0:00:00.000032 INFO: Moved old log file ./plasma_output/alphadia_2.1.0/log.txt to plasma_output/alphadia_2.1.0/log.2.bkp.txt
0:00:00.000178 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/plasma_output/alphadia_2.1.0, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000222 INFO: User provided config file: config_alphadia20_rs.yaml.
0:00:00.014195 PROGRESS:           _      _         ___ ___   _   
0:00:00.014265 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.014297 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.014321 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.014348 PROGRESS:            |_|                           
0:00:00.014373 PROGRESS: 
0:00:00.014395 PROGRESS: version: 2.1.0
0:00:00.014417 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.014444 INFO: hostname: thestral
0:00:00.014476 PROGRESS: os: Linux 6.12.48+deb13-amd64 (x86_64)
0:00:00.014505 PROGRESS: python: 3.11.11 (CPython)
0:00:00.014561 INFO: date: 2026-04-09 15:46:42
0:00:00.014586 INFO: ================ AlphaX Environment ===============
0:00:00.014610 INFO: alphabase       : 1.7.4
0:00:00.014631 INFO: alpharaw        : 0.4.8
0:00:00.014652 INFO: alphatims       : 1.0.9
0:00:00.014672 INFO: alphapeptdeep   : 1.4.1
0:00:00.014692 INFO: directlfq       : 0.3.3
0:00:00.014710 INFO: ===================================================
0:00:00.014730 INFO: ================= Pip Environment =================
0:00:00.071026 INFO: pytz==2025.2 et_xmlfile==2.0.0 scikit-learn==1.7.2 networkx==3.6 rdkit==2025.9.1 pyparsing==3.2.5 nvidia-nvjitlink-cu12==12.4.127 alpharaw==0.4.8 matplotlib==3.10.7 plotly==6.6.0 clr_loader==0.2.8 tqdm==4.67.1 MarkupSafe==3.0.3 regex==2025.11.3 pip==24.0 numpy==1.26.4 nvidia-nvshmem-cu12==3.3.20 dill==0.4.0 peptdeep==1.4.1 contextlib2==21.6.0 directlfq==0.3.3 argparse==1.4.0 nvidia-cuda-cupti-cu12==12.4.127 pandas==2.3.3 lightning-utilities==0.15.2 idna==3.11 tokenizers==0.22.1 safetensors==0.7.0 lxml==6.0.2 nvidia-cuda-nvrtc-cu12==12.4.127 pyteomics==4.7.5 PyYAML==6.0.3 mpmath==1.3.0 fonttools==4.60.1 six==1.17.0 narwhals==2.19.0 h5py==3.15.1 cycler==0.12.1 threadpoolctl==3.6.0 pythonnet==3.0.5 triton==3.2.0 pycparser==2.23 alphatims==1.0.9 typing_extensions==4.15.0 pyzstd==0.18.0 kiwisolver==1.4.9 multiprocess==0.70.18 alphabase==1.7.4 click==8.3.1 python-dateutil==2.9.0.post0 fsspec==2025.10.0 torch==2.6.0 openpyxl==3.1.5 huggingface-hub==0.36.0 nvidia-cusparse-cu12==12.3.1.170 contourpy==1.3.3 rocket-fft==0.2.5 numba==0.62.1 nvidia-cufile-cu12==1.13.1.3 certifi==2025.11.12 quantselect==0.1.3 joblib==1.5.2 pyahocorasick==2.2.0 seaborn==0.13.2 alphadia-search-rs==1.1.1 biopython==1.86 scipy==1.12.0 tzdata==2025.2 requests==2.32.5 urllib3==2.5.0 torchmetrics==1.8.2 Jinja2==3.1.6 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 pyarrow==22.0.0 filelock==3.20.0 llvmlite==0.45.1 nvidia-cufft-cu12==11.2.1.3 alphadia==2.1.0 pillow==12.0.0 charset-normalizer==3.4.4 transformers==4.57.3 sympy==1.13.1 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 packaging==25.0 nvidia-curand-cu12==10.3.5.147 cffi==2.0.0 setuptools==65.5.0 nvidia-cuda-runtime-cu12==12.4.127 nvidia-nccl-cu12==2.21.5 hf-xet==1.2.0 xxhash==3.6.0 nvidia-cusparselt-cu12==0.6.2 psutil==7.1.3
0:00:00.071119 INFO: ===================================================
0:00:00.071151 INFO: =================== Running step 'library' ===================
0:00:00.071215 INFO: loading default config from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.083402 INFO: loading additional config provided via CLI
0:00:00.083479 INFO: loading additional config provided via CLI parameters
0:00:00.083838 INFO: Updating config with 'user defined'
0:00:00.083900 WARNING: Key 'general.astral_ms1' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.083928 WARNING: Key 'general.mmap_detector_events' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.084014 WARNING: Key 'selection_config' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.084040 WARNING: Key 'scoring_config' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.084077 WARNING: Key 'fdr.enable_two_step_classifier' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.084099 WARNING: Key 'fdr.two_step_classifier_max_iterations' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.084178 INFO: Updating config with 'user defined (cli)'
0:00:00.084216 INFO: loading default config from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/default_python.yaml
0:00:00.084947 INFO: updating config with user defined values: [{'calibration': {'batch_size': 8000, 'optimization_lock_target': 200, 'min_steps': 2}, 'optimization': {'rt_error': {'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'maximal_decrease': 0.2, 'favour_narrower_optimum': True, 'maximum_decrease_from_maximum': 0.1}}}, {'version': 1, 'workflow_name': None, 'output_directory': None, 'library_path': None, 'raw_paths': ['/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d'], 'fasta_paths': [], 'quant_directory': None, 'general': {'thread_count': 80, 'transfer_step_enabled': False, 'mbr_step_enabled': True, 'reuse_calibration': False, 'reuse_quant': False, 'astral_ms1': False, 'log_level': 'INFO', 'mmap_detector_events': False, 'use_gpu': True, 'save_figures': True, 'save_library': True, 'save_flat_library': False, 'input_library_type': 'base', 'save_mbr_library': True, 'random_state': None}, 'library_prediction': {'enabled': False, 'enzyme': 'trypsin/p', 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M;Acetyl@Protein_N-term', 'max_var_mod_num': 1, 'missed_cleavages': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [400, 1000], 'fragment_mz': [50, 2000], 'nce': 25.0, 'fragment_types': ['b', 'y'], 'max_fragment_charge': 2, 'instrument': 'timsTOF', 'peptdeep_model_path': None, 'peptdeep_model_type': 'generic'}, 'custom_modifications': [{'name': 'Dimethyl:d12@K', 'composition': 'H(-2)2H(8)13C(2)'}, {'name': 'Dimethyl:d12@Any_N-term', 'composition': 'H(-2)2H(8)13C(2)'}, {'name': 'Dimethyl:d12@Protein_N-term', 'composition': 'H(-2)2H(8)13C(2)'}, {'name': 'mTRAQ:d12@K', 'composition': 'H(12)C(1)13C(10)15N(2)O(1)'}, {'name': 'mTRAQ:d12@Any_N-term', 'composition': 'H(12)C(1)13C(14)15N(2)O(1)'}, {'name': 'mTRAQ:d12@Protein_N-term', 'composition': 'H(12)C(1)13C(14)15N(2)O(1)'}, {'name': 'Label:13C(12)@K', 'composition': 'C(12)'}], 'search': {'extraction_backend': 'python', 'target_ms1_tolerance': 15, 'target_ms2_tolerance': 15, 'target_rt_tolerance': 0.0, 'target_mobility_tolerance': 0.0, 'quant_window': 3, 'target_num_candidates': 3, 'channel_filter': '', 'exclude_shared_ions': True, 'compete_for_fragments': True, 'quant_all': True, 'top_k_fragments_selection': 12, 'top_k_fragments_scoring': 12, 'min_fragment_intensity': 0.01, 'experimental_xic': True, 'optimized_peak_group_score': False}, 'calibration': {'batch_size': 200, 'optimization_lock_target': 200, 'max_steps': 20, 'min_steps': 2, 'max_skips': 1, 'max_fragments': 5000, 'min_correlation': 0.7}, 'search_initial': {'num_candidates': 1, 'ms1_tolerance': 30, 'ms2_tolerance': 30, 'mobility_tolerance': 0.1, 'rt_tolerance': 0.5}, 'selection_config': {'peak_len_rt': 10.0, 'sigma_scale_rt': 0.5, 'peak_len_mobility': 0.01, 'sigma_scale_mobility': 1.0, 'top_k_precursors': 3, 'kernel_size': 30, 'f_mobility': 1.0, 'f_rt': 0.99, 'center_fraction': 0.5, 'min_size_mobility': 8, 'min_size_rt': 3, 'max_size_mobility': 20, 'max_size_rt': 15, 'group_channels': False, 'use_weighted_score': True, 'join_close_candidates': False, 'join_close_candidates_scan_threshold': 0.6, 'join_close_candidates_cycle_threshold': 0.6}, 'scoring_config': {'score_grouped': False, 'top_k_isotopes': 3, 'reference_channel': -1, 'precursor_mz_tolerance': 10, 'fragment_mz_tolerance': 15}, 'library_multiplexing': {'enabled': False, 'input_channel': 0, 'multiplex_mapping': []}, 'multiplexing': {'enabled': False, 'target_channels': '4,8', 'decoy_channel': 12, 'reference_channel': 0, 'competitive_scoring': True}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins', 'inference_strategy': 'heuristic', 'competitive_scoring': True, 'keep_decoys': False, 'channel_wise_fdr': False, 'enable_two_step_classifier': False, 'two_step_classifier_max_iterations': 5, 'enable_nn_hyperparameter_tuning': True}, 'search_output': {'file_format': 'parquet', 'precursor_level_lfq': True, 'peptide_level_lfq': True, 'save_fragment_quant_matrix': False, 'min_k_fragments': 12, 'min_correlation': 0.9, 'num_samples_quadratic': 50, 'min_nonnan': 3}, 'optimization': {'order_of_optimization': None, 'ms2_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': True, 'maximal_decrease': 0.5, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.1}, 'ms1_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': False, 'maximal_decrease': 0.2, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.1}, 'mobility_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': False, 'maximal_decrease': 0.2, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.1}, 'rt_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': True, 'maximal_decrease': 0.2, 'favour_narrower_optimum': True, 'maximum_decrease_from_maximum': 0.1}}, 'optimization_manager': {'fwhm_rt': 5, 'fwhm_mobility': 0.01, 'score_cutoff': 0}, 'transfer_library': {'enabled': False, 'fragment_types': ['b', 'y'], 'max_charge': 2, 'top_k_samples': 3, 'norm_delta_max': True, 'precursor_correlation_cutoff': 0.5, 'fragment_correlation_ratio': 0.75}, 'transfer_learning': {'enabled': False, 'batch_size': 2000, 'max_lr': 0.0001, 'train_fraction': 0.7, 'validation_fraction': 0.2, 'test_fraction': 0.1, 'test_interval': 1, 'lr_patience': 3, 'epochs': 51, 'warmup_epochs': 5, 'nce': 25, 'instrument': 'Astral'}}, {'raw_paths': ['/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d'], 'library_path': '/home/robbe/ProteoBench_diaPASEF/plasma_output/alphadia_2.1.0/library/speclib.hdf', 'fasta_paths': ['./ProteoBenchFASTA_DDAQuantification.fasta']}, {'quant_directory': None, 'general': {'save_mbr_library': True, 'save_library': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'output_directory': 'plasma_output/alphadia_2.1.0/library'}]
0:00:00.085202 INFO: Updating config with 'default_python'
0:00:00.085244 INFO: Updating config with 'user defined'
0:00:00.085276 WARNING: Key 'general.astral_ms1' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.085300 WARNING: Key 'general.mmap_detector_events' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.085367 WARNING: Key 'selection_config' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.085390 WARNING: Key 'scoring_config' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.085424 WARNING: Key 'fdr.enable_two_step_classifier' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.085445 WARNING: Key 'fdr.two_step_classifier_max_iterations' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
0:00:00.085523 INFO: Updating config with 'user defined (cli)'
0:00:00.085549 INFO: Updating config with 'multistep search'
0:00:00.085591 INFO: [32;20m├──version: 1 [user defined, default: None][0m
0:00:00.085619 INFO: ├──workflow_name: None
0:00:00.085642 INFO: [32;20m├──output_directory: plasma_output/alphadia_2.1.0/library [multistep search, default: None][0m
0:00:00.085667 INFO: [32;20m├──library_path: /home/robbe/ProteoBench_diaPASEF/plasma_output/alphadia_2.1.0/library/speclib.hdf [user defined (cli), default: None][0m
0:00:00.085689 INFO: ├──raw_paths:
0:00:00.085710 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d [user defined (cli), default: None][0m
0:00:00.085730 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d [user defined (cli), default: None][0m
0:00:00.085752 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d [user defined (cli), default: None][0m
0:00:00.085779 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d [user defined (cli), default: None][0m
0:00:00.085800 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d [user defined (cli), default: None][0m
0:00:00.085821 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d [user defined (cli), default: None][0m
0:00:00.085840 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d [user defined (cli), default: None][0m
0:00:00.085860 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d [user defined (cli), default: None][0m
0:00:00.085902 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d [user defined (cli), default: None][0m
0:00:00.085933 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d [user defined (cli), default: None][0m
0:00:00.085965 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d [user defined (cli), default: None][0m
0:00:00.085997 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d [user defined (cli), default: None][0m
0:00:00.086029 INFO: ├──fasta_paths:
0:00:00.086057 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.086089 INFO: ├──quant_directory: None
0:00:00.086119 INFO: ├──general
0:00:00.086158 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:00:00.086189 INFO: │   ├──transfer_step_enabled: False
0:00:00.086220 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.086252 INFO: │   ├──reuse_calibration: False
0:00:00.086282 INFO: │   ├──reuse_quant: False
0:00:00.086311 INFO: │   ├──log_level: INFO
0:00:00.086339 INFO: │   ├──use_gpu: True
0:00:00.086363 INFO: │   ├──save_figures: True
0:00:00.086387 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.086412 INFO: │   ├──save_flat_library: False
0:00:00.086435 INFO: │   ├──input_library_type: base
0:00:00.086458 INFO: │   ├──save_mbr_library: True
0:00:00.086481 INFO: │   └──random_state: None
0:00:00.086506 INFO: ├──library_loading
0:00:00.086531 INFO: │   └──drop_decoys: False
0:00:00.086555 INFO: ├──library_prediction
0:00:00.086579 INFO: │   ├──enabled: False
0:00:00.086603 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.086627 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.086650 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.086674 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.086698 INFO: │   ├──missed_cleavages: 1
0:00:00.086721 INFO: │   ├──precursor_len:
0:00:00.086745 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.086769 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.086792 INFO: │   ├──precursor_charge:
0:00:00.086816 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.086838 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.086861 INFO: │   ├──precursor_mz:
0:00:00.086884 INFO: │   │   - 400
0:00:00.086908 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.086933 INFO: │   ├──fragment_mz:
0:00:00.086957 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.086982 INFO: │   │   - 2000
0:00:00.087007 INFO: │   ├──nce: 25.0
0:00:00.087031 INFO: │   ├──fragment_types:
0:00:00.087056 INFO: │   │   - b
0:00:00.087078 INFO: │   │   - y
0:00:00.087102 INFO: │   ├──max_fragment_charge: 2
0:00:00.087125 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.087148 INFO: │   ├──peptdeep_model_path: None
0:00:00.087171 INFO: │   ├──peptdeep_model_type: generic
0:00:00.087196 INFO: │   ├──predict_charge: False
0:00:00.087222 INFO: │   └──min_charge_probability: 0.1
0:00:00.087244 INFO: ├──custom_modifications:
0:00:00.087270 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.087291 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.087315 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.087337 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.087360 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.087383 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.087407 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.087431 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.087455 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.087479 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.087502 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.087527 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.087551 INFO: │   ├──name: Label:13C(12)@K
0:00:00.087576 INFO: │   └──composition: C(12)
0:00:00.087598 INFO: ├──search
0:00:00.087624 INFO: │   [32;20m├──extraction_backend: python [user defined, default: rust][0m
0:00:00.087650 INFO: │   [32;20m├──target_ms1_tolerance: 15 [user defined, default: 5][0m
0:00:00.087675 INFO: │   [32;20m├──target_ms2_tolerance: 15 [user defined, default: 10][0m
0:00:00.087707 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.087735 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.087759 INFO: │   ├──quant_window: 3
0:00:00.087783 INFO: │   ├──target_num_candidates: 3
0:00:00.087806 INFO: │   ├──channel_filter: 
0:00:00.087830 INFO: │   ├──compete_for_fragments: True
0:00:00.087853 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.087878 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.087903 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.087925 INFO: │   ├──optimized_peak_group_score: False
0:00:00.087946 INFO: │   ├──exclude_shared_ions: True
0:00:00.087967 INFO: │   ├──quant_all: True
0:00:00.087988 INFO: │   └──experimental_xic: True
0:00:00.088008 INFO: ├──calibration
0:00:00.088031 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 1000][0m
0:00:00.088052 INFO: │   [32;20m├──optimization_lock_target: 200 [user defined, default: 1000][0m
0:00:00.088074 INFO: │   ├──max_steps: 20
0:00:00.088094 INFO: │   [32;20m├──min_steps: 2 [user defined, default: 5][0m
0:00:00.088116 INFO: │   ├──max_skips: 1
0:00:00.088137 INFO: │   ├──max_fragments: 5000
0:00:00.088158 INFO: │   └──min_correlation: 0.7
0:00:00.088178 INFO: ├──search_initial
0:00:00.088202 INFO: │   ├──num_candidates: 1
0:00:00.088222 INFO: │   ├──ms1_tolerance: 30
0:00:00.088243 INFO: │   ├──ms2_tolerance: 30
0:00:00.088264 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.088286 INFO: │   └──rt_tolerance: 0.5
0:00:00.088306 INFO: ├──library_multiplexing
0:00:00.088328 INFO: │   ├──enabled: False
0:00:00.088348 INFO: │   ├──input_channel: 0
0:00:00.088368 INFO: │   └──multiplex_mapping:
0:00:00.088388 INFO: ├──multiplexing
0:00:00.088408 INFO: │   ├──enabled: False
0:00:00.088430 INFO: │   ├──target_channels: 4,8
0:00:00.088455 INFO: │   ├──decoy_channel: 12
0:00:00.088477 INFO: │   ├──reference_channel: 0
0:00:00.088500 INFO: │   └──competitive_scoring: True
0:00:00.088522 INFO: ├──fdr
0:00:00.088547 INFO: │   ├──fdr: 0.01
0:00:00.088569 INFO: │   ├──group_level: proteins
0:00:00.088591 INFO: │   ├──inference_strategy: heuristic
0:00:00.088612 INFO: │   ├──competitive_scoring: True
0:00:00.088636 INFO: │   ├──keep_decoys: False
0:00:00.088660 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.088683 INFO: │   ├──channel_wise_fdr: False
0:00:00.088706 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.088730 INFO: ├──search_output
0:00:00.088754 INFO: │   ├──file_format: parquet
0:00:00.088776 INFO: │   ├──precursor_level_lfq: True
0:00:00.088800 INFO: │   ├──peptide_level_lfq: True
0:00:00.088825 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.088848 INFO: │   ├──min_k_fragments: 12
0:00:00.088872 INFO: │   ├──min_correlation: 0.9
0:00:00.088896 INFO: │   ├──num_samples_quadratic: 50
0:00:00.088916 INFO: │   ├──min_nonnan: 3
0:00:00.088938 INFO: │   ├──normalization_method: directlfq
0:00:00.088959 INFO: │   └──normalize_directlfq: True
0:00:00.088980 INFO: ├──optimization
0:00:00.089002 INFO: │   ├──order_of_optimization: None
0:00:00.089023 INFO: │   ├──ms2_error
0:00:00.089044 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.089067 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.089090 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.089113 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.089135 INFO: │   │   ├──try_narrower_values: True
0:00:00.089158 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.089180 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.089206 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.089229 INFO: │   ├──ms1_error
0:00:00.089251 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.089274 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.089296 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.089319 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.089340 INFO: │   │   ├──try_narrower_values: False
0:00:00.089363 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.089383 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.089406 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.089428 INFO: │   ├──mobility_error
0:00:00.089451 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.089472 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.089494 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.089515 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.089538 INFO: │   │   ├──try_narrower_values: False
0:00:00.089559 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.089581 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.089601 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.089622 INFO: │   └──rt_error
0:00:00.089646 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.089667 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.089690 INFO: │       [32;20m├──automatic_update_percentile_range: 0.99 [user defined, default: 0.999][0m
0:00:00.089712 INFO: │       [32;20m├──automatic_update_factor: 1.1 [user defined, default: 1.5][0m
0:00:00.089734 INFO: │       ├──try_narrower_values: True
0:00:00.089756 INFO: │       [32;20m├──maximal_decrease: 0.2 [user defined, default: 0.1][0m
0:00:00.089778 INFO: │       [32;20m├──favour_narrower_optimum: True [user defined, default: False][0m
0:00:00.089800 INFO: │       [32;20m└──maximum_decrease_from_maximum: 0.1 [user defined, default: 0.5][0m
0:00:00.089822 INFO: ├──optimization_manager
0:00:00.089842 INFO: │   ├──fwhm_rt: 5
0:00:00.089876 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.089906 INFO: │   └──score_cutoff: 0
0:00:00.089927 INFO: ├──transfer_library
0:00:00.089947 INFO: │   ├──enabled: False
0:00:00.089970 INFO: │   ├──fragment_types:
0:00:00.089992 INFO: │   │   - b
0:00:00.090017 INFO: │   │   - y
0:00:00.090041 INFO: │   ├──max_charge: 2
0:00:00.090064 INFO: │   ├──top_k_samples: 3
0:00:00.090089 INFO: │   ├──norm_delta_max: True
0:00:00.090112 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.090137 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.090158 INFO: └──transfer_learning
0:00:00.090183 INFO:     ├──enabled: False
0:00:00.090205 INFO:     ├──batch_size: 2000
0:00:00.090230 INFO:     ├──max_lr: 0.0001
0:00:00.090253 INFO:     ├──train_fraction: 0.7
0:00:00.090277 INFO:     ├──validation_fraction: 0.2
0:00:00.090301 INFO:     ├──test_fraction: 0.1
0:00:00.090324 INFO:     ├──test_interval: 1
0:00:00.090347 INFO:     ├──lr_patience: 3
0:00:00.090370 INFO:     ├──epochs: 51
0:00:00.090393 INFO:     ├──warmup_epochs: 5
0:00:00.090416 INFO:     ├──nce: 25
0:00:00.090440 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:00:00.095551 INFO: Moved existing config file plasma_output/alphadia_2.1.0/library/frozen_config.yaml to plasma_output/alphadia_2.1.0/library/frozen_config.1.bkp.yaml
0:00:00.095773 INFO: Registering 7 custom modifications
0:00:00.129447 INFO: Searching 12 files:
0:00:00.129541 INFO:   A9_G_DIA_nLC_tTOF_R1.d
0:00:00.129572 INFO:   A9_G_DIA_nLC_tTOF_R2.d
0:00:00.129595 INFO:   A9_G_DIA_nLC_tTOF_R3.d
0:00:00.129617 INFO:   A9_G_DIA_nLC_tTOF_R4.d
0:00:00.129639 INFO:   A9_G_DIA_nLC_tTOF_R5.d
0:00:00.129673 INFO:   A9_G_DIA_nLC_tTOF_R6.d
0:00:00.129696 INFO:   B9_G_DIA_nLC_tTOF_R1.d
0:00:00.129720 INFO:   B9_G_DIA_nLC_tTOF_R2.d
0:00:00.129742 INFO:   B9_G_DIA_nLC_tTOF_R3.d
0:00:00.129763 INFO:   B9_G_DIA_nLC_tTOF_R4.d
0:00:00.129782 INFO:   B9_G_DIA_nLC_tTOF_R5.d
0:00:00.129803 INFO:   B9_G_DIA_nLC_tTOF_R6.d
0:00:00.129826 INFO: Using 1 fasta files:
0:00:00.129849 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:00:00.129885 INFO: Using library: /home/robbe/ProteoBench_diaPASEF/plasma_output/alphadia_2.1.0/library/speclib.hdf
0:00:00.129909 INFO: Saving output to: plasma_output/alphadia_2.1.0/library
0:00:00.129939 PROGRESS: Loading spectral library
0:00:00.129970 PROGRESS: Loading library (type: base) from disk..
0:00:00.129998 INFO: Running DynamicLoader
0:00:00.130057 INFO: Loading .hdf library from /home/robbe/ProteoBench_diaPASEF/plasma_output/alphadia_2.1.0/library/speclib.hdf
0:00:26.052980 INFO: Running PrecursorInitializer
0:00:26.056364 INFO: Channel column already present, skipping initialization
0:00:26.056467 INFO: Elution group indices already present, skipping initialization
0:00:26.056494 INFO: Precursor indices already present, skipping initialization
0:00:26.056523 INFO: Running AnnotateFasta
0:00:46.853598 INFO: Running IsotopeGenerator
0:00:46.854018 INFO: Isotope information already present, skipping isotope generation
0:00:46.854073 INFO: Running RTNormalization
0:00:46.854154 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:00:46.854223 INFO: Saving library to plasma_output/alphadia_2.1.0/library/speclib.hdf
0:01:19.451422 INFO: Running DecoyGenerator
0:04:30.460387 INFO: Running FlattenLibrary
0:05:01.204458 INFO: Running InitFlatColumns
0:05:01.488373 INFO: Running LogFlatLibraryStats
0:05:01.488537 INFO: ============ Library Stats ============
0:05:01.488579 INFO: Number of precursors: 12,218,312
0:05:02.927093 INFO: 	thereof targets:6,124,046
0:05:02.927259 INFO: 	thereof decoys: 6,094,266
0:05:03.028525 INFO: Number of elution groups: 6,124,046
0:05:03.028691 INFO: 	average size: 2.00
0:05:03.295303 INFO: Number of proteins: 117,993
0:05:03.328185 INFO: Number of channels: 1 ([0])
0:05:03.328404 INFO: Isotopes Distribution for 4 isotopes
0:05:03.328439 INFO: =======================================
0:05:03.328487 PROGRESS: =================== Starting Search Workflows for step library ===================
0:05:03.328553 PROGRESS: Loading raw file 1/12: A9_G_DIA_nLC_tTOF_R1 
0:05:03.328609 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
0:05:03.328702 INFO: Initializing TimingManager
0:05:03.329132 INFO: Initializing RawFileManager
0:05:03.329241 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:03.329302 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:03.329338 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:03.473433 INFO: Reading 22,623 frames with 335,647,195 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:09.528062 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d...
0:05:09.530965 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:09.534446 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:09.534756 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:09.535089 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:09.536337 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:09.561645 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:09.561897 INFO: Indexing quadrupole dimension
0:05:09.651637 INFO: Transposing detector events
0:05:12.252948 INFO: Finished transposing data
0:05:12.269490 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
0:05:12.270433 INFO: RT (min)            : 0.0 - 40.0
0:05:12.270556 INFO: RT duration (sec)   : 2399.9
0:05:12.270623 INFO: RT duration (min)   : 40.0
0:05:12.270680 INFO: Cycle len (scans)   : 12
0:05:12.270733 INFO: Cycle len (sec)     : 1.27
0:05:12.270781 INFO: Number of cycles    : 1885
0:05:12.270829 INFO: MS2 range (m/z)     : 374.4 - 1151.9
0:05:12.270894 INFO: Creating DIA data object took: 8.941654443740845
0:05:13.787162 INFO: Initializing CalibrationManager
0:05:13.787645 INFO: Setting up calibration estimators ..
0:05:13.787728 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:05:13.787821 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:05:13.787989 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:05:13.788068 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:05:13.788144 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:05:13.788229 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
0:05:13.788296 INFO: Done setting up calibration estimators.
0:05:13.788469 INFO: Initializing OptimizationManager
0:05:13.788601 INFO: initial parameter: ms1_error = 30
0:05:13.788664 INFO: initial parameter: ms2_error = 30
0:05:13.788729 INFO: initial parameter: rt_error = 1199.955978
0:05:13.788785 INFO: initial parameter: mobility_error = 0.1
0:05:13.788839 INFO: initial parameter: num_candidates = 1
0:05:13.788893 INFO: initial parameter: fwhm_rt = 5
0:05:13.788947 INFO: initial parameter: fwhm_mobility = 0.01
0:05:13.789004 INFO: initial parameter: score_cutoff = 0
0:05:13.789058 INFO: initial parameter: classifier_version = -1
0:05:13.789152 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R1
0:05:13.789500 INFO: FDRManager: loading saved state not requested, will be initialized.
0:05:13.789543 INFO: Initializing FDRManager
0:05:13.789595 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
0:05:15.250053 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
0:05:16.619605 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:05:16.620116 INFO: Updating optimization_manager: rt_error            : 1199.955978 -> 1199.955978
0:05:16.620222 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
0:05:16.620417 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
0:05:16.620529 PROGRESS: Starting initial search for precursors.
0:05:16.620620 INFO: Starting optimization step 0.
0:05:16.620685 PROGRESS: === Extracting elution groups 0 to 200 ===
0:05:16.620766 INFO: Using python extraction backend
0:05:16.620957 PROGRESS: Extracting batch of 395 precursors
0:05:16.621034 INFO: === Search parameters used ===
0:05:16.621087 INFO: rt_error       : 1199.955978
0:05:16.621133 INFO: mobility_error : 0.1
0:05:16.621177 INFO: num_candidates : 1
0:05:16.621222 INFO: ms1_error      : 30
0:05:16.621264 INFO: ms2_error      : 30
0:05:16.621306 INFO: fwhm_rt        : 5
0:05:16.621349 INFO: quant_window   : 3
0:05:16.621392 INFO: ==============================================
0:05:18.815475 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:05:18.815602 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:05:18.815651 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:05:18.815676 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:05:20.878129 INFO: Starting candidate selection
0:06:17.435569 INFO: Starting candidate scoring
0:09:55.834477 INFO: Finished candidate processing
0:09:55.834705 INFO: Collecting candidate features
0:09:56.900122 INFO: Collecting fragment features
0:09:58.262012 INFO: Finished candidate scoring
0:09:58.263743 INFO: performing precursor FDR with 47 features
0:09:58.263793 INFO: Decoy channel: -1
0:09:58.263820 INFO: competitive: True
0:09:58.265078 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:58.267028 INFO: Estimating optimal hyperparameters - samples: 272, batch_size: 128, learning_rate: 1.77e-04
0:09:58.267943 INFO: Using random state 929247 for train-test-split
0:09:58.293482 INFO: Test AUC: 0.473
0:09:58.293557 INFO: Train AUC: 0.506
0:09:58.293591 INFO: AUC difference: 6.46%
0:09:58.293616 WARNING: AUC difference > 5%. This may indicate overfitting.
0:09:58.573311 INFO: Resetting torch num_threads to 80
0:09:58.573841 PROGRESS: === Extracted 340 precursors and 2793 fragments ===
0:09:58.574342 INFO: === FDR correction performed with classifier version -1 ===
0:09:58.575109 PROGRESS: ============================= Precursor FDR =============================
0:09:58.575204 PROGRESS: Total precursors accumulated: 173
0:09:58.575272 PROGRESS: Target precursors: 82 (47.40%)
0:09:58.575332 PROGRESS: Decoy precursors: 91 (52.60%)
0:09:58.575393 PROGRESS: 
0:09:58.575447 PROGRESS: Precursor Summary:
0:09:58.576445 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:09:58.576538 PROGRESS: 
0:09:58.576604 PROGRESS: Protein Summary:
0:09:58.577672 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:09:58.577764 PROGRESS: =========================================================================
0:09:58.577950 INFO: Target number of precursors not reached yet.
0:09:58.661298 INFO: Starting optimization step 1.
0:09:58.661533 PROGRESS: === Extracting elution groups 200 to 600 ===
0:09:58.661634 INFO: Using python extraction backend
0:09:58.661782 PROGRESS: Extracting batch of 796 precursors
0:09:58.661873 INFO: === Search parameters used ===
0:09:58.661934 INFO: rt_error       : 1199.955978
0:09:58.661986 INFO: mobility_error : 0.1
0:09:58.662036 INFO: num_candidates : 1
0:09:58.662086 INFO: ms1_error      : 30
0:09:58.662134 INFO: ms2_error      : 30
0:09:58.662179 INFO: fwhm_rt        : 5
0:09:58.662226 INFO: quant_window   : 3
0:09:58.662271 INFO: ==============================================
0:09:58.663101 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:09:58.663152 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:09:58.663189 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:09:58.663216 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:09:58.664053 INFO: Starting candidate selection
0:10:01.570261 INFO: Starting candidate scoring
0:10:01.616072 INFO: Finished candidate processing
0:10:01.616188 INFO: Collecting candidate features
0:10:01.628097 INFO: Collecting fragment features
0:10:01.630661 INFO: Finished candidate scoring
0:10:01.632873 INFO: performing precursor FDR with 47 features
0:10:01.632927 INFO: Decoy channel: -1
0:10:01.632955 INFO: competitive: True
0:10:01.636242 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:01.638234 INFO: Estimating optimal hyperparameters - samples: 844, batch_size: 128, learning_rate: 1.77e-04
0:10:01.638325 INFO: Using random state 594567 for train-test-split
0:10:01.731895 INFO: Test AUC: 0.449
0:10:01.732198 INFO: Train AUC: 0.530
0:10:01.732234 INFO: AUC difference: 15.33%
0:10:01.732267 WARNING: AUC difference > 5%. This may indicate overfitting.
0:10:01.979367 INFO: Resetting torch num_threads to 80
0:10:01.980991 PROGRESS: === Extracted 1056 precursors and 8942 fragments ===
0:10:01.981572 INFO: === FDR correction performed with classifier version -1 ===
0:10:01.982280 PROGRESS: ============================= Precursor FDR =============================
0:10:01.982388 PROGRESS: Total precursors accumulated: 539
0:10:01.982456 PROGRESS: Target precursors: 286 (53.06%)
0:10:01.982518 PROGRESS: Decoy precursors: 253 (46.94%)
0:10:01.982572 PROGRESS: 
0:10:01.982625 PROGRESS: Precursor Summary:
0:10:01.983597 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:01.983687 PROGRESS: 
0:10:01.983756 PROGRESS: Protein Summary:
0:10:01.984797 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:01.984887 PROGRESS: =========================================================================
0:10:01.985072 INFO: Target number of precursors not reached yet.
0:10:02.086756 INFO: Starting optimization step 2.
0:10:02.087048 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:10:02.087193 INFO: Using python extraction backend
0:10:02.087367 PROGRESS: Extracting batch of 1598 precursors
0:10:02.087456 INFO: === Search parameters used ===
0:10:02.087514 INFO: rt_error       : 1199.955978
0:10:02.087564 INFO: mobility_error : 0.1
0:10:02.087612 INFO: num_candidates : 1
0:10:02.087660 INFO: ms1_error      : 30
0:10:02.087705 INFO: ms2_error      : 30
0:10:02.087753 INFO: fwhm_rt        : 5
0:10:02.087800 INFO: quant_window   : 3
0:10:02.087847 INFO: ==============================================
0:10:02.088987 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:10:02.089046 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:10:02.089108 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:10:02.089136 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:10:02.089885 INFO: Starting candidate selection
0:10:07.251269 INFO: Starting candidate scoring
0:10:07.308282 INFO: Finished candidate processing
0:10:07.308395 INFO: Collecting candidate features
0:10:07.320612 INFO: Collecting fragment features
0:10:07.323420 INFO: Finished candidate scoring
0:10:07.326126 INFO: performing precursor FDR with 47 features
0:10:07.326181 INFO: Decoy channel: -1
0:10:07.326207 INFO: competitive: True
0:10:07.329601 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:07.331828 INFO: Estimating optimal hyperparameters - samples: 1,979, batch_size: 128, learning_rate: 1.77e-04
0:10:07.331925 INFO: Using random state 635599 for train-test-split
0:10:07.527353 INFO: Test AUC: 0.522
0:10:07.527460 INFO: Train AUC: 0.557
0:10:07.527493 INFO: AUC difference: 6.27%
0:10:07.527518 WARNING: AUC difference > 5%. This may indicate overfitting.
0:10:07.775909 INFO: Resetting torch num_threads to 80
0:10:07.777652 PROGRESS: === Extracted 2474 precursors and 20799 fragments ===
0:10:07.778167 INFO: === FDR correction performed with classifier version -1 ===
0:10:07.778871 PROGRESS: ============================= Precursor FDR =============================
0:10:07.778966 PROGRESS: Total precursors accumulated: 1,262
0:10:07.779032 PROGRESS: Target precursors: 720 (57.05%)
0:10:07.779087 PROGRESS: Decoy precursors: 542 (42.95%)
0:10:07.779136 PROGRESS: 
0:10:07.779183 PROGRESS: Precursor Summary:
0:10:07.780159 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:07.780251 PROGRESS: 
0:10:07.780310 PROGRESS: Protein Summary:
0:10:07.781344 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:07.781435 PROGRESS: =========================================================================
0:10:07.781579 INFO: Target number of precursors not reached yet.
0:10:07.863579 INFO: Starting optimization step 3.
0:10:07.863841 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:10:07.863935 INFO: Using python extraction backend
0:10:07.864067 PROGRESS: Extracting batch of 3192 precursors
0:10:07.864143 INFO: === Search parameters used ===
0:10:07.864197 INFO: rt_error       : 1199.955978
0:10:07.864245 INFO: mobility_error : 0.1
0:10:07.864301 INFO: num_candidates : 1
0:10:07.864352 INFO: ms1_error      : 30
0:10:07.864397 INFO: ms2_error      : 30
0:10:07.864442 INFO: fwhm_rt        : 5
0:10:07.864491 INFO: quant_window   : 3
0:10:07.864534 INFO: ==============================================
0:10:07.865561 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:10:07.865615 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:10:07.865647 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:10:07.865671 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:10:07.866484 INFO: Starting candidate selection
0:10:16.438441 INFO: Starting candidate scoring
0:10:16.523529 INFO: Finished candidate processing
0:10:16.523646 INFO: Collecting candidate features
0:10:16.534241 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 2866)
0:10:16.538046 INFO: Collecting fragment features
0:10:16.541528 INFO: Finished candidate scoring
0:10:16.545552 INFO: performing precursor FDR with 47 features
0:10:16.545608 INFO: Decoy channel: -1
0:10:16.545635 INFO: competitive: True
0:10:16.549839 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:16.551580 WARNING: dropped 1 target PSMs due to missing features
0:10:16.552958 INFO: Estimating optimal hyperparameters - samples: 4,271, batch_size: 128, learning_rate: 1.77e-04
0:10:16.553053 INFO: Using random state 823065 for train-test-split
0:10:17.004379 INFO: Test AUC: 0.528
0:10:17.004493 INFO: Train AUC: 0.581
0:10:17.004527 INFO: AUC difference: 9.19%
0:10:17.004556 WARNING: AUC difference > 5%. This may indicate overfitting.
0:10:17.252255 INFO: Resetting torch num_threads to 80
0:10:17.254547 PROGRESS: === Extracted 5340 precursors and 44937 fragments ===
0:10:17.255045 INFO: === FDR correction performed with classifier version -1 ===
0:10:17.255894 PROGRESS: ============================= Precursor FDR =============================
0:10:17.255993 PROGRESS: Total precursors accumulated: 2,715
0:10:17.256062 PROGRESS: Target precursors: 1,580 (58.20%)
0:10:17.256125 PROGRESS: Decoy precursors: 1,135 (41.80%)
0:10:17.256186 PROGRESS: 
0:10:17.256237 PROGRESS: Precursor Summary:
0:10:17.257209 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:17.257303 PROGRESS: 
0:10:17.257365 PROGRESS: Protein Summary:
0:10:17.258451 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:17.258546 PROGRESS: =========================================================================
0:10:17.258725 INFO: Target number of precursors not reached yet.
0:10:17.356479 INFO: Starting optimization step 4.
0:10:17.356745 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:10:17.356857 INFO: Using python extraction backend
0:10:17.356988 PROGRESS: Extracting batch of 6381 precursors
0:10:17.357069 INFO: === Search parameters used ===
0:10:17.357126 INFO: rt_error       : 1199.955978
0:10:17.357175 INFO: mobility_error : 0.1
0:10:17.357232 INFO: num_candidates : 1
0:10:17.357278 INFO: ms1_error      : 30
0:10:17.357324 INFO: ms2_error      : 30
0:10:17.357371 INFO: fwhm_rt        : 5
0:10:17.357417 INFO: quant_window   : 3
0:10:17.357460 INFO: ==============================================
0:10:17.358917 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:10:17.358970 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:10:17.359004 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:10:17.359027 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:10:17.359786 INFO: Starting candidate selection
0:10:33.391752 INFO: Starting candidate scoring
0:10:33.538807 INFO: Finished candidate processing
0:10:33.538930 INFO: Collecting candidate features
0:10:33.553723 WARNING: intensity_correlation has 2 NaNs ( 0.03 % out of 5727)
0:10:33.557802 INFO: Collecting fragment features
0:10:33.562731 INFO: Finished candidate scoring
0:10:33.571181 INFO: performing precursor FDR with 47 features
0:10:33.571281 INFO: Decoy channel: -1
0:10:33.571320 INFO: competitive: True
0:10:33.577158 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:33.579495 WARNING: dropped 3 target PSMs due to missing features
0:10:33.581400 INFO: Estimating optimal hyperparameters - samples: 8,851, batch_size: 128, learning_rate: 1.77e-04
0:10:33.581527 INFO: Using random state 717782 for train-test-split
0:10:34.702651 INFO: Test AUC: 0.523
0:10:34.702781 INFO: Train AUC: 0.587
0:10:34.702820 INFO: AUC difference: 11.00%
0:10:34.702852 WARNING: AUC difference > 5%. This may indicate overfitting.
0:10:34.958132 INFO: Resetting torch num_threads to 80
0:10:34.961959 PROGRESS: === Extracted 11067 precursors and 92571 fragments ===
0:10:34.962476 INFO: === FDR correction performed with classifier version -1 ===
0:10:34.963683 PROGRESS: ============================= Precursor FDR =============================
0:10:34.963793 PROGRESS: Total precursors accumulated: 5,631
0:10:34.963874 PROGRESS: Target precursors: 3,317 (58.91%)
0:10:34.963949 PROGRESS: Decoy precursors: 2,314 (41.09%)
0:10:34.964016 PROGRESS: 
0:10:34.964081 PROGRESS: Precursor Summary:
0:10:34.965142 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:10:34.965247 PROGRESS: 
0:10:34.965329 PROGRESS: Protein Summary:
0:10:34.966504 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:10:34.966611 PROGRESS: =========================================================================
0:10:34.966864 INFO: Target number of precursors not reached yet.
0:10:35.104577 INFO: Starting optimization step 5.
0:10:35.104893 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:10:35.105009 INFO: Using python extraction backend
0:10:35.105155 PROGRESS: Extracting batch of 12763 precursors
0:10:35.105251 INFO: === Search parameters used ===
0:10:35.105323 INFO: rt_error       : 1199.955978
0:10:35.105390 INFO: mobility_error : 0.1
0:10:35.105453 INFO: num_candidates : 1
0:10:35.105514 INFO: ms1_error      : 30
0:10:35.105575 INFO: ms2_error      : 30
0:10:35.105637 INFO: fwhm_rt        : 5
0:10:35.105700 INFO: quant_window   : 3
0:10:35.105764 INFO: ==============================================
0:10:35.108499 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:10:35.108560 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:10:35.108604 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:10:35.108639 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:10:35.109433 INFO: Starting candidate selection
0:11:04.850089 INFO: Starting candidate scoring
0:11:05.068137 INFO: Finished candidate processing
0:11:05.068263 INFO: Collecting candidate features
0:11:05.101007 WARNING: intensity_correlation has 5 NaNs ( 0.04 % out of 11476)
0:11:05.105652 INFO: Collecting fragment features
0:11:05.118512 INFO: Finished candidate scoring
0:11:05.133990 INFO: performing precursor FDR with 47 features
0:11:05.134145 INFO: Decoy channel: -1
0:11:05.134176 INFO: competitive: True
0:11:05.144321 INFO: Setting torch num_threads to 2 for FDR classification task
0:11:05.148850 WARNING: dropped 5 target PSMs due to missing features
0:11:05.148944 WARNING: dropped 3 decoy PSMs due to missing features
0:11:05.152800 INFO: Estimating optimal hyperparameters - samples: 18,028, batch_size: 128, learning_rate: 1.77e-04
0:11:05.152962 INFO: Using random state 901929 for train-test-split
0:11:07.121599 INFO: Test AUC: 0.557
0:11:07.121756 INFO: Train AUC: 0.595
0:11:07.121790 INFO: AUC difference: 6.43%
0:11:07.121816 WARNING: AUC difference > 5%. This may indicate overfitting.
0:11:07.376532 INFO: Resetting torch num_threads to 80
0:11:07.395615 PROGRESS: === Extracted 22543 precursors and 188154 fragments ===
0:11:07.396259 INFO: === FDR correction performed with classifier version -1 ===
0:11:07.398661 PROGRESS: ============================= Precursor FDR =============================
0:11:07.398782 PROGRESS: Total precursors accumulated: 11,455
0:11:07.398860 PROGRESS: Target precursors: 6,907 (60.30%)
0:11:07.398921 PROGRESS: Decoy precursors: 4,548 (39.70%)
0:11:07.398973 PROGRESS: 
0:11:07.399025 PROGRESS: Precursor Summary:
0:11:07.400090 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
0:11:07.400184 PROGRESS: 
0:11:07.400245 PROGRESS: Protein Summary:
0:11:07.401369 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
0:11:07.401474 PROGRESS: =========================================================================
0:11:07.401780 INFO: Target number of precursors not reached yet.
0:11:07.562793 INFO: Starting optimization step 6.
0:11:07.563073 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:11:07.563184 INFO: Using python extraction backend
0:11:07.563328 PROGRESS: Extracting batch of 25523 precursors
0:11:07.563413 INFO: === Search parameters used ===
0:11:07.563473 INFO: rt_error       : 1199.955978
0:11:07.563522 INFO: mobility_error : 0.1
0:11:07.563568 INFO: num_candidates : 1
0:11:07.563615 INFO: ms1_error      : 30
0:11:07.563660 INFO: ms2_error      : 30
0:11:07.563704 INFO: fwhm_rt        : 5
0:11:07.563745 INFO: quant_window   : 3
0:11:07.563801 INFO: ==============================================
0:11:07.570226 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:11:07.570311 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:11:07.570345 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:11:07.570368 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:11:07.571176 INFO: Starting candidate selection
0:12:06.699552 INFO: Starting candidate scoring
0:12:07.056486 INFO: Finished candidate processing
0:12:07.056763 INFO: Collecting candidate features
0:12:07.096055 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 22859)
0:12:07.096335 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 22859)
0:12:07.100769 INFO: Collecting fragment features
0:12:07.114690 INFO: Finished candidate scoring
0:12:07.139475 INFO: performing precursor FDR with 47 features
0:12:07.139634 INFO: Decoy channel: -1
0:12:07.139663 INFO: competitive: True
0:12:07.158187 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:07.167427 WARNING: dropped 7 target PSMs due to missing features
0:12:07.167573 WARNING: dropped 4 decoy PSMs due to missing features
0:12:07.173946 INFO: Estimating optimal hyperparameters - samples: 36,312, batch_size: 148, learning_rate: 1.90e-04
0:12:07.174160 INFO: Using random state 848683 for train-test-split
0:12:10.811056 INFO: Test AUC: 0.551
0:12:10.811199 INFO: Train AUC: 0.609
0:12:10.811234 INFO: AUC difference: 9.53%
0:12:10.811261 WARNING: AUC difference > 5%. This may indicate overfitting.
0:12:11.073831 INFO: Resetting torch num_threads to 80
0:12:11.082817 PROGRESS: === Extracted 45402 precursors and 379719 fragments ===
0:12:11.083546 INFO: === FDR correction performed with classifier version -1 ===
0:12:11.087772 PROGRESS: ============================= Precursor FDR =============================
0:12:11.087900 PROGRESS: Total precursors accumulated: 23,078
0:12:11.087978 PROGRESS: Target precursors: 14,090 (61.05%)
0:12:11.088048 PROGRESS: Decoy precursors: 8,988 (38.95%)
0:12:11.088110 PROGRESS: 
0:12:11.088162 PROGRESS: Precursor Summary:
0:12:11.089314 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:12:11.089412 PROGRESS: 
0:12:11.089475 PROGRESS: Protein Summary:
0:12:11.090696 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:12:11.090795 PROGRESS: =========================================================================
0:12:11.091214 INFO: Target number of precursors not reached yet.
0:12:11.304470 INFO: Starting optimization step 7.
0:12:11.304769 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:12:11.304866 INFO: Using python extraction backend
0:12:11.305016 PROGRESS: Extracting batch of 51061 precursors
0:12:11.305103 INFO: === Search parameters used ===
0:12:11.305162 INFO: rt_error       : 1199.955978
0:12:11.305241 INFO: mobility_error : 0.1
0:12:11.305294 INFO: num_candidates : 1
0:12:11.305339 INFO: ms1_error      : 30
0:12:11.305384 INFO: ms2_error      : 30
0:12:11.305428 INFO: fwhm_rt        : 5
0:12:11.305473 INFO: quant_window   : 3
0:12:11.305517 INFO: ==============================================
0:12:11.319406 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:12:11.319542 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:12:11.319596 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:12:11.319623 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:12:11.321082 INFO: Starting candidate selection
0:14:06.251106 INFO: Starting candidate scoring
0:14:06.942220 INFO: Finished candidate processing
0:14:06.942410 INFO: Collecting candidate features
0:14:07.021326 WARNING: intensity_correlation has 14 NaNs ( 0.03 % out of 45735)
0:14:07.021624 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 45735)
0:14:07.026950 INFO: Collecting fragment features
0:14:07.054868 INFO: Finished candidate scoring
0:14:07.101060 INFO: performing precursor FDR with 47 features
0:14:07.101221 INFO: Decoy channel: -1
0:14:07.101251 INFO: competitive: True
0:14:07.143693 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:07.163262 WARNING: dropped 16 target PSMs due to missing features
0:14:07.163413 WARNING: dropped 11 decoy PSMs due to missing features
0:14:07.178880 INFO: Estimating optimal hyperparameters - samples: 72,888, batch_size: 298, learning_rate: 2.70e-04
0:14:07.179195 INFO: Using random state 189656 for train-test-split
0:14:12.017243 INFO: Test AUC: 0.545
0:14:12.017403 INFO: Train AUC: 0.608
0:14:12.017439 INFO: AUC difference: 10.34%
0:14:12.017470 WARNING: AUC difference > 5%. This may indicate overfitting.
0:14:12.299083 INFO: Resetting torch num_threads to 80
0:14:12.317888 PROGRESS: === Extracted 91137 precursors and 761898 fragments ===
0:14:12.318791 INFO: === FDR correction performed with classifier version -1 ===
0:14:12.328583 PROGRESS: ============================= Precursor FDR =============================
0:14:12.328753 PROGRESS: Total precursors accumulated: 46,297
0:14:12.328823 PROGRESS: Target precursors: 27,830 (60.11%)
0:14:12.328882 PROGRESS: Decoy precursors: 18,467 (39.89%)
0:14:12.328936 PROGRESS: 
0:14:12.328988 PROGRESS: Precursor Summary:
0:14:12.330411 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:14:12.330515 PROGRESS: 
0:14:12.330580 PROGRESS: Protein Summary:
0:14:12.331907 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:14:12.332007 PROGRESS: =========================================================================
0:14:12.332892 INFO: Target number of precursors not reached yet.
0:14:12.630853 INFO: Starting optimization step 8.
0:14:12.631222 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:14:12.631357 INFO: Using python extraction backend
0:14:12.631545 PROGRESS: Extracting batch of 102076 precursors
0:14:12.631639 INFO: === Search parameters used ===
0:14:12.631697 INFO: rt_error       : 1199.955978
0:14:12.631746 INFO: mobility_error : 0.1
0:14:12.631795 INFO: num_candidates : 1
0:14:12.631842 INFO: ms1_error      : 30
0:14:12.631889 INFO: ms2_error      : 30
0:14:12.631934 INFO: fwhm_rt        : 5
0:14:12.631980 INFO: quant_window   : 3
0:14:12.632027 INFO: ==============================================
0:14:12.658387 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:14:12.658540 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:14:12.658574 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:14:12.658599 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:14:12.659563 INFO: Starting candidate selection
0:18:01.609128 INFO: Starting candidate scoring
0:18:02.906028 INFO: Finished candidate processing
0:18:02.906213 INFO: Collecting candidate features
0:18:03.093009 WARNING: intensity_correlation has 33 NaNs ( 0.04 % out of 91464)
0:18:03.093348 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 91464)
0:18:03.100020 INFO: Collecting fragment features
0:18:03.158479 INFO: Finished candidate scoring
0:18:03.252867 INFO: performing precursor FDR with 47 features
0:18:03.253041 INFO: Decoy channel: -1
0:18:03.253072 INFO: competitive: True
0:18:03.329674 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:03.365495 WARNING: dropped 31 target PSMs due to missing features
0:18:03.365660 WARNING: dropped 31 decoy PSMs due to missing features
0:18:03.407628 INFO: Estimating optimal hyperparameters - samples: 146,031, batch_size: 598, learning_rate: 3.82e-04
0:18:03.408100 INFO: Using random state 476511 for train-test-split
0:18:09.640180 INFO: Test AUC: 0.543
0:18:09.640358 INFO: Train AUC: 0.587
0:18:09.640393 INFO: AUC difference: 7.50%
0:18:09.640419 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:09.953991 INFO: Resetting torch num_threads to 80
0:18:10.009606 PROGRESS: === Extracted 182601 precursors and 1528086 fragments ===
0:18:10.010529 INFO: === FDR correction performed with classifier version -1 ===
0:18:10.028996 PROGRESS: ============================= Precursor FDR =============================
0:18:10.029287 PROGRESS: Total precursors accumulated: 92,743
0:18:10.029361 PROGRESS: Target precursors: 54,588 (58.86%)
0:18:10.029422 PROGRESS: Decoy precursors: 38,155 (41.14%)
0:18:10.029477 PROGRESS: 
0:18:10.029537 PROGRESS: Precursor Summary:
0:18:10.031170 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:18:10.031283 PROGRESS: 
0:18:10.031345 PROGRESS: Protein Summary:
0:18:10.032855 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:18:10.032959 PROGRESS: =========================================================================
0:18:10.034755 INFO: Target number of precursors not reached yet.
0:18:10.449259 INFO: Starting optimization step 9.
0:18:10.449568 PROGRESS: === Extracting elution groups 102200 to 204600 ===
0:18:10.449678 INFO: Using python extraction backend
0:18:10.449827 PROGRESS: Extracting batch of 204132 precursors
0:18:10.449933 INFO: === Search parameters used ===
0:18:10.449996 INFO: rt_error       : 1199.955978
0:18:10.450051 INFO: mobility_error : 0.1
0:18:10.450106 INFO: num_candidates : 1
0:18:10.450158 INFO: ms1_error      : 30
0:18:10.450206 INFO: ms2_error      : 30
0:18:10.450253 INFO: fwhm_rt        : 5
0:18:10.450300 INFO: quant_window   : 3
0:18:10.450347 INFO: ==============================================
0:18:10.500220 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:18:10.500374 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:18:10.500411 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:18:10.500438 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:18:10.501374 INFO: Starting candidate selection
0:25:34.105851 INFO: Starting candidate scoring
0:25:36.599092 INFO: Finished candidate processing
0:25:36.599207 INFO: Collecting candidate features
0:25:36.982599 WARNING: intensity_correlation has 61 NaNs ( 0.03 % out of 183174)
0:25:36.983026 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 183174)
0:25:36.992625 INFO: Collecting fragment features
0:25:37.104986 INFO: Finished candidate scoring
0:25:37.324343 INFO: performing precursor FDR with 47 features
0:25:37.324498 INFO: Decoy channel: -1
0:25:37.324527 INFO: competitive: True
0:25:37.478368 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:37.548608 WARNING: dropped 62 target PSMs due to missing features
0:25:37.548760 WARNING: dropped 63 decoy PSMs due to missing features
0:25:37.651317 INFO: Estimating optimal hyperparameters - samples: 292,520, batch_size: 1,198, learning_rate: 5.41e-04
0:25:37.651923 INFO: Using random state 849162 for train-test-split
0:25:46.955394 INFO: Test AUC: 0.546
0:25:46.955572 INFO: Train AUC: 0.572
0:25:46.955606 INFO: AUC difference: 4.52%
0:25:47.329741 INFO: Resetting torch num_threads to 80
0:25:47.429520 PROGRESS: === Extracted 365775 precursors and 3060590 fragments ===
0:25:47.430587 INFO: === FDR correction performed with classifier version -1 ===
0:25:47.463376 PROGRESS: ============================= Precursor FDR =============================
0:25:47.463671 PROGRESS: Total precursors accumulated: 185,794
0:25:47.463765 PROGRESS: Target precursors: 107,141 (57.67%)
0:25:47.463835 PROGRESS: Decoy precursors: 78,653 (42.33%)
0:25:47.463891 PROGRESS: 
0:25:47.463946 PROGRESS: Precursor Summary:
0:25:47.466146 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:25:47.466260 PROGRESS: 
0:25:47.466342 PROGRESS: Protein Summary:
0:25:47.468362 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:25:47.468459 PROGRESS: =========================================================================
0:25:47.472064 INFO: Target number of precursors not reached yet.
0:25:48.164337 INFO: Starting optimization step 10.
0:25:48.164628 PROGRESS: === Extracting elution groups 204600 to 409400 ===
0:25:48.164795 INFO: Using python extraction backend
0:25:48.164996 PROGRESS: Extracting batch of 408390 precursors
0:25:48.165089 INFO: === Search parameters used ===
0:25:48.165147 INFO: rt_error       : 1199.955978
0:25:48.165196 INFO: mobility_error : 0.1
0:25:48.165247 INFO: num_candidates : 1
0:25:48.165302 INFO: ms1_error      : 30
0:25:48.165346 INFO: ms2_error      : 30
0:25:48.165391 INFO: fwhm_rt        : 5
0:25:48.165446 INFO: quant_window   : 3
0:25:48.165498 INFO: ==============================================
0:25:48.262364 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:25:48.262511 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:25:48.262563 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:25:48.262586 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:25:48.263707 INFO: Starting candidate selection
0:40:29.375542 INFO: Starting candidate scoring
0:40:34.243278 INFO: Finished candidate processing
0:40:34.243464 INFO: Collecting candidate features
0:40:35.109387 WARNING: intensity_correlation has 115 NaNs ( 0.03 % out of 365216)
0:40:35.110181 WARNING: height_correlation has 15 NaNs ( 0.00 % out of 365216)
0:40:35.125221 INFO: Collecting fragment features
0:40:35.356820 INFO: Finished candidate scoring
0:40:35.829750 INFO: performing precursor FDR with 47 features
0:40:35.829925 INFO: Decoy channel: -1
0:40:35.829958 INFO: competitive: True
0:40:36.131169 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:36.278958 WARNING: dropped 111 target PSMs due to missing features
0:40:36.279129 WARNING: dropped 138 decoy PSMs due to missing features
0:40:36.520875 INFO: Estimating optimal hyperparameters - samples: 584,593, batch_size: 2,394, learning_rate: 7.65e-04
0:40:36.521970 INFO: Using random state 394478 for train-test-split
0:40:51.758899 INFO: Test AUC: 0.547
0:40:51.759146 INFO: Train AUC: 0.575
0:40:51.759188 INFO: AUC difference: 4.93%
0:40:52.255052 INFO: Resetting torch num_threads to 80
0:40:52.373034 PROGRESS: === Extracted 730991 precursors and 6116688 fragments ===
0:40:52.374177 INFO: === FDR correction performed with classifier version -1 ===
0:40:52.437323 PROGRESS: ============================= Precursor FDR =============================
0:40:52.437620 PROGRESS: Total precursors accumulated: 371,329
0:40:52.437703 PROGRESS: Target precursors: 215,214 (57.96%)
0:40:52.437767 PROGRESS: Decoy precursors: 156,115 (42.04%)
0:40:52.437828 PROGRESS: 
0:40:52.437892 PROGRESS: Precursor Summary:
0:40:52.441313 PROGRESS: Channel   0:	 0.050 FDR:   158; 0.010 FDR:   128; 0.001 FDR:   108
0:40:52.441450 PROGRESS: 
0:40:52.441517 PROGRESS: Protein Summary:
0:40:52.444559 PROGRESS: Channel   0:	 0.050 FDR:   123; 0.010 FDR:    97; 0.001 FDR:    88
0:40:52.444663 PROGRESS: =========================================================================
0:40:52.450383 INFO: Target number of precursors not reached yet.
0:40:53.602088 INFO: Starting optimization step 11.
0:40:53.602363 PROGRESS: === Extracting elution groups 409400 to 819000 ===
0:40:53.602513 INFO: Using python extraction backend
0:40:53.602705 PROGRESS: Extracting batch of 816689 precursors
0:40:53.602805 INFO: === Search parameters used ===
0:40:53.602880 INFO: rt_error       : 1199.955978
0:40:53.602937 INFO: mobility_error : 0.1
0:40:53.602985 INFO: num_candidates : 1
0:40:53.603033 INFO: ms1_error      : 30
0:40:53.603079 INFO: ms2_error      : 30
0:40:53.603125 INFO: fwhm_rt        : 5
0:40:53.603168 INFO: quant_window   : 3
0:40:53.603213 INFO: ==============================================
0:40:53.851963 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
0:40:53.852108 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
0:40:53.852163 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
0:40:53.852188 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
0:40:53.853215 INFO: Starting candidate selection
1:10:45.577568 INFO: Starting candidate scoring
1:10:55.421056 INFO: Finished candidate processing
1:10:55.421255 INFO: Collecting candidate features
1:10:57.442974 WARNING: intensity_correlation has 240 NaNs ( 0.03 % out of 731852)
1:10:57.444026 WARNING: height_correlation has 26 NaNs ( 0.00 % out of 731852)
1:10:57.468779 INFO: Collecting fragment features
1:10:57.942835 INFO: Finished candidate scoring
1:10:58.943089 INFO: performing precursor FDR with 47 features
1:10:58.943259 INFO: Decoy channel: -1
1:10:58.943294 INFO: competitive: True
1:10:59.705518 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:59.998950 WARNING: dropped 218 target PSMs due to missing features
1:10:59.999123 WARNING: dropped 290 decoy PSMs due to missing features
1:11:00.537107 INFO: Estimating optimal hyperparameters - samples: 1,169,868, batch_size: 4,096, learning_rate: 1.00e-03
1:11:00.540396 INFO: Using random state 181241 for train-test-split
1:11:35.935429 INFO: Test AUC: 0.549
1:11:35.935825 INFO: Train AUC: 0.562
1:11:35.935873 INFO: AUC difference: 2.42%
1:11:37.605660 INFO: Resetting torch num_threads to 80
1:11:38.156083 PROGRESS: === Extracted 1462843 precursors and 12239663 fragments ===
1:11:38.157773 INFO: === FDR correction performed with classifier version -1 ===
1:11:38.303258 PROGRESS: ============================= Precursor FDR =============================
1:11:38.303611 PROGRESS: Total precursors accumulated: 743,082
1:11:38.303703 PROGRESS: Target precursors: 423,512 (56.99%)
1:11:38.303770 PROGRESS: Decoy precursors: 319,570 (43.01%)
1:11:38.303831 PROGRESS: 
1:11:38.303884 PROGRESS: Precursor Summary:
1:11:38.309827 PROGRESS: Channel   0:	 0.050 FDR:   647; 0.010 FDR:   306; 0.001 FDR:   189
1:11:38.310059 PROGRESS: 
1:11:38.310151 PROGRESS: Protein Summary:
1:11:38.315106 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   204; 0.001 FDR:   140
1:11:38.315219 PROGRESS: =========================================================================
1:11:38.326265 INFO: Target number of precursors reached.
1:11:39.673070 INFO: fragments_df: keeping 2897 of 12239663 [sum(precursor_idx_mask)=3407 sum(mass_error_mask)=12239596 stop_rank=2897
1:11:41.522430 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:11:41.680665 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:11:41.806798 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:11:41.935286 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:11:42.343997 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:11:42.344465 INFO: Using score_cutoff 39.87393434143066 (fac=0.99, q=1)
1:11:42.345012 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.8347771167755127
1:11:42.345098 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0076146116480231285
1:11:42.345162 INFO: Updating optimization_manager: score_cutoff        : 0 -> 39.87393434143066
1:11:42.345249 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:11:42.593924 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:11:43.728917 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:11:43.983333 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:11:46.129618 INFO: Updating optimization_manager: classifier_version  : -1 -> 11
1:11:46.129917 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:11:46.130086 INFO: Starting optimization step 12.
1:11:46.130169 PROGRESS: === Extracting elution groups 0 to 819000 ===
1:11:46.130320 INFO: Using python extraction backend
1:11:46.130603 PROGRESS: Extracting batch of 1632996 precursors
1:11:46.130705 INFO: === Search parameters used ===
1:11:46.130773 INFO: rt_error       : 1199.955978
1:11:46.130823 INFO: mobility_error : 0.1
1:11:46.130871 INFO: num_candidates : 3
1:11:46.130917 INFO: ms1_error      : 30
1:11:46.130961 INFO: ms2_error      : 30
1:11:46.131004 INFO: fwhm_rt        : 2.8347771167755127
1:11:46.131047 INFO: quant_window   : 3
1:11:46.131089 INFO: ==============================================
1:11:46.626227 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1:11:46.626389 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1:11:46.626476 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
1:11:46.626503 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.13
1:11:46.627512 INFO: Starting candidate selection
2:16:43.597422 INFO: Starting candidate scoring
2:17:42.196378 INFO: Finished candidate processing
2:17:42.196952 INFO: Collecting candidate features
2:17:51.399297 WARNING: intensity_correlation has 1486 NaNs ( 0.04 % out of 4200799)
2:17:51.403723 WARNING: height_correlation has 178 NaNs ( 0.00 % out of 4200799)
2:17:51.562963 INFO: Collecting fragment features
2:17:55.664872 INFO: Finished candidate scoring
2:17:59.230126 INFO: performing precursor FDR with 47 features
2:17:59.230275 INFO: Decoy channel: -1
2:17:59.230309 INFO: competitive: True
2:18:00.224384 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:00.824645 WARNING: dropped 718 target PSMs due to missing features
2:18:00.824810 WARNING: dropped 891 decoy PSMs due to missing features
2:18:02.590133 INFO: Estimating optimal hyperparameters - samples: 3,359,352, batch_size: 4,096, learning_rate: 1.00e-03
2:18:02.603461 INFO: Using random state 787549 for train-test-split
2:19:42.632135 INFO: Test AUC: 0.561
2:19:42.632403 INFO: Train AUC: 0.565
2:19:42.632443 INFO: AUC difference: 0.85%
2:19:44.259993 INFO: Resetting torch num_threads to 80
2:19:44.354758 PROGRESS: === Extracted 4200799 precursors and 34339454 fragments ===
2:19:44.356433 INFO: === FDR correction performed with classifier version 11 ===
2:19:44.509728 PROGRESS: ============================= Precursor FDR =============================
2:19:44.510046 PROGRESS: Total precursors accumulated: 749,547
2:19:44.510132 PROGRESS: Target precursors: 437,508 (58.37%)
2:19:44.510192 PROGRESS: Decoy precursors: 312,039 (41.63%)
2:19:44.510261 PROGRESS: 
2:19:44.510314 PROGRESS: Precursor Summary:
2:19:44.516335 PROGRESS: Channel   0:	 0.050 FDR:   724; 0.010 FDR:     0; 0.001 FDR:     0
2:19:44.516482 PROGRESS: 
2:19:44.516548 PROGRESS: Protein Summary:
2:19:44.521420 PROGRESS: Channel   0:	 0.050 FDR:   443; 0.010 FDR:     0; 0.001 FDR:     0
2:19:44.521531 PROGRESS: =========================================================================
2:19:44.548877 INFO: Target number of precursors not reached yet.
2:19:46.593968 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:19:46.844458 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:19:47.975225 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:19:48.235110 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:19:50.276676 INFO: === skipping optimization until target number of precursors are found ===
2:19:50.277044 INFO: Starting optimization step 13.
2:19:50.277158 PROGRESS: === Extracting elution groups 819000 to 1638200 ===
2:19:50.277273 INFO: Using python extraction backend
2:19:50.277470 PROGRESS: Extracting batch of 1633286 precursors
2:19:50.277585 INFO: === Search parameters used ===
2:19:50.277646 INFO: rt_error       : 1199.955978
2:19:50.277700 INFO: mobility_error : 0.1
2:19:50.277749 INFO: num_candidates : 3
2:19:50.277799 INFO: ms1_error      : 30
2:19:50.277845 INFO: ms2_error      : 30
2:19:50.277907 INFO: fwhm_rt        : 2.8347771167755127
2:19:50.277956 INFO: quant_window   : 3
2:19:50.278005 INFO: ==============================================
2:19:50.946308 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2:19:50.946465 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2:19:50.946544 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
2:19:50.946577 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.13
2:19:50.947579 INFO: Starting candidate selection
3:29:39.891544 INFO: Starting candidate scoring
3:30:32.711596 INFO: Finished candidate processing
3:30:32.712196 INFO: Collecting candidate features
3:30:42.284400 WARNING: intensity_correlation has 1523 NaNs ( 0.04 % out of 4201127)
3:30:42.288837 WARNING: height_correlation has 162 NaNs ( 0.00 % out of 4201127)
3:30:42.446069 INFO: Collecting fragment features
3:30:47.381449 INFO: Finished candidate scoring
3:30:52.079206 INFO: performing precursor FDR with 47 features
3:30:52.079490 INFO: Decoy channel: -1
3:30:52.079525 INFO: competitive: True
3:30:56.029326 INFO: Setting torch num_threads to 2 for FDR classification task
3:30:57.655511 WARNING: dropped 1446 target PSMs due to missing features
3:30:57.655678 WARNING: dropped 1793 decoy PSMs due to missing features
3:31:02.978401 INFO: Estimating optimal hyperparameters - samples: 6,718,949, batch_size: 4,096, learning_rate: 1.00e-03
3:31:03.008071 INFO: Using random state 787549 for train-test-split
3:34:33.865107 INFO: Test AUC: 0.569
3:34:33.865731 INFO: Train AUC: 0.570
3:34:33.865783 INFO: AUC difference: 0.30%
3:34:36.607497 INFO: Resetting torch num_threads to 80
3:34:38.907043 PROGRESS: === Extracted 8401926 precursors and 68681671 fragments ===
3:34:38.910505 INFO: === FDR correction performed with classifier version 11 ===
3:34:39.151476 PROGRESS: ============================= Precursor FDR =============================
3:34:39.151828 PROGRESS: Total precursors accumulated: 1,499,300
3:34:39.151922 PROGRESS: Target precursors: 883,007 (58.89%)
3:34:39.151990 PROGRESS: Decoy precursors: 616,293 (41.11%)
3:34:39.152047 PROGRESS: 
3:34:39.152125 PROGRESS: Precursor Summary:
3:34:39.162506 PROGRESS: Channel   0:	 0.050 FDR: 1,388; 0.010 FDR: 1,065; 0.001 FDR:   510
3:34:39.162672 PROGRESS: 
3:34:39.162753 PROGRESS: Protein Summary:
3:34:39.171754 PROGRESS: Channel   0:	 0.050 FDR:   638; 0.010 FDR:   465; 0.001 FDR:   257
3:34:39.171908 PROGRESS: =========================================================================
3:34:39.194612 INFO: Target number of precursors reached.
3:34:47.072719 INFO: fragments_df: keeping 5000 of 68681671 [sum(precursor_idx_mask)=31088 sum(mass_error_mask)=68681170 stop_rank=5000
3:34:48.601166 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:34:48.805463 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:34:49.012596 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:34:49.210342 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:34:49.931502 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:34:49.931979 INFO: Using score_cutoff 39.375123348999026 (fac=0.99, q=1)
3:34:49.932505 INFO: Updating optimization_manager: fwhm_rt             : 2.8347771167755127 -> 2.867489814758301
3:34:49.932593 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076146116480231285 -> 0.007631297223269939
3:34:49.932656 INFO: Updating optimization_manager: score_cutoff        : 39.87393434143066 -> 39.375123348999026
3:34:49.932745 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:34:50.038018 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:34:50.577945 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:34:50.685212 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:34:51.728232 INFO: === checking if optimization conditions were reached ===
3:34:51.730682 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
3:34:51.730879 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
3:34:51.730965 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
3:34:51.732232 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
3:34:51.732340 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
3:34:51.732411 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
3:34:51.732487 INFO: ==============================================
3:34:51.732586 INFO: Starting optimization step 14.
3:34:51.732657 PROGRESS: === Extracting elution groups 0 to 409400 ===
3:34:51.732791 INFO: Using python extraction backend
3:34:51.733197 PROGRESS: Extracting batch of 816307 precursors
3:34:51.733299 INFO: === Search parameters used ===
3:34:51.733356 INFO: rt_error       : 1199.955978
3:34:51.733405 INFO: mobility_error : 0.1
3:34:51.733452 INFO: num_candidates : 3
3:34:51.733497 INFO: ms1_error      : 15.0
3:34:51.733540 INFO: ms2_error      : 15.0
3:34:51.733588 INFO: fwhm_rt        : 2.867489814758301
3:34:51.733632 INFO: quant_window   : 3
3:34:51.733676 INFO: ==============================================
3:34:52.007401 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3:34:52.007547 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3:34:52.007625 INFO: FWHM in RT is 2.87 seconds, sigma is 0.48
3:34:52.007652 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.14
3:34:52.008546 INFO: Starting candidate selection
4:04:20.991720 INFO: Starting candidate scoring
4:04:44.805234 INFO: Finished candidate processing
4:04:44.805694 INFO: Collecting candidate features
4:04:48.905739 WARNING: intensity_correlation has 2490 NaNs ( 0.12 % out of 2047657)
4:04:48.907986 WARNING: height_correlation has 161 NaNs ( 0.01 % out of 2047657)
4:04:48.984528 INFO: Collecting fragment features
4:04:50.195259 INFO: Finished candidate scoring
4:04:51.802918 INFO: performing precursor FDR with 47 features
4:04:51.803169 INFO: Decoy channel: -1
4:04:51.803202 INFO: competitive: True
4:04:52.308309 INFO: Setting torch num_threads to 2 for FDR classification task
4:04:52.619555 WARNING: dropped 1273 target PSMs due to missing features
4:04:52.619748 WARNING: dropped 1321 decoy PSMs due to missing features
4:04:53.616660 INFO: Estimating optimal hyperparameters - samples: 1,636,050, batch_size: 4,096, learning_rate: 1.00e-03
4:04:53.620516 INFO: Using random state 610008 for train-test-split
4:05:31.482341 INFO: Test AUC: 0.563
4:05:31.482605 INFO: Train AUC: 0.574
4:05:31.482645 INFO: AUC difference: 2.04%
4:05:32.413284 INFO: Resetting torch num_threads to 80
4:05:32.449054 PROGRESS: === Extracted 2047657 precursors and 14241526 fragments ===
4:05:32.450431 INFO: === FDR correction performed with classifier version 13 ===
4:05:32.513717 PROGRESS: ============================= Precursor FDR =============================
4:05:32.514017 PROGRESS: Total precursors accumulated: 373,063
4:05:32.514095 PROGRESS: Target precursors: 220,269 (59.04%)
4:05:32.514159 PROGRESS: Decoy precursors: 152,794 (40.96%)
4:05:32.514215 PROGRESS: 
4:05:32.514269 PROGRESS: Precursor Summary:
4:05:32.518078 PROGRESS: Channel   0:	 0.050 FDR:   510; 0.010 FDR:   403; 0.001 FDR:   229
4:05:32.518221 PROGRESS: 
4:05:32.518291 PROGRESS: Protein Summary:
4:05:32.521640 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   296; 0.001 FDR:   162
4:05:32.521754 PROGRESS: =========================================================================
4:05:32.572182 INFO: Target number of precursors reached.
4:05:34.087383 INFO: fragments_df: keeping 5000 of 14241526 [sum(precursor_idx_mask)=10753 sum(mass_error_mask)=14241312 stop_rank=5000
4:05:34.693786 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:05:34.816094 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:05:34.942269 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:05:35.069805 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:05:35.717969 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:05:35.718424 INFO: Using score_cutoff 29.309723286437986 (fac=0.99, q=1)
4:05:35.718841 INFO: Updating optimization_manager: fwhm_rt             : 2.867489814758301 -> 2.6639857292175293
4:05:35.718929 INFO: Updating optimization_manager: fwhm_mobility       : 0.007631297223269939 -> 0.006135737057775259
4:05:35.718994 INFO: Updating optimization_manager: score_cutoff        : 39.375123348999026 -> 29.309723286437986
4:05:35.719080 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:05:35.770935 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:05:36.022013 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:05:36.075206 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:05:36.567079 INFO: === checking if optimization conditions were reached ===
4:05:36.569434 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
4:05:36.569630 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
4:05:36.569732 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
4:05:36.570900 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
4:05:36.571021 INFO: Updating optimization_manager: classifier_version  : 14 -> 14
4:05:36.571105 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
4:05:36.571181 INFO: ==============================================
4:05:36.571288 PROGRESS: Optimization finished for ms2_error, ms1_error.
4:05:37.134733 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:05:37.186585 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:05:37.442864 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:05:37.495811 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:05:37.977332 INFO: Starting optimization step 0.
4:05:37.977596 PROGRESS: === Extracting elution groups 0 to 204600 ===
4:05:37.977736 INFO: Using python extraction backend
4:05:37.977945 PROGRESS: Extracting batch of 407917 precursors
4:05:37.978047 INFO: === Search parameters used ===
4:05:37.978106 INFO: rt_error       : 1199.955978
4:05:37.978157 INFO: mobility_error : 0.1
4:05:37.978204 INFO: num_candidates : 3
4:05:37.978250 INFO: ms1_error      : 15.0
4:05:37.978307 INFO: ms2_error      : 15.0
4:05:37.978357 INFO: fwhm_rt        : 2.6639857292175293
4:05:37.978403 INFO: quant_window   : 3
4:05:37.978447 INFO: ==============================================
4:05:38.083921 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
4:05:38.084061 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
4:05:38.084135 INFO: FWHM in RT is 2.66 seconds, sigma is 0.44
4:05:38.084162 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.33
4:05:38.084988 INFO: Starting candidate selection
4:20:40.850354 INFO: Starting candidate scoring
4:20:53.068590 INFO: Finished candidate processing
4:20:53.068768 INFO: Collecting candidate features
4:20:55.592234 WARNING: intensity_correlation has 1190 NaNs ( 0.12 % out of 1019995)
4:20:55.593788 WARNING: height_correlation has 83 NaNs ( 0.01 % out of 1019995)
4:20:55.633634 INFO: Collecting fragment features
4:20:56.441549 INFO: Finished candidate scoring
4:20:57.650307 INFO: performing precursor FDR with 47 features
4:20:57.650454 INFO: Decoy channel: -1
4:20:57.650484 INFO: competitive: True
4:20:58.118848 INFO: Setting torch num_threads to 2 for FDR classification task
4:20:58.306036 WARNING: dropped 612 target PSMs due to missing features
4:20:58.306198 WARNING: dropped 633 decoy PSMs due to missing features
4:20:58.665784 INFO: Estimating optimal hyperparameters - samples: 815,000, batch_size: 3,338, learning_rate: 9.03e-04
4:20:58.668150 INFO: Using random state 355727 for train-test-split
4:21:23.787322 INFO: Test AUC: 0.569
4:21:23.787671 INFO: Train AUC: 0.587
4:21:23.787741 INFO: AUC difference: 2.98%
4:21:24.377047 INFO: Resetting torch num_threads to 80
4:21:24.400169 PROGRESS: === Extracted 1019995 precursors and 7041032 fragments ===
4:21:24.401140 INFO: === FDR correction performed with classifier version 14 ===
4:21:24.439515 PROGRESS: ============================= Precursor FDR =============================
4:21:24.439804 PROGRESS: Total precursors accumulated: 186,355
4:21:24.439879 PROGRESS: Target precursors: 111,818 (60.00%)
4:21:24.439939 PROGRESS: Decoy precursors: 74,537 (40.00%)
4:21:24.439993 PROGRESS: 
4:21:24.440051 PROGRESS: Precursor Summary:
4:21:24.442477 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   187; 0.001 FDR:   174
4:21:24.442585 PROGRESS: 
4:21:24.442652 PROGRESS: Protein Summary:
4:21:24.444818 PROGRESS: Channel   0:	 0.050 FDR:   216; 0.010 FDR:   147; 0.001 FDR:   139
4:21:24.444915 PROGRESS: =========================================================================
4:21:24.483555 INFO: Target number of precursors not reached yet.
4:21:25.120545 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:21:25.172954 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:21:25.427631 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:21:25.482018 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:21:25.991273 INFO: === skipping optimization until target number of precursors are found ===
4:21:25.991604 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
4:21:25.991744 INFO: Starting optimization step 1.
4:21:25.991819 PROGRESS: === Extracting elution groups 204600 to 409400 ===
4:21:25.991916 INFO: Using python extraction backend
4:21:25.992085 PROGRESS: Extracting batch of 408390 precursors
4:21:25.992180 INFO: === Search parameters used ===
4:21:25.992235 INFO: rt_error       : 1199.955978
4:21:25.992284 INFO: mobility_error : 0.1
4:21:25.992330 INFO: num_candidates : 3
4:21:25.992376 INFO: ms1_error      : 15.0
4:21:25.992420 INFO: ms2_error      : 15.0
4:21:25.992462 INFO: fwhm_rt        : 2.6639857292175293
4:21:25.992504 INFO: quant_window   : 3
4:21:25.992546 INFO: ==============================================
4:21:26.111343 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
4:21:26.111492 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
4:21:26.111552 INFO: FWHM in RT is 2.66 seconds, sigma is 0.44
4:21:26.111576 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.33
4:21:26.112397 INFO: Starting candidate selection
4:36:48.300056 INFO: Starting candidate scoring
4:37:00.070500 INFO: Finished candidate processing
4:37:00.070992 INFO: Collecting candidate features
4:37:02.218097 WARNING: intensity_correlation has 1295 NaNs ( 0.13 % out of 1019119)
4:37:02.219328 WARNING: height_correlation has 75 NaNs ( 0.01 % out of 1019119)
4:37:02.255577 INFO: Collecting fragment features
4:37:02.961696 INFO: Finished candidate scoring
4:37:04.640828 INFO: performing precursor FDR with 47 features
4:37:04.640983 INFO: Decoy channel: -1
4:37:04.641016 INFO: competitive: True
4:37:05.958494 INFO: Setting torch num_threads to 2 for FDR classification task
4:37:06.368222 WARNING: dropped 1248 target PSMs due to missing features
4:37:06.368389 WARNING: dropped 1341 decoy PSMs due to missing features
4:37:07.622290 INFO: Estimating optimal hyperparameters - samples: 1,629,220, batch_size: 4,096, learning_rate: 1.00e-03
4:37:07.625484 INFO: Using random state 355727 for train-test-split
4:37:55.013726 INFO: Test AUC: 0.569
4:37:55.014045 INFO: Train AUC: 0.579
4:37:55.014086 INFO: AUC difference: 1.82%
4:37:55.911611 INFO: Resetting torch num_threads to 80
4:37:56.655386 PROGRESS: === Extracted 2039114 precursors and 14074171 fragments ===
4:37:56.656752 INFO: === FDR correction performed with classifier version 14 ===
4:37:56.723667 PROGRESS: ============================= Precursor FDR =============================
4:37:56.723973 PROGRESS: Total precursors accumulated: 372,520
4:37:56.724072 PROGRESS: Target precursors: 221,039 (59.34%)
4:37:56.724138 PROGRESS: Decoy precursors: 151,481 (40.66%)
4:37:56.724199 PROGRESS: 
4:37:56.724250 PROGRESS: Precursor Summary:
4:37:56.728362 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   370; 0.001 FDR:   339
4:37:56.728512 PROGRESS: 
4:37:56.728592 PROGRESS: Protein Summary:
4:37:56.732122 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   269; 0.001 FDR:   241
4:37:56.732230 PROGRESS: =========================================================================
4:37:56.738583 INFO: Target number of precursors reached.
4:37:58.341022 INFO: fragments_df: keeping 5000 of 14074171 [sum(precursor_idx_mask)=9981 sum(mass_error_mask)=14073989 stop_rank=5000
4:37:59.390279 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:37:59.527821 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:37:59.650907 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:37:59.780962 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:38:00.445436 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:38:00.445935 INFO: Using score_cutoff 28.64835895729065 (fac=0.99, q=1)
4:38:00.446357 INFO: Updating optimization_manager: fwhm_rt             : 2.6639857292175293 -> 2.7232935428619385
4:38:00.446451 INFO: Updating optimization_manager: fwhm_mobility       : 0.006135737057775259 -> 0.0063267359510064125
4:38:00.446522 INFO: Updating optimization_manager: score_cutoff        : 29.309723286437986 -> 28.64835895729065
4:38:00.446611 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:38:00.552148 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:38:01.070507 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:38:01.184209 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:38:02.198488 INFO: === checking if optimization conditions were reached ===
4:38:02.198793 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
4:38:02.201063 INFO: Updating optimization_manager: rt_error            : 1199.955978 -> 673.0758844355967
4:38:02.201199 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 673.0759.
4:38:02.201281 INFO: ==============================================
4:38:02.201375 INFO: Starting optimization step 2.
4:38:02.201449 PROGRESS: === Extracting elution groups 0 to 409400 ===
4:38:02.201545 INFO: Using python extraction backend
4:38:02.201720 PROGRESS: Extracting batch of 816307 precursors
4:38:02.201808 INFO: === Search parameters used ===
4:38:02.201888 INFO: rt_error       : 673.0758844355967
4:38:02.201956 INFO: mobility_error : 0.1
4:38:02.202014 INFO: num_candidates : 3
4:38:02.202067 INFO: ms1_error      : 15.0
4:38:02.202122 INFO: ms2_error      : 15.0
4:38:02.202176 INFO: fwhm_rt        : 2.7232935428619385
4:38:02.202245 INFO: quant_window   : 3
4:38:02.202304 INFO: ==============================================
4:38:02.438523 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
4:38:02.438668 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
4:38:02.438729 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
4:38:02.438755 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.43
4:38:02.439583 INFO: Starting candidate selection
4:58:07.228240 INFO: Starting candidate scoring
4:58:30.468707 INFO: Finished candidate processing
4:58:30.468911 INFO: Collecting candidate features
4:58:35.664563 WARNING: intensity_correlation has 3336 NaNs ( 0.17 % out of 2006596)
4:58:35.666749 WARNING: height_correlation has 237 NaNs ( 0.01 % out of 2006596)
4:58:35.741118 INFO: Collecting fragment features
4:58:36.956755 INFO: Finished candidate scoring
4:58:39.034302 INFO: performing precursor FDR with 47 features
4:58:39.034468 INFO: Decoy channel: -1
4:58:39.034504 INFO: competitive: True
4:58:39.719224 INFO: Setting torch num_threads to 2 for FDR classification task
4:58:40.181106 WARNING: dropped 1696 target PSMs due to missing features
4:58:40.181269 WARNING: dropped 1782 decoy PSMs due to missing features
4:58:40.977642 INFO: Estimating optimal hyperparameters - samples: 1,602,494, batch_size: 4,096, learning_rate: 1.00e-03
4:58:40.984766 INFO: Using random state 355727 for train-test-split
4:59:19.324781 INFO: Test AUC: 0.562
4:59:19.324990 INFO: Train AUC: 0.575
4:59:19.325027 INFO: AUC difference: 2.17%
4:59:20.237905 INFO: Resetting torch num_threads to 80
4:59:20.300103 PROGRESS: === Extracted 2006596 precursors and 13531660 fragments ===
4:59:20.301494 INFO: === FDR correction performed with classifier version 14 ===
4:59:20.392981 PROGRESS: ============================= Precursor FDR =============================
4:59:20.393319 PROGRESS: Total precursors accumulated: 371,292
4:59:20.393409 PROGRESS: Target precursors: 217,370 (58.54%)
4:59:20.393473 PROGRESS: Decoy precursors: 153,922 (41.46%)
4:59:20.393537 PROGRESS: 
4:59:20.393591 PROGRESS: Precursor Summary:
4:59:20.397553 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:   377; 0.001 FDR:   373
4:59:20.397701 PROGRESS: 
4:59:20.397775 PROGRESS: Protein Summary:
4:59:20.401090 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   269; 0.001 FDR:   266
4:59:20.401200 PROGRESS: =========================================================================
4:59:20.417514 INFO: Target number of precursors reached.
4:59:21.871069 INFO: fragments_df: keeping 5000 of 13531660 [sum(precursor_idx_mask)=10229 sum(mass_error_mask)=13531423 stop_rank=5000
4:59:23.509498 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:59:23.655699 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:59:23.809218 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:59:23.961159 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:59:24.676159 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:59:24.676681 INFO: Using score_cutoff 31.226599758911135 (fac=0.99, q=1)
4:59:24.677097 INFO: Updating optimization_manager: fwhm_rt             : 2.7232935428619385 -> 2.6674482822418213
4:59:24.677188 INFO: Updating optimization_manager: fwhm_mobility       : 0.0063267359510064125 -> 0.006153266876935959
4:59:24.677250 INFO: Updating optimization_manager: score_cutoff        : 28.64835895729065 -> 31.226599758911135
4:59:24.677333 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:59:24.787016 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:59:25.316369 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:59:25.424712 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:59:26.631314 INFO: === checking if optimization conditions were reached ===
4:59:26.631697 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
4:59:26.634326 INFO: Updating optimization_manager: rt_error            : 673.0758844355967 -> 346.1962488910027
4:59:26.634473 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 346.1962.
4:59:26.634561 INFO: ==============================================
4:59:26.634668 INFO: Starting optimization step 3.
4:59:26.634749 PROGRESS: === Extracting elution groups 0 to 409400 ===
4:59:26.634864 INFO: Using python extraction backend
4:59:26.635074 PROGRESS: Extracting batch of 816307 precursors
4:59:26.635184 INFO: === Search parameters used ===
4:59:26.635255 INFO: rt_error       : 346.1962488910027
4:59:26.635315 INFO: mobility_error : 0.1
4:59:26.635375 INFO: num_candidates : 3
4:59:26.635433 INFO: ms1_error      : 15.0
4:59:26.635490 INFO: ms2_error      : 15.0
4:59:26.635546 INFO: fwhm_rt        : 2.6674482822418213
4:59:26.635602 INFO: quant_window   : 3
4:59:26.635659 INFO: ==============================================
4:59:26.907963 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
4:59:26.908126 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
4:59:26.908203 INFO: FWHM in RT is 2.67 seconds, sigma is 0.44
4:59:26.908235 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.34
4:59:26.909132 INFO: Starting candidate selection
5:09:04.284359 INFO: Starting candidate scoring
5:09:28.056536 INFO: Finished candidate processing
5:09:28.056994 INFO: Collecting candidate features
5:09:32.156168 WARNING: intensity_correlation has 4906 NaNs ( 0.25 % out of 1926413)
5:09:32.158170 WARNING: height_correlation has 446 NaNs ( 0.02 % out of 1926413)
5:09:32.242906 INFO: Collecting fragment features
5:09:33.527929 INFO: Finished candidate scoring
5:09:34.779671 INFO: performing precursor FDR with 47 features
5:09:34.779829 INFO: Decoy channel: -1
5:09:34.779867 INFO: competitive: True
5:09:35.340293 INFO: Setting torch num_threads to 2 for FDR classification task
5:09:35.657841 WARNING: dropped 2508 target PSMs due to missing features
5:09:35.658057 WARNING: dropped 2639 decoy PSMs due to missing features
5:09:36.459814 INFO: Estimating optimal hyperparameters - samples: 1,537,012, batch_size: 4,096, learning_rate: 1.00e-03
5:09:36.462862 INFO: Using random state 355727 for train-test-split
5:10:20.186938 INFO: Test AUC: 0.556
5:10:20.187192 INFO: Train AUC: 0.568
5:10:20.187229 INFO: AUC difference: 2.02%
5:10:21.070012 INFO: Resetting torch num_threads to 80
5:10:21.123288 PROGRESS: === Extracted 1926413 precursors and 11844379 fragments ===
5:10:21.124490 INFO: === FDR correction performed with classifier version 14 ===
5:10:21.196426 PROGRESS: ============================= Precursor FDR =============================
5:10:21.196704 PROGRESS: Total precursors accumulated: 367,880
5:10:21.196792 PROGRESS: Target precursors: 212,121 (57.66%)
5:10:21.196857 PROGRESS: Decoy precursors: 155,759 (42.34%)
5:10:21.196912 PROGRESS: 
5:10:21.196973 PROGRESS: Precursor Summary:
5:10:21.200695 PROGRESS: Channel   0:	 0.050 FDR:   551; 0.010 FDR:   439; 0.001 FDR:   388
5:10:21.200831 PROGRESS: 
5:10:21.200895 PROGRESS: Protein Summary:
5:10:21.204184 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   319; 0.001 FDR:   280
5:10:21.204316 PROGRESS: =========================================================================
5:10:21.218655 INFO: Target number of precursors reached.
5:10:22.499616 INFO: fragments_df: keeping 5000 of 11844379 [sum(precursor_idx_mask)=11869 sum(mass_error_mask)=11843915 stop_rank=5000
5:10:23.369653 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:10:23.489394 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:10:23.610790 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:10:23.737662 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:10:24.387444 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:10:24.387909 INFO: Using score_cutoff 25.53247663536072 (fac=0.99, q=1)
5:10:24.388269 INFO: Updating optimization_manager: fwhm_rt             : 2.6674482822418213 -> 2.63781476020813
5:10:24.388355 INFO: Updating optimization_manager: fwhm_mobility       : 0.006153266876935959 -> 0.005494628567248583
5:10:24.388420 INFO: Updating optimization_manager: score_cutoff        : 31.226599758911135 -> 25.53247663536072
5:10:24.388486 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:10:24.438803 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:10:24.698206 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:10:24.751414 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:10:25.251621 INFO: === checking if optimization conditions were reached ===
5:10:25.251902 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
5:10:25.254274 INFO: Updating optimization_manager: rt_error            : 346.1962488910027 -> 232.40270040041872
5:10:25.254436 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 232.4027.
5:10:25.254514 INFO: ==============================================
5:10:25.254592 INFO: Starting optimization step 4.
5:10:25.254658 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:10:25.254729 INFO: Using python extraction backend
5:10:25.254855 PROGRESS: Extracting batch of 407917 precursors
5:10:25.254931 INFO: === Search parameters used ===
5:10:25.254987 INFO: rt_error       : 232.40270040041872
5:10:25.255038 INFO: mobility_error : 0.1
5:10:25.255087 INFO: num_candidates : 3
5:10:25.255134 INFO: ms1_error      : 15.0
5:10:25.255181 INFO: ms2_error      : 15.0
5:10:25.255227 INFO: fwhm_rt        : 2.63781476020813
5:10:25.255275 INFO: quant_window   : 3
5:10:25.255322 INFO: ==============================================
5:10:25.383490 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:10:25.383658 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:10:25.383707 INFO: FWHM in RT is 2.64 seconds, sigma is 0.44
5:10:25.383734 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.98
5:10:25.384473 INFO: Starting candidate selection
5:13:49.504575 INFO: Starting candidate scoring
5:14:01.010420 INFO: Finished candidate processing
5:14:01.010622 INFO: Collecting candidate features
5:14:02.913329 WARNING: intensity_correlation has 2951 NaNs ( 0.32 % out of 934073)
5:14:02.914461 WARNING: height_correlation has 300 NaNs ( 0.03 % out of 934073)
5:14:02.948875 INFO: Collecting fragment features
5:14:03.394863 INFO: Finished candidate scoring
5:14:04.040218 INFO: performing precursor FDR with 47 features
5:14:04.040399 INFO: Decoy channel: -1
5:14:04.040433 INFO: competitive: True
5:14:04.305634 INFO: Setting torch num_threads to 2 for FDR classification task
5:14:04.482148 WARNING: dropped 1508 target PSMs due to missing features
5:14:04.482319 WARNING: dropped 1607 decoy PSMs due to missing features
5:14:04.807774 INFO: Estimating optimal hyperparameters - samples: 744,766, batch_size: 3,050, learning_rate: 8.63e-04
5:14:04.809447 INFO: Using random state 355727 for train-test-split
5:14:24.516758 INFO: Test AUC: 0.556
5:14:24.517020 INFO: Train AUC: 0.571
5:14:24.517059 INFO: AUC difference: 2.79%
5:14:25.069199 INFO: Resetting torch num_threads to 80
5:14:25.093567 PROGRESS: === Extracted 934073 precursors and 5479691 fragments ===
5:14:25.094491 INFO: === FDR correction performed with classifier version 14 ===
5:14:25.130553 PROGRESS: ============================= Precursor FDR =============================
5:14:25.130822 PROGRESS: Total precursors accumulated: 182,721
5:14:25.130897 PROGRESS: Target precursors: 105,906 (57.96%)
5:14:25.130982 PROGRESS: Decoy precursors: 76,815 (42.04%)
5:14:25.131044 PROGRESS: 
5:14:25.131095 PROGRESS: Precursor Summary:
5:14:25.133373 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   245; 0.001 FDR:   235
5:14:25.133477 PROGRESS: 
5:14:25.133539 PROGRESS: Protein Summary:
5:14:25.135692 PROGRESS: Channel   0:	 0.050 FDR:   254; 0.010 FDR:   196; 0.001 FDR:   186
5:14:25.135812 PROGRESS: =========================================================================
5:14:25.156242 INFO: Target number of precursors reached.
5:14:25.732718 INFO: fragments_df: keeping 4016 of 5479691 [sum(precursor_idx_mask)=6398 sum(mass_error_mask)=5479545 stop_rank=4016
5:14:26.429045 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:14:26.559381 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:14:27.719477 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:14:27.857685 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:14:28.426265 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:14:28.426730 INFO: Using score_cutoff 21.523825490570065 (fac=0.99, q=1)
5:14:28.427046 INFO: Updating optimization_manager: fwhm_rt             : 2.63781476020813 -> 2.700646162033081
5:14:28.427131 INFO: Updating optimization_manager: fwhm_mobility       : 0.005494628567248583 -> 0.00567212700843811
5:14:28.427194 INFO: Updating optimization_manager: score_cutoff        : 25.53247663536072 -> 21.523825490570065
5:14:28.427253 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:14:28.480075 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:14:28.736219 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:14:28.790513 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:14:29.325609 INFO: === checking if optimization conditions were reached ===
5:14:29.325929 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
5:14:29.328187 INFO: Updating optimization_manager: rt_error            : 232.40270040041872 -> 205.27020360928935
5:14:29.328325 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 205.2702.
5:14:29.328402 INFO: ==============================================
5:14:29.328499 INFO: Starting optimization step 5.
5:14:29.328568 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:14:29.328633 INFO: Using python extraction backend
5:14:29.328745 PROGRESS: Extracting batch of 407917 precursors
5:14:29.328817 INFO: === Search parameters used ===
5:14:29.328870 INFO: rt_error       : 205.27020360928935
5:14:29.328918 INFO: mobility_error : 0.1
5:14:29.328965 INFO: num_candidates : 3
5:14:29.329011 INFO: ms1_error      : 15.0
5:14:29.329057 INFO: ms2_error      : 15.0
5:14:29.329102 INFO: fwhm_rt        : 2.700646162033081
5:14:29.329149 INFO: quant_window   : 3
5:14:29.329203 INFO: ==============================================
5:14:29.451246 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:14:29.451399 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:14:29.451447 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
5:14:29.451473 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.08
5:14:29.452225 INFO: Starting candidate selection
5:17:28.922109 INFO: Starting candidate scoring
5:17:39.952938 INFO: Finished candidate processing
5:17:39.953219 INFO: Collecting candidate features
5:17:41.847999 WARNING: intensity_correlation has 3159 NaNs ( 0.35 % out of 913487)
5:17:41.849088 WARNING: height_correlation has 337 NaNs ( 0.04 % out of 913487)
5:17:41.883573 INFO: Collecting fragment features
5:17:42.381048 INFO: Finished candidate scoring
5:17:43.026554 INFO: performing precursor FDR with 47 features
5:17:43.026707 INFO: Decoy channel: -1
5:17:43.026737 INFO: competitive: True
5:17:43.315774 INFO: Setting torch num_threads to 2 for FDR classification task
5:17:43.479682 WARNING: dropped 1608 target PSMs due to missing features
5:17:43.479847 WARNING: dropped 1728 decoy PSMs due to missing features
5:17:43.799620 INFO: Estimating optimal hyperparameters - samples: 728,120, batch_size: 2,982, learning_rate: 8.53e-04
5:17:43.801636 INFO: Using random state 355727 for train-test-split
5:18:02.949368 INFO: Test AUC: 0.555
5:18:02.949608 INFO: Train AUC: 0.571
5:18:02.949644 INFO: AUC difference: 2.82%
5:18:03.506099 INFO: Resetting torch num_threads to 80
5:18:03.529805 PROGRESS: === Extracted 913487 precursors and 5285260 fragments ===
5:18:03.530694 INFO: === FDR correction performed with classifier version 14 ===
5:18:03.567646 PROGRESS: ============================= Precursor FDR =============================
5:18:03.567960 PROGRESS: Total precursors accumulated: 180,403
5:18:03.568044 PROGRESS: Target precursors: 103,995 (57.65%)
5:18:03.568107 PROGRESS: Decoy precursors: 76,408 (42.35%)
5:18:03.568168 PROGRESS: 
5:18:03.568220 PROGRESS: Precursor Summary:
5:18:03.570563 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   218; 0.001 FDR:   208
5:18:03.570705 PROGRESS: 
5:18:03.570772 PROGRESS: Protein Summary:
5:18:03.572957 PROGRESS: Channel   0:	 0.050 FDR:   242; 0.010 FDR:   171; 0.001 FDR:   162
5:18:03.573065 PROGRESS: =========================================================================
5:18:03.579648 INFO: Target number of precursors reached.
5:18:04.144253 INFO: fragments_df: keeping 3798 of 5285260 [sum(precursor_idx_mask)=5863 sum(mass_error_mask)=5285106 stop_rank=3798
5:18:04.840486 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:18:04.954440 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:18:05.067265 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:18:05.187291 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:18:05.659696 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:18:05.660162 INFO: Using score_cutoff 29.859271703338624 (fac=0.99, q=1)
5:18:05.660516 INFO: Updating optimization_manager: fwhm_rt             : 2.700646162033081 -> 2.6674604415893555
5:18:05.660606 INFO: Updating optimization_manager: fwhm_mobility       : 0.00567212700843811 -> 0.0057892752811312675
5:18:05.660671 INFO: Updating optimization_manager: score_cutoff        : 21.523825490570065 -> 29.859271703338624
5:18:05.660740 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:18:05.709591 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:18:05.969594 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:18:06.030892 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:18:06.563195 INFO: === checking if optimization conditions were reached ===
5:18:06.563510 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
5:18:06.565775 INFO: Updating optimization_manager: rt_error            : 205.27020360928935 -> 171.55160938517332
5:18:06.565921 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 171.5516.
5:18:06.566000 INFO: ==============================================
5:18:06.566077 INFO: Starting optimization step 6.
5:18:06.566141 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:18:06.566210 INFO: Using python extraction backend
5:18:06.566336 PROGRESS: Extracting batch of 407917 precursors
5:18:06.566411 INFO: === Search parameters used ===
5:18:06.566485 INFO: rt_error       : 171.55160938517332
5:18:06.566537 INFO: mobility_error : 0.1
5:18:06.566587 INFO: num_candidates : 3
5:18:06.566633 INFO: ms1_error      : 15.0
5:18:06.566678 INFO: ms2_error      : 15.0
5:18:06.566721 INFO: fwhm_rt        : 2.6674604415893555
5:18:06.566764 INFO: quant_window   : 3
5:18:06.566808 INFO: ==============================================
5:18:06.688105 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:18:06.688254 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:18:06.688300 INFO: FWHM in RT is 2.67 seconds, sigma is 0.44
5:18:06.688323 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.14
5:18:06.689078 INFO: Starting candidate selection
5:20:34.206351 INFO: Starting candidate scoring
5:20:45.469148 INFO: Finished candidate processing
5:20:45.469430 INFO: Collecting candidate features
5:20:47.320782 WARNING: intensity_correlation has 3625 NaNs ( 0.40 % out of 898423)
5:20:47.321844 WARNING: height_correlation has 404 NaNs ( 0.04 % out of 898423)
5:20:47.355356 INFO: Collecting fragment features
5:20:47.805275 INFO: Finished candidate scoring
5:20:48.429075 INFO: performing precursor FDR with 47 features
5:20:48.429229 INFO: Decoy channel: -1
5:20:48.429260 INFO: competitive: True
5:20:48.684414 INFO: Setting torch num_threads to 2 for FDR classification task
5:20:48.843304 WARNING: dropped 1912 target PSMs due to missing features
5:20:48.843472 WARNING: dropped 1918 decoy PSMs due to missing features
5:20:49.219514 INFO: Estimating optimal hyperparameters - samples: 715,674, batch_size: 2,931, learning_rate: 8.46e-04
5:20:49.221175 INFO: Using random state 355727 for train-test-split
5:21:10.863562 INFO: Test AUC: 0.551
5:21:10.863882 INFO: Train AUC: 0.568
5:21:10.863923 INFO: AUC difference: 3.08%
5:21:11.394341 INFO: Resetting torch num_threads to 80
5:21:11.413902 PROGRESS: === Extracted 898423 precursors and 5061958 fragments ===
5:21:11.414877 INFO: === FDR correction performed with classifier version 14 ===
5:21:11.453303 PROGRESS: ============================= Precursor FDR =============================
5:21:11.453573 PROGRESS: Total precursors accumulated: 179,955
5:21:11.453645 PROGRESS: Target precursors: 102,960 (57.21%)
5:21:11.453706 PROGRESS: Decoy precursors: 76,995 (42.79%)
5:21:11.453762 PROGRESS: 
5:21:11.453813 PROGRESS: Precursor Summary:
5:21:11.456145 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   301; 0.001 FDR:   283
5:21:11.456249 PROGRESS: 
5:21:11.456313 PROGRESS: Protein Summary:
5:21:11.458554 PROGRESS: Channel   0:	 0.050 FDR:   280; 0.010 FDR:   246; 0.001 FDR:   228
5:21:11.458658 PROGRESS: =========================================================================
5:21:11.464489 INFO: Target number of precursors reached.
5:21:12.014665 INFO: fragments_df: keeping 4479 of 5061958 [sum(precursor_idx_mask)=7736 sum(mass_error_mask)=5061815 stop_rank=4479
5:21:12.753120 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:21:12.887346 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:21:13.041245 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:21:13.181143 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:21:13.822671 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:21:13.823252 INFO: Using score_cutoff 22.049887390136718 (fac=0.99, q=1)
5:21:13.823667 INFO: Updating optimization_manager: fwhm_rt             : 2.6674604415893555 -> 2.648247718811035
5:21:13.823755 INFO: Updating optimization_manager: fwhm_mobility       : 0.0057892752811312675 -> 0.005587052088230848
5:21:13.823817 INFO: Updating optimization_manager: score_cutoff        : 29.859271703338624 -> 22.049887390136718
5:21:13.823883 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:21:13.883348 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:21:14.141695 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:21:14.199263 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:21:14.729831 INFO: === checking if optimization conditions were reached ===
5:21:14.730220 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
5:21:14.733140 INFO: Updating optimization_manager: rt_error            : 171.55160938517332 -> 165.27476451181877
5:21:14.733300 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 165.2748.
5:21:14.733387 INFO: ==============================================
5:21:14.733484 INFO: Starting optimization step 7.
5:21:14.733563 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:21:14.733644 INFO: Using python extraction backend
5:21:14.733787 PROGRESS: Extracting batch of 407917 precursors
5:21:14.733891 INFO: === Search parameters used ===
5:21:14.733964 INFO: rt_error       : 165.27476451181877
5:21:14.734024 INFO: mobility_error : 0.1
5:21:14.734082 INFO: num_candidates : 3
5:21:14.734137 INFO: ms1_error      : 15.0
5:21:14.734191 INFO: ms2_error      : 15.0
5:21:14.734251 INFO: fwhm_rt        : 2.648247718811035
5:21:14.734308 INFO: quant_window   : 3
5:21:14.734362 INFO: ==============================================
5:21:14.909601 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:21:14.909786 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:21:14.909852 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
5:21:14.909901 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.03
5:21:14.910768 INFO: Starting candidate selection
5:23:43.283763 INFO: Starting candidate scoring
5:23:54.128261 INFO: Finished candidate processing
5:23:54.128837 INFO: Collecting candidate features
5:23:55.991476 WARNING: intensity_correlation has 3548 NaNs ( 0.39 % out of 901926)
5:23:55.992635 WARNING: height_correlation has 399 NaNs ( 0.04 % out of 901926)
5:23:56.026052 INFO: Collecting fragment features
5:23:56.466789 INFO: Finished candidate scoring
5:23:57.119825 INFO: performing precursor FDR with 47 features
5:23:57.119978 INFO: Decoy channel: -1
5:23:57.120009 INFO: competitive: True
5:23:57.395164 INFO: Setting torch num_threads to 2 for FDR classification task
5:23:57.558341 WARNING: dropped 1879 target PSMs due to missing features
5:23:57.558511 WARNING: dropped 1868 decoy PSMs due to missing features
5:23:57.935666 INFO: Estimating optimal hyperparameters - samples: 718,543, batch_size: 2,943, learning_rate: 8.48e-04
5:23:57.937310 INFO: Using random state 355727 for train-test-split
5:24:16.669686 INFO: Test AUC: 0.552
5:24:16.670041 INFO: Train AUC: 0.571
5:24:16.670080 INFO: AUC difference: 3.42%
5:24:17.219094 INFO: Resetting torch num_threads to 80
5:24:17.241982 PROGRESS: === Extracted 901926 precursors and 5094430 fragments ===
5:24:17.242975 INFO: === FDR correction performed with classifier version 14 ===
5:24:17.278735 PROGRESS: ============================= Precursor FDR =============================
5:24:17.278986 PROGRESS: Total precursors accumulated: 180,241
5:24:17.279062 PROGRESS: Target precursors: 104,004 (57.70%)
5:24:17.279140 PROGRESS: Decoy precursors: 76,237 (42.30%)
5:24:17.279203 PROGRESS: 
5:24:17.279257 PROGRESS: Precursor Summary:
5:24:17.281557 PROGRESS: Channel   0:	 0.050 FDR:   306; 0.010 FDR:   247; 0.001 FDR:   229
5:24:17.281660 PROGRESS: 
5:24:17.281719 PROGRESS: Protein Summary:
5:24:17.283885 PROGRESS: Channel   0:	 0.050 FDR:   250; 0.010 FDR:   196; 0.001 FDR:   184
5:24:17.283995 PROGRESS: =========================================================================
5:24:17.291164 INFO: Target number of precursors reached.
5:24:17.843533 INFO: fragments_df: keeping 3923 of 5094430 [sum(precursor_idx_mask)=6395 sum(mass_error_mask)=5094285 stop_rank=3923
5:24:18.629031 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:24:18.771893 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:24:18.910784 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:24:19.054766 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:24:19.607859 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:24:19.608333 INFO: Using score_cutoff 22.478168624496462 (fac=0.99, q=1)
5:24:19.608692 INFO: Updating optimization_manager: fwhm_rt             : 2.648247718811035 -> 2.6846108436584473
5:24:19.608780 INFO: Updating optimization_manager: fwhm_mobility       : 0.005587052088230848 -> 0.005909050814807415
5:24:19.608847 INFO: Updating optimization_manager: score_cutoff        : 22.049887390136718 -> 22.478168624496462
5:24:19.608918 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:24:19.662545 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:24:19.915254 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:24:19.972216 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:24:20.515838 INFO: === checking if optimization conditions were reached ===
5:24:20.516135 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
5:24:20.517618 INFO: Updating optimization_manager: rt_error            : 165.27476451181877 -> 171.55160938517332
5:24:20.517780 INFO: Updating optimization_manager: classifier_version  : 14 -> 21
5:24:20.517919 INFO: Updating optimization_manager: score_cutoff        : 22.478168624496462 -> 22.049887390136718
5:24:20.518043 INFO: Updating optimization_manager: fwhm_rt             : 2.6846108436584473 -> 2.648247718811035
5:24:20.518158 INFO: Updating optimization_manager: fwhm_mobility       : 0.005909050814807415 -> 0.005587052088230848
5:24:20.518267 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 171.5516 found after 7 searches.
5:24:20.518345 INFO: ==============================================
5:24:20.518435 PROGRESS: Optimization finished for rt_error.
5:24:21.194702 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:24:21.249177 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:24:21.501175 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:24:21.563305 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:24:22.110066 INFO: Starting optimization step 0.
5:24:22.110333 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:24:22.110445 INFO: Using python extraction backend
5:24:22.110598 PROGRESS: Extracting batch of 407917 precursors
5:24:22.110686 INFO: === Search parameters used ===
5:24:22.110744 INFO: rt_error       : 171.55160938517332
5:24:22.110794 INFO: mobility_error : 0.1
5:24:22.110842 INFO: num_candidates : 3
5:24:22.110889 INFO: ms1_error      : 15.0
5:24:22.110935 INFO: ms2_error      : 15.0
5:24:22.110980 INFO: fwhm_rt        : 2.648247718811035
5:24:22.111026 INFO: quant_window   : 3
5:24:22.111071 INFO: ==============================================
5:24:22.229446 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:24:22.229585 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:24:22.229638 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
5:24:22.229664 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.03
5:24:22.230474 INFO: Starting candidate selection
5:26:49.149829 INFO: Starting candidate scoring
5:27:00.113942 INFO: Finished candidate processing
5:27:00.114289 INFO: Collecting candidate features
5:27:01.940955 WARNING: intensity_correlation has 3818 NaNs ( 0.43 % out of 882048)
5:27:01.941979 WARNING: height_correlation has 485 NaNs ( 0.05 % out of 882048)
5:27:01.974335 INFO: Collecting fragment features
5:27:02.401247 INFO: Finished candidate scoring
5:27:03.026966 INFO: performing precursor FDR with 47 features
5:27:03.027103 INFO: Decoy channel: -1
5:27:03.027136 INFO: competitive: True
5:27:03.275089 INFO: Setting torch num_threads to 2 for FDR classification task
5:27:03.432856 WARNING: dropped 2031 target PSMs due to missing features
5:27:03.433026 WARNING: dropped 2022 decoy PSMs due to missing features
5:27:03.831987 INFO: Estimating optimal hyperparameters - samples: 702,396, batch_size: 2,877, learning_rate: 8.38e-04
5:27:03.833567 INFO: Using random state 162299 for train-test-split
5:27:23.380745 INFO: Test AUC: 0.556
5:27:23.380938 INFO: Train AUC: 0.576
5:27:23.380975 INFO: AUC difference: 3.49%
5:27:23.917926 INFO: Resetting torch num_threads to 80
5:27:23.940028 PROGRESS: === Extracted 882048 precursors and 4900330 fragments ===
5:27:23.940900 INFO: === FDR correction performed with classifier version 21 ===
5:27:23.974598 PROGRESS: ============================= Precursor FDR =============================
5:27:23.974849 PROGRESS: Total precursors accumulated: 179,036
5:27:23.974922 PROGRESS: Target precursors: 103,481 (57.80%)
5:27:23.974988 PROGRESS: Decoy precursors: 75,555 (42.20%)
5:27:23.975041 PROGRESS: 
5:27:23.975095 PROGRESS: Precursor Summary:
5:27:23.977340 PROGRESS: Channel   0:	 0.050 FDR:   335; 0.010 FDR:   257; 0.001 FDR:   233
5:27:23.977469 PROGRESS: 
5:27:23.977549 PROGRESS: Protein Summary:
5:27:23.979897 PROGRESS: Channel   0:	 0.050 FDR:   279; 0.010 FDR:   210; 0.001 FDR:   188
5:27:23.980014 PROGRESS: =========================================================================
5:27:23.986188 INFO: Target number of precursors reached.
5:27:24.503030 INFO: fragments_df: keeping 4043 of 4900330 [sum(precursor_idx_mask)=6652 sum(mass_error_mask)=4900200 stop_rank=4043
5:27:25.199673 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:27:25.310175 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:27:25.425667 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:27:25.546036 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:27:26.050380 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:27:26.050850 INFO: Using score_cutoff 22.979633663177488 (fac=0.99, q=1)
5:27:26.051210 INFO: Updating optimization_manager: fwhm_rt             : 2.648247718811035 -> 2.6867687702178955
5:27:26.051301 INFO: Updating optimization_manager: fwhm_mobility       : 0.005587052088230848 -> 0.006111645605415106
5:27:26.051369 INFO: Updating optimization_manager: score_cutoff        : 22.049887390136718 -> 22.979633663177488
5:27:26.051436 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:27:26.108015 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:27:26.363736 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:27:26.422098 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:27:26.985835 INFO: === checking if optimization conditions were reached ===
5:27:26.986172 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
5:27:26.988077 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.08220444133992512
5:27:26.988207 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0822.
5:27:26.988282 INFO: ==============================================
5:27:26.988360 INFO: Starting optimization step 1.
5:27:26.988425 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:27:26.988498 INFO: Using python extraction backend
5:27:26.988627 PROGRESS: Extracting batch of 407917 precursors
5:27:26.988701 INFO: === Search parameters used ===
5:27:26.988753 INFO: rt_error       : 171.55160938517332
5:27:26.988800 INFO: mobility_error : 0.08220444133992512
5:27:26.988844 INFO: num_candidates : 3
5:27:26.988887 INFO: ms1_error      : 15.0
5:27:26.988937 INFO: ms2_error      : 15.0
5:27:26.988982 INFO: fwhm_rt        : 2.6867687702178955
5:27:26.989027 INFO: quant_window   : 3
5:27:26.989070 INFO: ==============================================
5:27:27.108591 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:27:27.108742 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:27:27.108788 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
5:27:27.108814 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.31
5:27:27.109517 INFO: Starting candidate selection
5:29:29.994504 INFO: Starting candidate scoring
5:29:40.958337 INFO: Finished candidate processing
5:29:40.958596 INFO: Collecting candidate features
5:29:42.698872 WARNING: intensity_correlation has 3910 NaNs ( 0.45 % out of 863082)
5:29:42.699905 WARNING: height_correlation has 480 NaNs ( 0.06 % out of 863082)
5:29:42.732512 INFO: Collecting fragment features
5:29:43.234186 INFO: Finished candidate scoring
5:29:44.059047 INFO: performing precursor FDR with 47 features
5:29:44.059200 INFO: Decoy channel: -1
5:29:44.059228 INFO: competitive: True
5:29:44.309991 INFO: Setting torch num_threads to 2 for FDR classification task
5:29:44.462980 WARNING: dropped 2087 target PSMs due to missing features
5:29:44.463148 WARNING: dropped 2052 decoy PSMs due to missing features
5:29:44.761513 INFO: Estimating optimal hyperparameters - samples: 687,154, batch_size: 2,814, learning_rate: 8.29e-04
5:29:44.762933 INFO: Using random state 162299 for train-test-split
5:30:04.153699 INFO: Test AUC: 0.555
5:30:04.153918 INFO: Train AUC: 0.577
5:30:04.153957 INFO: AUC difference: 3.69%
5:30:04.684123 INFO: Resetting torch num_threads to 80
5:30:04.705681 PROGRESS: === Extracted 863082 precursors and 4766775 fragments ===
5:30:04.706505 INFO: === FDR correction performed with classifier version 21 ===
5:30:04.744192 PROGRESS: ============================= Precursor FDR =============================
5:30:04.744453 PROGRESS: Total precursors accumulated: 176,129
5:30:04.744528 PROGRESS: Target precursors: 102,102 (57.97%)
5:30:04.744595 PROGRESS: Decoy precursors: 74,027 (42.03%)
5:30:04.744649 PROGRESS: 
5:30:04.744706 PROGRESS: Precursor Summary:
5:30:04.746892 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   143; 0.001 FDR:   118
5:30:04.747001 PROGRESS: 
5:30:04.747064 PROGRESS: Protein Summary:
5:30:04.749175 PROGRESS: Channel   0:	 0.050 FDR:   230; 0.010 FDR:   116; 0.001 FDR:    97
5:30:04.749274 PROGRESS: =========================================================================
5:30:04.755430 INFO: Target number of precursors not reached yet.
5:30:05.448869 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:30:05.504797 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:30:05.764714 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:30:05.826114 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:30:06.373297 INFO: === skipping optimization until target number of precursors are found ===
5:30:06.373567 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
5:30:06.373677 INFO: Starting optimization step 2.
5:30:06.373754 PROGRESS: === Extracting elution groups 204600 to 409400 ===
5:30:06.373827 INFO: Using python extraction backend
5:30:06.373994 PROGRESS: Extracting batch of 408390 precursors
5:30:06.374091 INFO: === Search parameters used ===
5:30:06.374151 INFO: rt_error       : 171.55160938517332
5:30:06.374202 INFO: mobility_error : 0.08220444133992512
5:30:06.374250 INFO: num_candidates : 3
5:30:06.374299 INFO: ms1_error      : 15.0
5:30:06.374346 INFO: ms2_error      : 15.0
5:30:06.374393 INFO: fwhm_rt        : 2.6867687702178955
5:30:06.374448 INFO: quant_window   : 3
5:30:06.374493 INFO: ==============================================
5:30:06.492766 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:30:06.492908 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:30:06.492953 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
5:30:06.492976 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.31
5:30:06.493707 INFO: Starting candidate selection
5:32:10.246613 INFO: Starting candidate scoring
5:32:20.979001 INFO: Finished candidate processing
5:32:20.979494 INFO: Collecting candidate features
5:32:22.642560 WARNING: intensity_correlation has 3962 NaNs ( 0.46 % out of 862025)
5:32:22.643587 WARNING: height_correlation has 510 NaNs ( 0.06 % out of 862025)
5:32:22.674824 INFO: Collecting fragment features
5:32:23.125820 INFO: Finished candidate scoring
5:32:24.190202 INFO: performing precursor FDR with 47 features
5:32:24.190360 INFO: Decoy channel: -1
5:32:24.190394 INFO: competitive: True
5:32:25.088037 INFO: Setting torch num_threads to 2 for FDR classification task
5:32:25.367898 WARNING: dropped 4195 target PSMs due to missing features
5:32:25.368058 WARNING: dropped 4132 decoy PSMs due to missing features
5:32:26.093040 INFO: Estimating optimal hyperparameters - samples: 1,373,424, batch_size: 4,096, learning_rate: 1.00e-03
5:32:26.097787 INFO: Using random state 162299 for train-test-split
5:32:59.808272 INFO: Test AUC: 0.553
5:32:59.808464 INFO: Train AUC: 0.566
5:32:59.808500 INFO: AUC difference: 2.34%
5:33:00.631699 INFO: Resetting torch num_threads to 80
5:33:01.124358 PROGRESS: === Extracted 1725107 precursors and 9523391 fragments ===
5:33:01.125443 INFO: === FDR correction performed with classifier version 21 ===
5:33:01.191579 PROGRESS: ============================= Precursor FDR =============================
5:33:01.191884 PROGRESS: Total precursors accumulated: 351,995
5:33:01.191964 PROGRESS: Target precursors: 201,341 (57.20%)
5:33:01.192031 PROGRESS: Decoy precursors: 150,654 (42.80%)
5:33:01.192085 PROGRESS: 
5:33:01.192135 PROGRESS: Precursor Summary:
5:33:01.195612 PROGRESS: Channel   0:	 0.050 FDR:   554; 0.010 FDR:   385; 0.001 FDR:   350
5:33:01.195745 PROGRESS: 
5:33:01.195813 PROGRESS: Protein Summary:
5:33:01.198943 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   280; 0.001 FDR:   252
5:33:01.199067 PROGRESS: =========================================================================
5:33:01.207100 INFO: Target number of precursors reached.
5:33:02.283216 INFO: fragments_df: keeping 5000 of 9523391 [sum(precursor_idx_mask)=10306 sum(mass_error_mask)=9523134 stop_rank=5000
5:33:03.318211 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:33:03.468404 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:33:03.617989 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:33:03.766454 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:33:04.483461 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:33:04.483924 INFO: Using score_cutoff 26.423378105163575 (fac=0.99, q=1)
5:33:04.484278 INFO: Updating optimization_manager: fwhm_rt             : 2.6867687702178955 -> 2.6867687702178955
5:33:04.484365 INFO: Updating optimization_manager: fwhm_mobility       : 0.006111645605415106 -> 0.005961200222373009
5:33:04.484428 INFO: Updating optimization_manager: score_cutoff        : 22.979633663177488 -> 26.423378105163575
5:33:04.484490 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:33:04.594262 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:33:05.117985 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:33:05.231735 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:33:06.291750 INFO: === checking if optimization conditions were reached ===
5:33:06.292066 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
5:33:06.294159 INFO: Updating optimization_manager: mobility_error      : 0.08220444133992512 -> 0.06757198270863912
5:33:06.294302 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0676.
5:33:06.294373 INFO: ==============================================
5:33:06.294454 INFO: Starting optimization step 3.
5:33:06.294517 PROGRESS: === Extracting elution groups 0 to 409400 ===
5:33:06.294598 INFO: Using python extraction backend
5:33:06.294728 PROGRESS: Extracting batch of 816307 precursors
5:33:06.294799 INFO: === Search parameters used ===
5:33:06.294852 INFO: rt_error       : 171.55160938517332
5:33:06.294903 INFO: mobility_error : 0.06757198270863912
5:33:06.294946 INFO: num_candidates : 3
5:33:06.294989 INFO: ms1_error      : 15.0
5:33:06.295031 INFO: ms2_error      : 15.0
5:33:06.295073 INFO: fwhm_rt        : 2.6867687702178955
5:33:06.295114 INFO: quant_window   : 3
5:33:06.295155 INFO: ==============================================
5:33:06.527532 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:33:06.527679 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:33:06.527736 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
5:33:06.527761 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.23
5:33:06.529422 INFO: Starting candidate selection
5:36:22.603936 INFO: Starting candidate scoring
5:36:44.458919 INFO: Finished candidate processing
5:36:44.459258 INFO: Collecting candidate features
5:36:48.349435 WARNING: intensity_correlation has 7656 NaNs ( 0.44 % out of 1723082)
5:36:48.351190 WARNING: height_correlation has 883 NaNs ( 0.05 % out of 1723082)
5:36:48.409654 INFO: Collecting fragment features
5:36:49.461033 INFO: Finished candidate scoring
5:36:50.818116 INFO: performing precursor FDR with 47 features
5:36:50.818256 INFO: Decoy channel: -1
5:36:50.818286 INFO: competitive: True
5:36:51.365093 INFO: Setting torch num_threads to 2 for FDR classification task
5:36:51.722089 WARNING: dropped 4049 target PSMs due to missing features
5:36:51.722251 WARNING: dropped 4050 decoy PSMs due to missing features
5:36:52.478859 INFO: Estimating optimal hyperparameters - samples: 1,371,986, batch_size: 4,096, learning_rate: 1.00e-03
5:36:52.482047 INFO: Using random state 162299 for train-test-split
5:37:27.050462 INFO: Test AUC: 0.552
5:37:27.050661 INFO: Train AUC: 0.564
5:37:27.050698 INFO: AUC difference: 2.19%
5:37:27.868257 INFO: Resetting torch num_threads to 80
5:37:27.912273 PROGRESS: === Extracted 1723082 precursors and 9563427 fragments ===
5:37:27.913402 INFO: === FDR correction performed with classifier version 21 ===
5:37:27.979488 PROGRESS: ============================= Precursor FDR =============================
5:37:27.979803 PROGRESS: Total precursors accumulated: 348,437
5:37:27.979877 PROGRESS: Target precursors: 198,394 (56.94%)
5:37:27.979956 PROGRESS: Decoy precursors: 150,043 (43.06%)
5:37:27.980013 PROGRESS: 
5:37:27.980063 PROGRESS: Precursor Summary:
5:37:27.983746 PROGRESS: Channel   0:	 0.050 FDR:   629; 0.010 FDR:   461; 0.001 FDR:   265
5:37:27.983854 PROGRESS: 
5:37:27.983916 PROGRESS: Protein Summary:
5:37:27.987028 PROGRESS: Channel   0:	 0.050 FDR:   494; 0.010 FDR:   343; 0.001 FDR:   191
5:37:27.987133 PROGRESS: =========================================================================
5:37:27.999717 INFO: Target number of precursors reached.
5:37:29.067426 INFO: fragments_df: keeping 5000 of 9563427 [sum(precursor_idx_mask)=11909 sum(mass_error_mask)=9563145 stop_rank=5000
5:37:29.820154 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:37:29.941835 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:37:30.075548 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:37:30.201492 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:37:30.853971 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:37:30.854427 INFO: Using score_cutoff 20.881499393463134 (fac=0.99, q=1)
5:37:30.854784 INFO: Updating optimization_manager: fwhm_rt             : 2.6867687702178955 -> 2.63781476020813
5:37:30.854872 INFO: Updating optimization_manager: fwhm_mobility       : 0.005961200222373009 -> 0.005502923391759396
5:37:30.854944 INFO: Updating optimization_manager: score_cutoff        : 26.423378105163575 -> 20.881499393463134
5:37:30.855021 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:37:30.907439 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:37:31.166618 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:37:31.224145 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:37:31.752429 INFO: === checking if optimization conditions were reached ===
5:37:31.752696 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
5:37:31.754969 INFO: Updating optimization_manager: mobility_error      : 0.06757198270863912 -> 0.06550505858141463
5:37:31.755099 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0655.
5:37:31.755172 INFO: ==============================================
5:37:31.755247 INFO: Starting optimization step 4.
5:37:31.755308 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:37:31.755373 INFO: Using python extraction backend
5:37:31.755510 PROGRESS: Extracting batch of 407917 precursors
5:37:31.755587 INFO: === Search parameters used ===
5:37:31.755640 INFO: rt_error       : 171.55160938517332
5:37:31.755694 INFO: mobility_error : 0.06550505858141463
5:37:31.755742 INFO: num_candidates : 3
5:37:31.755789 INFO: ms1_error      : 15.0
5:37:31.755835 INFO: ms2_error      : 15.0
5:37:31.755879 INFO: fwhm_rt        : 2.63781476020813
5:37:31.755944 INFO: quant_window   : 3
5:37:31.755996 INFO: ==============================================
5:37:31.882200 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:37:31.882342 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:37:31.882395 INFO: FWHM in RT is 2.64 seconds, sigma is 0.44
5:37:31.882419 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.98
5:37:31.883158 INFO: Starting candidate selection
5:39:10.452492 INFO: Starting candidate scoring
5:39:21.361391 INFO: Finished candidate processing
5:39:21.361666 INFO: Collecting candidate features
5:39:23.072628 WARNING: intensity_correlation has 3882 NaNs ( 0.45 % out of 853244)
5:39:23.073611 WARNING: height_correlation has 440 NaNs ( 0.05 % out of 853244)
5:39:23.104210 INFO: Collecting fragment features
5:39:23.518621 INFO: Finished candidate scoring
5:39:24.189084 INFO: performing precursor FDR with 47 features
5:39:24.189238 INFO: Decoy channel: -1
5:39:24.189275 INFO: competitive: True
5:39:24.412569 INFO: Setting torch num_threads to 2 for FDR classification task
5:39:24.556254 WARNING: dropped 2075 target PSMs due to missing features
5:39:24.556415 WARNING: dropped 2027 decoy PSMs due to missing features
5:39:24.935342 INFO: Estimating optimal hyperparameters - samples: 679,313, batch_size: 2,782, learning_rate: 8.24e-04
5:39:24.936843 INFO: Using random state 162299 for train-test-split
5:39:42.791431 INFO: Test AUC: 0.558
5:39:42.791633 INFO: Train AUC: 0.577
5:39:42.791672 INFO: AUC difference: 3.31%
5:39:43.315670 INFO: Resetting torch num_threads to 80
5:39:43.334269 PROGRESS: === Extracted 853244 precursors and 4714585 fragments ===
5:39:43.335156 INFO: === FDR correction performed with classifier version 21 ===
5:39:43.365766 PROGRESS: ============================= Precursor FDR =============================
5:39:43.366066 PROGRESS: Total precursors accumulated: 173,398
5:39:43.366144 PROGRESS: Target precursors: 100,560 (57.99%)
5:39:43.366210 PROGRESS: Decoy precursors: 72,838 (42.01%)
5:39:43.366267 PROGRESS: 
5:39:43.366321 PROGRESS: Precursor Summary:
5:39:43.368551 PROGRESS: Channel   0:	 0.050 FDR:   288; 0.010 FDR:   212; 0.001 FDR:   184
5:39:43.368653 PROGRESS: 
5:39:43.368716 PROGRESS: Protein Summary:
5:39:43.370862 PROGRESS: Channel   0:	 0.050 FDR:   239; 0.010 FDR:   173; 0.001 FDR:   150
5:39:43.370968 PROGRESS: =========================================================================
5:39:43.401029 INFO: Target number of precursors reached.
5:39:43.922892 INFO: fragments_df: keeping 3519 of 4714585 [sum(precursor_idx_mask)=5441 sum(mass_error_mask)=4714429 stop_rank=3519
5:39:44.617648 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:39:44.747296 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:39:44.877303 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:39:45.003991 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:39:45.482282 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:39:45.482732 INFO: Using score_cutoff 22.460289944458008 (fac=0.99, q=1)
5:39:45.483076 INFO: Updating optimization_manager: fwhm_rt             : 2.63781476020813 -> 2.6699066162109375
5:39:45.483162 INFO: Updating optimization_manager: fwhm_mobility       : 0.005502923391759396 -> 0.0061647929251194
5:39:45.483224 INFO: Updating optimization_manager: score_cutoff        : 20.881499393463134 -> 22.460289944458008
5:39:45.483283 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:39:45.538275 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:39:45.799319 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:39:45.868275 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:39:46.400166 INFO: === checking if optimization conditions were reached ===
5:39:46.400463 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
5:39:46.402577 INFO: Updating optimization_manager: mobility_error      : 0.06550505858141463 -> 0.05404613732846459
5:39:46.402716 PROGRESS: ❌ mobility_error : optimization incomplete after 4 search(es). Will search with parameter 0.0540.
5:39:46.402791 INFO: ==============================================
5:39:46.402869 INFO: Starting optimization step 5.
5:39:46.402935 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:39:46.403008 INFO: Using python extraction backend
5:39:46.403134 PROGRESS: Extracting batch of 407917 precursors
5:39:46.403227 INFO: === Search parameters used ===
5:39:46.403285 INFO: rt_error       : 171.55160938517332
5:39:46.403337 INFO: mobility_error : 0.05404613732846459
5:39:46.403385 INFO: num_candidates : 3
5:39:46.403433 INFO: ms1_error      : 15.0
5:39:46.403481 INFO: ms2_error      : 15.0
5:39:46.403528 INFO: fwhm_rt        : 2.6699066162109375
5:39:46.403575 INFO: quant_window   : 3
5:39:46.403621 INFO: ==============================================
5:39:46.513583 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:39:46.513733 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:39:46.513782 INFO: FWHM in RT is 2.67 seconds, sigma is 0.45
5:39:46.513807 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.34
5:39:46.514529 INFO: Starting candidate selection
5:41:05.578344 INFO: Starting candidate scoring
5:41:15.843724 INFO: Finished candidate processing
5:41:15.843966 INFO: Collecting candidate features
5:41:17.496876 WARNING: intensity_correlation has 4046 NaNs ( 0.49 % out of 831067)
5:41:17.497918 WARNING: height_correlation has 506 NaNs ( 0.06 % out of 831067)
5:41:17.527569 INFO: Collecting fragment features
5:41:17.953274 INFO: Finished candidate scoring
5:41:18.643535 INFO: performing precursor FDR with 47 features
5:41:18.643687 INFO: Decoy channel: -1
5:41:18.643718 INFO: competitive: True
5:41:18.861402 INFO: Setting torch num_threads to 2 for FDR classification task
5:41:18.999709 WARNING: dropped 2161 target PSMs due to missing features
5:41:18.999872 WARNING: dropped 2135 decoy PSMs due to missing features
5:41:19.268994 INFO: Estimating optimal hyperparameters - samples: 661,416, batch_size: 2,709, learning_rate: 8.13e-04
5:41:19.270318 INFO: Using random state 162299 for train-test-split
5:41:36.287304 INFO: Test AUC: 0.557
5:41:36.287533 INFO: Train AUC: 0.577
5:41:36.287572 INFO: AUC difference: 3.45%
5:41:37.957359 INFO: Resetting torch num_threads to 80
5:41:37.975446 PROGRESS: === Extracted 831067 precursors and 4536564 fragments ===
5:41:37.976233 INFO: === FDR correction performed with classifier version 21 ===
5:41:38.006965 PROGRESS: ============================= Precursor FDR =============================
5:41:38.007222 PROGRESS: Total precursors accumulated: 170,244
5:41:38.007295 PROGRESS: Target precursors: 98,858 (58.07%)
5:41:38.007355 PROGRESS: Decoy precursors: 71,386 (41.93%)
5:41:38.007413 PROGRESS: 
5:41:38.007469 PROGRESS: Precursor Summary:
5:41:38.009785 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   276; 0.001 FDR:   244
5:41:38.009904 PROGRESS: 
5:41:38.009973 PROGRESS: Protein Summary:
5:41:38.012161 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   226; 0.001 FDR:   196
5:41:38.012288 PROGRESS: =========================================================================
5:41:38.017744 INFO: Target number of precursors reached.
5:41:38.526699 INFO: fragments_df: keeping 4118 of 4536564 [sum(precursor_idx_mask)=7019 sum(mass_error_mask)=4536429 stop_rank=4118
5:41:39.224138 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:41:39.333329 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:41:39.454335 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:41:39.572696 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:41:40.096492 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:41:40.096955 INFO: Using score_cutoff 23.153745660781862 (fac=0.99, q=1)
5:41:40.097272 INFO: Updating optimization_manager: fwhm_rt             : 2.6699066162109375 -> 2.688504219055176
5:41:40.097357 INFO: Updating optimization_manager: fwhm_mobility       : 0.0061647929251194 -> 0.005544987507164478
5:41:40.097420 INFO: Updating optimization_manager: score_cutoff        : 22.460289944458008 -> 23.153745660781862
5:41:40.097490 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:41:40.153387 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:41:40.417252 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:41:40.478551 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:41:41.044341 INFO: === checking if optimization conditions were reached ===
5:41:41.044635 PROGRESS: === Optimization of mobility_error has been performed 5 time(s); minimum number is 2 ===
5:41:41.046711 INFO: Updating optimization_manager: mobility_error      : 0.05404613732846459 -> 0.05051033891606621
5:41:41.046864 PROGRESS: ❌ mobility_error : optimization incomplete after 5 search(es). Will search with parameter 0.0505.
5:41:41.046940 INFO: ==============================================
5:41:41.047018 INFO: Starting optimization step 6.
5:41:41.047084 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:41:41.047150 INFO: Using python extraction backend
5:41:41.047265 PROGRESS: Extracting batch of 407917 precursors
5:41:41.047340 INFO: === Search parameters used ===
5:41:41.047397 INFO: rt_error       : 171.55160938517332
5:41:41.047447 INFO: mobility_error : 0.05051033891606621
5:41:41.047496 INFO: num_candidates : 3
5:41:41.047544 INFO: ms1_error      : 15.0
5:41:41.047590 INFO: ms2_error      : 15.0
5:41:41.047637 INFO: fwhm_rt        : 2.688504219055176
5:41:41.047683 INFO: quant_window   : 3
5:41:41.047729 INFO: ==============================================
5:41:41.233170 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:41:41.233320 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:41:41.233374 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
5:41:41.233401 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.01
5:41:41.234151 INFO: Starting candidate selection
5:42:55.804760 INFO: Starting candidate scoring
5:43:06.281333 INFO: Finished candidate processing
5:43:06.281558 INFO: Collecting candidate features
5:43:07.890322 WARNING: intensity_correlation has 4003 NaNs ( 0.48 % out of 831032)
5:43:07.891273 WARNING: height_correlation has 496 NaNs ( 0.06 % out of 831032)
5:43:07.921077 INFO: Collecting fragment features
5:43:08.322699 INFO: Finished candidate scoring
5:43:08.898955 INFO: performing precursor FDR with 47 features
5:43:08.899097 INFO: Decoy channel: -1
5:43:08.899126 INFO: competitive: True
5:43:09.106432 INFO: Setting torch num_threads to 2 for FDR classification task
5:43:09.240518 WARNING: dropped 2161 target PSMs due to missing features
5:43:09.240678 WARNING: dropped 2095 decoy PSMs due to missing features
5:43:09.598339 INFO: Estimating optimal hyperparameters - samples: 661,420, batch_size: 2,709, learning_rate: 8.13e-04
5:43:09.599897 INFO: Using random state 162299 for train-test-split
5:43:26.517812 INFO: Test AUC: 0.556
5:43:26.517992 INFO: Train AUC: 0.576
5:43:26.518031 INFO: AUC difference: 3.40%
5:43:27.041712 INFO: Resetting torch num_threads to 80
5:43:27.059784 PROGRESS: === Extracted 831032 precursors and 4519448 fragments ===
5:43:27.060608 INFO: === FDR correction performed with classifier version 21 ===
5:43:27.090390 PROGRESS: ============================= Precursor FDR =============================
5:43:27.090657 PROGRESS: Total precursors accumulated: 170,381
5:43:27.090734 PROGRESS: Target precursors: 98,712 (57.94%)
5:43:27.090816 PROGRESS: Decoy precursors: 71,669 (42.06%)
5:43:27.090874 PROGRESS: 
5:43:27.090925 PROGRESS: Precursor Summary:
5:43:27.093163 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   253; 0.001 FDR:   199
5:43:27.093272 PROGRESS: 
5:43:27.093336 PROGRESS: Protein Summary:
5:43:27.095461 PROGRESS: Channel   0:	 0.050 FDR:   287; 0.010 FDR:   204; 0.001 FDR:   157
5:43:27.095579 PROGRESS: =========================================================================
5:43:27.100744 INFO: Target number of precursors reached.
5:43:27.589943 INFO: fragments_df: keeping 3951 of 4519448 [sum(precursor_idx_mask)=6523 sum(mass_error_mask)=4519291 stop_rank=3951
5:43:28.244732 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:43:28.372811 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:43:28.512162 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:43:28.636124 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:43:29.197366 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:43:29.197834 INFO: Using score_cutoff 20.216635523986817 (fac=0.99, q=1)
5:43:29.198189 INFO: Updating optimization_manager: fwhm_rt             : 2.688504219055176 -> 2.6846108436584473
5:43:29.198277 INFO: Updating optimization_manager: fwhm_mobility       : 0.005544987507164478 -> 0.0060001565143466
5:43:29.198345 INFO: Updating optimization_manager: score_cutoff        : 23.153745660781862 -> 20.216635523986817
5:43:29.198408 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:43:29.247506 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:43:29.508953 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:43:29.566567 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:43:30.107478 INFO: === checking if optimization conditions were reached ===
5:43:30.107775 PROGRESS: === Optimization of mobility_error has been performed 6 time(s); minimum number is 2 ===
5:43:30.109818 INFO: Updating optimization_manager: mobility_error      : 0.05051033891606621 -> 0.045145447499816235
5:43:30.109971 PROGRESS: ❌ mobility_error : optimization incomplete after 6 search(es). Will search with parameter 0.0451.
5:43:30.110050 INFO: ==============================================
5:43:30.110131 INFO: Starting optimization step 7.
5:43:30.110198 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:43:30.110268 INFO: Using python extraction backend
5:43:30.110382 PROGRESS: Extracting batch of 407917 precursors
5:43:30.110454 INFO: === Search parameters used ===
5:43:30.110509 INFO: rt_error       : 171.55160938517332
5:43:30.110560 INFO: mobility_error : 0.045145447499816235
5:43:30.110610 INFO: num_candidates : 3
5:43:30.110659 INFO: ms1_error      : 15.0
5:43:30.110708 INFO: ms2_error      : 15.0
5:43:30.110756 INFO: fwhm_rt        : 2.6846108436584473
5:43:30.110805 INFO: quant_window   : 3
5:43:30.110869 INFO: ==============================================
5:43:30.220883 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:43:30.221035 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:43:30.221083 INFO: FWHM in RT is 2.68 seconds, sigma is 0.45
5:43:30.221107 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.25
5:43:30.221928 INFO: Starting candidate selection
5:44:40.834406 INFO: Starting candidate scoring
5:44:50.970134 INFO: Finished candidate processing
5:44:50.970297 INFO: Collecting candidate features
5:44:52.373807 WARNING: intensity_correlation has 4188 NaNs ( 0.52 % out of 812524)
5:44:52.374745 WARNING: height_correlation has 537 NaNs ( 0.07 % out of 812524)
5:44:52.403665 INFO: Collecting fragment features
5:44:52.801531 INFO: Finished candidate scoring
5:44:53.391829 INFO: performing precursor FDR with 47 features
5:44:53.391970 INFO: Decoy channel: -1
5:44:53.391999 INFO: competitive: True
5:44:53.592493 INFO: Setting torch num_threads to 2 for FDR classification task
5:44:53.722509 WARNING: dropped 2259 target PSMs due to missing features
5:44:53.722674 WARNING: dropped 2193 decoy PSMs due to missing features
5:44:54.067723 INFO: Estimating optimal hyperparameters - samples: 646,457, batch_size: 2,647, learning_rate: 8.04e-04
5:44:54.068952 INFO: Using random state 162299 for train-test-split
5:45:11.014309 INFO: Test AUC: 0.555
5:45:11.014559 INFO: Train AUC: 0.578
5:45:11.014596 INFO: AUC difference: 3.95%
5:45:11.538344 INFO: Resetting torch num_threads to 80
5:45:11.561026 PROGRESS: === Extracted 812524 precursors and 4375035 fragments ===
5:45:11.561910 INFO: === FDR correction performed with classifier version 21 ===
5:45:11.592598 PROGRESS: ============================= Precursor FDR =============================
5:45:11.592859 PROGRESS: Total precursors accumulated: 168,066
5:45:11.592937 PROGRESS: Target precursors: 97,592 (58.07%)
5:45:11.593001 PROGRESS: Decoy precursors: 70,474 (41.93%)
5:45:11.593058 PROGRESS: 
5:45:11.593114 PROGRESS: Precursor Summary:
5:45:11.595510 PROGRESS: Channel   0:	 0.050 FDR:   393; 0.010 FDR:   279; 0.001 FDR:   193
5:45:11.595660 PROGRESS: 
5:45:11.595728 PROGRESS: Protein Summary:
5:45:11.597934 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   229; 0.001 FDR:   162
5:45:11.598044 PROGRESS: =========================================================================
5:45:11.603304 INFO: Target number of precursors reached.
5:45:12.091286 INFO: fragments_df: keeping 4116 of 4375035 [sum(precursor_idx_mask)=7124 sum(mass_error_mask)=4374891 stop_rank=4116
5:45:12.792045 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:45:12.906418 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:45:13.025327 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:45:13.140189 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:45:13.656408 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:45:13.656869 INFO: Using score_cutoff 22.194901558685302 (fac=0.99, q=1)
5:45:13.657274 INFO: Updating optimization_manager: fwhm_rt             : 2.6846108436584473 -> 2.648247718811035
5:45:13.657367 INFO: Updating optimization_manager: fwhm_mobility       : 0.0060001565143466 -> 0.005446931812912226
5:45:13.657439 INFO: Updating optimization_manager: score_cutoff        : 20.216635523986817 -> 22.194901558685302
5:45:13.657513 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:45:13.712872 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:45:13.970739 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:45:14.026490 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:45:14.602105 INFO: === checking if optimization conditions were reached ===
5:45:14.602416 PROGRESS: === Optimization of mobility_error has been performed 7 time(s); minimum number is 2 ===
5:45:14.604654 INFO: Updating optimization_manager: mobility_error      : 0.045145447499816235 -> 0.04301708599577289
5:45:14.604789 PROGRESS: ❌ mobility_error : optimization incomplete after 7 search(es). Will search with parameter 0.0430.
5:45:14.604879 INFO: ==============================================
5:45:14.604959 INFO: Starting optimization step 8.
5:45:14.605025 PROGRESS: === Extracting elution groups 0 to 204600 ===
5:45:14.605092 INFO: Using python extraction backend
5:45:14.605213 PROGRESS: Extracting batch of 407917 precursors
5:45:14.605293 INFO: === Search parameters used ===
5:45:14.605348 INFO: rt_error       : 171.55160938517332
5:45:14.605396 INFO: mobility_error : 0.04301708599577289
5:45:14.605443 INFO: num_candidates : 3
5:45:14.605489 INFO: ms1_error      : 15.0
5:45:14.605535 INFO: ms2_error      : 15.0
5:45:14.605581 INFO: fwhm_rt        : 2.648247718811035
5:45:14.605627 INFO: quant_window   : 3
5:45:14.605670 INFO: ==============================================
5:45:14.783242 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:45:14.783388 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:45:14.783435 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
5:45:14.783460 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.95
5:45:14.784226 INFO: Starting candidate selection
5:46:14.362678 INFO: Starting candidate scoring
5:46:24.555314 INFO: Finished candidate processing
5:46:24.555820 INFO: Collecting candidate features
5:46:26.104141 WARNING: intensity_correlation has 4319 NaNs ( 0.54 % out of 803576)
5:46:26.105085 WARNING: height_correlation has 538 NaNs ( 0.07 % out of 803576)
5:46:26.134059 INFO: Collecting fragment features
5:46:26.526904 INFO: Finished candidate scoring
5:46:27.107254 INFO: performing precursor FDR with 47 features
5:46:27.107396 INFO: Decoy channel: -1
5:46:27.107428 INFO: competitive: True
5:46:27.320482 INFO: Setting torch num_threads to 2 for FDR classification task
5:46:27.457050 WARNING: dropped 2301 target PSMs due to missing features
5:46:27.457211 WARNING: dropped 2287 decoy PSMs due to missing features
5:46:27.820312 INFO: Estimating optimal hyperparameters - samples: 639,190, batch_size: 2,618, learning_rate: 7.99e-04
5:46:27.821644 INFO: Using random state 162299 for train-test-split
5:46:44.973542 INFO: Test AUC: 0.558
5:46:44.973765 INFO: Train AUC: 0.578
5:46:44.973808 INFO: AUC difference: 3.43%
5:46:45.487132 INFO: Resetting torch num_threads to 80
5:46:45.504577 PROGRESS: === Extracted 803576 precursors and 4294140 fragments ===
5:46:45.505375 INFO: === FDR correction performed with classifier version 21 ===
5:46:45.534426 PROGRESS: ============================= Precursor FDR =============================
5:46:45.534678 PROGRESS: Total precursors accumulated: 166,455
5:46:45.534752 PROGRESS: Target precursors: 96,896 (58.21%)
5:46:45.534812 PROGRESS: Decoy precursors: 69,559 (41.79%)
5:46:45.534868 PROGRESS: 
5:46:45.534921 PROGRESS: Precursor Summary:
5:46:45.537097 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   252; 0.001 FDR:   228
5:46:45.537203 PROGRESS: 
5:46:45.537266 PROGRESS: Protein Summary:
5:46:45.539346 PROGRESS: Channel   0:	 0.050 FDR:   245; 0.010 FDR:   204; 0.001 FDR:   184
5:46:45.539447 PROGRESS: =========================================================================
5:46:45.544980 INFO: Target number of precursors reached.
5:46:46.011852 INFO: fragments_df: keeping 3816 of 4294140 [sum(precursor_idx_mask)=6266 sum(mass_error_mask)=4293984 stop_rank=3816
5:46:46.688617 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:46:46.807731 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:46:46.925349 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:46:47.036941 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:46:47.509408 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:46:47.509878 INFO: Using score_cutoff 12.830958580112457 (fac=0.99, q=1)
5:46:47.510223 INFO: Updating optimization_manager: fwhm_rt             : 2.648247718811035 -> 2.665308952331543
5:46:47.510309 INFO: Updating optimization_manager: fwhm_mobility       : 0.005446931812912226 -> 0.005736278370022774
5:46:47.510381 INFO: Updating optimization_manager: score_cutoff        : 22.194901558685302 -> 12.830958580112457
5:46:47.510443 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:46:47.565054 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:46:47.820585 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:46:47.877286 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:46:48.448350 INFO: === checking if optimization conditions were reached ===
5:46:48.448645 PROGRESS: === Optimization of mobility_error has been performed 8 time(s); minimum number is 2 ===
5:46:48.449686 INFO: Updating optimization_manager: mobility_error      : 0.04301708599577289 -> 0.045145447499816235
5:46:48.449880 INFO: Updating optimization_manager: classifier_version  : 21 -> 30
5:46:48.450012 INFO: Updating optimization_manager: score_cutoff        : 12.830958580112457 -> 22.194901558685302
5:46:48.450121 INFO: Updating optimization_manager: fwhm_rt             : 2.665308952331543 -> 2.648247718811035
5:46:48.450227 INFO: Updating optimization_manager: fwhm_mobility       : 0.005736278370022774 -> 0.005446931812912226
5:46:48.450337 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0451 found after 8 searches.
5:46:48.450412 INFO: ==============================================
5:46:48.450493 PROGRESS: Optimization finished for mobility_error.
5:46:49.090737 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:46:49.144504 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:46:49.400318 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:46:49.457337 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:46:49.997176 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
5:46:49.997552 PROGRESS: ==============================================
5:46:49.997657 PROGRESS: ms2_error      : 15.0000
5:46:49.997732 PROGRESS: ms1_error      : 15.0000
5:46:49.997803 PROGRESS: rt_error       : 171.5516
5:46:49.997878 PROGRESS: mobility_error : 0.0451
5:46:49.997953 PROGRESS: ==============================================
5:46:50.005164 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:46:51.755442 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:47:00.233744 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:47:02.054620 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:47:46.709515 INFO: Using python extraction backend
5:47:46.710001 PROGRESS: Extracting batch of 12210649 precursors
5:47:46.710121 INFO: === Search parameters used ===
5:47:46.710188 INFO: rt_error       : 171.55160938517332
5:47:46.710245 INFO: mobility_error : 0.045145447499816235
5:47:46.710304 INFO: num_candidates : 3
5:47:46.710355 INFO: ms1_error      : 15.0
5:47:46.710418 INFO: ms2_error      : 15.0
5:47:46.710467 INFO: fwhm_rt        : 2.648247718811035
5:47:46.710516 INFO: quant_window   : 3
5:47:46.710564 INFO: ==============================================
5:47:49.863877 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
5:47:49.864068 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
5:47:49.864120 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
5:47:49.864146 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.95
5:47:49.865006 INFO: Starting candidate selection
6:20:26.774307 INFO: Removed 24387500 precursors with score below cutoff 22.194901558685302
6:20:30.040149 INFO: Starting candidate scoring
6:21:57.733531 INFO: Finished candidate processing
6:21:57.734047 INFO: Collecting candidate features
6:22:28.794645 WARNING: intensity_correlation has 6030 NaNs ( 0.09 % out of 6718222)
6:22:28.801818 WARNING: height_correlation has 333 NaNs ( 0.00 % out of 6718222)
6:22:29.059295 INFO: Collecting fragment features
6:22:46.767058 INFO: Finished candidate scoring
6:22:54.471887 INFO: === Performing FDR correction with classifier version 30 ===
6:22:54.472761 INFO: performing precursor FDR with 47 features
6:22:54.472816 INFO: Decoy channel: -1
6:22:54.472849 INFO: competitive: True
6:22:56.402503 INFO: Setting torch num_threads to 2 for FDR classification task
6:22:57.377705 WARNING: dropped 3127 target PSMs due to missing features
6:22:57.377874 WARNING: dropped 3133 decoy PSMs due to missing features
6:23:00.171788 INFO: Estimating optimal hyperparameters - samples: 5,369,569, batch_size: 4,096, learning_rate: 1.00e-03
6:23:00.184302 INFO: Using random state 935326 for train-test-split
6:25:32.997841 INFO: Test AUC: 0.557
6:25:32.998240 INFO: Train AUC: 0.561
6:25:32.998284 INFO: AUC difference: 0.68%
6:25:35.267439 INFO: Resetting torch num_threads to 80
6:25:35.478122 INFO: Removing fragments below FDR threshold
6:25:35.943837 PROGRESS: ============================= Precursor FDR =============================
6:25:35.944105 PROGRESS: Total precursors accumulated: 7,756
6:25:35.944184 PROGRESS: Target precursors: 7,680 (99.02%)
6:25:35.944242 PROGRESS: Decoy precursors: 76 (0.98%)
6:25:35.944317 PROGRESS: 
6:25:35.944370 PROGRESS: Precursor Summary:
6:25:35.947383 PROGRESS: Channel   0:	 0.050 FDR: 7,680; 0.010 FDR: 7,680; 0.001 FDR: 5,580
6:25:35.947493 PROGRESS: 
6:25:35.947558 PROGRESS: Protein Summary:
6:25:35.951322 PROGRESS: Channel   0:	 0.050 FDR: 1,710; 0.010 FDR: 1,710; 0.001 FDR: 1,251
6:25:35.951429 PROGRESS: =========================================================================
6:25:36.604620 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R1/psm.parquet
6:25:36.660051 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R1/frag.parquet
6:25:36.704272 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R1
6:25:37.221264 PROGRESS: Loading raw file 2/12: A9_G_DIA_nLC_tTOF_R2 
6:25:37.221465 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
6:25:37.221612 INFO: Initializing TimingManager
6:25:37.222202 INFO: Initializing RawFileManager
6:25:37.222355 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:37.222421 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:37.222489 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:37.397322 INFO: Reading 22,623 frames with 354,406,482 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:43.119663 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d...
6:25:43.121394 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:43.128526 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:43.128788 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:43.129211 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:43.130650 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:43.141696 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:43.142272 INFO: Indexing quadrupole dimension
6:25:43.229297 INFO: Transposing detector events
6:25:44.676586 INFO: Finished transposing data
6:25:44.687159 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
6:25:44.688069 INFO: RT (min)            : 0.0 - 40.0
6:25:44.688174 INFO: RT duration (sec)   : 2399.9
6:25:44.688241 INFO: RT duration (min)   : 40.0
6:25:44.688299 INFO: Cycle len (scans)   : 12
6:25:44.688369 INFO: Cycle len (sec)     : 1.27
6:25:44.688425 INFO: Number of cycles    : 1885
6:25:44.688479 INFO: MS2 range (m/z)     : 374.4 - 1151.9
6:25:44.688552 INFO: Creating DIA data object took: 7.466235876083374
6:25:48.853244 INFO: Initializing CalibrationManager
6:25:48.853674 INFO: Setting up calibration estimators ..
6:25:48.853764 INFO: Found 1 estimator(s) in calibration group 'fragment'
6:25:48.853886 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
6:25:48.854054 INFO: Found 3 estimator(s) in calibration group 'precursor'
6:25:48.854132 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
6:25:48.854213 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
6:25:48.854285 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
6:25:48.854348 INFO: Done setting up calibration estimators.
6:25:48.854505 INFO: Initializing OptimizationManager
6:25:48.854622 INFO: initial parameter: ms1_error = 30
6:25:48.854678 INFO: initial parameter: ms2_error = 30
6:25:48.854730 INFO: initial parameter: rt_error = 1199.9447605
6:25:48.854780 INFO: initial parameter: mobility_error = 0.1
6:25:48.854826 INFO: initial parameter: num_candidates = 1
6:25:48.854872 INFO: initial parameter: fwhm_rt = 5
6:25:48.854918 INFO: initial parameter: fwhm_mobility = 0.01
6:25:48.854962 INFO: initial parameter: score_cutoff = 0
6:25:48.855004 INFO: initial parameter: classifier_version = -1
6:25:48.855087 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R2
6:25:48.855347 INFO: FDRManager: loading saved state not requested, will be initialized.
6:25:48.855385 INFO: Initializing FDRManager
6:25:48.855448 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
6:25:50.461275 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
6:25:51.850594 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
6:25:51.851080 INFO: Updating optimization_manager: rt_error            : 1199.9447605 -> 1199.9447605
6:25:51.851199 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
6:25:51.851391 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
6:25:51.851516 PROGRESS: Starting initial search for precursors.
6:25:51.851614 INFO: Starting optimization step 0.
6:25:51.851689 PROGRESS: === Extracting elution groups 0 to 200 ===
6:25:51.851777 INFO: Using python extraction backend
6:25:51.851952 PROGRESS: Extracting batch of 395 precursors
6:25:51.852038 INFO: === Search parameters used ===
6:25:51.852096 INFO: rt_error       : 1199.9447605
6:25:51.852146 INFO: mobility_error : 0.1
6:25:51.852194 INFO: num_candidates : 1
6:25:51.852243 INFO: ms1_error      : 30
6:25:51.852290 INFO: ms2_error      : 30
6:25:51.852335 INFO: fwhm_rt        : 5
6:25:51.852380 INFO: quant_window   : 3
6:25:51.852424 INFO: ==============================================
6:25:51.853430 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:25:51.853482 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:25:51.853546 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:25:51.853571 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:25:51.860483 INFO: Starting candidate selection
6:25:53.744392 INFO: Starting candidate scoring
6:25:53.785771 INFO: Finished candidate processing
6:25:53.785875 INFO: Collecting candidate features
6:25:53.796210 INFO: Collecting fragment features
6:25:53.798481 INFO: Finished candidate scoring
6:25:53.799351 INFO: performing precursor FDR with 47 features
6:25:53.799399 INFO: Decoy channel: -1
6:25:53.799427 INFO: competitive: True
6:25:53.800693 INFO: Setting torch num_threads to 2 for FDR classification task
6:25:53.802602 INFO: Estimating optimal hyperparameters - samples: 275, batch_size: 128, learning_rate: 1.77e-04
6:25:53.803415 INFO: Using random state 159096 for train-test-split
6:25:53.827179 INFO: Test AUC: 0.469
6:25:53.827258 INFO: Train AUC: 0.493
6:25:53.827289 INFO: AUC difference: 4.91%
6:25:54.079740 INFO: Resetting torch num_threads to 80
6:25:54.080195 PROGRESS: === Extracted 344 precursors and 2818 fragments ===
6:25:54.080643 INFO: === FDR correction performed with classifier version -1 ===
6:25:54.081181 PROGRESS: ============================= Precursor FDR =============================
6:25:54.081275 PROGRESS: Total precursors accumulated: 175
6:25:54.081340 PROGRESS: Target precursors: 86 (49.14%)
6:25:54.081395 PROGRESS: Decoy precursors: 89 (50.86%)
6:25:54.081449 PROGRESS: 
6:25:54.081499 PROGRESS: Precursor Summary:
6:25:54.082474 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
6:25:54.082572 PROGRESS: 
6:25:54.082633 PROGRESS: Protein Summary:
6:25:54.083683 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
6:25:54.083777 PROGRESS: =========================================================================
6:25:54.083886 INFO: Target number of precursors not reached yet.
6:25:54.146490 INFO: Starting optimization step 1.
6:25:54.146707 PROGRESS: === Extracting elution groups 200 to 600 ===
6:25:54.146790 INFO: Using python extraction backend
6:25:54.146899 PROGRESS: Extracting batch of 796 precursors
6:25:54.146970 INFO: === Search parameters used ===
6:25:54.147025 INFO: rt_error       : 1199.9447605
6:25:54.147076 INFO: mobility_error : 0.1
6:25:54.147126 INFO: num_candidates : 1
6:25:54.147173 INFO: ms1_error      : 30
6:25:54.147218 INFO: ms2_error      : 30
6:25:54.147262 INFO: fwhm_rt        : 5
6:25:54.147310 INFO: quant_window   : 3
6:25:54.147357 INFO: ==============================================
6:25:54.148022 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:25:54.148069 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:25:54.148099 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:25:54.148123 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:25:54.148868 INFO: Starting candidate selection
6:25:57.262770 INFO: Starting candidate scoring
6:25:57.304617 INFO: Finished candidate processing
6:25:57.304718 INFO: Collecting candidate features
6:25:57.315782 INFO: Collecting fragment features
6:25:57.318259 INFO: Finished candidate scoring
6:25:57.320507 INFO: performing precursor FDR with 47 features
6:25:57.320564 INFO: Decoy channel: -1
6:25:57.320590 INFO: competitive: True
6:25:57.323689 INFO: Setting torch num_threads to 2 for FDR classification task
6:25:57.325504 INFO: Estimating optimal hyperparameters - samples: 846, batch_size: 128, learning_rate: 1.77e-04
6:25:57.325587 INFO: Using random state 844388 for train-test-split
6:25:57.412794 INFO: Test AUC: 0.463
6:25:57.412903 INFO: Train AUC: 0.499
6:25:57.412936 INFO: AUC difference: 7.21%
6:25:57.412961 WARNING: AUC difference > 5%. This may indicate overfitting.
6:25:57.660629 INFO: Resetting torch num_threads to 80
6:25:57.661884 PROGRESS: === Extracted 1058 precursors and 8930 fragments ===
6:25:57.662335 INFO: === FDR correction performed with classifier version -1 ===
6:25:57.662910 PROGRESS: ============================= Precursor FDR =============================
6:25:57.663007 PROGRESS: Total precursors accumulated: 539
6:25:57.663074 PROGRESS: Target precursors: 273 (50.65%)
6:25:57.663140 PROGRESS: Decoy precursors: 266 (49.35%)
6:25:57.663194 PROGRESS: 
6:25:57.663246 PROGRESS: Precursor Summary:
6:25:57.664216 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
6:25:57.664312 PROGRESS: 
6:25:57.664375 PROGRESS: Protein Summary:
6:25:57.665419 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
6:25:57.665514 PROGRESS: =========================================================================
6:25:57.665663 INFO: Target number of precursors not reached yet.
6:25:57.737905 INFO: Starting optimization step 2.
6:25:57.738159 PROGRESS: === Extracting elution groups 600 to 1400 ===
6:25:57.738242 INFO: Using python extraction backend
6:25:57.738351 PROGRESS: Extracting batch of 1598 precursors
6:25:57.738427 INFO: === Search parameters used ===
6:25:57.738483 INFO: rt_error       : 1199.9447605
6:25:57.738539 INFO: mobility_error : 0.1
6:25:57.738588 INFO: num_candidates : 1
6:25:57.738633 INFO: ms1_error      : 30
6:25:57.738680 INFO: ms2_error      : 30
6:25:57.738727 INFO: fwhm_rt        : 5
6:25:57.738774 INFO: quant_window   : 3
6:25:57.738818 INFO: ==============================================
6:25:57.739607 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:25:57.739656 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:25:57.739689 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:25:57.739713 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:25:57.741885 INFO: Starting candidate selection
6:26:02.843450 INFO: Starting candidate scoring
6:26:02.914491 INFO: Finished candidate processing
6:26:02.914600 INFO: Collecting candidate features
6:26:02.922489 WARNING: intensity_correlation has 1 NaNs ( 0.07 % out of 1426)
6:26:02.926237 INFO: Collecting fragment features
6:26:02.929076 INFO: Finished candidate scoring
6:26:02.932597 INFO: performing precursor FDR with 47 features
6:26:02.932661 INFO: Decoy channel: -1
6:26:02.932691 INFO: competitive: True
6:26:02.935962 INFO: Setting torch num_threads to 2 for FDR classification task
6:26:02.937278 WARNING: dropped 1 target PSMs due to missing features
6:26:02.938232 INFO: Estimating optimal hyperparameters - samples: 1,986, batch_size: 128, learning_rate: 1.77e-04
6:26:02.938316 INFO: Using random state 871287 for train-test-split
6:26:03.142132 INFO: Test AUC: 0.497
6:26:03.142238 INFO: Train AUC: 0.513
6:26:03.142276 INFO: AUC difference: 3.15%
6:26:03.376989 INFO: Resetting torch num_threads to 80
6:26:03.378625 PROGRESS: === Extracted 2484 precursors and 20921 fragments ===
6:26:03.379062 INFO: === FDR correction performed with classifier version -1 ===
6:26:03.379712 PROGRESS: ============================= Precursor FDR =============================
6:26:03.379812 PROGRESS: Total precursors accumulated: 1,265
6:26:03.379879 PROGRESS: Target precursors: 675 (53.36%)
6:26:03.379936 PROGRESS: Decoy precursors: 590 (46.64%)
6:26:03.379987 PROGRESS: 
6:26:03.380038 PROGRESS: Precursor Summary:
6:26:03.380970 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
6:26:03.381064 PROGRESS: 
6:26:03.381125 PROGRESS: Protein Summary:
6:26:03.382155 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
6:26:03.382250 PROGRESS: =========================================================================
6:26:03.382403 INFO: Target number of precursors not reached yet.
6:26:03.484591 INFO: Starting optimization step 3.
6:26:03.484864 PROGRESS: === Extracting elution groups 1400 to 3000 ===
6:26:03.484949 INFO: Using python extraction backend
6:26:03.485060 PROGRESS: Extracting batch of 3192 precursors
6:26:03.485142 INFO: === Search parameters used ===
6:26:03.485199 INFO: rt_error       : 1199.9447605
6:26:03.485249 INFO: mobility_error : 0.1
6:26:03.485312 INFO: num_candidates : 1
6:26:03.485363 INFO: ms1_error      : 30
6:26:03.485411 INFO: ms2_error      : 30
6:26:03.485460 INFO: fwhm_rt        : 5
6:26:03.485505 INFO: quant_window   : 3
6:26:03.485551 INFO: ==============================================
6:26:03.486608 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:26:03.486663 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:26:03.486693 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:26:03.486720 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:26:03.487508 INFO: Starting candidate selection
6:26:12.340024 INFO: Starting candidate scoring
6:26:12.424401 INFO: Finished candidate processing
6:26:12.424508 INFO: Collecting candidate features
6:26:12.438185 INFO: Collecting fragment features
6:26:12.441957 INFO: Finished candidate scoring
6:26:12.446418 INFO: performing precursor FDR with 47 features
6:26:12.446479 INFO: Decoy channel: -1
6:26:12.446507 INFO: competitive: True
6:26:12.450516 INFO: Setting torch num_threads to 2 for FDR classification task
6:26:12.452127 WARNING: dropped 1 target PSMs due to missing features
6:26:12.453462 INFO: Estimating optimal hyperparameters - samples: 4,288, batch_size: 128, learning_rate: 1.77e-04
6:26:12.453551 INFO: Using random state 194708 for train-test-split
6:26:12.901393 INFO: Test AUC: 0.526
6:26:12.901499 INFO: Train AUC: 0.550
6:26:12.901531 INFO: AUC difference: 4.32%
6:26:13.142686 INFO: Resetting torch num_threads to 80
6:26:13.144809 PROGRESS: === Extracted 5362 precursors and 45254 fragments ===
6:26:13.145234 INFO: === FDR correction performed with classifier version -1 ===
6:26:13.146049 PROGRESS: ============================= Precursor FDR =============================
6:26:13.146152 PROGRESS: Total precursors accumulated: 2,721
6:26:13.146219 PROGRESS: Target precursors: 1,520 (55.86%)
6:26:13.146278 PROGRESS: Decoy precursors: 1,201 (44.14%)
6:26:13.146330 PROGRESS: 
6:26:13.146382 PROGRESS: Precursor Summary:
6:26:13.147337 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
6:26:13.147433 PROGRESS: 
6:26:13.147495 PROGRESS: Protein Summary:
6:26:13.148517 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
6:26:13.148610 PROGRESS: =========================================================================
6:26:13.148784 INFO: Target number of precursors not reached yet.
6:26:13.276540 INFO: Starting optimization step 4.
6:26:13.276814 PROGRESS: === Extracting elution groups 3000 to 6200 ===
6:26:13.276900 INFO: Using python extraction backend
6:26:13.277010 PROGRESS: Extracting batch of 6381 precursors
6:26:13.277084 INFO: === Search parameters used ===
6:26:13.277136 INFO: rt_error       : 1199.9447605
6:26:13.277183 INFO: mobility_error : 0.1
6:26:13.277229 INFO: num_candidates : 1
6:26:13.277274 INFO: ms1_error      : 30
6:26:13.277317 INFO: ms2_error      : 30
6:26:13.277360 INFO: fwhm_rt        : 5
6:26:13.277404 INFO: quant_window   : 3
6:26:13.277445 INFO: ==============================================
6:26:13.278842 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:26:13.278895 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:26:13.278924 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:26:13.278947 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:26:13.279699 INFO: Starting candidate selection
6:26:29.367209 INFO: Starting candidate scoring
6:26:29.509338 INFO: Finished candidate processing
6:26:29.509452 INFO: Collecting candidate features
6:26:29.525401 WARNING: intensity_correlation has 1 NaNs ( 0.02 % out of 5746)
6:26:29.529412 INFO: Collecting fragment features
6:26:29.534761 INFO: Finished candidate scoring
6:26:29.541641 INFO: performing precursor FDR with 47 features
6:26:29.541736 INFO: Decoy channel: -1
6:26:29.541765 INFO: competitive: True
6:26:29.547238 INFO: Setting torch num_threads to 2 for FDR classification task
6:26:29.549512 WARNING: dropped 2 target PSMs due to missing features
6:26:29.551334 INFO: Estimating optimal hyperparameters - samples: 8,884, batch_size: 128, learning_rate: 1.77e-04
6:26:29.551430 INFO: Using random state 101574 for train-test-split
6:26:30.524794 INFO: Test AUC: 0.520
6:26:30.524929 INFO: Train AUC: 0.562
6:26:30.524963 INFO: AUC difference: 7.49%
6:26:30.524988 WARNING: AUC difference > 5%. This may indicate overfitting.
6:26:30.780304 INFO: Resetting torch num_threads to 80
6:26:30.783530 PROGRESS: === Extracted 11108 precursors and 93209 fragments ===
6:26:30.783992 INFO: === FDR correction performed with classifier version -1 ===
6:26:30.785130 PROGRESS: ============================= Precursor FDR =============================
6:26:30.785236 PROGRESS: Total precursors accumulated: 5,643
6:26:30.785304 PROGRESS: Target precursors: 3,180 (56.35%)
6:26:30.785363 PROGRESS: Decoy precursors: 2,463 (43.65%)
6:26:30.785418 PROGRESS: 
6:26:30.785483 PROGRESS: Precursor Summary:
6:26:30.786505 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
6:26:30.786606 PROGRESS: 
6:26:30.786675 PROGRESS: Protein Summary:
6:26:30.787856 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
6:26:30.787951 PROGRESS: =========================================================================
6:26:30.788144 INFO: Target number of precursors not reached yet.
6:26:30.957064 INFO: Starting optimization step 5.
6:26:30.957324 PROGRESS: === Extracting elution groups 6200 to 12600 ===
6:26:30.957407 INFO: Using python extraction backend
6:26:30.957518 PROGRESS: Extracting batch of 12763 precursors
6:26:30.957591 INFO: === Search parameters used ===
6:26:30.957644 INFO: rt_error       : 1199.9447605
6:26:30.957696 INFO: mobility_error : 0.1
6:26:30.957746 INFO: num_candidates : 1
6:26:30.957821 INFO: ms1_error      : 30
6:26:30.957880 INFO: ms2_error      : 30
6:26:30.957933 INFO: fwhm_rt        : 5
6:26:30.957980 INFO: quant_window   : 3
6:26:30.958024 INFO: ==============================================
6:26:30.960462 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:26:30.960518 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:26:30.960551 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:26:30.960575 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:26:30.961310 INFO: Starting candidate selection
6:27:02.760818 INFO: Starting candidate scoring
6:27:02.986016 INFO: Finished candidate processing
6:27:02.986154 INFO: Collecting candidate features
6:27:03.021482 WARNING: intensity_correlation has 3 NaNs ( 0.03 % out of 11488)
6:27:03.028377 INFO: Collecting fragment features
6:27:03.038989 INFO: Finished candidate scoring
6:27:03.051228 INFO: performing precursor FDR with 47 features
6:27:03.051372 INFO: Decoy channel: -1
6:27:03.051402 INFO: competitive: True
6:27:03.060430 INFO: Setting torch num_threads to 2 for FDR classification task
6:27:03.064568 WARNING: dropped 2 target PSMs due to missing features
6:27:03.064657 WARNING: dropped 3 decoy PSMs due to missing features
6:27:03.068102 INFO: Estimating optimal hyperparameters - samples: 18,072, batch_size: 128, learning_rate: 1.77e-04
6:27:03.068235 INFO: Using random state 91674 for train-test-split
6:27:05.030062 INFO: Test AUC: 0.516
6:27:05.030205 INFO: Train AUC: 0.564
6:27:05.030238 INFO: AUC difference: 8.59%
6:27:05.030263 WARNING: AUC difference > 5%. This may indicate overfitting.
6:27:05.288743 INFO: Resetting torch num_threads to 80
6:27:05.293743 PROGRESS: === Extracted 22596 precursors and 189784 fragments ===
6:27:05.294320 INFO: === FDR correction performed with classifier version -1 ===
6:27:05.296193 PROGRESS: ============================= Precursor FDR =============================
6:27:05.296304 PROGRESS: Total precursors accumulated: 11,472
6:27:05.296394 PROGRESS: Target precursors: 6,568 (57.25%)
6:27:05.296460 PROGRESS: Decoy precursors: 4,904 (42.75%)
6:27:05.296519 PROGRESS: 
6:27:05.296573 PROGRESS: Precursor Summary:
6:27:05.297620 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
6:27:05.297718 PROGRESS: 
6:27:05.297787 PROGRESS: Protein Summary:
6:27:05.298930 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
6:27:05.299031 PROGRESS: =========================================================================
6:27:05.299278 INFO: Target number of precursors not reached yet.
6:27:05.511316 INFO: Starting optimization step 6.
6:27:05.511601 PROGRESS: === Extracting elution groups 12600 to 25400 ===
6:27:05.511690 INFO: Using python extraction backend
6:27:05.511804 PROGRESS: Extracting batch of 25523 precursors
6:27:05.511885 INFO: === Search parameters used ===
6:27:05.511949 INFO: rt_error       : 1199.9447605
6:27:05.512002 INFO: mobility_error : 0.1
6:27:05.512055 INFO: num_candidates : 1
6:27:05.512105 INFO: ms1_error      : 30
6:27:05.512157 INFO: ms2_error      : 30
6:27:05.512206 INFO: fwhm_rt        : 5
6:27:05.512254 INFO: quant_window   : 3
6:27:05.512319 INFO: ==============================================
6:27:05.518101 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:27:05.518177 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:27:05.518209 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:27:05.518235 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:27:05.519035 INFO: Starting candidate selection
6:28:05.524510 INFO: Starting candidate scoring
6:28:05.939438 INFO: Finished candidate processing
6:28:05.939549 INFO: Collecting candidate features
6:28:05.979052 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 22925)
6:28:05.983592 INFO: Collecting fragment features
6:28:05.998676 INFO: Finished candidate scoring
6:28:06.021168 INFO: performing precursor FDR with 47 features
6:28:06.021318 INFO: Decoy channel: -1
6:28:06.021346 INFO: competitive: True
6:28:06.038957 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:06.047404 WARNING: dropped 5 target PSMs due to missing features
6:28:06.047544 WARNING: dropped 5 decoy PSMs due to missing features
6:28:06.054034 INFO: Estimating optimal hyperparameters - samples: 36,408, batch_size: 149, learning_rate: 1.91e-04
6:28:06.054259 INFO: Using random state 191399 for train-test-split
6:28:09.760750 INFO: Test AUC: 0.534
6:28:09.760887 INFO: Train AUC: 0.568
6:28:09.760921 INFO: AUC difference: 6.00%
6:28:09.760945 WARNING: AUC difference > 5%. This may indicate overfitting.
6:28:10.018100 INFO: Resetting torch num_threads to 80
6:28:10.026356 PROGRESS: === Extracted 45521 precursors and 383164 fragments ===
6:28:10.027035 INFO: === FDR correction performed with classifier version -1 ===
6:28:10.031096 PROGRESS: ============================= Precursor FDR =============================
6:28:10.031223 PROGRESS: Total precursors accumulated: 23,104
6:28:10.031295 PROGRESS: Target precursors: 13,190 (57.09%)
6:28:10.031354 PROGRESS: Decoy precursors: 9,914 (42.91%)
6:28:10.031410 PROGRESS: 
6:28:10.031464 PROGRESS: Precursor Summary:
6:28:10.032610 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
6:28:10.032711 PROGRESS: 
6:28:10.032774 PROGRESS: Protein Summary:
6:28:10.034015 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
6:28:10.034115 PROGRESS: =========================================================================
6:28:10.034487 INFO: Target number of precursors not reached yet.
6:28:10.275399 INFO: Starting optimization step 7.
6:28:10.275686 PROGRESS: === Extracting elution groups 25400 to 51000 ===
6:28:10.275772 INFO: Using python extraction backend
6:28:10.275901 PROGRESS: Extracting batch of 51061 precursors
6:28:10.275983 INFO: === Search parameters used ===
6:28:10.276042 INFO: rt_error       : 1199.9447605
6:28:10.276114 INFO: mobility_error : 0.1
6:28:10.276167 INFO: num_candidates : 1
6:28:10.276216 INFO: ms1_error      : 30
6:28:10.276263 INFO: ms2_error      : 30
6:28:10.276310 INFO: fwhm_rt        : 5
6:28:10.276357 INFO: quant_window   : 3
6:28:10.276403 INFO: ==============================================
6:28:10.289072 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:28:10.289202 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:28:10.289236 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:28:10.289261 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:28:10.290173 INFO: Starting candidate selection
6:30:06.055703 INFO: Starting candidate scoring
6:30:06.746876 INFO: Finished candidate processing
6:30:06.746986 INFO: Collecting candidate features
6:30:06.820260 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 45807)
6:30:06.826466 INFO: Collecting fragment features
6:30:06.853749 INFO: Finished candidate scoring
6:30:06.897004 INFO: performing precursor FDR with 47 features
6:30:06.897163 INFO: Decoy channel: -1
6:30:06.897193 INFO: competitive: True
6:30:06.933822 INFO: Setting torch num_threads to 2 for FDR classification task
6:30:06.952342 WARNING: dropped 8 target PSMs due to missing features
6:30:06.952493 WARNING: dropped 8 decoy PSMs due to missing features
6:30:06.966546 INFO: Estimating optimal hyperparameters - samples: 73,049, batch_size: 299, learning_rate: 2.70e-04
6:30:06.966853 INFO: Using random state 356712 for train-test-split
6:30:11.796550 INFO: Test AUC: 0.547
6:30:11.796683 INFO: Train AUC: 0.570
6:30:11.796722 INFO: AUC difference: 4.11%
6:30:12.068995 INFO: Resetting torch num_threads to 80
6:30:12.099467 PROGRESS: === Extracted 91328 precursors and 768632 fragments ===
6:30:12.100182 INFO: === FDR correction performed with classifier version -1 ===
6:30:12.108472 PROGRESS: ============================= Precursor FDR =============================
6:30:12.108660 PROGRESS: Total precursors accumulated: 46,340
6:30:12.108731 PROGRESS: Target precursors: 26,608 (57.42%)
6:30:12.108792 PROGRESS: Decoy precursors: 19,732 (42.58%)
6:30:12.108847 PROGRESS: 
6:30:12.108900 PROGRESS: Precursor Summary:
6:30:12.110245 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
6:30:12.110357 PROGRESS: 
6:30:12.110421 PROGRESS: Protein Summary:
6:30:12.111737 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
6:30:12.111836 PROGRESS: =========================================================================
6:30:12.112720 INFO: Target number of precursors not reached yet.
6:30:12.627458 INFO: Starting optimization step 8.
6:30:12.627856 PROGRESS: === Extracting elution groups 51000 to 102200 ===
6:30:12.627961 INFO: Using python extraction backend
6:30:12.628095 PROGRESS: Extracting batch of 102076 precursors
6:30:12.628181 INFO: === Search parameters used ===
6:30:12.628240 INFO: rt_error       : 1199.9447605
6:30:12.628293 INFO: mobility_error : 0.1
6:30:12.628343 INFO: num_candidates : 1
6:30:12.628393 INFO: ms1_error      : 30
6:30:12.628440 INFO: ms2_error      : 30
6:30:12.628486 INFO: fwhm_rt        : 5
6:30:12.628533 INFO: quant_window   : 3
6:30:12.628580 INFO: ==============================================
6:30:12.656638 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:30:12.656780 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:30:12.656821 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:30:12.656848 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:30:12.657834 INFO: Starting candidate selection
6:34:09.085790 INFO: Starting candidate scoring
6:34:10.518827 INFO: Finished candidate processing
6:34:10.519003 INFO: Collecting candidate features
6:34:10.694387 WARNING: intensity_correlation has 23 NaNs ( 0.03 % out of 91607)
6:34:10.694728 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 91607)
6:34:10.701429 INFO: Collecting fragment features
6:34:10.756094 INFO: Finished candidate scoring
6:34:10.863341 INFO: performing precursor FDR with 47 features
6:34:10.863492 INFO: Decoy channel: -1
6:34:10.863523 INFO: competitive: True
6:34:10.937617 INFO: Setting torch num_threads to 2 for FDR classification task
6:34:10.971498 WARNING: dropped 16 target PSMs due to missing features
6:34:10.971652 WARNING: dropped 24 decoy PSMs due to missing features
6:34:11.020824 INFO: Estimating optimal hyperparameters - samples: 146,316, batch_size: 599, learning_rate: 3.82e-04
6:34:11.021326 INFO: Using random state 572100 for train-test-split
6:34:17.641273 INFO: Test AUC: 0.549
6:34:17.641429 INFO: Train AUC: 0.569
6:34:17.641465 INFO: AUC difference: 3.43%
6:34:17.942182 INFO: Resetting torch num_threads to 80
6:34:17.991158 PROGRESS: === Extracted 182935 precursors and 1542008 fragments ===
6:34:17.991984 INFO: === FDR correction performed with classifier version -1 ===
6:34:18.009622 PROGRESS: ============================= Precursor FDR =============================
6:34:18.009924 PROGRESS: Total precursors accumulated: 92,825
6:34:18.009997 PROGRESS: Target precursors: 53,515 (57.65%)
6:34:18.010057 PROGRESS: Decoy precursors: 39,310 (42.35%)
6:34:18.010110 PROGRESS: 
6:34:18.010163 PROGRESS: Precursor Summary:
6:34:18.011812 PROGRESS: Channel   0:	 0.050 FDR:    43; 0.010 FDR:     2; 0.001 FDR:     2
6:34:18.011934 PROGRESS: 
6:34:18.011998 PROGRESS: Protein Summary:
6:34:18.013539 PROGRESS: Channel   0:	 0.050 FDR:    43; 0.010 FDR:     2; 0.001 FDR:     2
6:34:18.013635 PROGRESS: =========================================================================
6:34:18.015031 INFO: Target number of precursors not reached yet.
6:34:18.641253 INFO: Starting optimization step 9.
6:34:18.641575 PROGRESS: === Extracting elution groups 102200 to 204600 ===
6:34:18.641679 INFO: Using python extraction backend
6:34:18.641808 PROGRESS: Extracting batch of 204132 precursors
6:34:18.641900 INFO: === Search parameters used ===
6:34:18.641966 INFO: rt_error       : 1199.9447605
6:34:18.642017 INFO: mobility_error : 0.1
6:34:18.642065 INFO: num_candidates : 1
6:34:18.642110 INFO: ms1_error      : 30
6:34:18.642154 INFO: ms2_error      : 30
6:34:18.642197 INFO: fwhm_rt        : 5
6:34:18.642241 INFO: quant_window   : 3
6:34:18.642284 INFO: ==============================================
6:34:18.690838 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:34:18.690986 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:34:18.691023 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:34:18.691050 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:34:18.692050 INFO: Starting candidate selection
6:42:12.179260 INFO: Starting candidate scoring
6:42:14.828625 INFO: Finished candidate processing
6:42:14.828800 INFO: Collecting candidate features
6:42:15.202246 WARNING: intensity_correlation has 42 NaNs ( 0.02 % out of 183363)
6:42:15.212404 INFO: Collecting fragment features
6:42:15.328390 INFO: Finished candidate scoring
6:42:15.562724 INFO: performing precursor FDR with 47 features
6:42:15.562873 INFO: Decoy channel: -1
6:42:15.562902 INFO: competitive: True
6:42:15.708050 INFO: Setting torch num_threads to 2 for FDR classification task
6:42:15.773190 WARNING: dropped 34 target PSMs due to missing features
6:42:15.773345 WARNING: dropped 48 decoy PSMs due to missing features
6:42:15.886227 INFO: Estimating optimal hyperparameters - samples: 292,972, batch_size: 1,200, learning_rate: 5.41e-04
6:42:15.886789 INFO: Using random state 333479 for train-test-split
6:42:25.691976 INFO: Test AUC: 0.545
6:42:25.692133 INFO: Train AUC: 0.565
6:42:25.692168 INFO: AUC difference: 3.52%
6:42:27.069366 INFO: Resetting torch num_threads to 80
6:42:27.299663 PROGRESS: === Extracted 366298 precursors and 3088299 fragments ===
6:42:27.300772 INFO: === FDR correction performed with classifier version -1 ===
6:42:27.336607 PROGRESS: ============================= Precursor FDR =============================
6:42:27.337034 PROGRESS: Total precursors accumulated: 185,902
6:42:27.337111 PROGRESS: Target precursors: 106,282 (57.17%)
6:42:27.337170 PROGRESS: Decoy precursors: 79,620 (42.83%)
6:42:27.337223 PROGRESS: 
6:42:27.337275 PROGRESS: Precursor Summary:
6:42:27.339680 PROGRESS: Channel   0:	 0.050 FDR:   104; 0.010 FDR:    34; 0.001 FDR:    34
6:42:27.339799 PROGRESS: 
6:42:27.339864 PROGRESS: Protein Summary:
6:42:27.341953 PROGRESS: Channel   0:	 0.050 FDR:    95; 0.010 FDR:    32; 0.001 FDR:    32
6:42:27.342054 PROGRESS: =========================================================================
6:42:27.344724 INFO: Target number of precursors not reached yet.
6:42:28.464835 INFO: Starting optimization step 10.
6:42:28.465160 PROGRESS: === Extracting elution groups 204600 to 409400 ===
6:42:28.465309 INFO: Using python extraction backend
6:42:28.465497 PROGRESS: Extracting batch of 408390 precursors
6:42:28.465592 INFO: === Search parameters used ===
6:42:28.465652 INFO: rt_error       : 1199.9447605
6:42:28.465706 INFO: mobility_error : 0.1
6:42:28.465758 INFO: num_candidates : 1
6:42:28.465816 INFO: ms1_error      : 30
6:42:28.465873 INFO: ms2_error      : 30
6:42:28.465929 INFO: fwhm_rt        : 5
6:42:28.465995 INFO: quant_window   : 3
6:42:28.466047 INFO: ==============================================
6:42:28.561082 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:42:28.561227 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:42:28.561270 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
6:42:28.561313 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
6:42:28.562413 INFO: Starting candidate selection
6:58:09.590734 INFO: Starting candidate scoring
6:58:14.816170 INFO: Finished candidate processing
6:58:14.816295 INFO: Collecting candidate features
6:58:15.663478 WARNING: intensity_correlation has 108 NaNs ( 0.03 % out of 365809)
6:58:15.664061 WARNING: height_correlation has 12 NaNs ( 0.00 % out of 365809)
6:58:15.680002 INFO: Collecting fragment features
6:58:15.902133 INFO: Finished candidate scoring
6:58:16.428643 INFO: performing precursor FDR with 47 features
6:58:16.428800 INFO: Decoy channel: -1
6:58:16.428828 INFO: competitive: True
6:58:16.846025 INFO: Setting torch num_threads to 2 for FDR classification task
6:58:17.020574 WARNING: dropped 93 target PSMs due to missing features
6:58:17.020732 WARNING: dropped 106 decoy PSMs due to missing features
6:58:17.280705 INFO: Estimating optimal hyperparameters - samples: 585,526, batch_size: 2,398, learning_rate: 7.65e-04
6:58:17.282500 INFO: Using random state 34853 for train-test-split
6:58:33.760871 INFO: Test AUC: 0.547
6:58:33.761043 INFO: Train AUC: 0.562
6:58:33.761079 INFO: AUC difference: 2.63%
6:58:34.259824 INFO: Resetting torch num_threads to 80
6:58:34.395727 PROGRESS: === Extracted 732107 precursors and 6171109 fragments ===
6:58:34.396799 INFO: === FDR correction performed with classifier version -1 ===
6:58:34.454485 PROGRESS: ============================= Precursor FDR =============================
6:58:34.454790 PROGRESS: Total precursors accumulated: 371,568
6:58:34.454870 PROGRESS: Target precursors: 211,418 (56.90%)
6:58:34.454930 PROGRESS: Decoy precursors: 160,150 (43.10%)
6:58:34.454988 PROGRESS: 
6:58:34.455042 PROGRESS: Precursor Summary:
6:58:34.458669 PROGRESS: Channel   0:	 0.050 FDR:   276; 0.010 FDR:   203; 0.001 FDR:   166
6:58:34.458808 PROGRESS: 
6:58:34.458875 PROGRESS: Protein Summary:
6:58:34.462194 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   155; 0.001 FDR:   128
6:58:34.462315 PROGRESS: =========================================================================
6:58:34.467615 INFO: Target number of precursors reached.
6:58:35.147487 INFO: fragments_df: keeping 1924 of 6171109 [sum(precursor_idx_mask)=2179 sum(mass_error_mask)=6171067 stop_rank=1924
6:58:36.514819 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:58:36.622569 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:58:36.732881 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
6:58:36.851238 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:58:37.085269 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
6:58:37.085724 INFO: Using score_cutoff 39.4700921836853 (fac=0.99, q=1)
6:58:37.086079 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.796626091003418
6:58:37.086172 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008695457130670547
6:58:37.086237 INFO: Updating optimization_manager: score_cutoff        : 0 -> 39.4700921836853
6:58:37.086306 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:58:37.204152 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:58:37.734893 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
6:58:37.865467 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:58:38.960296 INFO: Updating optimization_manager: classifier_version  : -1 -> 10
6:58:38.960583 PROGRESS: Required number of precursors found. Starting search parameter optimization.
6:58:38.960702 INFO: Starting optimization step 11.
6:58:38.960778 PROGRESS: === Extracting elution groups 0 to 409400 ===
6:58:38.960865 INFO: Using python extraction backend
6:58:38.961006 PROGRESS: Extracting batch of 816307 precursors
6:58:38.961098 INFO: === Search parameters used ===
6:58:38.961162 INFO: rt_error       : 1199.9447605
6:58:38.961216 INFO: mobility_error : 0.1
6:58:38.961269 INFO: num_candidates : 3
6:58:38.961338 INFO: ms1_error      : 30
6:58:38.961394 INFO: ms2_error      : 30
6:58:38.961440 INFO: fwhm_rt        : 2.796626091003418
6:58:38.961485 INFO: quant_window   : 3
6:58:38.961530 INFO: ==============================================
6:58:39.153433 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
6:58:39.153574 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
6:58:39.153630 INFO: FWHM in RT is 2.80 seconds, sigma is 0.47
6:58:39.153655 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.71
6:58:39.154470 INFO: Starting candidate selection
7:34:33.543221 INFO: Starting candidate scoring
7:35:02.027680 INFO: Finished candidate processing
7:35:02.027966 INFO: Collecting candidate features
7:35:10.029353 WARNING: intensity_correlation has 668 NaNs ( 0.03 % out of 2111110)
7:35:10.031830 WARNING: height_correlation has 53 NaNs ( 0.00 % out of 2111110)
7:35:10.117029 INFO: Collecting fragment features
7:35:15.741204 INFO: Finished candidate scoring
7:35:17.987255 INFO: performing precursor FDR with 47 features
7:35:17.987437 INFO: Decoy channel: -1
7:35:17.987477 INFO: competitive: True
7:35:18.539238 INFO: Setting torch num_threads to 2 for FDR classification task
7:35:18.859061 WARNING: dropped 316 target PSMs due to missing features
7:35:18.859236 WARNING: dropped 380 decoy PSMs due to missing features
7:35:20.197560 INFO: Estimating optimal hyperparameters - samples: 1,688,331, batch_size: 4,096, learning_rate: 1.00e-03
7:35:20.201814 INFO: Using random state 280662 for train-test-split
7:36:08.559324 INFO: Test AUC: 0.552
7:36:08.559556 INFO: Train AUC: 0.560
7:36:08.559594 INFO: AUC difference: 1.49%
7:36:09.520212 INFO: Resetting torch num_threads to 80
7:36:09.574782 PROGRESS: === Extracted 2111110 precursors and 17408951 fragments ===
7:36:09.575980 INFO: === FDR correction performed with classifier version 10 ===
7:36:09.639765 PROGRESS: ============================= Precursor FDR =============================
7:36:09.640054 PROGRESS: Total precursors accumulated: 375,172
7:36:09.640131 PROGRESS: Target precursors: 217,955 (58.09%)
7:36:09.640193 PROGRESS: Decoy precursors: 157,217 (41.91%)
7:36:09.640250 PROGRESS: 
7:36:09.640305 PROGRESS: Precursor Summary:
7:36:09.643753 PROGRESS: Channel   0:	 0.050 FDR:   267; 0.010 FDR:     0; 0.001 FDR:     0
7:36:09.643898 PROGRESS: 
7:36:09.643965 PROGRESS: Protein Summary:
7:36:09.646931 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:     0; 0.001 FDR:     0
7:36:09.647036 PROGRESS: =========================================================================
7:36:09.656987 INFO: Target number of precursors not reached yet.
7:36:10.887983 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:36:11.001720 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:36:11.519839 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:36:11.636590 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:36:12.659352 INFO: === skipping optimization until target number of precursors are found ===
7:36:12.659682 INFO: Starting optimization step 12.
7:36:12.659768 PROGRESS: === Extracting elution groups 409400 to 819000 ===
7:36:12.659899 INFO: Using python extraction backend
7:36:12.660082 PROGRESS: Extracting batch of 816689 precursors
7:36:12.660179 INFO: === Search parameters used ===
7:36:12.660245 INFO: rt_error       : 1199.9447605
7:36:12.660296 INFO: mobility_error : 0.1
7:36:12.660346 INFO: num_candidates : 3
7:36:12.660394 INFO: ms1_error      : 30
7:36:12.660439 INFO: ms2_error      : 30
7:36:12.660485 INFO: fwhm_rt        : 2.796626091003418
7:36:12.660531 INFO: quant_window   : 3
7:36:12.660575 INFO: ==============================================
7:36:12.860551 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
7:36:12.860696 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
7:36:12.860754 INFO: FWHM in RT is 2.80 seconds, sigma is 0.47
7:36:12.860779 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.71
7:36:12.861670 INFO: Starting candidate selection
8:12:12.195216 INFO: Starting candidate scoring
8:12:39.019206 INFO: Finished candidate processing
8:12:39.020549 INFO: Collecting candidate features
8:12:46.843230 WARNING: intensity_correlation has 620 NaNs ( 0.03 % out of 2113417)
8:12:46.845544 WARNING: height_correlation has 36 NaNs ( 0.00 % out of 2113417)
8:12:46.928337 INFO: Collecting fragment features
8:12:52.460364 INFO: Finished candidate scoring
8:12:57.766513 INFO: performing precursor FDR with 47 features
8:12:57.766670 INFO: Decoy channel: -1
8:12:57.766704 INFO: competitive: True
8:13:06.678551 INFO: Setting torch num_threads to 2 for FDR classification task
8:13:10.939164 WARNING: dropped 617 target PSMs due to missing features
8:13:10.939355 WARNING: dropped 723 decoy PSMs due to missing features
8:13:17.426117 INFO: Estimating optimal hyperparameters - samples: 3,378,549, batch_size: 4,096, learning_rate: 1.00e-03
8:13:17.435252 INFO: Using random state 280662 for train-test-split
8:14:47.965135 INFO: Test AUC: 0.560
8:14:47.965806 INFO: Train AUC: 0.564
8:14:47.965862 INFO: AUC difference: 0.67%
8:14:49.586226 INFO: Resetting torch num_threads to 80
8:14:51.260562 PROGRESS: === Extracted 4224527 precursors and 34835472 fragments ===
8:14:51.262582 INFO: === FDR correction performed with classifier version 10 ===
8:14:51.461145 PROGRESS: ============================= Precursor FDR =============================
8:14:51.461563 PROGRESS: Total precursors accumulated: 750,683
8:14:51.461666 PROGRESS: Target precursors: 437,713 (58.31%)
8:14:51.461748 PROGRESS: Decoy precursors: 312,970 (41.69%)
8:14:51.461814 PROGRESS: 
8:14:51.461895 PROGRESS: Precursor Summary:
8:14:51.467836 PROGRESS: Channel   0:	 0.050 FDR:   761; 0.010 FDR:   469; 0.001 FDR:   208
8:14:51.467985 PROGRESS: 
8:14:51.468064 PROGRESS: Protein Summary:
8:14:51.473145 PROGRESS: Channel   0:	 0.050 FDR:   451; 0.010 FDR:   277; 0.001 FDR:   132
8:14:51.473263 PROGRESS: =========================================================================
8:14:51.486499 INFO: Target number of precursors reached.
8:14:55.329903 INFO: fragments_df: keeping 5000 of 34835472 [sum(precursor_idx_mask)=14089 sum(mass_error_mask)=34835326 stop_rank=5000
8:14:57.343125 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:14:57.494754 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:14:57.631361 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
8:14:57.766721 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:14:58.422321 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:14:58.422800 INFO: Using score_cutoff 41.805527879333496 (fac=0.99, q=1)
8:14:58.423272 INFO: Updating optimization_manager: fwhm_rt             : 2.796626091003418 -> 2.8502037525177
8:14:58.423362 INFO: Updating optimization_manager: fwhm_mobility       : 0.008695457130670547 -> 0.008098438382148743
8:14:58.423425 INFO: Updating optimization_manager: score_cutoff        : 39.4700921836853 -> 41.805527879333496
8:14:58.423502 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:14:58.529484 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:14:59.071510 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
8:14:59.181436 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:15:00.254238 INFO: === checking if optimization conditions were reached ===
8:15:00.256684 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
8:15:00.256859 INFO: Updating optimization_manager: classifier_version  : 10 -> 12
8:15:00.256968 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
8:15:00.258175 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
8:15:00.258294 INFO: Updating optimization_manager: classifier_version  : 12 -> 12
8:15:00.258366 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
8:15:00.258428 INFO: ==============================================
8:15:00.258530 INFO: Starting optimization step 13.
8:15:00.258603 PROGRESS: === Extracting elution groups 0 to 409400 ===
8:15:00.258728 INFO: Using python extraction backend
8:15:00.259003 PROGRESS: Extracting batch of 816307 precursors
8:15:00.259093 INFO: === Search parameters used ===
8:15:00.259151 INFO: rt_error       : 1199.9447605
8:15:00.259200 INFO: mobility_error : 0.1
8:15:00.259248 INFO: num_candidates : 3
8:15:00.259302 INFO: ms1_error      : 15.0
8:15:00.259349 INFO: ms2_error      : 15.0
8:15:00.259394 INFO: fwhm_rt        : 2.8502037525177
8:15:00.259439 INFO: quant_window   : 3
8:15:00.259483 INFO: ==============================================
8:15:00.498488 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
8:15:00.498626 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
8:15:00.498694 INFO: FWHM in RT is 2.85 seconds, sigma is 0.48
8:15:00.498720 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.39
8:15:00.499522 INFO: Starting candidate selection
8:45:17.150629 INFO: Starting candidate scoring
8:45:41.209883 INFO: Finished candidate processing
8:45:41.210290 INFO: Collecting candidate features
8:45:45.086469 WARNING: intensity_correlation has 2354 NaNs ( 0.11 % out of 2054129)
8:45:45.088556 WARNING: height_correlation has 156 NaNs ( 0.01 % out of 2054129)
8:45:45.158095 INFO: Collecting fragment features
8:45:46.402932 INFO: Finished candidate scoring
8:45:48.040245 INFO: performing precursor FDR with 47 features
8:45:48.040388 INFO: Decoy channel: -1
8:45:48.040419 INFO: competitive: True
8:45:48.573743 INFO: Setting torch num_threads to 2 for FDR classification task
8:45:48.899105 WARNING: dropped 1182 target PSMs due to missing features
8:45:48.899273 WARNING: dropped 1274 decoy PSMs due to missing features
8:45:50.267258 INFO: Estimating optimal hyperparameters - samples: 1,641,338, batch_size: 4,096, learning_rate: 1.00e-03
8:45:50.272852 INFO: Using random state 795075 for train-test-split
8:46:33.503879 INFO: Test AUC: 0.559
8:46:33.504126 INFO: Train AUC: 0.568
8:46:33.504164 INFO: AUC difference: 1.57%
8:46:34.436127 INFO: Resetting torch num_threads to 80
8:46:34.474818 PROGRESS: === Extracted 2054129 precursors and 14451276 fragments ===
8:46:34.476179 INFO: === FDR correction performed with classifier version 12 ===
8:46:34.561627 PROGRESS: ============================= Precursor FDR =============================
8:46:34.561960 PROGRESS: Total precursors accumulated: 373,017
8:46:34.562037 PROGRESS: Target precursors: 216,951 (58.16%)
8:46:34.562100 PROGRESS: Decoy precursors: 156,066 (41.84%)
8:46:34.562156 PROGRESS: 
8:46:34.562211 PROGRESS: Precursor Summary:
8:46:34.565668 PROGRESS: Channel   0:	 0.050 FDR:   543; 0.010 FDR:   407; 0.001 FDR:   341
8:46:34.565778 PROGRESS: 
8:46:34.565852 PROGRESS: Protein Summary:
8:46:34.569051 PROGRESS: Channel   0:	 0.050 FDR:   398; 0.010 FDR:   291; 0.001 FDR:   243
8:46:34.569161 PROGRESS: =========================================================================
8:46:34.591708 INFO: Target number of precursors reached.
8:46:36.075615 INFO: fragments_df: keeping 5000 of 14451276 [sum(precursor_idx_mask)=11054 sum(mass_error_mask)=14451166 stop_rank=5000
8:46:37.858658 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:46:38.005291 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:46:38.151962 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
8:46:38.307023 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:46:39.027287 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:46:39.027744 INFO: Using score_cutoff 27.42136339416504 (fac=0.99, q=1)
8:46:39.028123 INFO: Updating optimization_manager: fwhm_rt             : 2.8502037525177 -> 2.6160049438476562
8:46:39.028213 INFO: Updating optimization_manager: fwhm_mobility       : 0.008098438382148743 -> 0.006175293121486902
8:46:39.028277 INFO: Updating optimization_manager: score_cutoff        : 41.805527879333496 -> 27.42136339416504
8:46:39.028355 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:46:39.080254 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:46:39.335717 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
8:46:39.389138 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:46:39.893568 INFO: === checking if optimization conditions were reached ===
8:46:39.895918 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
8:46:39.896070 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
8:46:39.896147 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
8:46:39.897260 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
8:46:39.897369 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
8:46:39.897439 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
8:46:39.897510 INFO: ==============================================
8:46:39.897584 PROGRESS: Optimization finished for ms2_error, ms1_error.
8:46:40.568841 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:46:40.621188 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:46:40.874736 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
8:46:40.931884 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:46:41.412903 INFO: Starting optimization step 0.
8:46:41.413221 PROGRESS: === Extracting elution groups 0 to 204600 ===
8:46:41.413335 INFO: Using python extraction backend
8:46:41.413476 PROGRESS: Extracting batch of 407917 precursors
8:46:41.413569 INFO: === Search parameters used ===
8:46:41.413634 INFO: rt_error       : 1199.9447605
8:46:41.413691 INFO: mobility_error : 0.1
8:46:41.413746 INFO: num_candidates : 3
8:46:41.413801 INFO: ms1_error      : 15.0
8:46:41.413856 INFO: ms2_error      : 15.0
8:46:41.413929 INFO: fwhm_rt        : 2.6160049438476562
8:46:41.413984 INFO: quant_window   : 3
8:46:41.414037 INFO: ==============================================
8:46:41.527885 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
8:46:41.528033 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
8:46:41.528098 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
8:46:41.528129 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.35
8:46:41.529016 INFO: Starting candidate selection
9:02:20.665279 INFO: Starting candidate scoring
9:02:32.741684 INFO: Finished candidate processing
9:02:32.742186 INFO: Collecting candidate features
9:02:34.654461 WARNING: intensity_correlation has 1184 NaNs ( 0.12 % out of 1024372)
9:02:34.655684 WARNING: height_correlation has 76 NaNs ( 0.01 % out of 1024372)
9:02:34.694140 INFO: Collecting fragment features
9:02:35.229100 INFO: Finished candidate scoring
9:02:35.949283 INFO: performing precursor FDR with 47 features
9:02:35.949417 INFO: Decoy channel: -1
9:02:35.949447 INFO: competitive: True
9:02:36.205842 INFO: Setting torch num_threads to 2 for FDR classification task
9:02:36.361447 WARNING: dropped 591 target PSMs due to missing features
9:02:36.361613 WARNING: dropped 647 decoy PSMs due to missing features
9:02:36.712024 INFO: Estimating optimal hyperparameters - samples: 818,507, batch_size: 3,352, learning_rate: 9.05e-04
9:02:36.714002 INFO: Using random state 594839 for train-test-split
9:02:58.919494 INFO: Test AUC: 0.561
9:02:58.919658 INFO: Train AUC: 0.581
9:02:58.919695 INFO: AUC difference: 3.35%
9:02:59.504967 INFO: Resetting torch num_threads to 80
9:02:59.525009 PROGRESS: === Extracted 1024372 precursors and 7134075 fragments ===
9:02:59.525974 INFO: === FDR correction performed with classifier version 13 ===
9:02:59.559463 PROGRESS: ============================= Precursor FDR =============================
9:02:59.559736 PROGRESS: Total precursors accumulated: 186,580
9:02:59.559808 PROGRESS: Target precursors: 110,624 (59.29%)
9:02:59.559867 PROGRESS: Decoy precursors: 75,956 (40.71%)
9:02:59.559920 PROGRESS: 
9:02:59.559971 PROGRESS: Precursor Summary:
9:02:59.562268 PROGRESS: Channel   0:	 0.050 FDR:   302; 0.010 FDR:   221; 0.001 FDR:   165
9:02:59.562376 PROGRESS: 
9:02:59.562444 PROGRESS: Protein Summary:
9:02:59.564624 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:   172; 0.001 FDR:   133
9:02:59.564742 PROGRESS: =========================================================================
9:02:59.606540 INFO: Target number of precursors reached.
9:03:00.375264 INFO: fragments_df: keeping 3894 of 7134075 [sum(precursor_idx_mask)=5980 sum(mass_error_mask)=7134037 stop_rank=3894
9:03:01.775983 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:03:01.913003 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:03:02.043412 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:03:02.171034 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:03:02.711873 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:03:02.712344 INFO: Using score_cutoff 30.580163566589356 (fac=0.99, q=1)
9:03:02.712728 INFO: Updating optimization_manager: fwhm_rt             : 2.6160049438476562 -> 2.716982126235962
9:03:02.712840 INFO: Updating optimization_manager: fwhm_mobility       : 0.006175293121486902 -> 0.006066923029720783
9:03:02.712916 INFO: Updating optimization_manager: score_cutoff        : 27.42136339416504 -> 30.580163566589356
9:03:02.713000 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:03:02.765509 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:03:03.026750 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:03:03.089821 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:03:03.674699 INFO: === checking if optimization conditions were reached ===
9:03:03.675036 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
9:03:03.677130 INFO: Updating optimization_manager: rt_error            : 1199.9447605 -> 412.18432799287785
9:03:03.677262 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 412.1843.
9:03:03.677341 INFO: ==============================================
9:03:03.677436 INFO: Starting optimization step 1.
9:03:03.677510 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:03:03.677619 INFO: Using python extraction backend
9:03:03.677778 PROGRESS: Extracting batch of 407917 precursors
9:03:03.677876 INFO: === Search parameters used ===
9:03:03.677948 INFO: rt_error       : 412.18432799287785
9:03:03.678000 INFO: mobility_error : 0.1
9:03:03.678049 INFO: num_candidates : 3
9:03:03.678106 INFO: ms1_error      : 15.0
9:03:03.678157 INFO: ms2_error      : 15.0
9:03:03.678204 INFO: fwhm_rt        : 2.716982126235962
9:03:03.678249 INFO: quant_window   : 3
9:03:03.678294 INFO: ==============================================
9:03:03.788742 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:03:03.788883 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:03:03.788968 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
9:03:03.788996 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.29
9:03:03.789798 INFO: Starting candidate selection
9:09:19.084034 INFO: Starting candidate scoring
9:09:30.905280 INFO: Finished candidate processing
9:09:30.905622 INFO: Collecting candidate features
9:09:32.755650 WARNING: intensity_correlation has 1879 NaNs ( 0.19 % out of 982577)
9:09:32.756880 WARNING: height_correlation has 143 NaNs ( 0.01 % out of 982577)
9:09:32.793997 INFO: Collecting fragment features
9:09:33.278096 INFO: Finished candidate scoring
9:09:33.985024 INFO: performing precursor FDR with 47 features
9:09:33.985180 INFO: Decoy channel: -1
9:09:33.985215 INFO: competitive: True
9:09:34.237243 INFO: Setting torch num_threads to 2 for FDR classification task
9:09:34.394156 WARNING: dropped 1000 target PSMs due to missing features
9:09:34.394323 WARNING: dropped 965 decoy PSMs due to missing features
9:09:34.727895 INFO: Estimating optimal hyperparameters - samples: 784,489, batch_size: 3,213, learning_rate: 8.86e-04
9:09:34.729825 INFO: Using random state 594839 for train-test-split
9:09:54.647173 INFO: Test AUC: 0.553
9:09:54.647337 INFO: Train AUC: 0.571
9:09:54.647376 INFO: AUC difference: 3.21%
9:09:55.222333 INFO: Resetting torch num_threads to 80
9:09:55.241372 PROGRESS: === Extracted 982577 precursors and 6378585 fragments ===
9:09:55.242251 INFO: === FDR correction performed with classifier version 13 ===
9:09:55.274414 PROGRESS: ============================= Precursor FDR =============================
9:09:55.274664 PROGRESS: Total precursors accumulated: 183,889
9:09:55.274736 PROGRESS: Target precursors: 106,544 (57.94%)
9:09:55.274796 PROGRESS: Decoy precursors: 77,345 (42.06%)
9:09:55.274848 PROGRESS: 
9:09:55.274901 PROGRESS: Precursor Summary:
9:09:55.277127 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   218; 0.001 FDR:   206
9:09:55.277230 PROGRESS: 
9:09:55.277295 PROGRESS: Protein Summary:
9:09:55.279438 PROGRESS: Channel   0:	 0.050 FDR:   217; 0.010 FDR:   169; 0.001 FDR:   162
9:09:55.279541 PROGRESS: =========================================================================
9:09:55.284829 INFO: Target number of precursors reached.
9:09:55.964050 INFO: fragments_df: keeping 3783 of 6378585 [sum(precursor_idx_mask)=5904 sum(mass_error_mask)=6378506 stop_rank=3783
9:09:56.991080 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:09:57.102329 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:09:57.225153 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:09:57.342173 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:09:57.802104 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:09:57.802552 INFO: Using score_cutoff 29.07503338279724 (fac=0.99, q=1)
9:09:57.802887 INFO: Updating optimization_manager: fwhm_rt             : 2.716982126235962 -> 2.753133773803711
9:09:57.802980 INFO: Updating optimization_manager: fwhm_mobility       : 0.006066923029720783 -> 0.006320829503238201
9:09:57.803047 INFO: Updating optimization_manager: score_cutoff        : 30.580163566589356 -> 29.07503338279724
9:09:57.803111 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:09:57.852497 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:09:58.109982 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:09:58.160683 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:09:58.698063 INFO: === checking if optimization conditions were reached ===
9:09:58.698357 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
9:09:58.700438 INFO: Updating optimization_manager: rt_error            : 412.18432799287785 -> 289.12889183015307
9:09:58.700569 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 289.1289.
9:09:58.700649 INFO: ==============================================
9:09:58.700727 INFO: Starting optimization step 2.
9:09:58.700810 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:09:58.700886 INFO: Using python extraction backend
9:09:58.701001 PROGRESS: Extracting batch of 407917 precursors
9:09:58.701082 INFO: === Search parameters used ===
9:09:58.701144 INFO: rt_error       : 289.12889183015307
9:09:58.701195 INFO: mobility_error : 0.1
9:09:58.701246 INFO: num_candidates : 3
9:09:58.701295 INFO: ms1_error      : 15.0
9:09:58.701343 INFO: ms2_error      : 15.0
9:09:58.701391 INFO: fwhm_rt        : 2.753133773803711
9:09:58.701442 INFO: quant_window   : 3
9:09:58.701491 INFO: ==============================================
9:09:58.812090 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:09:58.812232 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:09:58.812285 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
9:09:58.812312 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.43
9:09:58.813059 INFO: Starting candidate selection
9:14:11.000189 INFO: Starting candidate scoring
9:14:22.332976 INFO: Finished candidate processing
9:14:22.333145 INFO: Collecting candidate features
9:14:24.195364 WARNING: intensity_correlation has 2442 NaNs ( 0.26 % out of 955777)
9:14:24.196563 WARNING: height_correlation has 233 NaNs ( 0.02 % out of 955777)
9:14:24.233582 INFO: Collecting fragment features
9:14:24.742975 INFO: Finished candidate scoring
9:14:25.513704 INFO: performing precursor FDR with 47 features
9:14:25.513843 INFO: Decoy channel: -1
9:14:25.513906 INFO: competitive: True
9:14:25.754440 INFO: Setting torch num_threads to 2 for FDR classification task
9:14:25.905093 WARNING: dropped 1275 target PSMs due to missing features
9:14:25.905254 WARNING: dropped 1283 decoy PSMs due to missing features
9:14:26.322549 INFO: Estimating optimal hyperparameters - samples: 762,575, batch_size: 3,123, learning_rate: 8.73e-04
9:14:26.324128 INFO: Using random state 594839 for train-test-split
9:14:47.446855 INFO: Test AUC: 0.551
9:14:47.447079 INFO: Train AUC: 0.567
9:14:47.447117 INFO: AUC difference: 2.84%
9:14:47.999415 INFO: Resetting torch num_threads to 80
9:14:48.018212 PROGRESS: === Extracted 955777 precursors and 5859890 fragments ===
9:14:48.019031 INFO: === FDR correction performed with classifier version 13 ===
9:14:48.052281 PROGRESS: ============================= Precursor FDR =============================
9:14:48.052546 PROGRESS: Total precursors accumulated: 182,675
9:14:48.052617 PROGRESS: Target precursors: 104,896 (57.42%)
9:14:48.052677 PROGRESS: Decoy precursors: 77,779 (42.58%)
9:14:48.052733 PROGRESS: 
9:14:48.052787 PROGRESS: Precursor Summary:
9:14:48.055073 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   236; 0.001 FDR:   215
9:14:48.055180 PROGRESS: 
9:14:48.055254 PROGRESS: Protein Summary:
9:14:48.057381 PROGRESS: Channel   0:	 0.050 FDR:   287; 0.010 FDR:   181; 0.001 FDR:   166
9:14:48.057482 PROGRESS: =========================================================================
9:14:48.062720 INFO: Target number of precursors reached.
9:14:48.696163 INFO: fragments_df: keeping 4034 of 5859890 [sum(precursor_idx_mask)=6295 sum(mass_error_mask)=5859762 stop_rank=4034
9:14:49.559259 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:14:49.664752 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:14:49.775870 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:14:49.888882 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:14:50.383970 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:14:50.384413 INFO: Using score_cutoff 28.310007997512816 (fac=0.99, q=1)
9:14:50.384745 INFO: Updating optimization_manager: fwhm_rt             : 2.753133773803711 -> 2.7237534523010254
9:14:50.384832 INFO: Updating optimization_manager: fwhm_mobility       : 0.006320829503238201 -> 0.006320829503238201
9:14:50.384900 INFO: Updating optimization_manager: score_cutoff        : 29.07503338279724 -> 28.310007997512816
9:14:50.384970 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:14:50.434221 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:14:50.693041 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:14:50.747659 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:14:51.292053 INFO: === checking if optimization conditions were reached ===
9:14:51.292357 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
9:14:51.294632 INFO: Updating optimization_manager: rt_error            : 289.12889183015307 -> 246.51951075910048
9:14:51.294770 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 246.5195.
9:14:51.294848 INFO: ==============================================
9:14:51.294944 INFO: Starting optimization step 3.
9:14:51.295013 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:14:51.295082 INFO: Using python extraction backend
9:14:51.295199 PROGRESS: Extracting batch of 407917 precursors
9:14:51.295276 INFO: === Search parameters used ===
9:14:51.295333 INFO: rt_error       : 246.51951075910048
9:14:51.295383 INFO: mobility_error : 0.1
9:14:51.295432 INFO: num_candidates : 3
9:14:51.295480 INFO: ms1_error      : 15.0
9:14:51.295528 INFO: ms2_error      : 15.0
9:14:51.295575 INFO: fwhm_rt        : 2.7237534523010254
9:14:51.295630 INFO: quant_window   : 3
9:14:51.295676 INFO: ==============================================
9:14:51.406499 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:14:51.406639 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:14:51.406691 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
9:14:51.406719 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.43
9:14:51.407465 INFO: Starting candidate selection
9:18:19.752175 INFO: Starting candidate scoring
9:18:31.085626 INFO: Finished candidate processing
9:18:31.085849 INFO: Collecting candidate features
9:18:32.787593 WARNING: intensity_correlation has 2671 NaNs ( 0.28 % out of 943398)
9:18:32.788784 WARNING: height_correlation has 266 NaNs ( 0.03 % out of 943398)
9:18:32.824680 INFO: Collecting fragment features
9:18:33.275084 INFO: Finished candidate scoring
9:18:33.883721 INFO: performing precursor FDR with 47 features
9:18:33.883858 INFO: Decoy channel: -1
9:18:33.883889 INFO: competitive: True
9:18:34.118055 INFO: Setting torch num_threads to 2 for FDR classification task
9:18:34.266544 WARNING: dropped 1400 target PSMs due to missing features
9:18:34.266705 WARNING: dropped 1400 decoy PSMs due to missing features
9:18:34.765610 INFO: Estimating optimal hyperparameters - samples: 752,478, batch_size: 3,082, learning_rate: 8.67e-04
9:18:34.767203 INFO: Using random state 594839 for train-test-split
9:18:57.465691 INFO: Test AUC: 0.549
9:18:57.465878 INFO: Train AUC: 0.567
9:18:57.465919 INFO: AUC difference: 3.23%
9:18:58.022302 INFO: Resetting torch num_threads to 80
9:18:58.041252 PROGRESS: === Extracted 943398 precursors and 5665954 fragments ===
9:18:58.042165 INFO: === FDR correction performed with classifier version 13 ===
9:18:58.074243 PROGRESS: ============================= Precursor FDR =============================
9:18:58.074544 PROGRESS: Total precursors accumulated: 182,258
9:18:58.074617 PROGRESS: Target precursors: 104,698 (57.44%)
9:18:58.074677 PROGRESS: Decoy precursors: 77,560 (42.56%)
9:18:58.074729 PROGRESS: 
9:18:58.074779 PROGRESS: Precursor Summary:
9:18:58.077063 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   273; 0.001 FDR:   186
9:18:58.077166 PROGRESS: 
9:18:58.077230 PROGRESS: Protein Summary:
9:18:58.079354 PROGRESS: Channel   0:	 0.050 FDR:   279; 0.010 FDR:   216; 0.001 FDR:   141
9:18:58.079455 PROGRESS: =========================================================================
9:18:58.084874 INFO: Target number of precursors reached.
9:18:58.699219 INFO: fragments_df: keeping 4354 of 5665954 [sum(precursor_idx_mask)=7080 sum(mass_error_mask)=5665855 stop_rank=4354
9:18:59.562896 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:18:59.680345 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:18:59.792321 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:18:59.904244 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:19:00.448225 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:19:00.448678 INFO: Using score_cutoff 24.45284349975586 (fac=0.99, q=1)
9:19:00.449030 INFO: Updating optimization_manager: fwhm_rt             : 2.7237534523010254 -> 2.659209728240967
9:19:00.449119 INFO: Updating optimization_manager: fwhm_mobility       : 0.006320829503238201 -> 0.005721577908843756
9:19:00.449189 INFO: Updating optimization_manager: score_cutoff        : 28.310007997512816 -> 24.45284349975586
9:19:00.449252 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:19:00.498896 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:19:00.749616 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:19:00.800792 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:19:01.305212 INFO: === checking if optimization conditions were reached ===
9:19:01.305484 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
9:19:01.307925 INFO: Updating optimization_manager: rt_error            : 246.51951075910048 -> 234.0893862779673
9:19:01.308083 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 234.0894.
9:19:01.308161 INFO: ==============================================
9:19:01.308237 INFO: Starting optimization step 4.
9:19:01.308300 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:19:01.308371 INFO: Using python extraction backend
9:19:01.308481 PROGRESS: Extracting batch of 407917 precursors
9:19:01.308560 INFO: === Search parameters used ===
9:19:01.308617 INFO: rt_error       : 234.0893862779673
9:19:01.308667 INFO: mobility_error : 0.1
9:19:01.308715 INFO: num_candidates : 3
9:19:01.308761 INFO: ms1_error      : 15.0
9:19:01.308814 INFO: ms2_error      : 15.0
9:19:01.308861 INFO: fwhm_rt        : 2.659209728240967
9:19:01.308906 INFO: quant_window   : 3
9:19:01.308951 INFO: ==============================================
9:19:01.418746 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:19:01.418891 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:19:01.418941 INFO: FWHM in RT is 2.66 seconds, sigma is 0.44
9:19:01.418967 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.10
9:19:01.419718 INFO: Starting candidate selection
9:22:22.864540 INFO: Starting candidate scoring
9:22:34.210920 INFO: Finished candidate processing
9:22:34.211082 INFO: Collecting candidate features
9:22:36.189555 WARNING: intensity_correlation has 2875 NaNs ( 0.31 % out of 937811)
9:22:36.190675 WARNING: height_correlation has 279 NaNs ( 0.03 % out of 937811)
9:22:36.224869 INFO: Collecting fragment features
9:22:36.688891 INFO: Finished candidate scoring
9:22:37.404452 INFO: performing precursor FDR with 47 features
9:22:37.404601 INFO: Decoy channel: -1
9:22:37.404639 INFO: competitive: True
9:22:37.630473 INFO: Setting torch num_threads to 2 for FDR classification task
9:22:37.775969 WARNING: dropped 1505 target PSMs due to missing features
9:22:37.776131 WARNING: dropped 1495 decoy PSMs due to missing features
9:22:38.095017 INFO: Estimating optimal hyperparameters - samples: 747,848, batch_size: 3,063, learning_rate: 8.65e-04
9:22:38.096770 INFO: Using random state 594839 for train-test-split
9:22:58.780903 INFO: Test AUC: 0.551
9:22:58.781123 INFO: Train AUC: 0.567
9:22:58.781159 INFO: AUC difference: 2.72%
9:22:59.332673 INFO: Resetting torch num_threads to 80
9:22:59.351212 PROGRESS: === Extracted 937811 precursors and 5578523 fragments ===
9:22:59.352030 INFO: === FDR correction performed with classifier version 13 ===
9:22:59.384814 PROGRESS: ============================= Precursor FDR =============================
9:22:59.385113 PROGRESS: Total precursors accumulated: 182,009
9:22:59.385185 PROGRESS: Target precursors: 104,275 (57.29%)
9:22:59.385247 PROGRESS: Decoy precursors: 77,734 (42.71%)
9:22:59.385301 PROGRESS: 
9:22:59.385353 PROGRESS: Precursor Summary:
9:22:59.387601 PROGRESS: Channel   0:	 0.050 FDR:   275; 0.010 FDR:    54; 0.001 FDR:    54
9:22:59.387711 PROGRESS: 
9:22:59.387776 PROGRESS: Protein Summary:
9:22:59.389831 PROGRESS: Channel   0:	 0.050 FDR:   221; 0.010 FDR:    47; 0.001 FDR:    47
9:22:59.389952 PROGRESS: =========================================================================
9:22:59.395420 INFO: Target number of precursors not reached yet.
9:23:00.309936 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:23:00.360187 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:23:00.613923 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:23:00.665709 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:23:01.198560 INFO: === skipping optimization until target number of precursors are found ===
9:23:01.198877 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
9:23:01.199018 INFO: Starting optimization step 5.
9:23:01.199106 PROGRESS: === Extracting elution groups 204600 to 409400 ===
9:23:01.199180 INFO: Using python extraction backend
9:23:01.199300 PROGRESS: Extracting batch of 408390 precursors
9:23:01.199405 INFO: === Search parameters used ===
9:23:01.199466 INFO: rt_error       : 234.0893862779673
9:23:01.199516 INFO: mobility_error : 0.1
9:23:01.199564 INFO: num_candidates : 3
9:23:01.199610 INFO: ms1_error      : 15.0
9:23:01.199655 INFO: ms2_error      : 15.0
9:23:01.199700 INFO: fwhm_rt        : 2.659209728240967
9:23:01.199743 INFO: quant_window   : 3
9:23:01.199787 INFO: ==============================================
9:23:01.306474 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:23:01.306610 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:23:01.306659 INFO: FWHM in RT is 2.66 seconds, sigma is 0.44
9:23:01.306683 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.10
9:23:01.307491 INFO: Starting candidate selection
9:26:21.246271 INFO: Starting candidate scoring
9:26:32.579466 INFO: Finished candidate processing
9:26:32.579849 INFO: Collecting candidate features
9:26:34.352359 WARNING: intensity_correlation has 2861 NaNs ( 0.31 % out of 936122)
9:26:34.353409 WARNING: height_correlation has 313 NaNs ( 0.03 % out of 936122)
9:26:34.386372 INFO: Collecting fragment features
9:26:34.834084 INFO: Finished candidate scoring
9:26:35.784851 INFO: performing precursor FDR with 47 features
9:26:35.785039 INFO: Decoy channel: -1
9:26:35.785080 INFO: competitive: True
9:26:36.477139 INFO: Setting torch num_threads to 2 for FDR classification task
9:26:36.778426 WARNING: dropped 3026 target PSMs due to missing features
9:26:36.778586 WARNING: dropped 2988 decoy PSMs due to missing features
9:26:37.411957 INFO: Estimating optimal hyperparameters - samples: 1,494,335, batch_size: 4,096, learning_rate: 1.00e-03
9:26:37.415074 INFO: Using random state 594839 for train-test-split
9:27:15.948645 INFO: Test AUC: 0.551
9:27:15.948821 INFO: Train AUC: 0.561
9:27:15.948861 INFO: AUC difference: 1.81%
9:27:16.798616 INFO: Resetting torch num_threads to 80
9:27:17.334830 PROGRESS: === Extracted 1873933 precursors and 11144060 fragments ===
9:27:17.336004 INFO: === FDR correction performed with classifier version 13 ===
9:27:17.402478 PROGRESS: ============================= Precursor FDR =============================
9:27:17.402794 PROGRESS: Total precursors accumulated: 363,804
9:27:17.402875 PROGRESS: Target precursors: 205,941 (56.61%)
9:27:17.402950 PROGRESS: Decoy precursors: 157,863 (43.39%)
9:27:17.403016 PROGRESS: 
9:27:17.403090 PROGRESS: Precursor Summary:
9:27:17.406576 PROGRESS: Channel   0:	 0.050 FDR:   625; 0.010 FDR:   438; 0.001 FDR:   381
9:27:17.406711 PROGRESS: 
9:27:17.406777 PROGRESS: Protein Summary:
9:27:17.409926 PROGRESS: Channel   0:	 0.050 FDR:   464; 0.010 FDR:   316; 0.001 FDR:   274
9:27:17.410037 PROGRESS: =========================================================================
9:27:17.415393 INFO: Target number of precursors reached.
9:27:18.699601 INFO: fragments_df: keeping 5000 of 11144060 [sum(precursor_idx_mask)=11472 sum(mass_error_mask)=11143875 stop_rank=5000
9:27:19.570165 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:27:19.693817 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:27:19.824444 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:27:19.955093 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:27:20.605196 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:27:20.605650 INFO: Using score_cutoff 25.18183447723389 (fac=0.99, q=1)
9:27:20.606003 INFO: Updating optimization_manager: fwhm_rt             : 2.659209728240967 -> 2.6628012657165527
9:27:20.606095 INFO: Updating optimization_manager: fwhm_mobility       : 0.005721577908843756 -> 0.00620730547234416
9:27:20.606157 INFO: Updating optimization_manager: score_cutoff        : 24.45284349975586 -> 25.18183447723389
9:27:20.606224 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:27:20.659611 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:27:20.923515 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:27:20.982180 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:27:21.519106 INFO: === checking if optimization conditions were reached ===
9:27:21.519387 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
9:27:21.521807 INFO: Updating optimization_manager: rt_error            : 234.0893862779673 -> 184.763934189306
9:27:21.521955 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 184.7639.
9:27:21.522036 INFO: ==============================================
9:27:21.522113 INFO: Starting optimization step 6.
9:27:21.522183 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:27:21.522252 INFO: Using python extraction backend
9:27:21.522362 PROGRESS: Extracting batch of 407917 precursors
9:27:21.522437 INFO: === Search parameters used ===
9:27:21.522492 INFO: rt_error       : 184.763934189306
9:27:21.522542 INFO: mobility_error : 0.1
9:27:21.522589 INFO: num_candidates : 3
9:27:21.522637 INFO: ms1_error      : 15.0
9:27:21.522684 INFO: ms2_error      : 15.0
9:27:21.522731 INFO: fwhm_rt        : 2.6628012657165527
9:27:21.522786 INFO: quant_window   : 3
9:27:21.522835 INFO: ==============================================
9:27:21.633013 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:27:21.633155 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:27:21.633205 INFO: FWHM in RT is 2.66 seconds, sigma is 0.44
9:27:21.633229 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.36
9:27:21.634009 INFO: Starting candidate selection
9:30:04.966213 INFO: Starting candidate scoring
9:30:16.175635 INFO: Finished candidate processing
9:30:16.175914 INFO: Collecting candidate features
9:30:18.033092 WARNING: intensity_correlation has 3119 NaNs ( 0.34 % out of 930571)
9:30:18.034943 WARNING: height_correlation has 287 NaNs ( 0.03 % out of 930571)
9:30:18.090240 INFO: Collecting fragment features
9:30:18.627735 INFO: Finished candidate scoring
9:30:19.466660 INFO: performing precursor FDR with 47 features
9:30:19.466874 INFO: Decoy channel: -1
9:30:19.466907 INFO: competitive: True
9:30:19.700855 INFO: Setting torch num_threads to 2 for FDR classification task
9:30:19.845650 WARNING: dropped 1615 target PSMs due to missing features
9:30:19.845829 WARNING: dropped 1644 decoy PSMs due to missing features
9:30:20.165083 INFO: Estimating optimal hyperparameters - samples: 741,849, batch_size: 3,038, learning_rate: 8.61e-04
9:30:20.168059 INFO: Using random state 594839 for train-test-split
9:30:42.102753 INFO: Test AUC: 0.550
9:30:42.102983 INFO: Train AUC: 0.567
9:30:42.103021 INFO: AUC difference: 3.04%
9:30:42.651131 INFO: Resetting torch num_threads to 80
9:30:42.669648 PROGRESS: === Extracted 930571 precursors and 5457422 fragments ===
9:30:42.670497 INFO: === FDR correction performed with classifier version 13 ===
9:30:42.702938 PROGRESS: ============================= Precursor FDR =============================
9:30:42.703254 PROGRESS: Total precursors accumulated: 181,611
9:30:42.703326 PROGRESS: Target precursors: 103,856 (57.19%)
9:30:42.703387 PROGRESS: Decoy precursors: 77,755 (42.81%)
9:30:42.703443 PROGRESS: 
9:30:42.703497 PROGRESS: Precursor Summary:
9:30:42.705784 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:   134; 0.001 FDR:   133
9:30:42.705909 PROGRESS: 
9:30:42.705976 PROGRESS: Protein Summary:
9:30:42.708061 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:   106; 0.001 FDR:   106
9:30:42.708171 PROGRESS: =========================================================================
9:30:42.720051 INFO: Target number of precursors not reached yet.
9:30:43.563406 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:30:43.617579 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:30:43.878857 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:30:43.937886 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:30:44.458016 INFO: === skipping optimization until target number of precursors are found ===
9:30:44.458319 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
9:30:44.458472 INFO: Starting optimization step 7.
9:30:44.458550 PROGRESS: === Extracting elution groups 204600 to 409400 ===
9:30:44.458622 INFO: Using python extraction backend
9:30:44.458743 PROGRESS: Extracting batch of 408390 precursors
9:30:44.458828 INFO: === Search parameters used ===
9:30:44.458883 INFO: rt_error       : 184.763934189306
9:30:44.458932 INFO: mobility_error : 0.1
9:30:44.458980 INFO: num_candidates : 3
9:30:44.459026 INFO: ms1_error      : 15.0
9:30:44.459072 INFO: ms2_error      : 15.0
9:30:44.459118 INFO: fwhm_rt        : 2.6628012657165527
9:30:44.459165 INFO: quant_window   : 3
9:30:44.459209 INFO: ==============================================
9:30:44.573562 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:30:44.573703 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:30:44.573749 INFO: FWHM in RT is 2.66 seconds, sigma is 0.44
9:30:44.573772 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.36
9:30:44.574538 INFO: Starting candidate selection
9:33:30.191770 INFO: Starting candidate scoring
9:33:41.746646 INFO: Finished candidate processing
9:33:41.747161 INFO: Collecting candidate features
9:33:43.661692 WARNING: intensity_correlation has 3063 NaNs ( 0.33 % out of 928727)
9:33:43.662917 WARNING: height_correlation has 345 NaNs ( 0.04 % out of 928727)
9:33:43.696409 INFO: Collecting fragment features
9:33:44.176224 INFO: Finished candidate scoring
9:33:45.614978 INFO: performing precursor FDR with 47 features
9:33:45.615138 INFO: Decoy channel: -1
9:33:45.615170 INFO: competitive: True
9:33:46.376683 INFO: Setting torch num_threads to 2 for FDR classification task
9:33:46.705670 WARNING: dropped 3277 target PSMs due to missing features
9:33:46.705842 WARNING: dropped 3215 decoy PSMs due to missing features
9:33:47.338346 INFO: Estimating optimal hyperparameters - samples: 1,482,244, batch_size: 4,096, learning_rate: 1.00e-03
9:33:47.341562 INFO: Using random state 594839 for train-test-split
9:34:24.695977 INFO: Test AUC: 0.551
9:34:24.696219 INFO: Train AUC: 0.561
9:34:24.696262 INFO: AUC difference: 1.82%
9:34:25.553296 INFO: Resetting torch num_threads to 80
9:34:26.118668 PROGRESS: === Extracted 1859298 precursors and 10903526 fragments ===
9:34:26.119856 INFO: === FDR correction performed with classifier version 13 ===
9:34:26.192381 PROGRESS: ============================= Precursor FDR =============================
9:34:26.192709 PROGRESS: Total precursors accumulated: 362,963
9:34:26.192784 PROGRESS: Target precursors: 205,892 (56.73%)
9:34:26.192843 PROGRESS: Decoy precursors: 157,071 (43.27%)
9:34:26.192910 PROGRESS: 
9:34:26.192968 PROGRESS: Precursor Summary:
9:34:26.196444 PROGRESS: Channel   0:	 0.050 FDR:   649; 0.010 FDR:   423; 0.001 FDR:   367
9:34:26.196554 PROGRESS: 
9:34:26.196621 PROGRESS: Protein Summary:
9:34:26.199775 PROGRESS: Channel   0:	 0.050 FDR:   479; 0.010 FDR:   307; 0.001 FDR:   269
9:34:26.199883 PROGRESS: =========================================================================
9:34:26.207504 INFO: Target number of precursors reached.
9:34:27.437452 INFO: fragments_df: keeping 5000 of 10903526 [sum(precursor_idx_mask)=11287 sum(mass_error_mask)=10903369 stop_rank=5000
9:34:28.378923 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:34:28.509051 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:34:28.639245 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:34:28.769443 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:34:30.736653 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:34:30.737092 INFO: Using score_cutoff 27.579919932174683 (fac=0.99, q=1)
9:34:30.737414 INFO: Updating optimization_manager: fwhm_rt             : 2.6628012657165527 -> 2.652177333831787
9:34:30.737501 INFO: Updating optimization_manager: fwhm_mobility       : 0.00620730547234416 -> 0.006093875039368868
9:34:30.737563 INFO: Updating optimization_manager: score_cutoff        : 25.18183447723389 -> 27.579919932174683
9:34:30.737635 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:34:30.787215 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:34:31.053016 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:34:31.104995 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:34:31.603391 INFO: === checking if optimization conditions were reached ===
9:34:31.603690 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
9:34:31.606115 INFO: Updating optimization_manager: rt_error            : 184.763934189306 -> 148.9745138373568
9:34:31.606266 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 148.9745.
9:34:31.606357 INFO: ==============================================
9:34:31.606458 INFO: Starting optimization step 8.
9:34:31.606544 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:34:31.606629 INFO: Using python extraction backend
9:34:31.606754 PROGRESS: Extracting batch of 407917 precursors
9:34:31.606844 INFO: === Search parameters used ===
9:34:31.606916 INFO: rt_error       : 148.9745138373568
9:34:31.606984 INFO: mobility_error : 0.1
9:34:31.607053 INFO: num_candidates : 3
9:34:31.607119 INFO: ms1_error      : 15.0
9:34:31.607185 INFO: ms2_error      : 15.0
9:34:31.607250 INFO: fwhm_rt        : 2.652177333831787
9:34:31.607313 INFO: quant_window   : 3
9:34:31.607377 INFO: ==============================================
9:34:31.736870 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:34:31.737020 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:34:31.737078 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
9:34:31.737108 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.30
9:34:31.737913 INFO: Starting candidate selection
9:36:34.766933 INFO: Starting candidate scoring
9:36:45.743223 INFO: Finished candidate processing
9:36:45.743466 INFO: Collecting candidate features
9:36:47.623057 WARNING: intensity_correlation has 3610 NaNs ( 0.40 % out of 900358)
9:36:47.624069 WARNING: height_correlation has 382 NaNs ( 0.04 % out of 900358)
9:36:47.655855 INFO: Collecting fragment features
9:36:48.078204 INFO: Finished candidate scoring
9:36:48.660627 INFO: performing precursor FDR with 47 features
9:36:48.660764 INFO: Decoy channel: -1
9:36:48.660792 INFO: competitive: True
9:36:48.893741 INFO: Setting torch num_threads to 2 for FDR classification task
9:36:49.044960 WARNING: dropped 1850 target PSMs due to missing features
9:36:49.045120 WARNING: dropped 1922 decoy PSMs due to missing features
9:36:49.341344 INFO: Estimating optimal hyperparameters - samples: 717,268, batch_size: 2,937, learning_rate: 8.47e-04
9:36:49.342864 INFO: Using random state 594839 for train-test-split
9:37:10.123115 INFO: Test AUC: 0.548
9:37:10.123312 INFO: Train AUC: 0.565
9:37:10.123355 INFO: AUC difference: 3.01%
9:37:10.677336 INFO: Resetting torch num_threads to 80
9:37:10.699197 PROGRESS: === Extracted 900358 precursors and 5074477 fragments ===
9:37:10.700115 INFO: === FDR correction performed with classifier version 13 ===
9:37:10.753258 PROGRESS: ============================= Precursor FDR =============================
9:37:10.753542 PROGRESS: Total precursors accumulated: 179,685
9:37:10.753614 PROGRESS: Target precursors: 102,356 (56.96%)
9:37:10.753675 PROGRESS: Decoy precursors: 77,329 (43.04%)
9:37:10.753730 PROGRESS: 
9:37:10.753782 PROGRESS: Precursor Summary:
9:37:10.756076 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:    13; 0.001 FDR:    13
9:37:10.756181 PROGRESS: 
9:37:10.756244 PROGRESS: Protein Summary:
9:37:10.758380 PROGRESS: Channel   0:	 0.050 FDR:   241; 0.010 FDR:    11; 0.001 FDR:    11
9:37:10.758481 PROGRESS: =========================================================================
9:37:10.771480 INFO: Target number of precursors not reached yet.
9:37:11.692316 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:37:11.744100 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:37:12.004232 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:37:12.057280 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:37:12.577147 INFO: === skipping optimization until target number of precursors are found ===
9:37:12.577470 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
9:37:12.577607 INFO: Starting optimization step 9.
9:37:12.577691 PROGRESS: === Extracting elution groups 204600 to 409400 ===
9:37:12.577767 INFO: Using python extraction backend
9:37:12.577899 PROGRESS: Extracting batch of 408390 precursors
9:37:12.577993 INFO: === Search parameters used ===
9:37:12.578054 INFO: rt_error       : 148.9745138373568
9:37:12.578114 INFO: mobility_error : 0.1
9:37:12.578168 INFO: num_candidates : 3
9:37:12.578223 INFO: ms1_error      : 15.0
9:37:12.578275 INFO: ms2_error      : 15.0
9:37:12.578328 INFO: fwhm_rt        : 2.652177333831787
9:37:12.578379 INFO: quant_window   : 3
9:37:12.578431 INFO: ==============================================
9:37:12.700219 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:37:12.700366 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:37:12.700422 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
9:37:12.700451 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.30
9:37:12.701212 INFO: Starting candidate selection
9:39:16.283906 INFO: Starting candidate scoring
9:39:26.994841 INFO: Finished candidate processing
9:39:26.995088 INFO: Collecting candidate features
9:39:28.871934 WARNING: intensity_correlation has 3569 NaNs ( 0.40 % out of 898959)
9:39:28.872935 WARNING: height_correlation has 406 NaNs ( 0.05 % out of 898959)
9:39:28.905444 INFO: Collecting fragment features
9:39:29.441842 INFO: Finished candidate scoring
9:39:30.645052 INFO: performing precursor FDR with 47 features
9:39:30.645302 INFO: Decoy channel: -1
9:39:30.645334 INFO: competitive: True
9:39:31.408045 INFO: Setting torch num_threads to 2 for FDR classification task
9:39:31.700724 WARNING: dropped 3762 target PSMs due to missing features
9:39:31.700908 WARNING: dropped 3740 decoy PSMs due to missing features
9:39:32.301282 INFO: Estimating optimal hyperparameters - samples: 1,433,452, batch_size: 4,096, learning_rate: 1.00e-03
9:39:32.304247 INFO: Using random state 594839 for train-test-split
9:40:07.402714 INFO: Test AUC: 0.548
9:40:07.402964 INFO: Train AUC: 0.560
9:40:07.403002 INFO: AUC difference: 2.13%
9:40:08.258592 INFO: Resetting torch num_threads to 80
9:40:08.679891 PROGRESS: === Extracted 1799317 precursors and 10138428 fragments ===
9:40:08.680960 INFO: === FDR correction performed with classifier version 13 ===
9:40:08.752358 PROGRESS: ============================= Precursor FDR =============================
9:40:08.752670 PROGRESS: Total precursors accumulated: 359,172
9:40:08.752743 PROGRESS: Target precursors: 203,232 (56.58%)
9:40:08.752802 PROGRESS: Decoy precursors: 155,940 (43.42%)
9:40:08.752855 PROGRESS: 
9:40:08.752907 PROGRESS: Precursor Summary:
9:40:08.756324 PROGRESS: Channel   0:	 0.050 FDR:   658; 0.010 FDR:   434; 0.001 FDR:   329
9:40:08.756450 PROGRESS: 
9:40:08.756514 PROGRESS: Protein Summary:
9:40:08.759639 PROGRESS: Channel   0:	 0.050 FDR:   489; 0.010 FDR:   308; 0.001 FDR:   232
9:40:08.759826 PROGRESS: =========================================================================
9:40:08.766565 INFO: Target number of precursors reached.
9:40:09.884414 INFO: fragments_df: keeping 5000 of 10138428 [sum(precursor_idx_mask)=11412 sum(mass_error_mask)=10138222 stop_rank=5000
9:40:10.802330 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:40:10.935446 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:40:11.068264 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:40:11.198086 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:40:11.853944 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:40:11.854409 INFO: Using score_cutoff 27.869410167503357 (fac=0.99, q=1)
9:40:11.854759 INFO: Updating optimization_manager: fwhm_rt             : 2.652177333831787 -> 2.650113821029663
9:40:11.854843 INFO: Updating optimization_manager: fwhm_mobility       : 0.006093875039368868 -> 0.006109865382313728
9:40:11.854902 INFO: Updating optimization_manager: score_cutoff        : 27.579919932174683 -> 27.869410167503357
9:40:11.854968 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:40:11.905387 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:40:12.161615 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:40:12.216183 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:40:12.736431 INFO: === checking if optimization conditions were reached ===
9:40:12.736705 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
9:40:12.739069 INFO: Updating optimization_manager: rt_error            : 148.9745138373568 -> 135.10706715795777
9:40:12.739202 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 135.1071.
9:40:12.739274 INFO: ==============================================
9:40:12.739351 INFO: Starting optimization step 10.
9:40:12.739413 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:40:12.739476 INFO: Using python extraction backend
9:40:12.739591 PROGRESS: Extracting batch of 407917 precursors
9:40:12.739664 INFO: === Search parameters used ===
9:40:12.739717 INFO: rt_error       : 135.10706715795777
9:40:12.739763 INFO: mobility_error : 0.1
9:40:12.739807 INFO: num_candidates : 3
9:40:12.739853 INFO: ms1_error      : 15.0
9:40:12.739896 INFO: ms2_error      : 15.0
9:40:12.739939 INFO: fwhm_rt        : 2.650113821029663
9:40:12.739981 INFO: quant_window   : 3
9:40:12.740023 INFO: ==============================================
9:40:12.858061 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:40:12.858198 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:40:12.858246 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
9:40:12.858271 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.31
9:40:12.858992 INFO: Starting candidate selection
9:42:09.489806 INFO: Starting candidate scoring
9:42:20.194269 INFO: Finished candidate processing
9:42:20.194492 INFO: Collecting candidate features
9:42:21.943288 WARNING: intensity_correlation has 3673 NaNs ( 0.41 % out of 895026)
9:42:21.944281 WARNING: height_correlation has 378 NaNs ( 0.04 % out of 895026)
9:42:21.975983 INFO: Collecting fragment features
9:42:22.432768 INFO: Finished candidate scoring
9:42:23.245486 INFO: performing precursor FDR with 47 features
9:42:23.245625 INFO: Decoy channel: -1
9:42:23.245652 INFO: competitive: True
9:42:23.503541 INFO: Setting torch num_threads to 2 for FDR classification task
9:42:23.654667 WARNING: dropped 1910 target PSMs due to missing features
9:42:23.654829 WARNING: dropped 1918 decoy PSMs due to missing features
9:42:23.940828 INFO: Estimating optimal hyperparameters - samples: 712,958, batch_size: 2,920, learning_rate: 8.44e-04
9:42:23.942264 INFO: Using random state 594839 for train-test-split
9:42:42.599506 INFO: Test AUC: 0.549
9:42:42.599678 INFO: Train AUC: 0.566
9:42:42.599718 INFO: AUC difference: 2.99%
9:42:43.134503 INFO: Resetting torch num_threads to 80
9:42:43.156175 PROGRESS: === Extracted 895026 precursors and 5018741 fragments ===
9:42:43.157059 INFO: === FDR correction performed with classifier version 13 ===
9:42:43.193187 PROGRESS: ============================= Precursor FDR =============================
9:42:43.193454 PROGRESS: Total precursors accumulated: 179,101
9:42:43.193527 PROGRESS: Target precursors: 102,152 (57.04%)
9:42:43.193589 PROGRESS: Decoy precursors: 76,949 (42.96%)
9:42:43.193642 PROGRESS: 
9:42:43.193694 PROGRESS: Precursor Summary:
9:42:43.196034 PROGRESS: Channel   0:	 0.050 FDR:   363; 0.010 FDR:   204; 0.001 FDR:   201
9:42:43.196146 PROGRESS: 
9:42:43.196211 PROGRESS: Protein Summary:
9:42:43.198364 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   163; 0.001 FDR:   160
9:42:43.198478 PROGRESS: =========================================================================
9:42:43.210745 INFO: Target number of precursors reached.
9:42:43.765523 INFO: fragments_df: keeping 3458 of 5018741 [sum(precursor_idx_mask)=5243 sum(mass_error_mask)=5018627 stop_rank=3458
9:42:44.682712 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:42:44.795049 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:42:44.903336 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:42:45.018831 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:42:45.447805 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:42:45.448252 INFO: Using score_cutoff 27.717233299255373 (fac=0.99, q=1)
9:42:45.448599 INFO: Updating optimization_manager: fwhm_rt             : 2.650113821029663 -> 2.6544008255004883
9:42:45.448687 INFO: Updating optimization_manager: fwhm_mobility       : 0.006109865382313728 -> 0.006191889755427837
9:42:45.448750 INFO: Updating optimization_manager: score_cutoff        : 27.869410167503357 -> 27.717233299255373
9:42:45.448812 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:42:45.503417 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:42:45.767822 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:42:45.828572 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:42:46.348578 INFO: === checking if optimization conditions were reached ===
9:42:46.348886 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
9:42:46.351235 INFO: Updating optimization_manager: rt_error            : 135.10706715795777 -> 104.35897262139244
9:42:46.351381 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 104.3590.
9:42:46.351468 INFO: ==============================================
9:42:46.351555 INFO: Starting optimization step 11.
9:42:46.351630 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:42:46.351704 INFO: Using python extraction backend
9:42:46.351814 PROGRESS: Extracting batch of 407917 precursors
9:42:46.351893 INFO: === Search parameters used ===
9:42:46.351954 INFO: rt_error       : 104.35897262139244
9:42:46.352010 INFO: mobility_error : 0.1
9:42:46.352077 INFO: num_candidates : 3
9:42:46.352134 INFO: ms1_error      : 15.0
9:42:46.352187 INFO: ms2_error      : 15.0
9:42:46.352241 INFO: fwhm_rt        : 2.6544008255004883
9:42:46.352294 INFO: quant_window   : 3
9:42:46.352346 INFO: ==============================================
9:42:46.469416 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:42:46.469561 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:42:46.469614 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
9:42:46.469643 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.36
9:42:46.470328 INFO: Starting candidate selection
9:44:20.064027 INFO: Starting candidate scoring
9:44:30.623201 INFO: Finished candidate processing
9:44:30.623467 INFO: Collecting candidate features
9:44:32.404370 WARNING: intensity_correlation has 4062 NaNs ( 0.46 % out of 884096)
9:44:32.405416 WARNING: height_correlation has 387 NaNs ( 0.04 % out of 884096)
9:44:32.438096 INFO: Collecting fragment features
9:44:32.894066 INFO: Finished candidate scoring
9:44:33.688135 INFO: performing precursor FDR with 47 features
9:44:33.688267 INFO: Decoy channel: -1
9:44:33.688295 INFO: competitive: True
9:44:33.924170 INFO: Setting torch num_threads to 2 for FDR classification task
9:44:34.073591 WARNING: dropped 2124 target PSMs due to missing features
9:44:34.073748 WARNING: dropped 2089 decoy PSMs due to missing features
9:44:34.369152 INFO: Estimating optimal hyperparameters - samples: 703,906, batch_size: 2,883, learning_rate: 8.39e-04
9:44:34.370669 INFO: Using random state 594839 for train-test-split
9:44:53.712687 INFO: Test AUC: 0.545
9:44:53.712849 INFO: Train AUC: 0.562
9:44:53.712885 INFO: AUC difference: 3.18%
9:44:54.253178 INFO: Resetting torch num_threads to 80
9:44:54.274661 PROGRESS: === Extracted 884096 precursors and 4868865 fragments ===
9:44:54.275630 INFO: === FDR correction performed with classifier version 13 ===
9:44:54.313976 PROGRESS: ============================= Precursor FDR =============================
9:44:54.314256 PROGRESS: Total precursors accumulated: 178,357
9:44:54.314328 PROGRESS: Target precursors: 101,214 (56.75%)
9:44:54.314389 PROGRESS: Decoy precursors: 77,143 (43.25%)
9:44:54.314448 PROGRESS: 
9:44:54.314503 PROGRESS: Precursor Summary:
9:44:54.316813 PROGRESS: Channel   0:	 0.050 FDR:   382; 0.010 FDR:   287; 0.001 FDR:   235
9:44:54.316920 PROGRESS: 
9:44:54.316983 PROGRESS: Protein Summary:
9:44:54.319135 PROGRESS: Channel   0:	 0.050 FDR:   309; 0.010 FDR:   224; 0.001 FDR:   184
9:44:54.319242 PROGRESS: =========================================================================
9:44:54.327305 INFO: Target number of precursors reached.
9:44:54.867068 INFO: fragments_df: keeping 4325 of 4868865 [sum(precursor_idx_mask)=7202 sum(mass_error_mask)=4868777 stop_rank=4325
9:44:55.766279 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:44:55.883927 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:44:55.999989 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:44:56.118356 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:44:56.659283 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:44:56.659723 INFO: Using score_cutoff 21.651165819168092 (fac=0.99, q=1)
9:44:56.660057 INFO: Updating optimization_manager: fwhm_rt             : 2.6544008255004883 -> 2.6531221866607666
9:44:56.660148 INFO: Updating optimization_manager: fwhm_mobility       : 0.006191889755427837 -> 0.005278964526951313
9:44:56.660213 INFO: Updating optimization_manager: score_cutoff        : 27.717233299255373 -> 21.651165819168092
9:44:56.660276 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:44:56.710306 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:44:56.968311 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:44:57.022305 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:44:57.541086 INFO: === checking if optimization conditions were reached ===
9:44:57.541417 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
9:44:57.543757 INFO: Updating optimization_manager: rt_error            : 104.35897262139244 -> 101.29716523302102
9:44:57.543911 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 101.2972.
9:44:57.544015 INFO: ==============================================
9:44:57.544137 INFO: Starting optimization step 12.
9:44:57.544228 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:44:57.544335 INFO: Using python extraction backend
9:44:57.544476 PROGRESS: Extracting batch of 407917 precursors
9:44:57.544576 INFO: === Search parameters used ===
9:44:57.544654 INFO: rt_error       : 101.29716523302102
9:44:57.544729 INFO: mobility_error : 0.1
9:44:57.544804 INFO: num_candidates : 3
9:44:57.544879 INFO: ms1_error      : 15.0
9:44:57.544951 INFO: ms2_error      : 15.0
9:44:57.545024 INFO: fwhm_rt        : 2.6531221866607666
9:44:57.545095 INFO: quant_window   : 3
9:44:57.545167 INFO: ==============================================
9:44:57.658520 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:44:57.658664 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:44:57.658711 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
9:44:57.658738 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.86
9:44:57.659465 INFO: Starting candidate selection
9:46:20.971243 INFO: Starting candidate scoring
9:46:31.787646 INFO: Finished candidate processing
9:46:31.787835 INFO: Collecting candidate features
9:46:33.540337 WARNING: intensity_correlation has 4274 NaNs ( 0.49 % out of 876359)
9:46:33.541301 WARNING: height_correlation has 436 NaNs ( 0.05 % out of 876359)
9:46:33.573464 INFO: Collecting fragment features
9:46:33.999816 INFO: Finished candidate scoring
9:46:34.574015 INFO: performing precursor FDR with 47 features
9:46:34.574157 INFO: Decoy channel: -1
9:46:34.574184 INFO: competitive: True
9:46:34.799599 INFO: Setting torch num_threads to 2 for FDR classification task
9:46:34.944340 WARNING: dropped 2211 target PSMs due to missing features
9:46:34.944497 WARNING: dropped 2237 decoy PSMs due to missing features
9:46:35.230467 INFO: Estimating optimal hyperparameters - samples: 697,528, batch_size: 2,857, learning_rate: 8.35e-04
9:46:35.231879 INFO: Using random state 594839 for train-test-split
9:46:54.628958 INFO: Test AUC: 0.549
9:46:54.629106 INFO: Train AUC: 0.565
9:46:54.629142 INFO: AUC difference: 2.95%
9:46:55.166553 INFO: Resetting torch num_threads to 80
9:46:55.187884 PROGRESS: === Extracted 876359 precursors and 4778789 fragments ===
9:46:55.188687 INFO: === FDR correction performed with classifier version 13 ===
9:46:55.223472 PROGRESS: ============================= Precursor FDR =============================
9:46:55.223770 PROGRESS: Total precursors accumulated: 177,848
9:46:55.223844 PROGRESS: Target precursors: 100,914 (56.74%)
9:46:55.223912 PROGRESS: Decoy precursors: 76,934 (43.26%)
9:46:55.223969 PROGRESS: 
9:46:55.224020 PROGRESS: Precursor Summary:
9:46:55.226339 PROGRESS: Channel   0:	 0.050 FDR:   330; 0.010 FDR:   221; 0.001 FDR:   149
9:46:55.226458 PROGRESS: 
9:46:55.226525 PROGRESS: Protein Summary:
9:46:55.228656 PROGRESS: Channel   0:	 0.050 FDR:   262; 0.010 FDR:   176; 0.001 FDR:   117
9:46:55.228759 PROGRESS: =========================================================================
9:46:55.234903 INFO: Target number of precursors reached.
9:46:55.752252 INFO: fragments_df: keeping 3601 of 4778789 [sum(precursor_idx_mask)=5598 sum(mass_error_mask)=4778708 stop_rank=3601
9:46:56.647097 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:46:56.782674 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:46:56.920323 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:46:57.053952 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:46:57.489288 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:46:57.489742 INFO: Using score_cutoff 21.166880081176757 (fac=0.99, q=1)
9:46:57.490078 INFO: Updating optimization_manager: fwhm_rt             : 2.6531221866607666 -> 2.6557726860046387
9:46:57.490170 INFO: Updating optimization_manager: fwhm_mobility       : 0.005278964526951313 -> 0.005526528228074312
9:46:57.490237 INFO: Updating optimization_manager: score_cutoff        : 21.651165819168092 -> 21.166880081176757
9:46:57.490302 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:46:57.543240 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:46:57.791939 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:46:57.849502 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:46:58.349480 INFO: === checking if optimization conditions were reached ===
9:46:58.349767 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
9:46:58.351138 INFO: Updating optimization_manager: rt_error            : 101.29716523302102 -> 104.35897262139244
9:46:58.351306 INFO: Updating optimization_manager: classifier_version  : 13 -> 25
9:46:58.351419 INFO: Updating optimization_manager: score_cutoff        : 21.166880081176757 -> 21.651165819168092
9:46:58.351525 INFO: Updating optimization_manager: fwhm_rt             : 2.6557726860046387 -> 2.6531221866607666
9:46:58.351626 INFO: Updating optimization_manager: fwhm_mobility       : 0.005526528228074312 -> 0.005278964526951313
9:46:58.351727 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 104.3590 found after 10 searches.
9:46:58.351803 INFO: ==============================================
9:46:58.351885 PROGRESS: Optimization finished for rt_error.
9:46:58.970710 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:46:59.023788 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:46:59.273936 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:46:59.336329 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:46:59.859123 INFO: Starting optimization step 0.
9:46:59.859406 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:46:59.859502 INFO: Using python extraction backend
9:46:59.859633 PROGRESS: Extracting batch of 407917 precursors
9:46:59.859731 INFO: === Search parameters used ===
9:46:59.859793 INFO: rt_error       : 104.35897262139244
9:46:59.859844 INFO: mobility_error : 0.1
9:46:59.859893 INFO: num_candidates : 3
9:46:59.859940 INFO: ms1_error      : 15.0
9:46:59.859985 INFO: ms2_error      : 15.0
9:46:59.860030 INFO: fwhm_rt        : 2.6531221866607666
9:46:59.860075 INFO: quant_window   : 3
9:46:59.860119 INFO: ==============================================
9:46:59.989744 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:46:59.989901 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:46:59.989951 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
9:46:59.989974 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.86
9:46:59.990695 INFO: Starting candidate selection
9:48:33.150047 INFO: Starting candidate scoring
9:48:45.195491 INFO: Finished candidate processing
9:48:45.195692 INFO: Collecting candidate features
9:48:47.601763 WARNING: intensity_correlation has 4056 NaNs ( 0.46 % out of 880390)
9:48:47.602876 WARNING: height_correlation has 403 NaNs ( 0.05 % out of 880390)
9:48:47.634523 INFO: Collecting fragment features
9:48:48.090680 INFO: Finished candidate scoring
9:48:48.714726 INFO: performing precursor FDR with 47 features
9:48:48.714887 INFO: Decoy channel: -1
9:48:48.714916 INFO: competitive: True
9:48:48.959676 INFO: Setting torch num_threads to 2 for FDR classification task
9:48:49.114826 WARNING: dropped 2133 target PSMs due to missing features
9:48:49.115013 WARNING: dropped 2085 decoy PSMs due to missing features
9:48:49.405367 INFO: Estimating optimal hyperparameters - samples: 700,937, batch_size: 2,871, learning_rate: 8.37e-04
9:48:49.407468 INFO: Using random state 325412 for train-test-split
9:49:11.677421 INFO: Test AUC: 0.553
9:49:11.677611 INFO: Train AUC: 0.574
9:49:11.677649 INFO: AUC difference: 3.80%
9:49:12.217273 INFO: Resetting torch num_threads to 80
9:49:12.240664 PROGRESS: === Extracted 880390 precursors and 4834648 fragments ===
9:49:12.242095 INFO: === FDR correction performed with classifier version 25 ===
9:49:12.281600 PROGRESS: ============================= Precursor FDR =============================
9:49:12.281919 PROGRESS: Total precursors accumulated: 177,911
9:49:12.281995 PROGRESS: Target precursors: 102,309 (57.51%)
9:49:12.282054 PROGRESS: Decoy precursors: 75,602 (42.49%)
9:49:12.282107 PROGRESS: 
9:49:12.282161 PROGRESS: Precursor Summary:
9:49:12.284484 PROGRESS: Channel   0:	 0.050 FDR:   366; 0.010 FDR:   205; 0.001 FDR:   159
9:49:12.284593 PROGRESS: 
9:49:12.284659 PROGRESS: Protein Summary:
9:49:12.286805 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   165; 0.001 FDR:   127
9:49:12.286909 PROGRESS: =========================================================================
9:49:12.295194 INFO: Target number of precursors reached.
9:49:12.816273 INFO: fragments_df: keeping 3381 of 4834648 [sum(precursor_idx_mask)=5275 sum(mass_error_mask)=4834557 stop_rank=3381
9:49:13.720643 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:49:13.838777 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:49:13.948373 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:49:14.064319 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:49:14.469249 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:49:14.469696 INFO: Using score_cutoff 26.085123825073243 (fac=0.99, q=1)
9:49:14.470029 INFO: Updating optimization_manager: fwhm_rt             : 2.6531221866607666 -> 2.730525016784668
9:49:14.470129 INFO: Updating optimization_manager: fwhm_mobility       : 0.005278964526951313 -> 0.005897653754800558
9:49:14.470190 INFO: Updating optimization_manager: score_cutoff        : 21.651165819168092 -> 26.085123825073243
9:49:14.470249 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:49:14.520729 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:49:14.774405 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:49:14.831306 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:49:15.348961 INFO: === checking if optimization conditions were reached ===
9:49:15.349229 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
9:49:15.351092 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.05744408857504864
9:49:15.351240 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0574.
9:49:15.351320 INFO: ==============================================
9:49:15.351396 INFO: Starting optimization step 1.
9:49:15.351462 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:49:15.351538 INFO: Using python extraction backend
9:49:15.351649 PROGRESS: Extracting batch of 407917 precursors
9:49:15.351729 INFO: === Search parameters used ===
9:49:15.351785 INFO: rt_error       : 104.35897262139244
9:49:15.351835 INFO: mobility_error : 0.05744408857504864
9:49:15.351883 INFO: num_candidates : 3
9:49:15.351931 INFO: ms1_error      : 15.0
9:49:15.351976 INFO: ms2_error      : 15.0
9:49:15.352022 INFO: fwhm_rt        : 2.730525016784668
9:49:15.352067 INFO: quant_window   : 3
9:49:15.352110 INFO: ==============================================
9:49:15.468225 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:49:15.468359 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:49:15.468412 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
9:49:15.468437 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.20
9:49:15.469193 INFO: Starting candidate selection
9:50:12.530524 INFO: Starting candidate scoring
9:50:23.493508 INFO: Finished candidate processing
9:50:23.493799 INFO: Collecting candidate features
9:50:25.711732 WARNING: intensity_correlation has 4306 NaNs ( 0.52 % out of 823091)
9:50:25.712664 WARNING: height_correlation has 452 NaNs ( 0.05 % out of 823091)
9:50:25.742778 INFO: Collecting fragment features
9:50:26.179011 INFO: Finished candidate scoring
9:50:26.748075 INFO: performing precursor FDR with 47 features
9:50:26.748207 INFO: Decoy channel: -1
9:50:26.748236 INFO: competitive: True
9:50:26.982888 INFO: Setting torch num_threads to 2 for FDR classification task
9:50:27.126484 WARNING: dropped 2256 target PSMs due to missing features
9:50:27.126640 WARNING: dropped 2244 decoy PSMs due to missing features
9:50:27.397552 INFO: Estimating optimal hyperparameters - samples: 654,872, batch_size: 2,682, learning_rate: 8.09e-04
9:50:27.398819 INFO: Using random state 325412 for train-test-split
9:50:45.753078 INFO: Test AUC: 0.554
9:50:45.753239 INFO: Train AUC: 0.573
9:50:45.753275 INFO: AUC difference: 3.23%
9:50:46.269047 INFO: Resetting torch num_threads to 80
9:50:46.289025 PROGRESS: === Extracted 823091 precursors and 4416241 fragments ===
9:50:46.289818 INFO: === FDR correction performed with classifier version 25 ===
9:50:46.321960 PROGRESS: ============================= Precursor FDR =============================
9:50:46.322274 PROGRESS: Total precursors accumulated: 169,396
9:50:46.322347 PROGRESS: Target precursors: 97,719 (57.69%)
9:50:46.322406 PROGRESS: Decoy precursors: 71,677 (42.31%)
9:50:46.322474 PROGRESS: 
9:50:46.322527 PROGRESS: Precursor Summary:
9:50:46.324697 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:     1; 0.001 FDR:     1
9:50:46.324799 PROGRESS: 
9:50:46.324861 PROGRESS: Protein Summary:
9:50:46.326858 PROGRESS: Channel   0:	 0.050 FDR:   289; 0.010 FDR:     1; 0.001 FDR:     1
9:50:46.326962 PROGRESS: =========================================================================
9:50:46.335604 INFO: Target number of precursors not reached yet.
9:50:47.243107 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:50:47.295232 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:50:47.554923 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:50:47.613293 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:50:48.118501 INFO: === skipping optimization until target number of precursors are found ===
9:50:48.118830 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
9:50:48.118959 INFO: Starting optimization step 2.
9:50:48.119045 PROGRESS: === Extracting elution groups 204600 to 409400 ===
9:50:48.119126 INFO: Using python extraction backend
9:50:48.119267 PROGRESS: Extracting batch of 408390 precursors
9:50:48.119360 INFO: === Search parameters used ===
9:50:48.119421 INFO: rt_error       : 104.35897262139244
9:50:48.119493 INFO: mobility_error : 0.05744408857504864
9:50:48.119557 INFO: num_candidates : 3
9:50:48.119613 INFO: ms1_error      : 15.0
9:50:48.119668 INFO: ms2_error      : 15.0
9:50:48.119727 INFO: fwhm_rt        : 2.730525016784668
9:50:48.119781 INFO: quant_window   : 3
9:50:48.119834 INFO: ==============================================
9:50:48.245724 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:50:48.245881 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:50:48.245940 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
9:50:48.245970 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.20
9:50:48.246749 INFO: Starting candidate selection
9:51:45.242784 INFO: Starting candidate scoring
9:51:55.425555 INFO: Finished candidate processing
9:51:55.425724 INFO: Collecting candidate features
9:51:56.900063 WARNING: intensity_correlation has 4460 NaNs ( 0.54 % out of 822146)
9:51:56.901004 WARNING: height_correlation has 491 NaNs ( 0.06 % out of 822146)
9:51:56.930365 INFO: Collecting fragment features
9:51:57.324188 INFO: Finished candidate scoring
9:51:58.168618 INFO: performing precursor FDR with 47 features
9:51:58.168780 INFO: Decoy channel: -1
9:51:58.168809 INFO: competitive: True
9:51:58.824488 INFO: Setting torch num_threads to 2 for FDR classification task
9:51:59.106712 WARNING: dropped 4568 target PSMs due to missing features
9:51:59.106875 WARNING: dropped 4598 decoy PSMs due to missing features
9:51:59.656125 INFO: Estimating optimal hyperparameters - samples: 1,308,856, batch_size: 4,096, learning_rate: 1.00e-03
9:51:59.658846 INFO: Using random state 325412 for train-test-split
9:52:31.281791 INFO: Test AUC: 0.552
9:52:31.281990 INFO: Train AUC: 0.564
9:52:31.282027 INFO: AUC difference: 2.26%
9:52:32.076132 INFO: Resetting torch num_threads to 80
9:52:32.326589 PROGRESS: === Extracted 1645237 precursors and 8827825 fragments ===
9:52:32.327670 INFO: === FDR correction performed with classifier version 25 ===
9:52:32.392895 PROGRESS: ============================= Precursor FDR =============================
9:52:32.393215 PROGRESS: Total precursors accumulated: 338,654
9:52:32.393291 PROGRESS: Target precursors: 192,121 (56.73%)
9:52:32.393353 PROGRESS: Decoy precursors: 146,533 (43.27%)
9:52:32.393406 PROGRESS: 
9:52:32.393461 PROGRESS: Precursor Summary:
9:52:32.396734 PROGRESS: Channel   0:	 0.050 FDR:   665; 0.010 FDR:   511; 0.001 FDR:   351
9:52:32.396847 PROGRESS: 
9:52:32.396912 PROGRESS: Protein Summary:
9:52:32.399980 PROGRESS: Channel   0:	 0.050 FDR:   498; 0.010 FDR:   373; 0.001 FDR:   257
9:52:32.400089 PROGRESS: =========================================================================
9:52:32.406090 INFO: Target number of precursors reached.
9:52:33.397325 INFO: fragments_df: keeping 5000 of 8827825 [sum(precursor_idx_mask)=13344 sum(mass_error_mask)=8827557 stop_rank=5000
9:52:34.051502 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:52:34.180851 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:52:34.321005 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:52:34.447253 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:52:35.097980 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:52:35.098430 INFO: Using score_cutoff 22.85252744293213 (fac=0.99, q=1)
9:52:35.098782 INFO: Updating optimization_manager: fwhm_rt             : 2.730525016784668 -> 2.597942352294922
9:52:35.098870 INFO: Updating optimization_manager: fwhm_mobility       : 0.005897653754800558 -> 0.005333321169018745
9:52:35.098933 INFO: Updating optimization_manager: score_cutoff        : 26.085123825073243 -> 22.85252744293213
9:52:35.098993 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:52:35.149860 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:52:35.408581 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:52:35.462586 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:52:35.943760 INFO: === checking if optimization conditions were reached ===
9:52:35.944081 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
9:52:35.946225 INFO: Updating optimization_manager: mobility_error      : 0.05744408857504864 -> 0.053657629114340855
9:52:35.946376 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0537.
9:52:35.946480 INFO: ==============================================
9:52:35.946573 INFO: Starting optimization step 3.
9:52:35.946652 PROGRESS: === Extracting elution groups 0 to 204600 ===
9:52:35.946730 INFO: Using python extraction backend
9:52:35.946846 PROGRESS: Extracting batch of 407917 precursors
9:52:35.946929 INFO: === Search parameters used ===
9:52:35.946995 INFO: rt_error       : 104.35897262139244
9:52:35.947057 INFO: mobility_error : 0.053657629114340855
9:52:35.947120 INFO: num_candidates : 3
9:52:35.947179 INFO: ms1_error      : 15.0
9:52:35.947238 INFO: ms2_error      : 15.0
9:52:35.947294 INFO: fwhm_rt        : 2.597942352294922
9:52:35.947353 INFO: quant_window   : 3
9:52:35.947408 INFO: ==============================================
9:52:36.060634 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:52:36.060790 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:52:36.060846 INFO: FWHM in RT is 2.60 seconds, sigma is 0.43
9:52:36.060875 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.89
9:52:36.061659 INFO: Starting candidate selection
9:53:27.745454 INFO: Starting candidate scoring
9:53:37.597672 INFO: Finished candidate processing
9:53:37.597860 INFO: Collecting candidate features
9:53:39.129653 WARNING: intensity_correlation has 4307 NaNs ( 0.53 % out of 819133)
9:53:39.130833 WARNING: height_correlation has 437 NaNs ( 0.05 % out of 819133)
9:53:39.160884 INFO: Collecting fragment features
9:53:39.582012 INFO: Finished candidate scoring
9:53:40.201404 INFO: performing precursor FDR with 47 features
9:53:40.201562 INFO: Decoy channel: -1
9:53:40.201595 INFO: competitive: True
9:53:40.423868 INFO: Setting torch num_threads to 2 for FDR classification task
9:53:40.570500 WARNING: dropped 2238 target PSMs due to missing features
9:53:40.570667 WARNING: dropped 2255 decoy PSMs due to missing features
9:53:40.851250 INFO: Estimating optimal hyperparameters - samples: 651,712, batch_size: 2,669, learning_rate: 8.07e-04
9:53:40.852511 INFO: Using random state 325412 for train-test-split
9:53:58.662111 INFO: Test AUC: 0.552
9:53:58.662372 INFO: Train AUC: 0.573
9:53:58.662413 INFO: AUC difference: 3.74%
9:53:59.174637 INFO: Resetting torch num_threads to 80
9:53:59.194455 PROGRESS: === Extracted 819133 precursors and 4378781 fragments ===
9:53:59.195375 INFO: === FDR correction performed with classifier version 25 ===
9:53:59.234349 PROGRESS: ============================= Precursor FDR =============================
9:53:59.234680 PROGRESS: Total precursors accumulated: 168,155
9:53:59.234754 PROGRESS: Target precursors: 96,748 (57.54%)
9:53:59.234814 PROGRESS: Decoy precursors: 71,407 (42.46%)
9:53:59.234869 PROGRESS: 
9:53:59.234936 PROGRESS: Precursor Summary:
9:53:59.237181 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   201; 0.001 FDR:   131
9:53:59.237282 PROGRESS: 
9:53:59.237344 PROGRESS: Protein Summary:
9:53:59.239425 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   162; 0.001 FDR:   113
9:53:59.239531 PROGRESS: =========================================================================
9:53:59.251744 INFO: Target number of precursors reached.
9:53:59.724473 INFO: fragments_df: keeping 3314 of 4378781 [sum(precursor_idx_mask)=5219 sum(mass_error_mask)=4378680 stop_rank=3314
9:54:00.623210 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:54:00.739005 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:54:00.852461 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:54:00.957510 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:54:01.347061 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:54:01.347540 INFO: Using score_cutoff 24.4248069190979 (fac=0.99, q=1)
9:54:01.347896 INFO: Updating optimization_manager: fwhm_rt             : 2.597942352294922 -> 2.6681737899780273
9:54:01.347993 INFO: Updating optimization_manager: fwhm_mobility       : 0.005333321169018745 -> 0.0057528321631252766
9:54:01.348069 INFO: Updating optimization_manager: score_cutoff        : 22.85252744293213 -> 24.4248069190979
9:54:01.348142 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:54:01.401326 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:54:01.659607 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:54:01.717374 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:54:02.260014 INFO: === checking if optimization conditions were reached ===
9:54:02.260313 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
9:54:02.261392 INFO: Updating optimization_manager: mobility_error      : 0.053657629114340855 -> 0.05744408857504864
9:54:02.261548 INFO: Updating optimization_manager: classifier_version  : 25 -> 29
9:54:02.261659 INFO: Updating optimization_manager: score_cutoff        : 24.4248069190979 -> 22.85252744293213
9:54:02.261762 INFO: Updating optimization_manager: fwhm_rt             : 2.6681737899780273 -> 2.597942352294922
9:54:02.261861 INFO: Updating optimization_manager: fwhm_mobility       : 0.0057528321631252766 -> 0.005333321169018745
9:54:02.261977 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0574 found after 3 searches.
9:54:02.262052 INFO: ==============================================
9:54:02.262128 PROGRESS: Optimization finished for mobility_error.
9:54:02.912361 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:54:02.965681 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:54:03.219050 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:54:03.275667 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:54:03.778077 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
9:54:03.778331 PROGRESS: ==============================================
9:54:03.778434 PROGRESS: ms2_error      : 15.0000
9:54:03.778506 PROGRESS: ms1_error      : 15.0000
9:54:03.778568 PROGRESS: rt_error       : 104.3590
9:54:03.778625 PROGRESS: mobility_error : 0.0574
9:54:03.778681 PROGRESS: ==============================================
9:54:03.786578 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:54:05.446018 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:54:13.301272 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:54:15.019459 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:54:29.641462 INFO: Using python extraction backend
9:54:29.642086 PROGRESS: Extracting batch of 12210649 precursors
9:54:29.642199 INFO: === Search parameters used ===
9:54:29.642261 INFO: rt_error       : 104.35897262139244
9:54:29.642316 INFO: mobility_error : 0.05744408857504864
9:54:29.642379 INFO: num_candidates : 3
9:54:29.642428 INFO: ms1_error      : 15.0
9:54:29.642477 INFO: ms2_error      : 15.0
9:54:29.642524 INFO: fwhm_rt        : 2.597942352294922
9:54:29.642570 INFO: quant_window   : 3
9:54:29.642627 INFO: ==============================================
9:54:32.283988 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
9:54:32.284143 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
9:54:32.284191 INFO: FWHM in RT is 2.60 seconds, sigma is 0.43
9:54:32.284217 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.89
9:54:32.310835 INFO: Starting candidate selection
10:22:51.827774 INFO: Removed 25882322 precursors with score below cutoff 22.85252744293213
10:22:54.798180 INFO: Starting candidate scoring
10:24:02.231061 INFO: Finished candidate processing
10:24:02.231325 INFO: Collecting candidate features
10:24:12.897909 WARNING: intensity_correlation has 4295 NaNs ( 0.08 % out of 5401855)
10:24:12.902877 WARNING: height_correlation has 213 NaNs ( 0.00 % out of 5401855)
10:24:13.082706 INFO: Collecting fragment features
10:24:16.920660 INFO: Finished candidate scoring
10:24:19.919416 INFO: === Performing FDR correction with classifier version 29 ===
10:24:19.919977 INFO: performing precursor FDR with 47 features
10:24:19.920019 INFO: Decoy channel: -1
10:24:19.920049 INFO: competitive: True
10:24:21.212728 INFO: Setting torch num_threads to 2 for FDR classification task
10:24:22.005770 WARNING: dropped 2300 target PSMs due to missing features
10:24:22.005953 WARNING: dropped 2135 decoy PSMs due to missing features
10:24:24.141988 INFO: Estimating optimal hyperparameters - samples: 4,317,936, batch_size: 4,096, learning_rate: 1.00e-03
10:24:24.150535 INFO: Using random state 695266 for train-test-split
10:26:08.084507 INFO: Test AUC: 0.551
10:26:08.084813 INFO: Train AUC: 0.556
10:26:08.084853 INFO: AUC difference: 0.95%
10:26:09.913899 INFO: Resetting torch num_threads to 80
10:26:10.124636 INFO: Removing fragments below FDR threshold
10:26:10.428578 PROGRESS: ============================= Precursor FDR =============================
10:26:10.428819 PROGRESS: Total precursors accumulated: 8,499
10:26:10.428897 PROGRESS: Target precursors: 8,415 (99.01%)
10:26:10.428957 PROGRESS: Decoy precursors: 84 (0.99%)
10:26:10.429010 PROGRESS: 
10:26:10.429062 PROGRESS: Precursor Summary:
10:26:10.432965 PROGRESS: Channel   0:	 0.050 FDR: 8,415; 0.010 FDR: 8,415; 0.001 FDR: 5,520
10:26:10.433120 PROGRESS: 
10:26:10.433186 PROGRESS: Protein Summary:
10:26:10.437320 PROGRESS: Channel   0:	 0.050 FDR: 1,884; 0.010 FDR: 1,884; 0.001 FDR: 1,232
10:26:10.437434 PROGRESS: =========================================================================
10:26:10.558306 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R2/psm.parquet
10:26:10.597113 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R2/frag.parquet
10:26:10.645008 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R2
10:26:11.886045 PROGRESS: Loading raw file 3/12: A9_G_DIA_nLC_tTOF_R3 
10:26:11.886204 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
10:26:11.886342 INFO: Initializing TimingManager
10:26:11.886878 INFO: Initializing RawFileManager
10:26:11.887001 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:11.887069 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:11.887121 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:12.059641 INFO: Reading 22,623 frames with 375,308,789 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:17.836764 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d...
10:26:17.838871 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:17.846370 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:17.846620 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:17.847058 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:17.848480 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:17.862018 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:17.862557 INFO: Indexing quadrupole dimension
10:26:18.185759 INFO: Transposing detector events
10:26:20.013755 INFO: Finished transposing data
10:26:20.138197 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
10:26:20.138846 INFO: RT (min)            : 0.0 - 40.0
10:26:20.138901 INFO: RT duration (sec)   : 2400.0
10:26:20.138926 INFO: RT duration (min)   : 40.0
10:26:20.138948 INFO: Cycle len (scans)   : 12
10:26:20.138970 INFO: Cycle len (sec)     : 1.27
10:26:20.138989 INFO: Number of cycles    : 1885
10:26:20.139010 INFO: MS2 range (m/z)     : 374.4 - 1151.9
10:26:20.139047 INFO: Creating DIA data object took: 8.252062559127808
10:26:22.761822 INFO: Initializing CalibrationManager
10:26:22.762162 INFO: Setting up calibration estimators ..
10:26:22.762245 INFO: Found 1 estimator(s) in calibration group 'fragment'
10:26:22.762353 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
10:26:22.762448 INFO: Found 3 estimator(s) in calibration group 'precursor'
10:26:22.762525 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
10:26:22.762614 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
10:26:22.762691 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
10:26:22.762754 INFO: Done setting up calibration estimators.
10:26:22.762894 INFO: Initializing OptimizationManager
10:26:22.763003 INFO: initial parameter: ms1_error = 30
10:26:22.763059 INFO: initial parameter: ms2_error = 30
10:26:22.763113 INFO: initial parameter: rt_error = 1199.9776575
10:26:22.763163 INFO: initial parameter: mobility_error = 0.1
10:26:22.763210 INFO: initial parameter: num_candidates = 1
10:26:22.763255 INFO: initial parameter: fwhm_rt = 5
10:26:22.763301 INFO: initial parameter: fwhm_mobility = 0.01
10:26:22.763347 INFO: initial parameter: score_cutoff = 0
10:26:22.763395 INFO: initial parameter: classifier_version = -1
10:26:22.763971 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R3
10:26:22.764233 INFO: FDRManager: loading saved state not requested, will be initialized.
10:26:22.764274 INFO: Initializing FDRManager
10:26:22.764320 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
10:26:24.391485 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
10:26:25.599853 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
10:26:25.600270 INFO: Updating optimization_manager: rt_error            : 1199.9776575 -> 1199.9776575
10:26:25.600392 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
10:26:25.600582 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
10:26:25.600675 PROGRESS: Starting initial search for precursors.
10:26:25.600765 INFO: Starting optimization step 0.
10:26:25.600831 PROGRESS: === Extracting elution groups 0 to 200 ===
10:26:25.600906 INFO: Using python extraction backend
10:26:25.601016 PROGRESS: Extracting batch of 395 precursors
10:26:25.601084 INFO: === Search parameters used ===
10:26:25.601137 INFO: rt_error       : 1199.9776575
10:26:25.601186 INFO: mobility_error : 0.1
10:26:25.601232 INFO: num_candidates : 1
10:26:25.601279 INFO: ms1_error      : 30
10:26:25.601327 INFO: ms2_error      : 30
10:26:25.601372 INFO: fwhm_rt        : 5
10:26:25.601416 INFO: quant_window   : 3
10:26:25.601460 INFO: ==============================================
10:26:25.602185 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:26:25.602234 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:26:25.602268 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:26:25.602291 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:26:25.630873 INFO: Starting candidate selection
10:26:27.527065 INFO: Starting candidate scoring
10:26:27.566892 INFO: Finished candidate processing
10:26:27.566978 INFO: Collecting candidate features
10:26:27.576759 INFO: Collecting fragment features
10:26:27.578998 INFO: Finished candidate scoring
10:26:27.579913 INFO: performing precursor FDR with 47 features
10:26:27.579960 INFO: Decoy channel: -1
10:26:27.579988 INFO: competitive: True
10:26:27.581484 INFO: Setting torch num_threads to 2 for FDR classification task
10:26:27.583383 INFO: Estimating optimal hyperparameters - samples: 275, batch_size: 128, learning_rate: 1.77e-04
10:26:27.584174 INFO: Using random state 254013 for train-test-split
10:26:27.607314 INFO: Test AUC: 0.475
10:26:27.607387 INFO: Train AUC: 0.477
10:26:27.607419 INFO: AUC difference: 0.60%
10:26:27.844900 INFO: Resetting torch num_threads to 80
10:26:27.845382 PROGRESS: === Extracted 344 precursors and 2809 fragments ===
10:26:27.845810 INFO: === FDR correction performed with classifier version -1 ===
10:26:27.846375 PROGRESS: ============================= Precursor FDR =============================
10:26:27.846476 PROGRESS: Total precursors accumulated: 174
10:26:27.846543 PROGRESS: Target precursors: 83 (47.70%)
10:26:27.846603 PROGRESS: Decoy precursors: 91 (52.30%)
10:26:27.846656 PROGRESS: 
10:26:27.846708 PROGRESS: Precursor Summary:
10:26:27.847656 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
10:26:27.847752 PROGRESS: 
10:26:27.847816 PROGRESS: Protein Summary:
10:26:27.848865 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
10:26:27.848959 PROGRESS: =========================================================================
10:26:27.849069 INFO: Target number of precursors not reached yet.
10:26:27.910265 INFO: Starting optimization step 1.
10:26:27.910481 PROGRESS: === Extracting elution groups 200 to 600 ===
10:26:27.910565 INFO: Using python extraction backend
10:26:27.910676 PROGRESS: Extracting batch of 796 precursors
10:26:27.910751 INFO: === Search parameters used ===
10:26:27.910805 INFO: rt_error       : 1199.9776575
10:26:27.910856 INFO: mobility_error : 0.1
10:26:27.910909 INFO: num_candidates : 1
10:26:27.910957 INFO: ms1_error      : 30
10:26:27.911003 INFO: ms2_error      : 30
10:26:27.911049 INFO: fwhm_rt        : 5
10:26:27.911094 INFO: quant_window   : 3
10:26:27.911139 INFO: ==============================================
10:26:27.911824 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:26:27.911873 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:26:27.911904 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:26:27.911929 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:26:27.912600 INFO: Starting candidate selection
10:26:30.860452 INFO: Starting candidate scoring
10:26:30.902158 INFO: Finished candidate processing
10:26:30.902254 INFO: Collecting candidate features
10:26:30.912968 INFO: Collecting fragment features
10:26:30.915442 INFO: Finished candidate scoring
10:26:30.917589 INFO: performing precursor FDR with 47 features
10:26:30.917640 INFO: Decoy channel: -1
10:26:30.917667 INFO: competitive: True
10:26:30.920643 INFO: Setting torch num_threads to 2 for FDR classification task
10:26:30.922514 INFO: Estimating optimal hyperparameters - samples: 847, batch_size: 128, learning_rate: 1.77e-04
10:26:30.922598 INFO: Using random state 648953 for train-test-split
10:26:30.982214 INFO: Test AUC: 0.511
10:26:30.982301 INFO: Train AUC: 0.524
10:26:30.982332 INFO: AUC difference: 2.48%
10:26:31.221211 INFO: Resetting torch num_threads to 80
10:26:31.222489 PROGRESS: === Extracted 1059 precursors and 8942 fragments ===
10:26:31.222915 INFO: === FDR correction performed with classifier version -1 ===
10:26:31.223487 PROGRESS: ============================= Precursor FDR =============================
10:26:31.223583 PROGRESS: Total precursors accumulated: 540
10:26:31.223649 PROGRESS: Target precursors: 281 (52.04%)
10:26:31.223712 PROGRESS: Decoy precursors: 259 (47.96%)
10:26:31.223767 PROGRESS: 
10:26:31.223817 PROGRESS: Precursor Summary:
10:26:31.224763 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
10:26:31.224854 PROGRESS: 
10:26:31.224913 PROGRESS: Protein Summary:
10:26:31.225945 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
10:26:31.226041 PROGRESS: =========================================================================
10:26:31.226188 INFO: Target number of precursors not reached yet.
10:26:31.290534 INFO: Starting optimization step 2.
10:26:31.290752 PROGRESS: === Extracting elution groups 600 to 1400 ===
10:26:31.290834 INFO: Using python extraction backend
10:26:31.290948 PROGRESS: Extracting batch of 1598 precursors
10:26:31.291024 INFO: === Search parameters used ===
10:26:31.291082 INFO: rt_error       : 1199.9776575
10:26:31.291133 INFO: mobility_error : 0.1
10:26:31.291183 INFO: num_candidates : 1
10:26:31.291230 INFO: ms1_error      : 30
10:26:31.291276 INFO: ms2_error      : 30
10:26:31.291322 INFO: fwhm_rt        : 5
10:26:31.291367 INFO: quant_window   : 3
10:26:31.291411 INFO: ==============================================
10:26:31.292206 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:26:31.292255 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:26:31.292286 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:26:31.292311 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:26:31.293118 INFO: Starting candidate selection
10:26:36.269584 INFO: Starting candidate scoring
10:26:36.326176 INFO: Finished candidate processing
10:26:36.326276 INFO: Collecting candidate features
10:26:36.337851 INFO: Collecting fragment features
10:26:36.340615 INFO: Finished candidate scoring
10:26:36.343449 INFO: performing precursor FDR with 47 features
10:26:36.343505 INFO: Decoy channel: -1
10:26:36.343534 INFO: competitive: True
10:26:36.346805 INFO: Setting torch num_threads to 2 for FDR classification task
10:26:36.348799 INFO: Estimating optimal hyperparameters - samples: 1,990, batch_size: 128, learning_rate: 1.77e-04
10:26:36.348896 INFO: Using random state 176314 for train-test-split
10:26:36.549082 INFO: Test AUC: 0.498
10:26:36.549180 INFO: Train AUC: 0.561
10:26:36.549214 INFO: AUC difference: 11.27%
10:26:36.549241 WARNING: AUC difference > 5%. This may indicate overfitting.
10:26:36.789634 INFO: Resetting torch num_threads to 80
10:26:36.791353 PROGRESS: === Extracted 2488 precursors and 20820 fragments ===
10:26:36.791785 INFO: === FDR correction performed with classifier version -1 ===
10:26:36.792450 PROGRESS: ============================= Precursor FDR =============================
10:26:36.792553 PROGRESS: Total precursors accumulated: 1,268
10:26:36.792629 PROGRESS: Target precursors: 716 (56.47%)
10:26:36.792692 PROGRESS: Decoy precursors: 552 (43.53%)
10:26:36.792749 PROGRESS: 
10:26:36.792804 PROGRESS: Precursor Summary:
10:26:36.793762 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:26:36.793860 PROGRESS: 
10:26:36.793944 PROGRESS: Protein Summary:
10:26:36.794969 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:26:36.795066 PROGRESS: =========================================================================
10:26:36.795232 INFO: Target number of precursors not reached yet.
10:26:36.862719 INFO: Starting optimization step 3.
10:26:36.862949 PROGRESS: === Extracting elution groups 1400 to 3000 ===
10:26:36.863037 INFO: Using python extraction backend
10:26:36.863150 PROGRESS: Extracting batch of 3192 precursors
10:26:36.863235 INFO: === Search parameters used ===
10:26:36.863297 INFO: rt_error       : 1199.9776575
10:26:36.863349 INFO: mobility_error : 0.1
10:26:36.863413 INFO: num_candidates : 1
10:26:36.863464 INFO: ms1_error      : 30
10:26:36.863513 INFO: ms2_error      : 30
10:26:36.863560 INFO: fwhm_rt        : 5
10:26:36.863606 INFO: quant_window   : 3
10:26:36.863650 INFO: ==============================================
10:26:36.864664 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:26:36.864714 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:26:36.864745 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:26:36.864770 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:26:36.865832 INFO: Starting candidate selection
10:26:46.041497 INFO: Starting candidate scoring
10:26:46.124582 INFO: Finished candidate processing
10:26:46.124686 INFO: Collecting candidate features
10:26:46.138569 INFO: Collecting fragment features
10:26:46.142116 INFO: Finished candidate scoring
10:26:46.146538 INFO: performing precursor FDR with 47 features
10:26:46.146597 INFO: Decoy channel: -1
10:26:46.146627 INFO: competitive: True
10:26:46.151797 INFO: Setting torch num_threads to 2 for FDR classification task
10:26:46.154308 INFO: Estimating optimal hyperparameters - samples: 4,292, batch_size: 128, learning_rate: 1.77e-04
10:26:46.154403 INFO: Using random state 16518 for train-test-split
10:26:46.604187 INFO: Test AUC: 0.511
10:26:46.604293 INFO: Train AUC: 0.569
10:26:46.604326 INFO: AUC difference: 10.35%
10:26:46.604352 WARNING: AUC difference > 5%. This may indicate overfitting.
10:26:46.840505 INFO: Resetting torch num_threads to 80
10:26:46.842837 PROGRESS: === Extracted 5366 precursors and 45226 fragments ===
10:26:46.843278 INFO: === FDR correction performed with classifier version -1 ===
10:26:46.844110 PROGRESS: ============================= Precursor FDR =============================
10:26:46.844213 PROGRESS: Total precursors accumulated: 2,730
10:26:46.844282 PROGRESS: Target precursors: 1,551 (56.81%)
10:26:46.844342 PROGRESS: Decoy precursors: 1,179 (43.19%)
10:26:46.844398 PROGRESS: 
10:26:46.844453 PROGRESS: Precursor Summary:
10:26:46.845431 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
10:26:46.845529 PROGRESS: 
10:26:46.845596 PROGRESS: Protein Summary:
10:26:46.846668 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
10:26:46.846769 PROGRESS: =========================================================================
10:26:46.846939 INFO: Target number of precursors not reached yet.
10:26:46.918628 INFO: Starting optimization step 4.
10:26:46.918885 PROGRESS: === Extracting elution groups 3000 to 6200 ===
10:26:46.918972 INFO: Using python extraction backend
10:26:46.919086 PROGRESS: Extracting batch of 6381 precursors
10:26:46.919164 INFO: === Search parameters used ===
10:26:46.919221 INFO: rt_error       : 1199.9776575
10:26:46.919273 INFO: mobility_error : 0.1
10:26:46.919323 INFO: num_candidates : 1
10:26:46.919374 INFO: ms1_error      : 30
10:26:46.919424 INFO: ms2_error      : 30
10:26:46.919475 INFO: fwhm_rt        : 5
10:26:46.919523 INFO: quant_window   : 3
10:26:46.919572 INFO: ==============================================
10:26:46.921034 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:26:46.921089 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:26:46.921122 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:26:46.921147 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:26:46.921997 INFO: Starting candidate selection
10:27:03.402362 INFO: Starting candidate scoring
10:27:03.561129 INFO: Finished candidate processing
10:27:03.561250 INFO: Collecting candidate features
10:27:03.579686 INFO: Collecting fragment features
10:27:03.584713 INFO: Finished candidate scoring
10:27:03.591444 INFO: performing precursor FDR with 47 features
10:27:03.591542 INFO: Decoy channel: -1
10:27:03.591570 INFO: competitive: True
10:27:03.596998 INFO: Setting torch num_threads to 2 for FDR classification task
10:27:03.600532 INFO: Estimating optimal hyperparameters - samples: 8,884, batch_size: 128, learning_rate: 1.77e-04
10:27:03.600644 INFO: Using random state 447539 for train-test-split
10:27:04.590058 INFO: Test AUC: 0.545
10:27:04.590166 INFO: Train AUC: 0.579
10:27:04.590199 INFO: AUC difference: 5.81%
10:27:04.590224 WARNING: AUC difference > 5%. This may indicate overfitting.
10:27:04.836357 INFO: Resetting torch num_threads to 80
10:27:04.839780 PROGRESS: === Extracted 11106 precursors and 93128 fragments ===
10:27:04.840239 INFO: === FDR correction performed with classifier version -1 ===
10:27:04.841415 PROGRESS: ============================= Precursor FDR =============================
10:27:04.841523 PROGRESS: Total precursors accumulated: 5,653
10:27:04.841599 PROGRESS: Target precursors: 3,309 (58.54%)
10:27:04.841663 PROGRESS: Decoy precursors: 2,344 (41.46%)
10:27:04.841722 PROGRESS: 
10:27:04.841778 PROGRESS: Precursor Summary:
10:27:04.842780 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:27:04.842889 PROGRESS: 
10:27:04.842961 PROGRESS: Protein Summary:
10:27:04.843999 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:27:04.844092 PROGRESS: =========================================================================
10:27:04.844296 INFO: Target number of precursors not reached yet.
10:27:04.924625 INFO: Starting optimization step 5.
10:27:04.924881 PROGRESS: === Extracting elution groups 6200 to 12600 ===
10:27:04.924969 INFO: Using python extraction backend
10:27:04.925084 PROGRESS: Extracting batch of 12763 precursors
10:27:04.925164 INFO: === Search parameters used ===
10:27:04.925221 INFO: rt_error       : 1199.9776575
10:27:04.925274 INFO: mobility_error : 0.1
10:27:04.925326 INFO: num_candidates : 1
10:27:04.925375 INFO: ms1_error      : 30
10:27:04.925428 INFO: ms2_error      : 30
10:27:04.925478 INFO: fwhm_rt        : 5
10:27:04.925525 INFO: quant_window   : 3
10:27:04.925570 INFO: ==============================================
10:27:04.928232 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:27:04.928292 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:27:04.928327 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:27:04.928354 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:27:04.929094 INFO: Starting candidate selection
10:27:36.539523 INFO: Starting candidate scoring
10:27:36.777712 INFO: Finished candidate processing
10:27:36.777843 INFO: Collecting candidate features
10:27:36.802298 WARNING: intensity_correlation has 5 NaNs ( 0.04 % out of 11484)
10:27:36.808935 INFO: Collecting fragment features
10:27:36.827662 INFO: Finished candidate scoring
10:27:36.841564 INFO: performing precursor FDR with 47 features
10:27:36.841718 INFO: Decoy channel: -1
10:27:36.841747 INFO: competitive: True
10:27:36.853560 INFO: Setting torch num_threads to 2 for FDR classification task
10:27:36.858235 WARNING: dropped 1 target PSMs due to missing features
10:27:36.858336 WARNING: dropped 4 decoy PSMs due to missing features
10:27:36.861544 INFO: Estimating optimal hyperparameters - samples: 18,068, batch_size: 128, learning_rate: 1.77e-04
10:27:36.861680 INFO: Using random state 949167 for train-test-split
10:27:38.829177 INFO: Test AUC: 0.548
10:27:38.829305 INFO: Train AUC: 0.588
10:27:38.829340 INFO: AUC difference: 6.79%
10:27:38.829364 WARNING: AUC difference > 5%. This may indicate overfitting.
10:27:40.270456 INFO: Resetting torch num_threads to 80
10:27:40.275913 PROGRESS: === Extracted 22590 precursors and 189469 fragments ===
10:27:40.276480 INFO: === FDR correction performed with classifier version -1 ===
10:27:40.278533 PROGRESS: ============================= Precursor FDR =============================
10:27:40.278664 PROGRESS: Total precursors accumulated: 11,485
10:27:40.278743 PROGRESS: Target precursors: 6,822 (59.40%)
10:27:40.278806 PROGRESS: Decoy precursors: 4,663 (40.60%)
10:27:40.278857 PROGRESS: 
10:27:40.278906 PROGRESS: Precursor Summary:
10:27:40.279952 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
10:27:40.280045 PROGRESS: 
10:27:40.280107 PROGRESS: Protein Summary:
10:27:40.281208 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
10:27:40.281299 PROGRESS: =========================================================================
10:27:40.281568 INFO: Target number of precursors not reached yet.
10:27:40.378001 INFO: Starting optimization step 6.
10:27:40.378271 PROGRESS: === Extracting elution groups 12600 to 25400 ===
10:27:40.378361 INFO: Using python extraction backend
10:27:40.378481 PROGRESS: Extracting batch of 25523 precursors
10:27:40.378564 INFO: === Search parameters used ===
10:27:40.378621 INFO: rt_error       : 1199.9776575
10:27:40.378671 INFO: mobility_error : 0.1
10:27:40.378720 INFO: num_candidates : 1
10:27:40.378767 INFO: ms1_error      : 30
10:27:40.378814 INFO: ms2_error      : 30
10:27:40.378860 INFO: fwhm_rt        : 5
10:27:40.378905 INFO: quant_window   : 3
10:27:40.378963 INFO: ==============================================
10:27:40.386271 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:27:40.386353 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:27:40.386385 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:27:40.386416 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:27:40.387127 INFO: Starting candidate selection
10:28:41.295417 INFO: Starting candidate scoring
10:28:41.691197 INFO: Finished candidate processing
10:28:41.691381 INFO: Collecting candidate features
10:28:41.761518 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 22943)
10:28:41.761816 WARNING: height_correlation has 2 NaNs ( 0.01 % out of 22943)
10:28:41.766194 INFO: Collecting fragment features
10:28:41.781530 INFO: Finished candidate scoring
10:28:41.808856 INFO: performing precursor FDR with 47 features
10:28:41.809018 INFO: Decoy channel: -1
10:28:41.809056 INFO: competitive: True
10:28:41.829711 INFO: Setting torch num_threads to 2 for FDR classification task
10:28:41.840356 WARNING: dropped 7 target PSMs due to missing features
10:28:41.840484 WARNING: dropped 8 decoy PSMs due to missing features
10:28:41.847319 INFO: Estimating optimal hyperparameters - samples: 36,414, batch_size: 149, learning_rate: 1.91e-04
10:28:41.847539 INFO: Using random state 560715 for train-test-split
10:28:45.800989 INFO: Test AUC: 0.545
10:28:45.801312 INFO: Train AUC: 0.590
10:28:45.801349 INFO: AUC difference: 7.57%
10:28:45.801374 WARNING: AUC difference > 5%. This may indicate overfitting.
10:28:46.059667 INFO: Resetting torch num_threads to 80
10:28:46.070752 PROGRESS: === Extracted 45533 precursors and 382564 fragments ===
10:28:46.071448 INFO: === FDR correction performed with classifier version -1 ===
10:28:46.076291 PROGRESS: ============================= Precursor FDR =============================
10:28:46.076429 PROGRESS: Total precursors accumulated: 23,125
10:28:46.076500 PROGRESS: Target precursors: 13,704 (59.26%)
10:28:46.076559 PROGRESS: Decoy precursors: 9,421 (40.74%)
10:28:46.076614 PROGRESS: 
10:28:46.076666 PROGRESS: Precursor Summary:
10:28:46.077766 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:28:46.077875 PROGRESS: 
10:28:46.077944 PROGRESS: Protein Summary:
10:28:46.079181 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:28:46.079282 PROGRESS: =========================================================================
10:28:46.079915 INFO: Target number of precursors not reached yet.
10:28:46.324112 INFO: Starting optimization step 7.
10:28:46.324389 PROGRESS: === Extracting elution groups 25400 to 51000 ===
10:28:46.324477 INFO: Using python extraction backend
10:28:46.324626 PROGRESS: Extracting batch of 51061 precursors
10:28:46.324709 INFO: === Search parameters used ===
10:28:46.324766 INFO: rt_error       : 1199.9776575
10:28:46.324822 INFO: mobility_error : 0.1
10:28:46.324871 INFO: num_candidates : 1
10:28:46.324917 INFO: ms1_error      : 30
10:28:46.324961 INFO: ms2_error      : 30
10:28:46.325003 INFO: fwhm_rt        : 5
10:28:46.325049 INFO: quant_window   : 3
10:28:46.325093 INFO: ==============================================
10:28:46.340510 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:28:46.340635 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:28:46.340669 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:28:46.340694 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:28:46.341475 INFO: Starting candidate selection
10:30:45.934539 INFO: Starting candidate scoring
10:30:46.646443 INFO: Finished candidate processing
10:30:46.646578 INFO: Collecting candidate features
10:30:46.726387 WARNING: intensity_correlation has 13 NaNs ( 0.03 % out of 45814)
10:30:46.726687 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 45814)
10:30:46.732056 INFO: Collecting fragment features
10:30:46.757567 INFO: Finished candidate scoring
10:30:46.818073 INFO: performing precursor FDR with 47 features
10:30:46.818220 INFO: Decoy channel: -1
10:30:46.818249 INFO: competitive: True
10:30:46.858139 INFO: Setting torch num_threads to 2 for FDR classification task
10:30:46.878460 WARNING: dropped 14 target PSMs due to missing features
10:30:46.878595 WARNING: dropped 15 decoy PSMs due to missing features
10:30:46.891368 INFO: Estimating optimal hyperparameters - samples: 73,054, batch_size: 299, learning_rate: 2.70e-04
10:30:46.891687 INFO: Using random state 124555 for train-test-split
10:30:52.395296 INFO: Test AUC: 0.549
10:30:52.395421 INFO: Train AUC: 0.596
10:30:52.395454 INFO: AUC difference: 7.91%
10:30:52.395479 WARNING: AUC difference > 5%. This may indicate overfitting.
10:30:52.674160 INFO: Resetting torch num_threads to 80
10:30:52.693471 PROGRESS: === Extracted 91347 precursors and 767216 fragments ===
10:30:52.694243 INFO: === FDR correction performed with classifier version -1 ===
10:30:52.704716 PROGRESS: ============================= Precursor FDR =============================
10:30:52.704915 PROGRESS: Total precursors accumulated: 46,377
10:30:52.704991 PROGRESS: Target precursors: 27,504 (59.31%)
10:30:52.705052 PROGRESS: Decoy precursors: 18,873 (40.69%)
10:30:52.705107 PROGRESS: 
10:30:52.705161 PROGRESS: Precursor Summary:
10:30:52.706483 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:30:52.706595 PROGRESS: 
10:30:52.706661 PROGRESS: Protein Summary:
10:30:52.707946 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:30:52.708049 PROGRESS: =========================================================================
10:30:52.709052 INFO: Target number of precursors not reached yet.
10:30:53.044052 INFO: Starting optimization step 8.
10:30:53.044350 PROGRESS: === Extracting elution groups 51000 to 102200 ===
10:30:53.044439 INFO: Using python extraction backend
10:30:53.044564 PROGRESS: Extracting batch of 102076 precursors
10:30:53.044644 INFO: === Search parameters used ===
10:30:53.044700 INFO: rt_error       : 1199.9776575
10:30:53.044750 INFO: mobility_error : 0.1
10:30:53.044799 INFO: num_candidates : 1
10:30:53.044846 INFO: ms1_error      : 30
10:30:53.044894 INFO: ms2_error      : 30
10:30:53.044941 INFO: fwhm_rt        : 5
10:30:53.044988 INFO: quant_window   : 3
10:30:53.045038 INFO: ==============================================
10:30:53.073342 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:30:53.073482 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:30:53.073519 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:30:53.073543 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:30:53.075306 INFO: Starting candidate selection
10:34:48.895238 INFO: Starting candidate scoring
10:34:50.353674 INFO: Finished candidate processing
10:34:50.353899 INFO: Collecting candidate features
10:34:50.541120 WARNING: intensity_correlation has 19 NaNs ( 0.02 % out of 91723)
10:34:50.541439 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 91723)
10:34:50.548426 INFO: Collecting fragment features
10:34:50.602648 INFO: Finished candidate scoring
10:34:50.711564 INFO: performing precursor FDR with 47 features
10:34:50.711714 INFO: Decoy channel: -1
10:34:50.711742 INFO: competitive: True
10:34:50.796176 INFO: Setting torch num_threads to 2 for FDR classification task
10:34:50.835979 WARNING: dropped 22 target PSMs due to missing features
10:34:50.836116 WARNING: dropped 27 decoy PSMs due to missing features
10:34:50.886515 INFO: Estimating optimal hyperparameters - samples: 146,416, batch_size: 599, learning_rate: 3.82e-04
10:34:50.887643 INFO: Using random state 671636 for train-test-split
10:34:58.271637 INFO: Test AUC: 0.543
10:34:58.271773 INFO: Train AUC: 0.585
10:34:58.271808 INFO: AUC difference: 7.14%
10:34:58.271835 WARNING: AUC difference > 5%. This may indicate overfitting.
10:34:58.581579 INFO: Resetting torch num_threads to 80
10:34:58.618649 PROGRESS: === Extracted 183070 precursors and 1539176 fragments ===
10:34:58.619523 INFO: === FDR correction performed with classifier version -1 ===
10:34:58.640230 PROGRESS: ============================= Precursor FDR =============================
10:34:58.640506 PROGRESS: Total precursors accumulated: 92,922
10:34:58.640581 PROGRESS: Target precursors: 54,514 (58.67%)
10:34:58.640644 PROGRESS: Decoy precursors: 38,408 (41.33%)
10:34:58.640700 PROGRESS: 
10:34:58.640753 PROGRESS: Precursor Summary:
10:34:58.642478 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:34:58.642600 PROGRESS: 
10:34:58.642680 PROGRESS: Protein Summary:
10:34:58.644193 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:34:58.644293 PROGRESS: =========================================================================
10:34:58.646249 INFO: Target number of precursors not reached yet.
10:34:59.142862 INFO: Starting optimization step 9.
10:34:59.143176 PROGRESS: === Extracting elution groups 102200 to 204600 ===
10:34:59.143283 INFO: Using python extraction backend
10:34:59.143424 PROGRESS: Extracting batch of 204132 precursors
10:34:59.143512 INFO: === Search parameters used ===
10:34:59.143570 INFO: rt_error       : 1199.9776575
10:34:59.143620 INFO: mobility_error : 0.1
10:34:59.143669 INFO: num_candidates : 1
10:34:59.143718 INFO: ms1_error      : 30
10:34:59.143766 INFO: ms2_error      : 30
10:34:59.143814 INFO: fwhm_rt        : 5
10:34:59.143863 INFO: quant_window   : 3
10:34:59.143912 INFO: ==============================================
10:34:59.200402 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:34:59.200536 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:34:59.200572 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:34:59.200596 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:34:59.201470 INFO: Starting candidate selection
10:42:51.573008 INFO: Starting candidate scoring
10:42:54.229760 INFO: Finished candidate processing
10:42:54.230123 INFO: Collecting candidate features
10:42:54.670598 WARNING: intensity_correlation has 51 NaNs ( 0.03 % out of 183600)
10:42:54.680667 INFO: Collecting fragment features
10:42:54.800498 INFO: Finished candidate scoring
10:42:55.012787 INFO: performing precursor FDR with 47 features
10:42:55.012954 INFO: Decoy channel: -1
10:42:55.012984 INFO: competitive: True
10:42:55.191092 INFO: Setting torch num_threads to 2 for FDR classification task
10:42:55.265698 WARNING: dropped 41 target PSMs due to missing features
10:42:55.265878 WARNING: dropped 59 decoy PSMs due to missing features
10:42:55.391614 INFO: Estimating optimal hyperparameters - samples: 293,256, batch_size: 1,201, learning_rate: 5.41e-04
10:42:55.392231 INFO: Using random state 862652 for train-test-split
10:43:06.179441 INFO: Test AUC: 0.545
10:43:06.179584 INFO: Train AUC: 0.580
10:43:06.179629 INFO: AUC difference: 6.02%
10:43:06.179656 WARNING: AUC difference > 5%. This may indicate overfitting.
10:43:06.545223 INFO: Resetting torch num_threads to 80
10:43:06.651513 PROGRESS: === Extracted 366670 precursors and 3083422 fragments ===
10:43:06.652462 INFO: === FDR correction performed with classifier version -1 ===
10:43:06.689640 PROGRESS: ============================= Precursor FDR =============================
10:43:06.689998 PROGRESS: Total precursors accumulated: 186,096
10:43:06.690098 PROGRESS: Target precursors: 107,953 (58.01%)
10:43:06.690162 PROGRESS: Decoy precursors: 78,143 (41.99%)
10:43:06.690217 PROGRESS: 
10:43:06.690267 PROGRESS: Precursor Summary:
10:43:06.692361 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:43:06.692465 PROGRESS: 
10:43:06.692530 PROGRESS: Protein Summary:
10:43:06.694440 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
10:43:06.694547 PROGRESS: =========================================================================
10:43:06.699505 INFO: Target number of precursors not reached yet.
10:43:07.562584 INFO: Starting optimization step 10.
10:43:07.563071 PROGRESS: === Extracting elution groups 204600 to 409400 ===
10:43:07.563180 INFO: Using python extraction backend
10:43:07.563391 PROGRESS: Extracting batch of 408390 precursors
10:43:07.563511 INFO: === Search parameters used ===
10:43:07.563575 INFO: rt_error       : 1199.9776575
10:43:07.563629 INFO: mobility_error : 0.1
10:43:07.563678 INFO: num_candidates : 1
10:43:07.563725 INFO: ms1_error      : 30
10:43:07.563772 INFO: ms2_error      : 30
10:43:07.563818 INFO: fwhm_rt        : 5
10:43:07.563875 INFO: quant_window   : 3
10:43:07.563927 INFO: ==============================================
10:43:07.681272 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:43:07.681415 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:43:07.681459 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:43:07.681484 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:43:07.682583 INFO: Starting candidate selection
10:58:23.554319 INFO: Starting candidate scoring
10:58:28.841236 INFO: Finished candidate processing
10:58:28.841574 INFO: Collecting candidate features
10:58:29.718937 WARNING: intensity_correlation has 100 NaNs ( 0.03 % out of 366156)
10:58:29.719527 WARNING: height_correlation has 7 NaNs ( 0.00 % out of 366156)
10:58:29.734810 INFO: Collecting fragment features
10:58:29.967190 INFO: Finished candidate scoring
10:58:30.466688 INFO: performing precursor FDR with 47 features
10:58:30.466840 INFO: Decoy channel: -1
10:58:30.466870 INFO: competitive: True
10:58:30.795528 INFO: Setting torch num_threads to 2 for FDR classification task
10:58:30.928106 WARNING: dropped 83 target PSMs due to missing features
10:58:30.928269 WARNING: dropped 121 decoy PSMs due to missing features
10:58:31.216370 INFO: Estimating optimal hyperparameters - samples: 586,097, batch_size: 2,400, learning_rate: 7.65e-04
10:58:31.217438 INFO: Using random state 399536 for train-test-split
10:58:47.480981 INFO: Test AUC: 0.545
10:58:47.481128 INFO: Train AUC: 0.565
10:58:47.481165 INFO: AUC difference: 3.70%
10:58:47.961126 INFO: Resetting torch num_threads to 80
10:58:48.184016 PROGRESS: === Extracted 732826 precursors and 6162588 fragments ===
10:58:48.185156 INFO: === FDR correction performed with classifier version -1 ===
10:58:48.253172 PROGRESS: ============================= Precursor FDR =============================
10:58:48.253473 PROGRESS: Total precursors accumulated: 371,952
10:58:48.253549 PROGRESS: Target precursors: 211,984 (56.99%)
10:58:48.253612 PROGRESS: Decoy precursors: 159,968 (43.01%)
10:58:48.253667 PROGRESS: 
10:58:48.253721 PROGRESS: Precursor Summary:
10:58:48.257214 PROGRESS: Channel   0:	 0.050 FDR:   230; 0.010 FDR:   138; 0.001 FDR:   124
10:58:48.257338 PROGRESS: 
10:58:48.257409 PROGRESS: Protein Summary:
10:58:48.260447 PROGRESS: Channel   0:	 0.050 FDR:   187; 0.010 FDR:   111; 0.001 FDR:    98
10:58:48.260576 PROGRESS: =========================================================================
10:58:48.267077 INFO: Target number of precursors not reached yet.
10:58:49.467192 INFO: Starting optimization step 11.
10:58:49.467488 PROGRESS: === Extracting elution groups 409400 to 819000 ===
10:58:49.467611 INFO: Using python extraction backend
10:58:49.467764 PROGRESS: Extracting batch of 816689 precursors
10:58:49.467856 INFO: === Search parameters used ===
10:58:49.467926 INFO: rt_error       : 1199.9776575
10:58:49.467984 INFO: mobility_error : 0.1
10:58:49.468038 INFO: num_candidates : 1
10:58:49.468087 INFO: ms1_error      : 30
10:58:49.468133 INFO: ms2_error      : 30
10:58:49.468176 INFO: fwhm_rt        : 5
10:58:49.468221 INFO: quant_window   : 3
10:58:49.468265 INFO: ==============================================
10:58:49.675982 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
10:58:49.676124 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
10:58:49.676168 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
10:58:49.676191 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
10:58:49.677107 INFO: Starting candidate selection
11:28:26.449163 INFO: Starting candidate scoring
11:28:36.798993 INFO: Finished candidate processing
11:28:36.799180 INFO: Collecting candidate features
11:28:38.851233 WARNING: intensity_correlation has 219 NaNs ( 0.03 % out of 733728)
11:28:38.852333 WARNING: height_correlation has 14 NaNs ( 0.00 % out of 733728)
11:28:38.880242 INFO: Collecting fragment features
11:28:39.441213 INFO: Finished candidate scoring
11:28:40.565745 INFO: performing precursor FDR with 47 features
11:28:40.565915 INFO: Decoy channel: -1
11:28:40.565949 INFO: competitive: True
11:28:41.111473 INFO: Setting torch num_threads to 2 for FDR classification task
11:28:41.357464 WARNING: dropped 191 target PSMs due to missing features
11:28:41.357636 WARNING: dropped 241 decoy PSMs due to missing features
11:28:41.849020 INFO: Estimating optimal hyperparameters - samples: 1,172,897, batch_size: 4,096, learning_rate: 1.00e-03
11:28:41.851752 INFO: Using random state 755798 for train-test-split
11:29:17.735666 INFO: Test AUC: 0.547
11:29:17.736103 INFO: Train AUC: 0.560
11:29:17.736149 INFO: AUC difference: 2.24%
11:29:18.490035 INFO: Resetting torch num_threads to 80
11:29:19.221670 PROGRESS: === Extracted 1466554 precursors and 12330606 fragments ===
11:29:19.224139 INFO: === FDR correction performed with classifier version -1 ===
11:29:19.386037 PROGRESS: ============================= Precursor FDR =============================
11:29:19.386376 PROGRESS: Total precursors accumulated: 744,328
11:29:19.386467 PROGRESS: Target precursors: 423,127 (56.85%)
11:29:19.386529 PROGRESS: Decoy precursors: 321,201 (43.15%)
11:29:19.386584 PROGRESS: 
11:29:19.386637 PROGRESS: Precursor Summary:
11:29:19.392938 PROGRESS: Channel   0:	 0.050 FDR:   493; 0.010 FDR:   348; 0.001 FDR:   168
11:29:19.393108 PROGRESS: 
11:29:19.393183 PROGRESS: Protein Summary:
11:29:19.398558 PROGRESS: Channel   0:	 0.050 FDR:   320; 0.010 FDR:   232; 0.001 FDR:   128
11:29:19.398680 PROGRESS: =========================================================================
11:29:19.418422 INFO: Target number of precursors reached.
11:29:20.835585 INFO: fragments_df: keeping 3344 of 12330606 [sum(precursor_idx_mask)=3796 sum(mass_error_mask)=12330538 stop_rank=3344
11:29:23.475786 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
11:29:23.604896 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
11:29:23.734755 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
11:29:23.871468 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
11:29:24.279155 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
11:29:24.279633 INFO: Using score_cutoff 34.76848424263 (fac=0.99, q=1)
11:29:24.279993 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.9673566818237305
11:29:24.280080 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008403213694691658
11:29:24.280142 INFO: Updating optimization_manager: score_cutoff        : 0 -> 34.76848424263
11:29:24.280218 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
11:29:24.489239 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
11:29:25.604962 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
11:29:25.839474 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
11:29:27.825180 INFO: Updating optimization_manager: classifier_version  : -1 -> 11
11:29:27.825461 PROGRESS: Required number of precursors found. Starting search parameter optimization.
11:29:27.825596 INFO: Starting optimization step 12.
11:29:27.825670 PROGRESS: === Extracting elution groups 0 to 819000 ===
11:29:27.825778 INFO: Using python extraction backend
11:29:27.825999 PROGRESS: Extracting batch of 1632996 precursors
11:29:27.826126 INFO: === Search parameters used ===
11:29:27.826202 INFO: rt_error       : 1199.9776575
11:29:27.826268 INFO: mobility_error : 0.1
11:29:27.826330 INFO: num_candidates : 3
11:29:27.826384 INFO: ms1_error      : 30
11:29:27.826433 INFO: ms2_error      : 30
11:29:27.826480 INFO: fwhm_rt        : 2.9673566818237305
11:29:27.826528 INFO: quant_window   : 3
11:29:27.826577 INFO: ==============================================
11:29:28.299261 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
11:29:28.299408 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
11:29:28.299469 INFO: FWHM in RT is 2.97 seconds, sigma is 0.49
11:29:28.299496 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.55
11:29:28.304008 INFO: Starting candidate selection
12:36:14.707385 INFO: Starting candidate scoring
12:37:09.647150 INFO: Finished candidate processing
12:37:09.647414 INFO: Collecting candidate features
12:37:17.300646 WARNING: intensity_correlation has 1259 NaNs ( 0.03 % out of 4219291)
12:37:17.304570 WARNING: height_correlation has 99 NaNs ( 0.00 % out of 4219291)
12:37:17.446183 INFO: Collecting fragment features
12:37:20.212050 INFO: Finished candidate scoring
12:37:23.942898 INFO: performing precursor FDR with 47 features
12:37:23.943042 INFO: Decoy channel: -1
12:37:23.943074 INFO: competitive: True
12:37:24.942260 INFO: Setting torch num_threads to 2 for FDR classification task
12:37:25.526404 WARNING: dropped 618 target PSMs due to missing features
12:37:25.526589 WARNING: dropped 709 decoy PSMs due to missing features
12:37:27.153850 INFO: Estimating optimal hyperparameters - samples: 3,374,371, batch_size: 4,096, learning_rate: 1.00e-03
12:37:27.162495 INFO: Using random state 980248 for train-test-split
12:39:04.390074 INFO: Test AUC: 0.560
12:39:04.390319 INFO: Train AUC: 0.565
12:39:04.390368 INFO: AUC difference: 0.82%
12:39:05.924488 INFO: Resetting torch num_threads to 80
12:39:06.111625 PROGRESS: === Extracted 4219291 precursors and 34736348 fragments ===
12:39:06.113021 INFO: === FDR correction performed with classifier version 11 ===
12:39:06.231420 PROGRESS: ============================= Precursor FDR =============================
12:39:06.231739 PROGRESS: Total precursors accumulated: 750,957
12:39:06.231822 PROGRESS: Target precursors: 437,465 (58.25%)
12:39:06.231885 PROGRESS: Decoy precursors: 313,492 (41.75%)
12:39:06.231938 PROGRESS: 
12:39:06.231991 PROGRESS: Precursor Summary:
12:39:06.237824 PROGRESS: Channel   0:	 0.050 FDR:   569; 0.010 FDR:   408; 0.001 FDR:   275
12:39:06.238001 PROGRESS: 
12:39:06.238072 PROGRESS: Protein Summary:
12:39:06.243014 PROGRESS: Channel   0:	 0.050 FDR:   380; 0.010 FDR:   253; 0.001 FDR:   169
12:39:06.243129 PROGRESS: =========================================================================
12:39:06.262971 INFO: Target number of precursors reached.
12:39:09.792263 INFO: fragments_df: keeping 5000 of 34736348 [sum(precursor_idx_mask)=12033 sum(mass_error_mask)=34736199 stop_rank=5000
12:39:11.391020 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:39:11.549185 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:39:11.692957 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:39:11.834857 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:39:12.559541 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:39:12.560002 INFO: Using score_cutoff 28.68405710105896 (fac=0.99, q=1)
12:39:12.560405 INFO: Updating optimization_manager: fwhm_rt             : 2.9673566818237305 -> 2.9406070709228516
12:39:12.560495 INFO: Updating optimization_manager: fwhm_mobility       : 0.008403213694691658 -> 0.008328871801495552
12:39:12.560559 INFO: Updating optimization_manager: score_cutoff        : 34.76848424263 -> 28.68405710105896
12:39:12.560626 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:39:12.665597 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:39:13.190225 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:39:13.280874 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:39:14.348627 INFO: === checking if optimization conditions were reached ===
12:39:14.351000 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
12:39:14.351195 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
12:39:14.351282 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
12:39:14.352414 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
12:39:14.352521 INFO: Updating optimization_manager: classifier_version  : 12 -> 12
12:39:14.352594 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
12:39:14.352655 INFO: ==============================================
12:39:14.352736 INFO: Starting optimization step 13.
12:39:14.352802 PROGRESS: === Extracting elution groups 0 to 409400 ===
12:39:14.352886 INFO: Using python extraction backend
12:39:14.353065 PROGRESS: Extracting batch of 816307 precursors
12:39:14.353143 INFO: === Search parameters used ===
12:39:14.353198 INFO: rt_error       : 1199.9776575
12:39:14.353245 INFO: mobility_error : 0.1
12:39:14.353293 INFO: num_candidates : 3
12:39:14.353338 INFO: ms1_error      : 15.0
12:39:14.353382 INFO: ms2_error      : 15.0
12:39:14.353426 INFO: fwhm_rt        : 2.9406070709228516
12:39:14.353469 INFO: quant_window   : 3
12:39:14.353512 INFO: ==============================================
12:39:14.568968 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
12:39:14.569114 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
12:39:14.569176 INFO: FWHM in RT is 2.94 seconds, sigma is 0.49
12:39:14.569201 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.51
12:39:14.593683 INFO: Starting candidate selection
13:08:18.401452 INFO: Starting candidate scoring
13:08:42.501722 INFO: Finished candidate processing
13:08:42.501907 INFO: Collecting candidate features
13:08:46.109776 WARNING: intensity_correlation has 2294 NaNs ( 0.11 % out of 2051364)
13:08:46.111819 WARNING: height_correlation has 132 NaNs ( 0.01 % out of 2051364)
13:08:46.182120 INFO: Collecting fragment features
13:08:47.290799 INFO: Finished candidate scoring
13:08:49.045134 INFO: performing precursor FDR with 47 features
13:08:49.045272 INFO: Decoy channel: -1
13:08:49.045303 INFO: competitive: True
13:08:49.524182 INFO: Setting torch num_threads to 2 for FDR classification task
13:08:49.810732 WARNING: dropped 1110 target PSMs due to missing features
13:08:49.810896 WARNING: dropped 1270 decoy PSMs due to missing features
13:08:50.574083 INFO: Estimating optimal hyperparameters - samples: 1,639,187, batch_size: 4,096, learning_rate: 1.00e-03
13:08:50.582988 INFO: Using random state 115939 for train-test-split
13:09:37.543875 INFO: Test AUC: 0.560
13:09:37.544158 INFO: Train AUC: 0.569
13:09:37.544196 INFO: AUC difference: 1.61%
13:09:38.441767 INFO: Resetting torch num_threads to 80
13:09:38.478455 PROGRESS: === Extracted 2051364 precursors and 14457756 fragments ===
13:09:38.479630 INFO: === FDR correction performed with classifier version 12 ===
13:09:38.546559 PROGRESS: ============================= Precursor FDR =============================
13:09:38.546868 PROGRESS: Total precursors accumulated: 372,391
13:09:38.546952 PROGRESS: Target precursors: 216,859 (58.23%)
13:09:38.547009 PROGRESS: Decoy precursors: 155,532 (41.77%)
13:09:38.547058 PROGRESS: 
13:09:38.547107 PROGRESS: Precursor Summary:
13:09:38.550497 PROGRESS: Channel   0:	 0.050 FDR:   446; 0.010 FDR:   243; 0.001 FDR:   222
13:09:38.550603 PROGRESS: 
13:09:38.550667 PROGRESS: Protein Summary:
13:09:38.553695 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   178; 0.001 FDR:   163
13:09:38.553793 PROGRESS: =========================================================================
13:09:38.587523 INFO: Target number of precursors reached.
13:09:40.149288 INFO: fragments_df: keeping 4549 of 14457756 [sum(precursor_idx_mask)=6939 sum(mass_error_mask)=14457503 stop_rank=4549
13:09:41.478780 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:09:41.586195 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:09:41.698641 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:09:41.822557 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:09:42.404540 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:09:42.404994 INFO: Using score_cutoff 31.636692220687866 (fac=0.99, q=1)
13:09:42.405368 INFO: Updating optimization_manager: fwhm_rt             : 2.9406070709228516 -> 2.8567535877227783
13:09:42.405458 INFO: Updating optimization_manager: fwhm_mobility       : 0.008328871801495552 -> 0.007348875515162945
13:09:42.405522 INFO: Updating optimization_manager: score_cutoff        : 28.68405710105896 -> 31.636692220687866
13:09:42.405590 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:09:42.508317 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:09:43.033251 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:09:43.142463 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:09:44.123394 INFO: === checking if optimization conditions were reached ===
13:09:44.125632 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
13:09:44.125792 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
13:09:44.125882 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
13:09:44.126980 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
13:09:44.127087 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
13:09:44.127158 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
13:09:44.127220 INFO: ==============================================
13:09:44.127297 PROGRESS: Optimization finished for ms2_error, ms1_error.
13:09:45.011013 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:09:45.120035 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:09:45.632838 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:09:45.748578 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:09:46.773818 INFO: Starting optimization step 0.
13:09:46.774103 PROGRESS: === Extracting elution groups 0 to 409400 ===
13:09:46.774222 INFO: Using python extraction backend
13:09:46.774444 PROGRESS: Extracting batch of 816307 precursors
13:09:46.774543 INFO: === Search parameters used ===
13:09:46.774607 INFO: rt_error       : 1199.9776575
13:09:46.774661 INFO: mobility_error : 0.1
13:09:46.774712 INFO: num_candidates : 3
13:09:46.774764 INFO: ms1_error      : 15.0
13:09:46.774813 INFO: ms2_error      : 15.0
13:09:46.774863 INFO: fwhm_rt        : 2.8567535877227783
13:09:46.774914 INFO: quant_window   : 3
13:09:46.774964 INFO: ==============================================
13:09:46.979163 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
13:09:46.979307 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
13:09:46.979367 INFO: FWHM in RT is 2.86 seconds, sigma is 0.48
13:09:46.979397 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.98
13:09:46.980211 INFO: Starting candidate selection
13:40:09.123573 INFO: Starting candidate scoring
13:40:32.852286 INFO: Finished candidate processing
13:40:32.853239 INFO: Collecting candidate features
13:40:36.924768 WARNING: intensity_correlation has 2257 NaNs ( 0.11 % out of 2052053)
13:40:36.926853 WARNING: height_correlation has 124 NaNs ( 0.01 % out of 2052053)
13:40:36.997115 INFO: Collecting fragment features
13:40:38.169649 INFO: Finished candidate scoring
13:40:39.704165 INFO: performing precursor FDR with 47 features
13:40:39.704308 INFO: Decoy channel: -1
13:40:39.704340 INFO: competitive: True
13:40:40.217665 INFO: Setting torch num_threads to 2 for FDR classification task
13:40:40.516001 WARNING: dropped 1099 target PSMs due to missing features
13:40:40.516173 WARNING: dropped 1241 decoy PSMs due to missing features
13:40:41.447239 INFO: Estimating optimal hyperparameters - samples: 1,639,770, batch_size: 4,096, learning_rate: 1.00e-03
13:40:41.451131 INFO: Using random state 318981 for train-test-split
13:41:27.260078 INFO: Test AUC: 0.564
13:41:27.260520 INFO: Train AUC: 0.573
13:41:27.260567 INFO: AUC difference: 1.59%
13:41:28.191323 INFO: Resetting torch num_threads to 80
13:41:28.227858 PROGRESS: === Extracted 2052053 precursors and 14388529 fragments ===
13:41:28.229146 INFO: === FDR correction performed with classifier version 13 ===
13:41:28.292184 PROGRESS: ============================= Precursor FDR =============================
13:41:28.292495 PROGRESS: Total precursors accumulated: 373,195
13:41:28.292575 PROGRESS: Target precursors: 218,499 (58.55%)
13:41:28.292637 PROGRESS: Decoy precursors: 154,696 (41.45%)
13:41:28.292691 PROGRESS: 
13:41:28.292743 PROGRESS: Precursor Summary:
13:41:28.296086 PROGRESS: Channel   0:	 0.050 FDR:   438; 0.010 FDR:   356; 0.001 FDR:   325
13:41:28.296204 PROGRESS: 
13:41:28.296271 PROGRESS: Protein Summary:
13:41:28.299502 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   268; 0.001 FDR:   245
13:41:28.299617 PROGRESS: =========================================================================
13:41:28.314131 INFO: Target number of precursors reached.
13:41:29.888436 INFO: fragments_df: keeping 5000 of 14388529 [sum(precursor_idx_mask)=9995 sum(mass_error_mask)=14388271 stop_rank=5000
13:41:31.104310 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:41:31.252790 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:41:31.389409 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:41:31.538877 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:41:32.255353 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:41:32.255820 INFO: Using score_cutoff 27.79900137233734 (fac=0.99, q=1)
13:41:32.256184 INFO: Updating optimization_manager: fwhm_rt             : 2.8567535877227783 -> 2.8256094455718994
13:41:32.256275 INFO: Updating optimization_manager: fwhm_mobility       : 0.007348875515162945 -> 0.006199275143444538
13:41:32.256339 INFO: Updating optimization_manager: score_cutoff        : 31.636692220687866 -> 27.79900137233734
13:41:32.256408 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:41:32.356245 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:41:32.884198 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:41:32.986306 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:41:34.007055 INFO: === checking if optimization conditions were reached ===
13:41:34.007640 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
13:41:34.009855 INFO: Updating optimization_manager: rt_error            : 1199.9776575 -> 930.0969959695981
13:41:34.009998 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 930.0970.
13:41:34.010078 INFO: ==============================================
13:41:34.010160 INFO: Starting optimization step 1.
13:41:34.010235 PROGRESS: === Extracting elution groups 0 to 409400 ===
13:41:34.010325 INFO: Using python extraction backend
13:41:34.010474 PROGRESS: Extracting batch of 816307 precursors
13:41:34.010572 INFO: === Search parameters used ===
13:41:34.010628 INFO: rt_error       : 930.0969959695981
13:41:34.010676 INFO: mobility_error : 0.1
13:41:34.010723 INFO: num_candidates : 3
13:41:34.010769 INFO: ms1_error      : 15.0
13:41:34.010814 INFO: ms2_error      : 15.0
13:41:34.010858 INFO: fwhm_rt        : 2.8256094455718994
13:41:34.010905 INFO: quant_window   : 3
13:41:34.010949 INFO: ==============================================
13:41:34.213841 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
13:41:34.214001 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
13:41:34.214066 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
13:41:34.214091 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.36
13:41:34.214914 INFO: Starting candidate selection
14:05:56.324106 INFO: Starting candidate scoring
14:06:20.952741 INFO: Finished candidate processing
14:06:20.953103 INFO: Collecting candidate features
14:06:24.682822 WARNING: intensity_correlation has 2447 NaNs ( 0.12 % out of 2047597)
14:06:24.684833 WARNING: height_correlation has 151 NaNs ( 0.01 % out of 2047597)
14:06:24.753259 INFO: Collecting fragment features
14:06:25.835693 INFO: Finished candidate scoring
14:06:27.113702 INFO: performing precursor FDR with 47 features
14:06:27.113833 INFO: Decoy channel: -1
14:06:27.113871 INFO: competitive: True
14:06:27.573401 INFO: Setting torch num_threads to 2 for FDR classification task
14:06:27.873004 WARNING: dropped 1211 target PSMs due to missing features
14:06:27.873176 WARNING: dropped 1332 decoy PSMs due to missing features
14:06:28.571234 INFO: Estimating optimal hyperparameters - samples: 1,636,043, batch_size: 4,096, learning_rate: 1.00e-03
14:06:28.578338 INFO: Using random state 318981 for train-test-split
14:07:11.550258 INFO: Test AUC: 0.560
14:07:11.550565 INFO: Train AUC: 0.572
14:07:11.550605 INFO: AUC difference: 2.08%
14:07:12.462562 INFO: Resetting torch num_threads to 80
14:07:12.498378 PROGRESS: === Extracted 2047597 precursors and 14149363 fragments ===
14:07:12.499743 INFO: === FDR correction performed with classifier version 13 ===
14:07:12.562590 PROGRESS: ============================= Precursor FDR =============================
14:07:12.562895 PROGRESS: Total precursors accumulated: 374,099
14:07:12.562967 PROGRESS: Target precursors: 217,730 (58.20%)
14:07:12.563025 PROGRESS: Decoy precursors: 156,369 (41.80%)
14:07:12.563076 PROGRESS: 
14:07:12.563127 PROGRESS: Precursor Summary:
14:07:12.566504 PROGRESS: Channel   0:	 0.050 FDR:   491; 0.010 FDR:   287; 0.001 FDR:   144
14:07:12.566618 PROGRESS: 
14:07:12.566682 PROGRESS: Protein Summary:
14:07:12.569743 PROGRESS: Channel   0:	 0.050 FDR:   376; 0.010 FDR:   206; 0.001 FDR:   100
14:07:12.569844 PROGRESS: =========================================================================
14:07:12.580833 INFO: Target number of precursors reached.
14:07:14.080446 INFO: fragments_df: keeping 5000 of 14149363 [sum(precursor_idx_mask)=7940 sum(mass_error_mask)=14149091 stop_rank=5000
14:07:15.317755 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
14:07:15.460957 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
14:07:15.599624 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
14:07:15.704418 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
14:07:16.354476 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
14:07:16.354920 INFO: Using score_cutoff 32.18756209030151 (fac=0.99, q=1)
14:07:16.355285 INFO: Updating optimization_manager: fwhm_rt             : 2.8256094455718994 -> 2.9192686080932617
14:07:16.355372 INFO: Updating optimization_manager: fwhm_mobility       : 0.006199275143444538 -> 0.007038189098238945
14:07:16.355433 INFO: Updating optimization_manager: score_cutoff        : 27.79900137233734 -> 32.18756209030151
14:07:16.355497 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:07:16.464101 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:07:16.993751 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:07:17.106599 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:07:18.190186 INFO: === checking if optimization conditions were reached ===
14:07:18.190473 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
14:07:18.192701 INFO: Updating optimization_manager: rt_error            : 930.0969959695981 -> 477.47704185340797
14:07:18.192842 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 477.4770.
14:07:18.192920 INFO: ==============================================
14:07:18.193005 INFO: Starting optimization step 2.
14:07:18.193074 PROGRESS: === Extracting elution groups 0 to 409400 ===
14:07:18.193164 INFO: Using python extraction backend
14:07:18.193336 PROGRESS: Extracting batch of 816307 precursors
14:07:18.193421 INFO: === Search parameters used ===
14:07:18.193478 INFO: rt_error       : 477.47704185340797
14:07:18.193533 INFO: mobility_error : 0.1
14:07:18.193594 INFO: num_candidates : 3
14:07:18.193642 INFO: ms1_error      : 15.0
14:07:18.193687 INFO: ms2_error      : 15.0
14:07:18.193732 INFO: fwhm_rt        : 2.9192686080932617
14:07:18.193775 INFO: quant_window   : 3
14:07:18.193820 INFO: ==============================================
14:07:18.389577 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
14:07:18.389720 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
14:07:18.389779 INFO: FWHM in RT is 2.92 seconds, sigma is 0.49
14:07:18.389802 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.81
14:07:18.390588 INFO: Starting candidate selection
14:21:37.162246 INFO: Starting candidate scoring
14:22:01.480039 INFO: Finished candidate processing
14:22:01.480542 INFO: Collecting candidate features
14:22:05.434156 WARNING: intensity_correlation has 3762 NaNs ( 0.19 % out of 1972150)
14:22:05.436190 WARNING: height_correlation has 304 NaNs ( 0.02 % out of 1972150)
14:22:05.502055 INFO: Collecting fragment features
14:22:06.655710 INFO: Finished candidate scoring
14:22:07.869301 INFO: performing precursor FDR with 47 features
14:22:07.869459 INFO: Decoy channel: -1
14:22:07.869491 INFO: competitive: True
14:22:08.405463 INFO: Setting torch num_threads to 2 for FDR classification task
14:22:08.749820 WARNING: dropped 1905 target PSMs due to missing features
14:22:08.749999 WARNING: dropped 2024 decoy PSMs due to missing features
14:22:09.542503 INFO: Estimating optimal hyperparameters - samples: 1,574,576, batch_size: 4,096, learning_rate: 1.00e-03
14:22:09.547072 INFO: Using random state 318981 for train-test-split
14:22:46.984979 INFO: Test AUC: 0.556
14:22:46.985244 INFO: Train AUC: 0.567
14:22:46.985283 INFO: AUC difference: 2.05%
14:22:47.893031 INFO: Resetting torch num_threads to 80
14:22:47.943857 PROGRESS: === Extracted 1972150 precursors and 12727192 fragments ===
14:22:47.944988 INFO: === FDR correction performed with classifier version 13 ===
14:22:48.021370 PROGRESS: ============================= Precursor FDR =============================
14:22:48.021674 PROGRESS: Total precursors accumulated: 369,688
14:22:48.021753 PROGRESS: Target precursors: 213,237 (57.68%)
14:22:48.021813 PROGRESS: Decoy precursors: 156,451 (42.32%)
14:22:48.021878 PROGRESS: 
14:22:48.021935 PROGRESS: Precursor Summary:
14:22:48.025550 PROGRESS: Channel   0:	 0.050 FDR:   449; 0.010 FDR:   367; 0.001 FDR:   350
14:22:48.025694 PROGRESS: 
14:22:48.025762 PROGRESS: Protein Summary:
14:22:48.029081 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   271; 0.001 FDR:   256
14:22:48.029198 PROGRESS: =========================================================================
14:22:48.047742 INFO: Target number of precursors reached.
14:22:49.611681 INFO: fragments_df: keeping 5000 of 12727192 [sum(precursor_idx_mask)=10230 sum(mass_error_mask)=12726921 stop_rank=5000
14:22:50.864357 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
14:22:51.006995 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
14:22:51.150205 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
14:22:51.297347 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
14:22:52.007069 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
14:22:52.007535 INFO: Using score_cutoff 31.481700028610227 (fac=0.99, q=1)
14:22:52.007898 INFO: Updating optimization_manager: fwhm_rt             : 2.9192686080932617 -> 2.8844618797302246
14:22:52.007980 INFO: Updating optimization_manager: fwhm_mobility       : 0.007038189098238945 -> 0.006455347407609224
14:22:52.008037 INFO: Updating optimization_manager: score_cutoff        : 32.18756209030151 -> 31.481700028610227
14:22:52.008101 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:22:52.112962 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:22:52.639823 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:22:52.741212 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:22:53.758548 INFO: === checking if optimization conditions were reached ===
14:22:53.758855 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
14:22:53.761343 INFO: Updating optimization_manager: rt_error            : 477.47704185340797 -> 344.92772497598946
14:22:53.761483 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 344.9277.
14:22:53.761561 INFO: ==============================================
14:22:53.761658 INFO: Starting optimization step 3.
14:22:53.761727 PROGRESS: === Extracting elution groups 0 to 409400 ===
14:22:53.761810 INFO: Using python extraction backend
14:22:53.761978 PROGRESS: Extracting batch of 816307 precursors
14:22:53.762069 INFO: === Search parameters used ===
14:22:53.762131 INFO: rt_error       : 344.92772497598946
14:22:53.762182 INFO: mobility_error : 0.1
14:22:53.762230 INFO: num_candidates : 3
14:22:53.762278 INFO: ms1_error      : 15.0
14:22:53.762327 INFO: ms2_error      : 15.0
14:22:53.762373 INFO: fwhm_rt        : 2.8844618797302246
14:22:53.762418 INFO: quant_window   : 3
14:22:53.762462 INFO: ==============================================
14:22:54.011642 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
14:22:54.011787 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
14:22:54.011848 INFO: FWHM in RT is 2.88 seconds, sigma is 0.48
14:22:54.011874 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.50
14:22:54.012665 INFO: Starting candidate selection
14:32:53.466831 INFO: Starting candidate scoring
14:33:16.226325 INFO: Finished candidate processing
14:33:16.226525 INFO: Collecting candidate features
14:33:19.914397 WARNING: intensity_correlation has 4320 NaNs ( 0.22 % out of 1936753)
14:33:19.916487 WARNING: height_correlation has 397 NaNs ( 0.02 % out of 1936753)
14:33:19.981489 INFO: Collecting fragment features
14:33:21.043611 INFO: Finished candidate scoring
14:33:22.543953 INFO: performing precursor FDR with 47 features
14:33:22.544117 INFO: Decoy channel: -1
14:33:22.544149 INFO: competitive: True
14:33:23.051736 INFO: Setting torch num_threads to 2 for FDR classification task
14:33:23.364699 WARNING: dropped 2218 target PSMs due to missing features
14:33:23.364866 WARNING: dropped 2306 decoy PSMs due to missing features
14:33:24.052165 INFO: Estimating optimal hyperparameters - samples: 1,545,783, batch_size: 4,096, learning_rate: 1.00e-03
14:33:24.056324 INFO: Using random state 318981 for train-test-split
14:34:07.914606 INFO: Test AUC: 0.552
14:34:07.915066 INFO: Train AUC: 0.565
14:34:07.915109 INFO: AUC difference: 2.43%
14:34:08.823518 INFO: Resetting torch num_threads to 80
14:34:08.875820 PROGRESS: === Extracted 1936753 precursors and 12067010 fragments ===
14:34:08.877169 INFO: === FDR correction performed with classifier version 13 ===
14:34:08.944404 PROGRESS: ============================= Precursor FDR =============================
14:34:08.944725 PROGRESS: Total precursors accumulated: 368,150
14:34:08.944813 PROGRESS: Target precursors: 211,205 (57.37%)
14:34:08.944876 PROGRESS: Decoy precursors: 156,945 (42.63%)
14:34:08.944953 PROGRESS: 
14:34:08.945007 PROGRESS: Precursor Summary:
14:34:08.948827 PROGRESS: Channel   0:	 0.050 FDR:   565; 0.010 FDR:   426; 0.001 FDR:   324
14:34:08.948972 PROGRESS: 
14:34:08.949039 PROGRESS: Protein Summary:
14:34:08.952235 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   311; 0.001 FDR:   233
14:34:08.952338 PROGRESS: =========================================================================
14:34:08.963827 INFO: Target number of precursors reached.
14:34:10.259204 INFO: fragments_df: keeping 5000 of 12067010 [sum(precursor_idx_mask)=11532 sum(mass_error_mask)=12066613 stop_rank=5000
14:34:11.049849 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
14:34:11.206146 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
14:34:11.354914 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
14:34:11.509660 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
14:34:12.224232 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
14:34:12.224749 INFO: Using score_cutoff 27.80780809879303 (fac=0.99, q=1)
14:34:12.225147 INFO: Updating optimization_manager: fwhm_rt             : 2.8844618797302246 -> 2.753053665161133
14:34:12.225237 INFO: Updating optimization_manager: fwhm_mobility       : 0.006455347407609224 -> 0.005941587500274181
14:34:12.225299 INFO: Updating optimization_manager: score_cutoff        : 31.481700028610227 -> 27.80780809879303
14:34:12.225365 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:34:12.276859 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:34:12.537701 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:34:12.595405 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:34:13.107823 INFO: === checking if optimization conditions were reached ===
14:34:13.108129 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
14:34:13.110738 INFO: Updating optimization_manager: rt_error            : 344.92772497598946 -> 268.36033587801575
14:34:13.110887 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 268.3603.
14:34:13.110964 INFO: ==============================================
14:34:13.111046 INFO: Starting optimization step 4.
14:34:13.111116 PROGRESS: === Extracting elution groups 0 to 204600 ===
14:34:13.111197 INFO: Using python extraction backend
14:34:13.111329 PROGRESS: Extracting batch of 407917 precursors
14:34:13.111408 INFO: === Search parameters used ===
14:34:13.111465 INFO: rt_error       : 268.36033587801575
14:34:13.111513 INFO: mobility_error : 0.1
14:34:13.111561 INFO: num_candidates : 3
14:34:13.111607 INFO: ms1_error      : 15.0
14:34:13.111653 INFO: ms2_error      : 15.0
14:34:13.111697 INFO: fwhm_rt        : 2.753053665161133
14:34:13.111741 INFO: quant_window   : 3
14:34:13.111784 INFO: ==============================================
14:34:13.218599 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
14:34:13.218753 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
14:34:13.218814 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
14:34:13.218838 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.22
14:34:13.219611 INFO: Starting candidate selection
14:38:02.960146 INFO: Starting candidate scoring
14:38:14.426853 INFO: Finished candidate processing
14:38:14.427217 INFO: Collecting candidate features
14:38:16.312365 WARNING: intensity_correlation has 2458 NaNs ( 0.26 % out of 951816)
14:38:16.313582 WARNING: height_correlation has 234 NaNs ( 0.02 % out of 951816)
14:38:16.350665 INFO: Collecting fragment features
14:38:16.865075 INFO: Finished candidate scoring
14:38:17.619349 INFO: performing precursor FDR with 47 features
14:38:17.619497 INFO: Decoy channel: -1
14:38:17.619527 INFO: competitive: True
14:38:17.919554 INFO: Setting torch num_threads to 2 for FDR classification task
14:38:18.076653 WARNING: dropped 1258 target PSMs due to missing features
14:38:18.076833 WARNING: dropped 1302 decoy PSMs due to missing features
14:38:18.639297 INFO: Estimating optimal hyperparameters - samples: 759,404, batch_size: 3,110, learning_rate: 8.71e-04
14:38:18.641242 INFO: Using random state 318981 for train-test-split
14:38:41.561050 INFO: Test AUC: 0.553
14:38:41.561524 INFO: Train AUC: 0.569
14:38:41.561562 INFO: AUC difference: 2.86%
14:38:42.122913 INFO: Resetting torch num_threads to 80
14:38:42.164779 PROGRESS: === Extracted 951816 precursors and 5769441 fragments ===
14:38:42.165839 INFO: === FDR correction performed with classifier version 13 ===
14:38:42.199528 PROGRESS: ============================= Precursor FDR =============================
14:38:42.199843 PROGRESS: Total precursors accumulated: 183,496
14:38:42.199927 PROGRESS: Target precursors: 105,920 (57.72%)
14:38:42.199987 PROGRESS: Decoy precursors: 77,576 (42.28%)
14:38:42.200041 PROGRESS: 
14:38:42.200091 PROGRESS: Precursor Summary:
14:38:42.202661 PROGRESS: Channel   0:	 0.050 FDR:   281; 0.010 FDR:   186; 0.001 FDR:   175
14:38:42.202793 PROGRESS: 
14:38:42.202866 PROGRESS: Protein Summary:
14:38:42.205242 PROGRESS: Channel   0:	 0.050 FDR:   233; 0.010 FDR:   151; 0.001 FDR:   142
14:38:42.205357 PROGRESS: =========================================================================
14:38:42.236909 INFO: Target number of precursors not reached yet.
14:38:42.981593 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:38:43.035338 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:38:43.295834 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:38:43.354175 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:38:43.875875 INFO: === skipping optimization until target number of precursors are found ===
14:38:43.876220 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
14:38:43.876367 INFO: Starting optimization step 5.
14:38:43.876464 PROGRESS: === Extracting elution groups 204600 to 409400 ===
14:38:43.876838 INFO: Using python extraction backend
14:38:43.877021 PROGRESS: Extracting batch of 408390 precursors
14:38:43.877126 INFO: === Search parameters used ===
14:38:43.877190 INFO: rt_error       : 268.36033587801575
14:38:43.877243 INFO: mobility_error : 0.1
14:38:43.877294 INFO: num_candidates : 3
14:38:43.877342 INFO: ms1_error      : 15.0
14:38:43.877391 INFO: ms2_error      : 15.0
14:38:43.877438 INFO: fwhm_rt        : 2.753053665161133
14:38:43.877485 INFO: quant_window   : 3
14:38:43.877530 INFO: ==============================================
14:38:43.984630 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
14:38:43.984784 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
14:38:43.984869 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
14:38:43.984900 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.22
14:38:43.985817 INFO: Starting candidate selection
14:42:33.771688 INFO: Starting candidate scoring
14:42:45.028457 INFO: Finished candidate processing
14:42:45.028827 INFO: Collecting candidate features
14:42:46.645885 WARNING: intensity_correlation has 2498 NaNs ( 0.26 % out of 950866)
14:42:46.647010 WARNING: height_correlation has 247 NaNs ( 0.03 % out of 950866)
14:42:46.680736 INFO: Collecting fragment features
14:42:47.126653 INFO: Finished candidate scoring
14:42:48.119350 INFO: performing precursor FDR with 47 features
14:42:48.119992 INFO: Decoy channel: -1
14:42:48.120036 INFO: competitive: True
14:42:48.920139 INFO: Setting torch num_threads to 2 for FDR classification task
14:42:49.275061 WARNING: dropped 2577 target PSMs due to missing features
14:42:49.275227 WARNING: dropped 2600 decoy PSMs due to missing features
14:42:49.941848 INFO: Estimating optimal hyperparameters - samples: 1,518,004, batch_size: 4,096, learning_rate: 1.00e-03
14:42:49.945434 INFO: Using random state 318981 for train-test-split
14:43:28.846189 INFO: Test AUC: 0.552
14:43:28.846435 INFO: Train AUC: 0.562
14:43:28.846476 INFO: AUC difference: 1.75%
14:43:29.708183 INFO: Resetting torch num_threads to 80
14:43:29.968526 PROGRESS: === Extracted 1902682 precursors and 11530426 fragments ===
14:43:29.969766 INFO: === FDR correction performed with classifier version 13 ===
14:43:30.030381 PROGRESS: ============================= Precursor FDR =============================
14:43:30.030730 PROGRESS: Total precursors accumulated: 366,843
14:43:30.030825 PROGRESS: Target precursors: 209,483 (57.10%)
14:43:30.030885 PROGRESS: Decoy precursors: 157,360 (42.90%)
14:43:30.030938 PROGRESS: 
14:43:30.030990 PROGRESS: Precursor Summary:
14:43:30.034451 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   415; 0.001 FDR:   282
14:43:30.034561 PROGRESS: 
14:43:30.034651 PROGRESS: Protein Summary:
14:43:30.037761 PROGRESS: Channel   0:	 0.050 FDR:   386; 0.010 FDR:   309; 0.001 FDR:   206
14:43:30.037860 PROGRESS: =========================================================================
14:43:30.043516 INFO: Target number of precursors reached.
14:43:31.309668 INFO: fragments_df: keeping 5000 of 11530426 [sum(precursor_idx_mask)=11342 sum(mass_error_mask)=11530060 stop_rank=5000
14:43:32.028840 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
14:43:32.177042 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
14:43:32.327481 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
14:43:32.478809 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
14:43:33.193393 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
14:43:33.193903 INFO: Using score_cutoff 22.768825606155396 (fac=0.99, q=1)
14:43:33.194282 INFO: Updating optimization_manager: fwhm_rt             : 2.753053665161133 -> 2.7343080043792725
14:43:33.194371 INFO: Updating optimization_manager: fwhm_mobility       : 0.005941587500274181 -> 0.0058025759644806385
14:43:33.194435 INFO: Updating optimization_manager: score_cutoff        : 27.80780809879303 -> 22.768825606155396
14:43:33.194500 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:43:33.245394 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:43:33.507674 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:43:33.564419 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:43:34.109119 INFO: === checking if optimization conditions were reached ===
14:43:34.109431 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
14:43:34.111981 INFO: Updating optimization_manager: rt_error            : 268.36033587801575 -> 213.21223561543724
14:43:34.112123 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 213.2122.
14:43:34.112201 INFO: ==============================================
14:43:34.112288 INFO: Starting optimization step 6.
14:43:34.112357 PROGRESS: === Extracting elution groups 0 to 204600 ===
14:43:34.112445 INFO: Using python extraction backend
14:43:34.112641 PROGRESS: Extracting batch of 407917 precursors
14:43:34.112726 INFO: === Search parameters used ===
14:43:34.112800 INFO: rt_error       : 213.21223561543724
14:43:34.112854 INFO: mobility_error : 0.1
14:43:34.112905 INFO: num_candidates : 3
14:43:34.112952 INFO: ms1_error      : 15.0
14:43:34.112999 INFO: ms2_error      : 15.0
14:43:34.113046 INFO: fwhm_rt        : 2.7343080043792725
14:43:34.113093 INFO: quant_window   : 3
14:43:34.113139 INFO: ==============================================
14:43:34.218513 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
14:43:34.218656 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
14:43:34.218717 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
14:43:34.218743 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.14
14:43:34.219551 INFO: Starting candidate selection
14:46:36.702932 INFO: Starting candidate scoring
14:46:48.132475 INFO: Finished candidate processing
14:46:48.132897 INFO: Collecting candidate features
14:46:49.732847 WARNING: intensity_correlation has 2755 NaNs ( 0.30 % out of 929099)
14:46:49.733955 WARNING: height_correlation has 280 NaNs ( 0.03 % out of 929099)
14:46:49.767580 INFO: Collecting fragment features
14:46:50.225849 INFO: Finished candidate scoring
14:46:50.822849 INFO: performing precursor FDR with 47 features
14:46:50.822990 INFO: Decoy channel: -1
14:46:50.823017 INFO: competitive: True
14:46:51.048138 INFO: Setting torch num_threads to 2 for FDR classification task
14:46:51.187264 WARNING: dropped 1464 target PSMs due to missing features
14:46:51.187423 WARNING: dropped 1419 decoy PSMs due to missing features
14:46:51.509484 INFO: Estimating optimal hyperparameters - samples: 740,972, batch_size: 3,035, learning_rate: 8.61e-04
14:46:51.511126 INFO: Using random state 318981 for train-test-split
14:47:12.484976 INFO: Test AUC: 0.550
14:47:12.485204 INFO: Train AUC: 0.564
14:47:12.485240 INFO: AUC difference: 2.50%
14:47:13.023375 INFO: Resetting torch num_threads to 80
14:47:13.088467 PROGRESS: === Extracted 929099 precursors and 5479719 fragments ===
14:47:13.089460 INFO: === FDR correction performed with classifier version 13 ===
14:47:13.122242 PROGRESS: ============================= Precursor FDR =============================
14:47:13.122553 PROGRESS: Total precursors accumulated: 181,434
14:47:13.122626 PROGRESS: Target precursors: 103,526 (57.06%)
14:47:13.122684 PROGRESS: Decoy precursors: 77,908 (42.94%)
14:47:13.122736 PROGRESS: 
14:47:13.122785 PROGRESS: Precursor Summary:
14:47:13.124994 PROGRESS: Channel   0:	 0.050 FDR:   251; 0.010 FDR:     0; 0.001 FDR:     0
14:47:13.125104 PROGRESS: 
14:47:13.125166 PROGRESS: Protein Summary:
14:47:13.127189 PROGRESS: Channel   0:	 0.050 FDR:   203; 0.010 FDR:     0; 0.001 FDR:     0
14:47:13.127297 PROGRESS: =========================================================================
14:47:13.150892 INFO: Target number of precursors not reached yet.
14:47:13.788674 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:47:13.838166 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:47:14.099232 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:47:14.154140 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:47:14.652598 INFO: === skipping optimization until target number of precursors are found ===
14:47:14.652913 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
14:47:14.653051 INFO: Starting optimization step 7.
14:47:14.653153 PROGRESS: === Extracting elution groups 204600 to 409400 ===
14:47:14.653238 INFO: Using python extraction backend
14:47:14.653386 PROGRESS: Extracting batch of 408390 precursors
14:47:14.653487 INFO: === Search parameters used ===
14:47:14.653552 INFO: rt_error       : 213.21223561543724
14:47:14.653606 INFO: mobility_error : 0.1
14:47:14.653661 INFO: num_candidates : 3
14:47:14.653710 INFO: ms1_error      : 15.0
14:47:14.653758 INFO: ms2_error      : 15.0
14:47:14.653805 INFO: fwhm_rt        : 2.7343080043792725
14:47:14.653851 INFO: quant_window   : 3
14:47:14.653909 INFO: ==============================================
14:47:14.803566 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
14:47:14.803713 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
14:47:14.803781 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
14:47:14.803808 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.14
14:47:14.804745 INFO: Starting candidate selection
14:50:14.717915 INFO: Starting candidate scoring
14:50:27.096694 INFO: Finished candidate processing
14:50:27.097009 INFO: Collecting candidate features
14:50:28.866486 WARNING: intensity_correlation has 2793 NaNs ( 0.30 % out of 927829)
14:50:28.867639 WARNING: height_correlation has 272 NaNs ( 0.03 % out of 927829)
14:50:28.900549 INFO: Collecting fragment features
14:50:29.393424 INFO: Finished candidate scoring
14:50:30.588481 INFO: performing precursor FDR with 47 features
14:50:30.588658 INFO: Decoy channel: -1
14:50:30.588691 INFO: competitive: True
14:50:31.259268 INFO: Setting torch num_threads to 2 for FDR classification task
14:50:31.570082 WARNING: dropped 2940 target PSMs due to missing features
14:50:31.570261 WARNING: dropped 2863 decoy PSMs due to missing features
14:50:32.225929 INFO: Estimating optimal hyperparameters - samples: 1,480,900, batch_size: 4,096, learning_rate: 1.00e-03
14:50:32.229136 INFO: Using random state 318981 for train-test-split
14:51:14.246778 INFO: Test AUC: 0.552
14:51:14.246993 INFO: Train AUC: 0.563
14:51:14.247031 INFO: AUC difference: 1.96%
14:51:15.124053 INFO: Resetting torch num_threads to 80
14:51:15.619190 PROGRESS: === Extracted 1856928 precursors and 10949156 fragments ===
14:51:15.620378 INFO: === FDR correction performed with classifier version 13 ===
14:51:15.691133 PROGRESS: ============================= Precursor FDR =============================
14:51:15.691454 PROGRESS: Total precursors accumulated: 362,688
14:51:15.691546 PROGRESS: Target precursors: 205,822 (56.75%)
14:51:15.691610 PROGRESS: Decoy precursors: 156,866 (43.25%)
14:51:15.691665 PROGRESS: 
14:51:15.691715 PROGRESS: Precursor Summary:
14:51:15.696102 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   352; 0.001 FDR:   301
14:51:15.696259 PROGRESS: 
14:51:15.696335 PROGRESS: Protein Summary:
14:51:15.699575 PROGRESS: Channel   0:	 0.050 FDR:   399; 0.010 FDR:   256; 0.001 FDR:   217
14:51:15.699726 PROGRESS: =========================================================================
14:51:15.707366 INFO: Target number of precursors reached.
14:51:16.954609 INFO: fragments_df: keeping 5000 of 10949156 [sum(precursor_idx_mask)=9874 sum(mass_error_mask)=10948836 stop_rank=5000
14:51:18.211995 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
14:51:18.331505 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
14:51:18.455485 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
14:51:18.584235 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
14:51:19.235492 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
14:51:19.235969 INFO: Using score_cutoff 32.073140736007694 (fac=0.99, q=1)
14:51:19.236328 INFO: Updating optimization_manager: fwhm_rt             : 2.7343080043792725 -> 2.7834627628326416
14:51:19.236418 INFO: Updating optimization_manager: fwhm_mobility       : 0.0058025759644806385 -> 0.006225107703357935
14:51:19.236483 INFO: Updating optimization_manager: score_cutoff        : 22.768825606155396 -> 32.073140736007694
14:51:19.236561 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:51:19.338222 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:51:19.858405 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:51:19.965765 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:51:21.073668 INFO: === checking if optimization conditions were reached ===
14:51:21.074033 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
14:51:21.076606 INFO: Updating optimization_manager: rt_error            : 213.21223561543724 -> 162.496001721281
14:51:21.076752 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 162.4960.
14:51:21.076826 INFO: ==============================================
14:51:21.076917 INFO: Starting optimization step 8.
14:51:21.076988 PROGRESS: === Extracting elution groups 0 to 409400 ===
14:51:21.077091 INFO: Using python extraction backend
14:51:21.077262 PROGRESS: Extracting batch of 816307 precursors
14:51:21.077340 INFO: === Search parameters used ===
14:51:21.077394 INFO: rt_error       : 162.496001721281
14:51:21.077442 INFO: mobility_error : 0.1
14:51:21.077489 INFO: num_candidates : 3
14:51:21.077534 INFO: ms1_error      : 15.0
14:51:21.077580 INFO: ms2_error      : 15.0
14:51:21.077624 INFO: fwhm_rt        : 2.7834627628326416
14:51:21.077669 INFO: quant_window   : 3
14:51:21.077715 INFO: ==============================================
14:51:21.280649 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
14:51:21.280804 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
14:51:21.280897 INFO: FWHM in RT is 2.78 seconds, sigma is 0.46
14:51:21.280925 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.37
14:51:21.281796 INFO: Starting candidate selection
14:55:44.222957 INFO: Starting candidate scoring
14:56:06.735476 INFO: Finished candidate processing
14:56:06.735831 INFO: Collecting candidate features
14:56:10.119419 WARNING: intensity_correlation has 6493 NaNs ( 0.35 % out of 1829219)
14:56:10.121192 WARNING: height_correlation has 695 NaNs ( 0.04 % out of 1829219)
14:56:10.182346 INFO: Collecting fragment features
14:56:11.182840 INFO: Finished candidate scoring
14:56:12.510497 INFO: performing precursor FDR with 47 features
14:56:12.510644 INFO: Decoy channel: -1
14:56:12.510673 INFO: competitive: True
14:56:12.943430 INFO: Setting torch num_threads to 2 for FDR classification task
14:56:13.213995 WARNING: dropped 3375 target PSMs due to missing features
14:56:13.214186 WARNING: dropped 3445 decoy PSMs due to missing features
14:56:13.844939 INFO: Estimating optimal hyperparameters - samples: 1,457,919, batch_size: 4,096, learning_rate: 1.00e-03
14:56:13.848510 INFO: Using random state 318981 for train-test-split
14:56:54.073008 INFO: Test AUC: 0.549
14:56:54.073443 INFO: Train AUC: 0.561
14:56:54.073490 INFO: AUC difference: 2.25%
14:56:56.256808 INFO: Resetting torch num_threads to 80
14:56:56.289412 PROGRESS: === Extracted 1829219 precursors and 10464165 fragments ===
14:56:56.290510 INFO: === FDR correction performed with classifier version 13 ===
14:56:56.351815 PROGRESS: ============================= Precursor FDR =============================
14:56:56.352138 PROGRESS: Total precursors accumulated: 362,285
14:56:56.352210 PROGRESS: Target precursors: 205,296 (56.67%)
14:56:56.352285 PROGRESS: Decoy precursors: 156,989 (43.33%)
14:56:56.352341 PROGRESS: 
14:56:56.352392 PROGRESS: Precursor Summary:
14:56:56.355857 PROGRESS: Channel   0:	 0.050 FDR:   625; 0.010 FDR:   457; 0.001 FDR:   337
14:56:56.355981 PROGRESS: 
14:56:56.356044 PROGRESS: Protein Summary:
14:56:56.359197 PROGRESS: Channel   0:	 0.050 FDR:   467; 0.010 FDR:   334; 0.001 FDR:   241
14:56:56.359306 PROGRESS: =========================================================================
14:56:56.369002 INFO: Target number of precursors reached.
14:56:57.468358 INFO: fragments_df: keeping 5000 of 10464165 [sum(precursor_idx_mask)=12311 sum(mass_error_mask)=10463936 stop_rank=5000
14:56:58.091883 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
14:56:58.219439 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
14:56:58.349105 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
14:56:58.481890 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
14:56:59.131508 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
14:56:59.131962 INFO: Using score_cutoff 25.315270346832275 (fac=0.99, q=1)
14:56:59.132288 INFO: Updating optimization_manager: fwhm_rt             : 2.7834627628326416 -> 2.7409701347351074
14:56:59.132376 INFO: Updating optimization_manager: fwhm_mobility       : 0.006225107703357935 -> 0.00559806264936924
14:56:59.132441 INFO: Updating optimization_manager: score_cutoff        : 32.073140736007694 -> 25.315270346832275
14:56:59.132509 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:56:59.183063 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:56:59.446846 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:56:59.504972 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:56:59.987524 INFO: === checking if optimization conditions were reached ===
14:56:59.987805 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
14:56:59.990175 INFO: Updating optimization_manager: rt_error            : 162.496001721281 -> 132.42557153041997
14:56:59.990317 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 132.4256.
14:56:59.990395 INFO: ==============================================
14:56:59.990485 INFO: Starting optimization step 9.
14:56:59.990550 PROGRESS: === Extracting elution groups 0 to 204600 ===
14:56:59.990617 INFO: Using python extraction backend
14:56:59.990726 PROGRESS: Extracting batch of 407917 precursors
14:56:59.990795 INFO: === Search parameters used ===
14:56:59.990848 INFO: rt_error       : 132.42557153041997
14:56:59.990894 INFO: mobility_error : 0.1
14:56:59.990939 INFO: num_candidates : 3
14:56:59.990983 INFO: ms1_error      : 15.0
14:56:59.991026 INFO: ms2_error      : 15.0
14:56:59.991070 INFO: fwhm_rt        : 2.7409701347351074
14:56:59.991120 INFO: quant_window   : 3
14:56:59.991168 INFO: ==============================================
14:57:00.097417 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
14:57:00.097559 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
14:57:00.097609 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
14:57:00.097633 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.03
14:57:00.098430 INFO: Starting candidate selection
14:58:54.943666 INFO: Starting candidate scoring
14:59:06.049752 INFO: Finished candidate processing
14:59:06.050059 INFO: Collecting candidate features
14:59:07.633457 WARNING: intensity_correlation has 3447 NaNs ( 0.38 % out of 908849)
14:59:07.634481 WARNING: height_correlation has 358 NaNs ( 0.04 % out of 908849)
14:59:07.666980 INFO: Collecting fragment features
14:59:08.134045 INFO: Finished candidate scoring
14:59:08.770424 INFO: performing precursor FDR with 47 features
14:59:08.770561 INFO: Decoy channel: -1
14:59:08.770590 INFO: competitive: True
14:59:09.003426 INFO: Setting torch num_threads to 2 for FDR classification task
14:59:09.146315 WARNING: dropped 1760 target PSMs due to missing features
14:59:09.146473 WARNING: dropped 1863 decoy PSMs due to missing features
14:59:09.461345 INFO: Estimating optimal hyperparameters - samples: 724,180, batch_size: 2,966, learning_rate: 8.51e-04
14:59:09.463045 INFO: Using random state 318981 for train-test-split
14:59:30.118621 INFO: Test AUC: 0.549
14:59:30.118759 INFO: Train AUC: 0.566
14:59:30.118795 INFO: AUC difference: 3.02%
14:59:30.659929 INFO: Resetting torch num_threads to 80
14:59:30.677681 PROGRESS: === Extracted 908849 precursors and 5133640 fragments ===
14:59:30.678541 INFO: === FDR correction performed with classifier version 13 ===
14:59:30.712036 PROGRESS: ============================= Precursor FDR =============================
14:59:30.712342 PROGRESS: Total precursors accumulated: 180,806
14:59:30.712415 PROGRESS: Target precursors: 103,194 (57.07%)
14:59:30.712476 PROGRESS: Decoy precursors: 77,612 (42.93%)
14:59:30.712530 PROGRESS: 
14:59:30.712582 PROGRESS: Precursor Summary:
14:59:30.714867 PROGRESS: Channel   0:	 0.050 FDR:   283; 0.010 FDR:   175; 0.001 FDR:   170
14:59:30.714974 PROGRESS: 
14:59:30.715039 PROGRESS: Protein Summary:
14:59:30.717147 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:   141; 0.001 FDR:   138
14:59:30.717252 PROGRESS: =========================================================================
14:59:30.729120 INFO: Target number of precursors not reached yet.
14:59:31.297608 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:59:31.347863 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:59:31.603760 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:59:31.656544 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:59:32.118697 INFO: === skipping optimization until target number of precursors are found ===
14:59:32.118971 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
14:59:32.119100 INFO: Starting optimization step 10.
14:59:32.119180 PROGRESS: === Extracting elution groups 204600 to 409400 ===
14:59:32.119255 INFO: Using python extraction backend
14:59:32.119373 PROGRESS: Extracting batch of 408390 precursors
14:59:32.119453 INFO: === Search parameters used ===
14:59:32.119509 INFO: rt_error       : 132.42557153041997
14:59:32.119563 INFO: mobility_error : 0.1
14:59:32.119630 INFO: num_candidates : 3
14:59:32.119680 INFO: ms1_error      : 15.0
14:59:32.119727 INFO: ms2_error      : 15.0
14:59:32.119773 INFO: fwhm_rt        : 2.7409701347351074
14:59:32.119819 INFO: quant_window   : 3
14:59:32.119864 INFO: ==============================================
14:59:32.225750 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
14:59:32.225911 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
14:59:32.225971 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
14:59:32.226003 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.03
14:59:32.226790 INFO: Starting candidate selection
15:01:23.500519 INFO: Starting candidate scoring
15:01:34.490815 INFO: Finished candidate processing
15:01:34.491074 INFO: Collecting candidate features
15:01:36.097678 WARNING: intensity_correlation has 3529 NaNs ( 0.39 % out of 908286)
15:01:36.098694 WARNING: height_correlation has 351 NaNs ( 0.04 % out of 908286)
15:01:36.130694 INFO: Collecting fragment features
15:01:36.593520 INFO: Finished candidate scoring
15:01:37.495110 INFO: performing precursor FDR with 47 features
15:01:37.495266 INFO: Decoy channel: -1
15:01:37.495296 INFO: competitive: True
15:01:38.132701 INFO: Setting torch num_threads to 2 for FDR classification task
15:01:38.432632 WARNING: dropped 3599 target PSMs due to missing features
15:01:38.432798 WARNING: dropped 3725 decoy PSMs due to missing features
15:01:39.040169 INFO: Estimating optimal hyperparameters - samples: 1,447,848, batch_size: 4,096, learning_rate: 1.00e-03
15:01:39.043861 INFO: Using random state 318981 for train-test-split
15:02:17.753765 INFO: Test AUC: 0.550
15:02:17.754018 INFO: Train AUC: 0.560
15:02:17.754059 INFO: AUC difference: 1.80%
15:02:18.576891 INFO: Resetting torch num_threads to 80
15:02:18.830804 PROGRESS: === Extracted 1817135 precursors and 10262881 fragments ===
15:02:18.831899 INFO: === FDR correction performed with classifier version 13 ===
15:02:18.894911 PROGRESS: ============================= Precursor FDR =============================
15:02:18.895229 PROGRESS: Total precursors accumulated: 361,300
15:02:18.895305 PROGRESS: Target precursors: 205,040 (56.75%)
15:02:18.895370 PROGRESS: Decoy precursors: 156,260 (43.25%)
15:02:18.895441 PROGRESS: 
15:02:18.895495 PROGRESS: Precursor Summary:
15:02:18.898937 PROGRESS: Channel   0:	 0.050 FDR:   616; 0.010 FDR:   503; 0.001 FDR:   361
15:02:18.899053 PROGRESS: 
15:02:18.899130 PROGRESS: Protein Summary:
15:02:18.902289 PROGRESS: Channel   0:	 0.050 FDR:   471; 0.010 FDR:   368; 0.001 FDR:   266
15:02:18.902399 PROGRESS: =========================================================================
15:02:18.907660 INFO: Target number of precursors reached.
15:02:20.044658 INFO: fragments_df: keeping 5000 of 10262881 [sum(precursor_idx_mask)=13526 sum(mass_error_mask)=10262669 stop_rank=5000
15:02:20.654176 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:02:20.793851 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:02:20.923958 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:02:21.057202 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:02:21.709173 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:02:21.709630 INFO: Using score_cutoff 25.561284727478025 (fac=0.99, q=1)
15:02:21.709999 INFO: Updating optimization_manager: fwhm_rt             : 2.7409701347351074 -> 2.682527780532837
15:02:21.710095 INFO: Updating optimization_manager: fwhm_mobility       : 0.00559806264936924 -> 0.005178255494683981
15:02:21.710159 INFO: Updating optimization_manager: score_cutoff        : 25.315270346832275 -> 25.561284727478025
15:02:21.710220 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:02:21.759172 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:02:22.015500 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:02:22.067069 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:02:22.570344 INFO: === checking if optimization conditions were reached ===
15:02:22.570636 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
15:02:22.573042 INFO: Updating optimization_manager: rt_error            : 132.42557153041997 -> 121.6966432451404
15:02:22.573181 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 121.6966.
15:02:22.573263 INFO: ==============================================
15:02:22.573347 INFO: Starting optimization step 11.
15:02:22.573421 PROGRESS: === Extracting elution groups 0 to 204600 ===
15:02:22.573499 INFO: Using python extraction backend
15:02:22.573617 PROGRESS: Extracting batch of 407917 precursors
15:02:22.573699 INFO: === Search parameters used ===
15:02:22.573764 INFO: rt_error       : 121.6966432451404
15:02:22.573819 INFO: mobility_error : 0.1
15:02:22.573881 INFO: num_candidates : 3
15:02:22.573940 INFO: ms1_error      : 15.0
15:02:22.573991 INFO: ms2_error      : 15.0
15:02:22.574042 INFO: fwhm_rt        : 2.682527780532837
15:02:22.574093 INFO: quant_window   : 3
15:02:22.574140 INFO: ==============================================
15:02:22.679510 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:02:22.679642 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:02:22.679688 INFO: FWHM in RT is 2.68 seconds, sigma is 0.45
15:02:22.679713 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.81
15:02:22.680407 INFO: Starting candidate selection
15:04:02.973873 INFO: Starting candidate scoring
15:04:14.198896 INFO: Finished candidate processing
15:04:14.199661 INFO: Collecting candidate features
15:04:15.788652 WARNING: intensity_correlation has 3681 NaNs ( 0.41 % out of 896044)
15:04:15.789687 WARNING: height_correlation has 394 NaNs ( 0.04 % out of 896044)
15:04:15.821301 INFO: Collecting fragment features
15:04:16.279191 INFO: Finished candidate scoring
15:04:16.983503 INFO: performing precursor FDR with 47 features
15:04:16.983723 INFO: Decoy channel: -1
15:04:16.983756 INFO: competitive: True
15:04:17.214835 INFO: Setting torch num_threads to 2 for FDR classification task
15:04:17.358204 WARNING: dropped 1912 target PSMs due to missing features
15:04:17.358373 WARNING: dropped 1951 decoy PSMs due to missing features
15:04:17.668529 INFO: Estimating optimal hyperparameters - samples: 713,744, batch_size: 2,923, learning_rate: 8.45e-04
15:04:17.670329 INFO: Using random state 318981 for train-test-split
15:04:37.175243 INFO: Test AUC: 0.546
15:04:37.175560 INFO: Train AUC: 0.562
15:04:37.175598 INFO: AUC difference: 2.96%
15:04:37.706203 INFO: Resetting torch num_threads to 80
15:04:37.723814 PROGRESS: === Extracted 896044 precursors and 4990396 fragments ===
15:04:37.724686 INFO: === FDR correction performed with classifier version 13 ===
15:04:37.757392 PROGRESS: ============================= Precursor FDR =============================
15:04:37.757701 PROGRESS: Total precursors accumulated: 179,852
15:04:37.757772 PROGRESS: Target precursors: 101,987 (56.71%)
15:04:37.757832 PROGRESS: Decoy precursors: 77,865 (43.29%)
15:04:37.757897 PROGRESS: 
15:04:37.757951 PROGRESS: Precursor Summary:
15:04:37.760203 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:     1; 0.001 FDR:     1
15:04:37.760305 PROGRESS: 
15:04:37.760368 PROGRESS: Protein Summary:
15:04:37.762444 PROGRESS: Channel   0:	 0.050 FDR:   276; 0.010 FDR:     1; 0.001 FDR:     1
15:04:37.762548 PROGRESS: =========================================================================
15:04:37.779016 INFO: Target number of precursors not reached yet.
15:04:38.345255 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:04:38.395912 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:04:38.659331 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:04:38.716346 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:04:39.222849 INFO: === skipping optimization until target number of precursors are found ===
15:04:39.223134 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
15:04:39.223282 INFO: Starting optimization step 12.
15:04:39.223360 PROGRESS: === Extracting elution groups 204600 to 409400 ===
15:04:39.223428 INFO: Using python extraction backend
15:04:39.223545 PROGRESS: Extracting batch of 408390 precursors
15:04:39.223622 INFO: === Search parameters used ===
15:04:39.223673 INFO: rt_error       : 121.6966432451404
15:04:39.223718 INFO: mobility_error : 0.1
15:04:39.223762 INFO: num_candidates : 3
15:04:39.223803 INFO: ms1_error      : 15.0
15:04:39.223845 INFO: ms2_error      : 15.0
15:04:39.223886 INFO: fwhm_rt        : 2.682527780532837
15:04:39.223929 INFO: quant_window   : 3
15:04:39.223971 INFO: ==============================================
15:04:39.331418 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:04:39.331555 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:04:39.331601 INFO: FWHM in RT is 2.68 seconds, sigma is 0.45
15:04:39.331626 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.81
15:04:39.332414 INFO: Starting candidate selection
15:06:24.669878 INFO: Starting candidate scoring
15:06:35.396440 INFO: Finished candidate processing
15:06:35.396796 INFO: Collecting candidate features
15:06:36.948085 WARNING: intensity_correlation has 3698 NaNs ( 0.41 % out of 895838)
15:06:36.949078 WARNING: height_correlation has 384 NaNs ( 0.04 % out of 895838)
15:06:36.980797 INFO: Collecting fragment features
15:06:37.422203 INFO: Finished candidate scoring
15:06:38.400563 INFO: performing precursor FDR with 47 features
15:06:38.400726 INFO: Decoy channel: -1
15:06:38.400758 INFO: competitive: True
15:06:39.061092 INFO: Setting torch num_threads to 2 for FDR classification task
15:06:39.345549 WARNING: dropped 3839 target PSMs due to missing features
15:06:39.345715 WARNING: dropped 3906 decoy PSMs due to missing features
15:06:39.943999 INFO: Estimating optimal hyperparameters - samples: 1,427,309, batch_size: 4,096, learning_rate: 1.00e-03
15:06:39.947301 INFO: Using random state 318981 for train-test-split
15:07:16.192192 INFO: Test AUC: 0.550
15:07:16.192412 INFO: Train AUC: 0.562
15:07:16.192451 INFO: AUC difference: 2.14%
15:07:17.038457 INFO: Resetting torch num_threads to 80
15:07:17.286489 PROGRESS: === Extracted 1791882 precursors and 9975774 fragments ===
15:07:17.287602 INFO: === FDR correction performed with classifier version 13 ===
15:07:17.347793 PROGRESS: ============================= Precursor FDR =============================
15:07:17.348108 PROGRESS: Total precursors accumulated: 359,416
15:07:17.348182 PROGRESS: Target precursors: 203,689 (56.67%)
15:07:17.348245 PROGRESS: Decoy precursors: 155,727 (43.33%)
15:07:17.348300 PROGRESS: 
15:07:17.348354 PROGRESS: Precursor Summary:
15:07:17.351795 PROGRESS: Channel   0:	 0.050 FDR:   595; 0.010 FDR:   503; 0.001 FDR:   456
15:07:17.351906 PROGRESS: 
15:07:17.351970 PROGRESS: Protein Summary:
15:07:17.355070 PROGRESS: Channel   0:	 0.050 FDR:   454; 0.010 FDR:   373; 0.001 FDR:   340
15:07:17.355179 PROGRESS: =========================================================================
15:07:17.360323 INFO: Target number of precursors reached.
15:07:18.488925 INFO: fragments_df: keeping 5000 of 9975774 [sum(precursor_idx_mask)=13187 sum(mass_error_mask)=9975560 stop_rank=5000
15:07:19.097462 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:07:19.226399 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:07:19.358222 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:07:19.495454 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:07:20.146443 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:07:20.146899 INFO: Using score_cutoff 22.599588455200198 (fac=0.99, q=1)
15:07:20.147250 INFO: Updating optimization_manager: fwhm_rt             : 2.682527780532837 -> 2.71462345123291
15:07:20.147344 INFO: Updating optimization_manager: fwhm_mobility       : 0.005178255494683981 -> 0.005090391729027033
15:07:20.147410 INFO: Updating optimization_manager: score_cutoff        : 25.561284727478025 -> 22.599588455200198
15:07:20.147485 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:07:20.198044 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:07:20.462403 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:07:20.518786 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:07:21.036777 INFO: === checking if optimization conditions were reached ===
15:07:21.037071 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
15:07:21.039474 INFO: Updating optimization_manager: rt_error            : 121.6966432451404 -> 115.12233583005342
15:07:21.039621 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 115.1223.
15:07:21.039700 INFO: ==============================================
15:07:21.039776 INFO: Starting optimization step 13.
15:07:21.039841 PROGRESS: === Extracting elution groups 0 to 204600 ===
15:07:21.039907 INFO: Using python extraction backend
15:07:21.040017 PROGRESS: Extracting batch of 407917 precursors
15:07:21.040088 INFO: === Search parameters used ===
15:07:21.040144 INFO: rt_error       : 115.12233583005342
15:07:21.040192 INFO: mobility_error : 0.1
15:07:21.040238 INFO: num_candidates : 3
15:07:21.040283 INFO: ms1_error      : 15.0
15:07:21.040327 INFO: ms2_error      : 15.0
15:07:21.040371 INFO: fwhm_rt        : 2.71462345123291
15:07:21.040418 INFO: quant_window   : 3
15:07:21.040462 INFO: ==============================================
15:07:21.147565 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:07:21.147712 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:07:21.147764 INFO: FWHM in RT is 2.71 seconds, sigma is 0.45
15:07:21.147789 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.76
15:07:21.148594 INFO: Starting candidate selection
15:09:01.934107 INFO: Starting candidate scoring
15:09:12.790881 INFO: Finished candidate processing
15:09:12.791201 INFO: Collecting candidate features
15:09:14.419468 WARNING: intensity_correlation has 3676 NaNs ( 0.41 % out of 897597)
15:09:14.420477 WARNING: height_correlation has 398 NaNs ( 0.04 % out of 897597)
15:09:14.452257 INFO: Collecting fragment features
15:09:14.911424 INFO: Finished candidate scoring
15:09:15.533219 INFO: performing precursor FDR with 47 features
15:09:15.533356 INFO: Decoy channel: -1
15:09:15.533384 INFO: competitive: True
15:09:15.762216 INFO: Setting torch num_threads to 2 for FDR classification task
15:09:15.906094 WARNING: dropped 1862 target PSMs due to missing features
15:09:15.906270 WARNING: dropped 1998 decoy PSMs due to missing features
15:09:16.319645 INFO: Estimating optimal hyperparameters - samples: 714,989, batch_size: 2,928, learning_rate: 8.45e-04
15:09:16.321399 INFO: Using random state 318981 for train-test-split
15:09:34.978331 INFO: Test AUC: 0.544
15:09:34.978562 INFO: Train AUC: 0.566
15:09:34.978599 INFO: AUC difference: 3.85%
15:09:35.506097 INFO: Resetting torch num_threads to 80
15:09:35.523809 PROGRESS: === Extracted 897597 precursors and 4992068 fragments ===
15:09:35.524693 INFO: === FDR correction performed with classifier version 13 ===
15:09:35.557155 PROGRESS: ============================= Precursor FDR =============================
15:09:35.557469 PROGRESS: Total precursors accumulated: 180,091
15:09:35.557541 PROGRESS: Target precursors: 102,351 (56.83%)
15:09:35.557601 PROGRESS: Decoy precursors: 77,740 (43.17%)
15:09:35.557656 PROGRESS: 
15:09:35.557709 PROGRESS: Precursor Summary:
15:09:35.559972 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   166; 0.001 FDR:   103
15:09:35.560077 PROGRESS: 
15:09:35.560141 PROGRESS: Protein Summary:
15:09:35.562289 PROGRESS: Channel   0:	 0.050 FDR:   254; 0.010 FDR:   136; 0.001 FDR:    88
15:09:35.562398 PROGRESS: =========================================================================
15:09:35.571959 INFO: Target number of precursors not reached yet.
15:09:36.144571 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:09:36.196882 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:09:36.451151 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:09:36.503712 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:09:37.028023 INFO: === skipping optimization until target number of precursors are found ===
15:09:37.028359 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
15:09:37.028491 INFO: Starting optimization step 14.
15:09:37.028576 PROGRESS: === Extracting elution groups 204600 to 409400 ===
15:09:37.028670 INFO: Using python extraction backend
15:09:37.028805 PROGRESS: Extracting batch of 408390 precursors
15:09:37.028902 INFO: === Search parameters used ===
15:09:37.028968 INFO: rt_error       : 115.12233583005342
15:09:37.029025 INFO: mobility_error : 0.1
15:09:37.029083 INFO: num_candidates : 3
15:09:37.029138 INFO: ms1_error      : 15.0
15:09:37.029198 INFO: ms2_error      : 15.0
15:09:37.029256 INFO: fwhm_rt        : 2.71462345123291
15:09:37.029315 INFO: quant_window   : 3
15:09:37.029370 INFO: ==============================================
15:09:37.137787 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:09:37.137959 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:09:37.138016 INFO: FWHM in RT is 2.71 seconds, sigma is 0.45
15:09:37.138047 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.76
15:09:37.138866 INFO: Starting candidate selection
15:11:23.768725 INFO: Starting candidate scoring
15:11:34.635037 INFO: Finished candidate processing
15:11:34.635361 INFO: Collecting candidate features
15:11:36.201700 WARNING: intensity_correlation has 3681 NaNs ( 0.41 % out of 896542)
15:11:36.202706 WARNING: height_correlation has 402 NaNs ( 0.04 % out of 896542)
15:11:36.234276 INFO: Collecting fragment features
15:11:36.694189 INFO: Finished candidate scoring
15:11:37.583158 INFO: performing precursor FDR with 47 features
15:11:37.583325 INFO: Decoy channel: -1
15:11:37.583356 INFO: competitive: True
15:11:38.223222 INFO: Setting torch num_threads to 2 for FDR classification task
15:11:38.505262 WARNING: dropped 3769 target PSMs due to missing features
15:11:38.505427 WARNING: dropped 3969 decoy PSMs due to missing features
15:11:39.107749 INFO: Estimating optimal hyperparameters - samples: 1,429,120, batch_size: 4,096, learning_rate: 1.00e-03
15:11:39.111767 INFO: Using random state 318981 for train-test-split
15:12:15.173294 INFO: Test AUC: 0.548
15:12:15.173538 INFO: Train AUC: 0.560
15:12:15.173578 INFO: AUC difference: 2.19%
15:12:15.979784 INFO: Resetting torch num_threads to 80
15:12:16.226696 PROGRESS: === Extracted 1794139 precursors and 9976357 fragments ===
15:12:16.227842 INFO: === FDR correction performed with classifier version 13 ===
15:12:16.289663 PROGRESS: ============================= Precursor FDR =============================
15:12:16.289989 PROGRESS: Total precursors accumulated: 359,787
15:12:16.290061 PROGRESS: Target precursors: 203,675 (56.61%)
15:12:16.290120 PROGRESS: Decoy precursors: 156,112 (43.39%)
15:12:16.290175 PROGRESS: 
15:12:16.290226 PROGRESS: Precursor Summary:
15:12:16.293647 PROGRESS: Channel   0:	 0.050 FDR:   652; 0.010 FDR:   416; 0.001 FDR:   278
15:12:16.293761 PROGRESS: 
15:12:16.293839 PROGRESS: Protein Summary:
15:12:16.296933 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   310; 0.001 FDR:   213
15:12:16.297038 PROGRESS: =========================================================================
15:12:16.302248 INFO: Target number of precursors reached.
15:12:17.447743 INFO: fragments_df: keeping 5000 of 9976357 [sum(precursor_idx_mask)=11138 sum(mass_error_mask)=9976146 stop_rank=5000
15:12:18.048254 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:12:18.197642 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:12:18.345605 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:12:18.495850 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:12:19.208186 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:12:19.208641 INFO: Using score_cutoff 24.685758708000183 (fac=0.99, q=1)
15:12:19.208979 INFO: Updating optimization_manager: fwhm_rt             : 2.71462345123291 -> 2.747404098510742
15:12:19.209064 INFO: Updating optimization_manager: fwhm_mobility       : 0.005090391729027033 -> 0.005359177477657795
15:12:19.209123 INFO: Updating optimization_manager: score_cutoff        : 22.599588455200198 -> 24.685758708000183
15:12:19.209186 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:12:19.261942 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:12:19.519797 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:12:19.572300 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:12:20.072375 INFO: === checking if optimization conditions were reached ===
15:12:20.072678 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
15:12:20.075141 INFO: Updating optimization_manager: rt_error            : 115.12233583005342 -> 111.24138866065493
15:12:20.075285 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 111.2414.
15:12:20.075365 INFO: ==============================================
15:12:20.075447 INFO: Starting optimization step 15.
15:12:20.075518 PROGRESS: === Extracting elution groups 0 to 204600 ===
15:12:20.075590 INFO: Using python extraction backend
15:12:20.075709 PROGRESS: Extracting batch of 407917 precursors
15:12:20.075789 INFO: === Search parameters used ===
15:12:20.075846 INFO: rt_error       : 111.24138866065493
15:12:20.075896 INFO: mobility_error : 0.1
15:12:20.075944 INFO: num_candidates : 3
15:12:20.075990 INFO: ms1_error      : 15.0
15:12:20.076037 INFO: ms2_error      : 15.0
15:12:20.076087 INFO: fwhm_rt        : 2.747404098510742
15:12:20.076134 INFO: quant_window   : 3
15:12:20.076180 INFO: ==============================================
15:12:20.183290 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:12:20.183435 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:12:20.183486 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
15:12:20.183511 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.90
15:12:20.184335 INFO: Starting candidate selection
15:13:54.842061 INFO: Starting candidate scoring
15:14:06.293654 INFO: Finished candidate processing
15:14:06.293896 INFO: Collecting candidate features
15:14:08.046461 WARNING: intensity_correlation has 3795 NaNs ( 0.43 % out of 891254)
15:14:08.047484 WARNING: height_correlation has 414 NaNs ( 0.05 % out of 891254)
15:14:08.079806 INFO: Collecting fragment features
15:14:08.658694 INFO: Finished candidate scoring
15:14:09.414762 INFO: performing precursor FDR with 47 features
15:14:09.414925 INFO: Decoy channel: -1
15:14:09.414954 INFO: competitive: True
15:14:09.798175 INFO: Setting torch num_threads to 2 for FDR classification task
15:14:10.046261 WARNING: dropped 1930 target PSMs due to missing features
15:14:10.046585 WARNING: dropped 2049 decoy PSMs due to missing features
15:14:10.528165 INFO: Estimating optimal hyperparameters - samples: 709,820, batch_size: 2,907, learning_rate: 8.42e-04
15:14:10.529954 INFO: Using random state 318981 for train-test-split
15:14:29.955861 INFO: Test AUC: 0.549
15:14:29.956138 INFO: Train AUC: 0.565
15:14:29.956178 INFO: AUC difference: 2.83%
15:14:30.502582 INFO: Resetting torch num_threads to 80
15:14:30.530363 PROGRESS: === Extracted 891254 precursors and 4931001 fragments ===
15:14:30.531236 INFO: === FDR correction performed with classifier version 13 ===
15:14:30.566268 PROGRESS: ============================= Precursor FDR =============================
15:14:30.566593 PROGRESS: Total precursors accumulated: 179,296
15:14:30.566669 PROGRESS: Target precursors: 101,842 (56.80%)
15:14:30.566729 PROGRESS: Decoy precursors: 77,454 (43.20%)
15:14:30.566782 PROGRESS: 
15:14:30.566833 PROGRESS: Precursor Summary:
15:14:30.569128 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   229; 0.001 FDR:    45
15:14:30.569239 PROGRESS: 
15:14:30.569302 PROGRESS: Protein Summary:
15:14:30.571472 PROGRESS: Channel   0:	 0.050 FDR:   269; 0.010 FDR:   183; 0.001 FDR:    40
15:14:30.571579 PROGRESS: =========================================================================
15:14:30.582237 INFO: Target number of precursors reached.
15:14:31.141000 INFO: fragments_df: keeping 3641 of 4931001 [sum(precursor_idx_mask)=6143 sum(mass_error_mask)=4930910 stop_rank=3641
15:14:31.952837 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:14:32.090463 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:14:32.222010 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:14:32.356314 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:14:32.856910 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:14:32.857359 INFO: Using score_cutoff 25.97963684463501 (fac=0.99, q=1)
15:14:32.857718 INFO: Updating optimization_manager: fwhm_rt             : 2.747404098510742 -> 2.7912838459014893
15:14:32.857804 INFO: Updating optimization_manager: fwhm_mobility       : 0.005359177477657795 -> 0.005291359964758158
15:14:32.857884 INFO: Updating optimization_manager: score_cutoff        : 24.685758708000183 -> 25.97963684463501
15:14:32.857957 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:14:32.908803 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:14:33.221234 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:14:33.283662 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:14:33.789671 INFO: === checking if optimization conditions were reached ===
15:14:33.789984 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
15:14:33.791346 INFO: Updating optimization_manager: rt_error            : 111.24138866065493 -> 111.24138866065493
15:14:33.791512 INFO: Updating optimization_manager: classifier_version  : 13 -> 29
15:14:33.791622 INFO: Updating optimization_manager: score_cutoff        : 25.97963684463501 -> 25.97963684463501
15:14:33.791722 INFO: Updating optimization_manager: fwhm_rt             : 2.7912838459014893 -> 2.7912838459014893
15:14:33.791816 INFO: Updating optimization_manager: fwhm_mobility       : 0.005291359964758158 -> 0.005291359964758158
15:14:33.791910 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 111.2414 found after 11 searches.
15:14:33.791982 INFO: ==============================================
15:14:33.792055 PROGRESS: Optimization finished for rt_error.
15:14:34.418364 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:14:34.470614 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:14:34.732451 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:14:34.795084 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:14:35.292566 INFO: Starting optimization step 0.
15:14:35.292844 PROGRESS: === Extracting elution groups 0 to 204600 ===
15:14:35.292930 INFO: Using python extraction backend
15:14:35.293062 PROGRESS: Extracting batch of 407917 precursors
15:14:35.293153 INFO: === Search parameters used ===
15:14:35.293211 INFO: rt_error       : 111.24138866065493
15:14:35.293260 INFO: mobility_error : 0.1
15:14:35.293307 INFO: num_candidates : 3
15:14:35.293351 INFO: ms1_error      : 15.0
15:14:35.293396 INFO: ms2_error      : 15.0
15:14:35.293438 INFO: fwhm_rt        : 2.7912838459014893
15:14:35.293482 INFO: quant_window   : 3
15:14:35.293525 INFO: ==============================================
15:14:35.395932 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:14:35.396086 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:14:35.396138 INFO: FWHM in RT is 2.79 seconds, sigma is 0.47
15:14:35.396163 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.87
15:14:35.396961 INFO: Starting candidate selection
15:16:10.196041 INFO: Starting candidate scoring
15:16:21.383870 INFO: Finished candidate processing
15:16:21.384273 INFO: Collecting candidate features
15:16:23.139373 WARNING: intensity_correlation has 3771 NaNs ( 0.42 % out of 887965)
15:16:23.140375 WARNING: height_correlation has 394 NaNs ( 0.04 % out of 887965)
15:16:23.172729 INFO: Collecting fragment features
15:16:23.763907 INFO: Finished candidate scoring
15:16:24.585265 INFO: performing precursor FDR with 47 features
15:16:24.585414 INFO: Decoy channel: -1
15:16:24.585444 INFO: competitive: True
15:16:24.879481 INFO: Setting torch num_threads to 2 for FDR classification task
15:16:25.012505 WARNING: dropped 1917 target PSMs due to missing features
15:16:25.012677 WARNING: dropped 2021 decoy PSMs due to missing features
15:16:25.394999 INFO: Estimating optimal hyperparameters - samples: 707,221, batch_size: 2,896, learning_rate: 8.41e-04
15:16:25.396383 INFO: Using random state 236813 for train-test-split
15:16:43.906165 INFO: Test AUC: 0.554
15:16:43.906556 INFO: Train AUC: 0.574
15:16:43.906597 INFO: AUC difference: 3.46%
15:16:44.445363 INFO: Resetting torch num_threads to 80
15:16:44.465693 PROGRESS: === Extracted 887965 precursors and 4907031 fragments ===
15:16:44.466676 INFO: === FDR correction performed with classifier version 29 ===
15:16:44.501876 PROGRESS: ============================= Precursor FDR =============================
15:16:44.502229 PROGRESS: Total precursors accumulated: 178,901
15:16:44.502305 PROGRESS: Target precursors: 102,895 (57.52%)
15:16:44.502367 PROGRESS: Decoy precursors: 76,006 (42.48%)
15:16:44.502421 PROGRESS: 
15:16:44.502485 PROGRESS: Precursor Summary:
15:16:44.504801 PROGRESS: Channel   0:	 0.050 FDR:   406; 0.010 FDR:   218; 0.001 FDR:    63
15:16:44.504905 PROGRESS: 
15:16:44.504968 PROGRESS: Protein Summary:
15:16:44.507059 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   180; 0.001 FDR:    57
15:16:44.507161 PROGRESS: =========================================================================
15:16:44.514351 INFO: Target number of precursors reached.
15:16:45.056799 INFO: fragments_df: keeping 3459 of 4907031 [sum(precursor_idx_mask)=5773 sum(mass_error_mask)=4906933 stop_rank=3459
15:16:45.917032 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:16:46.050125 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:16:46.187294 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:16:46.317477 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:16:46.793785 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:16:46.794306 INFO: Using score_cutoff 21.098532168388367 (fac=0.99, q=1)
15:16:46.794685 INFO: Updating optimization_manager: fwhm_rt             : 2.7912838459014893 -> 2.7529165744781494
15:16:46.794775 INFO: Updating optimization_manager: fwhm_mobility       : 0.005291359964758158 -> 0.005454482510685921
15:16:46.794837 INFO: Updating optimization_manager: score_cutoff        : 25.97963684463501 -> 21.098532168388367
15:16:46.794904 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:16:46.845618 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:16:47.109574 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:16:47.173986 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:16:47.677043 INFO: === checking if optimization conditions were reached ===
15:16:47.677326 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
15:16:47.679200 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0691412812886882
15:16:47.679343 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0691.
15:16:47.679429 INFO: ==============================================
15:16:47.679524 INFO: Starting optimization step 1.
15:16:47.679603 PROGRESS: === Extracting elution groups 0 to 204600 ===
15:16:47.679682 INFO: Using python extraction backend
15:16:47.679810 PROGRESS: Extracting batch of 407917 precursors
15:16:47.679910 INFO: === Search parameters used ===
15:16:47.679974 INFO: rt_error       : 111.24138866065493
15:16:47.680032 INFO: mobility_error : 0.0691412812886882
15:16:47.680086 INFO: num_candidates : 3
15:16:47.680141 INFO: ms1_error      : 15.0
15:16:47.680200 INFO: ms2_error      : 15.0
15:16:47.680259 INFO: fwhm_rt        : 2.7529165744781494
15:16:47.680315 INFO: quant_window   : 3
15:16:47.680369 INFO: ==============================================
15:16:47.783283 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:16:47.783434 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:16:47.783492 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
15:16:47.783523 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.96
15:16:47.784311 INFO: Starting candidate selection
15:17:53.777794 INFO: Starting candidate scoring
15:18:04.939111 INFO: Finished candidate processing
15:18:04.939570 INFO: Collecting candidate features
15:18:06.915649 WARNING: intensity_correlation has 3988 NaNs ( 0.47 % out of 843027)
15:18:06.916616 WARNING: height_correlation has 433 NaNs ( 0.05 % out of 843027)
15:18:06.946983 INFO: Collecting fragment features
15:18:07.410202 INFO: Finished candidate scoring
15:18:08.066664 INFO: performing precursor FDR with 47 features
15:18:08.066816 INFO: Decoy channel: -1
15:18:08.066846 INFO: competitive: True
15:18:08.323291 INFO: Setting torch num_threads to 2 for FDR classification task
15:18:08.486907 WARNING: dropped 2050 target PSMs due to missing features
15:18:08.487079 WARNING: dropped 2149 decoy PSMs due to missing features
15:18:08.848790 INFO: Estimating optimal hyperparameters - samples: 671,062, batch_size: 2,748, learning_rate: 8.19e-04
15:18:08.850368 INFO: Using random state 236813 for train-test-split
15:18:27.393266 INFO: Test AUC: 0.553
15:18:27.393441 INFO: Train AUC: 0.573
15:18:27.393478 INFO: AUC difference: 3.53%
15:18:27.924011 INFO: Resetting torch num_threads to 80
15:18:27.940742 PROGRESS: === Extracted 843027 precursors and 4566595 fragments ===
15:18:27.941626 INFO: === FDR correction performed with classifier version 29 ===
15:18:27.974467 PROGRESS: ============================= Precursor FDR =============================
15:18:27.974815 PROGRESS: Total precursors accumulated: 172,806
15:18:27.974890 PROGRESS: Target precursors: 99,273 (57.45%)
15:18:27.974953 PROGRESS: Decoy precursors: 73,533 (42.55%)
15:18:27.975006 PROGRESS: 
15:18:27.975057 PROGRESS: Precursor Summary:
15:18:27.977357 PROGRESS: Channel   0:	 0.050 FDR:   327; 0.010 FDR:   249; 0.001 FDR:   219
15:18:27.977460 PROGRESS: 
15:18:27.977524 PROGRESS: Protein Summary:
15:18:27.979587 PROGRESS: Channel   0:	 0.050 FDR:   277; 0.010 FDR:   206; 0.001 FDR:   178
15:18:27.979703 PROGRESS: =========================================================================
15:18:27.984915 INFO: Target number of precursors reached.
15:18:28.487652 INFO: fragments_df: keeping 3830 of 4566595 [sum(precursor_idx_mask)=6567 sum(mass_error_mask)=4566462 stop_rank=3830
15:18:29.240338 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:18:29.379541 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:18:29.519677 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:18:29.656921 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:18:30.188540 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:18:30.189021 INFO: Using score_cutoff 23.58550796813965 (fac=0.99, q=1)
15:18:30.189361 INFO: Updating optimization_manager: fwhm_rt             : 2.7529165744781494 -> 2.73333740234375
15:18:30.189450 INFO: Updating optimization_manager: fwhm_mobility       : 0.005454482510685921 -> 0.005093957297503948
15:18:30.189512 INFO: Updating optimization_manager: score_cutoff        : 21.098532168388367 -> 23.58550796813965
15:18:30.189573 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:18:30.242105 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:18:30.500688 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:18:30.559566 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:18:31.048515 INFO: === checking if optimization conditions were reached ===
15:18:31.048827 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
15:18:31.050939 INFO: Updating optimization_manager: mobility_error      : 0.0691412812886882 -> 0.06477394706734227
15:18:31.051082 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0648.
15:18:31.051162 INFO: ==============================================
15:18:31.051243 INFO: Starting optimization step 2.
15:18:31.051313 PROGRESS: === Extracting elution groups 0 to 204600 ===
15:18:31.051384 INFO: Using python extraction backend
15:18:31.051501 PROGRESS: Extracting batch of 407917 precursors
15:18:31.051579 INFO: === Search parameters used ===
15:18:31.051640 INFO: rt_error       : 111.24138866065493
15:18:31.051709 INFO: mobility_error : 0.06477394706734227
15:18:31.051763 INFO: num_candidates : 3
15:18:31.051814 INFO: ms1_error      : 15.0
15:18:31.051862 INFO: ms2_error      : 15.0
15:18:31.051914 INFO: fwhm_rt        : 2.73333740234375
15:18:31.051962 INFO: quant_window   : 3
15:18:31.052011 INFO: ==============================================
15:18:31.156452 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:18:31.156609 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:18:31.156660 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
15:18:31.156686 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.76
15:18:31.157396 INFO: Starting candidate selection
15:19:35.197564 INFO: Starting candidate scoring
15:19:45.582037 INFO: Finished candidate processing
15:19:45.582936 INFO: Collecting candidate features
15:19:47.229469 WARNING: intensity_correlation has 4014 NaNs ( 0.48 % out of 837736)
15:19:47.230436 WARNING: height_correlation has 411 NaNs ( 0.05 % out of 837736)
15:19:47.260837 INFO: Collecting fragment features
15:19:47.729329 INFO: Finished candidate scoring
15:19:48.405770 INFO: performing precursor FDR with 47 features
15:19:48.405921 INFO: Decoy channel: -1
15:19:48.405958 INFO: competitive: True
15:19:48.632348 INFO: Setting torch num_threads to 2 for FDR classification task
15:19:48.763827 WARNING: dropped 2082 target PSMs due to missing features
15:19:48.763992 WARNING: dropped 2123 decoy PSMs due to missing features
15:19:49.139796 INFO: Estimating optimal hyperparameters - samples: 666,824, batch_size: 2,731, learning_rate: 8.17e-04
15:19:49.140981 INFO: Using random state 236813 for train-test-split
15:20:08.018017 INFO: Test AUC: 0.553
15:20:08.018231 INFO: Train AUC: 0.573
15:20:08.018282 INFO: AUC difference: 3.54%
15:20:08.545634 INFO: Resetting torch num_threads to 80
15:20:08.562125 PROGRESS: === Extracted 837736 precursors and 4521430 fragments ===
15:20:08.562937 INFO: === FDR correction performed with classifier version 29 ===
15:20:08.592697 PROGRESS: ============================= Precursor FDR =============================
15:20:08.593005 PROGRESS: Total precursors accumulated: 171,964
15:20:08.593079 PROGRESS: Target precursors: 98,734 (57.42%)
15:20:08.593140 PROGRESS: Decoy precursors: 73,230 (42.58%)
15:20:08.593193 PROGRESS: 
15:20:08.593244 PROGRESS: Precursor Summary:
15:20:08.595463 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   215; 0.001 FDR:    50
15:20:08.595568 PROGRESS: 
15:20:08.595634 PROGRESS: Protein Summary:
15:20:08.597692 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   173; 0.001 FDR:    45
15:20:08.597793 PROGRESS: =========================================================================
15:20:08.605142 INFO: Target number of precursors reached.
15:20:09.093570 INFO: fragments_df: keeping 3482 of 4521430 [sum(precursor_idx_mask)=5780 sum(mass_error_mask)=4521313 stop_rank=3482
15:20:09.782475 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:20:09.912229 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:20:10.049873 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:20:10.184244 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:20:10.664139 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:20:10.664588 INFO: Using score_cutoff 26.527459869003295 (fac=0.99, q=1)
15:20:10.664916 INFO: Updating optimization_manager: fwhm_rt             : 2.73333740234375 -> 2.755783796310425
15:20:10.665001 INFO: Updating optimization_manager: fwhm_mobility       : 0.005093957297503948 -> 0.005291359964758158
15:20:10.665062 INFO: Updating optimization_manager: score_cutoff        : 23.58550796813965 -> 26.527459869003295
15:20:10.665122 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:20:10.714372 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:20:10.975039 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:20:11.039000 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:20:11.537963 INFO: === checking if optimization conditions were reached ===
15:20:11.538245 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
15:20:11.539259 INFO: Updating optimization_manager: mobility_error      : 0.06477394706734227 -> 0.0691412812886882
15:20:11.539440 INFO: Updating optimization_manager: classifier_version  : 29 -> 31
15:20:11.539557 INFO: Updating optimization_manager: score_cutoff        : 26.527459869003295 -> 23.58550796813965
15:20:11.539683 INFO: Updating optimization_manager: fwhm_rt             : 2.755783796310425 -> 2.73333740234375
15:20:11.539782 INFO: Updating optimization_manager: fwhm_mobility       : 0.005291359964758158 -> 0.005093957297503948
15:20:11.539878 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0691 found after 3 searches.
15:20:11.539948 INFO: ==============================================
15:20:11.540023 PROGRESS: Optimization finished for mobility_error.
15:20:12.102661 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:20:12.152356 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:20:12.413280 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:20:12.476695 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:20:12.964397 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
15:20:12.964669 PROGRESS: ==============================================
15:20:12.964756 PROGRESS: ms2_error      : 15.0000
15:20:12.964821 PROGRESS: ms1_error      : 15.0000
15:20:12.964881 PROGRESS: rt_error       : 111.2414
15:20:12.964940 PROGRESS: mobility_error : 0.0691
15:20:12.964990 PROGRESS: ==============================================
15:20:12.972206 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:20:14.503076 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:20:22.385122 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:20:24.087344 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:20:38.760343 INFO: Using python extraction backend
15:20:38.760802 PROGRESS: Extracting batch of 12210649 precursors
15:20:38.760917 INFO: === Search parameters used ===
15:20:38.760988 INFO: rt_error       : 111.24138866065493
15:20:38.761050 INFO: mobility_error : 0.0691412812886882
15:20:38.761109 INFO: num_candidates : 3
15:20:38.761168 INFO: ms1_error      : 15.0
15:20:38.761225 INFO: ms2_error      : 15.0
15:20:38.761282 INFO: fwhm_rt        : 2.73333740234375
15:20:38.761339 INFO: quant_window   : 3
15:20:38.761395 INFO: ==============================================
15:20:41.244019 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:20:41.244165 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:20:41.244214 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
15:20:41.244241 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.76
15:20:41.245086 INFO: Starting candidate selection
15:52:29.739497 INFO: Removed 26609062 precursors with score below cutoff 23.58550796813965
15:52:33.894843 INFO: Starting candidate scoring
15:53:41.255013 INFO: Finished candidate processing
15:53:41.255293 INFO: Collecting candidate features
15:54:06.900841 WARNING: intensity_correlation has 3099 NaNs ( 0.06 % out of 5051469)
15:54:06.906060 WARNING: height_correlation has 162 NaNs ( 0.00 % out of 5051469)
15:54:07.095548 INFO: Collecting fragment features
15:54:24.489265 INFO: Finished candidate scoring
15:54:28.771342 INFO: === Performing FDR correction with classifier version 31 ===
15:54:28.773348 INFO: performing precursor FDR with 47 features
15:54:28.773401 INFO: Decoy channel: -1
15:54:28.773432 INFO: competitive: True
15:54:30.021521 INFO: Setting torch num_threads to 2 for FDR classification task
15:54:30.747886 WARNING: dropped 1664 target PSMs due to missing features
15:54:30.748083 WARNING: dropped 1536 decoy PSMs due to missing features
15:54:32.755507 INFO: Estimating optimal hyperparameters - samples: 4,038,615, batch_size: 4,096, learning_rate: 1.00e-03
15:54:32.766049 INFO: Using random state 421079 for train-test-split
15:56:25.147135 INFO: Test AUC: 0.551
15:56:25.147573 INFO: Train AUC: 0.557
15:56:25.147615 INFO: AUC difference: 1.04%
15:56:26.951335 INFO: Resetting torch num_threads to 80
15:56:27.123137 INFO: Removing fragments below FDR threshold
15:56:27.430939 PROGRESS: ============================= Precursor FDR =============================
15:56:27.431211 PROGRESS: Total precursors accumulated: 7,608
15:56:27.431289 PROGRESS: Target precursors: 7,533 (99.01%)
15:56:27.431351 PROGRESS: Decoy precursors: 75 (0.99%)
15:56:27.431407 PROGRESS: 
15:56:27.431467 PROGRESS: Precursor Summary:
15:56:27.435186 PROGRESS: Channel   0:	 0.050 FDR: 7,533; 0.010 FDR: 7,533; 0.001 FDR: 5,191
15:56:27.435335 PROGRESS: 
15:56:27.435405 PROGRESS: Protein Summary:
15:56:27.439178 PROGRESS: Channel   0:	 0.050 FDR: 1,760; 0.010 FDR: 1,760; 0.001 FDR: 1,239
15:56:27.439286 PROGRESS: =========================================================================
15:56:27.857141 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R3/psm.parquet
15:56:27.886988 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R3/frag.parquet
15:56:27.929927 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R3
15:56:28.482667 PROGRESS: Loading raw file 4/12: A9_G_DIA_nLC_tTOF_R4 
15:56:28.482842 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
15:56:28.482973 INFO: Initializing TimingManager
15:56:28.483617 INFO: Initializing RawFileManager
15:56:28.483746 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:28.483808 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:28.483856 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:28.628006 INFO: Reading 22,622 frames with 404,833,767 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:34.058371 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d...
15:56:34.060245 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:34.062798 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:34.063138 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:34.063742 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:34.065744 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:34.087819 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:34.088167 INFO: Indexing quadrupole dimension
15:56:34.185137 INFO: Transposing detector events
15:56:36.303010 INFO: Finished transposing data
15:56:36.319557 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
15:56:36.320403 INFO: RT (min)            : 0.0 - 40.0
15:56:36.320500 INFO: RT duration (sec)   : 2399.9
15:56:36.320560 INFO: RT duration (min)   : 40.0
15:56:36.320621 INFO: Cycle len (scans)   : 12
15:56:36.320672 INFO: Cycle len (sec)     : 1.27
15:56:36.320720 INFO: Number of cycles    : 1885
15:56:36.320769 INFO: MS2 range (m/z)     : 374.4 - 1151.9
15:56:36.320840 INFO: Creating DIA data object took: 7.837111473083496
15:56:40.247477 INFO: Initializing CalibrationManager
15:56:40.247797 INFO: Setting up calibration estimators ..
15:56:40.247876 INFO: Found 1 estimator(s) in calibration group 'fragment'
15:56:40.247994 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
15:56:40.248108 INFO: Found 3 estimator(s) in calibration group 'precursor'
15:56:40.248195 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
15:56:40.248285 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
15:56:40.248364 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
15:56:40.248423 INFO: Done setting up calibration estimators.
15:56:40.248564 INFO: Initializing OptimizationManager
15:56:40.248688 INFO: initial parameter: ms1_error = 30
15:56:40.248746 INFO: initial parameter: ms2_error = 30
15:56:40.248799 INFO: initial parameter: rt_error = 1199.9717345
15:56:40.248850 INFO: initial parameter: mobility_error = 0.1
15:56:40.248896 INFO: initial parameter: num_candidates = 1
15:56:40.248943 INFO: initial parameter: fwhm_rt = 5
15:56:40.248990 INFO: initial parameter: fwhm_mobility = 0.01
15:56:40.249035 INFO: initial parameter: score_cutoff = 0
15:56:40.249084 INFO: initial parameter: classifier_version = -1
15:56:40.249184 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R4
15:56:40.249461 INFO: FDRManager: loading saved state not requested, will be initialized.
15:56:40.249502 INFO: Initializing FDRManager
15:56:40.249553 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
15:56:42.080124 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
15:56:44.102592 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
15:56:44.103207 INFO: Updating optimization_manager: rt_error            : 1199.9717345 -> 1199.9717345
15:56:44.103344 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
15:56:44.103537 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
15:56:44.103640 PROGRESS: Starting initial search for precursors.
15:56:44.103733 INFO: Starting optimization step 0.
15:56:44.103810 PROGRESS: === Extracting elution groups 0 to 200 ===
15:56:44.103894 INFO: Using python extraction backend
15:56:44.104042 PROGRESS: Extracting batch of 395 precursors
15:56:44.104122 INFO: === Search parameters used ===
15:56:44.104179 INFO: rt_error       : 1199.9717345
15:56:44.104234 INFO: mobility_error : 0.1
15:56:44.104283 INFO: num_candidates : 1
15:56:44.104330 INFO: ms1_error      : 30
15:56:44.104377 INFO: ms2_error      : 30
15:56:44.104425 INFO: fwhm_rt        : 5
15:56:44.104471 INFO: quant_window   : 3
15:56:44.104517 INFO: ==============================================
15:56:44.105764 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:56:44.105827 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:56:44.105887 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
15:56:44.105917 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
15:56:44.107141 INFO: Starting candidate selection
15:56:46.085210 INFO: Starting candidate scoring
15:56:46.128728 INFO: Finished candidate processing
15:56:46.128843 INFO: Collecting candidate features
15:56:46.144980 INFO: Collecting fragment features
15:56:46.147402 INFO: Finished candidate scoring
15:56:46.148392 INFO: performing precursor FDR with 47 features
15:56:46.148445 INFO: Decoy channel: -1
15:56:46.148476 INFO: competitive: True
15:56:46.149789 INFO: Setting torch num_threads to 2 for FDR classification task
15:56:46.151991 INFO: Estimating optimal hyperparameters - samples: 273, batch_size: 128, learning_rate: 1.77e-04
15:56:46.152830 INFO: Using random state 667329 for train-test-split
15:56:46.179047 INFO: Test AUC: 0.466
15:56:46.179138 INFO: Train AUC: 0.560
15:56:46.179178 INFO: AUC difference: 16.72%
15:56:46.179207 WARNING: AUC difference > 5%. This may indicate overfitting.
15:56:46.430010 INFO: Resetting torch num_threads to 80
15:56:46.430608 PROGRESS: === Extracted 342 precursors and 2876 fragments ===
15:56:46.431139 INFO: === FDR correction performed with classifier version -1 ===
15:56:46.431731 PROGRESS: ============================= Precursor FDR =============================
15:56:46.431826 PROGRESS: Total precursors accumulated: 173
15:56:46.431889 PROGRESS: Target precursors: 103 (59.54%)
15:56:46.431945 PROGRESS: Decoy precursors: 70 (40.46%)
15:56:46.431997 PROGRESS: 
15:56:46.432045 PROGRESS: Precursor Summary:
15:56:46.433015 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
15:56:46.433106 PROGRESS: 
15:56:46.433166 PROGRESS: Protein Summary:
15:56:46.434212 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
15:56:46.434310 PROGRESS: =========================================================================
15:56:46.434432 INFO: Target number of precursors not reached yet.
15:56:46.497265 INFO: Starting optimization step 1.
15:56:46.497514 PROGRESS: === Extracting elution groups 200 to 600 ===
15:56:46.497606 INFO: Using python extraction backend
15:56:46.497731 PROGRESS: Extracting batch of 796 precursors
15:56:46.497816 INFO: === Search parameters used ===
15:56:46.497885 INFO: rt_error       : 1199.9717345
15:56:46.497939 INFO: mobility_error : 0.1
15:56:46.497990 INFO: num_candidates : 1
15:56:46.498038 INFO: ms1_error      : 30
15:56:46.498083 INFO: ms2_error      : 30
15:56:46.498129 INFO: fwhm_rt        : 5
15:56:46.498176 INFO: quant_window   : 3
15:56:46.498223 INFO: ==============================================
15:56:46.498981 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:56:46.499031 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:56:46.499063 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
15:56:46.499087 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
15:56:46.499932 INFO: Starting candidate selection
15:56:49.697488 INFO: Starting candidate scoring
15:56:49.740492 INFO: Finished candidate processing
15:56:49.740593 INFO: Collecting candidate features
15:56:49.751301 INFO: Collecting fragment features
15:56:49.753752 INFO: Finished candidate scoring
15:56:49.756853 INFO: performing precursor FDR with 47 features
15:56:49.756911 INFO: Decoy channel: -1
15:56:49.756940 INFO: competitive: True
15:56:49.760036 INFO: Setting torch num_threads to 2 for FDR classification task
15:56:49.761848 INFO: Estimating optimal hyperparameters - samples: 850, batch_size: 128, learning_rate: 1.77e-04
15:56:49.761948 INFO: Using random state 204467 for train-test-split
15:56:49.842570 INFO: Test AUC: 0.535
15:56:49.842672 INFO: Train AUC: 0.533
15:56:49.842704 INFO: AUC difference: 0.24%
15:56:50.086298 INFO: Resetting torch num_threads to 80
15:56:50.087598 PROGRESS: === Extracted 1063 precursors and 9085 fragments ===
15:56:50.088042 INFO: === FDR correction performed with classifier version -1 ===
15:56:50.088623 PROGRESS: ============================= Precursor FDR =============================
15:56:50.088718 PROGRESS: Total precursors accumulated: 541
15:56:50.088783 PROGRESS: Target precursors: 307 (56.75%)
15:56:50.088851 PROGRESS: Decoy precursors: 234 (43.25%)
15:56:50.088905 PROGRESS: 
15:56:50.088957 PROGRESS: Precursor Summary:
15:56:50.089921 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
15:56:50.090017 PROGRESS: 
15:56:50.090075 PROGRESS: Protein Summary:
15:56:50.091115 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
15:56:50.091205 PROGRESS: =========================================================================
15:56:50.091380 INFO: Target number of precursors not reached yet.
15:56:50.193180 INFO: Starting optimization step 2.
15:56:50.193429 PROGRESS: === Extracting elution groups 600 to 1400 ===
15:56:50.193511 INFO: Using python extraction backend
15:56:50.193619 PROGRESS: Extracting batch of 1598 precursors
15:56:50.193693 INFO: === Search parameters used ===
15:56:50.193746 INFO: rt_error       : 1199.9717345
15:56:50.193796 INFO: mobility_error : 0.1
15:56:50.193844 INFO: num_candidates : 1
15:56:50.193902 INFO: ms1_error      : 30
15:56:50.193954 INFO: ms2_error      : 30
15:56:50.194001 INFO: fwhm_rt        : 5
15:56:50.194046 INFO: quant_window   : 3
15:56:50.194090 INFO: ==============================================
15:56:50.194895 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:56:50.194942 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:56:50.194973 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
15:56:50.194995 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
15:56:50.195741 INFO: Starting candidate selection
15:56:55.505555 INFO: Starting candidate scoring
15:56:55.562014 INFO: Finished candidate processing
15:56:55.562125 INFO: Collecting candidate features
15:56:55.574278 INFO: Collecting fragment features
15:56:55.577291 INFO: Finished candidate scoring
15:56:55.581047 INFO: performing precursor FDR with 47 features
15:56:55.581113 INFO: Decoy channel: -1
15:56:55.581145 INFO: competitive: True
15:56:55.584842 INFO: Setting torch num_threads to 2 for FDR classification task
15:56:55.587027 INFO: Estimating optimal hyperparameters - samples: 1,996, batch_size: 128, learning_rate: 1.77e-04
15:56:55.587128 INFO: Using random state 457963 for train-test-split
15:56:55.803200 INFO: Test AUC: 0.514
15:56:55.803309 INFO: Train AUC: 0.558
15:56:55.803342 INFO: AUC difference: 7.73%
15:56:55.803368 WARNING: AUC difference > 5%. This may indicate overfitting.
15:56:56.049205 INFO: Resetting torch num_threads to 80
15:56:56.050932 PROGRESS: === Extracted 2496 precursors and 21242 fragments ===
15:56:56.051404 INFO: === FDR correction performed with classifier version -1 ===
15:56:56.052058 PROGRESS: ============================= Precursor FDR =============================
15:56:56.052159 PROGRESS: Total precursors accumulated: 1,269
15:56:56.052234 PROGRESS: Target precursors: 706 (55.63%)
15:56:56.052295 PROGRESS: Decoy precursors: 563 (44.37%)
15:56:56.052350 PROGRESS: 
15:56:56.052404 PROGRESS: Precursor Summary:
15:56:56.053374 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
15:56:56.053472 PROGRESS: 
15:56:56.053536 PROGRESS: Protein Summary:
15:56:56.054597 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
15:56:56.054696 PROGRESS: =========================================================================
15:56:56.054886 INFO: Target number of precursors not reached yet.
15:56:56.194648 INFO: Starting optimization step 3.
15:56:56.194903 PROGRESS: === Extracting elution groups 1400 to 3000 ===
15:56:56.194999 INFO: Using python extraction backend
15:56:56.195112 PROGRESS: Extracting batch of 3192 precursors
15:56:56.195190 INFO: === Search parameters used ===
15:56:56.195248 INFO: rt_error       : 1199.9717345
15:56:56.195301 INFO: mobility_error : 0.1
15:56:56.195364 INFO: num_candidates : 1
15:56:56.195414 INFO: ms1_error      : 30
15:56:56.195470 INFO: ms2_error      : 30
15:56:56.195517 INFO: fwhm_rt        : 5
15:56:56.195561 INFO: quant_window   : 3
15:56:56.195606 INFO: ==============================================
15:56:56.196619 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:56:56.196674 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:56:56.196705 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
15:56:56.196730 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
15:56:56.197454 INFO: Starting candidate selection
15:57:05.895712 INFO: Starting candidate scoring
15:57:05.998391 INFO: Finished candidate processing
15:57:05.998510 INFO: Collecting candidate features
15:57:06.009626 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 2885)
15:57:06.013604 INFO: Collecting fragment features
15:57:06.017682 INFO: Finished candidate scoring
15:57:06.022203 INFO: performing precursor FDR with 47 features
15:57:06.022264 INFO: Decoy channel: -1
15:57:06.022293 INFO: competitive: True
15:57:06.026601 INFO: Setting torch num_threads to 2 for FDR classification task
15:57:06.028212 WARNING: dropped 1 decoy PSMs due to missing features
15:57:06.029413 INFO: Estimating optimal hyperparameters - samples: 4,304, batch_size: 128, learning_rate: 1.77e-04
15:57:06.029502 INFO: Using random state 134197 for train-test-split
15:57:06.453655 INFO: Test AUC: 0.475
15:57:06.453770 INFO: Train AUC: 0.579
15:57:06.453804 INFO: AUC difference: 17.94%
15:57:06.453830 WARNING: AUC difference > 5%. This may indicate overfitting.
15:57:06.692675 INFO: Resetting torch num_threads to 80
15:57:06.694988 PROGRESS: === Extracted 5381 precursors and 45968 fragments ===
15:57:06.695430 INFO: === FDR correction performed with classifier version -1 ===
15:57:06.696248 PROGRESS: ============================= Precursor FDR =============================
15:57:06.696346 PROGRESS: Total precursors accumulated: 2,731
15:57:06.696413 PROGRESS: Target precursors: 1,563 (57.23%)
15:57:06.696472 PROGRESS: Decoy precursors: 1,168 (42.77%)
15:57:06.696526 PROGRESS: 
15:57:06.696580 PROGRESS: Precursor Summary:
15:57:06.697542 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
15:57:06.697639 PROGRESS: 
15:57:06.697703 PROGRESS: Protein Summary:
15:57:06.698765 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
15:57:06.698862 PROGRESS: =========================================================================
15:57:06.699053 INFO: Target number of precursors not reached yet.
15:57:06.904330 INFO: Starting optimization step 4.
15:57:06.904600 PROGRESS: === Extracting elution groups 3000 to 6200 ===
15:57:06.904686 INFO: Using python extraction backend
15:57:06.904800 PROGRESS: Extracting batch of 6381 precursors
15:57:06.904880 INFO: === Search parameters used ===
15:57:06.904937 INFO: rt_error       : 1199.9717345
15:57:06.904989 INFO: mobility_error : 0.1
15:57:06.905040 INFO: num_candidates : 1
15:57:06.905088 INFO: ms1_error      : 30
15:57:06.905134 INFO: ms2_error      : 30
15:57:06.905182 INFO: fwhm_rt        : 5
15:57:06.905232 INFO: quant_window   : 3
15:57:06.905280 INFO: ==============================================
15:57:06.906698 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:57:06.906753 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:57:06.906787 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
15:57:06.906817 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
15:57:06.907538 INFO: Starting candidate selection
15:57:23.643384 INFO: Starting candidate scoring
15:57:23.778152 INFO: Finished candidate processing
15:57:23.778281 INFO: Collecting candidate features
15:57:23.799028 INFO: Collecting fragment features
15:57:23.804502 INFO: Finished candidate scoring
15:57:23.812910 INFO: performing precursor FDR with 47 features
15:57:23.813011 INFO: Decoy channel: -1
15:57:23.813041 INFO: competitive: True
15:57:23.819000 INFO: Setting torch num_threads to 2 for FDR classification task
15:57:23.821815 WARNING: dropped 1 decoy PSMs due to missing features
15:57:23.823838 INFO: Estimating optimal hyperparameters - samples: 8,919, batch_size: 128, learning_rate: 1.77e-04
15:57:23.823933 INFO: Using random state 337949 for train-test-split
15:57:24.714843 INFO: Test AUC: 0.533
15:57:24.714989 INFO: Train AUC: 0.587
15:57:24.715022 INFO: AUC difference: 9.14%
15:57:24.715045 WARNING: AUC difference > 5%. This may indicate overfitting.
15:57:24.958448 INFO: Resetting torch num_threads to 80
15:57:24.961707 PROGRESS: === Extracted 11150 precursors and 94600 fragments ===
15:57:24.962196 INFO: === FDR correction performed with classifier version -1 ===
15:57:24.963530 PROGRESS: ============================= Precursor FDR =============================
15:57:24.963633 PROGRESS: Total precursors accumulated: 5,655
15:57:24.963699 PROGRESS: Target precursors: 3,332 (58.92%)
15:57:24.963757 PROGRESS: Decoy precursors: 2,323 (41.08%)
15:57:24.963812 PROGRESS: 
15:57:24.963865 PROGRESS: Precursor Summary:
15:57:24.964840 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
15:57:24.964936 PROGRESS: 
15:57:24.965005 PROGRESS: Protein Summary:
15:57:24.966058 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
15:57:24.966154 PROGRESS: =========================================================================
15:57:24.966362 INFO: Target number of precursors not reached yet.
15:57:25.249618 INFO: Starting optimization step 5.
15:57:25.249918 PROGRESS: === Extracting elution groups 6200 to 12600 ===
15:57:25.250019 INFO: Using python extraction backend
15:57:25.250135 PROGRESS: Extracting batch of 12763 precursors
15:57:25.250217 INFO: === Search parameters used ===
15:57:25.250275 INFO: rt_error       : 1199.9717345
15:57:25.250329 INFO: mobility_error : 0.1
15:57:25.250381 INFO: num_candidates : 1
15:57:25.250429 INFO: ms1_error      : 30
15:57:25.250482 INFO: ms2_error      : 30
15:57:25.250531 INFO: fwhm_rt        : 5
15:57:25.250578 INFO: quant_window   : 3
15:57:25.250627 INFO: ==============================================
15:57:25.253087 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:57:25.253146 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:57:25.253180 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
15:57:25.253205 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
15:57:25.254043 INFO: Starting candidate selection
15:57:56.341282 INFO: Starting candidate scoring
15:57:56.599190 INFO: Finished candidate processing
15:57:56.599367 INFO: Collecting candidate features
15:57:56.647531 WARNING: intensity_correlation has 4 NaNs ( 0.03 % out of 11525)
15:57:56.654884 INFO: Collecting fragment features
15:57:56.667112 INFO: Finished candidate scoring
15:57:56.683091 INFO: performing precursor FDR with 47 features
15:57:56.683243 INFO: Decoy channel: -1
15:57:56.683272 INFO: competitive: True
15:57:56.694168 INFO: Setting torch num_threads to 2 for FDR classification task
15:57:56.698591 WARNING: dropped 3 target PSMs due to missing features
15:57:56.698687 WARNING: dropped 2 decoy PSMs due to missing features
15:57:56.702248 INFO: Estimating optimal hyperparameters - samples: 18,136, batch_size: 128, learning_rate: 1.77e-04
15:57:56.702390 INFO: Using random state 333484 for train-test-split
15:57:58.645081 INFO: Test AUC: 0.551
15:57:58.645223 INFO: Train AUC: 0.598
15:57:58.645257 INFO: AUC difference: 7.83%
15:57:58.645283 WARNING: AUC difference > 5%. This may indicate overfitting.
15:57:58.904637 INFO: Resetting torch num_threads to 80
15:57:58.909689 PROGRESS: === Extracted 22675 precursors and 192429 fragments ===
15:57:58.910290 INFO: === FDR correction performed with classifier version -1 ===
15:57:58.912127 PROGRESS: ============================= Precursor FDR =============================
15:57:58.912240 PROGRESS: Total precursors accumulated: 11,501
15:57:58.912411 PROGRESS: Target precursors: 6,869 (59.73%)
15:57:58.912474 PROGRESS: Decoy precursors: 4,632 (40.27%)
15:57:58.912528 PROGRESS: 
15:57:58.912579 PROGRESS: Precursor Summary:
15:57:58.913620 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
15:57:58.913724 PROGRESS: 
15:57:58.913785 PROGRESS: Protein Summary:
15:57:58.914923 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
15:57:58.915020 PROGRESS: =========================================================================
15:57:58.915323 INFO: Target number of precursors not reached yet.
15:57:59.307263 INFO: Starting optimization step 6.
15:57:59.307531 PROGRESS: === Extracting elution groups 12600 to 25400 ===
15:57:59.307620 INFO: Using python extraction backend
15:57:59.307738 PROGRESS: Extracting batch of 25523 precursors
15:57:59.307813 INFO: === Search parameters used ===
15:57:59.307867 INFO: rt_error       : 1199.9717345
15:57:59.307915 INFO: mobility_error : 0.1
15:57:59.307963 INFO: num_candidates : 1
15:57:59.308010 INFO: ms1_error      : 30
15:57:59.308056 INFO: ms2_error      : 30
15:57:59.308101 INFO: fwhm_rt        : 5
15:57:59.308145 INFO: quant_window   : 3
15:57:59.308203 INFO: ==============================================
15:57:59.314473 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:57:59.314547 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:57:59.314581 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
15:57:59.314605 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
15:57:59.315432 INFO: Starting candidate selection
15:58:58.951676 INFO: Starting candidate scoring
15:58:59.379889 INFO: Finished candidate processing
15:58:59.380140 INFO: Collecting candidate features
15:58:59.450109 WARNING: intensity_correlation has 4 NaNs ( 0.02 % out of 22997)
15:58:59.450373 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 22997)
15:58:59.454712 INFO: Collecting fragment features
15:58:59.469996 INFO: Finished candidate scoring
15:58:59.498191 INFO: performing precursor FDR with 47 features
15:58:59.498345 INFO: Decoy channel: -1
15:58:59.498374 INFO: competitive: True
15:58:59.517082 INFO: Setting torch num_threads to 2 for FDR classification task
15:58:59.526246 WARNING: dropped 5 target PSMs due to missing features
15:58:59.526386 WARNING: dropped 4 decoy PSMs due to missing features
15:58:59.532790 INFO: Estimating optimal hyperparameters - samples: 36,530, batch_size: 149, learning_rate: 1.91e-04
15:58:59.533016 INFO: Using random state 886522 for train-test-split
15:59:03.352088 INFO: Test AUC: 0.558
15:59:03.352213 INFO: Train AUC: 0.604
15:59:03.352249 INFO: AUC difference: 7.58%
15:59:03.352276 WARNING: AUC difference > 5%. This may indicate overfitting.
15:59:03.612345 INFO: Resetting torch num_threads to 80
15:59:03.621288 PROGRESS: === Extracted 45672 precursors and 388235 fragments ===
15:59:03.621996 INFO: === FDR correction performed with classifier version -1 ===
15:59:03.626221 PROGRESS: ============================= Precursor FDR =============================
15:59:03.626362 PROGRESS: Total precursors accumulated: 23,164
15:59:03.626433 PROGRESS: Target precursors: 14,031 (60.57%)
15:59:03.626494 PROGRESS: Decoy precursors: 9,133 (39.43%)
15:59:03.626555 PROGRESS: 
15:59:03.626608 PROGRESS: Precursor Summary:
15:59:03.627717 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
15:59:03.627815 PROGRESS: 
15:59:03.627878 PROGRESS: Protein Summary:
15:59:03.629011 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
15:59:03.629109 PROGRESS: =========================================================================
15:59:03.629501 INFO: Target number of precursors not reached yet.
15:59:04.108322 INFO: Starting optimization step 7.
15:59:04.108618 PROGRESS: === Extracting elution groups 25400 to 51000 ===
15:59:04.108706 INFO: Using python extraction backend
15:59:04.108830 PROGRESS: Extracting batch of 51061 precursors
15:59:04.108914 INFO: === Search parameters used ===
15:59:04.108973 INFO: rt_error       : 1199.9717345
15:59:04.109086 INFO: mobility_error : 0.1
15:59:04.109140 INFO: num_candidates : 1
15:59:04.109190 INFO: ms1_error      : 30
15:59:04.109236 INFO: ms2_error      : 30
15:59:04.109290 INFO: fwhm_rt        : 5
15:59:04.109336 INFO: quant_window   : 3
15:59:04.109380 INFO: ==============================================
15:59:04.122148 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
15:59:04.122281 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
15:59:04.122313 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
15:59:04.122337 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
15:59:04.123207 INFO: Starting candidate selection
16:01:02.611917 INFO: Starting candidate scoring
16:01:03.384778 INFO: Finished candidate processing
16:01:03.384902 INFO: Collecting candidate features
16:01:03.482629 WARNING: intensity_correlation has 11 NaNs ( 0.02 % out of 45942)
16:01:03.482939 WARNING: height_correlation has 4 NaNs ( 0.01 % out of 45942)
16:01:03.488431 INFO: Collecting fragment features
16:01:03.524014 INFO: Finished candidate scoring
16:01:03.596832 INFO: performing precursor FDR with 47 features
16:01:03.596998 INFO: Decoy channel: -1
16:01:03.597028 INFO: competitive: True
16:01:03.645147 INFO: Setting torch num_threads to 2 for FDR classification task
16:01:03.668797 WARNING: dropped 9 target PSMs due to missing features
16:01:03.668954 WARNING: dropped 13 decoy PSMs due to missing features
16:01:03.688434 INFO: Estimating optimal hyperparameters - samples: 73,273, batch_size: 300, learning_rate: 2.71e-04
16:01:03.688782 INFO: Using random state 669411 for train-test-split
16:01:09.655998 INFO: Test AUC: 0.543
16:01:09.656144 INFO: Train AUC: 0.603
16:01:09.656180 INFO: AUC difference: 9.94%
16:01:09.656206 WARNING: AUC difference > 5%. This may indicate overfitting.
16:01:09.948380 INFO: Resetting torch num_threads to 80
16:01:10.053573 PROGRESS: === Extracted 91614 precursors and 779371 fragments ===
16:01:10.054539 INFO: === FDR correction performed with classifier version -1 ===
16:01:10.067596 PROGRESS: ============================= Precursor FDR =============================
16:01:10.067801 PROGRESS: Total precursors accumulated: 46,451
16:01:10.067877 PROGRESS: Target precursors: 27,855 (59.97%)
16:01:10.067947 PROGRESS: Decoy precursors: 18,596 (40.03%)
16:01:10.068004 PROGRESS: 
16:01:10.068059 PROGRESS: Precursor Summary:
16:01:10.069436 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
16:01:10.069540 PROGRESS: 
16:01:10.069603 PROGRESS: Protein Summary:
16:01:10.070885 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
16:01:10.070993 PROGRESS: =========================================================================
16:01:10.072889 INFO: Target number of precursors not reached yet.
16:01:10.738005 INFO: Starting optimization step 8.
16:01:10.738436 PROGRESS: === Extracting elution groups 51000 to 102200 ===
16:01:10.738563 INFO: Using python extraction backend
16:01:10.738714 PROGRESS: Extracting batch of 102076 precursors
16:01:10.738815 INFO: === Search parameters used ===
16:01:10.738881 INFO: rt_error       : 1199.9717345
16:01:10.738942 INFO: mobility_error : 0.1
16:01:10.739001 INFO: num_candidates : 1
16:01:10.739058 INFO: ms1_error      : 30
16:01:10.739114 INFO: ms2_error      : 30
16:01:10.739180 INFO: fwhm_rt        : 5
16:01:10.739236 INFO: quant_window   : 3
16:01:10.739291 INFO: ==============================================
16:01:10.767714 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
16:01:10.767878 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
16:01:10.767947 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
16:01:10.767983 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
16:01:10.769051 INFO: Starting candidate selection
16:05:03.998210 INFO: Starting candidate scoring
16:05:05.471582 INFO: Finished candidate processing
16:05:05.471991 INFO: Collecting candidate features
16:05:05.686510 WARNING: intensity_correlation has 22 NaNs ( 0.02 % out of 91940)
16:05:05.686850 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 91940)
16:05:05.693695 INFO: Collecting fragment features
16:05:05.771360 INFO: Finished candidate scoring
16:05:05.941879 INFO: performing precursor FDR with 47 features
16:05:05.942047 INFO: Decoy channel: -1
16:05:05.942075 INFO: competitive: True
16:05:06.035322 INFO: Setting torch num_threads to 2 for FDR classification task
16:05:06.076171 WARNING: dropped 19 target PSMs due to missing features
16:05:06.076332 WARNING: dropped 28 decoy PSMs due to missing features
16:05:06.129845 INFO: Estimating optimal hyperparameters - samples: 146,805, batch_size: 601, learning_rate: 3.83e-04
16:05:06.130262 INFO: Using random state 774369 for train-test-split
16:05:14.252294 INFO: Test AUC: 0.545
16:05:14.252451 INFO: Train AUC: 0.592
16:05:14.252485 INFO: AUC difference: 7.92%
16:05:14.252511 WARNING: AUC difference > 5%. This may indicate overfitting.
16:05:14.563069 INFO: Resetting torch num_threads to 80
16:05:14.619466 PROGRESS: === Extracted 183554 precursors and 1563632 fragments ===
16:05:14.620409 INFO: === FDR correction performed with classifier version -1 ===
16:05:14.641501 PROGRESS: ============================= Precursor FDR =============================
16:05:14.641807 PROGRESS: Total precursors accumulated: 93,084
16:05:14.641929 PROGRESS: Target precursors: 55,127 (59.22%)
16:05:14.641994 PROGRESS: Decoy precursors: 37,957 (40.78%)
16:05:14.642049 PROGRESS: 
16:05:14.642105 PROGRESS: Precursor Summary:
16:05:14.643774 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
16:05:14.643892 PROGRESS: 
16:05:14.643957 PROGRESS: Protein Summary:
16:05:14.645496 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
16:05:14.645594 PROGRESS: =========================================================================
16:05:14.647642 INFO: Target number of precursors not reached yet.
16:05:16.062715 INFO: Starting optimization step 9.
16:05:16.063047 PROGRESS: === Extracting elution groups 102200 to 204600 ===
16:05:16.063162 INFO: Using python extraction backend
16:05:16.063320 PROGRESS: Extracting batch of 204132 precursors
16:05:16.063442 INFO: === Search parameters used ===
16:05:16.063503 INFO: rt_error       : 1199.9717345
16:05:16.063556 INFO: mobility_error : 0.1
16:05:16.063608 INFO: num_candidates : 1
16:05:16.063658 INFO: ms1_error      : 30
16:05:16.063707 INFO: ms2_error      : 30
16:05:16.063754 INFO: fwhm_rt        : 5
16:05:16.063802 INFO: quant_window   : 3
16:05:16.063850 INFO: ==============================================
16:05:16.129088 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
16:05:16.129240 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
16:05:16.129276 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
16:05:16.129300 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
16:05:16.130352 INFO: Starting candidate selection
16:12:54.476200 INFO: Starting candidate scoring
16:12:57.335378 INFO: Finished candidate processing
16:12:57.335563 INFO: Collecting candidate features
16:12:57.805599 WARNING: intensity_correlation has 44 NaNs ( 0.02 % out of 184178)
16:12:57.815919 INFO: Collecting fragment features
16:12:57.930837 INFO: Finished candidate scoring
16:12:58.486180 INFO: performing precursor FDR with 47 features
16:12:58.486350 INFO: Decoy channel: -1
16:12:58.486380 INFO: competitive: True
16:12:58.654976 INFO: Setting torch num_threads to 2 for FDR classification task
16:12:58.727482 WARNING: dropped 41 target PSMs due to missing features
16:12:58.727652 WARNING: dropped 50 decoy PSMs due to missing features
16:12:58.901533 INFO: Estimating optimal hyperparameters - samples: 294,112, batch_size: 1,204, learning_rate: 5.42e-04
16:12:58.902189 INFO: Using random state 955343 for train-test-split
16:13:09.993285 INFO: Test AUC: 0.549
16:13:09.993553 INFO: Train AUC: 0.581
16:13:09.993594 INFO: AUC difference: 5.46%
16:13:09.993619 WARNING: AUC difference > 5%. This may indicate overfitting.
16:13:11.944175 INFO: Resetting torch num_threads to 80
16:13:12.095406 PROGRESS: === Extracted 367732 precursors and 3133187 fragments ===
16:13:12.096416 INFO: === FDR correction performed with classifier version -1 ===
16:13:12.134031 PROGRESS: ============================= Precursor FDR =============================
16:13:12.134357 PROGRESS: Total precursors accumulated: 186,468
16:13:12.134428 PROGRESS: Target precursors: 108,882 (58.39%)
16:13:12.134483 PROGRESS: Decoy precursors: 77,586 (41.61%)
16:13:12.134533 PROGRESS: 
16:13:12.134582 PROGRESS: Precursor Summary:
16:13:12.136775 PROGRESS: Channel   0:	 0.050 FDR:    17; 0.010 FDR:    17; 0.001 FDR:    17
16:13:12.136871 PROGRESS: 
16:13:12.136931 PROGRESS: Protein Summary:
16:13:12.138992 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
16:13:12.139101 PROGRESS: =========================================================================
16:13:12.142477 INFO: Target number of precursors not reached yet.
16:13:13.699361 INFO: Starting optimization step 10.
16:13:13.699678 PROGRESS: === Extracting elution groups 204600 to 409400 ===
16:13:13.699771 INFO: Using python extraction backend
16:13:13.699914 PROGRESS: Extracting batch of 408390 precursors
16:13:13.699995 INFO: === Search parameters used ===
16:13:13.700051 INFO: rt_error       : 1199.9717345
16:13:13.700102 INFO: mobility_error : 0.1
16:13:13.700152 INFO: num_candidates : 1
16:13:13.700199 INFO: ms1_error      : 30
16:13:13.700245 INFO: ms2_error      : 30
16:13:13.700292 INFO: fwhm_rt        : 5
16:13:13.700351 INFO: quant_window   : 3
16:13:13.700399 INFO: ==============================================
16:13:13.818340 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
16:13:13.818493 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
16:13:13.818530 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
16:13:13.818554 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
16:13:13.819524 INFO: Starting candidate selection
16:28:56.115954 INFO: Starting candidate scoring
16:29:01.374055 INFO: Finished candidate processing
16:29:01.374506 INFO: Collecting candidate features
16:29:02.267016 WARNING: intensity_correlation has 102 NaNs ( 0.03 % out of 367032)
16:29:02.267690 WARNING: height_correlation has 14 NaNs ( 0.00 % out of 367032)
16:29:02.282702 INFO: Collecting fragment features
16:29:02.528565 INFO: Finished candidate scoring
16:29:02.956648 INFO: performing precursor FDR with 47 features
16:29:02.956797 INFO: Decoy channel: -1
16:29:02.956830 INFO: competitive: True
16:29:03.248750 INFO: Setting torch num_threads to 2 for FDR classification task
16:29:03.377170 WARNING: dropped 92 target PSMs due to missing features
16:29:03.377321 WARNING: dropped 110 decoy PSMs due to missing features
16:29:03.893616 INFO: Estimating optimal hyperparameters - samples: 587,649, batch_size: 2,407, learning_rate: 7.67e-04
16:29:03.894860 INFO: Using random state 378759 for train-test-split
16:29:21.545136 INFO: Test AUC: 0.546
16:29:21.545325 INFO: Train AUC: 0.573
16:29:21.545360 INFO: AUC difference: 4.68%
16:29:22.046416 INFO: Resetting torch num_threads to 80
16:29:22.191771 PROGRESS: === Extracted 734764 precursors and 6259603 fragments ===
16:29:22.193015 INFO: === FDR correction performed with classifier version -1 ===
16:29:22.256946 PROGRESS: ============================= Precursor FDR =============================
16:29:22.257267 PROGRESS: Total precursors accumulated: 372,590
16:29:22.257354 PROGRESS: Target precursors: 215,484 (57.83%)
16:29:22.257421 PROGRESS: Decoy precursors: 157,106 (42.17%)
16:29:22.257481 PROGRESS: 
16:29:22.257536 PROGRESS: Precursor Summary:
16:29:22.260754 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
16:29:22.260867 PROGRESS: 
16:29:22.260941 PROGRESS: Protein Summary:
16:29:22.263833 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
16:29:22.263938 PROGRESS: =========================================================================
16:29:22.269684 INFO: Target number of precursors not reached yet.
16:29:23.478013 INFO: Starting optimization step 11.
16:29:23.478317 PROGRESS: === Extracting elution groups 409400 to 819000 ===
16:29:23.478467 INFO: Using python extraction backend
16:29:23.478670 PROGRESS: Extracting batch of 816689 precursors
16:29:23.478784 INFO: === Search parameters used ===
16:29:23.478855 INFO: rt_error       : 1199.9717345
16:29:23.478913 INFO: mobility_error : 0.1
16:29:23.478966 INFO: num_candidates : 1
16:29:23.479020 INFO: ms1_error      : 30
16:29:23.479069 INFO: ms2_error      : 30
16:29:23.479117 INFO: fwhm_rt        : 5
16:29:23.479167 INFO: quant_window   : 3
16:29:23.479216 INFO: ==============================================
16:29:23.680858 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
16:29:23.681011 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
16:29:23.681075 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
16:29:23.681101 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
16:29:23.682184 INFO: Starting candidate selection
16:59:40.479644 INFO: Starting candidate scoring
16:59:50.877515 INFO: Finished candidate processing
16:59:50.877714 INFO: Collecting candidate features
16:59:52.595447 WARNING: intensity_correlation has 176 NaNs ( 0.02 % out of 735697)
16:59:52.596347 WARNING: height_correlation has 14 NaNs ( 0.00 % out of 735697)
16:59:52.622276 INFO: Collecting fragment features
16:59:53.235752 INFO: Finished candidate scoring
16:59:54.009099 INFO: performing precursor FDR with 47 features
16:59:54.009256 INFO: Decoy channel: -1
16:59:54.009293 INFO: competitive: True
16:59:54.532254 INFO: Setting torch num_threads to 2 for FDR classification task
16:59:54.760414 WARNING: dropped 162 target PSMs due to missing features
16:59:54.760580 WARNING: dropped 226 decoy PSMs due to missing features
16:59:55.257751 INFO: Estimating optimal hyperparameters - samples: 1,176,058, batch_size: 4,096, learning_rate: 1.00e-03
16:59:55.261082 INFO: Using random state 443491 for train-test-split
17:00:29.151712 INFO: Test AUC: 0.548
17:00:29.151941 INFO: Train AUC: 0.562
17:00:29.151979 INFO: AUC difference: 2.45%
17:00:29.884039 INFO: Resetting torch num_threads to 80
17:00:30.132194 PROGRESS: === Extracted 1470461 precursors and 12527657 fragments ===
17:00:30.134569 INFO: === FDR correction performed with classifier version -1 ===
17:00:30.248586 PROGRESS: ============================= Precursor FDR =============================
17:00:30.248929 PROGRESS: Total precursors accumulated: 745,589
17:00:30.249005 PROGRESS: Target precursors: 425,608 (57.08%)
17:00:30.249067 PROGRESS: Decoy precursors: 319,981 (42.92%)
17:00:30.249121 PROGRESS: 
17:00:30.249176 PROGRESS: Precursor Summary:
17:00:30.254736 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
17:00:30.254868 PROGRESS: 
17:00:30.254935 PROGRESS: Protein Summary:
17:00:30.259685 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
17:00:30.259806 PROGRESS: =========================================================================
17:00:30.269596 INFO: Target number of precursors not reached yet.
17:00:32.013122 INFO: Starting optimization step 12.
17:00:32.013428 PROGRESS: === Extracting elution groups 819000 to 1638200 ===
17:00:32.013680 INFO: Using python extraction backend
17:00:32.013839 PROGRESS: Extracting batch of 1633286 precursors
17:00:32.013942 INFO: === Search parameters used ===
17:00:32.014003 INFO: rt_error       : 1199.9717345
17:00:32.014085 INFO: mobility_error : 0.1
17:00:32.014138 INFO: num_candidates : 1
17:00:32.014187 INFO: ms1_error      : 30
17:00:32.014235 INFO: ms2_error      : 30
17:00:32.014283 INFO: fwhm_rt        : 5
17:00:32.014329 INFO: quant_window   : 3
17:00:32.014376 INFO: ==============================================
17:00:32.389004 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
17:00:32.389155 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
17:00:32.389199 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
17:00:32.389224 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
17:00:32.390156 INFO: Starting candidate selection
18:00:28.981848 INFO: Starting candidate scoring
18:00:49.511889 INFO: Finished candidate processing
18:00:49.512159 INFO: Collecting candidate features
18:00:55.406185 WARNING: intensity_correlation has 347 NaNs ( 0.02 % out of 1470726)
18:00:55.407930 WARNING: height_correlation has 36 NaNs ( 0.00 % out of 1470726)
18:00:55.458281 INFO: Collecting fragment features
18:00:58.235361 INFO: Finished candidate scoring
18:01:00.411256 INFO: performing precursor FDR with 47 features
18:01:00.411416 INFO: Decoy channel: -1
18:01:00.411450 INFO: competitive: True
18:01:04.805705 INFO: Setting torch num_threads to 2 for FDR classification task
18:01:06.554843 WARNING: dropped 353 target PSMs due to missing features
18:01:06.555017 WARNING: dropped 411 decoy PSMs due to missing features
18:01:10.356205 INFO: Estimating optimal hyperparameters - samples: 2,352,338, batch_size: 4,096, learning_rate: 1.00e-03
18:01:10.363203 INFO: Using random state 910446 for train-test-split
18:02:30.689704 INFO: Test AUC: 0.558
18:02:30.689976 INFO: Train AUC: 0.565
18:02:30.690017 INFO: AUC difference: 1.17%
18:02:31.897144 INFO: Resetting torch num_threads to 80
18:02:32.397818 PROGRESS: === Extracted 2941187 precursors and 25053733 fragments ===
18:02:32.400082 INFO: === FDR correction performed with classifier version -1 ===
18:02:32.628855 PROGRESS: ============================= Precursor FDR =============================
18:02:32.629197 PROGRESS: Total precursors accumulated: 1,491,423
18:02:32.629274 PROGRESS: Target precursors: 854,431 (57.29%)
18:02:32.629337 PROGRESS: Decoy precursors: 636,992 (42.71%)
18:02:32.629392 PROGRESS: 
18:02:32.629445 PROGRESS: Precursor Summary:
18:02:32.639714 PROGRESS: Channel   0:	 0.050 FDR: 1,123; 0.010 FDR:   732; 0.001 FDR:   311
18:02:32.639891 PROGRESS: 
18:02:32.639960 PROGRESS: Protein Summary:
18:02:32.648975 PROGRESS: Channel   0:	 0.050 FDR:   570; 0.010 FDR:   368; 0.001 FDR:   184
18:02:32.649136 PROGRESS: =========================================================================
18:02:32.668883 INFO: Target number of precursors reached.
18:02:35.499114 INFO: fragments_df: keeping 5000 of 25053733 [sum(precursor_idx_mask)=8032 sum(mass_error_mask)=25053662 stop_rank=5000
18:02:37.448219 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
18:02:37.625837 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
18:02:37.801158 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
18:02:37.977876 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
18:02:38.707305 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
18:02:38.707781 INFO: Using score_cutoff 36.67350850296021 (fac=0.99, q=1)
18:02:38.708180 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.9509620666503906
18:02:38.708273 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008910607546567917
18:02:38.708335 INFO: Updating optimization_manager: score_cutoff        : 0 -> 36.67350850296021
18:02:38.708407 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
18:02:38.913268 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
18:02:39.959277 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
18:02:40.165015 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
18:02:42.078795 INFO: Updating optimization_manager: classifier_version  : -1 -> 12
18:02:42.079084 PROGRESS: Required number of precursors found. Starting search parameter optimization.
18:02:42.079219 INFO: Starting optimization step 13.
18:02:42.079304 PROGRESS: === Extracting elution groups 0 to 819000 ===
18:02:42.079395 INFO: Using python extraction backend
18:02:42.079540 PROGRESS: Extracting batch of 1632996 precursors
18:02:42.079631 INFO: === Search parameters used ===
18:02:42.079709 INFO: rt_error       : 1199.9717345
18:02:42.079767 INFO: mobility_error : 0.1
18:02:42.079823 INFO: num_candidates : 3
18:02:42.079876 INFO: ms1_error      : 30
18:02:42.079930 INFO: ms2_error      : 30
18:02:42.079980 INFO: fwhm_rt        : 2.9509620666503906
18:02:42.080034 INFO: quant_window   : 3
18:02:42.080084 INFO: ==============================================
18:02:42.523346 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
18:02:42.523547 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
18:02:42.523607 INFO: FWHM in RT is 2.95 seconds, sigma is 0.49
18:02:42.523632 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.83
18:02:42.524471 INFO: Starting candidate selection
19:10:44.110237 INFO: Starting candidate scoring
19:11:39.076907 INFO: Finished candidate processing
19:11:39.077512 INFO: Collecting candidate features
19:11:57.253142 WARNING: intensity_correlation has 1266 NaNs ( 0.03 % out of 4218786)
19:11:57.257621 WARNING: height_correlation has 114 NaNs ( 0.00 % out of 4218786)
19:11:57.418730 INFO: Collecting fragment features
19:12:11.548476 INFO: Finished candidate scoring
19:12:14.580239 INFO: performing precursor FDR with 47 features
19:12:14.580380 INFO: Decoy channel: -1
19:12:14.580409 INFO: competitive: True
19:12:15.510694 INFO: Setting torch num_threads to 2 for FDR classification task
19:12:16.073933 WARNING: dropped 591 target PSMs due to missing features
19:12:16.074107 WARNING: dropped 753 decoy PSMs due to missing features
19:12:17.739114 INFO: Estimating optimal hyperparameters - samples: 3,373,953, batch_size: 4,096, learning_rate: 1.00e-03
19:12:17.751973 INFO: Using random state 233047 for train-test-split
19:13:47.632097 INFO: Test AUC: 0.564
19:13:47.632615 INFO: Train AUC: 0.570
19:13:47.632658 INFO: AUC difference: 0.95%
19:13:49.140238 INFO: Resetting torch num_threads to 80
19:13:49.208520 PROGRESS: === Extracted 4218786 precursors and 35167758 fragments ===
19:13:49.209930 INFO: === FDR correction performed with classifier version 12 ===
19:13:49.328070 PROGRESS: ============================= Precursor FDR =============================
19:13:49.328418 PROGRESS: Total precursors accumulated: 749,676
19:13:49.328492 PROGRESS: Target precursors: 439,838 (58.67%)
19:13:49.328571 PROGRESS: Decoy precursors: 309,838 (41.33%)
19:13:49.328627 PROGRESS: 
19:13:49.328678 PROGRESS: Precursor Summary:
19:13:49.334390 PROGRESS: Channel   0:	 0.050 FDR:   647; 0.010 FDR:   435; 0.001 FDR:   255
19:13:49.334533 PROGRESS: 
19:13:49.334601 PROGRESS: Protein Summary:
19:13:49.339573 PROGRESS: Channel   0:	 0.050 FDR:   425; 0.010 FDR:   275; 0.001 FDR:   167
19:13:49.339689 PROGRESS: =========================================================================
19:13:49.376553 INFO: Target number of precursors reached.
19:13:53.018477 INFO: fragments_df: keeping 5000 of 35167758 [sum(precursor_idx_mask)=12978 sum(mass_error_mask)=35167633 stop_rank=5000
19:13:54.412644 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:13:54.547315 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:13:54.706736 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:13:54.862730 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:13:55.581244 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:13:55.581692 INFO: Using score_cutoff 36.777632450866705 (fac=0.99, q=1)
19:13:55.582050 INFO: Updating optimization_manager: fwhm_rt             : 2.9509620666503906 -> 2.847290515899658
19:13:55.582139 INFO: Updating optimization_manager: fwhm_mobility       : 0.008910607546567917 -> 0.008373254910111427
19:13:55.582200 INFO: Updating optimization_manager: score_cutoff        : 36.67350850296021 -> 36.777632450866705
19:13:55.582284 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:13:55.684584 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:13:56.214360 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:13:56.323308 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:13:57.273262 INFO: === checking if optimization conditions were reached ===
19:13:57.275932 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
19:13:57.276096 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
19:13:57.276179 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
19:13:57.277300 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
19:13:57.277421 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
19:13:57.277493 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
19:13:57.277556 INFO: ==============================================
19:13:57.277633 INFO: Starting optimization step 14.
19:13:57.277701 PROGRESS: === Extracting elution groups 0 to 409400 ===
19:13:57.277784 INFO: Using python extraction backend
19:13:57.277948 PROGRESS: Extracting batch of 816307 precursors
19:13:57.278031 INFO: === Search parameters used ===
19:13:57.278090 INFO: rt_error       : 1199.9717345
19:13:57.278141 INFO: mobility_error : 0.1
19:13:57.278190 INFO: num_candidates : 3
19:13:57.278243 INFO: ms1_error      : 15.0
19:13:57.278290 INFO: ms2_error      : 15.0
19:13:57.278334 INFO: fwhm_rt        : 2.847290515899658
19:13:57.278378 INFO: quant_window   : 3
19:13:57.278421 INFO: ==============================================
19:13:57.480681 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
19:13:57.480832 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
19:13:57.480895 INFO: FWHM in RT is 2.85 seconds, sigma is 0.47
19:13:57.480919 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.54
19:13:57.481793 INFO: Starting candidate selection
19:43:17.954456 INFO: Starting candidate scoring
19:43:41.913362 INFO: Finished candidate processing
19:43:41.913645 INFO: Collecting candidate features
19:43:45.898400 WARNING: intensity_correlation has 2228 NaNs ( 0.11 % out of 2063250)
19:43:45.900469 WARNING: height_correlation has 135 NaNs ( 0.01 % out of 2063250)
19:43:45.969929 INFO: Collecting fragment features
19:43:46.992630 INFO: Finished candidate scoring
19:43:48.248649 INFO: performing precursor FDR with 47 features
19:43:48.248791 INFO: Decoy channel: -1
19:43:48.248822 INFO: competitive: True
19:43:48.714451 INFO: Setting torch num_threads to 2 for FDR classification task
19:43:49.009063 WARNING: dropped 1102 target PSMs due to missing features
19:43:49.009216 WARNING: dropped 1216 decoy PSMs due to missing features
19:43:49.788067 INFO: Estimating optimal hyperparameters - samples: 1,648,745, batch_size: 4,096, learning_rate: 1.00e-03
19:43:49.792138 INFO: Using random state 655426 for train-test-split
19:44:35.081756 INFO: Test AUC: 0.560
19:44:35.082047 INFO: Train AUC: 0.573
19:44:35.082086 INFO: AUC difference: 2.25%
19:44:35.986910 INFO: Resetting torch num_threads to 80
19:44:36.027552 PROGRESS: === Extracted 2063250 precursors and 14734908 fragments ===
19:44:36.028635 INFO: === FDR correction performed with classifier version 13 ===
19:44:36.090015 PROGRESS: ============================= Precursor FDR =============================
19:44:36.090340 PROGRESS: Total precursors accumulated: 373,720
19:44:36.090420 PROGRESS: Target precursors: 218,779 (58.54%)
19:44:36.090482 PROGRESS: Decoy precursors: 154,941 (41.46%)
19:44:36.090537 PROGRESS: 
19:44:36.090590 PROGRESS: Precursor Summary:
19:44:36.094381 PROGRESS: Channel   0:	 0.050 FDR:   451; 0.010 FDR:   307; 0.001 FDR:   262
19:44:36.094517 PROGRESS: 
19:44:36.094585 PROGRESS: Protein Summary:
19:44:36.097960 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   222; 0.001 FDR:   191
19:44:36.098072 PROGRESS: =========================================================================
19:44:36.118191 INFO: Target number of precursors reached.
19:44:37.703554 INFO: fragments_df: keeping 5000 of 14734908 [sum(precursor_idx_mask)=8728 sum(mass_error_mask)=14734770 stop_rank=5000
19:44:38.852218 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:44:38.967917 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:44:39.087782 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:44:39.211981 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:44:39.928456 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:44:39.928910 INFO: Using score_cutoff 36.075213054656984 (fac=0.99, q=1)
19:44:39.929290 INFO: Updating optimization_manager: fwhm_rt             : 2.847290515899658 -> 2.7775931358337402
19:44:39.929386 INFO: Updating optimization_manager: fwhm_mobility       : 0.008373254910111427 -> 0.0071370238438248634
19:44:39.929453 INFO: Updating optimization_manager: score_cutoff        : 36.777632450866705 -> 36.075213054656984
19:44:39.929518 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:44:40.032541 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:44:40.558026 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:44:40.664914 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:44:41.615527 INFO: === checking if optimization conditions were reached ===
19:44:41.617881 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
19:44:41.618052 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
19:44:41.618147 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
19:44:41.619241 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
19:44:41.619357 INFO: Updating optimization_manager: classifier_version  : 14 -> 14
19:44:41.619438 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
19:44:41.619531 INFO: ==============================================
19:44:41.619625 PROGRESS: Optimization finished for ms2_error, ms1_error.
19:44:42.629733 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:44:42.733737 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:44:43.260232 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:44:43.367325 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:44:44.326475 INFO: Starting optimization step 0.
19:44:44.326776 PROGRESS: === Extracting elution groups 0 to 409400 ===
19:44:44.326891 INFO: Using python extraction backend
19:44:44.327077 PROGRESS: Extracting batch of 816307 precursors
19:44:44.327179 INFO: === Search parameters used ===
19:44:44.327252 INFO: rt_error       : 1199.9717345
19:44:44.327319 INFO: mobility_error : 0.1
19:44:44.327381 INFO: num_candidates : 3
19:44:44.327441 INFO: ms1_error      : 15.0
19:44:44.327498 INFO: ms2_error      : 15.0
19:44:44.327557 INFO: fwhm_rt        : 2.7775931358337402
19:44:44.327613 INFO: quant_window   : 3
19:44:44.327671 INFO: ==============================================
19:44:44.547942 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
19:44:44.548101 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
19:44:44.548165 INFO: FWHM in RT is 2.78 seconds, sigma is 0.46
19:44:44.548197 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.87
19:44:44.549050 INFO: Starting candidate selection
20:14:58.805553 INFO: Starting candidate scoring
20:15:23.387248 INFO: Finished candidate processing
20:15:23.387446 INFO: Collecting candidate features
20:15:27.728829 WARNING: intensity_correlation has 2231 NaNs ( 0.11 % out of 2057117)
20:15:27.730938 WARNING: height_correlation has 145 NaNs ( 0.01 % out of 2057117)
20:15:27.800586 INFO: Collecting fragment features
20:15:28.826102 INFO: Finished candidate scoring
20:15:30.135378 INFO: performing precursor FDR with 47 features
20:15:30.135529 INFO: Decoy channel: -1
20:15:30.135569 INFO: competitive: True
20:15:30.724739 INFO: Setting torch num_threads to 2 for FDR classification task
20:15:31.140695 WARNING: dropped 1128 target PSMs due to missing features
20:15:31.140872 WARNING: dropped 1200 decoy PSMs due to missing features
20:15:31.902331 INFO: Estimating optimal hyperparameters - samples: 1,643,831, batch_size: 4,096, learning_rate: 1.00e-03
20:15:31.909116 INFO: Using random state 291852 for train-test-split
20:16:16.483916 INFO: Test AUC: 0.564
20:16:16.484740 INFO: Train AUC: 0.575
20:16:16.484785 INFO: AUC difference: 1.91%
20:16:17.418263 INFO: Resetting torch num_threads to 80
20:16:17.468201 PROGRESS: === Extracted 2057117 precursors and 14611444 fragments ===
20:16:17.469465 INFO: === FDR correction performed with classifier version 14 ===
20:16:17.555343 PROGRESS: ============================= Precursor FDR =============================
20:16:17.555686 PROGRESS: Total precursors accumulated: 373,341
20:16:17.555759 PROGRESS: Target precursors: 219,545 (58.81%)
20:16:17.555816 PROGRESS: Decoy precursors: 153,796 (41.19%)
20:16:17.555869 PROGRESS: 
20:16:17.555918 PROGRESS: Precursor Summary:
20:16:17.559390 PROGRESS: Channel   0:	 0.050 FDR:   481; 0.010 FDR:   336; 0.001 FDR:   270
20:16:17.559501 PROGRESS: 
20:16:17.559565 PROGRESS: Protein Summary:
20:16:17.562728 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   248; 0.001 FDR:   201
20:16:17.562835 PROGRESS: =========================================================================
20:16:17.581787 INFO: Target number of precursors reached.
20:16:19.212763 INFO: fragments_df: keeping 5000 of 14611444 [sum(precursor_idx_mask)=9692 sum(mass_error_mask)=14611314 stop_rank=5000
20:16:21.113461 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
20:16:21.229117 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
20:16:21.352206 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
20:16:21.476190 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
20:16:22.131435 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
20:16:22.131918 INFO: Using score_cutoff 33.08223085784912 (fac=0.99, q=1)
20:16:22.132297 INFO: Updating optimization_manager: fwhm_rt             : 2.7775931358337402 -> 2.7720723152160645
20:16:22.132397 INFO: Updating optimization_manager: fwhm_mobility       : 0.0071370238438248634 -> 0.0066372789442539215
20:16:22.132460 INFO: Updating optimization_manager: score_cutoff        : 36.075213054656984 -> 33.08223085784912
20:16:22.132527 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:16:22.238262 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:16:22.782780 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:16:22.889462 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:16:23.899815 INFO: === checking if optimization conditions were reached ===
20:16:23.900129 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
20:16:23.902503 INFO: Updating optimization_manager: rt_error            : 1199.9717345 -> 313.90915596916665
20:16:23.902644 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 313.9092.
20:16:23.902723 INFO: ==============================================
20:16:23.902808 INFO: Starting optimization step 1.
20:16:23.902880 PROGRESS: === Extracting elution groups 0 to 409400 ===
20:16:23.902969 INFO: Using python extraction backend
20:16:23.903112 PROGRESS: Extracting batch of 816307 precursors
20:16:23.903199 INFO: === Search parameters used ===
20:16:23.903262 INFO: rt_error       : 313.90915596916665
20:16:23.903314 INFO: mobility_error : 0.1
20:16:23.903365 INFO: num_candidates : 3
20:16:23.903428 INFO: ms1_error      : 15.0
20:16:23.903478 INFO: ms2_error      : 15.0
20:16:23.903525 INFO: fwhm_rt        : 2.7720723152160645
20:16:23.903573 INFO: quant_window   : 3
20:16:23.903620 INFO: ==============================================
20:16:24.145890 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
20:16:24.146053 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
20:16:24.146114 INFO: FWHM in RT is 2.77 seconds, sigma is 0.46
20:16:24.146143 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.60
20:16:24.146999 INFO: Starting candidate selection
20:25:49.643049 INFO: Starting candidate scoring
20:26:14.158880 INFO: Finished candidate processing
20:26:14.159145 INFO: Collecting candidate features
20:26:18.415338 WARNING: intensity_correlation has 4461 NaNs ( 0.23 % out of 1936708)
20:26:18.417550 WARNING: height_correlation has 448 NaNs ( 0.02 % out of 1936708)
20:26:18.492434 INFO: Collecting fragment features
20:26:19.523919 INFO: Finished candidate scoring
20:26:21.059154 INFO: performing precursor FDR with 47 features
20:26:21.059340 INFO: Decoy channel: -1
20:26:21.059393 INFO: competitive: True
20:26:21.576003 INFO: Setting torch num_threads to 2 for FDR classification task
20:26:21.900873 WARNING: dropped 2344 target PSMs due to missing features
20:26:21.901057 WARNING: dropped 2349 decoy PSMs due to missing features
20:26:22.622871 INFO: Estimating optimal hyperparameters - samples: 1,545,612, batch_size: 4,096, learning_rate: 1.00e-03
20:26:22.627920 INFO: Using random state 291852 for train-test-split
20:27:02.379791 INFO: Test AUC: 0.552
20:27:02.380008 INFO: Train AUC: 0.564
20:27:02.380045 INFO: AUC difference: 2.09%
20:27:03.291124 INFO: Resetting torch num_threads to 80
20:27:03.342185 PROGRESS: === Extracted 1936708 precursors and 12130785 fragments ===
20:27:03.343792 INFO: === FDR correction performed with classifier version 14 ===
20:27:03.425924 PROGRESS: ============================= Precursor FDR =============================
20:27:03.426269 PROGRESS: Total precursors accumulated: 368,042
20:27:03.426348 PROGRESS: Target precursors: 211,320 (57.42%)
20:27:03.426409 PROGRESS: Decoy precursors: 156,722 (42.58%)
20:27:03.426462 PROGRESS: 
20:27:03.426515 PROGRESS: Precursor Summary:
20:27:03.430022 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   362; 0.001 FDR:   116
20:27:03.430138 PROGRESS: 
20:27:03.430202 PROGRESS: Protein Summary:
20:27:03.433316 PROGRESS: Channel   0:	 0.050 FDR:   452; 0.010 FDR:   264; 0.001 FDR:    94
20:27:03.433420 PROGRESS: =========================================================================
20:27:03.453125 INFO: Target number of precursors reached.
20:27:04.766146 INFO: fragments_df: keeping 5000 of 12130785 [sum(precursor_idx_mask)=10128 sum(mass_error_mask)=12130543 stop_rank=5000
20:27:06.714454 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
20:27:06.833720 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
20:27:06.964891 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
20:27:07.084250 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
20:27:07.735125 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
20:27:07.735612 INFO: Using score_cutoff 21.52985448875427 (fac=0.99, q=1)
20:27:07.735964 INFO: Updating optimization_manager: fwhm_rt             : 2.7720723152160645 -> 2.7527899742126465
20:27:07.736053 INFO: Updating optimization_manager: fwhm_mobility       : 0.0066372789442539215 -> 0.0065730842761695385
20:27:07.736115 INFO: Updating optimization_manager: score_cutoff        : 33.08223085784912 -> 21.52985448875427
20:27:07.736175 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:27:07.845997 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:27:08.384908 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:27:08.490278 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:27:09.538309 INFO: === checking if optimization conditions were reached ===
20:27:09.538645 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
20:27:09.541013 INFO: Updating optimization_manager: rt_error            : 313.90915596916665 -> 186.78184574480488
20:27:09.541161 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 186.7818.
20:27:09.541239 INFO: ==============================================
20:27:09.541329 INFO: Starting optimization step 2.
20:27:09.541414 PROGRESS: === Extracting elution groups 0 to 409400 ===
20:27:09.541485 INFO: Using python extraction backend
20:27:09.541603 PROGRESS: Extracting batch of 816307 precursors
20:27:09.541696 INFO: === Search parameters used ===
20:27:09.541756 INFO: rt_error       : 186.78184574480488
20:27:09.541807 INFO: mobility_error : 0.1
20:27:09.541857 INFO: num_candidates : 3
20:27:09.541922 INFO: ms1_error      : 15.0
20:27:09.541969 INFO: ms2_error      : 15.0
20:27:09.542015 INFO: fwhm_rt        : 2.7527899742126465
20:27:09.542062 INFO: quant_window   : 3
20:27:09.542108 INFO: ==============================================
20:27:09.792374 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
20:27:09.792542 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
20:27:09.792594 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
20:27:09.792621 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.56
20:27:09.793447 INFO: Starting candidate selection
20:32:36.725938 INFO: Starting candidate scoring
20:32:59.801059 INFO: Finished candidate processing
20:32:59.801565 INFO: Collecting candidate features
20:33:03.770486 WARNING: intensity_correlation has 5673 NaNs ( 0.30 % out of 1875536)
20:33:03.772453 WARNING: height_correlation has 592 NaNs ( 0.03 % out of 1875536)
20:33:03.834965 INFO: Collecting fragment features
20:33:04.733046 INFO: Finished candidate scoring
20:33:05.944736 INFO: performing precursor FDR with 47 features
20:33:05.944881 INFO: Decoy channel: -1
20:33:05.944911 INFO: competitive: True
20:33:06.443618 INFO: Setting torch num_threads to 2 for FDR classification task
20:33:06.763938 WARNING: dropped 2992 target PSMs due to missing features
20:33:06.764092 WARNING: dropped 2982 decoy PSMs due to missing features
20:33:07.427989 INFO: Estimating optimal hyperparameters - samples: 1,495,649, batch_size: 4,096, learning_rate: 1.00e-03
20:33:07.432191 INFO: Using random state 291852 for train-test-split
20:33:44.303116 INFO: Test AUC: 0.552
20:33:44.303338 INFO: Train AUC: 0.564
20:33:44.303376 INFO: AUC difference: 2.06%
20:33:45.172586 INFO: Resetting torch num_threads to 80
20:33:45.222796 PROGRESS: === Extracted 1875536 precursors and 11163457 fragments ===
20:33:45.223970 INFO: === FDR correction performed with classifier version 14 ===
20:33:45.298837 PROGRESS: ============================= Precursor FDR =============================
20:33:45.299146 PROGRESS: Total precursors accumulated: 365,004
20:33:45.299222 PROGRESS: Target precursors: 208,697 (57.18%)
20:33:45.299281 PROGRESS: Decoy precursors: 156,307 (42.82%)
20:33:45.299333 PROGRESS: 
20:33:45.299384 PROGRESS: Precursor Summary:
20:33:45.302956 PROGRESS: Channel   0:	 0.050 FDR:   547; 0.010 FDR:   432; 0.001 FDR:   345
20:33:45.303120 PROGRESS: 
20:33:45.303202 PROGRESS: Protein Summary:
20:33:45.306401 PROGRESS: Channel   0:	 0.050 FDR:   415; 0.010 FDR:   319; 0.001 FDR:   257
20:33:45.306507 PROGRESS: =========================================================================
20:33:45.325308 INFO: Target number of precursors reached.
20:33:46.483916 INFO: fragments_df: keeping 5000 of 11163457 [sum(precursor_idx_mask)=11698 sum(mass_error_mask)=11163244 stop_rank=5000
20:33:47.402253 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
20:33:47.551530 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
20:33:47.706734 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
20:33:47.853378 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
20:33:48.571090 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
20:33:48.571562 INFO: Using score_cutoff 29.615377723503112 (fac=0.99, q=1)
20:33:48.571897 INFO: Updating optimization_manager: fwhm_rt             : 2.7527899742126465 -> 2.7380309104919434
20:33:48.571983 INFO: Updating optimization_manager: fwhm_mobility       : 0.0065730842761695385 -> 0.0059190294705331326
20:33:48.572042 INFO: Updating optimization_manager: score_cutoff        : 21.52985448875427 -> 29.615377723503112
20:33:48.572109 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:33:48.625199 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:33:48.878750 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:33:48.932728 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:33:49.432387 INFO: === checking if optimization conditions were reached ===
20:33:49.432662 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
20:33:49.435109 INFO: Updating optimization_manager: rt_error            : 186.78184574480488 -> 183.71276073795946
20:33:49.435238 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 183.7128.
20:33:49.435330 INFO: ==============================================
20:33:49.435414 INFO: Starting optimization step 3.
20:33:49.435481 PROGRESS: === Extracting elution groups 0 to 204600 ===
20:33:49.435548 INFO: Using python extraction backend
20:33:49.435660 PROGRESS: Extracting batch of 407917 precursors
20:33:49.435732 INFO: === Search parameters used ===
20:33:49.435784 INFO: rt_error       : 183.71276073795946
20:33:49.435832 INFO: mobility_error : 0.1
20:33:49.435877 INFO: num_candidates : 3
20:33:49.435922 INFO: ms1_error      : 15.0
20:33:49.435966 INFO: ms2_error      : 15.0
20:33:49.436009 INFO: fwhm_rt        : 2.7380309104919434
20:33:49.436053 INFO: quant_window   : 3
20:33:49.436097 INFO: ==============================================
20:33:49.561002 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
20:33:49.561153 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
20:33:49.561202 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
20:33:49.561228 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.21
20:33:49.562039 INFO: Starting candidate selection
20:36:29.407698 INFO: Starting candidate scoring
20:36:40.818235 INFO: Finished candidate processing
20:36:40.818542 INFO: Collecting candidate features
20:36:42.657462 WARNING: intensity_correlation has 2872 NaNs ( 0.31 % out of 936394)
20:36:42.658521 WARNING: height_correlation has 346 NaNs ( 0.04 % out of 936394)
20:36:42.691288 INFO: Collecting fragment features
20:36:43.151385 INFO: Finished candidate scoring
20:36:43.768201 INFO: performing precursor FDR with 47 features
20:36:43.768344 INFO: Decoy channel: -1
20:36:43.768373 INFO: competitive: True
20:36:44.031576 INFO: Setting torch num_threads to 2 for FDR classification task
20:36:44.198191 WARNING: dropped 1520 target PSMs due to missing features
20:36:44.198354 WARNING: dropped 1539 decoy PSMs due to missing features
20:36:44.491820 INFO: Estimating optimal hyperparameters - samples: 746,668, batch_size: 3,058, learning_rate: 8.64e-04
20:36:44.493817 INFO: Using random state 291852 for train-test-split
20:37:03.414247 INFO: Test AUC: 0.552
20:37:03.414428 INFO: Train AUC: 0.569
20:37:03.414465 INFO: AUC difference: 3.02%
20:37:03.963772 INFO: Resetting torch num_threads to 80
20:37:03.989673 PROGRESS: === Extracted 936394 precursors and 5541122 fragments ===
20:37:03.990581 INFO: === FDR correction performed with classifier version 14 ===
20:37:04.028733 PROGRESS: ============================= Precursor FDR =============================
20:37:04.029016 PROGRESS: Total precursors accumulated: 182,688
20:37:04.029088 PROGRESS: Target precursors: 105,303 (57.64%)
20:37:04.029146 PROGRESS: Decoy precursors: 77,385 (42.36%)
20:37:04.029199 PROGRESS: 
20:37:04.029265 PROGRESS: Precursor Summary:
20:37:04.031532 PROGRESS: Channel   0:	 0.050 FDR:   272; 0.010 FDR:   209; 0.001 FDR:   177
20:37:04.031647 PROGRESS: 
20:37:04.031709 PROGRESS: Protein Summary:
20:37:04.033831 PROGRESS: Channel   0:	 0.050 FDR:   223; 0.010 FDR:   171; 0.001 FDR:   146
20:37:04.033947 PROGRESS: =========================================================================
20:37:04.048272 INFO: Target number of precursors reached.
20:37:04.645921 INFO: fragments_df: keeping 3640 of 5541122 [sum(precursor_idx_mask)=5741 sum(mass_error_mask)=5541002 stop_rank=3640
20:37:05.329267 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
20:37:05.443347 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
20:37:05.551820 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
20:37:05.667283 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
20:37:06.115924 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
20:37:06.116401 INFO: Using score_cutoff 28.209907775115965 (fac=0.99, q=1)
20:37:06.116729 INFO: Updating optimization_manager: fwhm_rt             : 2.7380309104919434 -> 2.7388219833374023
20:37:06.116822 INFO: Updating optimization_manager: fwhm_mobility       : 0.0059190294705331326 -> 0.005941200535744429
20:37:06.116890 INFO: Updating optimization_manager: score_cutoff        : 29.615377723503112 -> 28.209907775115965
20:37:06.116954 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:37:06.169299 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:37:06.422765 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:37:06.482955 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:37:06.994583 INFO: === checking if optimization conditions were reached ===
20:37:06.994867 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
20:37:06.996325 INFO: Updating optimization_manager: rt_error            : 183.71276073795946 -> 183.71276073795946
20:37:06.996498 INFO: Updating optimization_manager: classifier_version  : 14 -> 18
20:37:06.996618 INFO: Updating optimization_manager: score_cutoff        : 28.209907775115965 -> 28.209907775115965
20:37:06.996723 INFO: Updating optimization_manager: fwhm_rt             : 2.7388219833374023 -> 2.7388219833374023
20:37:06.996824 INFO: Updating optimization_manager: fwhm_mobility       : 0.005941200535744429 -> 0.005941200535744429
20:37:06.996923 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 183.7128 found after 4 searches.
20:37:06.996997 INFO: ==============================================
20:37:06.997076 PROGRESS: Optimization finished for rt_error.
20:37:07.623651 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:37:07.676058 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:37:07.929888 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:37:07.990078 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:37:08.505460 INFO: Starting optimization step 0.
20:37:08.505738 PROGRESS: === Extracting elution groups 0 to 204600 ===
20:37:08.505828 INFO: Using python extraction backend
20:37:08.505966 PROGRESS: Extracting batch of 407917 precursors
20:37:08.506055 INFO: === Search parameters used ===
20:37:08.506117 INFO: rt_error       : 183.71276073795946
20:37:08.506171 INFO: mobility_error : 0.1
20:37:08.506226 INFO: num_candidates : 3
20:37:08.506277 INFO: ms1_error      : 15.0
20:37:08.506330 INFO: ms2_error      : 15.0
20:37:08.506380 INFO: fwhm_rt        : 2.7388219833374023
20:37:08.506428 INFO: quant_window   : 3
20:37:08.506476 INFO: ==============================================
20:37:08.629933 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
20:37:08.630090 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
20:37:08.630142 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
20:37:08.630169 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.22
20:37:08.630861 INFO: Starting candidate selection
20:39:52.937521 INFO: Starting candidate scoring
20:40:04.207218 INFO: Finished candidate processing
20:40:04.207386 INFO: Collecting candidate features
20:40:06.026870 WARNING: intensity_correlation has 2833 NaNs ( 0.30 % out of 939442)
20:40:06.027907 WARNING: height_correlation has 338 NaNs ( 0.04 % out of 939442)
20:40:06.061309 INFO: Collecting fragment features
20:40:06.531896 INFO: Finished candidate scoring
20:40:07.144960 INFO: performing precursor FDR with 47 features
20:40:07.145112 INFO: Decoy channel: -1
20:40:07.145141 INFO: competitive: True
20:40:07.427150 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:07.606282 WARNING: dropped 1493 target PSMs due to missing features
20:40:07.606448 WARNING: dropped 1525 decoy PSMs due to missing features
20:40:07.913507 INFO: Estimating optimal hyperparameters - samples: 749,139, batch_size: 3,068, learning_rate: 8.65e-04
20:40:07.914946 INFO: Using random state 558768 for train-test-split
20:40:26.593417 INFO: Test AUC: 0.556
20:40:26.593597 INFO: Train AUC: 0.578
20:40:26.593633 INFO: AUC difference: 3.74%
20:40:27.145923 INFO: Resetting torch num_threads to 80
20:40:27.172024 PROGRESS: === Extracted 939442 precursors and 5570678 fragments ===
20:40:27.172905 INFO: === FDR correction performed with classifier version 18 ===
20:40:27.210876 PROGRESS: ============================= Precursor FDR =============================
20:40:27.211169 PROGRESS: Total precursors accumulated: 183,033
20:40:27.211242 PROGRESS: Target precursors: 106,808 (58.35%)
20:40:27.211302 PROGRESS: Decoy precursors: 76,225 (41.65%)
20:40:27.211370 PROGRESS: 
20:40:27.211422 PROGRESS: Precursor Summary:
20:40:27.213710 PROGRESS: Channel   0:	 0.050 FDR:   289; 0.010 FDR:   179; 0.001 FDR:   158
20:40:27.213811 PROGRESS: 
20:40:27.213883 PROGRESS: Protein Summary:
20:40:27.216002 PROGRESS: Channel   0:	 0.050 FDR:   245; 0.010 FDR:   150; 0.001 FDR:   134
20:40:27.216099 PROGRESS: =========================================================================
20:40:27.223093 INFO: Target number of precursors not reached yet.
20:40:27.899143 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:40:27.951573 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:40:28.212661 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:40:28.278746 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:40:28.790766 INFO: === skipping optimization until target number of precursors are found ===
20:40:28.791080 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
20:40:28.791207 INFO: Starting optimization step 1.
20:40:28.791289 PROGRESS: === Extracting elution groups 204600 to 409400 ===
20:40:28.791360 INFO: Using python extraction backend
20:40:28.791476 PROGRESS: Extracting batch of 408390 precursors
20:40:28.791559 INFO: === Search parameters used ===
20:40:28.791613 INFO: rt_error       : 183.71276073795946
20:40:28.791677 INFO: mobility_error : 0.1
20:40:28.791727 INFO: num_candidates : 3
20:40:28.791772 INFO: ms1_error      : 15.0
20:40:28.791817 INFO: ms2_error      : 15.0
20:40:28.791862 INFO: fwhm_rt        : 2.7388219833374023
20:40:28.791906 INFO: quant_window   : 3
20:40:28.791948 INFO: ==============================================
20:40:28.914576 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
20:40:28.914728 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
20:40:28.914776 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
20:40:28.914799 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.22
20:40:28.915583 INFO: Starting candidate selection
20:43:10.987845 INFO: Starting candidate scoring
20:43:22.377746 INFO: Finished candidate processing
20:43:22.377990 INFO: Collecting candidate features
20:43:24.177447 WARNING: intensity_correlation has 2825 NaNs ( 0.30 % out of 937691)
20:43:24.178518 WARNING: height_correlation has 280 NaNs ( 0.03 % out of 937691)
20:43:24.211313 INFO: Collecting fragment features
20:43:24.652795 INFO: Finished candidate scoring
20:43:25.597390 INFO: performing precursor FDR with 47 features
20:43:25.597556 INFO: Decoy channel: -1
20:43:25.597585 INFO: competitive: True
20:43:26.361013 INFO: Setting torch num_threads to 2 for FDR classification task
20:43:26.682319 WARNING: dropped 2993 target PSMs due to missing features
20:43:26.682484 WARNING: dropped 2990 decoy PSMs due to missing features
20:43:27.551200 INFO: Estimating optimal hyperparameters - samples: 1,496,920, batch_size: 4,096, learning_rate: 1.00e-03
20:43:27.554106 INFO: Using random state 558768 for train-test-split
20:44:04.137029 INFO: Test AUC: 0.552
20:44:04.137218 INFO: Train AUC: 0.567
20:44:04.137256 INFO: AUC difference: 2.55%
20:44:04.970871 INFO: Resetting torch num_threads to 80
20:44:05.308754 PROGRESS: === Extracted 1877133 precursors and 11126732 fragments ===
20:44:05.309987 INFO: === FDR correction performed with classifier version 18 ===
20:44:05.385185 PROGRESS: ============================= Precursor FDR =============================
20:44:05.385510 PROGRESS: Total precursors accumulated: 365,747
20:44:05.385583 PROGRESS: Target precursors: 209,541 (57.29%)
20:44:05.385643 PROGRESS: Decoy precursors: 156,206 (42.71%)
20:44:05.385721 PROGRESS: 
20:44:05.385807 PROGRESS: Precursor Summary:
20:44:05.389345 PROGRESS: Channel   0:	 0.050 FDR:   545; 0.010 FDR:   381; 0.001 FDR:   293
20:44:05.389462 PROGRESS: 
20:44:05.389528 PROGRESS: Protein Summary:
20:44:05.392614 PROGRESS: Channel   0:	 0.050 FDR:   416; 0.010 FDR:   280; 0.001 FDR:   211
20:44:05.392721 PROGRESS: =========================================================================
20:44:05.400102 INFO: Target number of precursors reached.
20:44:06.653590 INFO: fragments_df: keeping 5000 of 11126732 [sum(precursor_idx_mask)=10633 sum(mass_error_mask)=11126527 stop_rank=5000
20:44:07.825329 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
20:44:07.974494 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
20:44:08.119841 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
20:44:08.265585 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
20:44:08.919915 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
20:44:08.920392 INFO: Using score_cutoff 29.152784660339353 (fac=0.99, q=1)
20:44:08.920723 INFO: Updating optimization_manager: fwhm_rt             : 2.7388219833374023 -> 2.7572174072265625
20:44:08.920807 INFO: Updating optimization_manager: fwhm_mobility       : 0.005941200535744429 -> 0.006357881706207991
20:44:08.920869 INFO: Updating optimization_manager: score_cutoff        : 28.209907775115965 -> 29.152784660339353
20:44:08.920934 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:44:09.023128 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:44:09.545832 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:44:09.651585 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:44:10.631780 INFO: === checking if optimization conditions were reached ===
20:44:10.632124 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
20:44:10.634240 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0836276498894171
20:44:10.634387 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0836.
20:44:10.634485 INFO: ==============================================
20:44:10.634572 INFO: Starting optimization step 2.
20:44:10.634647 PROGRESS: === Extracting elution groups 0 to 409400 ===
20:44:10.634718 INFO: Using python extraction backend
20:44:10.634833 PROGRESS: Extracting batch of 816307 precursors
20:44:10.634908 INFO: === Search parameters used ===
20:44:10.634966 INFO: rt_error       : 183.71276073795946
20:44:10.635019 INFO: mobility_error : 0.0836276498894171
20:44:10.635069 INFO: num_candidates : 3
20:44:10.635121 INFO: ms1_error      : 15.0
20:44:10.635171 INFO: ms2_error      : 15.0
20:44:10.635220 INFO: fwhm_rt        : 2.7572174072265625
20:44:10.635268 INFO: quant_window   : 3
20:44:10.635316 INFO: ==============================================
20:44:10.878661 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
20:44:10.878824 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
20:44:10.878877 INFO: FWHM in RT is 2.76 seconds, sigma is 0.46
20:44:10.878906 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.45
20:44:10.891554 INFO: Starting candidate selection
20:48:51.726947 INFO: Starting candidate scoring
20:49:14.697743 INFO: Finished candidate processing
20:49:14.698035 INFO: Collecting candidate features
20:49:18.225751 WARNING: intensity_correlation has 5947 NaNs ( 0.32 % out of 1841276)
20:49:18.227566 WARNING: height_correlation has 645 NaNs ( 0.04 % out of 1841276)
20:49:18.290896 INFO: Collecting fragment features
20:49:19.274919 INFO: Finished candidate scoring
20:49:20.605030 INFO: performing precursor FDR with 47 features
20:49:20.605186 INFO: Decoy channel: -1
20:49:20.605214 INFO: competitive: True
20:49:21.086570 INFO: Setting torch num_threads to 2 for FDR classification task
20:49:21.390692 WARNING: dropped 3144 target PSMs due to missing features
20:49:21.390903 WARNING: dropped 3126 decoy PSMs due to missing features
20:49:22.656443 INFO: Estimating optimal hyperparameters - samples: 1,468,004, batch_size: 4,096, learning_rate: 1.00e-03
20:49:22.661720 INFO: Using random state 558768 for train-test-split
20:50:05.047148 INFO: Test AUC: 0.553
20:50:05.047410 INFO: Train AUC: 0.567
20:50:05.047459 INFO: AUC difference: 2.45%
20:50:05.910173 INFO: Resetting torch num_threads to 80
20:50:05.944523 PROGRESS: === Extracted 1841276 precursors and 10851335 fragments ===
20:50:05.945860 INFO: === FDR correction performed with classifier version 18 ===
20:50:06.009631 PROGRESS: ============================= Precursor FDR =============================
20:50:06.009983 PROGRESS: Total precursors accumulated: 360,705
20:50:06.010074 PROGRESS: Target precursors: 206,539 (57.26%)
20:50:06.010137 PROGRESS: Decoy precursors: 154,166 (42.74%)
20:50:06.010192 PROGRESS: 
20:50:06.010247 PROGRESS: Precursor Summary:
20:50:06.013982 PROGRESS: Channel   0:	 0.050 FDR:   529; 0.010 FDR:   386; 0.001 FDR:   337
20:50:06.014130 PROGRESS: 
20:50:06.014195 PROGRESS: Protein Summary:
20:50:06.017345 PROGRESS: Channel   0:	 0.050 FDR:   397; 0.010 FDR:   284; 0.001 FDR:   246
20:50:06.017448 PROGRESS: =========================================================================
20:50:06.028531 INFO: Target number of precursors reached.
20:50:07.204066 INFO: fragments_df: keeping 5000 of 10851335 [sum(precursor_idx_mask)=10564 sum(mass_error_mask)=10851126 stop_rank=5000
20:50:08.523645 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
20:50:08.654034 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
20:50:08.787046 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
20:50:08.917449 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
20:50:09.572269 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
20:50:09.572767 INFO: Using score_cutoff 17.457315499305725 (fac=0.99, q=1)
20:50:09.573202 INFO: Updating optimization_manager: fwhm_rt             : 2.7572174072265625 -> 2.7439651489257812
20:50:09.573291 INFO: Updating optimization_manager: fwhm_mobility       : 0.006357881706207991 -> 0.006296937353909016
20:50:09.573354 INFO: Updating optimization_manager: score_cutoff        : 29.152784660339353 -> 17.457315499305725
20:50:09.573431 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:50:09.677673 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:50:10.200624 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:50:10.305455 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:50:11.331241 INFO: === checking if optimization conditions were reached ===
20:50:11.331602 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
20:50:11.333881 INFO: Updating optimization_manager: mobility_error      : 0.0836276498894171 -> 0.07764482365314451
20:50:11.334035 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0776.
20:50:11.334118 INFO: ==============================================
20:50:11.334202 INFO: Starting optimization step 3.
20:50:11.334275 PROGRESS: === Extracting elution groups 0 to 409400 ===
20:50:11.334372 INFO: Using python extraction backend
20:50:11.334510 PROGRESS: Extracting batch of 816307 precursors
20:50:11.334830 INFO: === Search parameters used ===
20:50:11.334916 INFO: rt_error       : 183.71276073795946
20:50:11.334970 INFO: mobility_error : 0.07764482365314451
20:50:11.335021 INFO: num_candidates : 3
20:50:11.335072 INFO: ms1_error      : 15.0
20:50:11.335122 INFO: ms2_error      : 15.0
20:50:11.335171 INFO: fwhm_rt        : 2.7439651489257812
20:50:11.335223 INFO: quant_window   : 3
20:50:11.335272 INFO: ==============================================
20:50:11.550633 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
20:50:11.550797 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
20:50:11.550849 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
20:50:11.550890 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.41
20:50:11.551749 INFO: Starting candidate selection
20:54:29.528182 INFO: Starting candidate scoring
20:54:51.813426 INFO: Finished candidate processing
20:54:51.814058 INFO: Collecting candidate features
20:54:56.040721 WARNING: intensity_correlation has 5933 NaNs ( 0.32 % out of 1831238)
20:54:56.042825 WARNING: height_correlation has 640 NaNs ( 0.03 % out of 1831238)
20:54:56.108482 INFO: Collecting fragment features
20:54:56.987415 INFO: Finished candidate scoring
20:54:58.250142 INFO: performing precursor FDR with 47 features
20:54:58.250284 INFO: Decoy channel: -1
20:54:58.250324 INFO: competitive: True
20:54:58.753046 INFO: Setting torch num_threads to 2 for FDR classification task
20:54:59.079095 WARNING: dropped 3106 target PSMs due to missing features
20:54:59.079264 WARNING: dropped 3144 decoy PSMs due to missing features
20:54:59.727407 INFO: Estimating optimal hyperparameters - samples: 1,459,990, batch_size: 4,096, learning_rate: 1.00e-03
20:54:59.730374 INFO: Using random state 558768 for train-test-split
20:55:39.071259 INFO: Test AUC: 0.552
20:55:39.071520 INFO: Train AUC: 0.565
20:55:39.071559 INFO: AUC difference: 2.27%
20:55:39.924378 INFO: Resetting torch num_threads to 80
20:55:39.972311 PROGRESS: === Extracted 1831238 precursors and 10804017 fragments ===
20:55:39.973573 INFO: === FDR correction performed with classifier version 18 ===
20:55:40.046124 PROGRESS: ============================= Precursor FDR =============================
20:55:40.046447 PROGRESS: Total precursors accumulated: 358,982
20:55:40.046516 PROGRESS: Target precursors: 205,117 (57.14%)
20:55:40.046573 PROGRESS: Decoy precursors: 153,865 (42.86%)
20:55:40.046625 PROGRESS: 
20:55:40.046675 PROGRESS: Precursor Summary:
20:55:40.050386 PROGRESS: Channel   0:	 0.050 FDR:   565; 0.010 FDR:   419; 0.001 FDR:   238
20:55:40.050492 PROGRESS: 
20:55:40.050554 PROGRESS: Protein Summary:
20:55:40.053678 PROGRESS: Channel   0:	 0.050 FDR:   424; 0.010 FDR:   310; 0.001 FDR:   179
20:55:40.053785 PROGRESS: =========================================================================
20:55:40.067810 INFO: Target number of precursors reached.
20:55:41.217148 INFO: fragments_df: keeping 5000 of 10804017 [sum(precursor_idx_mask)=11401 sum(mass_error_mask)=10803802 stop_rank=5000
20:55:41.954550 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
20:55:42.102543 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
20:55:42.257156 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
20:55:42.410897 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
20:55:43.129786 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
20:55:43.130247 INFO: Using score_cutoff 18.582918410110473 (fac=0.99, q=1)
20:55:43.130631 INFO: Updating optimization_manager: fwhm_rt             : 2.7439651489257812 -> 2.7572174072265625
20:55:43.130718 INFO: Updating optimization_manager: fwhm_mobility       : 0.006296937353909016 -> 0.006065457593649626
20:55:43.130779 INFO: Updating optimization_manager: score_cutoff        : 17.457315499305725 -> 18.582918410110473
20:55:43.130840 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:55:43.182087 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:55:43.438183 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:55:43.496085 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:55:44.052776 INFO: === checking if optimization conditions were reached ===
20:55:44.053064 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
20:55:44.055278 INFO: Updating optimization_manager: mobility_error      : 0.07764482365314451 -> 0.07298392081411945
20:55:44.055416 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0730.
20:55:44.055492 INFO: ==============================================
20:55:44.055586 INFO: Starting optimization step 4.
20:55:44.055653 PROGRESS: === Extracting elution groups 0 to 204600 ===
20:55:44.055715 INFO: Using python extraction backend
20:55:44.055823 PROGRESS: Extracting batch of 407917 precursors
20:55:44.055893 INFO: === Search parameters used ===
20:55:44.055946 INFO: rt_error       : 183.71276073795946
20:55:44.055994 INFO: mobility_error : 0.07298392081411945
20:55:44.056051 INFO: num_candidates : 3
20:55:44.056099 INFO: ms1_error      : 15.0
20:55:44.056144 INFO: ms2_error      : 15.0
20:55:44.056188 INFO: fwhm_rt        : 2.7572174072265625
20:55:44.056231 INFO: quant_window   : 3
20:55:44.056274 INFO: ==============================================
20:55:44.181404 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
20:55:44.181556 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
20:55:44.181603 INFO: FWHM in RT is 2.76 seconds, sigma is 0.46
20:55:44.181627 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.29
20:55:44.182692 INFO: Starting candidate selection
20:57:44.817413 INFO: Starting candidate scoring
20:57:55.711539 INFO: Finished candidate processing
20:57:55.711724 INFO: Collecting candidate features
20:57:57.381669 WARNING: intensity_correlation has 2943 NaNs ( 0.33 % out of 905206)
20:57:57.382928 WARNING: height_correlation has 356 NaNs ( 0.04 % out of 905206)
20:57:57.417380 INFO: Collecting fragment features
20:57:57.878606 INFO: Finished candidate scoring
20:57:58.516116 INFO: performing precursor FDR with 47 features
20:57:58.516262 INFO: Decoy channel: -1
20:57:58.516292 INFO: competitive: True
20:57:58.758705 INFO: Setting torch num_threads to 2 for FDR classification task
20:57:58.906945 WARNING: dropped 1526 target PSMs due to missing features
20:57:58.907112 WARNING: dropped 1606 decoy PSMs due to missing features
20:57:59.444085 INFO: Estimating optimal hyperparameters - samples: 721,659, batch_size: 2,955, learning_rate: 8.49e-04
20:57:59.445725 INFO: Using random state 558768 for train-test-split
20:58:22.023089 INFO: Test AUC: 0.554
20:58:22.023495 INFO: Train AUC: 0.576
20:58:22.023537 INFO: AUC difference: 3.86%
20:58:22.571268 INFO: Resetting torch num_threads to 80
20:58:22.589468 PROGRESS: === Extracted 905206 precursors and 5319836 fragments ===
20:58:22.590613 INFO: === FDR correction performed with classifier version 18 ===
20:58:22.621220 PROGRESS: ============================= Precursor FDR =============================
20:58:22.621490 PROGRESS: Total precursors accumulated: 177,886
20:58:22.621561 PROGRESS: Target precursors: 103,085 (57.95%)
20:58:22.621621 PROGRESS: Decoy precursors: 74,801 (42.05%)
20:58:22.621674 PROGRESS: 
20:58:22.621725 PROGRESS: Precursor Summary:
20:58:22.624128 PROGRESS: Channel   0:	 0.050 FDR:   261; 0.010 FDR:   203; 0.001 FDR:   180
20:58:22.624235 PROGRESS: 
20:58:22.624298 PROGRESS: Protein Summary:
20:58:22.626458 PROGRESS: Channel   0:	 0.050 FDR:   220; 0.010 FDR:   171; 0.001 FDR:   149
20:58:22.626558 PROGRESS: =========================================================================
20:58:22.640961 INFO: Target number of precursors reached.
20:58:23.199506 INFO: fragments_df: keeping 3551 of 5319836 [sum(precursor_idx_mask)=5603 sum(mass_error_mask)=5319705 stop_rank=3551
20:58:24.084228 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
20:58:24.199271 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
20:58:24.313158 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
20:58:24.423732 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
20:58:24.861687 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
20:58:24.862182 INFO: Using score_cutoff 30.91867676696777 (fac=0.99, q=1)
20:58:24.862540 INFO: Updating optimization_manager: fwhm_rt             : 2.7572174072265625 -> 2.7572174072265625
20:58:24.862626 INFO: Updating optimization_manager: fwhm_mobility       : 0.006065457593649626 -> 0.006065457593649626
20:58:24.862687 INFO: Updating optimization_manager: score_cutoff        : 18.582918410110473 -> 30.91867676696777
20:58:24.862758 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:58:24.917005 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:58:25.182110 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:58:25.248936 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:58:25.756054 INFO: === checking if optimization conditions were reached ===
20:58:25.756341 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
20:58:25.757401 INFO: Updating optimization_manager: mobility_error      : 0.07298392081411945 -> 0.07764482365314451
20:58:25.757564 INFO: Updating optimization_manager: classifier_version  : 18 -> 22
20:58:25.757676 INFO: Updating optimization_manager: score_cutoff        : 30.91867676696777 -> 18.582918410110473
20:58:25.757797 INFO: Updating optimization_manager: fwhm_rt             : 2.7572174072265625 -> 2.7572174072265625
20:58:25.757908 INFO: Updating optimization_manager: fwhm_mobility       : 0.006065457593649626 -> 0.006065457593649626
20:58:25.758014 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0776 found after 4 searches.
20:58:25.758091 INFO: ==============================================
20:58:25.758167 PROGRESS: Optimization finished for mobility_error.
20:58:26.449836 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:58:26.505112 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:58:26.770062 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:58:26.837148 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:58:27.343339 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
20:58:27.343608 PROGRESS: ==============================================
20:58:27.343710 PROGRESS: ms2_error      : 15.0000
20:58:27.343785 PROGRESS: ms1_error      : 15.0000
20:58:27.343849 PROGRESS: rt_error       : 183.7128
20:58:27.343902 PROGRESS: mobility_error : 0.0776
20:58:27.343950 PROGRESS: ==============================================
20:58:27.351483 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
20:58:29.127700 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
20:58:37.067896 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
20:58:38.982175 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
20:58:53.910007 INFO: Using python extraction backend
20:58:53.910816 PROGRESS: Extracting batch of 12210649 precursors
20:58:53.910975 INFO: === Search parameters used ===
20:58:53.911048 INFO: rt_error       : 183.71276073795946
20:58:53.911108 INFO: mobility_error : 0.07764482365314451
20:58:53.911162 INFO: num_candidates : 3
20:58:53.911214 INFO: ms1_error      : 15.0
20:58:53.911262 INFO: ms2_error      : 15.0
20:58:53.911309 INFO: fwhm_rt        : 2.7572174072265625
20:58:53.911356 INFO: quant_window   : 3
20:58:53.911402 INFO: ==============================================
20:58:56.238776 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
20:58:56.238927 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
20:58:56.238998 INFO: FWHM in RT is 2.76 seconds, sigma is 0.46
20:58:56.239028 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.29
20:58:56.240119 INFO: Starting candidate selection
22:00:47.543048 INFO: Removed 17533823 precursors with score below cutoff 18.582918410110473
22:00:50.068458 INFO: Starting candidate scoring
22:04:03.358843 INFO: Finished candidate processing
22:04:03.359161 INFO: Collecting candidate features
22:04:34.689670 WARNING: intensity_correlation has 19762 NaNs ( 0.14 % out of 14235877)
22:04:34.703945 WARNING: height_correlation has 965 NaNs ( 0.01 % out of 14235877)
22:04:35.238951 INFO: Collecting fragment features
22:04:51.634627 INFO: Finished candidate scoring
22:05:02.134102 INFO: === Performing FDR correction with classifier version 22 ===
22:05:02.134966 INFO: performing precursor FDR with 47 features
22:05:02.135027 INFO: Decoy channel: -1
22:05:02.135056 INFO: competitive: True
22:05:05.139222 INFO: Setting torch num_threads to 2 for FDR classification task
22:05:06.936509 WARNING: dropped 10386 target PSMs due to missing features
22:05:06.936791 WARNING: dropped 10007 decoy PSMs due to missing features
22:05:12.850313 INFO: Estimating optimal hyperparameters - samples: 11,372,387, batch_size: 4,096, learning_rate: 1.00e-03
22:05:12.876181 INFO: Using random state 699070 for train-test-split
22:10:11.560764 INFO: Test AUC: 0.551
22:10:11.561085 INFO: Train AUC: 0.553
22:10:11.561130 INFO: AUC difference: 0.36%
22:10:15.060202 INFO: Resetting torch num_threads to 80
22:10:15.293719 INFO: Removing fragments below FDR threshold
22:10:16.043756 PROGRESS: ============================= Precursor FDR =============================
22:10:16.044031 PROGRESS: Total precursors accumulated: 7,650
22:10:16.044105 PROGRESS: Target precursors: 7,575 (99.02%)
22:10:16.044164 PROGRESS: Decoy precursors: 75 (0.98%)
22:10:16.044219 PROGRESS: 
22:10:16.044272 PROGRESS: Precursor Summary:
22:10:16.047300 PROGRESS: Channel   0:	 0.050 FDR: 7,575; 0.010 FDR: 7,575; 0.001 FDR: 4,532
22:10:16.047417 PROGRESS: 
22:10:16.047482 PROGRESS: Protein Summary:
22:10:16.051126 PROGRESS: Channel   0:	 0.050 FDR: 1,699; 0.010 FDR: 1,699; 0.001 FDR: 1,115
22:10:16.051243 PROGRESS: =========================================================================
22:10:16.444993 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R4/psm.parquet
22:10:16.485450 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R4/frag.parquet
22:10:16.537887 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R4
22:10:18.058791 PROGRESS: Loading raw file 5/12: A9_G_DIA_nLC_tTOF_R5 
22:10:18.058981 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
22:10:18.059137 INFO: Initializing TimingManager
22:10:18.059791 INFO: Initializing RawFileManager
22:10:18.059952 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:18.060033 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:18.060117 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:18.202093 INFO: Reading 22,622 frames with 405,356,946 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:24.665629 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d...
22:10:24.667780 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:24.674853 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:24.675086 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:24.675485 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:24.676703 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:24.689457 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:24.689687 INFO: Indexing quadrupole dimension
22:10:24.795631 INFO: Transposing detector events
22:10:26.375783 INFO: Finished transposing data
22:10:26.375997 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
22:10:26.376567 INFO: RT (min)            : 0.0 - 40.0
22:10:26.376670 INFO: RT duration (sec)   : 2399.9
22:10:26.376739 INFO: RT duration (min)   : 40.0
22:10:26.376793 INFO: Cycle len (scans)   : 12
22:10:26.376853 INFO: Cycle len (sec)     : 1.27
22:10:26.376904 INFO: Number of cycles    : 1885
22:10:26.376956 INFO: MS2 range (m/z)     : 374.4 - 1151.9
22:10:26.377023 INFO: Creating DIA data object took: 8.317119836807251
22:10:28.061158 INFO: Initializing CalibrationManager
22:10:28.061596 INFO: Setting up calibration estimators ..
22:10:28.061682 INFO: Found 1 estimator(s) in calibration group 'fragment'
22:10:28.061836 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
22:10:28.061983 INFO: Found 3 estimator(s) in calibration group 'precursor'
22:10:28.062074 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
22:10:28.062169 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
22:10:28.062245 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
22:10:28.062304 INFO: Done setting up calibration estimators.
22:10:28.062478 INFO: Initializing OptimizationManager
22:10:28.062595 INFO: initial parameter: ms1_error = 30
22:10:28.062655 INFO: initial parameter: ms2_error = 30
22:10:28.062711 INFO: initial parameter: rt_error = 1199.943863
22:10:28.062760 INFO: initial parameter: mobility_error = 0.1
22:10:28.062809 INFO: initial parameter: num_candidates = 1
22:10:28.062855 INFO: initial parameter: fwhm_rt = 5
22:10:28.062906 INFO: initial parameter: fwhm_mobility = 0.01
22:10:28.062954 INFO: initial parameter: score_cutoff = 0
22:10:28.063001 INFO: initial parameter: classifier_version = -1
22:10:28.063097 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R5
22:10:28.063404 INFO: FDRManager: loading saved state not requested, will be initialized.
22:10:28.063443 INFO: Initializing FDRManager
22:10:28.063523 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
22:10:29.245618 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
22:10:29.948758 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
22:10:29.949242 INFO: Updating optimization_manager: rt_error            : 1199.943863 -> 1199.943863
22:10:29.949382 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
22:10:29.949573 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
22:10:29.949695 PROGRESS: Starting initial search for precursors.
22:10:29.949790 INFO: Starting optimization step 0.
22:10:29.949859 PROGRESS: === Extracting elution groups 0 to 200 ===
22:10:29.949971 INFO: Using python extraction backend
22:10:29.950141 PROGRESS: Extracting batch of 395 precursors
22:10:29.950223 INFO: === Search parameters used ===
22:10:29.950283 INFO: rt_error       : 1199.943863
22:10:29.950335 INFO: mobility_error : 0.1
22:10:29.950385 INFO: num_candidates : 1
22:10:29.950432 INFO: ms1_error      : 30
22:10:29.950479 INFO: ms2_error      : 30
22:10:29.950526 INFO: fwhm_rt        : 5
22:10:29.950573 INFO: quant_window   : 3
22:10:29.950621 INFO: ==============================================
22:10:29.951915 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:10:29.951970 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:10:29.952023 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:10:29.952050 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:10:29.953828 INFO: Starting candidate selection
22:10:31.912853 INFO: Starting candidate scoring
22:10:31.957074 INFO: Finished candidate processing
22:10:31.957183 INFO: Collecting candidate features
22:10:31.968672 INFO: Collecting fragment features
22:10:31.971047 INFO: Finished candidate scoring
22:10:31.972034 INFO: performing precursor FDR with 47 features
22:10:31.972082 INFO: Decoy channel: -1
22:10:31.972110 INFO: competitive: True
22:10:31.973423 INFO: Setting torch num_threads to 2 for FDR classification task
22:10:31.975620 INFO: Estimating optimal hyperparameters - samples: 276, batch_size: 128, learning_rate: 1.77e-04
22:10:31.976646 INFO: Using random state 657897 for train-test-split
22:10:32.004445 INFO: Test AUC: 0.580
22:10:32.004537 INFO: Train AUC: 0.457
22:10:32.004570 INFO: AUC difference: 26.88%
22:10:32.004594 WARNING: AUC difference > 5%. This may indicate overfitting.
22:10:32.255523 INFO: Resetting torch num_threads to 80
22:10:32.256127 PROGRESS: === Extracted 345 precursors and 2865 fragments ===
22:10:32.256647 INFO: === FDR correction performed with classifier version -1 ===
22:10:32.257227 PROGRESS: ============================= Precursor FDR =============================
22:10:32.257321 PROGRESS: Total precursors accumulated: 175
22:10:32.257387 PROGRESS: Target precursors: 87 (49.71%)
22:10:32.257443 PROGRESS: Decoy precursors: 88 (50.29%)
22:10:32.257493 PROGRESS: 
22:10:32.257543 PROGRESS: Precursor Summary:
22:10:32.258507 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:10:32.258604 PROGRESS: 
22:10:32.258665 PROGRESS: Protein Summary:
22:10:32.259685 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:10:32.259779 PROGRESS: =========================================================================
22:10:32.259902 INFO: Target number of precursors not reached yet.
22:10:32.323817 INFO: Starting optimization step 1.
22:10:32.324053 PROGRESS: === Extracting elution groups 200 to 600 ===
22:10:32.324143 INFO: Using python extraction backend
22:10:32.324273 PROGRESS: Extracting batch of 796 precursors
22:10:32.324352 INFO: === Search parameters used ===
22:10:32.324407 INFO: rt_error       : 1199.943863
22:10:32.324456 INFO: mobility_error : 0.1
22:10:32.324505 INFO: num_candidates : 1
22:10:32.324552 INFO: ms1_error      : 30
22:10:32.324598 INFO: ms2_error      : 30
22:10:32.324644 INFO: fwhm_rt        : 5
22:10:32.324690 INFO: quant_window   : 3
22:10:32.324735 INFO: ==============================================
22:10:32.325490 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:10:32.325538 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:10:32.325572 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:10:32.325595 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:10:32.326424 INFO: Starting candidate selection
22:10:35.568209 INFO: Starting candidate scoring
22:10:35.610360 INFO: Finished candidate processing
22:10:35.610457 INFO: Collecting candidate features
22:10:35.620993 INFO: Collecting fragment features
22:10:35.623421 INFO: Finished candidate scoring
22:10:35.625602 INFO: performing precursor FDR with 47 features
22:10:35.625658 INFO: Decoy channel: -1
22:10:35.625687 INFO: competitive: True
22:10:35.628688 INFO: Setting torch num_threads to 2 for FDR classification task
22:10:35.630504 INFO: Estimating optimal hyperparameters - samples: 856, batch_size: 128, learning_rate: 1.77e-04
22:10:35.630588 INFO: Using random state 969104 for train-test-split
22:10:35.711154 INFO: Test AUC: 0.484
22:10:35.711258 INFO: Train AUC: 0.613
22:10:35.711292 INFO: AUC difference: 21.07%
22:10:35.711317 WARNING: AUC difference > 5%. This may indicate overfitting.
22:10:35.961387 INFO: Resetting torch num_threads to 80
22:10:35.963025 PROGRESS: === Extracted 1070 precursors and 9098 fragments ===
22:10:35.963483 INFO: === FDR correction performed with classifier version -1 ===
22:10:35.964088 PROGRESS: ============================= Precursor FDR =============================
22:10:35.964197 PROGRESS: Total precursors accumulated: 544
22:10:35.964274 PROGRESS: Target precursors: 328 (60.29%)
22:10:35.964352 PROGRESS: Decoy precursors: 216 (39.71%)
22:10:35.964418 PROGRESS: 
22:10:35.964482 PROGRESS: Precursor Summary:
22:10:35.965456 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
22:10:35.965559 PROGRESS: 
22:10:35.965628 PROGRESS: Protein Summary:
22:10:35.966714 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
22:10:35.966824 PROGRESS: =========================================================================
22:10:35.967079 INFO: Target number of precursors not reached yet.
22:10:36.036508 INFO: Starting optimization step 2.
22:10:36.036744 PROGRESS: === Extracting elution groups 600 to 1400 ===
22:10:36.036827 INFO: Using python extraction backend
22:10:36.036932 PROGRESS: Extracting batch of 1598 precursors
22:10:36.037004 INFO: === Search parameters used ===
22:10:36.037057 INFO: rt_error       : 1199.943863
22:10:36.037105 INFO: mobility_error : 0.1
22:10:36.037152 INFO: num_candidates : 1
22:10:36.037197 INFO: ms1_error      : 30
22:10:36.037241 INFO: ms2_error      : 30
22:10:36.037288 INFO: fwhm_rt        : 5
22:10:36.037335 INFO: quant_window   : 3
22:10:36.037379 INFO: ==============================================
22:10:36.038227 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:10:36.038278 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:10:36.038312 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:10:36.038336 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:10:36.039123 INFO: Starting candidate selection
22:10:41.190184 INFO: Starting candidate scoring
22:10:41.259146 INFO: Finished candidate processing
22:10:41.259254 INFO: Collecting candidate features
22:10:41.267574 WARNING: intensity_correlation has 2 NaNs ( 0.14 % out of 1430)
22:10:41.271325 INFO: Collecting fragment features
22:10:41.274184 INFO: Finished candidate scoring
22:10:41.277290 INFO: performing precursor FDR with 47 features
22:10:41.277345 INFO: Decoy channel: -1
22:10:41.277377 INFO: competitive: True
22:10:41.280806 INFO: Setting torch num_threads to 2 for FDR classification task
22:10:41.282169 WARNING: dropped 2 target PSMs due to missing features
22:10:41.283288 INFO: Estimating optimal hyperparameters - samples: 1,998, batch_size: 128, learning_rate: 1.77e-04
22:10:41.283374 INFO: Using random state 615972 for train-test-split
22:10:41.481199 INFO: Test AUC: 0.538
22:10:41.481305 INFO: Train AUC: 0.606
22:10:41.481341 INFO: AUC difference: 11.22%
22:10:41.481366 WARNING: AUC difference > 5%. This may indicate overfitting.
22:10:41.716829 INFO: Resetting torch num_threads to 80
22:10:41.718505 PROGRESS: === Extracted 2500 precursors and 21135 fragments ===
22:10:41.718963 INFO: === FDR correction performed with classifier version -1 ===
22:10:41.719625 PROGRESS: ============================= Precursor FDR =============================
22:10:41.719725 PROGRESS: Total precursors accumulated: 1,269
22:10:41.719795 PROGRESS: Target precursors: 773 (60.91%)
22:10:41.719856 PROGRESS: Decoy precursors: 496 (39.09%)
22:10:41.719911 PROGRESS: 
22:10:41.719965 PROGRESS: Precursor Summary:
22:10:41.720899 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:10:41.721004 PROGRESS: 
22:10:41.721070 PROGRESS: Protein Summary:
22:10:41.722092 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:10:41.722188 PROGRESS: =========================================================================
22:10:41.722355 INFO: Target number of precursors not reached yet.
22:10:41.799343 INFO: Starting optimization step 3.
22:10:41.799590 PROGRESS: === Extracting elution groups 1400 to 3000 ===
22:10:41.799678 INFO: Using python extraction backend
22:10:41.799799 PROGRESS: Extracting batch of 3192 precursors
22:10:41.799881 INFO: === Search parameters used ===
22:10:41.799941 INFO: rt_error       : 1199.943863
22:10:41.799995 INFO: mobility_error : 0.1
22:10:41.800061 INFO: num_candidates : 1
22:10:41.800115 INFO: ms1_error      : 30
22:10:41.800163 INFO: ms2_error      : 30
22:10:41.800211 INFO: fwhm_rt        : 5
22:10:41.800258 INFO: quant_window   : 3
22:10:41.800310 INFO: ==============================================
22:10:41.801304 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:10:41.801356 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:10:41.801389 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:10:41.801420 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:10:41.802255 INFO: Starting candidate selection
22:10:50.918277 INFO: Starting candidate scoring
22:10:51.007749 INFO: Finished candidate processing
22:10:51.007874 INFO: Collecting candidate features
22:10:51.019495 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 2884)
22:10:51.023412 INFO: Collecting fragment features
22:10:51.027081 INFO: Finished candidate scoring
22:10:51.031454 INFO: performing precursor FDR with 47 features
22:10:51.031512 INFO: Decoy channel: -1
22:10:51.031541 INFO: competitive: True
22:10:51.037444 INFO: Setting torch num_threads to 2 for FDR classification task
22:10:51.039907 WARNING: dropped 2 target PSMs due to missing features
22:10:51.039967 WARNING: dropped 1 decoy PSMs due to missing features
22:10:51.041400 INFO: Estimating optimal hyperparameters - samples: 4,304, batch_size: 128, learning_rate: 1.77e-04
22:10:51.041489 INFO: Using random state 307381 for train-test-split
22:10:51.493421 INFO: Test AUC: 0.498
22:10:51.493533 INFO: Train AUC: 0.598
22:10:51.493568 INFO: AUC difference: 16.80%
22:10:51.493594 WARNING: AUC difference > 5%. This may indicate overfitting.
22:10:51.731752 INFO: Resetting torch num_threads to 80
22:10:51.734055 PROGRESS: === Extracted 5384 precursors and 45784 fragments ===
22:10:51.734499 INFO: === FDR correction performed with classifier version -1 ===
22:10:51.735309 PROGRESS: ============================= Precursor FDR =============================
22:10:51.735406 PROGRESS: Total precursors accumulated: 2,732
22:10:51.735474 PROGRESS: Target precursors: 1,628 (59.59%)
22:10:51.735533 PROGRESS: Decoy precursors: 1,104 (40.41%)
22:10:51.735587 PROGRESS: 
22:10:51.735639 PROGRESS: Precursor Summary:
22:10:51.736595 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:10:51.736691 PROGRESS: 
22:10:51.736753 PROGRESS: Protein Summary:
22:10:51.737764 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:10:51.737859 PROGRESS: =========================================================================
22:10:51.738053 INFO: Target number of precursors not reached yet.
22:10:51.832819 INFO: Starting optimization step 4.
22:10:51.833084 PROGRESS: === Extracting elution groups 3000 to 6200 ===
22:10:51.833176 INFO: Using python extraction backend
22:10:51.833289 PROGRESS: Extracting batch of 6381 precursors
22:10:51.833366 INFO: === Search parameters used ===
22:10:51.833421 INFO: rt_error       : 1199.943863
22:10:51.833472 INFO: mobility_error : 0.1
22:10:51.833521 INFO: num_candidates : 1
22:10:51.833570 INFO: ms1_error      : 30
22:10:51.833618 INFO: ms2_error      : 30
22:10:51.833665 INFO: fwhm_rt        : 5
22:10:51.833708 INFO: quant_window   : 3
22:10:51.833754 INFO: ==============================================
22:10:51.835152 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:10:51.835205 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:10:51.835237 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:10:51.835261 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:10:51.836056 INFO: Starting candidate selection
22:11:08.015648 INFO: Starting candidate scoring
22:11:08.170842 INFO: Finished candidate processing
22:11:08.170978 INFO: Collecting candidate features
22:11:08.189137 WARNING: intensity_correlation has 1 NaNs ( 0.02 % out of 5749)
22:11:08.193238 INFO: Collecting fragment features
22:11:08.198636 INFO: Finished candidate scoring
22:11:08.206701 INFO: performing precursor FDR with 47 features
22:11:08.206810 INFO: Decoy channel: -1
22:11:08.206843 INFO: competitive: True
22:11:08.212990 INFO: Setting torch num_threads to 2 for FDR classification task
22:11:08.215980 WARNING: dropped 2 target PSMs due to missing features
22:11:08.216057 WARNING: dropped 2 decoy PSMs due to missing features
22:11:08.218125 INFO: Estimating optimal hyperparameters - samples: 8,903, batch_size: 128, learning_rate: 1.77e-04
22:11:08.218239 INFO: Using random state 616232 for train-test-split
22:11:09.343312 INFO: Test AUC: 0.545
22:11:09.343456 INFO: Train AUC: 0.600
22:11:09.343489 INFO: AUC difference: 9.16%
22:11:09.343514 WARNING: AUC difference > 5%. This may indicate overfitting.
22:11:09.600282 INFO: Resetting torch num_threads to 80
22:11:09.604408 PROGRESS: === Extracted 11133 precursors and 94240 fragments ===
22:11:09.604962 INFO: === FDR correction performed with classifier version -1 ===
22:11:09.606356 PROGRESS: ============================= Precursor FDR =============================
22:11:09.606461 PROGRESS: Total precursors accumulated: 5,651
22:11:09.606527 PROGRESS: Target precursors: 3,418 (60.48%)
22:11:09.606584 PROGRESS: Decoy precursors: 2,233 (39.52%)
22:11:09.606635 PROGRESS: 
22:11:09.606684 PROGRESS: Precursor Summary:
22:11:09.607727 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
22:11:09.607821 PROGRESS: 
22:11:09.607889 PROGRESS: Protein Summary:
22:11:09.608989 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
22:11:09.609081 PROGRESS: =========================================================================
22:11:09.609328 INFO: Target number of precursors not reached yet.
22:11:09.792108 INFO: Starting optimization step 5.
22:11:09.792388 PROGRESS: === Extracting elution groups 6200 to 12600 ===
22:11:09.792479 INFO: Using python extraction backend
22:11:09.792605 PROGRESS: Extracting batch of 12763 precursors
22:11:09.792683 INFO: === Search parameters used ===
22:11:09.792735 INFO: rt_error       : 1199.943863
22:11:09.792782 INFO: mobility_error : 0.1
22:11:09.792827 INFO: num_candidates : 1
22:11:09.792870 INFO: ms1_error      : 30
22:11:09.792912 INFO: ms2_error      : 30
22:11:09.792953 INFO: fwhm_rt        : 5
22:11:09.792995 INFO: quant_window   : 3
22:11:09.793036 INFO: ==============================================
22:11:09.796170 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:11:09.796230 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:11:09.796261 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:11:09.796283 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:11:09.797101 INFO: Starting candidate selection
22:11:40.907823 INFO: Starting candidate scoring
22:11:41.166993 INFO: Finished candidate processing
22:11:41.167101 INFO: Collecting candidate features
22:11:41.189225 WARNING: intensity_correlation has 2 NaNs ( 0.02 % out of 11505)
22:11:41.193398 INFO: Collecting fragment features
22:11:41.202743 INFO: Finished candidate scoring
22:11:41.215430 INFO: performing precursor FDR with 47 features
22:11:41.215573 INFO: Decoy channel: -1
22:11:41.215602 INFO: competitive: True
22:11:41.225034 INFO: Setting torch num_threads to 2 for FDR classification task
22:11:41.229305 WARNING: dropped 2 target PSMs due to missing features
22:11:41.229394 WARNING: dropped 4 decoy PSMs due to missing features
22:11:41.232509 INFO: Estimating optimal hyperparameters - samples: 18,105, batch_size: 128, learning_rate: 1.77e-04
22:11:41.232665 INFO: Using random state 270165 for train-test-split
22:11:43.248443 INFO: Test AUC: 0.546
22:11:43.248598 INFO: Train AUC: 0.605
22:11:43.248641 INFO: AUC difference: 9.73%
22:11:43.248666 WARNING: AUC difference > 5%. This may indicate overfitting.
22:11:43.507947 INFO: Resetting torch num_threads to 80
22:11:43.513119 PROGRESS: === Extracted 22638 precursors and 191723 fragments ===
22:11:43.513690 INFO: === FDR correction performed with classifier version -1 ===
22:11:43.515551 PROGRESS: ============================= Precursor FDR =============================
22:11:43.515666 PROGRESS: Total precursors accumulated: 11,484
22:11:43.515747 PROGRESS: Target precursors: 7,028 (61.20%)
22:11:43.515808 PROGRESS: Decoy precursors: 4,456 (38.80%)
22:11:43.515862 PROGRESS: 
22:11:43.515912 PROGRESS: Precursor Summary:
22:11:43.516920 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:11:43.517015 PROGRESS: 
22:11:43.517081 PROGRESS: Protein Summary:
22:11:43.518177 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:11:43.518283 PROGRESS: =========================================================================
22:11:43.518542 INFO: Target number of precursors not reached yet.
22:11:43.667238 INFO: Starting optimization step 6.
22:11:43.667516 PROGRESS: === Extracting elution groups 12600 to 25400 ===
22:11:43.667613 INFO: Using python extraction backend
22:11:43.667728 PROGRESS: Extracting batch of 25523 precursors
22:11:43.667804 INFO: === Search parameters used ===
22:11:43.667857 INFO: rt_error       : 1199.943863
22:11:43.667907 INFO: mobility_error : 0.1
22:11:43.667956 INFO: num_candidates : 1
22:11:43.668003 INFO: ms1_error      : 30
22:11:43.668047 INFO: ms2_error      : 30
22:11:43.668091 INFO: fwhm_rt        : 5
22:11:43.668136 INFO: quant_window   : 3
22:11:43.668196 INFO: ==============================================
22:11:43.674652 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:11:43.674727 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:11:43.674758 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:11:43.674781 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:11:43.675576 INFO: Starting candidate selection
22:12:44.342117 INFO: Starting candidate scoring
22:12:44.751731 INFO: Finished candidate processing
22:12:44.752016 INFO: Collecting candidate features
22:12:44.821977 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 22985)
22:12:44.822302 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 22985)
22:12:44.826741 INFO: Collecting fragment features
22:12:44.842893 INFO: Finished candidate scoring
22:12:44.869110 INFO: performing precursor FDR with 47 features
22:12:44.869261 INFO: Decoy channel: -1
22:12:44.869295 INFO: competitive: True
22:12:44.887487 INFO: Setting torch num_threads to 2 for FDR classification task
22:12:44.897836 WARNING: dropped 3 target PSMs due to missing features
22:12:44.897993 WARNING: dropped 7 decoy PSMs due to missing features
22:12:44.904449 INFO: Estimating optimal hyperparameters - samples: 36,490, batch_size: 149, learning_rate: 1.91e-04
22:12:44.904668 INFO: Using random state 738709 for train-test-split
22:12:48.571224 INFO: Test AUC: 0.550
22:12:48.571380 INFO: Train AUC: 0.592
22:12:48.571417 INFO: AUC difference: 7.18%
22:12:48.571442 WARNING: AUC difference > 5%. This may indicate overfitting.
22:12:51.209768 INFO: Resetting torch num_threads to 80
22:12:51.218939 PROGRESS: === Extracted 45623 precursors and 387420 fragments ===
22:12:51.219647 INFO: === FDR correction performed with classifier version -1 ===
22:12:51.224151 PROGRESS: ============================= Precursor FDR =============================
22:12:51.224296 PROGRESS: Total precursors accumulated: 23,139
22:12:51.224370 PROGRESS: Target precursors: 13,663 (59.05%)
22:12:51.224434 PROGRESS: Decoy precursors: 9,476 (40.95%)
22:12:51.224489 PROGRESS: 
22:12:51.224542 PROGRESS: Precursor Summary:
22:12:51.225652 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:12:51.225753 PROGRESS: 
22:12:51.225818 PROGRESS: Protein Summary:
22:12:51.226984 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:12:51.227082 PROGRESS: =========================================================================
22:12:51.227487 INFO: Target number of precursors not reached yet.
22:12:51.412731 INFO: Starting optimization step 7.
22:12:51.413012 PROGRESS: === Extracting elution groups 25400 to 51000 ===
22:12:51.413098 INFO: Using python extraction backend
22:12:51.413222 PROGRESS: Extracting batch of 51061 precursors
22:12:51.413302 INFO: === Search parameters used ===
22:12:51.413360 INFO: rt_error       : 1199.943863
22:12:51.413430 INFO: mobility_error : 0.1
22:12:51.413481 INFO: num_candidates : 1
22:12:51.413529 INFO: ms1_error      : 30
22:12:51.413575 INFO: ms2_error      : 30
22:12:51.413621 INFO: fwhm_rt        : 5
22:12:51.413666 INFO: quant_window   : 3
22:12:51.413714 INFO: ==============================================
22:12:51.426690 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:12:51.426841 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:12:51.426873 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:12:51.426896 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:12:51.427723 INFO: Starting candidate selection
22:14:53.417793 INFO: Starting candidate scoring
22:14:54.202361 INFO: Finished candidate processing
22:14:54.202490 INFO: Collecting candidate features
22:14:54.276882 WARNING: intensity_correlation has 10 NaNs ( 0.02 % out of 45899)
22:14:54.282285 INFO: Collecting fragment features
22:14:54.309477 INFO: Finished candidate scoring
22:14:54.358256 INFO: performing precursor FDR with 47 features
22:14:54.358411 INFO: Decoy channel: -1
22:14:54.358439 INFO: competitive: True
22:14:54.395694 INFO: Setting torch num_threads to 2 for FDR classification task
22:14:54.413555 WARNING: dropped 8 target PSMs due to missing features
22:14:54.413697 WARNING: dropped 12 decoy PSMs due to missing features
22:14:54.428062 INFO: Estimating optimal hyperparameters - samples: 73,201, batch_size: 299, learning_rate: 2.70e-04
22:14:54.428377 INFO: Using random state 588595 for train-test-split
22:14:59.464885 INFO: Test AUC: 0.543
22:14:59.465031 INFO: Train AUC: 0.591
22:14:59.465073 INFO: AUC difference: 8.11%
22:14:59.465101 WARNING: AUC difference > 5%. This may indicate overfitting.
22:14:59.734545 INFO: Resetting torch num_threads to 80
22:14:59.754293 PROGRESS: === Extracted 91522 precursors and 776990 fragments ===
22:14:59.755060 INFO: === FDR correction performed with classifier version -1 ===
22:14:59.763894 PROGRESS: ============================= Precursor FDR =============================
22:14:59.764113 PROGRESS: Total precursors accumulated: 46,399
22:14:59.764195 PROGRESS: Target precursors: 27,383 (59.02%)
22:14:59.764266 PROGRESS: Decoy precursors: 19,016 (40.98%)
22:14:59.764331 PROGRESS: 
22:14:59.764395 PROGRESS: Precursor Summary:
22:14:59.765690 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:14:59.765797 PROGRESS: 
22:14:59.765884 PROGRESS: Protein Summary:
22:14:59.767189 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:14:59.767291 PROGRESS: =========================================================================
22:14:59.768008 INFO: Target number of precursors not reached yet.
22:15:00.048369 INFO: Starting optimization step 8.
22:15:00.048693 PROGRESS: === Extracting elution groups 51000 to 102200 ===
22:15:00.048794 INFO: Using python extraction backend
22:15:00.048926 PROGRESS: Extracting batch of 102076 precursors
22:15:00.049014 INFO: === Search parameters used ===
22:15:00.049079 INFO: rt_error       : 1199.943863
22:15:00.049138 INFO: mobility_error : 0.1
22:15:00.049197 INFO: num_candidates : 1
22:15:00.049254 INFO: ms1_error      : 30
22:15:00.049309 INFO: ms2_error      : 30
22:15:00.049364 INFO: fwhm_rt        : 5
22:15:00.049419 INFO: quant_window   : 3
22:15:00.049474 INFO: ==============================================
22:15:00.075215 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:15:00.075366 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:15:00.075409 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:15:00.075437 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:15:00.076308 INFO: Starting candidate selection
22:18:57.842264 INFO: Starting candidate scoring
22:18:59.346385 INFO: Finished candidate processing
22:18:59.346561 INFO: Collecting candidate features
22:18:59.520077 WARNING: intensity_correlation has 30 NaNs ( 0.03 % out of 91818)
22:18:59.520430 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 91818)
22:18:59.527245 INFO: Collecting fragment features
22:18:59.585926 INFO: Finished candidate scoring
22:18:59.691073 INFO: performing precursor FDR with 47 features
22:18:59.691235 INFO: Decoy channel: -1
22:18:59.691271 INFO: competitive: True
22:18:59.765294 INFO: Setting torch num_threads to 2 for FDR classification task
22:18:59.800350 WARNING: dropped 24 target PSMs due to missing features
22:18:59.800532 WARNING: dropped 29 decoy PSMs due to missing features
22:18:59.855507 INFO: Estimating optimal hyperparameters - samples: 146,629, batch_size: 600, learning_rate: 3.83e-04
22:18:59.855894 INFO: Using random state 899884 for train-test-split
22:19:06.327550 INFO: Test AUC: 0.543
22:19:06.327709 INFO: Train AUC: 0.583
22:19:06.327742 INFO: AUC difference: 6.94%
22:19:06.327768 WARNING: AUC difference > 5%. This may indicate overfitting.
22:19:06.635264 INFO: Resetting torch num_threads to 80
22:19:06.670183 PROGRESS: === Extracted 183340 precursors and 1559135 fragments ===
22:19:06.671053 INFO: === FDR correction performed with classifier version -1 ===
22:19:06.688366 PROGRESS: ============================= Precursor FDR =============================
22:19:06.688656 PROGRESS: Total precursors accumulated: 92,949
22:19:06.688731 PROGRESS: Target precursors: 54,332 (58.45%)
22:19:06.688792 PROGRESS: Decoy precursors: 38,617 (41.55%)
22:19:06.688847 PROGRESS: 
22:19:06.688901 PROGRESS: Precursor Summary:
22:19:06.690507 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:19:06.690630 PROGRESS: 
22:19:06.690695 PROGRESS: Protein Summary:
22:19:06.692186 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:19:06.692284 PROGRESS: =========================================================================
22:19:06.694338 INFO: Target number of precursors not reached yet.
22:19:07.128093 INFO: Starting optimization step 9.
22:19:07.128402 PROGRESS: === Extracting elution groups 102200 to 204600 ===
22:19:07.128505 INFO: Using python extraction backend
22:19:07.128634 PROGRESS: Extracting batch of 204132 precursors
22:19:07.128716 INFO: === Search parameters used ===
22:19:07.128776 INFO: rt_error       : 1199.943863
22:19:07.128828 INFO: mobility_error : 0.1
22:19:07.128879 INFO: num_candidates : 1
22:19:07.128927 INFO: ms1_error      : 30
22:19:07.128974 INFO: ms2_error      : 30
22:19:07.129022 INFO: fwhm_rt        : 5
22:19:07.129069 INFO: quant_window   : 3
22:19:07.129116 INFO: ==============================================
22:19:07.178473 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:19:07.178613 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:19:07.178649 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:19:07.178674 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:19:07.179666 INFO: Starting candidate selection
22:27:03.176379 INFO: Starting candidate scoring
22:27:06.105850 INFO: Finished candidate processing
22:27:06.106511 INFO: Collecting candidate features
22:27:06.601527 WARNING: intensity_correlation has 40 NaNs ( 0.02 % out of 183859)
22:27:06.602005 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 183859)
22:27:06.612291 INFO: Collecting fragment features
22:27:06.778772 INFO: Finished candidate scoring
22:27:07.225525 INFO: performing precursor FDR with 47 features
22:27:07.225693 INFO: Decoy channel: -1
22:27:07.225725 INFO: competitive: True
22:27:07.423043 INFO: Setting torch num_threads to 2 for FDR classification task
22:27:07.506861 WARNING: dropped 42 target PSMs due to missing features
22:27:07.507022 WARNING: dropped 53 decoy PSMs due to missing features
22:27:07.692091 INFO: Estimating optimal hyperparameters - samples: 293,683, batch_size: 1,202, learning_rate: 5.42e-04
22:27:07.694870 INFO: Using random state 550052 for train-test-split
22:27:17.752929 INFO: Test AUC: 0.539
22:27:17.753113 INFO: Train AUC: 0.572
22:27:17.753146 INFO: AUC difference: 5.85%
22:27:17.753174 WARNING: AUC difference > 5%. This may indicate overfitting.
22:27:18.115682 INFO: Resetting torch num_threads to 80
22:27:18.225981 PROGRESS: === Extracted 367199 precursors and 3123066 fragments ===
22:27:18.226985 INFO: === FDR correction performed with classifier version -1 ===
22:27:18.259795 PROGRESS: ============================= Precursor FDR =============================
22:27:18.260135 PROGRESS: Total precursors accumulated: 186,171
22:27:18.260211 PROGRESS: Target precursors: 106,671 (57.30%)
22:27:18.260280 PROGRESS: Decoy precursors: 79,500 (42.70%)
22:27:18.260332 PROGRESS: 
22:27:18.260382 PROGRESS: Precursor Summary:
22:27:18.262507 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:27:18.262611 PROGRESS: 
22:27:18.262674 PROGRESS: Protein Summary:
22:27:18.264592 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
22:27:18.264687 PROGRESS: =========================================================================
22:27:18.267951 INFO: Target number of precursors not reached yet.
22:27:19.068989 INFO: Starting optimization step 10.
22:27:19.069323 PROGRESS: === Extracting elution groups 204600 to 409400 ===
22:27:19.069435 INFO: Using python extraction backend
22:27:19.069587 PROGRESS: Extracting batch of 408390 precursors
22:27:19.069679 INFO: === Search parameters used ===
22:27:19.069740 INFO: rt_error       : 1199.943863
22:27:19.069793 INFO: mobility_error : 0.1
22:27:19.069845 INFO: num_candidates : 1
22:27:19.069917 INFO: ms1_error      : 30
22:27:19.069967 INFO: ms2_error      : 30
22:27:19.070016 INFO: fwhm_rt        : 5
22:27:19.070080 INFO: quant_window   : 3
22:27:19.070127 INFO: ==============================================
22:27:19.228953 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:27:19.229109 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:27:19.229153 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:27:19.229178 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:27:19.230278 INFO: Starting candidate selection
22:42:54.283378 INFO: Starting candidate scoring
22:42:59.583111 INFO: Finished candidate processing
22:42:59.583546 INFO: Collecting candidate features
22:43:00.515638 WARNING: intensity_correlation has 109 NaNs ( 0.03 % out of 366682)
22:43:00.516467 WARNING: height_correlation has 12 NaNs ( 0.00 % out of 366682)
22:43:00.532338 INFO: Collecting fragment features
22:43:00.796669 INFO: Finished candidate scoring
22:43:01.275690 INFO: performing precursor FDR with 47 features
22:43:01.275856 INFO: Decoy channel: -1
22:43:01.275900 INFO: competitive: True
22:43:01.586948 INFO: Setting torch num_threads to 2 for FDR classification task
22:43:01.720460 WARNING: dropped 99 target PSMs due to missing features
22:43:01.720633 WARNING: dropped 113 decoy PSMs due to missing features
22:43:01.966242 INFO: Estimating optimal hyperparameters - samples: 586,935, batch_size: 2,404, learning_rate: 7.66e-04
22:43:01.967417 INFO: Using random state 208234 for train-test-split
22:43:18.317933 INFO: Test AUC: 0.546
22:43:18.318108 INFO: Train AUC: 0.567
22:43:18.318145 INFO: AUC difference: 3.76%
22:43:18.817434 INFO: Resetting torch num_threads to 80
22:43:19.034611 PROGRESS: === Extracted 733881 precursors and 6240065 fragments ===
22:43:19.035871 INFO: === FDR correction performed with classifier version -1 ===
22:43:19.104592 PROGRESS: ============================= Precursor FDR =============================
22:43:19.104925 PROGRESS: Total precursors accumulated: 372,078
22:43:19.105011 PROGRESS: Target precursors: 212,904 (57.22%)
22:43:19.105072 PROGRESS: Decoy precursors: 159,174 (42.78%)
22:43:19.105128 PROGRESS: 
22:43:19.105183 PROGRESS: Precursor Summary:
22:43:19.108948 PROGRESS: Channel   0:	 0.050 FDR:   122; 0.010 FDR:     3; 0.001 FDR:     3
22:43:19.109095 PROGRESS: 
22:43:19.109165 PROGRESS: Protein Summary:
22:43:19.112334 PROGRESS: Channel   0:	 0.050 FDR:    97; 0.010 FDR:     3; 0.001 FDR:     3
22:43:19.112452 PROGRESS: =========================================================================
22:43:19.124098 INFO: Target number of precursors not reached yet.
22:43:20.304582 INFO: Starting optimization step 11.
22:43:20.304903 PROGRESS: === Extracting elution groups 409400 to 819000 ===
22:43:20.305022 INFO: Using python extraction backend
22:43:20.305192 PROGRESS: Extracting batch of 816689 precursors
22:43:20.305286 INFO: === Search parameters used ===
22:43:20.305363 INFO: rt_error       : 1199.943863
22:43:20.305418 INFO: mobility_error : 0.1
22:43:20.305469 INFO: num_candidates : 1
22:43:20.305525 INFO: ms1_error      : 30
22:43:20.305571 INFO: ms2_error      : 30
22:43:20.305614 INFO: fwhm_rt        : 5
22:43:20.305659 INFO: quant_window   : 3
22:43:20.305706 INFO: ==============================================
22:43:20.554919 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
22:43:20.555070 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
22:43:20.555111 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
22:43:20.555135 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
22:43:20.556365 INFO: Starting candidate selection
23:14:24.427935 INFO: Starting candidate scoring
23:14:34.917242 INFO: Finished candidate processing
23:14:34.917425 INFO: Collecting candidate features
23:14:36.647140 WARNING: intensity_correlation has 193 NaNs ( 0.03 % out of 734694)
23:14:36.647999 WARNING: height_correlation has 24 NaNs ( 0.00 % out of 734694)
23:14:36.672969 INFO: Collecting fragment features
23:14:37.133352 INFO: Finished candidate scoring
23:14:38.106930 INFO: performing precursor FDR with 47 features
23:14:38.107084 INFO: Decoy channel: -1
23:14:38.107113 INFO: competitive: True
23:14:38.626518 INFO: Setting torch num_threads to 2 for FDR classification task
23:14:38.853790 WARNING: dropped 186 target PSMs due to missing features
23:14:38.853971 WARNING: dropped 237 decoy PSMs due to missing features
23:14:39.508150 INFO: Estimating optimal hyperparameters - samples: 1,174,521, batch_size: 4,096, learning_rate: 1.00e-03
23:14:39.510444 INFO: Using random state 868586 for train-test-split
23:15:07.402278 INFO: Test AUC: 0.546
23:15:07.402455 INFO: Train AUC: 0.560
23:15:07.402492 INFO: AUC difference: 2.60%
23:15:08.138937 INFO: Resetting torch num_threads to 80
23:15:08.356630 PROGRESS: === Extracted 1468575 precursors and 12487450 fragments ===
23:15:08.358037 INFO: === FDR correction performed with classifier version -1 ===
23:15:08.471991 PROGRESS: ============================= Precursor FDR =============================
23:15:08.472300 PROGRESS: Total precursors accumulated: 744,578
23:15:08.472377 PROGRESS: Target precursors: 423,716 (56.91%)
23:15:08.472441 PROGRESS: Decoy precursors: 320,862 (43.09%)
23:15:08.472496 PROGRESS: 
23:15:08.472550 PROGRESS: Precursor Summary:
23:15:08.478297 PROGRESS: Channel   0:	 0.050 FDR:   486; 0.010 FDR:   346; 0.001 FDR:     2
23:15:08.478460 PROGRESS: 
23:15:08.478526 PROGRESS: Protein Summary:
23:15:08.483407 PROGRESS: Channel   0:	 0.050 FDR:   320; 0.010 FDR:   221; 0.001 FDR:     2
23:15:08.483536 PROGRESS: =========================================================================
23:15:08.509468 INFO: Target number of precursors reached.
23:15:09.949216 INFO: fragments_df: keeping 3426 of 12487450 [sum(precursor_idx_mask)=3816 sum(mass_error_mask)=12487402 stop_rank=3426
23:15:11.616021 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
23:15:11.737297 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
23:15:11.860627 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
23:15:11.987610 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
23:15:12.403129 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
23:15:12.403592 INFO: Using score_cutoff 21.25205233669281 (fac=0.99, q=1)
23:15:12.403954 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.9998831748962402
23:15:12.404045 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008829397149384022
23:15:12.404106 INFO: Updating optimization_manager: score_cutoff        : 0 -> 21.25205233669281
23:15:12.404181 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
23:15:12.637530 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
23:15:13.724948 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
23:15:13.964636 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
23:15:15.888047 INFO: Updating optimization_manager: classifier_version  : -1 -> 11
23:15:15.888335 PROGRESS: Required number of precursors found. Starting search parameter optimization.
23:15:15.888478 INFO: Starting optimization step 12.
23:15:15.888556 PROGRESS: === Extracting elution groups 0 to 819000 ===
23:15:15.888639 INFO: Using python extraction backend
23:15:15.888763 PROGRESS: Extracting batch of 1632996 precursors
23:15:15.888837 INFO: === Search parameters used ===
23:15:15.888890 INFO: rt_error       : 1199.943863
23:15:15.888936 INFO: mobility_error : 0.1
23:15:15.888982 INFO: num_candidates : 3
23:15:15.889025 INFO: ms1_error      : 30
23:15:15.889070 INFO: ms2_error      : 30
23:15:15.889115 INFO: fwhm_rt        : 2.9998831748962402
23:15:15.889159 INFO: quant_window   : 3
23:15:15.889203 INFO: ==============================================
23:15:16.277963 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
23:15:16.278112 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
23:15:16.278159 INFO: FWHM in RT is 3.00 seconds, sigma is 0.50
23:15:16.278185 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.79
23:15:16.278924 INFO: Starting candidate selection
1 day, 0:23:58.261085 INFO: Starting candidate scoring
1 day, 0:24:55.146277 INFO: Finished candidate processing
1 day, 0:24:55.146543 INFO: Collecting candidate features
1 day, 0:25:08.265559 WARNING: intensity_correlation has 1254 NaNs ( 0.03 % out of 4219894)
1 day, 0:25:08.270025 WARNING: height_correlation has 104 NaNs ( 0.00 % out of 4219894)
1 day, 0:25:08.434265 INFO: Collecting fragment features
1 day, 0:25:11.342380 INFO: Finished candidate scoring
1 day, 0:25:14.061344 INFO: performing precursor FDR with 47 features
1 day, 0:25:14.061496 INFO: Decoy channel: -1
1 day, 0:25:14.061529 INFO: competitive: True
1 day, 0:25:15.124001 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:25:15.761537 WARNING: dropped 580 target PSMs due to missing features
1 day, 0:25:15.761706 WARNING: dropped 740 decoy PSMs due to missing features
1 day, 0:25:17.417804 INFO: Estimating optimal hyperparameters - samples: 3,374,859, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 0:25:17.426757 INFO: Using random state 66779 for train-test-split
1 day, 0:26:47.258242 INFO: Test AUC: 0.563
1 day, 0:26:47.258492 INFO: Train AUC: 0.566
1 day, 0:26:47.258531 INFO: AUC difference: 0.60%
1 day, 0:26:48.853426 INFO: Resetting torch num_threads to 80
1 day, 0:26:48.927478 PROGRESS: === Extracted 4219894 precursors and 35126572 fragments ===
1 day, 0:26:48.929649 INFO: === FDR correction performed with classifier version 11 ===
1 day, 0:26:49.058202 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:26:49.058548 PROGRESS: Total precursors accumulated: 750,708
1 day, 0:26:49.058629 PROGRESS: Target precursors: 438,306 (58.39%)
1 day, 0:26:49.058692 PROGRESS: Decoy precursors: 312,402 (41.61%)
1 day, 0:26:49.058748 PROGRESS: 
1 day, 0:26:49.058801 PROGRESS: Precursor Summary:
1 day, 0:26:49.065088 PROGRESS: Channel   0:	 0.050 FDR:   643; 0.010 FDR:   483; 0.001 FDR:   414
1 day, 0:26:49.065253 PROGRESS: 
1 day, 0:26:49.065323 PROGRESS: Protein Summary:
1 day, 0:26:49.070480 PROGRESS: Channel   0:	 0.050 FDR:   420; 0.010 FDR:   301; 0.001 FDR:   258
1 day, 0:26:49.070593 PROGRESS: =========================================================================
1 day, 0:26:49.090999 INFO: Target number of precursors reached.
1 day, 0:26:52.913842 INFO: fragments_df: keeping 5000 of 35126572 [sum(precursor_idx_mask)=14942 sum(mass_error_mask)=35126491 stop_rank=5000
1 day, 0:26:54.145998 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:26:54.301234 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:26:54.466862 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:26:54.602056 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:26:55.267780 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:26:55.268256 INFO: Using score_cutoff 40.82566346054077 (fac=0.99, q=1)
1 day, 0:26:55.268623 INFO: Updating optimization_manager: fwhm_rt             : 2.9998831748962402 -> 3.0845704078674316
1 day, 0:26:55.268722 INFO: Updating optimization_manager: fwhm_mobility       : 0.008829397149384022 -> 0.00820727925747633
1 day, 0:26:55.268785 INFO: Updating optimization_manager: score_cutoff        : 21.25205233669281 -> 40.82566346054077
1 day, 0:26:55.268852 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:26:55.377378 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:26:55.904657 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:26:56.011652 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:26:56.961413 INFO: === checking if optimization conditions were reached ===
1 day, 0:26:56.963874 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 0:26:56.964065 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1 day, 0:26:56.964146 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 0:26:56.965285 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 0:26:56.965390 INFO: Updating optimization_manager: classifier_version  : 12 -> 12
1 day, 0:26:56.965466 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 0:26:56.965530 INFO: ==============================================
1 day, 0:26:56.965607 INFO: Starting optimization step 13.
1 day, 0:26:56.965673 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 0:26:56.965748 INFO: Using python extraction backend
1 day, 0:26:56.965894 PROGRESS: Extracting batch of 816307 precursors
1 day, 0:26:56.965985 INFO: === Search parameters used ===
1 day, 0:26:56.966041 INFO: rt_error       : 1199.943863
1 day, 0:26:56.966092 INFO: mobility_error : 0.1
1 day, 0:26:56.966141 INFO: num_candidates : 3
1 day, 0:26:56.966189 INFO: ms1_error      : 15.0
1 day, 0:26:56.966238 INFO: ms2_error      : 15.0
1 day, 0:26:56.966285 INFO: fwhm_rt        : 3.0845704078674316
1 day, 0:26:56.966331 INFO: quant_window   : 3
1 day, 0:26:56.966375 INFO: ==============================================
1 day, 0:26:57.196059 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 0:26:57.196209 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 0:26:57.196271 INFO: FWHM in RT is 3.08 seconds, sigma is 0.51
1 day, 0:26:57.196311 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.45
1 day, 0:26:57.197056 INFO: Starting candidate selection
1 day, 0:56:38.607296 INFO: Starting candidate scoring
1 day, 0:57:02.748728 INFO: Finished candidate processing
1 day, 0:57:02.748918 INFO: Collecting candidate features
1 day, 0:57:06.813334 WARNING: intensity_correlation has 2095 NaNs ( 0.10 % out of 2060755)
1 day, 0:57:06.815449 WARNING: height_correlation has 120 NaNs ( 0.01 % out of 2060755)
1 day, 0:57:06.884504 INFO: Collecting fragment features
1 day, 0:57:08.219747 INFO: Finished candidate scoring
1 day, 0:57:09.481139 INFO: performing precursor FDR with 47 features
1 day, 0:57:09.481280 INFO: Decoy channel: -1
1 day, 0:57:09.481312 INFO: competitive: True
1 day, 0:57:09.951648 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:57:10.245525 WARNING: dropped 1012 target PSMs due to missing features
1 day, 0:57:10.245690 WARNING: dropped 1158 decoy PSMs due to missing features
1 day, 0:57:10.994820 INFO: Estimating optimal hyperparameters - samples: 1,646,868, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 0:57:10.998102 INFO: Using random state 648418 for train-test-split
1 day, 0:57:52.040349 INFO: Test AUC: 0.561
1 day, 0:57:52.040530 INFO: Train AUC: 0.570
1 day, 0:57:52.040568 INFO: AUC difference: 1.66%
1 day, 0:57:52.967337 INFO: Resetting torch num_threads to 80
1 day, 0:57:53.003475 PROGRESS: === Extracted 2060755 precursors and 14710099 fragments ===
1 day, 0:57:53.004599 INFO: === FDR correction performed with classifier version 12 ===
1 day, 0:57:53.066431 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:57:53.066760 PROGRESS: Total precursors accumulated: 373,401
1 day, 0:57:53.066829 PROGRESS: Target precursors: 217,914 (58.36%)
1 day, 0:57:53.066886 PROGRESS: Decoy precursors: 155,487 (41.64%)
1 day, 0:57:53.066936 PROGRESS: 
1 day, 0:57:53.066985 PROGRESS: Precursor Summary:
1 day, 0:57:53.070394 PROGRESS: Channel   0:	 0.050 FDR:   547; 0.010 FDR:   359; 0.001 FDR:   261
1 day, 0:57:53.070503 PROGRESS: 
1 day, 0:57:53.070567 PROGRESS: Protein Summary:
1 day, 0:57:53.073678 PROGRESS: Channel   0:	 0.050 FDR:   419; 0.010 FDR:   263; 0.001 FDR:   190
1 day, 0:57:53.073778 PROGRESS: =========================================================================
1 day, 0:57:53.106832 INFO: Target number of precursors reached.
1 day, 0:57:54.714104 INFO: fragments_df: keeping 5000 of 14710099 [sum(precursor_idx_mask)=10203 sum(mass_error_mask)=14709997 stop_rank=5000
1 day, 0:57:55.815332 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:57:55.940212 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:57:56.064882 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:57:56.193745 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:57:56.845745 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:57:56.846202 INFO: Using score_cutoff 34.83544553833008 (fac=0.99, q=1)
1 day, 0:57:56.846556 INFO: Updating optimization_manager: fwhm_rt             : 3.0845704078674316 -> 2.7801260948181152
1 day, 0:57:56.846642 INFO: Updating optimization_manager: fwhm_mobility       : 0.00820727925747633 -> 0.006789858918637037
1 day, 0:57:56.846701 INFO: Updating optimization_manager: score_cutoff        : 40.82566346054077 -> 34.83544553833008
1 day, 0:57:56.846764 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:57:56.948670 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:57:57.469429 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:57:57.572432 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:57:58.599874 INFO: === checking if optimization conditions were reached ===
1 day, 0:57:58.602298 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 0:57:58.602469 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
1 day, 0:57:58.602551 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 0:57:58.603656 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 0:57:58.603766 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
1 day, 0:57:58.603838 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 0:57:58.603903 INFO: ==============================================
1 day, 0:57:58.603985 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 0:57:59.537342 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:57:59.639550 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:58:00.158798 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:58:00.266927 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:58:01.241515 INFO: Starting optimization step 0.
1 day, 0:58:01.241845 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 0:58:01.241965 INFO: Using python extraction backend
1 day, 0:58:01.242110 PROGRESS: Extracting batch of 816307 precursors
1 day, 0:58:01.242199 INFO: === Search parameters used ===
1 day, 0:58:01.242260 INFO: rt_error       : 1199.943863
1 day, 0:58:01.242313 INFO: mobility_error : 0.1
1 day, 0:58:01.242363 INFO: num_candidates : 3
1 day, 0:58:01.242412 INFO: ms1_error      : 15.0
1 day, 0:58:01.242460 INFO: ms2_error      : 15.0
1 day, 0:58:01.242511 INFO: fwhm_rt        : 2.7801260948181152
1 day, 0:58:01.242561 INFO: quant_window   : 3
1 day, 0:58:01.242609 INFO: ==============================================
1 day, 0:58:01.455221 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 0:58:01.455388 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 0:58:01.455448 INFO: FWHM in RT is 2.78 seconds, sigma is 0.46
1 day, 0:58:01.455473 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.68
1 day, 0:58:01.456274 INFO: Starting candidate selection
1 day, 1:27:26.160818 INFO: Starting candidate scoring
1 day, 1:27:50.541401 INFO: Finished candidate processing
1 day, 1:27:50.541579 INFO: Collecting candidate features
1 day, 1:27:55.160461 WARNING: intensity_correlation has 2205 NaNs ( 0.11 % out of 2057212)
1 day, 1:27:55.162552 WARNING: height_correlation has 120 NaNs ( 0.01 % out of 2057212)
1 day, 1:27:55.231505 INFO: Collecting fragment features
1 day, 1:27:56.236318 INFO: Finished candidate scoring
1 day, 1:27:57.371947 INFO: performing precursor FDR with 47 features
1 day, 1:27:57.372095 INFO: Decoy channel: -1
1 day, 1:27:57.372125 INFO: competitive: True
1 day, 1:27:57.917906 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:27:58.268793 WARNING: dropped 1058 target PSMs due to missing features
1 day, 1:27:58.268963 WARNING: dropped 1223 decoy PSMs due to missing features
1 day, 1:27:59.020579 INFO: Estimating optimal hyperparameters - samples: 1,643,944, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 1:27:59.024058 INFO: Using random state 682675 for train-test-split
1 day, 1:28:44.017444 INFO: Test AUC: 0.564
1 day, 1:28:44.017693 INFO: Train AUC: 0.574
1 day, 1:28:44.017731 INFO: AUC difference: 1.74%
1 day, 1:28:44.973673 INFO: Resetting torch num_threads to 80
1 day, 1:28:45.027932 PROGRESS: === Extracted 2057212 precursors and 14555142 fragments ===
1 day, 1:28:45.029210 INFO: === FDR correction performed with classifier version 13 ===
1 day, 1:28:45.106777 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:28:45.107113 PROGRESS: Total precursors accumulated: 373,689
1 day, 1:28:45.107188 PROGRESS: Target precursors: 219,403 (58.71%)
1 day, 1:28:45.107248 PROGRESS: Decoy precursors: 154,286 (41.29%)
1 day, 1:28:45.107304 PROGRESS: 
1 day, 1:28:45.107380 PROGRESS: Precursor Summary:
1 day, 1:28:45.110995 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   387; 0.001 FDR:   355
1 day, 1:28:45.111111 PROGRESS: 
1 day, 1:28:45.111178 PROGRESS: Protein Summary:
1 day, 1:28:45.114380 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   283; 0.001 FDR:   258
1 day, 1:28:45.114488 PROGRESS: =========================================================================
1 day, 1:28:45.130258 INFO: Target number of precursors reached.
1 day, 1:28:46.718042 INFO: fragments_df: keeping 5000 of 14555142 [sum(precursor_idx_mask)=10928 sum(mass_error_mask)=14555043 stop_rank=5000
1 day, 1:28:47.840430 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:28:47.965735 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:28:48.092340 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:28:48.218235 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:28:48.871553 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:28:48.872042 INFO: Using score_cutoff 32.84056736526489 (fac=0.99, q=1)
1 day, 1:28:48.872409 INFO: Updating optimization_manager: fwhm_rt             : 2.7801260948181152 -> 2.738666534423828
1 day, 1:28:48.872501 INFO: Updating optimization_manager: fwhm_mobility       : 0.006789858918637037 -> 0.005967187695205212
1 day, 1:28:48.872568 INFO: Updating optimization_manager: score_cutoff        : 34.83544553833008 -> 32.84056736526489
1 day, 1:28:48.872636 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:28:48.975264 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:28:49.497153 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:28:49.598653 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:28:50.600065 INFO: === checking if optimization conditions were reached ===
1 day, 1:28:50.600416 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 1:28:50.602690 INFO: Updating optimization_manager: rt_error            : 1199.943863 -> 509.3205062828372
1 day, 1:28:50.602826 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 509.3205.
1 day, 1:28:50.602906 INFO: ==============================================
1 day, 1:28:50.602990 INFO: Starting optimization step 1.
1 day, 1:28:50.603064 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 1:28:50.603143 INFO: Using python extraction backend
1 day, 1:28:50.603284 PROGRESS: Extracting batch of 816307 precursors
1 day, 1:28:50.603363 INFO: === Search parameters used ===
1 day, 1:28:50.603423 INFO: rt_error       : 509.3205062828372
1 day, 1:28:50.603475 INFO: mobility_error : 0.1
1 day, 1:28:50.603527 INFO: num_candidates : 3
1 day, 1:28:50.603577 INFO: ms1_error      : 15.0
1 day, 1:28:50.603625 INFO: ms2_error      : 15.0
1 day, 1:28:50.603672 INFO: fwhm_rt        : 2.738666534423828
1 day, 1:28:50.603720 INFO: quant_window   : 3
1 day, 1:28:50.603769 INFO: ==============================================
1 day, 1:28:50.850079 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 1:28:50.850228 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 1:28:50.850285 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
1 day, 1:28:50.850310 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.23
1 day, 1:28:50.851118 INFO: Starting candidate selection
1 day, 1:44:24.740087 INFO: Starting candidate scoring
1 day, 1:44:48.346553 INFO: Finished candidate processing
1 day, 1:44:48.346808 INFO: Collecting candidate features
1 day, 1:44:52.785481 WARNING: intensity_correlation has 3409 NaNs ( 0.17 % out of 1988429)
1 day, 1:44:52.787531 WARNING: height_correlation has 251 NaNs ( 0.01 % out of 1988429)
1 day, 1:44:52.854051 INFO: Collecting fragment features
1 day, 1:44:53.798179 INFO: Finished candidate scoring
1 day, 1:44:55.302802 INFO: performing precursor FDR with 47 features
1 day, 1:44:55.302947 INFO: Decoy channel: -1
1 day, 1:44:55.302980 INFO: competitive: True
1 day, 1:44:55.833028 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:44:56.169315 WARNING: dropped 1690 target PSMs due to missing features
1 day, 1:44:56.169599 WARNING: dropped 1883 decoy PSMs due to missing features
1 day, 1:44:57.332466 INFO: Estimating optimal hyperparameters - samples: 1,587,884, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 1:44:57.336271 INFO: Using random state 682675 for train-test-split
1 day, 1:45:42.317407 INFO: Test AUC: 0.557
1 day, 1:45:42.317582 INFO: Train AUC: 0.566
1 day, 1:45:42.317621 INFO: AUC difference: 1.59%
1 day, 1:45:43.265198 INFO: Resetting torch num_threads to 80
1 day, 1:45:43.304140 PROGRESS: === Extracted 1988429 precursors and 13225871 fragments ===
1 day, 1:45:43.305544 INFO: === FDR correction performed with classifier version 13 ===
1 day, 1:45:43.376266 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:45:43.376609 PROGRESS: Total precursors accumulated: 370,206
1 day, 1:45:43.376692 PROGRESS: Target precursors: 214,709 (58.00%)
1 day, 1:45:43.376753 PROGRESS: Decoy precursors: 155,497 (42.00%)
1 day, 1:45:43.376808 PROGRESS: 
1 day, 1:45:43.376861 PROGRESS: Precursor Summary:
1 day, 1:45:43.380619 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   211; 0.001 FDR:   185
1 day, 1:45:43.380790 PROGRESS: 
1 day, 1:45:43.380863 PROGRESS: Protein Summary:
1 day, 1:45:43.384172 PROGRESS: Channel   0:	 0.050 FDR:   396; 0.010 FDR:   161; 0.001 FDR:   140
1 day, 1:45:43.384281 PROGRESS: =========================================================================
1 day, 1:45:43.396080 INFO: Target number of precursors reached.
1 day, 1:45:44.882949 INFO: fragments_df: keeping 4142 of 13225871 [sum(precursor_idx_mask)=6119 sum(mass_error_mask)=13225694 stop_rank=4142
1 day, 1:45:46.176200 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:45:46.316882 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:45:46.458650 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:45:46.591626 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:45:47.175857 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:45:47.176388 INFO: Using score_cutoff 7.596559380054474 (fac=0.99, q=1)
1 day, 1:45:47.176796 INFO: Updating optimization_manager: fwhm_rt             : 2.738666534423828 -> 2.826225519180298
1 day, 1:45:47.176882 INFO: Updating optimization_manager: fwhm_mobility       : 0.005967187695205212 -> 0.006942282896488905
1 day, 1:45:47.176942 INFO: Updating optimization_manager: score_cutoff        : 32.84056736526489 -> 7.596559380054474
1 day, 1:45:47.177013 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:45:47.288680 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:45:47.813076 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:45:47.924799 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:45:48.994228 INFO: === checking if optimization conditions were reached ===
1 day, 1:45:48.995476 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 1:45:48.998119 INFO: Updating optimization_manager: rt_error            : 509.3205062828372 -> 278.1184113891088
1 day, 1:45:48.998272 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 278.1184.
1 day, 1:45:48.998368 INFO: ==============================================
1 day, 1:45:48.998490 INFO: Starting optimization step 2.
1 day, 1:45:48.998582 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 1:45:48.998709 INFO: Using python extraction backend
1 day, 1:45:48.998876 PROGRESS: Extracting batch of 816307 precursors
1 day, 1:45:48.998992 INFO: === Search parameters used ===
1 day, 1:45:48.999081 INFO: rt_error       : 278.1184113891088
1 day, 1:45:48.999184 INFO: mobility_error : 0.1
1 day, 1:45:48.999258 INFO: num_candidates : 3
1 day, 1:45:48.999325 INFO: ms1_error      : 15.0
1 day, 1:45:48.999391 INFO: ms2_error      : 15.0
1 day, 1:45:48.999467 INFO: fwhm_rt        : 2.826225519180298
1 day, 1:45:48.999535 INFO: quant_window   : 3
1 day, 1:45:48.999600 INFO: ==============================================
1 day, 1:45:49.220453 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 1:45:49.220627 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 1:45:49.220712 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
1 day, 1:45:49.220738 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.76
1 day, 1:45:49.221631 INFO: Starting candidate selection
1 day, 1:53:42.403492 INFO: Starting candidate scoring
1 day, 1:54:06.384473 INFO: Finished candidate processing
1 day, 1:54:06.384877 INFO: Collecting candidate features
1 day, 1:54:10.602548 WARNING: intensity_correlation has 4401 NaNs ( 0.23 % out of 1943508)
1 day, 1:54:10.604459 WARNING: height_correlation has 395 NaNs ( 0.02 % out of 1943508)
1 day, 1:54:10.669580 INFO: Collecting fragment features
1 day, 1:54:11.603820 INFO: Finished candidate scoring
1 day, 1:54:12.786329 INFO: performing precursor FDR with 47 features
1 day, 1:54:12.786513 INFO: Decoy channel: -1
1 day, 1:54:12.786546 INFO: competitive: True
1 day, 1:54:13.308987 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:54:13.644531 WARNING: dropped 2307 target PSMs due to missing features
1 day, 1:54:13.644697 WARNING: dropped 2312 decoy PSMs due to missing features
1 day, 1:54:14.349698 INFO: Estimating optimal hyperparameters - samples: 1,551,111, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 1:54:14.353266 INFO: Using random state 682675 for train-test-split
1 day, 1:54:53.696860 INFO: Test AUC: 0.555
1 day, 1:54:53.697055 INFO: Train AUC: 0.565
1 day, 1:54:53.697093 INFO: AUC difference: 1.77%
1 day, 1:54:54.598375 INFO: Resetting torch num_threads to 80
1 day, 1:54:54.647179 PROGRESS: === Extracted 1943508 precursors and 12264476 fragments ===
1 day, 1:54:54.648348 INFO: === FDR correction performed with classifier version 13 ===
1 day, 1:54:54.724756 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:54:54.725084 PROGRESS: Total precursors accumulated: 368,530
1 day, 1:54:54.725160 PROGRESS: Target precursors: 211,595 (57.42%)
1 day, 1:54:54.725222 PROGRESS: Decoy precursors: 156,935 (42.58%)
1 day, 1:54:54.725278 PROGRESS: 
1 day, 1:54:54.725334 PROGRESS: Precursor Summary:
1 day, 1:54:54.729250 PROGRESS: Channel   0:	 0.050 FDR:   550; 0.010 FDR:   434; 0.001 FDR:   334
1 day, 1:54:54.729360 PROGRESS: 
1 day, 1:54:54.729432 PROGRESS: Protein Summary:
1 day, 1:54:54.732895 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   317; 0.001 FDR:   244
1 day, 1:54:54.733019 PROGRESS: =========================================================================
1 day, 1:54:54.746541 INFO: Target number of precursors reached.
1 day, 1:54:56.013408 INFO: fragments_df: keeping 5000 of 12264476 [sum(precursor_idx_mask)=11956 sum(mass_error_mask)=12264304 stop_rank=5000
1 day, 1:54:56.833730 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:54:56.959170 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:54:57.082370 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:54:57.216255 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:54:57.867789 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:54:57.868271 INFO: Using score_cutoff 26.540409754371645 (fac=0.99, q=1)
1 day, 1:54:57.868618 INFO: Updating optimization_manager: fwhm_rt             : 2.826225519180298 -> 2.730116605758667
1 day, 1:54:57.868708 INFO: Updating optimization_manager: fwhm_mobility       : 0.006942282896488905 -> 0.005819616839289665
1 day, 1:54:57.868772 INFO: Updating optimization_manager: score_cutoff        : 7.596559380054474 -> 26.540409754371645
1 day, 1:54:57.868838 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:54:57.918154 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:54:58.180053 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:54:58.236076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:54:58.739884 INFO: === checking if optimization conditions were reached ===
1 day, 1:54:58.740184 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 1:54:58.742583 INFO: Updating optimization_manager: rt_error            : 278.1184113891088 -> 214.504885880213
1 day, 1:54:58.742729 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 214.5049.
1 day, 1:54:58.742807 INFO: ==============================================
1 day, 1:54:58.742903 INFO: Starting optimization step 3.
1 day, 1:54:58.742973 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 1:54:58.743041 INFO: Using python extraction backend
1 day, 1:54:58.743163 PROGRESS: Extracting batch of 407917 precursors
1 day, 1:54:58.743238 INFO: === Search parameters used ===
1 day, 1:54:58.743294 INFO: rt_error       : 214.504885880213
1 day, 1:54:58.743344 INFO: mobility_error : 0.1
1 day, 1:54:58.743392 INFO: num_candidates : 3
1 day, 1:54:58.743441 INFO: ms1_error      : 15.0
1 day, 1:54:58.743489 INFO: ms2_error      : 15.0
1 day, 1:54:58.743535 INFO: fwhm_rt        : 2.730116605758667
1 day, 1:54:58.743582 INFO: quant_window   : 3
1 day, 1:54:58.743627 INFO: ==============================================
1 day, 1:54:58.867845 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 1:54:58.867997 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 1:54:58.868047 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
1 day, 1:54:58.868073 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.15
1 day, 1:54:58.868771 INFO: Starting candidate selection
1 day, 1:58:24.123692 INFO: Starting candidate scoring
1 day, 1:58:35.547367 INFO: Finished candidate processing
1 day, 1:58:35.547752 INFO: Collecting candidate features
1 day, 1:58:37.541384 WARNING: intensity_correlation has 2586 NaNs ( 0.27 % out of 946379)
1 day, 1:58:37.542442 WARNING: height_correlation has 314 NaNs ( 0.03 % out of 946379)
1 day, 1:58:37.575738 INFO: Collecting fragment features
1 day, 1:58:38.019146 INFO: Finished candidate scoring
1 day, 1:58:38.684733 INFO: performing precursor FDR with 47 features
1 day, 1:58:38.684870 INFO: Decoy channel: -1
1 day, 1:58:38.684900 INFO: competitive: True
1 day, 1:58:38.942110 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:58:39.110204 WARNING: dropped 1432 target PSMs due to missing features
1 day, 1:58:39.110498 WARNING: dropped 1325 decoy PSMs due to missing features
1 day, 1:58:39.429797 INFO: Estimating optimal hyperparameters - samples: 754,897, batch_size: 3,092, learning_rate: 8.69e-04
1 day, 1:58:39.431420 INFO: Using random state 682675 for train-test-split
1 day, 1:58:57.183511 INFO: Test AUC: 0.549
1 day, 1:58:57.183691 INFO: Train AUC: 0.564
1 day, 1:58:57.183727 INFO: AUC difference: 2.61%
1 day, 1:58:57.740208 INFO: Resetting torch num_threads to 80
1 day, 1:58:57.765426 PROGRESS: === Extracted 946379 precursors and 5719495 fragments ===
1 day, 1:58:57.766365 INFO: === FDR correction performed with classifier version 13 ===
1 day, 1:58:57.805466 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:58:57.805806 PROGRESS: Total precursors accumulated: 183,238
1 day, 1:58:57.805900 PROGRESS: Target precursors: 104,997 (57.30%)
1 day, 1:58:57.805970 PROGRESS: Decoy precursors: 78,241 (42.70%)
1 day, 1:58:57.806026 PROGRESS: 
1 day, 1:58:57.806081 PROGRESS: Precursor Summary:
1 day, 1:58:57.808534 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   219; 0.001 FDR:   180
1 day, 1:58:57.808664 PROGRESS: 
1 day, 1:58:57.808733 PROGRESS: Protein Summary:
1 day, 1:58:57.810955 PROGRESS: Channel   0:	 0.050 FDR:   291; 0.010 FDR:   177; 0.001 FDR:   146
1 day, 1:58:57.811060 PROGRESS: =========================================================================
1 day, 1:58:57.825963 INFO: Target number of precursors reached.
1 day, 1:58:58.446163 INFO: fragments_df: keeping 3630 of 5719495 [sum(precursor_idx_mask)=5939 sum(mass_error_mask)=5719389 stop_rank=3630
1 day, 1:58:59.165261 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:58:59.275005 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:58:59.381855 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:58:59.485897 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:58:59.919682 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:58:59.920147 INFO: Using score_cutoff 30.257443521881104 (fac=0.99, q=1)
1 day, 1:58:59.920501 INFO: Updating optimization_manager: fwhm_rt             : 2.730116605758667 -> 2.7630903720855713
1 day, 1:58:59.920599 INFO: Updating optimization_manager: fwhm_mobility       : 0.005819616839289665 -> 0.006060491781681776
1 day, 1:58:59.920664 INFO: Updating optimization_manager: score_cutoff        : 26.540409754371645 -> 30.257443521881104
1 day, 1:58:59.920733 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:58:59.968494 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:59:00.218977 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:59:00.274202 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:59:00.743082 INFO: === checking if optimization conditions were reached ===
1 day, 1:59:00.743370 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 1:59:00.745580 INFO: Updating optimization_manager: rt_error            : 214.504885880213 -> 205.15602391521952
1 day, 1:59:00.745720 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 205.1560.
1 day, 1:59:00.745821 INFO: ==============================================
1 day, 1:59:00.745912 INFO: Starting optimization step 4.
1 day, 1:59:00.745987 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 1:59:00.746052 INFO: Using python extraction backend
1 day, 1:59:00.746188 PROGRESS: Extracting batch of 407917 precursors
1 day, 1:59:00.746264 INFO: === Search parameters used ===
1 day, 1:59:00.746318 INFO: rt_error       : 205.15602391521952
1 day, 1:59:00.746366 INFO: mobility_error : 0.1
1 day, 1:59:00.746412 INFO: num_candidates : 3
1 day, 1:59:00.746457 INFO: ms1_error      : 15.0
1 day, 1:59:00.746501 INFO: ms2_error      : 15.0
1 day, 1:59:00.746545 INFO: fwhm_rt        : 2.7630903720855713
1 day, 1:59:00.746587 INFO: quant_window   : 3
1 day, 1:59:00.746630 INFO: ==============================================
1 day, 1:59:00.866465 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 1:59:00.866611 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 1:59:00.866659 INFO: FWHM in RT is 2.76 seconds, sigma is 0.46
1 day, 1:59:00.866684 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.28
1 day, 1:59:00.867402 INFO: Starting candidate selection
1 day, 2:02:24.107313 INFO: Starting candidate scoring
1 day, 2:02:35.411697 INFO: Finished candidate processing
1 day, 2:02:35.411974 INFO: Collecting candidate features
1 day, 2:02:37.402594 WARNING: intensity_correlation has 2576 NaNs ( 0.27 % out of 939213)
1 day, 2:02:37.403620 WARNING: height_correlation has 320 NaNs ( 0.03 % out of 939213)
1 day, 2:02:37.436442 INFO: Collecting fragment features
1 day, 2:02:37.881329 INFO: Finished candidate scoring
1 day, 2:02:38.468696 INFO: performing precursor FDR with 47 features
1 day, 2:02:38.468835 INFO: Decoy channel: -1
1 day, 2:02:38.468864 INFO: competitive: True
1 day, 2:02:38.736429 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:02:38.914696 WARNING: dropped 1384 target PSMs due to missing features
1 day, 2:02:38.914858 WARNING: dropped 1364 decoy PSMs due to missing features
1 day, 2:02:39.236268 INFO: Estimating optimal hyperparameters - samples: 749,172, batch_size: 3,068, learning_rate: 8.65e-04
1 day, 2:02:39.237746 INFO: Using random state 682675 for train-test-split
1 day, 2:02:58.231832 INFO: Test AUC: 0.549
1 day, 2:02:58.232059 INFO: Train AUC: 0.568
1 day, 2:02:58.232098 INFO: AUC difference: 3.45%
1 day, 2:02:58.765806 INFO: Resetting torch num_threads to 80
1 day, 2:02:58.790894 PROGRESS: === Extracted 939213 precursors and 5667459 fragments ===
1 day, 2:02:58.791802 INFO: === FDR correction performed with classifier version 13 ===
1 day, 2:02:58.829203 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:02:58.829531 PROGRESS: Total precursors accumulated: 181,994
1 day, 2:02:58.829608 PROGRESS: Target precursors: 104,304 (57.31%)
1 day, 2:02:58.829669 PROGRESS: Decoy precursors: 77,690 (42.69%)
1 day, 2:02:58.829723 PROGRESS: 
1 day, 2:02:58.829774 PROGRESS: Precursor Summary:
1 day, 2:02:58.832262 PROGRESS: Channel   0:	 0.050 FDR:   334; 0.010 FDR:   212; 0.001 FDR:   181
1 day, 2:02:58.832406 PROGRESS: 
1 day, 2:02:58.832478 PROGRESS: Protein Summary:
1 day, 2:02:58.834690 PROGRESS: Channel   0:	 0.050 FDR:   279; 0.010 FDR:   174; 0.001 FDR:   148
1 day, 2:02:58.834798 PROGRESS: =========================================================================
1 day, 2:02:58.841916 INFO: Target number of precursors reached.
1 day, 2:02:59.452522 INFO: fragments_df: keeping 3548 of 5667459 [sum(precursor_idx_mask)=5765 sum(mass_error_mask)=5667365 stop_rank=3548
1 day, 2:03:00.095073 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:03:00.202794 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:03:00.308639 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:03:00.424215 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:03:00.845805 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 2:03:00.846280 INFO: Using score_cutoff 31.04548824634552 (fac=0.99, q=1)
1 day, 2:03:00.846627 INFO: Updating optimization_manager: fwhm_rt             : 2.7630903720855713 -> 2.761960744857788
1 day, 2:03:00.846713 INFO: Updating optimization_manager: fwhm_mobility       : 0.006060491781681776 -> 0.006155543494969606
1 day, 2:03:00.846773 INFO: Updating optimization_manager: score_cutoff        : 30.257443521881104 -> 31.04548824634552
1 day, 2:03:00.846836 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:03:00.896793 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:03:01.156506 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:03:01.220008 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:03:01.718302 INFO: === checking if optimization conditions were reached ===
1 day, 2:03:01.718602 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 2:03:01.719946 INFO: Updating optimization_manager: rt_error            : 205.15602391521952 -> 205.15602391521952
1 day, 2:03:01.720119 INFO: Updating optimization_manager: classifier_version  : 13 -> 18
1 day, 2:03:01.720237 INFO: Updating optimization_manager: score_cutoff        : 31.04548824634552 -> 31.04548824634552
1 day, 2:03:01.720339 INFO: Updating optimization_manager: fwhm_rt             : 2.761960744857788 -> 2.761960744857788
1 day, 2:03:01.720434 INFO: Updating optimization_manager: fwhm_mobility       : 0.006155543494969606 -> 0.006155543494969606
1 day, 2:03:01.720531 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 205.1560 found after 5 searches.
1 day, 2:03:01.720600 INFO: ==============================================
1 day, 2:03:01.720674 PROGRESS: Optimization finished for rt_error.
1 day, 2:03:02.336662 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:03:02.388229 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:03:02.647965 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:03:02.710683 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:03:03.215908 INFO: Starting optimization step 0.
1 day, 2:03:03.216177 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 2:03:03.216265 INFO: Using python extraction backend
1 day, 2:03:03.216396 PROGRESS: Extracting batch of 407917 precursors
1 day, 2:03:03.216478 INFO: === Search parameters used ===
1 day, 2:03:03.216536 INFO: rt_error       : 205.15602391521952
1 day, 2:03:03.216588 INFO: mobility_error : 0.1
1 day, 2:03:03.216639 INFO: num_candidates : 3
1 day, 2:03:03.216686 INFO: ms1_error      : 15.0
1 day, 2:03:03.216732 INFO: ms2_error      : 15.0
1 day, 2:03:03.216777 INFO: fwhm_rt        : 2.761960744857788
1 day, 2:03:03.216823 INFO: quant_window   : 3
1 day, 2:03:03.216867 INFO: ==============================================
1 day, 2:03:03.338643 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 2:03:03.338794 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 2:03:03.338839 INFO: FWHM in RT is 2.76 seconds, sigma is 0.46
1 day, 2:03:03.338863 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.34
1 day, 2:03:03.339590 INFO: Starting candidate selection
1 day, 2:06:24.060010 INFO: Starting candidate scoring
1 day, 2:06:35.140988 INFO: Finished candidate processing
1 day, 2:06:35.141229 INFO: Collecting candidate features
1 day, 2:06:36.966489 WARNING: intensity_correlation has 2525 NaNs ( 0.27 % out of 941064)
1 day, 2:06:36.967520 WARNING: height_correlation has 306 NaNs ( 0.03 % out of 941064)
1 day, 2:06:37.000795 INFO: Collecting fragment features
1 day, 2:06:37.437800 INFO: Finished candidate scoring
1 day, 2:06:38.023824 INFO: performing precursor FDR with 47 features
1 day, 2:06:38.023971 INFO: Decoy channel: -1
1 day, 2:06:38.023999 INFO: competitive: True
1 day, 2:06:38.284369 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:06:38.457691 WARNING: dropped 1382 target PSMs due to missing features
1 day, 2:06:38.457851 WARNING: dropped 1313 decoy PSMs due to missing features
1 day, 2:06:38.770416 INFO: Estimating optimal hyperparameters - samples: 750,695, batch_size: 3,074, learning_rate: 8.66e-04
1 day, 2:06:38.771825 INFO: Using random state 328785 for train-test-split
1 day, 2:07:01.793117 INFO: Test AUC: 0.558
1 day, 2:07:01.793302 INFO: Train AUC: 0.576
1 day, 2:07:01.793341 INFO: AUC difference: 3.07%
1 day, 2:07:02.368766 INFO: Resetting torch num_threads to 80
1 day, 2:07:02.388818 PROGRESS: === Extracted 941064 precursors and 5689332 fragments ===
1 day, 2:07:02.389968 INFO: === FDR correction performed with classifier version 18 ===
1 day, 2:07:02.424712 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:07:02.425079 PROGRESS: Total precursors accumulated: 182,232
1 day, 2:07:02.425157 PROGRESS: Target precursors: 105,647 (57.97%)
1 day, 2:07:02.425233 PROGRESS: Decoy precursors: 76,585 (42.03%)
1 day, 2:07:02.425293 PROGRESS: 
1 day, 2:07:02.425346 PROGRESS: Precursor Summary:
1 day, 2:07:02.427878 PROGRESS: Channel   0:	 0.050 FDR:   391; 0.010 FDR:   256; 0.001 FDR:   211
1 day, 2:07:02.427999 PROGRESS: 
1 day, 2:07:02.428064 PROGRESS: Protein Summary:
1 day, 2:07:02.430270 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   209; 0.001 FDR:   175
1 day, 2:07:02.430378 PROGRESS: =========================================================================
1 day, 2:07:02.436286 INFO: Target number of precursors reached.
1 day, 2:07:03.068846 INFO: fragments_df: keeping 4127 of 5689332 [sum(precursor_idx_mask)=6902 sum(mass_error_mask)=5689209 stop_rank=4127
1 day, 2:07:03.864077 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:07:04.007434 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:07:04.137943 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:07:04.255976 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:07:04.764493 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 2:07:04.765023 INFO: Using score_cutoff 25.453512688636778 (fac=0.99, q=1)
1 day, 2:07:04.765414 INFO: Updating optimization_manager: fwhm_rt             : 2.761960744857788 -> 2.7106313705444336
1 day, 2:07:04.765514 INFO: Updating optimization_manager: fwhm_mobility       : 0.006155543494969606 -> 0.005732005462050438
1 day, 2:07:04.765579 INFO: Updating optimization_manager: score_cutoff        : 31.04548824634552 -> 25.453512688636778
1 day, 2:07:04.765666 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:07:04.814190 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:07:05.074279 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:07:05.127776 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:07:05.646046 INFO: === checking if optimization conditions were reached ===
1 day, 2:07:05.646352 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 2:07:05.648615 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06826904882329995
1 day, 2:07:05.648764 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0683.
1 day, 2:07:05.648848 INFO: ==============================================
1 day, 2:07:05.648933 INFO: Starting optimization step 1.
1 day, 2:07:05.649006 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 2:07:05.649084 INFO: Using python extraction backend
1 day, 2:07:05.649219 PROGRESS: Extracting batch of 407917 precursors
1 day, 2:07:05.649303 INFO: === Search parameters used ===
1 day, 2:07:05.649365 INFO: rt_error       : 205.15602391521952
1 day, 2:07:05.649420 INFO: mobility_error : 0.06826904882329995
1 day, 2:07:05.649472 INFO: num_candidates : 3
1 day, 2:07:05.649523 INFO: ms1_error      : 15.0
1 day, 2:07:05.649588 INFO: ms2_error      : 15.0
1 day, 2:07:05.649640 INFO: fwhm_rt        : 2.7106313705444336
1 day, 2:07:05.649698 INFO: quant_window   : 3
1 day, 2:07:05.649746 INFO: ==============================================
1 day, 2:07:05.771497 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 2:07:05.771659 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 2:07:05.771711 INFO: FWHM in RT is 2.71 seconds, sigma is 0.45
1 day, 2:07:05.771737 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.11
1 day, 2:07:05.772601 INFO: Starting candidate selection
1 day, 2:09:05.699516 INFO: Starting candidate scoring
1 day, 2:09:16.702576 INFO: Finished candidate processing
1 day, 2:09:16.702881 INFO: Collecting candidate features
1 day, 2:09:18.495668 WARNING: intensity_correlation has 2721 NaNs ( 0.30 % out of 898574)
1 day, 2:09:18.496665 WARNING: height_correlation has 310 NaNs ( 0.03 % out of 898574)
1 day, 2:09:18.529935 INFO: Collecting fragment features
1 day, 2:09:18.979122 INFO: Finished candidate scoring
1 day, 2:09:19.575982 INFO: performing precursor FDR with 47 features
1 day, 2:09:19.576123 INFO: Decoy channel: -1
1 day, 2:09:19.576154 INFO: competitive: True
1 day, 2:09:19.831426 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:09:20.003858 WARNING: dropped 1431 target PSMs due to missing features
1 day, 2:09:20.004021 WARNING: dropped 1448 decoy PSMs due to missing features
1 day, 2:09:20.316186 INFO: Estimating optimal hyperparameters - samples: 716,556, batch_size: 2,935, learning_rate: 8.46e-04
1 day, 2:09:20.317911 INFO: Using random state 328785 for train-test-split
1 day, 2:09:39.429578 INFO: Test AUC: 0.557
1 day, 2:09:39.429778 INFO: Train AUC: 0.575
1 day, 2:09:39.429820 INFO: AUC difference: 3.01%
1 day, 2:09:39.974285 INFO: Resetting torch num_threads to 80
1 day, 2:09:39.998534 PROGRESS: === Extracted 898574 precursors and 5337763 fragments ===
1 day, 2:09:39.999367 INFO: === FDR correction performed with classifier version 18 ===
1 day, 2:09:40.037829 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:09:40.038198 PROGRESS: Total precursors accumulated: 176,235
1 day, 2:09:40.038287 PROGRESS: Target precursors: 102,121 (57.95%)
1 day, 2:09:40.038355 PROGRESS: Decoy precursors: 74,114 (42.05%)
1 day, 2:09:40.038421 PROGRESS: 
1 day, 2:09:40.038481 PROGRESS: Precursor Summary:
1 day, 2:09:40.041035 PROGRESS: Channel   0:	 0.050 FDR:   375; 0.010 FDR:   236; 0.001 FDR:   137
1 day, 2:09:40.041187 PROGRESS: 
1 day, 2:09:40.041259 PROGRESS: Protein Summary:
1 day, 2:09:40.043583 PROGRESS: Channel   0:	 0.050 FDR:   317; 0.010 FDR:   195; 0.001 FDR:   115
1 day, 2:09:40.043707 PROGRESS: =========================================================================
1 day, 2:09:40.051039 INFO: Target number of precursors reached.
1 day, 2:09:40.629838 INFO: fragments_df: keeping 3768 of 5337763 [sum(precursor_idx_mask)=6259 sum(mass_error_mask)=5337677 stop_rank=3768
1 day, 2:09:41.324418 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:09:41.435900 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:09:41.542812 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:09:41.661227 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:09:42.112825 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 2:09:42.113273 INFO: Using score_cutoff 26.30267049407959 (fac=0.99, q=1)
1 day, 2:09:42.113595 INFO: Updating optimization_manager: fwhm_rt             : 2.7106313705444336 -> 2.740189552307129
1 day, 2:09:42.113683 INFO: Updating optimization_manager: fwhm_mobility       : 0.005732005462050438 -> 0.006134028546512127
1 day, 2:09:42.113744 INFO: Updating optimization_manager: score_cutoff        : 25.453512688636778 -> 26.30267049407959
1 day, 2:09:42.113811 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:09:42.163786 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:09:42.424260 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:09:42.485024 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:09:42.987388 INFO: === checking if optimization conditions were reached ===
1 day, 2:09:42.987663 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 2:09:42.989648 INFO: Updating optimization_manager: mobility_error      : 0.06826904882329995 -> 0.05452558592209694
1 day, 2:09:42.989784 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0545.
1 day, 2:09:42.989857 INFO: ==============================================
1 day, 2:09:42.989954 INFO: Starting optimization step 2.
1 day, 2:09:42.990024 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 2:09:42.990090 INFO: Using python extraction backend
1 day, 2:09:42.990203 PROGRESS: Extracting batch of 407917 precursors
1 day, 2:09:42.990293 INFO: === Search parameters used ===
1 day, 2:09:42.990350 INFO: rt_error       : 205.15602391521952
1 day, 2:09:42.990400 INFO: mobility_error : 0.05452558592209694
1 day, 2:09:42.990448 INFO: num_candidates : 3
1 day, 2:09:42.990494 INFO: ms1_error      : 15.0
1 day, 2:09:42.990540 INFO: ms2_error      : 15.0
1 day, 2:09:42.990586 INFO: fwhm_rt        : 2.740189552307129
1 day, 2:09:42.990633 INFO: quant_window   : 3
1 day, 2:09:42.990678 INFO: ==============================================
1 day, 2:09:43.115080 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 2:09:43.115225 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 2:09:43.115268 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
1 day, 2:09:43.115293 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.32
1 day, 2:09:43.116004 INFO: Starting candidate selection
1 day, 2:11:24.099271 INFO: Starting candidate scoring
1 day, 2:11:35.073316 INFO: Finished candidate processing
1 day, 2:11:35.073524 INFO: Collecting candidate features
1 day, 2:11:36.954796 WARNING: intensity_correlation has 2845 NaNs ( 0.32 % out of 877914)
1 day, 2:11:36.955845 WARNING: height_correlation has 310 NaNs ( 0.04 % out of 877914)
1 day, 2:11:36.990332 INFO: Collecting fragment features
1 day, 2:11:37.478740 INFO: Finished candidate scoring
1 day, 2:11:38.146998 INFO: performing precursor FDR with 47 features
1 day, 2:11:38.147162 INFO: Decoy channel: -1
1 day, 2:11:38.147192 INFO: competitive: True
1 day, 2:11:38.400790 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:11:38.552690 WARNING: dropped 1508 target PSMs due to missing features
1 day, 2:11:38.552866 WARNING: dropped 1492 decoy PSMs due to missing features
1 day, 2:11:39.048976 INFO: Estimating optimal hyperparameters - samples: 699,931, batch_size: 2,866, learning_rate: 8.36e-04
1 day, 2:11:39.050716 INFO: Using random state 328785 for train-test-split
1 day, 2:12:00.956719 INFO: Test AUC: 0.557
1 day, 2:12:00.956898 INFO: Train AUC: 0.575
1 day, 2:12:00.956936 INFO: AUC difference: 3.22%
1 day, 2:12:01.508691 INFO: Resetting torch num_threads to 80
1 day, 2:12:01.527703 PROGRESS: === Extracted 877914 precursors and 5156274 fragments ===
1 day, 2:12:01.528647 INFO: === FDR correction performed with classifier version 18 ===
1 day, 2:12:01.571746 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:12:01.572077 PROGRESS: Total precursors accumulated: 173,082
1 day, 2:12:01.572151 PROGRESS: Target precursors: 100,173 (57.88%)
1 day, 2:12:01.572212 PROGRESS: Decoy precursors: 72,909 (42.12%)
1 day, 2:12:01.572264 PROGRESS: 
1 day, 2:12:01.572319 PROGRESS: Precursor Summary:
1 day, 2:12:01.574639 PROGRESS: Channel   0:	 0.050 FDR:   310; 0.010 FDR:   202; 0.001 FDR:   156
1 day, 2:12:01.574756 PROGRESS: 
1 day, 2:12:01.574820 PROGRESS: Protein Summary:
1 day, 2:12:01.576889 PROGRESS: Channel   0:	 0.050 FDR:   261; 0.010 FDR:   170; 0.001 FDR:   132
1 day, 2:12:01.576994 PROGRESS: =========================================================================
1 day, 2:12:01.584131 INFO: Target number of precursors reached.
1 day, 2:12:02.134857 INFO: fragments_df: keeping 3411 of 5156274 [sum(precursor_idx_mask)=5491 sum(mass_error_mask)=5156179 stop_rank=3411
1 day, 2:12:02.888910 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:12:03.012244 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:12:03.127441 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:12:03.235901 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:12:03.654803 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 2:12:03.655332 INFO: Using score_cutoff 31.375980658149718 (fac=0.99, q=1)
1 day, 2:12:03.655672 INFO: Updating optimization_manager: fwhm_rt             : 2.740189552307129 -> 2.8347647190093994
1 day, 2:12:03.655761 INFO: Updating optimization_manager: fwhm_mobility       : 0.006134028546512127 -> 0.006359749473631382
1 day, 2:12:03.655821 INFO: Updating optimization_manager: score_cutoff        : 26.30267049407959 -> 31.375980658149718
1 day, 2:12:03.655883 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:12:03.707103 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:12:03.973034 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:12:04.038558 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:12:04.580171 INFO: === checking if optimization conditions were reached ===
1 day, 2:12:04.580474 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 2:12:04.581776 INFO: Updating optimization_manager: mobility_error      : 0.05452558592209694 -> 0.1
1 day, 2:12:04.581970 INFO: Updating optimization_manager: classifier_version  : 18 -> 19
1 day, 2:12:04.582097 INFO: Updating optimization_manager: score_cutoff        : 31.375980658149718 -> 25.453512688636778
1 day, 2:12:04.582201 INFO: Updating optimization_manager: fwhm_rt             : 2.8347647190093994 -> 2.7106313705444336
1 day, 2:12:04.582297 INFO: Updating optimization_manager: fwhm_mobility       : 0.006359749473631382 -> 0.005732005462050438
1 day, 2:12:04.582393 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 2:12:04.582464 INFO: ==============================================
1 day, 2:12:04.582546 PROGRESS: Optimization finished for mobility_error.
1 day, 2:12:05.324618 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:12:05.376147 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:12:05.643956 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:12:05.709346 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:12:06.249509 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 2:12:06.249804 PROGRESS: ==============================================
1 day, 2:12:06.249945 PROGRESS: ms2_error      : 15.0000
1 day, 2:12:06.250034 PROGRESS: ms1_error      : 15.0000
1 day, 2:12:06.250115 PROGRESS: rt_error       : 205.1560
1 day, 2:12:06.250179 PROGRESS: mobility_error : 0.1000
1 day, 2:12:06.250234 PROGRESS: ==============================================
1 day, 2:12:06.258162 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:12:07.967512 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:12:16.110265 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:12:18.015084 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:12:36.308053 INFO: Using python extraction backend
1 day, 2:12:36.308514 PROGRESS: Extracting batch of 12210649 precursors
1 day, 2:12:36.308633 INFO: === Search parameters used ===
1 day, 2:12:36.308702 INFO: rt_error       : 205.15602391521952
1 day, 2:12:36.308758 INFO: mobility_error : 0.1
1 day, 2:12:36.308831 INFO: num_candidates : 3
1 day, 2:12:36.308884 INFO: ms1_error      : 15.0
1 day, 2:12:36.308931 INFO: ms2_error      : 15.0
1 day, 2:12:36.308978 INFO: fwhm_rt        : 2.7106313705444336
1 day, 2:12:36.309022 INFO: quant_window   : 3
1 day, 2:12:36.309093 INFO: ==============================================
1 day, 2:12:38.590856 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 2:12:38.591027 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 2:12:38.591086 INFO: FWHM in RT is 2.71 seconds, sigma is 0.45
1 day, 2:12:38.591120 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.11
1 day, 2:12:38.591969 INFO: Starting candidate selection
1 day, 3:39:11.913116 INFO: Removed 25460379 precursors with score below cutoff 25.453512688636778
1 day, 3:39:15.072349 INFO: Starting candidate scoring
1 day, 3:40:40.463306 INFO: Finished candidate processing
1 day, 3:40:40.463581 INFO: Collecting candidate features
1 day, 3:40:54.394950 WARNING: intensity_correlation has 1993 NaNs ( 0.03 % out of 6714827)
1 day, 3:40:54.401845 WARNING: height_correlation has 149 NaNs ( 0.00 % out of 6714827)
1 day, 3:40:54.658064 INFO: Collecting fragment features
1 day, 3:41:00.057407 INFO: Finished candidate scoring
1 day, 3:41:04.623931 INFO: === Performing FDR correction with classifier version 19 ===
1 day, 3:41:04.624678 INFO: performing precursor FDR with 47 features
1 day, 3:41:04.624721 INFO: Decoy channel: -1
1 day, 3:41:04.624753 INFO: competitive: True
1 day, 3:41:06.798084 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:41:07.877023 WARNING: dropped 1064 target PSMs due to missing features
1 day, 3:41:07.877204 WARNING: dropped 1036 decoy PSMs due to missing features
1 day, 3:41:11.495414 INFO: Estimating optimal hyperparameters - samples: 5,370,181, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 3:41:11.506863 INFO: Using random state 88395 for train-test-split
1 day, 3:43:54.093720 INFO: Test AUC: 0.550
1 day, 3:43:54.094324 INFO: Train AUC: 0.554
1 day, 3:43:54.094373 INFO: AUC difference: 0.78%
1 day, 3:43:56.348243 INFO: Resetting torch num_threads to 80
1 day, 3:43:56.526066 INFO: Removing fragments below FDR threshold
1 day, 3:43:57.184815 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:43:57.185094 PROGRESS: Total precursors accumulated: 8,023
1 day, 3:43:57.185177 PROGRESS: Target precursors: 7,944 (99.02%)
1 day, 3:43:57.185237 PROGRESS: Decoy precursors: 79 (0.98%)
1 day, 3:43:57.185303 PROGRESS: 
1 day, 3:43:57.185359 PROGRESS: Precursor Summary:
1 day, 3:43:57.189151 PROGRESS: Channel   0:	 0.050 FDR: 7,944; 0.010 FDR: 7,944; 0.001 FDR: 5,763
1 day, 3:43:57.189287 PROGRESS: 
1 day, 3:43:57.189354 PROGRESS: Protein Summary:
1 day, 3:43:57.193411 PROGRESS: Channel   0:	 0.050 FDR: 1,823; 0.010 FDR: 1,823; 0.001 FDR: 1,337
1 day, 3:43:57.193524 PROGRESS: =========================================================================
1 day, 3:43:57.301393 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R5/psm.parquet
1 day, 3:43:57.333355 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R5/frag.parquet
1 day, 3:43:57.381348 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R5
1 day, 3:43:58.138023 PROGRESS: Loading raw file 6/12: A9_G_DIA_nLC_tTOF_R6 
1 day, 3:43:58.138205 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
1 day, 3:43:58.138362 INFO: Initializing TimingManager
1 day, 3:43:58.138943 INFO: Initializing RawFileManager
1 day, 3:43:58.139083 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:43:58.139148 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:43:58.139199 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:43:58.279766 INFO: Reading 22,622 frames with 397,467,912 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:44:04.057437 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d...
1 day, 3:44:04.059252 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:44:04.061541 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:44:04.061814 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:44:04.062300 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:44:04.064120 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:44:04.077235 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:44:04.077479 INFO: Indexing quadrupole dimension
1 day, 3:44:04.208502 INFO: Transposing detector events
1 day, 3:44:06.909641 INFO: Finished transposing data
1 day, 3:44:06.909847 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
1 day, 3:44:06.910385 INFO: RT (min)            : 0.0 - 40.0
1 day, 3:44:06.910485 INFO: RT duration (sec)   : 2399.9
1 day, 3:44:06.910548 INFO: RT duration (min)   : 40.0
1 day, 3:44:06.910602 INFO: Cycle len (scans)   : 12
1 day, 3:44:06.910654 INFO: Cycle len (sec)     : 1.27
1 day, 3:44:06.910704 INFO: Number of cycles    : 1885
1 day, 3:44:06.910753 INFO: MS2 range (m/z)     : 374.4 - 1151.9
1 day, 3:44:06.910815 INFO: Creating DIA data object took: 8.771765232086182
1 day, 3:44:08.566842 INFO: Initializing CalibrationManager
1 day, 3:44:08.567162 INFO: Setting up calibration estimators ..
1 day, 3:44:08.567237 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 3:44:08.567336 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 3:44:08.567438 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 3:44:08.567506 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 3:44:08.567580 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1 day, 3:44:08.567645 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
1 day, 3:44:08.567700 INFO: Done setting up calibration estimators.
1 day, 3:44:08.567846 INFO: Initializing OptimizationManager
1 day, 3:44:08.567951 INFO: initial parameter: ms1_error = 30
1 day, 3:44:08.568007 INFO: initial parameter: ms2_error = 30
1 day, 3:44:08.568058 INFO: initial parameter: rt_error = 1199.968138
1 day, 3:44:08.568107 INFO: initial parameter: mobility_error = 0.1
1 day, 3:44:08.568153 INFO: initial parameter: num_candidates = 1
1 day, 3:44:08.568200 INFO: initial parameter: fwhm_rt = 5
1 day, 3:44:08.568250 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 3:44:08.568300 INFO: initial parameter: score_cutoff = 0
1 day, 3:44:08.568348 INFO: initial parameter: classifier_version = -1
1 day, 3:44:08.568424 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R6
1 day, 3:44:08.568713 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 3:44:08.568751 INFO: Initializing FDRManager
1 day, 3:44:08.568806 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 3:44:10.164371 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
1 day, 3:44:10.993075 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 3:44:10.993556 INFO: Updating optimization_manager: rt_error            : 1199.968138 -> 1199.968138
1 day, 3:44:10.993683 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 3:44:10.993890 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 3:44:10.994008 PROGRESS: Starting initial search for precursors.
1 day, 3:44:10.994106 INFO: Starting optimization step 0.
1 day, 3:44:10.994179 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 3:44:10.994265 INFO: Using python extraction backend
1 day, 3:44:10.994461 PROGRESS: Extracting batch of 395 precursors
1 day, 3:44:10.994541 INFO: === Search parameters used ===
1 day, 3:44:10.994599 INFO: rt_error       : 1199.968138
1 day, 3:44:10.994650 INFO: mobility_error : 0.1
1 day, 3:44:10.994697 INFO: num_candidates : 1
1 day, 3:44:10.994745 INFO: ms1_error      : 30
1 day, 3:44:10.994792 INFO: ms2_error      : 30
1 day, 3:44:10.994846 INFO: fwhm_rt        : 5
1 day, 3:44:10.994894 INFO: quant_window   : 3
1 day, 3:44:10.994939 INFO: ==============================================
1 day, 3:44:10.995842 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:44:10.995898 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:44:10.995950 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:44:10.995976 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:44:10.996889 INFO: Starting candidate selection
1 day, 3:44:13.103446 INFO: Starting candidate scoring
1 day, 3:44:13.144494 INFO: Finished candidate processing
1 day, 3:44:13.144582 INFO: Collecting candidate features
1 day, 3:44:13.154688 INFO: Collecting fragment features
1 day, 3:44:13.156996 INFO: Finished candidate scoring
1 day, 3:44:13.157961 INFO: performing precursor FDR with 47 features
1 day, 3:44:13.158010 INFO: Decoy channel: -1
1 day, 3:44:13.158041 INFO: competitive: True
1 day, 3:44:13.159262 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:44:13.161349 INFO: Estimating optimal hyperparameters - samples: 272, batch_size: 128, learning_rate: 1.77e-04
1 day, 3:44:13.162149 INFO: Using random state 479845 for train-test-split
1 day, 3:44:13.184220 INFO: Test AUC: 0.489
1 day, 3:44:13.184299 INFO: Train AUC: 0.546
1 day, 3:44:13.184335 INFO: AUC difference: 10.40%
1 day, 3:44:13.184365 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:44:13.424788 INFO: Resetting torch num_threads to 80
1 day, 3:44:13.425308 PROGRESS: === Extracted 341 precursors and 2842 fragments ===
1 day, 3:44:13.425775 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:44:13.426358 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:44:13.426458 PROGRESS: Total precursors accumulated: 174
1 day, 3:44:13.426523 PROGRESS: Target precursors: 101 (58.05%)
1 day, 3:44:13.426582 PROGRESS: Decoy precursors: 73 (41.95%)
1 day, 3:44:13.426638 PROGRESS: 
1 day, 3:44:13.426691 PROGRESS: Precursor Summary:
1 day, 3:44:13.427642 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:44:13.427740 PROGRESS: 
1 day, 3:44:13.427804 PROGRESS: Protein Summary:
1 day, 3:44:13.428841 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:44:13.428936 PROGRESS: =========================================================================
1 day, 3:44:13.429060 INFO: Target number of precursors not reached yet.
1 day, 3:44:13.491197 INFO: Starting optimization step 1.
1 day, 3:44:13.491421 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 3:44:13.491509 INFO: Using python extraction backend
1 day, 3:44:13.491619 PROGRESS: Extracting batch of 796 precursors
1 day, 3:44:13.491706 INFO: === Search parameters used ===
1 day, 3:44:13.491762 INFO: rt_error       : 1199.968138
1 day, 3:44:13.491814 INFO: mobility_error : 0.1
1 day, 3:44:13.491864 INFO: num_candidates : 1
1 day, 3:44:13.491928 INFO: ms1_error      : 30
1 day, 3:44:13.491977 INFO: ms2_error      : 30
1 day, 3:44:13.492023 INFO: fwhm_rt        : 5
1 day, 3:44:13.492068 INFO: quant_window   : 3
1 day, 3:44:13.492113 INFO: ==============================================
1 day, 3:44:13.492820 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:44:13.492867 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:44:13.492899 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:44:13.492923 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:44:13.493693 INFO: Starting candidate selection
1 day, 3:44:16.625370 INFO: Starting candidate scoring
1 day, 3:44:16.667667 INFO: Finished candidate processing
1 day, 3:44:16.667770 INFO: Collecting candidate features
1 day, 3:44:16.679498 INFO: Collecting fragment features
1 day, 3:44:16.681945 INFO: Finished candidate scoring
1 day, 3:44:16.684177 INFO: performing precursor FDR with 47 features
1 day, 3:44:16.684235 INFO: Decoy channel: -1
1 day, 3:44:16.684268 INFO: competitive: True
1 day, 3:44:16.687238 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:44:16.689110 INFO: Estimating optimal hyperparameters - samples: 848, batch_size: 128, learning_rate: 1.77e-04
1 day, 3:44:16.689202 INFO: Using random state 129243 for train-test-split
1 day, 3:44:16.770657 INFO: Test AUC: 0.481
1 day, 3:44:16.770760 INFO: Train AUC: 0.588
1 day, 3:44:16.770797 INFO: AUC difference: 18.14%
1 day, 3:44:16.770827 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:44:17.015342 INFO: Resetting torch num_threads to 80
1 day, 3:44:17.016697 PROGRESS: === Extracted 1060 precursors and 9020 fragments ===
1 day, 3:44:17.017150 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:44:17.017785 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:44:17.017899 PROGRESS: Total precursors accumulated: 541
1 day, 3:44:17.017978 PROGRESS: Target precursors: 327 (60.44%)
1 day, 3:44:17.018052 PROGRESS: Decoy precursors: 214 (39.56%)
1 day, 3:44:17.018117 PROGRESS: 
1 day, 3:44:17.018175 PROGRESS: Precursor Summary:
1 day, 3:44:17.019171 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:44:17.019271 PROGRESS: 
1 day, 3:44:17.019341 PROGRESS: Protein Summary:
1 day, 3:44:17.020404 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:44:17.020506 PROGRESS: =========================================================================
1 day, 3:44:17.020678 INFO: Target number of precursors not reached yet.
1 day, 3:44:17.086664 INFO: Starting optimization step 2.
1 day, 3:44:17.086916 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 3:44:17.087014 INFO: Using python extraction backend
1 day, 3:44:17.087138 PROGRESS: Extracting batch of 1598 precursors
1 day, 3:44:17.087223 INFO: === Search parameters used ===
1 day, 3:44:17.087286 INFO: rt_error       : 1199.968138
1 day, 3:44:17.087346 INFO: mobility_error : 0.1
1 day, 3:44:17.087404 INFO: num_candidates : 1
1 day, 3:44:17.087460 INFO: ms1_error      : 30
1 day, 3:44:17.087517 INFO: ms2_error      : 30
1 day, 3:44:17.087572 INFO: fwhm_rt        : 5
1 day, 3:44:17.087626 INFO: quant_window   : 3
1 day, 3:44:17.087679 INFO: ==============================================
1 day, 3:44:17.088527 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:44:17.088584 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:44:17.088620 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:44:17.088651 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:44:17.089476 INFO: Starting candidate selection
1 day, 3:44:22.340748 INFO: Starting candidate scoring
1 day, 3:44:22.400383 INFO: Finished candidate processing
1 day, 3:44:22.400500 INFO: Collecting candidate features
1 day, 3:44:22.412777 INFO: Collecting fragment features
1 day, 3:44:22.415646 INFO: Finished candidate scoring
1 day, 3:44:22.418748 INFO: performing precursor FDR with 47 features
1 day, 3:44:22.418803 INFO: Decoy channel: -1
1 day, 3:44:22.418830 INFO: competitive: True
1 day, 3:44:22.422182 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:44:22.424257 INFO: Estimating optimal hyperparameters - samples: 1,990, batch_size: 128, learning_rate: 1.77e-04
1 day, 3:44:22.424342 INFO: Using random state 766849 for train-test-split
1 day, 3:44:23.605193 INFO: Test AUC: 0.509
1 day, 3:44:23.605303 INFO: Train AUC: 0.559
1 day, 3:44:23.605338 INFO: AUC difference: 8.84%
1 day, 3:44:23.605362 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:44:23.844641 INFO: Resetting torch num_threads to 80
1 day, 3:44:23.846498 PROGRESS: === Extracted 2488 precursors and 21195 fragments ===
1 day, 3:44:23.846949 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:44:23.847629 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:44:23.847731 PROGRESS: Total precursors accumulated: 1,267
1 day, 3:44:23.847800 PROGRESS: Target precursors: 695 (54.85%)
1 day, 3:44:23.847859 PROGRESS: Decoy precursors: 572 (45.15%)
1 day, 3:44:23.847917 PROGRESS: 
1 day, 3:44:23.847967 PROGRESS: Precursor Summary:
1 day, 3:44:23.848937 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 3:44:23.849035 PROGRESS: 
1 day, 3:44:23.849098 PROGRESS: Protein Summary:
1 day, 3:44:23.850168 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 3:44:23.850266 PROGRESS: =========================================================================
1 day, 3:44:23.850435 INFO: Target number of precursors not reached yet.
1 day, 3:44:23.920006 INFO: Starting optimization step 3.
1 day, 3:44:23.920250 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 3:44:23.920346 INFO: Using python extraction backend
1 day, 3:44:23.920461 PROGRESS: Extracting batch of 3192 precursors
1 day, 3:44:23.920542 INFO: === Search parameters used ===
1 day, 3:44:23.920605 INFO: rt_error       : 1199.968138
1 day, 3:44:23.920658 INFO: mobility_error : 0.1
1 day, 3:44:23.920723 INFO: num_candidates : 1
1 day, 3:44:23.920777 INFO: ms1_error      : 30
1 day, 3:44:23.920826 INFO: ms2_error      : 30
1 day, 3:44:23.920874 INFO: fwhm_rt        : 5
1 day, 3:44:23.920921 INFO: quant_window   : 3
1 day, 3:44:23.920968 INFO: ==============================================
1 day, 3:44:23.922016 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:44:23.922068 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:44:23.922100 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:44:23.922126 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:44:23.922923 INFO: Starting candidate selection
1 day, 3:44:33.518168 INFO: Starting candidate scoring
1 day, 3:44:33.610119 INFO: Finished candidate processing
1 day, 3:44:33.610250 INFO: Collecting candidate features
1 day, 3:44:33.623946 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 2884)
1 day, 3:44:33.628001 INFO: Collecting fragment features
1 day, 3:44:33.632988 INFO: Finished candidate scoring
1 day, 3:44:33.637821 INFO: performing precursor FDR with 47 features
1 day, 3:44:33.637888 INFO: Decoy channel: -1
1 day, 3:44:33.637918 INFO: competitive: True
1 day, 3:44:33.642162 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:44:33.643816 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 3:44:33.645210 INFO: Estimating optimal hyperparameters - samples: 4,296, batch_size: 128, learning_rate: 1.77e-04
1 day, 3:44:33.645295 INFO: Using random state 976862 for train-test-split
1 day, 3:44:34.075162 INFO: Test AUC: 0.504
1 day, 3:44:34.075274 INFO: Train AUC: 0.576
1 day, 3:44:34.075310 INFO: AUC difference: 12.57%
1 day, 3:44:34.075337 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:44:34.316626 INFO: Resetting torch num_threads to 80
1 day, 3:44:34.319095 PROGRESS: === Extracted 5372 precursors and 45959 fragments ===
1 day, 3:44:34.319565 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:44:34.320407 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:44:34.320505 PROGRESS: Total precursors accumulated: 2,727
1 day, 3:44:34.320573 PROGRESS: Target precursors: 1,577 (57.83%)
1 day, 3:44:34.320633 PROGRESS: Decoy precursors: 1,150 (42.17%)
1 day, 3:44:34.320688 PROGRESS: 
1 day, 3:44:34.320741 PROGRESS: Precursor Summary:
1 day, 3:44:34.321715 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 3:44:34.321810 PROGRESS: 
1 day, 3:44:34.321881 PROGRESS: Protein Summary:
1 day, 3:44:34.322937 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 3:44:34.323030 PROGRESS: =========================================================================
1 day, 3:44:34.323217 INFO: Target number of precursors not reached yet.
1 day, 3:44:34.398650 INFO: Starting optimization step 4.
1 day, 3:44:34.398917 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 3:44:34.399005 INFO: Using python extraction backend
1 day, 3:44:34.399117 PROGRESS: Extracting batch of 6381 precursors
1 day, 3:44:34.399197 INFO: === Search parameters used ===
1 day, 3:44:34.399253 INFO: rt_error       : 1199.968138
1 day, 3:44:34.399303 INFO: mobility_error : 0.1
1 day, 3:44:34.399352 INFO: num_candidates : 1
1 day, 3:44:34.399401 INFO: ms1_error      : 30
1 day, 3:44:34.399446 INFO: ms2_error      : 30
1 day, 3:44:34.399491 INFO: fwhm_rt        : 5
1 day, 3:44:34.399536 INFO: quant_window   : 3
1 day, 3:44:34.399581 INFO: ==============================================
1 day, 3:44:34.401101 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:44:34.401151 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:44:34.401182 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:44:34.401207 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:44:34.402216 INFO: Starting candidate selection
1 day, 3:45:23.951499 INFO: Starting candidate scoring
1 day, 3:45:24.098367 INFO: Finished candidate processing
1 day, 3:45:24.098506 INFO: Collecting candidate features
1 day, 3:45:24.119344 WARNING: intensity_correlation has 2 NaNs ( 0.03 % out of 5741)
1 day, 3:45:24.124444 INFO: Collecting fragment features
1 day, 3:45:24.129982 INFO: Finished candidate scoring
1 day, 3:45:24.137505 INFO: performing precursor FDR with 47 features
1 day, 3:45:24.137599 INFO: Decoy channel: -1
1 day, 3:45:24.137628 INFO: competitive: True
1 day, 3:45:24.145549 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:45:24.148586 WARNING: dropped 2 target PSMs due to missing features
1 day, 3:45:24.148650 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 3:45:24.150867 INFO: Estimating optimal hyperparameters - samples: 8,888, batch_size: 128, learning_rate: 1.77e-04
1 day, 3:45:24.150972 INFO: Using random state 981256 for train-test-split
1 day, 3:45:25.157155 INFO: Test AUC: 0.530
1 day, 3:45:25.157277 INFO: Train AUC: 0.579
1 day, 3:45:25.157311 INFO: AUC difference: 8.50%
1 day, 3:45:25.157338 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:45:25.404541 INFO: Resetting torch num_threads to 80
1 day, 3:45:25.408305 PROGRESS: === Extracted 11113 precursors and 94714 fragments ===
1 day, 3:45:25.408781 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:45:25.411000 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:45:25.411117 PROGRESS: Total precursors accumulated: 5,641
1 day, 3:45:25.411185 PROGRESS: Target precursors: 3,300 (58.50%)
1 day, 3:45:25.411244 PROGRESS: Decoy precursors: 2,341 (41.50%)
1 day, 3:45:25.411299 PROGRESS: 
1 day, 3:45:25.411352 PROGRESS: Precursor Summary:
1 day, 3:45:25.412344 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:45:25.412439 PROGRESS: 
1 day, 3:45:25.412510 PROGRESS: Protein Summary:
1 day, 3:45:25.413586 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:45:25.413685 PROGRESS: =========================================================================
1 day, 3:45:25.413899 INFO: Target number of precursors not reached yet.
1 day, 3:45:25.500937 INFO: Starting optimization step 5.
1 day, 3:45:25.501196 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1 day, 3:45:25.501283 INFO: Using python extraction backend
1 day, 3:45:25.501396 PROGRESS: Extracting batch of 12763 precursors
1 day, 3:45:25.501472 INFO: === Search parameters used ===
1 day, 3:45:25.501531 INFO: rt_error       : 1199.968138
1 day, 3:45:25.501580 INFO: mobility_error : 0.1
1 day, 3:45:25.501628 INFO: num_candidates : 1
1 day, 3:45:25.501674 INFO: ms1_error      : 30
1 day, 3:45:25.501722 INFO: ms2_error      : 30
1 day, 3:45:25.501768 INFO: fwhm_rt        : 5
1 day, 3:45:25.501814 INFO: quant_window   : 3
1 day, 3:45:25.501859 INFO: ==============================================
1 day, 3:45:25.504677 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:45:25.504732 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:45:25.504765 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:45:25.504791 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:45:25.505646 INFO: Starting candidate selection
1 day, 3:46:23.955407 INFO: Starting candidate scoring
1 day, 3:46:24.212194 INFO: Finished candidate processing
1 day, 3:46:24.212302 INFO: Collecting candidate features
1 day, 3:46:24.237355 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 11498)
1 day, 3:46:24.241613 INFO: Collecting fragment features
1 day, 3:46:24.250223 INFO: Finished candidate scoring
1 day, 3:46:24.264593 INFO: performing precursor FDR with 47 features
1 day, 3:46:24.264760 INFO: Decoy channel: -1
1 day, 3:46:24.264793 INFO: competitive: True
1 day, 3:46:24.275526 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:46:24.280289 WARNING: dropped 2 target PSMs due to missing features
1 day, 3:46:24.280401 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 3:46:24.283989 INFO: Estimating optimal hyperparameters - samples: 18,085, batch_size: 128, learning_rate: 1.77e-04
1 day, 3:46:24.284148 INFO: Using random state 739431 for train-test-split
1 day, 3:46:26.523189 INFO: Test AUC: 0.539
1 day, 3:46:26.523346 INFO: Train AUC: 0.578
1 day, 3:46:26.523381 INFO: AUC difference: 6.68%
1 day, 3:46:26.523408 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:46:26.779712 INFO: Resetting torch num_threads to 80
1 day, 3:46:26.785428 PROGRESS: === Extracted 22611 precursors and 192551 fragments ===
1 day, 3:46:26.786134 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:46:26.788273 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:46:26.788393 PROGRESS: Total precursors accumulated: 11,474
1 day, 3:46:26.788485 PROGRESS: Target precursors: 6,670 (58.13%)
1 day, 3:46:26.788544 PROGRESS: Decoy precursors: 4,804 (41.87%)
1 day, 3:46:26.788598 PROGRESS: 
1 day, 3:46:26.788649 PROGRESS: Precursor Summary:
1 day, 3:46:26.789715 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:46:26.789813 PROGRESS: 
1 day, 3:46:26.789889 PROGRESS: Protein Summary:
1 day, 3:46:26.791017 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:46:26.791119 PROGRESS: =========================================================================
1 day, 3:46:26.791420 INFO: Target number of precursors not reached yet.
1 day, 3:46:26.889653 INFO: Starting optimization step 6.
1 day, 3:46:26.889985 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1 day, 3:46:26.890079 INFO: Using python extraction backend
1 day, 3:46:26.890211 PROGRESS: Extracting batch of 25523 precursors
1 day, 3:46:26.890294 INFO: === Search parameters used ===
1 day, 3:46:26.890351 INFO: rt_error       : 1199.968138
1 day, 3:46:26.890404 INFO: mobility_error : 0.1
1 day, 3:46:26.890454 INFO: num_candidates : 1
1 day, 3:46:26.890521 INFO: ms1_error      : 30
1 day, 3:46:26.890570 INFO: ms2_error      : 30
1 day, 3:46:26.890616 INFO: fwhm_rt        : 5
1 day, 3:46:26.890661 INFO: quant_window   : 3
1 day, 3:46:26.890711 INFO: ==============================================
1 day, 3:46:26.897505 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:46:26.897592 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:46:26.897626 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:46:26.897652 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:46:26.898442 INFO: Starting candidate selection
1 day, 3:47:26.934718 INFO: Starting candidate scoring
1 day, 3:47:27.341642 INFO: Finished candidate processing
1 day, 3:47:27.341756 INFO: Collecting candidate features
1 day, 3:47:27.388190 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 22952)
1 day, 3:47:27.392865 INFO: Collecting fragment features
1 day, 3:47:27.409025 INFO: Finished candidate scoring
1 day, 3:47:27.436967 INFO: performing precursor FDR with 47 features
1 day, 3:47:27.437114 INFO: Decoy channel: -1
1 day, 3:47:27.437143 INFO: competitive: True
1 day, 3:47:27.457542 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:47:27.467749 WARNING: dropped 4 target PSMs due to missing features
1 day, 3:47:27.467882 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 3:47:27.475079 INFO: Estimating optimal hyperparameters - samples: 36,443, batch_size: 149, learning_rate: 1.91e-04
1 day, 3:47:27.475310 INFO: Using random state 304659 for train-test-split
1 day, 3:47:31.334798 INFO: Test AUC: 0.547
1 day, 3:47:31.334933 INFO: Train AUC: 0.592
1 day, 3:47:31.334969 INFO: AUC difference: 7.58%
1 day, 3:47:31.334997 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:47:31.594557 INFO: Resetting torch num_threads to 80
1 day, 3:47:31.604574 PROGRESS: === Extracted 45563 precursors and 388352 fragments ===
1 day, 3:47:31.605280 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:47:31.610213 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:47:31.610356 PROGRESS: Total precursors accumulated: 23,118
1 day, 3:47:31.610424 PROGRESS: Target precursors: 13,692 (59.23%)
1 day, 3:47:31.610482 PROGRESS: Decoy precursors: 9,426 (40.77%)
1 day, 3:47:31.610543 PROGRESS: 
1 day, 3:47:31.610596 PROGRESS: Precursor Summary:
1 day, 3:47:31.611732 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:47:31.611831 PROGRESS: 
1 day, 3:47:31.611895 PROGRESS: Protein Summary:
1 day, 3:47:31.613091 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 3:47:31.613189 PROGRESS: =========================================================================
1 day, 3:47:31.613644 INFO: Target number of precursors not reached yet.
1 day, 3:47:31.767569 INFO: Starting optimization step 7.
1 day, 3:47:31.767855 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1 day, 3:47:31.767950 INFO: Using python extraction backend
1 day, 3:47:31.768086 PROGRESS: Extracting batch of 51061 precursors
1 day, 3:47:31.768172 INFO: === Search parameters used ===
1 day, 3:47:31.768237 INFO: rt_error       : 1199.968138
1 day, 3:47:31.768305 INFO: mobility_error : 0.1
1 day, 3:47:31.768360 INFO: num_candidates : 1
1 day, 3:47:31.768412 INFO: ms1_error      : 30
1 day, 3:47:31.768461 INFO: ms2_error      : 30
1 day, 3:47:31.768510 INFO: fwhm_rt        : 5
1 day, 3:47:31.768561 INFO: quant_window   : 3
1 day, 3:47:31.768611 INFO: ==============================================
1 day, 3:47:31.784187 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:47:31.784317 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:47:31.784352 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:47:31.784379 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:47:31.785448 INFO: Starting candidate selection
1 day, 3:49:29.623139 INFO: Starting candidate scoring
1 day, 3:49:30.413944 INFO: Finished candidate processing
1 day, 3:49:30.414137 INFO: Collecting candidate features
1 day, 3:49:30.511638 WARNING: intensity_correlation has 12 NaNs ( 0.03 % out of 45818)
1 day, 3:49:30.517410 INFO: Collecting fragment features
1 day, 3:49:30.546227 INFO: Finished candidate scoring
1 day, 3:49:30.606299 INFO: performing precursor FDR with 47 features
1 day, 3:49:30.606460 INFO: Decoy channel: -1
1 day, 3:49:30.606494 INFO: competitive: True
1 day, 3:49:30.650689 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:49:30.672829 WARNING: dropped 10 target PSMs due to missing features
1 day, 3:49:30.672982 WARNING: dropped 11 decoy PSMs due to missing features
1 day, 3:49:30.688832 INFO: Estimating optimal hyperparameters - samples: 73,088, batch_size: 299, learning_rate: 2.70e-04
1 day, 3:49:30.689207 INFO: Using random state 123609 for train-test-split
1 day, 3:49:36.272750 INFO: Test AUC: 0.542
1 day, 3:49:36.272964 INFO: Train AUC: 0.594
1 day, 3:49:36.273001 INFO: AUC difference: 8.80%
1 day, 3:49:36.273029 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:49:36.554465 INFO: Resetting torch num_threads to 80
1 day, 3:49:36.574063 PROGRESS: === Extracted 91381 precursors and 778847 fragments ===
1 day, 3:49:36.574865 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:49:36.585268 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:49:36.585447 PROGRESS: Total precursors accumulated: 46,346
1 day, 3:49:36.585518 PROGRESS: Target precursors: 27,493 (59.32%)
1 day, 3:49:36.585576 PROGRESS: Decoy precursors: 18,853 (40.68%)
1 day, 3:49:36.585629 PROGRESS: 
1 day, 3:49:36.585682 PROGRESS: Precursor Summary:
1 day, 3:49:36.587096 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 3:49:36.587200 PROGRESS: 
1 day, 3:49:36.587265 PROGRESS: Protein Summary:
1 day, 3:49:36.588642 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 3:49:36.588740 PROGRESS: =========================================================================
1 day, 3:49:36.589798 INFO: Target number of precursors not reached yet.
1 day, 3:49:36.968487 INFO: Starting optimization step 8.
1 day, 3:49:36.968788 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1 day, 3:49:36.968891 INFO: Using python extraction backend
1 day, 3:49:36.969030 PROGRESS: Extracting batch of 102076 precursors
1 day, 3:49:36.969110 INFO: === Search parameters used ===
1 day, 3:49:36.969167 INFO: rt_error       : 1199.968138
1 day, 3:49:36.969218 INFO: mobility_error : 0.1
1 day, 3:49:36.969266 INFO: num_candidates : 1
1 day, 3:49:36.969314 INFO: ms1_error      : 30
1 day, 3:49:36.969360 INFO: ms2_error      : 30
1 day, 3:49:36.969412 INFO: fwhm_rt        : 5
1 day, 3:49:36.969461 INFO: quant_window   : 3
1 day, 3:49:36.969507 INFO: ==============================================
1 day, 3:49:36.999008 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:49:36.999167 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:49:36.999209 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:49:36.999240 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:49:37.000259 INFO: Starting candidate selection
1 day, 3:53:30.510669 INFO: Starting candidate scoring
1 day, 3:53:32.006855 INFO: Finished candidate processing
1 day, 3:53:32.007115 INFO: Collecting candidate features
1 day, 3:53:32.185719 WARNING: intensity_correlation has 24 NaNs ( 0.03 % out of 91706)
1 day, 3:53:32.186082 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 91706)
1 day, 3:53:32.192981 INFO: Collecting fragment features
1 day, 3:53:32.253824 INFO: Finished candidate scoring
1 day, 3:53:32.369787 INFO: performing precursor FDR with 47 features
1 day, 3:53:32.369951 INFO: Decoy channel: -1
1 day, 3:53:32.369983 INFO: competitive: True
1 day, 3:53:32.452689 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:53:32.490088 WARNING: dropped 21 target PSMs due to missing features
1 day, 3:53:32.490236 WARNING: dropped 26 decoy PSMs due to missing features
1 day, 3:53:32.538276 INFO: Estimating optimal hyperparameters - samples: 146,432, batch_size: 599, learning_rate: 3.82e-04
1 day, 3:53:32.538738 INFO: Using random state 861849 for train-test-split
1 day, 3:53:40.387543 INFO: Test AUC: 0.549
1 day, 3:53:40.387707 INFO: Train AUC: 0.578
1 day, 3:53:40.387744 INFO: AUC difference: 5.04%
1 day, 3:53:40.387772 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:53:40.701401 INFO: Resetting torch num_threads to 80
1 day, 3:53:40.739120 PROGRESS: === Extracted 183087 precursors and 1562452 fragments ===
1 day, 3:53:40.740014 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:53:40.758445 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:53:40.758740 PROGRESS: Total precursors accumulated: 92,844
1 day, 3:53:40.758815 PROGRESS: Target precursors: 53,844 (57.99%)
1 day, 3:53:40.758877 PROGRESS: Decoy precursors: 39,000 (42.01%)
1 day, 3:53:40.758931 PROGRESS: 
1 day, 3:53:40.758985 PROGRESS: Precursor Summary:
1 day, 3:53:40.760661 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 3:53:40.760776 PROGRESS: 
1 day, 3:53:40.760840 PROGRESS: Protein Summary:
1 day, 3:53:40.762413 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 3:53:40.762515 PROGRESS: =========================================================================
1 day, 3:53:40.764396 INFO: Target number of precursors not reached yet.
1 day, 3:53:41.280176 INFO: Starting optimization step 9.
1 day, 3:53:41.280502 PROGRESS: === Extracting elution groups 102200 to 204600 ===
1 day, 3:53:41.280611 INFO: Using python extraction backend
1 day, 3:53:41.280761 PROGRESS: Extracting batch of 204132 precursors
1 day, 3:53:41.280850 INFO: === Search parameters used ===
1 day, 3:53:41.280907 INFO: rt_error       : 1199.968138
1 day, 3:53:41.280961 INFO: mobility_error : 0.1
1 day, 3:53:41.281013 INFO: num_candidates : 1
1 day, 3:53:41.281062 INFO: ms1_error      : 30
1 day, 3:53:41.281108 INFO: ms2_error      : 30
1 day, 3:53:41.281155 INFO: fwhm_rt        : 5
1 day, 3:53:41.281204 INFO: quant_window   : 3
1 day, 3:53:41.281250 INFO: ==============================================
1 day, 3:53:41.339710 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 3:53:41.339859 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 3:53:41.339897 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 3:53:41.339924 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 3:53:41.340884 INFO: Starting candidate selection
1 day, 4:01:27.453545 INFO: Starting candidate scoring
1 day, 4:01:30.335161 INFO: Finished candidate processing
1 day, 4:01:30.335368 INFO: Collecting candidate features
1 day, 4:01:30.703753 WARNING: intensity_correlation has 44 NaNs ( 0.02 % out of 183637)
1 day, 4:01:30.704185 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 183637)
1 day, 4:01:30.714225 INFO: Collecting fragment features
1 day, 4:01:30.829363 INFO: Finished candidate scoring
1 day, 4:01:31.045040 INFO: performing precursor FDR with 47 features
1 day, 4:01:31.045197 INFO: Decoy channel: -1
1 day, 4:01:31.045228 INFO: competitive: True
1 day, 4:01:31.219991 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:01:31.293332 WARNING: dropped 40 target PSMs due to missing features
1 day, 4:01:31.293485 WARNING: dropped 55 decoy PSMs due to missing features
1 day, 4:01:31.429447 INFO: Estimating optimal hyperparameters - samples: 293,303, batch_size: 1,201, learning_rate: 5.41e-04
1 day, 4:01:31.430201 INFO: Using random state 436055 for train-test-split
1 day, 4:01:42.474917 INFO: Test AUC: 0.544
1 day, 4:01:42.475067 INFO: Train AUC: 0.570
1 day, 4:01:42.475104 INFO: AUC difference: 4.52%
1 day, 4:01:42.842007 INFO: Resetting torch num_threads to 80
1 day, 4:01:42.913101 PROGRESS: === Extracted 366724 precursors and 3130906 fragments ===
1 day, 4:01:42.914141 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:01:42.948789 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:01:42.949106 PROGRESS: Total precursors accumulated: 185,972
1 day, 4:01:42.949181 PROGRESS: Target precursors: 106,581 (57.31%)
1 day, 4:01:42.949241 PROGRESS: Decoy precursors: 79,391 (42.69%)
1 day, 4:01:42.949292 PROGRESS: 
1 day, 4:01:42.949344 PROGRESS: Precursor Summary:
1 day, 4:01:42.951573 PROGRESS: Channel   0:	 0.050 FDR:    49; 0.010 FDR:    34; 0.001 FDR:    34
1 day, 4:01:42.951678 PROGRESS: 
1 day, 4:01:42.951743 PROGRESS: Protein Summary:
1 day, 4:01:42.953753 PROGRESS: Channel   0:	 0.050 FDR:    45; 0.010 FDR:    32; 0.001 FDR:    32
1 day, 4:01:42.953855 PROGRESS: =========================================================================
1 day, 4:01:42.957275 INFO: Target number of precursors not reached yet.
1 day, 4:01:43.775708 INFO: Starting optimization step 10.
1 day, 4:01:43.776021 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 4:01:43.776131 INFO: Using python extraction backend
1 day, 4:01:43.776283 PROGRESS: Extracting batch of 408390 precursors
1 day, 4:01:43.776378 INFO: === Search parameters used ===
1 day, 4:01:43.776439 INFO: rt_error       : 1199.968138
1 day, 4:01:43.776495 INFO: mobility_error : 0.1
1 day, 4:01:43.776550 INFO: num_candidates : 1
1 day, 4:01:43.776601 INFO: ms1_error      : 30
1 day, 4:01:43.776650 INFO: ms2_error      : 30
1 day, 4:01:43.776699 INFO: fwhm_rt        : 5
1 day, 4:01:43.776761 INFO: quant_window   : 3
1 day, 4:01:43.776812 INFO: ==============================================
1 day, 4:01:43.893230 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 4:01:43.893374 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 4:01:43.893409 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 4:01:43.893437 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 4:01:43.894432 INFO: Starting candidate selection
1 day, 4:17:31.634399 INFO: Starting candidate scoring
1 day, 4:17:37.083293 INFO: Finished candidate processing
1 day, 4:17:37.083694 INFO: Collecting candidate features
1 day, 4:17:37.942990 WARNING: intensity_correlation has 99 NaNs ( 0.03 % out of 366187)
1 day, 4:17:37.943602 WARNING: height_correlation has 13 NaNs ( 0.00 % out of 366187)
1 day, 4:17:37.959765 INFO: Collecting fragment features
1 day, 4:17:38.202890 INFO: Finished candidate scoring
1 day, 4:17:41.087575 INFO: performing precursor FDR with 47 features
1 day, 4:17:41.087749 INFO: Decoy channel: -1
1 day, 4:17:41.087779 INFO: competitive: True
1 day, 4:17:41.395667 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:17:41.569958 WARNING: dropped 93 target PSMs due to missing features
1 day, 4:17:41.570133 WARNING: dropped 110 decoy PSMs due to missing features
1 day, 4:17:42.038422 INFO: Estimating optimal hyperparameters - samples: 586,166, batch_size: 2,400, learning_rate: 7.65e-04
1 day, 4:17:42.042928 INFO: Using random state 77645 for train-test-split
1 day, 4:17:59.726420 INFO: Test AUC: 0.547
1 day, 4:17:59.726589 INFO: Train AUC: 0.566
1 day, 4:17:59.726629 INFO: AUC difference: 3.31%
1 day, 4:18:00.211489 INFO: Resetting torch num_threads to 80
1 day, 4:18:00.343652 PROGRESS: === Extracted 732911 precursors and 6257806 fragments ===
1 day, 4:18:00.344779 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:18:00.412611 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:18:00.412955 PROGRESS: Total precursors accumulated: 371,691
1 day, 4:18:00.413032 PROGRESS: Target precursors: 212,591 (57.20%)
1 day, 4:18:00.413094 PROGRESS: Decoy precursors: 159,100 (42.80%)
1 day, 4:18:00.413149 PROGRESS: 
1 day, 4:18:00.413204 PROGRESS: Precursor Summary:
1 day, 4:18:00.416646 PROGRESS: Channel   0:	 0.050 FDR:   144; 0.010 FDR:    66; 0.001 FDR:    66
1 day, 4:18:00.416760 PROGRESS: 
1 day, 4:18:00.416825 PROGRESS: Protein Summary:
1 day, 4:18:00.419813 PROGRESS: Channel   0:	 0.050 FDR:   114; 0.010 FDR:    56; 0.001 FDR:    56
1 day, 4:18:00.419919 PROGRESS: =========================================================================
1 day, 4:18:00.427899 INFO: Target number of precursors not reached yet.
1 day, 4:18:01.727436 INFO: Starting optimization step 11.
1 day, 4:18:01.727895 PROGRESS: === Extracting elution groups 409400 to 819000 ===
1 day, 4:18:01.728020 INFO: Using python extraction backend
1 day, 4:18:01.728172 PROGRESS: Extracting batch of 816689 precursors
1 day, 4:18:01.728259 INFO: === Search parameters used ===
1 day, 4:18:01.728330 INFO: rt_error       : 1199.968138
1 day, 4:18:01.728383 INFO: mobility_error : 0.1
1 day, 4:18:01.728431 INFO: num_candidates : 1
1 day, 4:18:01.728478 INFO: ms1_error      : 30
1 day, 4:18:01.728523 INFO: ms2_error      : 30
1 day, 4:18:01.728570 INFO: fwhm_rt        : 5
1 day, 4:18:01.728616 INFO: quant_window   : 3
1 day, 4:18:01.728661 INFO: ==============================================
1 day, 4:18:01.933593 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 4:18:01.933748 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 4:18:01.933786 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 4:18:01.933811 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 4:18:01.934852 INFO: Starting candidate selection
1 day, 4:47:08.316159 INFO: Starting candidate scoring
1 day, 4:47:18.453755 INFO: Finished candidate processing
1 day, 4:47:18.453968 INFO: Collecting candidate features
1 day, 4:47:20.749962 WARNING: intensity_correlation has 169 NaNs ( 0.02 % out of 733803)
1 day, 4:47:20.750854 WARNING: height_correlation has 8 NaNs ( 0.00 % out of 733803)
1 day, 4:47:20.775895 INFO: Collecting fragment features
1 day, 4:47:21.272615 INFO: Finished candidate scoring
1 day, 4:47:22.512594 INFO: performing precursor FDR with 47 features
1 day, 4:47:22.512760 INFO: Decoy channel: -1
1 day, 4:47:22.512790 INFO: competitive: True
1 day, 4:47:23.188173 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:47:23.452196 WARNING: dropped 178 target PSMs due to missing features
1 day, 4:47:23.452372 WARNING: dropped 199 decoy PSMs due to missing features
1 day, 4:47:24.050601 INFO: Estimating optimal hyperparameters - samples: 1,173,069, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 4:47:24.052816 INFO: Using random state 143381 for train-test-split
1 day, 4:47:56.997887 INFO: Test AUC: 0.549
1 day, 4:47:56.998069 INFO: Train AUC: 0.561
1 day, 4:47:56.998107 INFO: AUC difference: 2.24%
1 day, 4:47:57.740110 INFO: Resetting torch num_threads to 80
1 day, 4:47:58.293322 PROGRESS: === Extracted 1466714 precursors and 12520783 fragments ===
1 day, 4:47:58.294987 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:47:58.438848 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:47:58.439199 PROGRESS: Total precursors accumulated: 743,777
1 day, 4:47:58.439283 PROGRESS: Target precursors: 423,815 (56.98%)
1 day, 4:47:58.439348 PROGRESS: Decoy precursors: 319,962 (43.02%)
1 day, 4:47:58.439412 PROGRESS: 
1 day, 4:47:58.439463 PROGRESS: Precursor Summary:
1 day, 4:47:58.445735 PROGRESS: Channel   0:	 0.050 FDR:   418; 0.010 FDR:   304; 0.001 FDR:   132
1 day, 4:47:58.445923 PROGRESS: 
1 day, 4:47:58.446005 PROGRESS: Protein Summary:
1 day, 4:47:58.451104 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   202; 0.001 FDR:    94
1 day, 4:47:58.451225 PROGRESS: =========================================================================
1 day, 4:47:58.474702 INFO: Target number of precursors reached.
1 day, 4:47:59.867101 INFO: fragments_df: keeping 3024 of 12520783 [sum(precursor_idx_mask)=3366 sum(mass_error_mask)=12520735 stop_rank=3024
1 day, 4:48:02.533541 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:48:02.684718 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:48:02.829672 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:48:02.971815 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:48:03.401226 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 4:48:03.401725 INFO: Using score_cutoff 19.399720847511293 (fac=0.99, q=1)
1 day, 4:48:03.402321 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1309814453125
1 day, 4:48:03.402416 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.009115289896726608
1 day, 4:48:03.402478 INFO: Updating optimization_manager: score_cutoff        : 0 -> 19.399720847511293
1 day, 4:48:03.402558 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:48:03.620399 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:48:04.664069 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:48:04.882993 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:48:07.013672 INFO: Updating optimization_manager: classifier_version  : -1 -> 11
1 day, 4:48:07.014007 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 4:48:07.014167 INFO: Starting optimization step 12.
1 day, 4:48:07.014251 PROGRESS: === Extracting elution groups 0 to 819000 ===
1 day, 4:48:07.014368 INFO: Using python extraction backend
1 day, 4:48:07.014549 PROGRESS: Extracting batch of 1632996 precursors
1 day, 4:48:07.014647 INFO: === Search parameters used ===
1 day, 4:48:07.014714 INFO: rt_error       : 1199.968138
1 day, 4:48:07.014767 INFO: mobility_error : 0.1
1 day, 4:48:07.014816 INFO: num_candidates : 3
1 day, 4:48:07.014865 INFO: ms1_error      : 30
1 day, 4:48:07.014913 INFO: ms2_error      : 30
1 day, 4:48:07.014961 INFO: fwhm_rt        : 3.1309814453125
1 day, 4:48:07.015008 INFO: quant_window   : 3
1 day, 4:48:07.015059 INFO: ==============================================
1 day, 4:48:07.449078 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 4:48:07.449228 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 4:48:07.449309 INFO: FWHM in RT is 3.13 seconds, sigma is 0.52
1 day, 4:48:07.449340 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.94
1 day, 4:48:07.450318 INFO: Starting candidate selection
1 day, 5:56:33.447393 INFO: Starting candidate scoring
1 day, 5:57:32.139219 INFO: Finished candidate processing
1 day, 5:57:32.139453 INFO: Collecting candidate features
1 day, 5:57:41.183706 WARNING: intensity_correlation has 1203 NaNs ( 0.03 % out of 4226830)
1 day, 5:57:41.188246 WARNING: height_correlation has 89 NaNs ( 0.00 % out of 4226830)
1 day, 5:57:41.345408 INFO: Collecting fragment features
1 day, 5:57:44.025218 INFO: Finished candidate scoring
1 day, 5:57:46.558769 INFO: performing precursor FDR with 47 features
1 day, 5:57:46.558918 INFO: Decoy channel: -1
1 day, 5:57:46.558951 INFO: competitive: True
1 day, 5:57:47.592149 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:57:48.206955 WARNING: dropped 558 target PSMs due to missing features
1 day, 5:57:48.207139 WARNING: dropped 702 decoy PSMs due to missing features
1 day, 5:57:50.110743 INFO: Estimating optimal hyperparameters - samples: 3,380,456, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 5:57:50.119594 INFO: Using random state 567531 for train-test-split
1 day, 5:59:25.510775 INFO: Test AUC: 0.564
1 day, 5:59:25.511022 INFO: Train AUC: 0.568
1 day, 5:59:25.511064 INFO: AUC difference: 0.80%
1 day, 5:59:27.104410 INFO: Resetting torch num_threads to 80
1 day, 5:59:27.171426 PROGRESS: === Extracted 4226830 precursors and 35353188 fragments ===
1 day, 5:59:27.173106 INFO: === FDR correction performed with classifier version 11 ===
1 day, 5:59:27.293651 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:59:27.294022 PROGRESS: Total precursors accumulated: 751,847
1 day, 5:59:27.294099 PROGRESS: Target precursors: 441,523 (58.73%)
1 day, 5:59:27.294162 PROGRESS: Decoy precursors: 310,324 (41.27%)
1 day, 5:59:27.294217 PROGRESS: 
1 day, 5:59:27.294284 PROGRESS: Precursor Summary:
1 day, 5:59:27.300368 PROGRESS: Channel   0:	 0.050 FDR:    89; 0.010 FDR:     4; 0.001 FDR:     4
1 day, 5:59:27.300491 PROGRESS: 
1 day, 5:59:27.300558 PROGRESS: Protein Summary:
1 day, 5:59:27.305425 PROGRESS: Channel   0:	 0.050 FDR:    76; 0.010 FDR:     4; 0.001 FDR:     4
1 day, 5:59:27.305538 PROGRESS: =========================================================================
1 day, 5:59:27.324997 INFO: Target number of precursors not reached yet.
1 day, 5:59:29.760747 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 5:59:29.979483 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 5:59:31.065917 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 5:59:31.283778 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 5:59:33.314611 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:59:33.314960 INFO: Starting optimization step 13.
1 day, 5:59:33.315061 PROGRESS: === Extracting elution groups 819000 to 1638200 ===
1 day, 5:59:33.315175 INFO: Using python extraction backend
1 day, 5:59:33.315353 PROGRESS: Extracting batch of 1633286 precursors
1 day, 5:59:33.315510 INFO: === Search parameters used ===
1 day, 5:59:33.315607 INFO: rt_error       : 1199.968138
1 day, 5:59:33.315682 INFO: mobility_error : 0.1
1 day, 5:59:33.315746 INFO: num_candidates : 3
1 day, 5:59:33.315809 INFO: ms1_error      : 30
1 day, 5:59:33.315881 INFO: ms2_error      : 30
1 day, 5:59:33.315941 INFO: fwhm_rt        : 3.1309814453125
1 day, 5:59:33.315998 INFO: quant_window   : 3
1 day, 5:59:33.316056 INFO: ==============================================
1 day, 5:59:33.735188 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 5:59:33.735347 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 5:59:33.735414 INFO: FWHM in RT is 3.13 seconds, sigma is 0.52
1 day, 5:59:33.735445 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.94
1 day, 5:59:33.736393 INFO: Starting candidate selection
1 day, 7:08:25.844627 INFO: Starting candidate scoring
1 day, 7:09:20.209590 INFO: Finished candidate processing
1 day, 7:09:20.210021 INFO: Collecting candidate features
1 day, 7:09:28.231736 WARNING: intensity_correlation has 1156 NaNs ( 0.03 % out of 4227317)
1 day, 7:09:28.235794 WARNING: height_correlation has 87 NaNs ( 0.00 % out of 4227317)
1 day, 7:09:28.377250 INFO: Collecting fragment features
1 day, 7:09:30.656963 INFO: Finished candidate scoring
1 day, 7:09:35.677162 INFO: performing precursor FDR with 47 features
1 day, 7:09:35.677328 INFO: Decoy channel: -1
1 day, 7:09:35.677365 INFO: competitive: True
1 day, 7:09:38.497428 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 7:09:39.950106 WARNING: dropped 1068 target PSMs due to missing features
1 day, 7:09:39.950276 WARNING: dropped 1399 decoy PSMs due to missing features
1 day, 7:09:43.294877 INFO: Estimating optimal hyperparameters - samples: 6,761,344, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 7:09:43.308524 INFO: Using random state 567531 for train-test-split
1 day, 7:13:00.960583 INFO: Test AUC: 0.567
1 day, 7:13:00.960775 INFO: Train AUC: 0.569
1 day, 7:13:00.960819 INFO: AUC difference: 0.42%
1 day, 7:13:03.568980 INFO: Resetting torch num_threads to 80
1 day, 7:13:06.494921 PROGRESS: === Extracted 8454147 precursors and 70715490 fragments ===
1 day, 7:13:06.497549 INFO: === FDR correction performed with classifier version 11 ===
1 day, 7:13:06.746273 PROGRESS: ============================= Precursor FDR =============================
1 day, 7:13:06.746638 PROGRESS: Total precursors accumulated: 1,503,805
1 day, 7:13:06.746719 PROGRESS: Target precursors: 887,566 (59.02%)
1 day, 7:13:06.746782 PROGRESS: Decoy precursors: 616,239 (40.98%)
1 day, 7:13:06.746838 PROGRESS: 
1 day, 7:13:06.746891 PROGRESS: Precursor Summary:
1 day, 7:13:06.756901 PROGRESS: Channel   0:	 0.050 FDR:   794; 0.010 FDR:   511; 0.001 FDR:   383
1 day, 7:13:06.757079 PROGRESS: 
1 day, 7:13:06.757163 PROGRESS: Protein Summary:
1 day, 7:13:06.766201 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   266; 0.001 FDR:   204
1 day, 7:13:06.766359 PROGRESS: =========================================================================
1 day, 7:13:06.787081 INFO: Target number of precursors reached.
1 day, 7:13:14.376546 INFO: fragments_df: keeping 5000 of 70715490 [sum(precursor_idx_mask)=15812 sum(mass_error_mask)=70715221 stop_rank=5000
1 day, 7:13:16.940018 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 7:13:17.078233 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 7:13:17.218913 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 7:13:17.349373 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 7:13:18.016665 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 7:13:18.017149 INFO: Using score_cutoff 45.322011474609376 (fac=0.99, q=1)
1 day, 7:13:18.017533 INFO: Updating optimization_manager: fwhm_rt             : 3.1309814453125 -> 3.160578489303589
1 day, 7:13:18.017622 INFO: Updating optimization_manager: fwhm_mobility       : 0.009115289896726608 -> 0.009396519511938095
1 day, 7:13:18.017685 INFO: Updating optimization_manager: score_cutoff        : 19.399720847511293 -> 45.322011474609376
1 day, 7:13:18.017767 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 7:13:18.219791 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 7:13:19.291688 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 7:13:19.479639 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 7:13:21.400124 INFO: === checking if optimization conditions were reached ===
1 day, 7:13:21.402763 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 7:13:21.402936 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
1 day, 7:13:21.403017 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 7:13:21.404198 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 7:13:21.404307 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
1 day, 7:13:21.404387 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 7:13:21.404455 INFO: ==============================================
1 day, 7:13:21.404543 INFO: Starting optimization step 14.
1 day, 7:13:21.404614 PROGRESS: === Extracting elution groups 0 to 819000 ===
1 day, 7:13:21.404717 INFO: Using python extraction backend
1 day, 7:13:21.404867 PROGRESS: Extracting batch of 1632996 precursors
1 day, 7:13:21.404945 INFO: === Search parameters used ===
1 day, 7:13:21.405007 INFO: rt_error       : 1199.968138
1 day, 7:13:21.405059 INFO: mobility_error : 0.1
1 day, 7:13:21.405107 INFO: num_candidates : 3
1 day, 7:13:21.405157 INFO: ms1_error      : 15.0
1 day, 7:13:21.405204 INFO: ms2_error      : 15.0
1 day, 7:13:21.405249 INFO: fwhm_rt        : 3.160578489303589
1 day, 7:13:21.405296 INFO: quant_window   : 3
1 day, 7:13:21.405343 INFO: ==============================================
1 day, 7:13:21.825433 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 7:13:21.825588 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 7:13:21.825666 INFO: FWHM in RT is 3.16 seconds, sigma is 0.53
1 day, 7:13:21.825694 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 5.09
1 day, 7:13:21.826602 INFO: Starting candidate selection
1 day, 8:15:33.554136 INFO: Starting candidate scoring
1 day, 8:16:23.347911 INFO: Finished candidate processing
1 day, 8:16:23.348234 INFO: Collecting candidate features
1 day, 8:16:31.747708 WARNING: intensity_correlation has 4049 NaNs ( 0.10 % out of 4119136)
1 day, 8:16:31.751561 WARNING: height_correlation has 234 NaNs ( 0.01 % out of 4119136)
1 day, 8:16:31.888846 INFO: Collecting fragment features
1 day, 8:16:34.344800 INFO: Finished candidate scoring
1 day, 8:16:36.919750 INFO: performing precursor FDR with 47 features
1 day, 8:16:36.919908 INFO: Decoy channel: -1
1 day, 8:16:36.919939 INFO: competitive: True
1 day, 8:16:37.888028 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:16:38.480907 WARNING: dropped 1990 target PSMs due to missing features
1 day, 8:16:38.481071 WARNING: dropped 2218 decoy PSMs due to missing features
1 day, 8:16:40.055959 INFO: Estimating optimal hyperparameters - samples: 3,291,942, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 8:16:40.063260 INFO: Using random state 832421 for train-test-split
1 day, 8:18:12.143303 INFO: Test AUC: 0.564
1 day, 8:18:12.143514 INFO: Train AUC: 0.569
1 day, 8:18:12.143553 INFO: AUC difference: 0.87%
1 day, 8:18:13.707092 INFO: Resetting torch num_threads to 80
1 day, 8:18:13.779753 PROGRESS: === Extracted 4119136 precursors and 29694633 fragments ===
1 day, 8:18:13.781363 INFO: === FDR correction performed with classifier version 13 ===
1 day, 8:18:13.907112 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:18:13.907480 PROGRESS: Total precursors accumulated: 745,408
1 day, 8:18:13.907565 PROGRESS: Target precursors: 436,365 (58.54%)
1 day, 8:18:13.907626 PROGRESS: Decoy precursors: 309,043 (41.46%)
1 day, 8:18:13.907681 PROGRESS: 
1 day, 8:18:13.907735 PROGRESS: Precursor Summary:
1 day, 8:18:13.914629 PROGRESS: Channel   0:	 0.050 FDR:   944; 0.010 FDR:   677; 0.001 FDR:   441
1 day, 8:18:13.914812 PROGRESS: 
1 day, 8:18:13.914898 PROGRESS: Protein Summary:
1 day, 8:18:13.920105 PROGRESS: Channel   0:	 0.050 FDR:   578; 0.010 FDR:   410; 0.001 FDR:   277
1 day, 8:18:13.920218 PROGRESS: =========================================================================
1 day, 8:18:13.974497 INFO: Target number of precursors reached.
1 day, 8:18:17.147245 INFO: fragments_df: keeping 5000 of 29694633 [sum(precursor_idx_mask)=19180 sum(mass_error_mask)=29694448 stop_rank=5000
1 day, 8:18:18.937719 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:18:19.110323 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:18:19.289684 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:18:19.464528 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:18:20.194679 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:18:20.195146 INFO: Using score_cutoff 32.813124458312984 (fac=0.99, q=1)
1 day, 8:18:20.195568 INFO: Updating optimization_manager: fwhm_rt             : 3.160578489303589 -> 2.9237990379333496
1 day, 8:18:20.195664 INFO: Updating optimization_manager: fwhm_mobility       : 0.009396519511938095 -> 0.006444309838116169
1 day, 8:18:20.195727 INFO: Updating optimization_manager: score_cutoff        : 45.322011474609376 -> 32.813124458312984
1 day, 8:18:20.195799 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:18:20.297083 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:18:20.848381 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:18:20.955189 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:18:21.943323 INFO: === checking if optimization conditions were reached ===
1 day, 8:18:21.945826 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 8:18:21.946022 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
1 day, 8:18:21.946113 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 8:18:21.947304 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 8:18:21.947414 INFO: Updating optimization_manager: classifier_version  : 14 -> 14
1 day, 8:18:21.947486 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 8:18:21.947549 INFO: ==============================================
1 day, 8:18:21.947632 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 8:18:23.020565 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:18:23.121142 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:18:23.640986 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:18:23.745529 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:18:24.724205 INFO: Starting optimization step 0.
1 day, 8:18:24.724542 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 8:18:24.724654 INFO: Using python extraction backend
1 day, 8:18:24.724805 PROGRESS: Extracting batch of 816307 precursors
1 day, 8:18:24.724896 INFO: === Search parameters used ===
1 day, 8:18:24.724961 INFO: rt_error       : 1199.968138
1 day, 8:18:24.725013 INFO: mobility_error : 0.1
1 day, 8:18:24.725062 INFO: num_candidates : 3
1 day, 8:18:24.725111 INFO: ms1_error      : 15.0
1 day, 8:18:24.725170 INFO: ms2_error      : 15.0
1 day, 8:18:24.725217 INFO: fwhm_rt        : 2.9237990379333496
1 day, 8:18:24.725262 INFO: quant_window   : 3
1 day, 8:18:24.725307 INFO: ==============================================
1 day, 8:18:24.979828 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 8:18:24.979977 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 8:18:24.980037 INFO: FWHM in RT is 2.92 seconds, sigma is 0.49
1 day, 8:18:24.980064 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.49
1 day, 8:18:24.980907 INFO: Starting candidate selection
1 day, 8:47:26.911083 INFO: Starting candidate scoring
1 day, 8:47:53.337490 INFO: Finished candidate processing
1 day, 8:47:53.337905 INFO: Collecting candidate features
1 day, 8:47:58.300410 WARNING: intensity_correlation has 2122 NaNs ( 0.10 % out of 2053602)
1 day, 8:47:58.302981 WARNING: height_correlation has 122 NaNs ( 0.01 % out of 2053602)
1 day, 8:47:58.394567 INFO: Collecting fragment features
1 day, 8:47:59.734122 INFO: Finished candidate scoring
1 day, 8:48:01.097910 INFO: performing precursor FDR with 47 features
1 day, 8:48:01.098066 INFO: Decoy channel: -1
1 day, 8:48:01.098101 INFO: competitive: True
1 day, 8:48:01.656838 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:48:01.956691 WARNING: dropped 1060 target PSMs due to missing features
1 day, 8:48:01.956860 WARNING: dropped 1144 decoy PSMs due to missing features
1 day, 8:48:02.755605 INFO: Estimating optimal hyperparameters - samples: 1,641,118, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 8:48:02.760739 INFO: Using random state 934384 for train-test-split
1 day, 8:48:43.589583 INFO: Test AUC: 0.568
1 day, 8:48:43.590209 INFO: Train AUC: 0.576
1 day, 8:48:43.590255 INFO: AUC difference: 1.34%
1 day, 8:48:44.524786 INFO: Resetting torch num_threads to 80
1 day, 8:48:44.561069 PROGRESS: === Extracted 2053602 precursors and 14591907 fragments ===
1 day, 8:48:44.562179 INFO: === FDR correction performed with classifier version 14 ===
1 day, 8:48:44.624736 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:48:44.625078 PROGRESS: Total precursors accumulated: 373,369
1 day, 8:48:44.625153 PROGRESS: Target precursors: 220,954 (59.18%)
1 day, 8:48:44.625219 PROGRESS: Decoy precursors: 152,415 (40.82%)
1 day, 8:48:44.625276 PROGRESS: 
1 day, 8:48:44.625329 PROGRESS: Precursor Summary:
1 day, 8:48:44.628812 PROGRESS: Channel   0:	 0.050 FDR:   563; 0.010 FDR:   416; 0.001 FDR:   303
1 day, 8:48:44.628926 PROGRESS: 
1 day, 8:48:44.629001 PROGRESS: Protein Summary:
1 day, 8:48:44.632407 PROGRESS: Channel   0:	 0.050 FDR:   436; 0.010 FDR:   310; 0.001 FDR:   218
1 day, 8:48:44.632514 PROGRESS: =========================================================================
1 day, 8:48:44.657752 INFO: Target number of precursors reached.
1 day, 8:48:46.156936 INFO: fragments_df: keeping 5000 of 14591907 [sum(precursor_idx_mask)=11228 sum(mass_error_mask)=14591823 stop_rank=5000
1 day, 8:48:47.052278 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:47.207922 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:47.363298 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:47.512152 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:48.234313 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:48:48.234763 INFO: Using score_cutoff 28.45447209262848 (fac=0.99, q=1)
1 day, 8:48:48.235136 INFO: Updating optimization_manager: fwhm_rt             : 2.9237990379333496 -> 2.8152780532836914
1 day, 8:48:48.235221 INFO: Updating optimization_manager: fwhm_mobility       : 0.006444309838116169 -> 0.006040048785507679
1 day, 8:48:48.235282 INFO: Updating optimization_manager: score_cutoff        : 32.813124458312984 -> 28.45447209262848
1 day, 8:48:48.235347 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:48.284551 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:48.543466 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:48.594993 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:49.112067 INFO: === checking if optimization conditions were reached ===
1 day, 8:48:49.112350 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:48:49.114587 INFO: Updating optimization_manager: rt_error            : 1199.968138 -> 646.7783957339904
1 day, 8:48:49.114728 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 646.7784.
1 day, 8:48:49.114803 INFO: ==============================================
1 day, 8:48:49.114882 INFO: Starting optimization step 1.
1 day, 8:48:49.114949 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 8:48:49.115043 INFO: Using python extraction backend
1 day, 8:48:49.115177 PROGRESS: Extracting batch of 407917 precursors
1 day, 8:48:49.115253 INFO: === Search parameters used ===
1 day, 8:48:49.115308 INFO: rt_error       : 646.7783957339904
1 day, 8:48:49.115356 INFO: mobility_error : 0.1
1 day, 8:48:49.115405 INFO: num_candidates : 3
1 day, 8:48:49.115454 INFO: ms1_error      : 15.0
1 day, 8:48:49.115502 INFO: ms2_error      : 15.0
1 day, 8:48:49.115546 INFO: fwhm_rt        : 2.8152780532836914
1 day, 8:48:49.115590 INFO: quant_window   : 3
1 day, 8:48:49.115636 INFO: ==============================================
1 day, 8:48:49.225070 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 8:48:49.225219 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 8:48:49.225275 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
1 day, 8:48:49.225301 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.27
1 day, 8:48:49.226438 INFO: Starting candidate selection
1 day, 8:59:07.901963 INFO: Starting candidate scoring
1 day, 8:59:21.470959 INFO: Finished candidate processing
1 day, 8:59:21.471220 INFO: Collecting candidate features
1 day, 8:59:23.447666 WARNING: intensity_correlation has 1402 NaNs ( 0.14 % out of 1007817)
1 day, 8:59:23.448797 WARNING: height_correlation has 98 NaNs ( 0.01 % out of 1007817)
1 day, 8:59:23.485474 INFO: Collecting fragment features
1 day, 8:59:24.043641 INFO: Finished candidate scoring
1 day, 8:59:24.692319 INFO: performing precursor FDR with 47 features
1 day, 8:59:24.692460 INFO: Decoy channel: -1
1 day, 8:59:24.692495 INFO: competitive: True
1 day, 8:59:24.951800 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:59:25.108585 WARNING: dropped 713 target PSMs due to missing features
1 day, 8:59:25.108755 WARNING: dropped 749 decoy PSMs due to missing features
1 day, 8:59:25.472770 INFO: Estimating optimal hyperparameters - samples: 805,084, batch_size: 3,297, learning_rate: 8.97e-04
1 day, 8:59:25.475113 INFO: Using random state 934384 for train-test-split
1 day, 8:59:48.180720 INFO: Test AUC: 0.563
1 day, 8:59:48.180872 INFO: Train AUC: 0.578
1 day, 8:59:48.180912 INFO: AUC difference: 2.60%
1 day, 8:59:48.771579 INFO: Resetting torch num_threads to 80
1 day, 8:59:48.790877 PROGRESS: === Extracted 1007817 precursors and 6978714 fragments ===
1 day, 8:59:48.791794 INFO: === FDR correction performed with classifier version 14 ===
1 day, 8:59:48.825414 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:59:48.825743 PROGRESS: Total precursors accumulated: 185,773
1 day, 8:59:48.825818 PROGRESS: Target precursors: 109,601 (59.00%)
1 day, 8:59:48.825891 PROGRESS: Decoy precursors: 76,172 (41.00%)
1 day, 8:59:48.825949 PROGRESS: 
1 day, 8:59:48.826004 PROGRESS: Precursor Summary:
1 day, 8:59:48.828262 PROGRESS: Channel   0:	 0.050 FDR:   289; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 8:59:48.828366 PROGRESS: 
1 day, 8:59:48.828438 PROGRESS: Protein Summary:
1 day, 8:59:48.830504 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 8:59:48.830608 PROGRESS: =========================================================================
1 day, 8:59:48.865986 INFO: Target number of precursors not reached yet.
1 day, 8:59:49.638665 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:49.688695 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:49.948894 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:50.003566 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:50.534976 INFO: === skipping optimization until target number of precursors are found ===
1 day, 8:59:50.535286 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 8:59:50.535427 INFO: Starting optimization step 2.
1 day, 8:59:50.535506 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 8:59:50.535591 INFO: Using python extraction backend
1 day, 8:59:50.535723 PROGRESS: Extracting batch of 408390 precursors
1 day, 8:59:50.535809 INFO: === Search parameters used ===
1 day, 8:59:50.535869 INFO: rt_error       : 646.7783957339904
1 day, 8:59:50.535919 INFO: mobility_error : 0.1
1 day, 8:59:50.535969 INFO: num_candidates : 3
1 day, 8:59:50.536016 INFO: ms1_error      : 15.0
1 day, 8:59:50.536062 INFO: ms2_error      : 15.0
1 day, 8:59:50.536107 INFO: fwhm_rt        : 2.8152780532836914
1 day, 8:59:50.536163 INFO: quant_window   : 3
1 day, 8:59:50.536209 INFO: ==============================================
1 day, 8:59:50.642727 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 8:59:50.642876 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 8:59:50.642931 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
1 day, 8:59:50.642958 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.27
1 day, 8:59:50.643766 INFO: Starting candidate selection
1 day, 9:09:53.903509 INFO: Starting candidate scoring
1 day, 9:10:05.901953 INFO: Finished candidate processing
1 day, 9:10:05.902191 INFO: Collecting candidate features
1 day, 9:10:07.889922 WARNING: intensity_correlation has 1496 NaNs ( 0.15 % out of 1006209)
1 day, 9:10:07.891058 WARNING: height_correlation has 89 NaNs ( 0.01 % out of 1006209)
1 day, 9:10:07.928657 INFO: Collecting fragment features
1 day, 9:10:08.437801 INFO: Finished candidate scoring
1 day, 9:10:09.664744 INFO: performing precursor FDR with 47 features
1 day, 9:10:09.664901 INFO: Decoy channel: -1
1 day, 9:10:09.664932 INFO: competitive: True
1 day, 9:10:10.497356 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:10:10.788411 WARNING: dropped 1482 target PSMs due to missing features
1 day, 9:10:10.788572 WARNING: dropped 1531 decoy PSMs due to missing features
1 day, 9:10:11.635822 INFO: Estimating optimal hyperparameters - samples: 1,608,810, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 9:10:11.640387 INFO: Using random state 934384 for train-test-split
1 day, 9:10:53.507929 INFO: Test AUC: 0.562
1 day, 9:10:53.508097 INFO: Train AUC: 0.573
1 day, 9:10:53.508135 INFO: AUC difference: 1.90%
1 day, 9:10:54.441805 INFO: Resetting torch num_threads to 80
1 day, 9:10:54.690193 PROGRESS: === Extracted 2014026 precursors and 13947609 fragments ===
1 day, 9:10:54.691391 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:10:54.752389 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:10:54.752745 PROGRESS: Total precursors accumulated: 371,315
1 day, 9:10:54.752818 PROGRESS: Target precursors: 217,339 (58.53%)
1 day, 9:10:54.752877 PROGRESS: Decoy precursors: 153,976 (41.47%)
1 day, 9:10:54.752930 PROGRESS: 
1 day, 9:10:54.752981 PROGRESS: Precursor Summary:
1 day, 9:10:54.756558 PROGRESS: Channel   0:	 0.050 FDR:   542; 0.010 FDR:   432; 0.001 FDR:   367
1 day, 9:10:54.756678 PROGRESS: 
1 day, 9:10:54.756744 PROGRESS: Protein Summary:
1 day, 9:10:54.759905 PROGRESS: Channel   0:	 0.050 FDR:   409; 0.010 FDR:   319; 0.001 FDR:   268
1 day, 9:10:54.760016 PROGRESS: =========================================================================
1 day, 9:10:54.765458 INFO: Target number of precursors reached.
1 day, 9:10:56.315056 INFO: fragments_df: keeping 5000 of 13947609 [sum(precursor_idx_mask)=11551 sum(mass_error_mask)=13947461 stop_rank=5000
1 day, 9:10:57.085926 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:57.230294 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:57.383140 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:57.544253 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:58.268025 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:10:58.268484 INFO: Using score_cutoff 25.201623808479308 (fac=0.99, q=1)
1 day, 9:10:58.268842 INFO: Updating optimization_manager: fwhm_rt             : 2.8152780532836914 -> 2.8342957496643066
1 day, 9:10:58.268929 INFO: Updating optimization_manager: fwhm_mobility       : 0.006040048785507679 -> 0.006076439283788204
1 day, 9:10:58.268992 INFO: Updating optimization_manager: score_cutoff        : 28.45447209262848 -> 25.201623808479308
1 day, 9:10:58.269059 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:58.321726 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:58.578418 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:58.633343 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:59.168868 INFO: === checking if optimization conditions were reached ===
1 day, 9:10:59.169144 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 9:10:59.171460 INFO: Updating optimization_manager: rt_error            : 646.7783957339904 -> 429.70308647070294
1 day, 9:10:59.171596 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 429.7031.
1 day, 9:10:59.171673 INFO: ==============================================
1 day, 9:10:59.171753 INFO: Starting optimization step 3.
1 day, 9:10:59.171821 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:10:59.171892 INFO: Using python extraction backend
1 day, 9:10:59.172013 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:10:59.172100 INFO: === Search parameters used ===
1 day, 9:10:59.172162 INFO: rt_error       : 429.70308647070294
1 day, 9:10:59.172214 INFO: mobility_error : 0.1
1 day, 9:10:59.172263 INFO: num_candidates : 3
1 day, 9:10:59.172311 INFO: ms1_error      : 15.0
1 day, 9:10:59.172358 INFO: ms2_error      : 15.0
1 day, 9:10:59.172406 INFO: fwhm_rt        : 2.8342957496643066
1 day, 9:10:59.172452 INFO: quant_window   : 3
1 day, 9:10:59.172498 INFO: ==============================================
1 day, 9:10:59.279902 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:10:59.280049 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:10:59.280098 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
1 day, 9:10:59.280124 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.29
1 day, 9:10:59.280886 INFO: Starting candidate selection
1 day, 9:17:28.214360 INFO: Starting candidate scoring
1 day, 9:17:39.860016 INFO: Finished candidate processing
1 day, 9:17:39.860281 INFO: Collecting candidate features
1 day, 9:17:41.728228 WARNING: intensity_correlation has 1868 NaNs ( 0.19 % out of 981064)
1 day, 9:17:41.729317 WARNING: height_correlation has 179 NaNs ( 0.02 % out of 981064)
1 day, 9:17:41.764231 INFO: Collecting fragment features
1 day, 9:17:42.241234 INFO: Finished candidate scoring
1 day, 9:17:42.873368 INFO: performing precursor FDR with 47 features
1 day, 9:17:42.873504 INFO: Decoy channel: -1
1 day, 9:17:42.873535 INFO: competitive: True
1 day, 9:17:43.109947 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:17:43.254044 WARNING: dropped 960 target PSMs due to missing features
1 day, 9:17:43.254206 WARNING: dropped 1002 decoy PSMs due to missing features
1 day, 9:17:43.591944 INFO: Estimating optimal hyperparameters - samples: 783,281, batch_size: 3,208, learning_rate: 8.85e-04
1 day, 9:17:43.593604 INFO: Using random state 934384 for train-test-split
1 day, 9:18:03.714141 INFO: Test AUC: 0.557
1 day, 9:18:03.714293 INFO: Train AUC: 0.573
1 day, 9:18:03.714330 INFO: AUC difference: 2.84%
1 day, 9:18:04.291674 INFO: Resetting torch num_threads to 80
1 day, 9:18:04.310515 PROGRESS: === Extracted 981064 precursors and 6355145 fragments ===
1 day, 9:18:04.311386 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:18:04.343843 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:18:04.344153 PROGRESS: Total precursors accumulated: 184,790
1 day, 9:18:04.344228 PROGRESS: Target precursors: 107,890 (58.39%)
1 day, 9:18:04.344289 PROGRESS: Decoy precursors: 76,900 (41.61%)
1 day, 9:18:04.344344 PROGRESS: 
1 day, 9:18:04.344400 PROGRESS: Precursor Summary:
1 day, 9:18:04.346640 PROGRESS: Channel   0:	 0.050 FDR:   291; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 9:18:04.346749 PROGRESS: 
1 day, 9:18:04.346816 PROGRESS: Protein Summary:
1 day, 9:18:04.348918 PROGRESS: Channel   0:	 0.050 FDR:   238; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 9:18:04.349037 PROGRESS: =========================================================================
1 day, 9:18:04.384207 INFO: Target number of precursors not reached yet.
1 day, 9:18:05.155906 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:18:05.210189 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:18:05.470124 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:18:05.524981 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:18:06.070844 INFO: === skipping optimization until target number of precursors are found ===
1 day, 9:18:06.071138 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 9:18:06.071268 INFO: Starting optimization step 4.
1 day, 9:18:06.071345 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 9:18:06.071428 INFO: Using python extraction backend
1 day, 9:18:06.071561 PROGRESS: Extracting batch of 408390 precursors
1 day, 9:18:06.071650 INFO: === Search parameters used ===
1 day, 9:18:06.071707 INFO: rt_error       : 429.70308647070294
1 day, 9:18:06.071757 INFO: mobility_error : 0.1
1 day, 9:18:06.071808 INFO: num_candidates : 3
1 day, 9:18:06.071856 INFO: ms1_error      : 15.0
1 day, 9:18:06.071902 INFO: ms2_error      : 15.0
1 day, 9:18:06.071948 INFO: fwhm_rt        : 2.8342957496643066
1 day, 9:18:06.071999 INFO: quant_window   : 3
1 day, 9:18:06.072046 INFO: ==============================================
1 day, 9:18:06.184865 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:18:06.185010 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:18:06.185071 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
1 day, 9:18:06.185098 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.29
1 day, 9:18:06.186001 INFO: Starting candidate selection
1 day, 9:24:42.947522 INFO: Starting candidate scoring
1 day, 9:24:54.950652 INFO: Finished candidate processing
1 day, 9:24:54.950852 INFO: Collecting candidate features
1 day, 9:24:56.793574 WARNING: intensity_correlation has 1922 NaNs ( 0.20 % out of 980722)
1 day, 9:24:56.794670 WARNING: height_correlation has 169 NaNs ( 0.02 % out of 980722)
1 day, 9:24:56.830961 INFO: Collecting fragment features
1 day, 9:24:57.315410 INFO: Finished candidate scoring
1 day, 9:24:58.439324 INFO: performing precursor FDR with 47 features
1 day, 9:24:58.439488 INFO: Decoy channel: -1
1 day, 9:24:58.439517 INFO: competitive: True
1 day, 9:24:59.234140 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:24:59.559245 WARNING: dropped 1982 target PSMs due to missing features
1 day, 9:24:59.559412 WARNING: dropped 1990 decoy PSMs due to missing features
1 day, 9:25:00.359218 INFO: Estimating optimal hyperparameters - samples: 1,566,251, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 9:25:00.364075 INFO: Using random state 934384 for train-test-split
1 day, 9:25:41.310189 INFO: Test AUC: 0.559
1 day, 9:25:41.310361 INFO: Train AUC: 0.568
1 day, 9:25:41.310397 INFO: AUC difference: 1.61%
1 day, 9:25:42.206471 INFO: Resetting torch num_threads to 80
1 day, 9:25:42.449449 PROGRESS: === Extracted 1961786 precursors and 12707397 fragments ===
1 day, 9:25:42.450545 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:25:42.511226 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:25:42.511562 PROGRESS: Total precursors accumulated: 369,449
1 day, 9:25:42.511640 PROGRESS: Target precursors: 213,548 (57.80%)
1 day, 9:25:42.511701 PROGRESS: Decoy precursors: 155,901 (42.20%)
1 day, 9:25:42.511764 PROGRESS: 
1 day, 9:25:42.511823 PROGRESS: Precursor Summary:
1 day, 9:25:42.515259 PROGRESS: Channel   0:	 0.050 FDR:   564; 0.010 FDR:   385; 0.001 FDR:   328
1 day, 9:25:42.515375 PROGRESS: 
1 day, 9:25:42.515446 PROGRESS: Protein Summary:
1 day, 9:25:42.518600 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   281; 0.001 FDR:   241
1 day, 9:25:42.518704 PROGRESS: =========================================================================
1 day, 9:25:42.524197 INFO: Target number of precursors reached.
1 day, 9:25:43.971650 INFO: fragments_df: keeping 5000 of 12707397 [sum(precursor_idx_mask)=10505 sum(mass_error_mask)=12707268 stop_rank=5000
1 day, 9:25:45.153571 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:25:45.277065 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:25:45.399966 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:25:45.530143 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:25:46.181961 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:25:46.182433 INFO: Using score_cutoff 27.246873628234862 (fac=0.99, q=1)
1 day, 9:25:46.182776 INFO: Updating optimization_manager: fwhm_rt             : 2.8342957496643066 -> 2.8896641731262207
1 day, 9:25:46.182863 INFO: Updating optimization_manager: fwhm_mobility       : 0.006076439283788204 -> 0.006448662374168634
1 day, 9:25:46.182925 INFO: Updating optimization_manager: score_cutoff        : 25.201623808479308 -> 27.246873628234862
1 day, 9:25:46.182989 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:25:46.290151 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:25:46.810214 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:25:46.917701 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:25:47.960329 INFO: === checking if optimization conditions were reached ===
1 day, 9:25:47.960679 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 9:25:47.963130 INFO: Updating optimization_manager: rt_error            : 429.70308647070294 -> 228.93364897716438
1 day, 9:25:47.963274 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 228.9336.
1 day, 9:25:47.963353 INFO: ==============================================
1 day, 9:25:47.963441 INFO: Starting optimization step 5.
1 day, 9:25:47.963513 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 9:25:47.963598 INFO: Using python extraction backend
1 day, 9:25:47.963737 PROGRESS: Extracting batch of 816307 precursors
1 day, 9:25:47.963816 INFO: === Search parameters used ===
1 day, 9:25:47.963883 INFO: rt_error       : 228.93364897716438
1 day, 9:25:47.963939 INFO: mobility_error : 0.1
1 day, 9:25:47.963988 INFO: num_candidates : 3
1 day, 9:25:47.964036 INFO: ms1_error      : 15.0
1 day, 9:25:47.964082 INFO: ms2_error      : 15.0
1 day, 9:25:47.964129 INFO: fwhm_rt        : 2.8896641731262207
1 day, 9:25:47.964175 INFO: quant_window   : 3
1 day, 9:25:47.964218 INFO: ==============================================
1 day, 9:25:48.169489 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:25:48.169639 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:25:48.169696 INFO: FWHM in RT is 2.89 seconds, sigma is 0.48
1 day, 9:25:48.169721 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.49
1 day, 9:25:48.170502 INFO: Starting candidate selection
1 day, 9:32:35.376433 INFO: Starting candidate scoring
1 day, 9:32:58.718960 INFO: Finished candidate processing
1 day, 9:32:58.719392 INFO: Collecting candidate features
1 day, 9:33:02.467579 WARNING: intensity_correlation has 5062 NaNs ( 0.27 % out of 1884002)
1 day, 9:33:02.469399 WARNING: height_correlation has 550 NaNs ( 0.03 % out of 1884002)
1 day, 9:33:02.531770 INFO: Collecting fragment features
1 day, 9:33:03.494935 INFO: Finished candidate scoring
1 day, 9:33:04.757342 INFO: performing precursor FDR with 47 features
1 day, 9:33:04.757486 INFO: Decoy channel: -1
1 day, 9:33:04.757514 INFO: competitive: True
1 day, 9:33:05.203162 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:33:05.475079 WARNING: dropped 2648 target PSMs due to missing features
1 day, 9:33:05.475249 WARNING: dropped 2675 decoy PSMs due to missing features
1 day, 9:33:06.163954 INFO: Estimating optimal hyperparameters - samples: 1,502,943, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 9:33:06.167889 INFO: Using random state 934384 for train-test-split
1 day, 9:33:43.659834 INFO: Test AUC: 0.554
1 day, 9:33:43.660008 INFO: Train AUC: 0.565
1 day, 9:33:43.660046 INFO: AUC difference: 1.88%
1 day, 9:33:44.524827 INFO: Resetting torch num_threads to 80
1 day, 9:33:44.558913 PROGRESS: === Extracted 1884002 precursors and 11442249 fragments ===
1 day, 9:33:44.560059 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:33:44.620445 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:33:44.620791 PROGRESS: Total precursors accumulated: 365,011
1 day, 9:33:44.620866 PROGRESS: Target precursors: 208,543 (57.13%)
1 day, 9:33:44.620927 PROGRESS: Decoy precursors: 156,468 (42.87%)
1 day, 9:33:44.620981 PROGRESS: 
1 day, 9:33:44.621034 PROGRESS: Precursor Summary:
1 day, 9:33:44.624533 PROGRESS: Channel   0:	 0.050 FDR:   645; 0.010 FDR:   469; 0.001 FDR:   377
1 day, 9:33:44.624644 PROGRESS: 
1 day, 9:33:44.624713 PROGRESS: Protein Summary:
1 day, 9:33:44.628035 PROGRESS: Channel   0:	 0.050 FDR:   492; 0.010 FDR:   345; 0.001 FDR:   272
1 day, 9:33:44.628145 PROGRESS: =========================================================================
1 day, 9:33:44.642431 INFO: Target number of precursors reached.
1 day, 9:33:45.784909 INFO: fragments_df: keeping 5000 of 11442249 [sum(precursor_idx_mask)=12354 sum(mass_error_mask)=11442058 stop_rank=5000
1 day, 9:33:46.573130 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:33:46.731783 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:33:46.886144 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:33:47.044755 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:33:47.763858 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:33:47.764323 INFO: Using score_cutoff 26.280404331207276 (fac=0.99, q=1)
1 day, 9:33:47.764688 INFO: Updating optimization_manager: fwhm_rt             : 2.8896641731262207 -> 2.8306021690368652
1 day, 9:33:47.764777 INFO: Updating optimization_manager: fwhm_mobility       : 0.006448662374168634 -> 0.005893845576792955
1 day, 9:33:47.764851 INFO: Updating optimization_manager: score_cutoff        : 27.246873628234862 -> 26.280404331207276
1 day, 9:33:47.764917 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:33:47.818549 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:33:48.074570 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:33:48.128084 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:33:48.655669 INFO: === checking if optimization conditions were reached ===
1 day, 9:33:48.655967 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 9:33:48.658508 INFO: Updating optimization_manager: rt_error            : 228.93364897716438 -> 179.3979342073846
1 day, 9:33:48.658648 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 179.3979.
1 day, 9:33:48.658737 INFO: ==============================================
1 day, 9:33:48.658820 INFO: Starting optimization step 6.
1 day, 9:33:48.658890 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:33:48.658959 INFO: Using python extraction backend
1 day, 9:33:48.659079 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:33:48.659154 INFO: === Search parameters used ===
1 day, 9:33:48.659210 INFO: rt_error       : 179.3979342073846
1 day, 9:33:48.659261 INFO: mobility_error : 0.1
1 day, 9:33:48.659314 INFO: num_candidates : 3
1 day, 9:33:48.659362 INFO: ms1_error      : 15.0
1 day, 9:33:48.659413 INFO: ms2_error      : 15.0
1 day, 9:33:48.659462 INFO: fwhm_rt        : 2.8306021690368652
1 day, 9:33:48.659509 INFO: quant_window   : 3
1 day, 9:33:48.659556 INFO: ==============================================
1 day, 9:33:48.771767 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:33:48.771914 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:33:48.771964 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
1 day, 9:33:48.771991 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.19
1 day, 9:33:48.772799 INFO: Starting candidate selection
1 day, 9:36:18.800354 INFO: Starting candidate scoring
1 day, 9:36:30.551249 INFO: Finished candidate processing
1 day, 9:36:30.551466 INFO: Collecting candidate features
1 day, 9:36:32.337302 WARNING: intensity_correlation has 2760 NaNs ( 0.30 % out of 928236)
1 day, 9:36:32.338341 WARNING: height_correlation has 326 NaNs ( 0.04 % out of 928236)
1 day, 9:36:32.371653 INFO: Collecting fragment features
1 day, 9:36:32.835085 INFO: Finished candidate scoring
1 day, 9:36:33.472646 INFO: performing precursor FDR with 47 features
1 day, 9:36:33.472795 INFO: Decoy channel: -1
1 day, 9:36:33.472823 INFO: competitive: True
1 day, 9:36:33.717107 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:36:33.855527 WARNING: dropped 1464 target PSMs due to missing features
1 day, 9:36:33.855693 WARNING: dropped 1466 decoy PSMs due to missing features
1 day, 9:36:34.171788 INFO: Estimating optimal hyperparameters - samples: 740,244, batch_size: 3,032, learning_rate: 8.60e-04
1 day, 9:36:34.173234 INFO: Using random state 934384 for train-test-split
1 day, 9:36:53.236251 INFO: Test AUC: 0.552
1 day, 9:36:53.236470 INFO: Train AUC: 0.566
1 day, 9:36:53.236508 INFO: AUC difference: 2.46%
1 day, 9:36:53.761422 INFO: Resetting torch num_threads to 80
1 day, 9:36:53.779542 PROGRESS: === Extracted 928236 precursors and 5510094 fragments ===
1 day, 9:36:53.780430 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:36:53.813966 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:36:53.814303 PROGRESS: Total precursors accumulated: 181,668
1 day, 9:36:53.814378 PROGRESS: Target precursors: 104,280 (57.40%)
1 day, 9:36:53.814438 PROGRESS: Decoy precursors: 77,388 (42.60%)
1 day, 9:36:53.814493 PROGRESS: 
1 day, 9:36:53.814561 PROGRESS: Precursor Summary:
1 day, 9:36:53.816887 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   236; 0.001 FDR:   216
1 day, 9:36:53.816988 PROGRESS: 
1 day, 9:36:53.817049 PROGRESS: Protein Summary:
1 day, 9:36:53.819220 PROGRESS: Channel   0:	 0.050 FDR:   233; 0.010 FDR:   192; 0.001 FDR:   175
1 day, 9:36:53.819324 PROGRESS: =========================================================================
1 day, 9:36:53.832764 INFO: Target number of precursors reached.
1 day, 9:36:54.403803 INFO: fragments_df: keeping 3748 of 5510094 [sum(precursor_idx_mask)=6225 sum(mass_error_mask)=5509994 stop_rank=3748
1 day, 9:36:55.171468 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:36:55.289099 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:36:55.404321 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:36:55.519940 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:36:55.986043 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:36:55.986481 INFO: Using score_cutoff 27.256727082252503 (fac=0.99, q=1)
1 day, 9:36:55.986816 INFO: Updating optimization_manager: fwhm_rt             : 2.8306021690368652 -> 2.84814453125
1 day, 9:36:55.986903 INFO: Updating optimization_manager: fwhm_mobility       : 0.005893845576792955 -> 0.00590379536151886
1 day, 9:36:55.986964 INFO: Updating optimization_manager: score_cutoff        : 26.280404331207276 -> 27.256727082252503
1 day, 9:36:55.987035 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:36:56.040749 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:36:56.298043 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:36:56.353524 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:36:56.879394 INFO: === checking if optimization conditions were reached ===
1 day, 9:36:56.879692 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 9:36:56.881950 INFO: Updating optimization_manager: rt_error            : 179.3979342073846 -> 158.56562261784416
1 day, 9:36:56.882091 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 158.5656.
1 day, 9:36:56.882173 INFO: ==============================================
1 day, 9:36:56.882256 INFO: Starting optimization step 7.
1 day, 9:36:56.882329 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:36:56.882399 INFO: Using python extraction backend
1 day, 9:36:56.882516 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:36:56.882593 INFO: === Search parameters used ===
1 day, 9:36:56.882655 INFO: rt_error       : 158.56562261784416
1 day, 9:36:56.882710 INFO: mobility_error : 0.1
1 day, 9:36:56.882762 INFO: num_candidates : 3
1 day, 9:36:56.882821 INFO: ms1_error      : 15.0
1 day, 9:36:56.882873 INFO: ms2_error      : 15.0
1 day, 9:36:56.882924 INFO: fwhm_rt        : 2.84814453125
1 day, 9:36:56.882973 INFO: quant_window   : 3
1 day, 9:36:56.883024 INFO: ==============================================
1 day, 9:36:56.991841 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:36:56.991983 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:36:56.992035 INFO: FWHM in RT is 2.85 seconds, sigma is 0.48
1 day, 9:36:56.992064 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.20
1 day, 9:36:56.992886 INFO: Starting candidate selection
1 day, 9:39:07.691491 INFO: Starting candidate scoring
1 day, 9:39:19.324190 INFO: Finished candidate processing
1 day, 9:39:19.324466 INFO: Collecting candidate features
1 day, 9:39:21.072986 WARNING: intensity_correlation has 2943 NaNs ( 0.32 % out of 917409)
1 day, 9:39:21.074004 WARNING: height_correlation has 326 NaNs ( 0.04 % out of 917409)
1 day, 9:39:21.108305 INFO: Collecting fragment features
1 day, 9:39:21.569709 INFO: Finished candidate scoring
1 day, 9:39:22.196717 INFO: performing precursor FDR with 47 features
1 day, 9:39:22.196853 INFO: Decoy channel: -1
1 day, 9:39:22.196883 INFO: competitive: True
1 day, 9:39:22.427409 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:39:22.568066 WARNING: dropped 1562 target PSMs due to missing features
1 day, 9:39:22.568227 WARNING: dropped 1533 decoy PSMs due to missing features
1 day, 9:39:23.006263 INFO: Estimating optimal hyperparameters - samples: 731,451, batch_size: 2,996, learning_rate: 8.55e-04
1 day, 9:39:23.008119 INFO: Using random state 934384 for train-test-split
1 day, 9:39:42.110667 INFO: Test AUC: 0.551
1 day, 9:39:42.110832 INFO: Train AUC: 0.569
1 day, 9:39:42.110872 INFO: AUC difference: 3.08%
1 day, 9:39:42.657024 INFO: Resetting torch num_threads to 80
1 day, 9:39:42.674922 PROGRESS: === Extracted 917409 precursors and 5393522 fragments ===
1 day, 9:39:42.675804 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:39:42.706101 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:39:42.706384 PROGRESS: Total precursors accumulated: 180,317
1 day, 9:39:42.706457 PROGRESS: Target precursors: 103,469 (57.38%)
1 day, 9:39:42.706517 PROGRESS: Decoy precursors: 76,848 (42.62%)
1 day, 9:39:42.706572 PROGRESS: 
1 day, 9:39:42.706624 PROGRESS: Precursor Summary:
1 day, 9:39:42.708754 PROGRESS: Channel   0:	 0.050 FDR:   286; 0.010 FDR:    32; 0.001 FDR:    32
1 day, 9:39:42.708856 PROGRESS: 
1 day, 9:39:42.708919 PROGRESS: Protein Summary:
1 day, 9:39:42.711009 PROGRESS: Channel   0:	 0.050 FDR:   233; 0.010 FDR:    30; 0.001 FDR:    30
1 day, 9:39:42.711114 PROGRESS: =========================================================================
1 day, 9:39:42.716079 INFO: Target number of precursors not reached yet.
1 day, 9:39:43.460983 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:39:43.515784 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:39:43.774427 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:39:43.828817 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:39:44.359867 INFO: === skipping optimization until target number of precursors are found ===
1 day, 9:39:44.360173 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 9:39:44.360313 INFO: Starting optimization step 8.
1 day, 9:39:44.360395 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 9:39:44.360470 INFO: Using python extraction backend
1 day, 9:39:44.360586 PROGRESS: Extracting batch of 408390 precursors
1 day, 9:39:44.360669 INFO: === Search parameters used ===
1 day, 9:39:44.360727 INFO: rt_error       : 158.56562261784416
1 day, 9:39:44.360779 INFO: mobility_error : 0.1
1 day, 9:39:44.360828 INFO: num_candidates : 3
1 day, 9:39:44.360876 INFO: ms1_error      : 15.0
1 day, 9:39:44.360922 INFO: ms2_error      : 15.0
1 day, 9:39:44.360972 INFO: fwhm_rt        : 2.84814453125
1 day, 9:39:44.361019 INFO: quant_window   : 3
1 day, 9:39:44.361067 INFO: ==============================================
1 day, 9:39:44.469314 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:39:44.469455 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:39:44.469502 INFO: FWHM in RT is 2.85 seconds, sigma is 0.48
1 day, 9:39:44.469528 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.20
1 day, 9:39:44.470277 INFO: Starting candidate selection
1 day, 9:41:54.741673 INFO: Starting candidate scoring
1 day, 9:42:06.210812 INFO: Finished candidate processing
1 day, 9:42:06.211051 INFO: Collecting candidate features
1 day, 9:42:07.924323 WARNING: intensity_correlation has 2990 NaNs ( 0.33 % out of 916523)
1 day, 9:42:07.925328 WARNING: height_correlation has 347 NaNs ( 0.04 % out of 916523)
1 day, 9:42:07.957371 INFO: Collecting fragment features
1 day, 9:42:08.432184 INFO: Finished candidate scoring
1 day, 9:42:09.441281 INFO: performing precursor FDR with 47 features
1 day, 9:42:09.441448 INFO: Decoy channel: -1
1 day, 9:42:09.441481 INFO: competitive: True
1 day, 9:42:10.194628 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:42:10.504607 WARNING: dropped 3121 target PSMs due to missing features
1 day, 9:42:10.504775 WARNING: dropped 3117 decoy PSMs due to missing features
1 day, 9:42:11.244043 INFO: Estimating optimal hyperparameters - samples: 1,462,155, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 9:42:11.247256 INFO: Using random state 934384 for train-test-split
1 day, 9:42:49.278461 INFO: Test AUC: 0.551
1 day, 9:42:49.278629 INFO: Train AUC: 0.563
1 day, 9:42:49.278668 INFO: AUC difference: 2.24%
1 day, 9:42:50.139071 INFO: Resetting torch num_threads to 80
1 day, 9:42:50.364726 PROGRESS: === Extracted 1833932 precursors and 10777210 fragments ===
1 day, 9:42:50.365944 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:42:50.427277 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:42:50.427628 PROGRESS: Total precursors accumulated: 360,468
1 day, 9:42:50.427700 PROGRESS: Target precursors: 205,228 (56.93%)
1 day, 9:42:50.427759 PROGRESS: Decoy precursors: 155,240 (43.07%)
1 day, 9:42:50.427813 PROGRESS: 
1 day, 9:42:50.427877 PROGRESS: Precursor Summary:
1 day, 9:42:50.431362 PROGRESS: Channel   0:	 0.050 FDR:   579; 0.010 FDR:   442; 0.001 FDR:   351
1 day, 9:42:50.431481 PROGRESS: 
1 day, 9:42:50.431548 PROGRESS: Protein Summary:
1 day, 9:42:50.434669 PROGRESS: Channel   0:	 0.050 FDR:   435; 0.010 FDR:   321; 0.001 FDR:   258
1 day, 9:42:50.434776 PROGRESS: =========================================================================
1 day, 9:42:50.440019 INFO: Target number of precursors reached.
1 day, 9:42:51.617659 INFO: fragments_df: keeping 5000 of 10777210 [sum(precursor_idx_mask)=11715 sum(mass_error_mask)=10777033 stop_rank=5000
1 day, 9:42:52.383116 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:42:52.532610 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:42:52.686981 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:42:52.843412 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:42:53.565497 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:42:53.565969 INFO: Using score_cutoff 28.10390746707916 (fac=0.99, q=1)
1 day, 9:42:53.566325 INFO: Updating optimization_manager: fwhm_rt             : 2.84814453125 -> 2.8460347652435303
1 day, 9:42:53.566411 INFO: Updating optimization_manager: fwhm_mobility       : 0.00590379536151886 -> 0.005862313788384199
1 day, 9:42:53.566473 INFO: Updating optimization_manager: score_cutoff        : 27.256727082252503 -> 28.10390746707916
1 day, 9:42:53.566534 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:42:53.617688 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:42:53.871500 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:42:53.924198 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:42:54.439265 INFO: === checking if optimization conditions were reached ===
1 day, 9:42:54.439557 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 9:42:54.441960 INFO: Updating optimization_manager: rt_error            : 158.56562261784416 -> 139.81606600879147
1 day, 9:42:54.442105 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 139.8161.
1 day, 9:42:54.442189 INFO: ==============================================
1 day, 9:42:54.442278 INFO: Starting optimization step 9.
1 day, 9:42:54.442354 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:42:54.442430 INFO: Using python extraction backend
1 day, 9:42:54.442544 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:42:54.442625 INFO: === Search parameters used ===
1 day, 9:42:54.442687 INFO: rt_error       : 139.81606600879147
1 day, 9:42:54.442746 INFO: mobility_error : 0.1
1 day, 9:42:54.442802 INFO: num_candidates : 3
1 day, 9:42:54.442858 INFO: ms1_error      : 15.0
1 day, 9:42:54.442929 INFO: ms2_error      : 15.0
1 day, 9:42:54.442983 INFO: fwhm_rt        : 2.8460347652435303
1 day, 9:42:54.443035 INFO: quant_window   : 3
1 day, 9:42:54.443088 INFO: ==============================================
1 day, 9:42:54.548523 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:42:54.548680 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:42:54.548736 INFO: FWHM in RT is 2.85 seconds, sigma is 0.47
1 day, 9:42:54.548767 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.18
1 day, 9:42:54.549547 INFO: Starting candidate selection
1 day, 9:44:53.009350 INFO: Starting candidate scoring
1 day, 9:45:04.290864 INFO: Finished candidate processing
1 day, 9:45:04.291175 INFO: Collecting candidate features
1 day, 9:45:05.950587 WARNING: intensity_correlation has 3184 NaNs ( 0.35 % out of 911060)
1 day, 9:45:05.951620 WARNING: height_correlation has 372 NaNs ( 0.04 % out of 911060)
1 day, 9:45:05.983617 INFO: Collecting fragment features
1 day, 9:45:06.449038 INFO: Finished candidate scoring
1 day, 9:45:07.100029 INFO: performing precursor FDR with 47 features
1 day, 9:45:07.100164 INFO: Decoy channel: -1
1 day, 9:45:07.100208 INFO: competitive: True
1 day, 9:45:07.323185 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:45:07.462539 WARNING: dropped 1680 target PSMs due to missing features
1 day, 9:45:07.462704 WARNING: dropped 1674 decoy PSMs due to missing features
1 day, 9:45:07.775713 INFO: Estimating optimal hyperparameters - samples: 726,164, batch_size: 2,974, learning_rate: 8.52e-04
1 day, 9:45:07.777295 INFO: Using random state 934384 for train-test-split
1 day, 9:45:27.538171 INFO: Test AUC: 0.550
1 day, 9:45:27.538323 INFO: Train AUC: 0.568
1 day, 9:45:27.538359 INFO: AUC difference: 3.16%
1 day, 9:45:28.061450 INFO: Resetting torch num_threads to 80
1 day, 9:45:28.079058 PROGRESS: === Extracted 911060 precursors and 5282015 fragments ===
1 day, 9:45:28.079925 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:45:28.110077 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:45:28.110374 PROGRESS: Total precursors accumulated: 180,398
1 day, 9:45:28.110445 PROGRESS: Target precursors: 103,338 (57.28%)
1 day, 9:45:28.110505 PROGRESS: Decoy precursors: 77,060 (42.72%)
1 day, 9:45:28.110559 PROGRESS: 
1 day, 9:45:28.110611 PROGRESS: Precursor Summary:
1 day, 9:45:28.112853 PROGRESS: Channel   0:	 0.050 FDR:   327; 0.010 FDR:   221; 0.001 FDR:   211
1 day, 9:45:28.112959 PROGRESS: 
1 day, 9:45:28.113024 PROGRESS: Protein Summary:
1 day, 9:45:28.115230 PROGRESS: Channel   0:	 0.050 FDR:   275; 0.010 FDR:   182; 0.001 FDR:   173
1 day, 9:45:28.115333 PROGRESS: =========================================================================
1 day, 9:45:28.125154 INFO: Target number of precursors reached.
1 day, 9:45:28.690517 INFO: fragments_df: keeping 3454 of 5282015 [sum(precursor_idx_mask)=5810 sum(mass_error_mask)=5281928 stop_rank=3454
1 day, 9:45:29.454627 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:45:29.588897 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:45:29.719377 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:45:29.858871 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:45:30.352684 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:45:30.353136 INFO: Using score_cutoff 26.712508152008056 (fac=0.99, q=1)
1 day, 9:45:30.353462 INFO: Updating optimization_manager: fwhm_rt             : 2.8460347652435303 -> 2.8471150398254395
1 day, 9:45:30.353557 INFO: Updating optimization_manager: fwhm_mobility       : 0.005862313788384199 -> 0.0058995746076107025
1 day, 9:45:30.353622 INFO: Updating optimization_manager: score_cutoff        : 28.10390746707916 -> 26.712508152008056
1 day, 9:45:30.353687 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:45:30.407082 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:45:30.659478 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:45:30.717947 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:45:31.240993 INFO: === checking if optimization conditions were reached ===
1 day, 9:45:31.241270 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 9:45:31.243542 INFO: Updating optimization_manager: rt_error            : 139.81606600879147 -> 130.93273513085327
1 day, 9:45:31.243686 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 130.9327.
1 day, 9:45:31.243761 INFO: ==============================================
1 day, 9:45:31.243836 INFO: Starting optimization step 10.
1 day, 9:45:31.243903 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:45:31.243965 INFO: Using python extraction backend
1 day, 9:45:31.244067 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:45:31.244135 INFO: === Search parameters used ===
1 day, 9:45:31.244189 INFO: rt_error       : 130.93273513085327
1 day, 9:45:31.244236 INFO: mobility_error : 0.1
1 day, 9:45:31.244284 INFO: num_candidates : 3
1 day, 9:45:31.244347 INFO: ms1_error      : 15.0
1 day, 9:45:31.244395 INFO: ms2_error      : 15.0
1 day, 9:45:31.244442 INFO: fwhm_rt        : 2.8471150398254395
1 day, 9:45:31.244488 INFO: quant_window   : 3
1 day, 9:45:31.244535 INFO: ==============================================
1 day, 9:45:31.356042 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:45:31.356189 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:45:31.356236 INFO: FWHM in RT is 2.85 seconds, sigma is 0.47
1 day, 9:45:31.356260 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.20
1 day, 9:45:31.357014 INFO: Starting candidate selection
1 day, 9:47:22.022665 INFO: Starting candidate scoring
1 day, 9:47:33.559075 INFO: Finished candidate processing
1 day, 9:47:33.559527 INFO: Collecting candidate features
1 day, 9:47:35.223775 WARNING: intensity_correlation has 3324 NaNs ( 0.37 % out of 903743)
1 day, 9:47:35.224815 WARNING: height_correlation has 394 NaNs ( 0.04 % out of 903743)
1 day, 9:47:35.257395 INFO: Collecting fragment features
1 day, 9:47:35.717643 INFO: Finished candidate scoring
1 day, 9:47:36.369950 INFO: performing precursor FDR with 47 features
1 day, 9:47:36.370087 INFO: Decoy channel: -1
1 day, 9:47:36.370122 INFO: competitive: True
1 day, 9:47:36.605692 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:47:36.755553 WARNING: dropped 1773 target PSMs due to missing features
1 day, 9:47:36.755709 WARNING: dropped 1729 decoy PSMs due to missing features
1 day, 9:47:37.193279 INFO: Estimating optimal hyperparameters - samples: 720,192, batch_size: 2,949, learning_rate: 8.49e-04
1 day, 9:47:37.194861 INFO: Using random state 934384 for train-test-split
1 day, 9:47:58.670949 INFO: Test AUC: 0.553
1 day, 9:47:58.671110 INFO: Train AUC: 0.566
1 day, 9:47:58.671154 INFO: AUC difference: 2.38%
1 day, 9:47:59.214852 INFO: Resetting torch num_threads to 80
1 day, 9:47:59.232354 PROGRESS: === Extracted 903743 precursors and 5199906 fragments ===
1 day, 9:47:59.233238 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:47:59.265232 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:47:59.265556 PROGRESS: Total precursors accumulated: 179,581
1 day, 9:47:59.265657 PROGRESS: Target precursors: 102,647 (57.16%)
1 day, 9:47:59.265742 PROGRESS: Decoy precursors: 76,934 (42.84%)
1 day, 9:47:59.265820 PROGRESS: 
1 day, 9:47:59.265911 PROGRESS: Precursor Summary:
1 day, 9:47:59.268244 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   221; 0.001 FDR:   211
1 day, 9:47:59.268366 PROGRESS: 
1 day, 9:47:59.268458 PROGRESS: Protein Summary:
1 day, 9:47:59.270682 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   179; 0.001 FDR:   169
1 day, 9:47:59.270805 PROGRESS: =========================================================================
1 day, 9:47:59.276005 INFO: Target number of precursors reached.
1 day, 9:47:59.829192 INFO: fragments_df: keeping 3453 of 5199906 [sum(precursor_idx_mask)=5764 sum(mass_error_mask)=5199813 stop_rank=3453
1 day, 9:48:00.604992 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:48:00.709171 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:48:00.819293 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:48:00.926246 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:48:01.362623 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:48:01.363066 INFO: Using score_cutoff 27.998337421417236 (fac=0.99, q=1)
1 day, 9:48:01.363386 INFO: Updating optimization_manager: fwhm_rt             : 2.8471150398254395 -> 2.8471150398254395
1 day, 9:48:01.363471 INFO: Updating optimization_manager: fwhm_mobility       : 0.0058995746076107025 -> 0.005902942270040512
1 day, 9:48:01.363535 INFO: Updating optimization_manager: score_cutoff        : 26.712508152008056 -> 27.998337421417236
1 day, 9:48:01.363595 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:48:01.417289 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:48:01.672365 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:48:01.730209 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:48:02.245667 INFO: === checking if optimization conditions were reached ===
1 day, 9:48:02.245946 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 9:48:02.248164 INFO: Updating optimization_manager: rt_error            : 130.93273513085327 -> 114.60968605280435
1 day, 9:48:02.248290 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 114.6097.
1 day, 9:48:02.248361 INFO: ==============================================
1 day, 9:48:02.248436 INFO: Starting optimization step 11.
1 day, 9:48:02.248513 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:48:02.248578 INFO: Using python extraction backend
1 day, 9:48:02.248685 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:48:02.248753 INFO: === Search parameters used ===
1 day, 9:48:02.248811 INFO: rt_error       : 114.60968605280435
1 day, 9:48:02.248859 INFO: mobility_error : 0.1
1 day, 9:48:02.248905 INFO: num_candidates : 3
1 day, 9:48:02.248950 INFO: ms1_error      : 15.0
1 day, 9:48:02.248993 INFO: ms2_error      : 15.0
1 day, 9:48:02.249037 INFO: fwhm_rt        : 2.8471150398254395
1 day, 9:48:02.249081 INFO: quant_window   : 3
1 day, 9:48:02.249126 INFO: ==============================================
1 day, 9:48:02.358087 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:48:02.358237 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:48:02.358291 INFO: FWHM in RT is 2.85 seconds, sigma is 0.47
1 day, 9:48:02.358319 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.20
1 day, 9:48:02.359127 INFO: Starting candidate selection
1 day, 9:49:39.905671 INFO: Starting candidate scoring
1 day, 9:49:50.662893 INFO: Finished candidate processing
1 day, 9:49:50.663229 INFO: Collecting candidate features
1 day, 9:49:52.396925 WARNING: intensity_correlation has 3574 NaNs ( 0.40 % out of 890479)
1 day, 9:49:52.397943 WARNING: height_correlation has 447 NaNs ( 0.05 % out of 890479)
1 day, 9:49:52.429388 INFO: Collecting fragment features
1 day, 9:49:52.888045 INFO: Finished candidate scoring
1 day, 9:49:53.598926 INFO: performing precursor FDR with 47 features
1 day, 9:49:53.599064 INFO: Decoy channel: -1
1 day, 9:49:53.599094 INFO: competitive: True
1 day, 9:49:53.833698 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:49:53.983049 WARNING: dropped 1849 target PSMs due to missing features
1 day, 9:49:53.983235 WARNING: dropped 1921 decoy PSMs due to missing features
1 day, 9:49:54.571573 INFO: Estimating optimal hyperparameters - samples: 709,367, batch_size: 2,905, learning_rate: 8.42e-04
1 day, 9:49:54.573388 INFO: Using random state 934384 for train-test-split
1 day, 9:50:14.530526 INFO: Test AUC: 0.548
1 day, 9:50:14.530682 INFO: Train AUC: 0.567
1 day, 9:50:14.530719 INFO: AUC difference: 3.34%
1 day, 9:50:15.075534 INFO: Resetting torch num_threads to 80
1 day, 9:50:15.093127 PROGRESS: === Extracted 890479 precursors and 5053765 fragments ===
1 day, 9:50:15.093992 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:50:15.125671 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:50:15.126040 PROGRESS: Total precursors accumulated: 178,366
1 day, 9:50:15.126115 PROGRESS: Target precursors: 101,637 (56.98%)
1 day, 9:50:15.126175 PROGRESS: Decoy precursors: 76,729 (43.02%)
1 day, 9:50:15.126230 PROGRESS: 
1 day, 9:50:15.126286 PROGRESS: Precursor Summary:
1 day, 9:50:15.128564 PROGRESS: Channel   0:	 0.050 FDR:   329; 0.010 FDR:   216; 0.001 FDR:   187
1 day, 9:50:15.128670 PROGRESS: 
1 day, 9:50:15.128748 PROGRESS: Protein Summary:
1 day, 9:50:15.130892 PROGRESS: Channel   0:	 0.050 FDR:   275; 0.010 FDR:   174; 0.001 FDR:   149
1 day, 9:50:15.130994 PROGRESS: =========================================================================
1 day, 9:50:15.136226 INFO: Target number of precursors reached.
1 day, 9:50:15.675368 INFO: fragments_df: keeping 3388 of 5053765 [sum(precursor_idx_mask)=5674 sum(mass_error_mask)=5053667 stop_rank=3388
1 day, 9:50:16.442311 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:50:16.545823 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:50:16.655349 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:50:16.786644 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:50:17.268986 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:50:17.269454 INFO: Using score_cutoff 27.973544746398925 (fac=0.99, q=1)
1 day, 9:50:17.269778 INFO: Updating optimization_manager: fwhm_rt             : 2.8471150398254395 -> 2.84814453125
1 day, 9:50:17.269877 INFO: Updating optimization_manager: fwhm_mobility       : 0.005902942270040512 -> 0.005985443480312824
1 day, 9:50:17.269945 INFO: Updating optimization_manager: score_cutoff        : 27.998337421417236 -> 27.973544746398925
1 day, 9:50:17.270012 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:50:17.322682 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:50:17.583017 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:50:17.636793 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:50:18.171391 INFO: === checking if optimization conditions were reached ===
1 day, 9:50:18.171669 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1 day, 9:50:18.173875 INFO: Updating optimization_manager: rt_error            : 114.60968605280435 -> 117.51568035906206
1 day, 9:50:18.174022 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 117.5157.
1 day, 9:50:18.174100 INFO: ==============================================
1 day, 9:50:18.174181 INFO: Starting optimization step 12.
1 day, 9:50:18.174251 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:50:18.174319 INFO: Using python extraction backend
1 day, 9:50:18.174429 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:50:18.174506 INFO: === Search parameters used ===
1 day, 9:50:18.174565 INFO: rt_error       : 117.51568035906206
1 day, 9:50:18.174618 INFO: mobility_error : 0.1
1 day, 9:50:18.174669 INFO: num_candidates : 3
1 day, 9:50:18.174721 INFO: ms1_error      : 15.0
1 day, 9:50:18.174772 INFO: ms2_error      : 15.0
1 day, 9:50:18.174820 INFO: fwhm_rt        : 2.84814453125
1 day, 9:50:18.174868 INFO: quant_window   : 3
1 day, 9:50:18.174915 INFO: ==============================================
1 day, 9:50:18.281620 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:50:18.281779 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:50:18.281833 INFO: FWHM in RT is 2.85 seconds, sigma is 0.48
1 day, 9:50:18.281862 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.24
1 day, 9:50:18.282620 INFO: Starting candidate selection
1 day, 9:52:00.884766 INFO: Starting candidate scoring
1 day, 9:52:12.173842 INFO: Finished candidate processing
1 day, 9:52:12.174201 INFO: Collecting candidate features
1 day, 9:52:13.744115 WARNING: intensity_correlation has 3535 NaNs ( 0.40 % out of 888875)
1 day, 9:52:13.745106 WARNING: height_correlation has 448 NaNs ( 0.05 % out of 888875)
1 day, 9:52:13.776400 INFO: Collecting fragment features
1 day, 9:52:14.224619 INFO: Finished candidate scoring
1 day, 9:52:14.850921 INFO: performing precursor FDR with 47 features
1 day, 9:52:14.851056 INFO: Decoy channel: -1
1 day, 9:52:14.851084 INFO: competitive: True
1 day, 9:52:15.067658 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:52:15.209228 WARNING: dropped 1887 target PSMs due to missing features
1 day, 9:52:15.209396 WARNING: dropped 1838 decoy PSMs due to missing features
1 day, 9:52:15.794574 INFO: Estimating optimal hyperparameters - samples: 708,120, batch_size: 2,900, learning_rate: 8.41e-04
1 day, 9:52:15.796221 INFO: Using random state 934384 for train-test-split
1 day, 9:52:33.837460 INFO: Test AUC: 0.547
1 day, 9:52:33.837628 INFO: Train AUC: 0.566
1 day, 9:52:33.837669 INFO: AUC difference: 3.36%
1 day, 9:52:34.358128 INFO: Resetting torch num_threads to 80
1 day, 9:52:34.375420 PROGRESS: === Extracted 888875 precursors and 5049787 fragments ===
1 day, 9:52:34.376210 INFO: === FDR correction performed with classifier version 14 ===
1 day, 9:52:34.408344 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:52:34.408650 PROGRESS: Total precursors accumulated: 178,055
1 day, 9:52:34.408723 PROGRESS: Target precursors: 101,592 (57.06%)
1 day, 9:52:34.408784 PROGRESS: Decoy precursors: 76,463 (42.94%)
1 day, 9:52:34.408840 PROGRESS: 
1 day, 9:52:34.408891 PROGRESS: Precursor Summary:
1 day, 9:52:34.411490 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   245; 0.001 FDR:   231
1 day, 9:52:34.411617 PROGRESS: 
1 day, 9:52:34.411681 PROGRESS: Protein Summary:
1 day, 9:52:34.413810 PROGRESS: Channel   0:	 0.050 FDR:   267; 0.010 FDR:   200; 0.001 FDR:   188
1 day, 9:52:34.413930 PROGRESS: =========================================================================
1 day, 9:52:34.419022 INFO: Target number of precursors reached.
1 day, 9:52:34.957342 INFO: fragments_df: keeping 3653 of 5049787 [sum(precursor_idx_mask)=6274 sum(mass_error_mask)=5049689 stop_rank=3653
1 day, 9:52:35.589751 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:52:35.702042 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:52:35.813665 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:52:35.926521 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:52:36.378421 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:52:36.378878 INFO: Using score_cutoff 25.560237867736816 (fac=0.99, q=1)
1 day, 9:52:36.379198 INFO: Updating optimization_manager: fwhm_rt             : 2.84814453125 -> 2.8471150398254395
1 day, 9:52:36.379287 INFO: Updating optimization_manager: fwhm_mobility       : 0.005985443480312824 -> 0.005893845576792955
1 day, 9:52:36.379359 INFO: Updating optimization_manager: score_cutoff        : 27.973544746398925 -> 25.560237867736816
1 day, 9:52:36.379428 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:52:36.434141 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:52:36.696333 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:52:36.756391 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:52:37.301158 INFO: === checking if optimization conditions were reached ===
1 day, 9:52:37.301458 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
1 day, 9:52:37.302838 INFO: Updating optimization_manager: rt_error            : 117.51568035906206 -> 117.51568035906206
1 day, 9:52:37.303012 INFO: Updating optimization_manager: classifier_version  : 14 -> 27
1 day, 9:52:37.303124 INFO: Updating optimization_manager: score_cutoff        : 25.560237867736816 -> 25.560237867736816
1 day, 9:52:37.303225 INFO: Updating optimization_manager: fwhm_rt             : 2.8471150398254395 -> 2.8471150398254395
1 day, 9:52:37.303319 INFO: Updating optimization_manager: fwhm_mobility       : 0.005893845576792955 -> 0.005893845576792955
1 day, 9:52:37.303415 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 117.5157 found after 10 searches.
1 day, 9:52:37.303489 INFO: ==============================================
1 day, 9:52:37.303567 PROGRESS: Optimization finished for rt_error.
1 day, 9:52:37.915102 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:52:37.970448 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:52:38.229806 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:52:38.288422 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:52:38.831524 INFO: Starting optimization step 0.
1 day, 9:52:38.831797 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:52:38.831891 INFO: Using python extraction backend
1 day, 9:52:38.832022 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:52:38.832111 INFO: === Search parameters used ===
1 day, 9:52:38.832170 INFO: rt_error       : 117.51568035906206
1 day, 9:52:38.832220 INFO: mobility_error : 0.1
1 day, 9:52:38.832271 INFO: num_candidates : 3
1 day, 9:52:38.832319 INFO: ms1_error      : 15.0
1 day, 9:52:38.832365 INFO: ms2_error      : 15.0
1 day, 9:52:38.832411 INFO: fwhm_rt        : 2.8471150398254395
1 day, 9:52:38.832458 INFO: quant_window   : 3
1 day, 9:52:38.832504 INFO: ==============================================
1 day, 9:52:38.936376 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:52:38.936527 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:52:38.936577 INFO: FWHM in RT is 2.85 seconds, sigma is 0.47
1 day, 9:52:38.936602 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.19
1 day, 9:52:38.937301 INFO: Starting candidate selection
1 day, 9:54:22.324186 INFO: Starting candidate scoring
1 day, 9:54:33.413464 INFO: Finished candidate processing
1 day, 9:54:33.413694 INFO: Collecting candidate features
1 day, 9:54:35.274011 WARNING: intensity_correlation has 3560 NaNs ( 0.40 % out of 891544)
1 day, 9:54:35.275090 WARNING: height_correlation has 448 NaNs ( 0.05 % out of 891544)
1 day, 9:54:35.309409 INFO: Collecting fragment features
1 day, 9:54:35.793650 INFO: Finished candidate scoring
1 day, 9:54:36.455921 INFO: performing precursor FDR with 47 features
1 day, 9:54:36.456088 INFO: Decoy channel: -1
1 day, 9:54:36.456118 INFO: competitive: True
1 day, 9:54:36.723965 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:54:36.890910 WARNING: dropped 1865 target PSMs due to missing features
1 day, 9:54:36.891097 WARNING: dropped 1887 decoy PSMs due to missing features
1 day, 9:54:37.193640 INFO: Estimating optimal hyperparameters - samples: 710,233, batch_size: 2,909, learning_rate: 8.43e-04
1 day, 9:54:37.195423 INFO: Using random state 384917 for train-test-split
1 day, 9:54:59.723594 INFO: Test AUC: 0.556
1 day, 9:54:59.723788 INFO: Train AUC: 0.575
1 day, 9:54:59.723827 INFO: AUC difference: 3.33%
1 day, 9:55:00.270884 INFO: Resetting torch num_threads to 80
1 day, 9:55:00.296221 PROGRESS: === Extracted 891544 precursors and 5063598 fragments ===
1 day, 9:55:00.297174 INFO: === FDR correction performed with classifier version 27 ===
1 day, 9:55:00.336311 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:55:00.336621 PROGRESS: Total precursors accumulated: 178,517
1 day, 9:55:00.336720 PROGRESS: Target precursors: 103,075 (57.74%)
1 day, 9:55:00.336780 PROGRESS: Decoy precursors: 75,442 (42.26%)
1 day, 9:55:00.336834 PROGRESS: 
1 day, 9:55:00.336893 PROGRESS: Precursor Summary:
1 day, 9:55:00.339194 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   239; 0.001 FDR:   221
1 day, 9:55:00.339308 PROGRESS: 
1 day, 9:55:00.339371 PROGRESS: Protein Summary:
1 day, 9:55:00.341515 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   194; 0.001 FDR:   179
1 day, 9:55:00.341610 PROGRESS: =========================================================================
1 day, 9:55:00.348775 INFO: Target number of precursors reached.
1 day, 9:55:00.897020 INFO: fragments_df: keeping 3612 of 5063598 [sum(precursor_idx_mask)=6105 sum(mass_error_mask)=5063504 stop_rank=3612
1 day, 9:55:01.661819 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:55:01.776577 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:55:01.893411 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:55:02.014636 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:55:02.464478 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:55:02.464999 INFO: Using score_cutoff 21.298051455688476 (fac=0.99, q=1)
1 day, 9:55:02.465368 INFO: Updating optimization_manager: fwhm_rt             : 2.8471150398254395 -> 2.879823684692383
1 day, 9:55:02.465460 INFO: Updating optimization_manager: fwhm_mobility       : 0.005893845576792955 -> 0.005893845576792955
1 day, 9:55:02.465524 INFO: Updating optimization_manager: score_cutoff        : 25.560237867736816 -> 21.298051455688476
1 day, 9:55:02.465590 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:55:02.519605 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:55:02.780180 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:55:02.838684 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:55:03.344672 INFO: === checking if optimization conditions were reached ===
1 day, 9:55:03.344986 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 9:55:03.347231 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0663510160348284
1 day, 9:55:03.347390 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0664.
1 day, 9:55:03.347471 INFO: ==============================================
1 day, 9:55:03.347553 INFO: Starting optimization step 1.
1 day, 9:55:03.347627 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:55:03.347699 INFO: Using python extraction backend
1 day, 9:55:03.347823 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:55:03.347901 INFO: === Search parameters used ===
1 day, 9:55:03.347959 INFO: rt_error       : 117.51568035906206
1 day, 9:55:03.348011 INFO: mobility_error : 0.0663510160348284
1 day, 9:55:03.348062 INFO: num_candidates : 3
1 day, 9:55:03.348112 INFO: ms1_error      : 15.0
1 day, 9:55:03.348160 INFO: ms2_error      : 15.0
1 day, 9:55:03.348208 INFO: fwhm_rt        : 2.879823684692383
1 day, 9:55:03.348254 INFO: quant_window   : 3
1 day, 9:55:03.348302 INFO: ==============================================
1 day, 9:55:03.478323 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:55:03.478497 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:55:03.478547 INFO: FWHM in RT is 2.88 seconds, sigma is 0.48
1 day, 9:55:03.478573 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.19
1 day, 9:55:03.479344 INFO: Starting candidate selection
1 day, 9:56:10.970724 INFO: Starting candidate scoring
1 day, 9:56:21.728653 INFO: Finished candidate processing
1 day, 9:56:21.728912 INFO: Collecting candidate features
1 day, 9:56:23.263390 WARNING: intensity_correlation has 3706 NaNs ( 0.44 % out of 847810)
1 day, 9:56:23.264367 WARNING: height_correlation has 440 NaNs ( 0.05 % out of 847810)
1 day, 9:56:23.295500 INFO: Collecting fragment features
1 day, 9:56:23.716477 INFO: Finished candidate scoring
1 day, 9:56:24.352813 INFO: performing precursor FDR with 47 features
1 day, 9:56:24.352957 INFO: Decoy channel: -1
1 day, 9:56:24.352986 INFO: competitive: True
1 day, 9:56:24.571297 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:56:24.705989 WARNING: dropped 1928 target PSMs due to missing features
1 day, 9:56:24.706152 WARNING: dropped 1970 decoy PSMs due to missing features
1 day, 9:56:25.240385 INFO: Estimating optimal hyperparameters - samples: 675,129, batch_size: 2,765, learning_rate: 8.22e-04
1 day, 9:56:25.242091 INFO: Using random state 384917 for train-test-split
1 day, 9:56:44.637848 INFO: Test AUC: 0.556
1 day, 9:56:44.638020 INFO: Train AUC: 0.575
1 day, 9:56:44.638058 INFO: AUC difference: 3.25%
1 day, 9:56:45.167936 INFO: Resetting torch num_threads to 80
1 day, 9:56:45.184893 PROGRESS: === Extracted 847810 precursors and 4735115 fragments ===
1 day, 9:56:45.185759 INFO: === FDR correction performed with classifier version 27 ===
1 day, 9:56:45.214892 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:56:45.215165 PROGRESS: Total precursors accumulated: 171,702
1 day, 9:56:45.215240 PROGRESS: Target precursors: 99,248 (57.80%)
1 day, 9:56:45.215301 PROGRESS: Decoy precursors: 72,454 (42.20%)
1 day, 9:56:45.215356 PROGRESS: 
1 day, 9:56:45.215412 PROGRESS: Precursor Summary:
1 day, 9:56:45.217643 PROGRESS: Channel   0:	 0.050 FDR:   364; 0.010 FDR:   243; 0.001 FDR:   230
1 day, 9:56:45.217752 PROGRESS: 
1 day, 9:56:45.217817 PROGRESS: Protein Summary:
1 day, 9:56:45.219913 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   199; 0.001 FDR:   187
1 day, 9:56:45.220035 PROGRESS: =========================================================================
1 day, 9:56:45.225148 INFO: Target number of precursors reached.
1 day, 9:56:45.741447 INFO: fragments_df: keeping 3660 of 4735115 [sum(precursor_idx_mask)=6240 sum(mass_error_mask)=4734991 stop_rank=3660
1 day, 9:56:46.375332 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:56:46.490516 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:56:46.602121 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:56:46.709044 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:56:47.161698 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:56:47.162177 INFO: Using score_cutoff 23.822524528884887 (fac=0.99, q=1)
1 day, 9:56:47.162506 INFO: Updating optimization_manager: fwhm_rt             : 2.879823684692383 -> 2.844954490661621
1 day, 9:56:47.162595 INFO: Updating optimization_manager: fwhm_mobility       : 0.005893845576792955 -> 0.005835250020027161
1 day, 9:56:47.162659 INFO: Updating optimization_manager: score_cutoff        : 21.298051455688476 -> 23.822524528884887
1 day, 9:56:47.162729 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:56:47.217089 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:56:47.476978 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:56:47.536041 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:56:48.061534 INFO: === checking if optimization conditions were reached ===
1 day, 9:56:48.061811 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 9:56:48.063851 INFO: Updating optimization_manager: mobility_error      : 0.0663510160348284 -> 0.055496445374204555
1 day, 9:56:48.063986 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0555.
1 day, 9:56:48.064065 INFO: ==============================================
1 day, 9:56:48.064145 INFO: Starting optimization step 2.
1 day, 9:56:48.064216 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 9:56:48.064284 INFO: Using python extraction backend
1 day, 9:56:48.064407 PROGRESS: Extracting batch of 407917 precursors
1 day, 9:56:48.064482 INFO: === Search parameters used ===
1 day, 9:56:48.064536 INFO: rt_error       : 117.51568035906206
1 day, 9:56:48.064594 INFO: mobility_error : 0.055496445374204555
1 day, 9:56:48.064644 INFO: num_candidates : 3
1 day, 9:56:48.064690 INFO: ms1_error      : 15.0
1 day, 9:56:48.064736 INFO: ms2_error      : 15.0
1 day, 9:56:48.064781 INFO: fwhm_rt        : 2.844954490661621
1 day, 9:56:48.064825 INFO: quant_window   : 3
1 day, 9:56:48.064870 INFO: ==============================================
1 day, 9:56:48.169296 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:56:48.169447 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:56:48.169495 INFO: FWHM in RT is 2.84 seconds, sigma is 0.47
1 day, 9:56:48.169520 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.16
1 day, 9:56:48.170281 INFO: Starting candidate selection
1 day, 9:57:42.599982 INFO: Starting candidate scoring
1 day, 9:57:53.145325 INFO: Finished candidate processing
1 day, 9:57:53.145511 INFO: Collecting candidate features
1 day, 9:57:54.615279 WARNING: intensity_correlation has 3860 NaNs ( 0.47 % out of 821910)
1 day, 9:57:54.616223 WARNING: height_correlation has 464 NaNs ( 0.06 % out of 821910)
1 day, 9:57:54.645650 INFO: Collecting fragment features
1 day, 9:57:55.075969 INFO: Finished candidate scoring
1 day, 9:57:55.701031 INFO: performing precursor FDR with 47 features
1 day, 9:57:55.701174 INFO: Decoy channel: -1
1 day, 9:57:55.701204 INFO: competitive: True
1 day, 9:57:55.910252 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:57:56.039961 WARNING: dropped 2042 target PSMs due to missing features
1 day, 9:57:56.040121 WARNING: dropped 2027 decoy PSMs due to missing features
1 day, 9:57:56.320711 INFO: Estimating optimal hyperparameters - samples: 654,272, batch_size: 2,679, learning_rate: 8.09e-04
1 day, 9:57:56.322238 INFO: Using random state 384917 for train-test-split
1 day, 9:58:15.631487 INFO: Test AUC: 0.556
1 day, 9:58:15.631634 INFO: Train AUC: 0.574
1 day, 9:58:15.631670 INFO: AUC difference: 3.29%
1 day, 9:58:16.143443 INFO: Resetting torch num_threads to 80
1 day, 9:58:16.160002 PROGRESS: === Extracted 821910 precursors and 4537817 fragments ===
1 day, 9:58:16.160856 INFO: === FDR correction performed with classifier version 27 ===
1 day, 9:58:16.189362 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:58:16.189656 PROGRESS: Total precursors accumulated: 167,540
1 day, 9:58:16.189728 PROGRESS: Target precursors: 97,017 (57.91%)
1 day, 9:58:16.189790 PROGRESS: Decoy precursors: 70,523 (42.09%)
1 day, 9:58:16.189846 PROGRESS: 
1 day, 9:58:16.189916 PROGRESS: Precursor Summary:
1 day, 9:58:16.192151 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   243; 0.001 FDR:   215
1 day, 9:58:16.192258 PROGRESS: 
1 day, 9:58:16.192323 PROGRESS: Protein Summary:
1 day, 9:58:16.194414 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:   199; 0.001 FDR:   173
1 day, 9:58:16.194520 PROGRESS: =========================================================================
1 day, 9:58:16.199240 INFO: Target number of precursors reached.
1 day, 9:58:16.691501 INFO: fragments_df: keeping 3658 of 4537817 [sum(precursor_idx_mask)=6380 sum(mass_error_mask)=4537703 stop_rank=3658
1 day, 9:58:17.464305 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:58:17.580929 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:58:17.692145 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:58:17.803008 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:58:18.259221 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:58:18.259691 INFO: Using score_cutoff 26.058719091796874 (fac=0.99, q=1)
1 day, 9:58:18.260023 INFO: Updating optimization_manager: fwhm_rt             : 2.844954490661621 -> 2.8401901721954346
1 day, 9:58:18.260112 INFO: Updating optimization_manager: fwhm_mobility       : 0.005835250020027161 -> 0.005700021516531706
1 day, 9:58:18.260187 INFO: Updating optimization_manager: score_cutoff        : 23.822524528884887 -> 26.058719091796874
1 day, 9:58:18.260249 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:58:18.312495 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:58:18.571319 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:58:18.629429 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:58:19.150218 INFO: === checking if optimization conditions were reached ===
1 day, 9:58:19.150493 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 9:58:19.151537 INFO: Updating optimization_manager: mobility_error      : 0.055496445374204555 -> 0.055496445374204555
1 day, 9:58:19.151695 INFO: Updating optimization_manager: classifier_version  : 27 -> 30
1 day, 9:58:19.151828 INFO: Updating optimization_manager: score_cutoff        : 26.058719091796874 -> 26.058719091796874
1 day, 9:58:19.151931 INFO: Updating optimization_manager: fwhm_rt             : 2.8401901721954346 -> 2.8401901721954346
1 day, 9:58:19.152028 INFO: Updating optimization_manager: fwhm_mobility       : 0.005700021516531706 -> 0.005700021516531706
1 day, 9:58:19.152126 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0555 found after 3 searches.
1 day, 9:58:19.152204 INFO: ==============================================
1 day, 9:58:19.152286 PROGRESS: Optimization finished for mobility_error.
1 day, 9:58:19.763386 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:58:19.816669 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:58:20.075505 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:58:20.133816 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:58:20.654765 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 9:58:20.655043 PROGRESS: ==============================================
1 day, 9:58:20.655138 PROGRESS: ms2_error      : 15.0000
1 day, 9:58:20.655207 PROGRESS: ms1_error      : 15.0000
1 day, 9:58:20.655270 PROGRESS: rt_error       : 117.5157
1 day, 9:58:20.655325 PROGRESS: mobility_error : 0.0555
1 day, 9:58:20.655378 PROGRESS: ==============================================
1 day, 9:58:20.662423 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:58:22.264456 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:58:30.020540 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:58:31.596180 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:58:47.396197 INFO: Using python extraction backend
1 day, 9:58:47.396610 PROGRESS: Extracting batch of 12210649 precursors
1 day, 9:58:47.396710 INFO: === Search parameters used ===
1 day, 9:58:47.396774 INFO: rt_error       : 117.51568035906206
1 day, 9:58:47.396832 INFO: mobility_error : 0.055496445374204555
1 day, 9:58:47.396887 INFO: num_candidates : 3
1 day, 9:58:47.396941 INFO: ms1_error      : 15.0
1 day, 9:58:47.396991 INFO: ms2_error      : 15.0
1 day, 9:58:47.397040 INFO: fwhm_rt        : 2.8401901721954346
1 day, 9:58:47.397090 INFO: quant_window   : 3
1 day, 9:58:47.397138 INFO: ==============================================
1 day, 9:58:49.612613 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 9:58:49.612765 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 9:58:49.612812 INFO: FWHM in RT is 2.84 seconds, sigma is 0.47
1 day, 9:58:49.612839 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.09
1 day, 9:58:49.613618 INFO: Starting candidate selection
1 day, 10:23:50.892334 INFO: Removed 27711033 precursors with score below cutoff 26.058719091796874
1 day, 10:23:53.863930 INFO: Starting candidate scoring
1 day, 10:24:37.167776 INFO: Finished candidate processing
1 day, 10:24:37.168104 INFO: Collecting candidate features
1 day, 10:24:46.686340 WARNING: intensity_correlation has 1083 NaNs ( 0.03 % out of 3475327)
1 day, 10:24:46.689726 WARNING: height_correlation has 68 NaNs ( 0.00 % out of 3475327)
1 day, 10:24:46.808449 INFO: Collecting fragment features
1 day, 10:24:49.217934 INFO: Finished candidate scoring
1 day, 10:24:51.605584 INFO: === Performing FDR correction with classifier version 30 ===
1 day, 10:24:51.606245 INFO: performing precursor FDR with 47 features
1 day, 10:24:51.606287 INFO: Decoy channel: -1
1 day, 10:24:51.606318 INFO: competitive: True
1 day, 10:24:52.479900 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:24:52.947701 WARNING: dropped 602 target PSMs due to missing features
1 day, 10:24:52.947870 WARNING: dropped 536 decoy PSMs due to missing features
1 day, 10:24:52.947966 WARNING: FDR calculation for 1839151 target and 1635038 decoy PSMs
1 day, 10:24:52.947993 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 10:24:54.263247 INFO: Estimating optimal hyperparameters - samples: 2,779,351, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 10:24:54.269779 INFO: Using random state 883257 for train-test-split
1 day, 10:26:01.852914 INFO: Test AUC: 0.557
1 day, 10:26:01.853097 INFO: Train AUC: 0.563
1 day, 10:26:01.853137 INFO: AUC difference: 1.14%
1 day, 10:26:03.256083 INFO: Resetting torch num_threads to 80
1 day, 10:26:03.343941 INFO: Removing fragments below FDR threshold
1 day, 10:26:03.568174 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:26:03.568436 PROGRESS: Total precursors accumulated: 8,520
1 day, 10:26:03.568512 PROGRESS: Target precursors: 8,436 (99.01%)
1 day, 10:26:03.568573 PROGRESS: Decoy precursors: 84 (0.99%)
1 day, 10:26:03.568633 PROGRESS: 
1 day, 10:26:03.568688 PROGRESS: Precursor Summary:
1 day, 10:26:03.571942 PROGRESS: Channel   0:	 0.050 FDR: 8,436; 0.010 FDR: 8,436; 0.001 FDR: 5,687
1 day, 10:26:03.572056 PROGRESS: 
1 day, 10:26:03.572119 PROGRESS: Protein Summary:
1 day, 10:26:03.576230 PROGRESS: Channel   0:	 0.050 FDR: 1,974; 0.010 FDR: 1,974; 0.001 FDR: 1,342
1 day, 10:26:03.576340 PROGRESS: =========================================================================
1 day, 10:26:03.629384 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R6/psm.parquet
1 day, 10:26:03.681949 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R6/frag.parquet
1 day, 10:26:03.721342 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R6
1 day, 10:26:04.802017 PROGRESS: Loading raw file 7/12: B9_G_DIA_nLC_tTOF_R1 
1 day, 10:26:04.802180 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
1 day, 10:26:04.802253 INFO: Creating folder plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R1/figures
1 day, 10:26:04.802444 INFO: Initializing TimingManager
1 day, 10:26:04.802993 INFO: Initializing RawFileManager
1 day, 10:26:04.803114 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:04.803185 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:04.803232 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:04.939873 INFO: Reading 22,622 frames with 343,415,986 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:10.176603 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d...
1 day, 10:26:10.179561 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:10.182543 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:10.182976 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:10.183697 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:10.186117 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:10.198108 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:10.198430 INFO: Indexing quadrupole dimension
1 day, 10:26:10.294983 INFO: Transposing detector events
1 day, 10:26:11.618631 INFO: Finished transposing data
1 day, 10:26:11.618833 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
1 day, 10:26:11.619414 INFO: RT (min)            : 0.0 - 40.0
1 day, 10:26:11.619518 INFO: RT duration (sec)   : 2399.9
1 day, 10:26:11.619607 INFO: RT duration (min)   : 40.0
1 day, 10:26:11.619682 INFO: Cycle len (scans)   : 12
1 day, 10:26:11.619754 INFO: Cycle len (sec)     : 1.27
1 day, 10:26:11.619826 INFO: Number of cycles    : 1885
1 day, 10:26:11.619899 INFO: MS2 range (m/z)     : 374.4 - 1151.9
1 day, 10:26:11.619984 INFO: Creating DIA data object took: 6.816879749298096
1 day, 10:26:13.615646 INFO: Initializing CalibrationManager
1 day, 10:26:13.615990 INFO: Setting up calibration estimators ..
1 day, 10:26:13.616098 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 10:26:13.616236 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 10:26:13.616344 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 10:26:13.616436 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 10:26:13.616536 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1 day, 10:26:13.616628 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
1 day, 10:26:13.616710 INFO: Done setting up calibration estimators.
1 day, 10:26:13.616882 INFO: Initializing OptimizationManager
1 day, 10:26:13.617017 INFO: initial parameter: ms1_error = 30
1 day, 10:26:13.617090 INFO: initial parameter: ms2_error = 30
1 day, 10:26:13.617160 INFO: initial parameter: rt_error = 1199.951526
1 day, 10:26:13.617224 INFO: initial parameter: mobility_error = 0.1
1 day, 10:26:13.617285 INFO: initial parameter: num_candidates = 1
1 day, 10:26:13.617346 INFO: initial parameter: fwhm_rt = 5
1 day, 10:26:13.617407 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 10:26:13.617467 INFO: initial parameter: score_cutoff = 0
1 day, 10:26:13.617527 INFO: initial parameter: classifier_version = -1
1 day, 10:26:13.617626 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R1
1 day, 10:26:13.617890 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 10:26:13.617936 INFO: Initializing FDRManager
1 day, 10:26:13.618016 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 10:26:15.191867 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
1 day, 10:26:15.881129 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 10:26:15.881565 INFO: Updating optimization_manager: rt_error            : 1199.951526 -> 1199.951526
1 day, 10:26:15.881674 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 10:26:15.881860 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 10:26:15.881967 PROGRESS: Starting initial search for precursors.
1 day, 10:26:15.882063 INFO: Starting optimization step 0.
1 day, 10:26:15.882128 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 10:26:15.882192 INFO: Using python extraction backend
1 day, 10:26:15.882296 PROGRESS: Extracting batch of 395 precursors
1 day, 10:26:15.882359 INFO: === Search parameters used ===
1 day, 10:26:15.882411 INFO: rt_error       : 1199.951526
1 day, 10:26:15.882457 INFO: mobility_error : 0.1
1 day, 10:26:15.882501 INFO: num_candidates : 1
1 day, 10:26:15.882545 INFO: ms1_error      : 30
1 day, 10:26:15.882590 INFO: ms2_error      : 30
1 day, 10:26:15.882634 INFO: fwhm_rt        : 5
1 day, 10:26:15.882679 INFO: quant_window   : 3
1 day, 10:26:15.882723 INFO: ==============================================
1 day, 10:26:15.883431 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:26:15.883479 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:26:15.883512 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:26:15.883536 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:26:15.884356 INFO: Starting candidate selection
1 day, 10:26:17.920142 INFO: Starting candidate scoring
1 day, 10:26:17.960118 INFO: Finished candidate processing
1 day, 10:26:17.960218 INFO: Collecting candidate features
1 day, 10:26:17.970224 INFO: Collecting fragment features
1 day, 10:26:17.972437 INFO: Finished candidate scoring
1 day, 10:26:17.973420 INFO: performing precursor FDR with 47 features
1 day, 10:26:17.973467 INFO: Decoy channel: -1
1 day, 10:26:17.973494 INFO: competitive: True
1 day, 10:26:17.974729 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:26:17.976384 INFO: Estimating optimal hyperparameters - samples: 275, batch_size: 128, learning_rate: 1.77e-04
1 day, 10:26:17.977210 INFO: Using random state 457623 for train-test-split
1 day, 10:26:18.000699 INFO: Test AUC: 0.427
1 day, 10:26:18.000767 INFO: Train AUC: 0.526
1 day, 10:26:18.000800 INFO: AUC difference: 18.89%
1 day, 10:26:18.000826 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 10:26:18.244313 INFO: Resetting torch num_threads to 80
1 day, 10:26:18.244790 PROGRESS: === Extracted 344 precursors and 2791 fragments ===
1 day, 10:26:18.245226 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:26:18.245776 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:26:18.245877 PROGRESS: Total precursors accumulated: 174
1 day, 10:26:18.245949 PROGRESS: Target precursors: 141 (81.03%)
1 day, 10:26:18.246006 PROGRESS: Decoy precursors: 33 (18.97%)
1 day, 10:26:18.246056 PROGRESS: 
1 day, 10:26:18.246106 PROGRESS: Precursor Summary:
1 day, 10:26:18.247042 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 10:26:18.247133 PROGRESS: 
1 day, 10:26:18.247193 PROGRESS: Protein Summary:
1 day, 10:26:18.248221 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 10:26:18.248312 PROGRESS: =========================================================================
1 day, 10:26:18.248424 INFO: Target number of precursors not reached yet.
1 day, 10:26:18.310327 INFO: Starting optimization step 1.
1 day, 10:26:18.310553 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 10:26:18.310635 INFO: Using python extraction backend
1 day, 10:26:18.310751 PROGRESS: Extracting batch of 796 precursors
1 day, 10:26:18.310827 INFO: === Search parameters used ===
1 day, 10:26:18.310880 INFO: rt_error       : 1199.951526
1 day, 10:26:18.310928 INFO: mobility_error : 0.1
1 day, 10:26:18.310976 INFO: num_candidates : 1
1 day, 10:26:18.311023 INFO: ms1_error      : 30
1 day, 10:26:18.311071 INFO: ms2_error      : 30
1 day, 10:26:18.311116 INFO: fwhm_rt        : 5
1 day, 10:26:18.311160 INFO: quant_window   : 3
1 day, 10:26:18.311205 INFO: ==============================================
1 day, 10:26:18.311909 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:26:18.311958 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:26:18.311999 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:26:18.312025 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:26:18.312735 INFO: Starting candidate selection
1 day, 10:26:21.324293 INFO: Starting candidate scoring
1 day, 10:26:21.365894 INFO: Finished candidate processing
1 day, 10:26:21.365983 INFO: Collecting candidate features
1 day, 10:26:21.372828 WARNING: intensity_correlation has 3 NaNs ( 0.42 % out of 720)
1 day, 10:26:21.376433 INFO: Collecting fragment features
1 day, 10:26:21.378816 INFO: Finished candidate scoring
1 day, 10:26:21.381140 INFO: performing precursor FDR with 47 features
1 day, 10:26:21.381195 INFO: Decoy channel: -1
1 day, 10:26:21.381221 INFO: competitive: True
1 day, 10:26:21.384145 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:26:21.385440 WARNING: dropped 1 target PSMs due to missing features
1 day, 10:26:21.385492 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 10:26:21.386307 INFO: Estimating optimal hyperparameters - samples: 848, batch_size: 128, learning_rate: 1.77e-04
1 day, 10:26:21.386388 INFO: Using random state 846687 for train-test-split
1 day, 10:26:21.466248 INFO: Test AUC: 0.590
1 day, 10:26:21.466348 INFO: Train AUC: 0.545
1 day, 10:26:21.466382 INFO: AUC difference: 8.26%
1 day, 10:26:21.466407 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 10:26:21.705633 INFO: Resetting torch num_threads to 80
1 day, 10:26:21.706936 PROGRESS: === Extracted 1064 precursors and 8861 fragments ===
1 day, 10:26:21.707364 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:26:21.707952 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:26:21.708047 PROGRESS: Total precursors accumulated: 540
1 day, 10:26:21.708114 PROGRESS: Target precursors: 427 (79.07%)
1 day, 10:26:21.708181 PROGRESS: Decoy precursors: 113 (20.93%)
1 day, 10:26:21.708236 PROGRESS: 
1 day, 10:26:21.708288 PROGRESS: Precursor Summary:
1 day, 10:26:21.709239 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
1 day, 10:26:21.709331 PROGRESS: 
1 day, 10:26:21.709392 PROGRESS: Protein Summary:
1 day, 10:26:21.710450 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
1 day, 10:26:21.710545 PROGRESS: =========================================================================
1 day, 10:26:21.710698 INFO: Target number of precursors not reached yet.
1 day, 10:26:21.778471 INFO: Starting optimization step 2.
1 day, 10:26:21.778703 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 10:26:21.778789 INFO: Using python extraction backend
1 day, 10:26:21.778902 PROGRESS: Extracting batch of 1598 precursors
1 day, 10:26:21.778979 INFO: === Search parameters used ===
1 day, 10:26:21.779037 INFO: rt_error       : 1199.951526
1 day, 10:26:21.779089 INFO: mobility_error : 0.1
1 day, 10:26:21.779142 INFO: num_candidates : 1
1 day, 10:26:21.779193 INFO: ms1_error      : 30
1 day, 10:26:21.779243 INFO: ms2_error      : 30
1 day, 10:26:21.779291 INFO: fwhm_rt        : 5
1 day, 10:26:21.779340 INFO: quant_window   : 3
1 day, 10:26:21.779387 INFO: ==============================================
1 day, 10:26:21.780207 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:26:21.780259 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:26:21.780292 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:26:21.780317 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:26:21.781010 INFO: Starting candidate selection
1 day, 10:26:27.914520 INFO: Starting candidate scoring
1 day, 10:26:27.976062 INFO: Finished candidate processing
1 day, 10:26:27.976164 INFO: Collecting candidate features
1 day, 10:26:27.988147 INFO: Collecting fragment features
1 day, 10:26:27.990999 INFO: Finished candidate scoring
1 day, 10:26:27.994214 INFO: performing precursor FDR with 47 features
1 day, 10:26:27.994276 INFO: Decoy channel: -1
1 day, 10:26:27.994316 INFO: competitive: True
1 day, 10:26:27.997665 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:26:27.999227 WARNING: dropped 1 target PSMs due to missing features
1 day, 10:26:27.999286 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 10:26:28.000269 INFO: Estimating optimal hyperparameters - samples: 1,986, batch_size: 128, learning_rate: 1.77e-04
1 day, 10:26:28.000350 INFO: Using random state 806338 for train-test-split
1 day, 10:26:28.212529 INFO: Test AUC: 0.491
1 day, 10:26:28.212627 INFO: Train AUC: 0.572
1 day, 10:26:28.212662 INFO: AUC difference: 14.17%
1 day, 10:26:28.212687 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 10:26:28.450753 INFO: Resetting torch num_threads to 80
1 day, 10:26:28.452461 PROGRESS: === Extracted 2486 precursors and 20742 fragments ===
1 day, 10:26:28.452898 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:26:28.453564 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:26:28.453663 PROGRESS: Total precursors accumulated: 1,266
1 day, 10:26:28.453731 PROGRESS: Target precursors: 730 (57.66%)
1 day, 10:26:28.453793 PROGRESS: Decoy precursors: 536 (42.34%)
1 day, 10:26:28.453849 PROGRESS: 
1 day, 10:26:28.453919 PROGRESS: Precursor Summary:
1 day, 10:26:28.454879 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:26:28.454977 PROGRESS: 
1 day, 10:26:28.455040 PROGRESS: Protein Summary:
1 day, 10:26:28.456048 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:26:28.456141 PROGRESS: =========================================================================
1 day, 10:26:28.456301 INFO: Target number of precursors not reached yet.
1 day, 10:26:28.525464 INFO: Starting optimization step 3.
1 day, 10:26:28.525696 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 10:26:28.525785 INFO: Using python extraction backend
1 day, 10:26:28.525912 PROGRESS: Extracting batch of 3192 precursors
1 day, 10:26:28.525999 INFO: === Search parameters used ===
1 day, 10:26:28.526061 INFO: rt_error       : 1199.951526
1 day, 10:26:28.526113 INFO: mobility_error : 0.1
1 day, 10:26:28.526184 INFO: num_candidates : 1
1 day, 10:26:28.526237 INFO: ms1_error      : 30
1 day, 10:26:28.526284 INFO: ms2_error      : 30
1 day, 10:26:28.526331 INFO: fwhm_rt        : 5
1 day, 10:26:28.526377 INFO: quant_window   : 3
1 day, 10:26:28.526423 INFO: ==============================================
1 day, 10:26:28.527465 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:26:28.527515 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:26:28.527550 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:26:28.527575 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:26:28.528317 INFO: Starting candidate selection
1 day, 10:26:37.729293 INFO: Starting candidate scoring
1 day, 10:26:37.805028 INFO: Finished candidate processing
1 day, 10:26:37.805156 INFO: Collecting candidate features
1 day, 10:26:37.816835 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 2871)
1 day, 10:26:37.820932 INFO: Collecting fragment features
1 day, 10:26:37.824645 INFO: Finished candidate scoring
1 day, 10:26:37.829410 INFO: performing precursor FDR with 47 features
1 day, 10:26:37.829473 INFO: Decoy channel: -1
1 day, 10:26:37.829502 INFO: competitive: True
1 day, 10:26:37.833792 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:26:37.835814 WARNING: dropped 2 target PSMs due to missing features
1 day, 10:26:37.835874 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 10:26:37.837118 INFO: Estimating optimal hyperparameters - samples: 4,282, batch_size: 128, learning_rate: 1.77e-04
1 day, 10:26:37.837214 INFO: Using random state 676045 for train-test-split
1 day, 10:26:38.310794 INFO: Test AUC: 0.555
1 day, 10:26:38.310900 INFO: Train AUC: 0.568
1 day, 10:26:38.310935 INFO: AUC difference: 2.29%
1 day, 10:26:38.554716 INFO: Resetting torch num_threads to 80
1 day, 10:26:38.557048 PROGRESS: === Extracted 5357 precursors and 44799 fragments ===
1 day, 10:26:38.557490 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:26:38.558321 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:26:38.558423 PROGRESS: Total precursors accumulated: 2,723
1 day, 10:26:38.558489 PROGRESS: Target precursors: 1,582 (58.10%)
1 day, 10:26:38.558547 PROGRESS: Decoy precursors: 1,141 (41.90%)
1 day, 10:26:38.558599 PROGRESS: 
1 day, 10:26:38.558647 PROGRESS: Precursor Summary:
1 day, 10:26:38.559613 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 10:26:38.559707 PROGRESS: 
1 day, 10:26:38.559766 PROGRESS: Protein Summary:
1 day, 10:26:38.560835 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 10:26:38.560929 PROGRESS: =========================================================================
1 day, 10:26:38.561097 INFO: Target number of precursors not reached yet.
1 day, 10:26:38.654171 INFO: Starting optimization step 4.
1 day, 10:26:38.654451 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 10:26:38.654538 INFO: Using python extraction backend
1 day, 10:26:38.654659 PROGRESS: Extracting batch of 6381 precursors
1 day, 10:26:38.654734 INFO: === Search parameters used ===
1 day, 10:26:38.654785 INFO: rt_error       : 1199.951526
1 day, 10:26:38.654832 INFO: mobility_error : 0.1
1 day, 10:26:38.654876 INFO: num_candidates : 1
1 day, 10:26:38.654919 INFO: ms1_error      : 30
1 day, 10:26:38.654963 INFO: ms2_error      : 30
1 day, 10:26:38.655006 INFO: fwhm_rt        : 5
1 day, 10:26:38.655052 INFO: quant_window   : 3
1 day, 10:26:38.655095 INFO: ==============================================
1 day, 10:26:38.657164 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:26:38.657213 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:26:38.657245 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:26:38.657268 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:26:38.658070 INFO: Starting candidate selection
1 day, 10:26:56.924804 INFO: Starting candidate scoring
1 day, 10:26:57.079612 INFO: Finished candidate processing
1 day, 10:26:57.079742 INFO: Collecting candidate features
1 day, 10:26:57.098322 WARNING: intensity_correlation has 2 NaNs ( 0.03 % out of 5729)
1 day, 10:26:57.102340 INFO: Collecting fragment features
1 day, 10:26:57.108226 INFO: Finished candidate scoring
1 day, 10:26:57.118247 INFO: performing precursor FDR with 47 features
1 day, 10:26:57.118376 INFO: Decoy channel: -1
1 day, 10:26:57.118406 INFO: competitive: True
1 day, 10:26:57.124542 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:26:57.127383 WARNING: dropped 4 target PSMs due to missing features
1 day, 10:26:57.127447 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 10:26:57.129558 INFO: Estimating optimal hyperparameters - samples: 8,864, batch_size: 128, learning_rate: 1.77e-04
1 day, 10:26:57.129667 INFO: Using random state 497136 for train-test-split
1 day, 10:26:58.304269 INFO: Test AUC: 0.534
1 day, 10:26:58.304401 INFO: Train AUC: 0.578
1 day, 10:26:58.304440 INFO: AUC difference: 7.58%
1 day, 10:26:58.304465 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 10:26:58.553197 INFO: Resetting torch num_threads to 80
1 day, 10:26:58.557268 PROGRESS: === Extracted 11086 precursors and 92339 fragments ===
1 day, 10:26:58.557849 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:26:58.559186 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:26:58.559305 PROGRESS: Total precursors accumulated: 5,641
1 day, 10:26:58.559381 PROGRESS: Target precursors: 3,226 (57.19%)
1 day, 10:26:58.559444 PROGRESS: Decoy precursors: 2,415 (42.81%)
1 day, 10:26:58.559501 PROGRESS: 
1 day, 10:26:58.559556 PROGRESS: Precursor Summary:
1 day, 10:26:58.560545 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:26:58.560651 PROGRESS: 
1 day, 10:26:58.560722 PROGRESS: Protein Summary:
1 day, 10:26:58.561763 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:26:58.561854 PROGRESS: =========================================================================
1 day, 10:26:58.562145 INFO: Target number of precursors not reached yet.
1 day, 10:26:58.736080 INFO: Starting optimization step 5.
1 day, 10:26:58.736406 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1 day, 10:26:58.736506 INFO: Using python extraction backend
1 day, 10:26:58.736650 PROGRESS: Extracting batch of 12763 precursors
1 day, 10:26:58.736739 INFO: === Search parameters used ===
1 day, 10:26:58.736796 INFO: rt_error       : 1199.951526
1 day, 10:26:58.736847 INFO: mobility_error : 0.1
1 day, 10:26:58.736893 INFO: num_candidates : 1
1 day, 10:26:58.736939 INFO: ms1_error      : 30
1 day, 10:26:58.736985 INFO: ms2_error      : 30
1 day, 10:26:58.737030 INFO: fwhm_rt        : 5
1 day, 10:26:58.737075 INFO: quant_window   : 3
1 day, 10:26:58.737119 INFO: ==============================================
1 day, 10:26:58.742799 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:26:58.742875 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:26:58.742908 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:26:58.742935 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:26:58.743692 INFO: Starting candidate selection
1 day, 10:27:29.568248 INFO: Starting candidate scoring
1 day, 10:27:29.804581 INFO: Finished candidate processing
1 day, 10:27:29.804690 INFO: Collecting candidate features
1 day, 10:27:29.828357 WARNING: intensity_correlation has 2 NaNs ( 0.02 % out of 11468)
1 day, 10:27:29.828656 WARNING: height_correlation has 1 NaNs ( 0.01 % out of 11468)
1 day, 10:27:29.833012 INFO: Collecting fragment features
1 day, 10:27:29.844712 INFO: Finished candidate scoring
1 day, 10:27:29.863721 INFO: performing precursor FDR with 47 features
1 day, 10:27:29.863888 INFO: Decoy channel: -1
1 day, 10:27:29.863917 INFO: competitive: True
1 day, 10:27:29.876644 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:27:29.881604 WARNING: dropped 5 target PSMs due to missing features
1 day, 10:27:29.881717 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 10:27:29.885423 INFO: Estimating optimal hyperparameters - samples: 18,036, batch_size: 128, learning_rate: 1.77e-04
1 day, 10:27:29.885584 INFO: Using random state 472168 for train-test-split
1 day, 10:27:32.148950 INFO: Test AUC: 0.543
1 day, 10:27:32.149095 INFO: Train AUC: 0.582
1 day, 10:27:32.149129 INFO: AUC difference: 6.72%
1 day, 10:27:32.149156 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 10:27:32.409406 INFO: Resetting torch num_threads to 80
1 day, 10:27:32.415776 PROGRESS: === Extracted 22554 precursors and 187930 fragments ===
1 day, 10:27:32.416492 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:27:32.418719 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:27:32.418843 PROGRESS: Total precursors accumulated: 11,471
1 day, 10:27:32.418934 PROGRESS: Target precursors: 6,668 (58.13%)
1 day, 10:27:32.418995 PROGRESS: Decoy precursors: 4,803 (41.87%)
1 day, 10:27:32.419051 PROGRESS: 
1 day, 10:27:32.419123 PROGRESS: Precursor Summary:
1 day, 10:27:32.420181 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:27:32.420277 PROGRESS: 
1 day, 10:27:32.420341 PROGRESS: Protein Summary:
1 day, 10:27:32.421429 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:27:32.421523 PROGRESS: =========================================================================
1 day, 10:27:32.421836 INFO: Target number of precursors not reached yet.
1 day, 10:27:32.620187 INFO: Starting optimization step 6.
1 day, 10:27:32.620513 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1 day, 10:27:32.620631 INFO: Using python extraction backend
1 day, 10:27:32.620773 PROGRESS: Extracting batch of 25523 precursors
1 day, 10:27:32.620857 INFO: === Search parameters used ===
1 day, 10:27:32.620914 INFO: rt_error       : 1199.951526
1 day, 10:27:32.620964 INFO: mobility_error : 0.1
1 day, 10:27:32.621011 INFO: num_candidates : 1
1 day, 10:27:32.621058 INFO: ms1_error      : 30
1 day, 10:27:32.621105 INFO: ms2_error      : 30
1 day, 10:27:32.621150 INFO: fwhm_rt        : 5
1 day, 10:27:32.621197 INFO: quant_window   : 3
1 day, 10:27:32.621250 INFO: ==============================================
1 day, 10:27:32.629242 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:27:32.629336 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:27:32.629370 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:27:32.629395 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:27:32.630207 INFO: Starting candidate selection
1 day, 10:28:30.597108 INFO: Starting candidate scoring
1 day, 10:28:30.991246 INFO: Finished candidate processing
1 day, 10:28:30.991354 INFO: Collecting candidate features
1 day, 10:28:31.033935 WARNING: intensity_correlation has 9 NaNs ( 0.04 % out of 22870)
1 day, 10:28:31.038658 INFO: Collecting fragment features
1 day, 10:28:31.054283 INFO: Finished candidate scoring
1 day, 10:28:31.082249 INFO: performing precursor FDR with 47 features
1 day, 10:28:31.082425 INFO: Decoy channel: -1
1 day, 10:28:31.082456 INFO: competitive: True
1 day, 10:28:31.103938 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:28:31.114941 WARNING: dropped 12 target PSMs due to missing features
1 day, 10:28:31.115103 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 10:28:31.122403 INFO: Estimating optimal hyperparameters - samples: 36,324, batch_size: 148, learning_rate: 1.90e-04
1 day, 10:28:31.122646 INFO: Using random state 312914 for train-test-split
1 day, 10:28:35.458266 INFO: Test AUC: 0.538
1 day, 10:28:35.458417 INFO: Train AUC: 0.583
1 day, 10:28:35.458452 INFO: AUC difference: 7.65%
1 day, 10:28:35.458478 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 10:28:35.726246 INFO: Resetting torch num_threads to 80
1 day, 10:28:35.736300 PROGRESS: === Extracted 45424 precursors and 379372 fragments ===
1 day, 10:28:35.737029 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:28:35.741555 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:28:35.741701 PROGRESS: Total precursors accumulated: 23,089
1 day, 10:28:35.741782 PROGRESS: Target precursors: 13,428 (58.16%)
1 day, 10:28:35.741847 PROGRESS: Decoy precursors: 9,661 (41.84%)
1 day, 10:28:35.741940 PROGRESS: 
1 day, 10:28:35.741999 PROGRESS: Precursor Summary:
1 day, 10:28:35.743149 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:28:35.743250 PROGRESS: 
1 day, 10:28:35.743315 PROGRESS: Protein Summary:
1 day, 10:28:35.744442 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:28:35.744536 PROGRESS: =========================================================================
1 day, 10:28:35.744965 INFO: Target number of precursors not reached yet.
1 day, 10:28:35.954095 INFO: Starting optimization step 7.
1 day, 10:28:35.954431 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1 day, 10:28:35.954528 INFO: Using python extraction backend
1 day, 10:28:35.954676 PROGRESS: Extracting batch of 51061 precursors
1 day, 10:28:35.954766 INFO: === Search parameters used ===
1 day, 10:28:35.954828 INFO: rt_error       : 1199.951526
1 day, 10:28:35.954896 INFO: mobility_error : 0.1
1 day, 10:28:35.954948 INFO: num_candidates : 1
1 day, 10:28:35.954998 INFO: ms1_error      : 30
1 day, 10:28:35.955045 INFO: ms2_error      : 30
1 day, 10:28:35.955090 INFO: fwhm_rt        : 5
1 day, 10:28:35.955137 INFO: quant_window   : 3
1 day, 10:28:35.955182 INFO: ==============================================
1 day, 10:28:35.971567 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:28:35.971732 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:28:35.971781 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:28:35.971807 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:28:35.972689 INFO: Starting candidate selection
1 day, 10:30:31.917796 INFO: Starting candidate scoring
1 day, 10:30:32.613670 INFO: Finished candidate processing
1 day, 10:30:32.613902 INFO: Collecting candidate features
1 day, 10:30:32.693231 WARNING: intensity_correlation has 21 NaNs ( 0.05 % out of 45760)
1 day, 10:30:32.693524 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 45760)
1 day, 10:30:32.699110 INFO: Collecting fragment features
1 day, 10:30:32.726931 INFO: Finished candidate scoring
1 day, 10:30:32.779612 INFO: performing precursor FDR with 47 features
1 day, 10:30:32.779760 INFO: Decoy channel: -1
1 day, 10:30:32.779789 INFO: competitive: True
1 day, 10:30:32.819715 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:30:32.839851 WARNING: dropped 23 target PSMs due to missing features
1 day, 10:30:32.839994 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 10:30:32.854329 INFO: Estimating optimal hyperparameters - samples: 72,915, batch_size: 298, learning_rate: 2.70e-04
1 day, 10:30:32.854657 INFO: Using random state 994131 for train-test-split
1 day, 10:30:38.214954 INFO: Test AUC: 0.547
1 day, 10:30:38.215083 INFO: Train AUC: 0.585
1 day, 10:30:38.215118 INFO: AUC difference: 6.47%
1 day, 10:30:38.215143 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 10:30:38.489337 INFO: Resetting torch num_threads to 80
1 day, 10:30:38.507701 PROGRESS: === Extracted 91184 precursors and 761365 fragments ===
1 day, 10:30:38.508481 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:30:38.518617 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:30:38.518791 PROGRESS: Total precursors accumulated: 46,311
1 day, 10:30:38.518867 PROGRESS: Target precursors: 27,066 (58.44%)
1 day, 10:30:38.518929 PROGRESS: Decoy precursors: 19,245 (41.56%)
1 day, 10:30:38.518986 PROGRESS: 
1 day, 10:30:38.519038 PROGRESS: Precursor Summary:
1 day, 10:30:38.520385 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:30:38.520494 PROGRESS: 
1 day, 10:30:38.520560 PROGRESS: Protein Summary:
1 day, 10:30:38.521900 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 10:30:38.522005 PROGRESS: =========================================================================
1 day, 10:30:38.522951 INFO: Target number of precursors not reached yet.
1 day, 10:30:38.777637 INFO: Starting optimization step 8.
1 day, 10:30:38.777955 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1 day, 10:30:38.778061 INFO: Using python extraction backend
1 day, 10:30:38.778198 PROGRESS: Extracting batch of 102076 precursors
1 day, 10:30:38.778280 INFO: === Search parameters used ===
1 day, 10:30:38.778337 INFO: rt_error       : 1199.951526
1 day, 10:30:38.778388 INFO: mobility_error : 0.1
1 day, 10:30:38.778439 INFO: num_candidates : 1
1 day, 10:30:38.778487 INFO: ms1_error      : 30
1 day, 10:30:38.778536 INFO: ms2_error      : 30
1 day, 10:30:38.778582 INFO: fwhm_rt        : 5
1 day, 10:30:38.778627 INFO: quant_window   : 3
1 day, 10:30:38.778673 INFO: ==============================================
1 day, 10:30:38.805492 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:30:38.805631 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:30:38.805666 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:30:38.805692 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:30:38.806546 INFO: Starting candidate selection
1 day, 10:34:31.007816 INFO: Starting candidate scoring
1 day, 10:34:32.355489 INFO: Finished candidate processing
1 day, 10:34:32.355693 INFO: Collecting candidate features
1 day, 10:34:32.509258 WARNING: intensity_correlation has 19 NaNs ( 0.02 % out of 91493)
1 day, 10:34:32.509603 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 91493)
1 day, 10:34:32.516434 INFO: Collecting fragment features
1 day, 10:34:32.573647 INFO: Finished candidate scoring
1 day, 10:34:32.690853 INFO: performing precursor FDR with 47 features
1 day, 10:34:32.691006 INFO: Decoy channel: -1
1 day, 10:34:32.691034 INFO: competitive: True
1 day, 10:34:32.764016 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:34:32.797554 WARNING: dropped 30 target PSMs due to missing features
1 day, 10:34:32.797703 WARNING: dropped 33 decoy PSMs due to missing features
1 day, 10:34:32.853333 INFO: Estimating optimal hyperparameters - samples: 146,091, batch_size: 598, learning_rate: 3.82e-04
1 day, 10:34:32.853770 INFO: Using random state 574696 for train-test-split
1 day, 10:34:39.942102 INFO: Test AUC: 0.543
1 day, 10:34:39.942259 INFO: Train AUC: 0.571
1 day, 10:34:39.942295 INFO: AUC difference: 4.88%
1 day, 10:34:40.248883 INFO: Resetting torch num_threads to 80
1 day, 10:34:40.283248 PROGRESS: === Extracted 182677 precursors and 1527533 fragments ===
1 day, 10:34:40.284159 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:34:40.301729 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:34:40.302036 PROGRESS: Total precursors accumulated: 92,766
1 day, 10:34:40.302123 PROGRESS: Target precursors: 53,169 (57.32%)
1 day, 10:34:40.302185 PROGRESS: Decoy precursors: 39,597 (42.68%)
1 day, 10:34:40.302243 PROGRESS: 
1 day, 10:34:40.302307 PROGRESS: Precursor Summary:
1 day, 10:34:40.304013 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 10:34:40.304128 PROGRESS: 
1 day, 10:34:40.304192 PROGRESS: Protein Summary:
1 day, 10:34:40.305752 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 10:34:40.305852 PROGRESS: =========================================================================
1 day, 10:34:40.308079 INFO: Target number of precursors not reached yet.
1 day, 10:34:40.887842 INFO: Starting optimization step 9.
1 day, 10:34:40.888148 PROGRESS: === Extracting elution groups 102200 to 204600 ===
1 day, 10:34:40.888244 INFO: Using python extraction backend
1 day, 10:34:40.888382 PROGRESS: Extracting batch of 204132 precursors
1 day, 10:34:40.888463 INFO: === Search parameters used ===
1 day, 10:34:40.888517 INFO: rt_error       : 1199.951526
1 day, 10:34:40.888565 INFO: mobility_error : 0.1
1 day, 10:34:40.888613 INFO: num_candidates : 1
1 day, 10:34:40.888660 INFO: ms1_error      : 30
1 day, 10:34:40.888706 INFO: ms2_error      : 30
1 day, 10:34:40.888752 INFO: fwhm_rt        : 5
1 day, 10:34:40.888798 INFO: quant_window   : 3
1 day, 10:34:40.888843 INFO: ==============================================
1 day, 10:34:40.942355 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:34:40.942498 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:34:40.942532 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:34:40.942559 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:34:40.943432 INFO: Starting candidate selection
1 day, 10:42:24.735830 INFO: Starting candidate scoring
1 day, 10:42:27.258132 INFO: Finished candidate processing
1 day, 10:42:27.258263 INFO: Collecting candidate features
1 day, 10:42:27.606033 WARNING: intensity_correlation has 55 NaNs ( 0.03 % out of 183157)
1 day, 10:42:27.606512 WARNING: height_correlation has 8 NaNs ( 0.00 % out of 183157)
1 day, 10:42:27.616382 INFO: Collecting fragment features
1 day, 10:42:27.727763 INFO: Finished candidate scoring
1 day, 10:42:27.940011 INFO: performing precursor FDR with 47 features
1 day, 10:42:27.940184 INFO: Decoy channel: -1
1 day, 10:42:27.940220 INFO: competitive: True
1 day, 10:42:28.085927 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:42:28.151734 WARNING: dropped 61 target PSMs due to missing features
1 day, 10:42:28.151899 WARNING: dropped 63 decoy PSMs due to missing features
1 day, 10:42:28.256004 INFO: Estimating optimal hyperparameters - samples: 292,568, batch_size: 1,198, learning_rate: 5.41e-04
1 day, 10:42:28.256556 INFO: Using random state 25336 for train-test-split
1 day, 10:42:38.861574 INFO: Test AUC: 0.544
1 day, 10:42:38.861731 INFO: Train AUC: 0.568
1 day, 10:42:38.861767 INFO: AUC difference: 4.28%
1 day, 10:42:39.227264 INFO: Resetting torch num_threads to 80
1 day, 10:42:39.292869 PROGRESS: === Extracted 365834 precursors and 3057986 fragments ===
1 day, 10:42:39.293954 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:42:39.325506 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:42:39.325823 PROGRESS: Total precursors accumulated: 185,791
1 day, 10:42:39.325924 PROGRESS: Target precursors: 106,710 (57.44%)
1 day, 10:42:39.325990 PROGRESS: Decoy precursors: 79,081 (42.56%)
1 day, 10:42:39.326050 PROGRESS: 
1 day, 10:42:39.326102 PROGRESS: Precursor Summary:
1 day, 10:42:39.328386 PROGRESS: Channel   0:	 0.050 FDR:    42; 0.010 FDR:    12; 0.001 FDR:    12
1 day, 10:42:39.328490 PROGRESS: 
1 day, 10:42:39.328554 PROGRESS: Protein Summary:
1 day, 10:42:39.330603 PROGRESS: Channel   0:	 0.050 FDR:    42; 0.010 FDR:    12; 0.001 FDR:    12
1 day, 10:42:39.330706 PROGRESS: =========================================================================
1 day, 10:42:39.333642 INFO: Target number of precursors not reached yet.
1 day, 10:42:40.410733 INFO: Starting optimization step 10.
1 day, 10:42:40.411058 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 10:42:40.411179 INFO: Using python extraction backend
1 day, 10:42:40.411331 PROGRESS: Extracting batch of 408390 precursors
1 day, 10:42:40.411421 INFO: === Search parameters used ===
1 day, 10:42:40.411481 INFO: rt_error       : 1199.951526
1 day, 10:42:40.411535 INFO: mobility_error : 0.1
1 day, 10:42:40.411586 INFO: num_candidates : 1
1 day, 10:42:40.411633 INFO: ms1_error      : 30
1 day, 10:42:40.411680 INFO: ms2_error      : 30
1 day, 10:42:40.411726 INFO: fwhm_rt        : 5
1 day, 10:42:40.411782 INFO: quant_window   : 3
1 day, 10:42:40.411833 INFO: ==============================================
1 day, 10:42:40.513623 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:42:40.513770 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:42:40.513808 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:42:40.513834 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:42:40.514645 INFO: Starting candidate selection
1 day, 10:57:56.540999 INFO: Starting candidate scoring
1 day, 10:58:01.372024 INFO: Finished candidate processing
1 day, 10:58:01.372140 INFO: Collecting candidate features
1 day, 10:58:02.147342 WARNING: intensity_correlation has 116 NaNs ( 0.03 % out of 365257)
1 day, 10:58:02.147919 WARNING: height_correlation has 18 NaNs ( 0.00 % out of 365257)
1 day, 10:58:02.162514 INFO: Collecting fragment features
1 day, 10:58:02.386161 INFO: Finished candidate scoring
1 day, 10:58:02.758008 INFO: performing precursor FDR with 47 features
1 day, 10:58:02.758175 INFO: Decoy channel: -1
1 day, 10:58:02.758205 INFO: competitive: True
1 day, 10:58:03.041612 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:58:03.170955 WARNING: dropped 129 target PSMs due to missing features
1 day, 10:58:03.171120 WARNING: dropped 125 decoy PSMs due to missing features
1 day, 10:58:03.528507 INFO: Estimating optimal hyperparameters - samples: 584,669, batch_size: 2,394, learning_rate: 7.65e-04
1 day, 10:58:03.529556 INFO: Using random state 199268 for train-test-split
1 day, 10:58:21.485851 INFO: Test AUC: 0.541
1 day, 10:58:21.486076 INFO: Train AUC: 0.561
1 day, 10:58:21.486116 INFO: AUC difference: 3.61%
1 day, 10:58:21.954100 INFO: Resetting torch num_threads to 80
1 day, 10:58:22.079483 PROGRESS: === Extracted 731091 precursors and 6111980 fragments ===
1 day, 10:58:22.080709 INFO: === FDR correction performed with classifier version -1 ===
1 day, 10:58:22.146656 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:58:22.146995 PROGRESS: Total precursors accumulated: 371,352
1 day, 10:58:22.147068 PROGRESS: Target precursors: 210,133 (56.59%)
1 day, 10:58:22.147130 PROGRESS: Decoy precursors: 161,219 (43.41%)
1 day, 10:58:22.147183 PROGRESS: 
1 day, 10:58:22.147236 PROGRESS: Precursor Summary:
1 day, 10:58:22.150784 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 10:58:22.150896 PROGRESS: 
1 day, 10:58:22.150959 PROGRESS: Protein Summary:
1 day, 10:58:22.153982 PROGRESS: Channel   0:	 0.050 FDR:   161; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 10:58:22.154089 PROGRESS: =========================================================================
1 day, 10:58:22.159502 INFO: Target number of precursors not reached yet.
1 day, 10:58:23.294036 INFO: Starting optimization step 11.
1 day, 10:58:23.294345 PROGRESS: === Extracting elution groups 409400 to 819000 ===
1 day, 10:58:23.294453 INFO: Using python extraction backend
1 day, 10:58:23.294585 PROGRESS: Extracting batch of 816689 precursors
1 day, 10:58:23.294671 INFO: === Search parameters used ===
1 day, 10:58:23.294743 INFO: rt_error       : 1199.951526
1 day, 10:58:23.294795 INFO: mobility_error : 0.1
1 day, 10:58:23.294843 INFO: num_candidates : 1
1 day, 10:58:23.294891 INFO: ms1_error      : 30
1 day, 10:58:23.294937 INFO: ms2_error      : 30
1 day, 10:58:23.294981 INFO: fwhm_rt        : 5
1 day, 10:58:23.295026 INFO: quant_window   : 3
1 day, 10:58:23.295069 INFO: ==============================================
1 day, 10:58:23.490084 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 10:58:23.490226 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 10:58:23.490268 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 10:58:23.490293 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 10:58:23.491280 INFO: Starting candidate selection
1 day, 11:28:46.579902 INFO: Starting candidate scoring
1 day, 11:28:56.100694 INFO: Finished candidate processing
1 day, 11:28:56.100888 INFO: Collecting candidate features
1 day, 11:28:58.005843 WARNING: intensity_correlation has 242 NaNs ( 0.03 % out of 731997)
1 day, 11:28:58.006736 WARNING: height_correlation has 29 NaNs ( 0.00 % out of 731997)
1 day, 11:28:58.032431 INFO: Collecting fragment features
1 day, 11:28:58.507618 INFO: Finished candidate scoring
1 day, 11:28:59.356592 INFO: performing precursor FDR with 47 features
1 day, 11:28:59.356743 INFO: Decoy channel: -1
1 day, 11:28:59.356775 INFO: competitive: True
1 day, 11:28:59.903399 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 11:29:00.133136 WARNING: dropped 260 target PSMs due to missing features
1 day, 11:29:00.133308 WARNING: dropped 258 decoy PSMs due to missing features
1 day, 11:29:00.783454 INFO: Estimating optimal hyperparameters - samples: 1,170,056, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 11:29:00.786074 INFO: Using random state 46399 for train-test-split
1 day, 11:29:32.025756 INFO: Test AUC: 0.545
1 day, 11:29:32.025948 INFO: Train AUC: 0.558
1 day, 11:29:32.025987 INFO: AUC difference: 2.31%
1 day, 11:29:32.728209 INFO: Resetting torch num_threads to 80
1 day, 11:29:33.038126 PROGRESS: === Extracted 1463088 precursors and 12228732 fragments ===
1 day, 11:29:33.039803 INFO: === FDR correction performed with classifier version -1 ===
1 day, 11:29:33.157686 PROGRESS: ============================= Precursor FDR =============================
1 day, 11:29:33.158084 PROGRESS: Total precursors accumulated: 743,151
1 day, 11:29:33.158172 PROGRESS: Target precursors: 420,715 (56.61%)
1 day, 11:29:33.158241 PROGRESS: Decoy precursors: 322,436 (43.39%)
1 day, 11:29:33.158298 PROGRESS: 
1 day, 11:29:33.158355 PROGRESS: Precursor Summary:
1 day, 11:29:33.164114 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 11:29:33.164282 PROGRESS: 
1 day, 11:29:33.164353 PROGRESS: Protein Summary:
1 day, 11:29:33.169030 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 11:29:33.169155 PROGRESS: =========================================================================
1 day, 11:29:33.179504 INFO: Target number of precursors not reached yet.
1 day, 11:29:34.889079 INFO: Starting optimization step 12.
1 day, 11:29:34.889392 PROGRESS: === Extracting elution groups 819000 to 1638200 ===
1 day, 11:29:34.889498 INFO: Using python extraction backend
1 day, 11:29:34.889641 PROGRESS: Extracting batch of 1633286 precursors
1 day, 11:29:34.889724 INFO: === Search parameters used ===
1 day, 11:29:34.889779 INFO: rt_error       : 1199.951526
1 day, 11:29:34.889830 INFO: mobility_error : 0.1
1 day, 11:29:34.889912 INFO: num_candidates : 1
1 day, 11:29:34.889966 INFO: ms1_error      : 30
1 day, 11:29:34.890011 INFO: ms2_error      : 30
1 day, 11:29:34.890054 INFO: fwhm_rt        : 5
1 day, 11:29:34.890100 INFO: quant_window   : 3
1 day, 11:29:34.890143 INFO: ==============================================
1 day, 11:29:35.307578 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 11:29:35.307716 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 11:29:35.307752 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 11:29:35.307776 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 11:29:35.308743 INFO: Starting candidate selection
1 day, 12:30:27.635717 INFO: Starting candidate scoring
1 day, 12:30:47.272465 INFO: Finished candidate processing
1 day, 12:30:47.272734 INFO: Collecting candidate features
1 day, 12:30:51.195313 WARNING: intensity_correlation has 457 NaNs ( 0.03 % out of 1462810)
1 day, 12:30:51.196957 WARNING: height_correlation has 61 NaNs ( 0.00 % out of 1462810)
1 day, 12:30:51.245119 INFO: Collecting fragment features
1 day, 12:30:52.218151 INFO: Finished candidate scoring
1 day, 12:30:54.057454 INFO: performing precursor FDR with 47 features
1 day, 12:30:54.057619 INFO: Decoy channel: -1
1 day, 12:30:54.057654 INFO: competitive: True
1 day, 12:30:55.170974 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:30:55.695556 WARNING: dropped 475 target PSMs due to missing features
1 day, 12:30:55.695727 WARNING: dropped 536 decoy PSMs due to missing features
1 day, 12:30:57.049911 INFO: Estimating optimal hyperparameters - samples: 2,339,909, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 12:30:57.056438 INFO: Using random state 875001 for train-test-split
1 day, 12:32:01.223249 INFO: Test AUC: 0.554
1 day, 12:32:01.223425 INFO: Train AUC: 0.560
1 day, 12:32:01.223463 INFO: AUC difference: 1.06%
1 day, 12:32:02.457639 INFO: Resetting torch num_threads to 80
1 day, 12:32:03.389855 PROGRESS: === Extracted 2925898 precursors and 24457609 fragments ===
1 day, 12:32:03.392036 INFO: === FDR correction performed with classifier version -1 ===
1 day, 12:32:03.617540 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:32:03.617925 PROGRESS: Total precursors accumulated: 1,486,253
1 day, 12:32:03.618003 PROGRESS: Target precursors: 844,685 (56.83%)
1 day, 12:32:03.618064 PROGRESS: Decoy precursors: 641,568 (43.17%)
1 day, 12:32:03.618117 PROGRESS: 
1 day, 12:32:03.618171 PROGRESS: Precursor Summary:
1 day, 12:32:03.628005 PROGRESS: Channel   0:	 0.050 FDR: 1,465; 0.010 FDR:   924; 0.001 FDR:   529
1 day, 12:32:03.628178 PROGRESS: 
1 day, 12:32:03.628244 PROGRESS: Protein Summary:
1 day, 12:32:03.637251 PROGRESS: Channel   0:	 0.050 FDR:   758; 0.010 FDR:   448; 0.001 FDR:   281
1 day, 12:32:03.637417 PROGRESS: =========================================================================
1 day, 12:32:03.656701 INFO: Target number of precursors reached.
1 day, 12:32:06.363581 INFO: fragments_df: keeping 5000 of 24457609 [sum(precursor_idx_mask)=10044 sum(mass_error_mask)=24457387 stop_rank=5000
1 day, 12:32:07.620489 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:32:07.813079 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:32:08.002956 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:32:08.171383 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:32:08.824022 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 12:32:08.824491 INFO: Using score_cutoff 37.62803925590515 (fac=0.99, q=1)
1 day, 12:32:08.824869 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.897521495819092
1 day, 12:32:08.824959 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007725381292402744
1 day, 12:32:08.825023 INFO: Updating optimization_manager: score_cutoff        : 0 -> 37.62803925590515
1 day, 12:32:08.825092 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:32:08.925996 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:32:09.451861 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:32:09.551786 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:32:10.546980 INFO: Updating optimization_manager: classifier_version  : -1 -> 12
1 day, 12:32:10.547269 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 12:32:10.547411 INFO: Starting optimization step 13.
1 day, 12:32:10.547489 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 12:32:10.547573 INFO: Using python extraction backend
1 day, 12:32:10.547711 PROGRESS: Extracting batch of 816307 precursors
1 day, 12:32:10.547799 INFO: === Search parameters used ===
1 day, 12:32:10.547856 INFO: rt_error       : 1199.951526
1 day, 12:32:10.547905 INFO: mobility_error : 0.1
1 day, 12:32:10.547952 INFO: num_candidates : 3
1 day, 12:32:10.547998 INFO: ms1_error      : 30
1 day, 12:32:10.548043 INFO: ms2_error      : 30
1 day, 12:32:10.548087 INFO: fwhm_rt        : 2.897521495819092
1 day, 12:32:10.548134 INFO: quant_window   : 3
1 day, 12:32:10.548179 INFO: ==============================================
1 day, 12:32:10.753481 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 12:32:10.753622 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 12:32:10.753681 INFO: FWHM in RT is 2.90 seconds, sigma is 0.48
1 day, 12:32:10.753707 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.19
1 day, 12:32:10.754523 INFO: Starting candidate selection
1 day, 13:05:18.987852 INFO: Starting candidate scoring
1 day, 13:05:45.644369 INFO: Finished candidate processing
1 day, 13:05:45.644873 INFO: Collecting candidate features
1 day, 13:05:50.290176 WARNING: intensity_correlation has 713 NaNs ( 0.03 % out of 2100352)
1 day, 13:05:50.292313 WARNING: height_correlation has 70 NaNs ( 0.00 % out of 2100352)
1 day, 13:05:50.362663 INFO: Collecting fragment features
1 day, 13:05:51.768924 INFO: Finished candidate scoring
1 day, 13:05:53.277472 INFO: performing precursor FDR with 47 features
1 day, 13:05:53.277618 INFO: Decoy channel: -1
1 day, 13:05:53.277663 INFO: competitive: True
1 day, 13:05:53.791359 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 13:05:54.089769 WARNING: dropped 366 target PSMs due to missing features
1 day, 13:05:54.089983 WARNING: dropped 397 decoy PSMs due to missing features
1 day, 13:05:54.945630 INFO: Estimating optimal hyperparameters - samples: 1,679,671, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 13:05:54.949492 INFO: Using random state 235139 for train-test-split
1 day, 13:06:38.577923 INFO: Test AUC: 0.560
1 day, 13:06:38.578169 INFO: Train AUC: 0.571
1 day, 13:06:38.578209 INFO: AUC difference: 1.79%
1 day, 13:06:39.532212 INFO: Resetting torch num_threads to 80
1 day, 13:06:39.568860 PROGRESS: === Extracted 2100352 precursors and 17158322 fragments ===
1 day, 13:06:39.570019 INFO: === FDR correction performed with classifier version 12 ===
1 day, 13:06:39.634948 PROGRESS: ============================= Precursor FDR =============================
1 day, 13:06:39.635300 PROGRESS: Total precursors accumulated: 374,604
1 day, 13:06:39.635375 PROGRESS: Target precursors: 219,650 (58.64%)
1 day, 13:06:39.635448 PROGRESS: Decoy precursors: 154,954 (41.36%)
1 day, 13:06:39.635511 PROGRESS: 
1 day, 13:06:39.635562 PROGRESS: Precursor Summary:
1 day, 13:06:39.639074 PROGRESS: Channel   0:	 0.050 FDR:   381; 0.010 FDR:   255; 0.001 FDR:   221
1 day, 13:06:39.639184 PROGRESS: 
1 day, 13:06:39.639250 PROGRESS: Protein Summary:
1 day, 13:06:39.642378 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   193; 0.001 FDR:   163
1 day, 13:06:39.642484 PROGRESS: =========================================================================
1 day, 13:06:39.703219 INFO: Target number of precursors reached.
1 day, 13:06:41.565930 INFO: fragments_df: keeping 4856 of 17158322 [sum(precursor_idx_mask)=7659 sum(mass_error_mask)=17158141 stop_rank=4856
1 day, 13:06:42.854948 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 13:06:42.986395 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 13:06:43.124043 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 13:06:43.248682 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 13:06:43.878952 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 13:06:43.879401 INFO: Using score_cutoff 33.82262256088257 (fac=0.99, q=1)
1 day, 13:06:43.879753 INFO: Updating optimization_manager: fwhm_rt             : 2.897521495819092 -> 2.9160120487213135
1 day, 13:06:43.879836 INFO: Updating optimization_manager: fwhm_mobility       : 0.007725381292402744 -> 0.007399494294077158
1 day, 13:06:43.879894 INFO: Updating optimization_manager: score_cutoff        : 37.62803925590515 -> 33.82262256088257
1 day, 13:06:43.879956 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 13:06:43.989176 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 13:06:44.518813 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 13:06:44.627774 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 13:06:45.730801 INFO: === checking if optimization conditions were reached ===
1 day, 13:06:45.733217 INFO: Updating optimization_manager: ms2_error           : 30 -> 16.700235515689997
1 day, 13:06:45.733377 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
1 day, 13:06:45.733462 PROGRESS: ❌ ms2_error      : 16.7002 > 15.0000 or insufficient steps taken.
1 day, 13:06:45.734573 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 13:06:45.734683 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
1 day, 13:06:45.734757 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 13:06:45.734826 INFO: ==============================================
1 day, 13:06:45.734911 INFO: Starting optimization step 14.
1 day, 13:06:45.734980 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 13:06:45.735068 INFO: Using python extraction backend
1 day, 13:06:45.735219 PROGRESS: Extracting batch of 816307 precursors
1 day, 13:06:45.735299 INFO: === Search parameters used ===
1 day, 13:06:45.735361 INFO: rt_error       : 1199.951526
1 day, 13:06:45.735412 INFO: mobility_error : 0.1
1 day, 13:06:45.735462 INFO: num_candidates : 3
1 day, 13:06:45.735511 INFO: ms1_error      : 15.0
1 day, 13:06:45.735572 INFO: ms2_error      : 16.700235515689997
1 day, 13:06:45.735622 INFO: fwhm_rt        : 2.9160120487213135
1 day, 13:06:45.735668 INFO: quant_window   : 3
1 day, 13:06:45.735717 INFO: ==============================================
1 day, 13:06:45.942391 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 13:06:45.942537 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 13:06:45.942595 INFO: FWHM in RT is 2.92 seconds, sigma is 0.49
1 day, 13:06:45.942627 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 4.01
1 day, 13:06:45.943457 INFO: Starting candidate selection
1 day, 13:37:54.901943 INFO: Starting candidate scoring
1 day, 13:38:19.488987 INFO: Finished candidate processing
1 day, 13:38:19.489178 INFO: Collecting candidate features
1 day, 13:38:23.782048 WARNING: intensity_correlation has 2337 NaNs ( 0.11 % out of 2052356)
1 day, 13:38:23.784149 WARNING: height_correlation has 188 NaNs ( 0.01 % out of 2052356)
1 day, 13:38:23.873140 INFO: Collecting fragment features
1 day, 13:38:25.039299 INFO: Finished candidate scoring
1 day, 13:38:26.433595 INFO: performing precursor FDR with 47 features
1 day, 13:38:26.433733 INFO: Decoy channel: -1
1 day, 13:38:26.433764 INFO: competitive: True
1 day, 13:38:26.917924 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 13:38:27.209194 WARNING: dropped 1190 target PSMs due to missing features
1 day, 13:38:27.209353 WARNING: dropped 1274 decoy PSMs due to missing features
1 day, 13:38:28.489235 INFO: Estimating optimal hyperparameters - samples: 1,639,913, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 13:38:28.493136 INFO: Using random state 703382 for train-test-split
1 day, 13:39:07.412287 INFO: Test AUC: 0.559
1 day, 13:39:07.412547 INFO: Train AUC: 0.571
1 day, 13:39:07.412589 INFO: AUC difference: 2.06%
1 day, 13:39:08.308136 INFO: Resetting torch num_threads to 80
1 day, 13:39:08.343843 PROGRESS: === Extracted 2052356 precursors and 14533394 fragments ===
1 day, 13:39:08.344963 INFO: === FDR correction performed with classifier version 13 ===
1 day, 13:39:08.407543 PROGRESS: ============================= Precursor FDR =============================
1 day, 13:39:08.407890 PROGRESS: Total precursors accumulated: 372,405
1 day, 13:39:08.407964 PROGRESS: Target precursors: 217,707 (58.46%)
1 day, 13:39:08.408025 PROGRESS: Decoy precursors: 154,698 (41.54%)
1 day, 13:39:08.408080 PROGRESS: 
1 day, 13:39:08.408133 PROGRESS: Precursor Summary:
1 day, 13:39:08.411592 PROGRESS: Channel   0:	 0.050 FDR:   494; 0.010 FDR:   340; 0.001 FDR:     9
1 day, 13:39:08.411699 PROGRESS: 
1 day, 13:39:08.411766 PROGRESS: Protein Summary:
1 day, 13:39:08.414904 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   250; 0.001 FDR:     7
1 day, 13:39:08.415012 PROGRESS: =========================================================================
1 day, 13:39:08.425652 INFO: Target number of precursors reached.
1 day, 13:39:10.033982 INFO: fragments_df: keeping 5000 of 14533394 [sum(precursor_idx_mask)=9136 sum(mass_error_mask)=14533220 stop_rank=5000
1 day, 13:39:11.425952 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 13:39:11.568964 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 13:39:11.720319 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 13:39:11.867421 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 13:39:12.591343 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 13:39:12.591793 INFO: Using score_cutoff 31.0075186964035 (fac=0.99, q=1)
1 day, 13:39:12.592145 INFO: Updating optimization_manager: fwhm_rt             : 2.9160120487213135 -> 2.7996773719787598
1 day, 13:39:12.592232 INFO: Updating optimization_manager: fwhm_mobility       : 0.007399494294077158 -> 0.006609410513192415
1 day, 13:39:12.592294 INFO: Updating optimization_manager: score_cutoff        : 33.82262256088257 -> 31.0075186964035
1 day, 13:39:12.592365 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 13:39:12.700621 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 13:39:13.223124 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 13:39:13.330415 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 13:39:14.383838 INFO: === checking if optimization conditions were reached ===
1 day, 13:39:14.386290 INFO: Updating optimization_manager: ms2_error           : 16.700235515689997 -> 15.0
1 day, 13:39:14.386458 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
1 day, 13:39:14.386539 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 13:39:14.387669 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 13:39:14.387779 INFO: Updating optimization_manager: classifier_version  : 14 -> 14
1 day, 13:39:14.387863 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 13:39:14.387931 INFO: ==============================================
1 day, 13:39:14.388013 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 13:39:15.399944 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 13:39:15.508495 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 13:39:16.031538 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 13:39:16.139255 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 13:39:17.138950 INFO: Starting optimization step 0.
1 day, 13:39:17.139239 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 13:39:17.139356 INFO: Using python extraction backend
1 day, 13:39:17.139543 PROGRESS: Extracting batch of 816307 precursors
1 day, 13:39:17.139638 INFO: === Search parameters used ===
1 day, 13:39:17.139703 INFO: rt_error       : 1199.951526
1 day, 13:39:17.139757 INFO: mobility_error : 0.1
1 day, 13:39:17.139808 INFO: num_candidates : 3
1 day, 13:39:17.139858 INFO: ms1_error      : 15.0
1 day, 13:39:17.139909 INFO: ms2_error      : 15.0
1 day, 13:39:17.139959 INFO: fwhm_rt        : 2.7996773719787598
1 day, 13:39:17.140008 INFO: quant_window   : 3
1 day, 13:39:17.140056 INFO: ==============================================
1 day, 13:39:17.354497 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 13:39:17.354644 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 13:39:17.354703 INFO: FWHM in RT is 2.80 seconds, sigma is 0.47
1 day, 13:39:17.354729 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.58
1 day, 13:39:17.355534 INFO: Starting candidate selection
1 day, 14:08:28.084516 INFO: Starting candidate scoring
1 day, 14:08:52.473288 INFO: Finished candidate processing
1 day, 14:08:52.473722 INFO: Collecting candidate features
1 day, 14:08:56.559900 WARNING: intensity_correlation has 2587 NaNs ( 0.13 % out of 2044611)
1 day, 14:08:56.561839 WARNING: height_correlation has 204 NaNs ( 0.01 % out of 2044611)
1 day, 14:08:56.630875 INFO: Collecting fragment features
1 day, 14:08:57.706663 INFO: Finished candidate scoring
1 day, 14:08:59.065426 INFO: performing precursor FDR with 47 features
1 day, 14:08:59.065571 INFO: Decoy channel: -1
1 day, 14:08:59.065601 INFO: competitive: True
1 day, 14:08:59.528845 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 14:08:59.821003 WARNING: dropped 1343 target PSMs due to missing features
1 day, 14:08:59.821183 WARNING: dropped 1378 decoy PSMs due to missing features
1 day, 14:09:01.144460 INFO: Estimating optimal hyperparameters - samples: 1,633,512, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 14:09:01.148111 INFO: Using random state 368128 for train-test-split
1 day, 14:09:40.470896 INFO: Test AUC: 0.562
1 day, 14:09:40.471075 INFO: Train AUC: 0.573
1 day, 14:09:40.471114 INFO: AUC difference: 2.01%
1 day, 14:09:41.347889 INFO: Resetting torch num_threads to 80
1 day, 14:09:41.383707 PROGRESS: === Extracted 2044611 precursors and 14113607 fragments ===
1 day, 14:09:41.384842 INFO: === FDR correction performed with classifier version 14 ===
1 day, 14:09:41.446115 PROGRESS: ============================= Precursor FDR =============================
1 day, 14:09:41.446459 PROGRESS: Total precursors accumulated: 372,915
1 day, 14:09:41.446534 PROGRESS: Target precursors: 218,939 (58.71%)
1 day, 14:09:41.446595 PROGRESS: Decoy precursors: 153,976 (41.29%)
1 day, 14:09:41.446663 PROGRESS: 
1 day, 14:09:41.446718 PROGRESS: Precursor Summary:
1 day, 14:09:41.450357 PROGRESS: Channel   0:	 0.050 FDR:   532; 0.010 FDR:   373; 0.001 FDR:   303
1 day, 14:09:41.450478 PROGRESS: 
1 day, 14:09:41.450542 PROGRESS: Protein Summary:
1 day, 14:09:41.453691 PROGRESS: Channel   0:	 0.050 FDR:   417; 0.010 FDR:   279; 0.001 FDR:   224
1 day, 14:09:41.453796 PROGRESS: =========================================================================
1 day, 14:09:41.463871 INFO: Target number of precursors reached.
1 day, 14:09:43.014621 INFO: fragments_df: keeping 5000 of 14113607 [sum(precursor_idx_mask)=10173 sum(mass_error_mask)=14113434 stop_rank=5000
1 day, 14:09:44.191566 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:09:44.331372 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:09:44.449517 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:09:44.573218 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:09:45.223671 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 14:09:45.224130 INFO: Using score_cutoff 30.487988774871823 (fac=0.99, q=1)
1 day, 14:09:45.224482 INFO: Updating optimization_manager: fwhm_rt             : 2.7996773719787598 -> 2.765390634536743
1 day, 14:09:45.224573 INFO: Updating optimization_manager: fwhm_mobility       : 0.006609410513192415 -> 0.006117984186857939
1 day, 14:09:45.224634 INFO: Updating optimization_manager: score_cutoff        : 31.0075186964035 -> 30.487988774871823
1 day, 14:09:45.224698 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:09:45.332708 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:09:45.853736 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:09:45.964748 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:09:46.945853 INFO: === checking if optimization conditions were reached ===
1 day, 14:09:46.946167 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 14:09:46.948346 INFO: Updating optimization_manager: rt_error            : 1199.951526 -> 549.5177366140446
1 day, 14:09:46.948486 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 549.5177.
1 day, 14:09:46.948572 INFO: ==============================================
1 day, 14:09:46.948663 INFO: Starting optimization step 1.
1 day, 14:09:46.948740 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 14:09:46.948820 INFO: Using python extraction backend
1 day, 14:09:46.948951 PROGRESS: Extracting batch of 816307 precursors
1 day, 14:09:46.949035 INFO: === Search parameters used ===
1 day, 14:09:46.949101 INFO: rt_error       : 549.5177366140446
1 day, 14:09:46.949163 INFO: mobility_error : 0.1
1 day, 14:09:46.949226 INFO: num_candidates : 3
1 day, 14:09:46.949300 INFO: ms1_error      : 15.0
1 day, 14:09:46.949358 INFO: ms2_error      : 15.0
1 day, 14:09:46.949414 INFO: fwhm_rt        : 2.765390634536743
1 day, 14:09:46.949470 INFO: quant_window   : 3
1 day, 14:09:46.949523 INFO: ==============================================
1 day, 14:09:47.147134 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 14:09:47.147282 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 14:09:47.147333 INFO: FWHM in RT is 2.77 seconds, sigma is 0.46
1 day, 14:09:47.147361 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.32
1 day, 14:09:47.148142 INFO: Starting candidate selection
1 day, 14:24:34.620203 INFO: Starting candidate scoring
1 day, 14:24:58.858055 INFO: Finished candidate processing
1 day, 14:24:58.858319 INFO: Collecting candidate features
1 day, 14:25:02.696186 WARNING: intensity_correlation has 3758 NaNs ( 0.19 % out of 1979169)
1 day, 14:25:02.698210 WARNING: height_correlation has 338 NaNs ( 0.02 % out of 1979169)
1 day, 14:25:02.763933 INFO: Collecting fragment features
1 day, 14:25:03.676349 INFO: Finished candidate scoring
1 day, 14:25:04.894168 INFO: performing precursor FDR with 47 features
1 day, 14:25:04.894301 INFO: Decoy channel: -1
1 day, 14:25:04.894332 INFO: competitive: True
1 day, 14:25:05.382043 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 14:25:05.655349 WARNING: dropped 1957 target PSMs due to missing features
1 day, 14:25:05.655516 WARNING: dropped 1993 decoy PSMs due to missing features
1 day, 14:25:06.378997 INFO: Estimating optimal hyperparameters - samples: 1,580,175, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 14:25:06.383008 INFO: Using random state 368128 for train-test-split
1 day, 14:25:42.962048 INFO: Test AUC: 0.555
1 day, 14:25:42.962200 INFO: Train AUC: 0.566
1 day, 14:25:42.962237 INFO: AUC difference: 2.02%
1 day, 14:25:43.869192 INFO: Resetting torch num_threads to 80
1 day, 14:25:43.903805 PROGRESS: === Extracted 1979169 precursors and 12881579 fragments ===
1 day, 14:25:43.904917 INFO: === FDR correction performed with classifier version 14 ===
1 day, 14:25:43.966739 PROGRESS: ============================= Precursor FDR =============================
1 day, 14:25:43.967085 PROGRESS: Total precursors accumulated: 369,680
1 day, 14:25:43.967162 PROGRESS: Target precursors: 213,065 (57.63%)
1 day, 14:25:43.967225 PROGRESS: Decoy precursors: 156,615 (42.37%)
1 day, 14:25:43.967280 PROGRESS: 
1 day, 14:25:43.967333 PROGRESS: Precursor Summary:
1 day, 14:25:43.970784 PROGRESS: Channel   0:	 0.050 FDR:   508; 0.010 FDR:   116; 0.001 FDR:    99
1 day, 14:25:43.970895 PROGRESS: 
1 day, 14:25:43.970962 PROGRESS: Protein Summary:
1 day, 14:25:43.974048 PROGRESS: Channel   0:	 0.050 FDR:   399; 0.010 FDR:    90; 0.001 FDR:    78
1 day, 14:25:43.974156 PROGRESS: =========================================================================
1 day, 14:25:43.984311 INFO: Target number of precursors not reached yet.
1 day, 14:25:45.142674 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:25:45.249089 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:25:45.779505 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:25:45.894649 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:25:46.888231 INFO: === skipping optimization until target number of precursors are found ===
1 day, 14:25:46.888532 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 14:25:46.888661 INFO: Starting optimization step 2.
1 day, 14:25:46.888741 PROGRESS: === Extracting elution groups 409400 to 819000 ===
1 day, 14:25:46.888831 INFO: Using python extraction backend
1 day, 14:25:46.888962 PROGRESS: Extracting batch of 816689 precursors
1 day, 14:25:46.889052 INFO: === Search parameters used ===
1 day, 14:25:46.889111 INFO: rt_error       : 549.5177366140446
1 day, 14:25:46.889167 INFO: mobility_error : 0.1
1 day, 14:25:46.889218 INFO: num_candidates : 3
1 day, 14:25:46.889267 INFO: ms1_error      : 15.0
1 day, 14:25:46.889315 INFO: ms2_error      : 15.0
1 day, 14:25:46.889363 INFO: fwhm_rt        : 2.765390634536743
1 day, 14:25:46.889413 INFO: quant_window   : 3
1 day, 14:25:46.889463 INFO: ==============================================
1 day, 14:25:47.090294 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 14:25:47.090434 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 14:25:47.090493 INFO: FWHM in RT is 2.77 seconds, sigma is 0.46
1 day, 14:25:47.090524 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.32
1 day, 14:25:47.091307 INFO: Starting candidate selection
1 day, 14:40:51.168199 INFO: Starting candidate scoring
1 day, 14:41:15.508955 INFO: Finished candidate processing
1 day, 14:41:15.509200 INFO: Collecting candidate features
1 day, 14:41:19.394387 WARNING: intensity_correlation has 3907 NaNs ( 0.20 % out of 1982688)
1 day, 14:41:19.396298 WARNING: height_correlation has 359 NaNs ( 0.02 % out of 1982688)
1 day, 14:41:19.462057 INFO: Collecting fragment features
1 day, 14:41:20.468387 INFO: Finished candidate scoring
1 day, 14:41:22.972783 INFO: performing precursor FDR with 47 features
1 day, 14:41:22.973035 INFO: Decoy channel: -1
1 day, 14:41:22.973068 INFO: competitive: True
1 day, 14:41:24.580165 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 14:41:25.166399 WARNING: dropped 4043 target PSMs due to missing features
1 day, 14:41:25.166584 WARNING: dropped 4018 decoy PSMs due to missing features
1 day, 14:41:26.954596 INFO: Estimating optimal hyperparameters - samples: 3,163,036, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 14:41:26.961824 INFO: Using random state 368128 for train-test-split
1 day, 14:42:49.258113 INFO: Test AUC: 0.558
1 day, 14:42:49.258309 INFO: Train AUC: 0.563
1 day, 14:42:49.258353 INFO: AUC difference: 1.01%
1 day, 14:42:50.761515 INFO: Resetting torch num_threads to 80
1 day, 14:42:51.423784 PROGRESS: === Extracted 3961857 precursors and 25792328 fragments ===
1 day, 14:42:51.425399 INFO: === FDR correction performed with classifier version 14 ===
1 day, 14:42:51.544481 PROGRESS: ============================= Precursor FDR =============================
1 day, 14:42:51.544861 PROGRESS: Total precursors accumulated: 739,887
1 day, 14:42:51.544955 PROGRESS: Target precursors: 425,026 (57.44%)
1 day, 14:42:51.545020 PROGRESS: Decoy precursors: 314,861 (42.56%)
1 day, 14:42:51.545080 PROGRESS: 
1 day, 14:42:51.545132 PROGRESS: Precursor Summary:
1 day, 14:42:51.550930 PROGRESS: Channel   0:	 0.050 FDR: 1,030; 0.010 FDR:   702; 0.001 FDR:   434
1 day, 14:42:51.551050 PROGRESS: 
1 day, 14:42:51.551145 PROGRESS: Protein Summary:
1 day, 14:42:51.556340 PROGRESS: Channel   0:	 0.050 FDR:   641; 0.010 FDR:   433; 0.001 FDR:   268
1 day, 14:42:51.556453 PROGRESS: =========================================================================
1 day, 14:42:51.566685 INFO: Target number of precursors reached.
1 day, 14:42:54.425114 INFO: fragments_df: keeping 5000 of 25792328 [sum(precursor_idx_mask)=19280 sum(mass_error_mask)=25791906 stop_rank=5000
1 day, 14:42:55.655630 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:42:55.828808 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:42:55.998761 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:42:56.172198 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:42:56.888789 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 14:42:56.889244 INFO: Using score_cutoff 29.932785351562497 (fac=0.99, q=1)
1 day, 14:42:56.889612 INFO: Updating optimization_manager: fwhm_rt             : 2.765390634536743 -> 2.7101197242736816
1 day, 14:42:56.889701 INFO: Updating optimization_manager: fwhm_mobility       : 0.006117984186857939 -> 0.0060933781787753105
1 day, 14:42:56.889771 INFO: Updating optimization_manager: score_cutoff        : 30.487988774871823 -> 29.932785351562497
1 day, 14:42:56.889838 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:42:56.992075 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:42:57.532067 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:42:57.638077 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:42:58.631295 INFO: === checking if optimization conditions were reached ===
1 day, 14:42:58.631692 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 14:42:58.634234 INFO: Updating optimization_manager: rt_error            : 549.5177366140446 -> 184.84240834373455
1 day, 14:42:58.634377 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 184.8424.
1 day, 14:42:58.634458 INFO: ==============================================
1 day, 14:42:58.634546 INFO: Starting optimization step 3.
1 day, 14:42:58.634619 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 14:42:58.634698 INFO: Using python extraction backend
1 day, 14:42:58.634832 PROGRESS: Extracting batch of 816307 precursors
1 day, 14:42:58.634915 INFO: === Search parameters used ===
1 day, 14:42:58.634978 INFO: rt_error       : 184.84240834373455
1 day, 14:42:58.635030 INFO: mobility_error : 0.1
1 day, 14:42:58.635082 INFO: num_candidates : 3
1 day, 14:42:58.635130 INFO: ms1_error      : 15.0
1 day, 14:42:58.635178 INFO: ms2_error      : 15.0
1 day, 14:42:58.635239 INFO: fwhm_rt        : 2.7101197242736816
1 day, 14:42:58.635290 INFO: quant_window   : 3
1 day, 14:42:58.635339 INFO: ==============================================
1 day, 14:42:58.833658 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 14:42:58.833820 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 14:42:58.833889 INFO: FWHM in RT is 2.71 seconds, sigma is 0.45
1 day, 14:42:58.833916 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.30
1 day, 14:42:58.834716 INFO: Starting candidate selection
1 day, 14:48:28.570470 INFO: Starting candidate scoring
1 day, 14:48:51.160325 INFO: Finished candidate processing
1 day, 14:48:51.160487 INFO: Collecting candidate features
1 day, 14:48:54.799531 WARNING: intensity_correlation has 6716 NaNs ( 0.37 % out of 1836896)
1 day, 14:48:54.801287 WARNING: height_correlation has 817 NaNs ( 0.04 % out of 1836896)
1 day, 14:48:54.864568 INFO: Collecting fragment features
1 day, 14:48:55.751195 INFO: Finished candidate scoring
1 day, 14:48:57.108240 INFO: performing precursor FDR with 47 features
1 day, 14:48:57.108372 INFO: Decoy channel: -1
1 day, 14:48:57.108401 INFO: competitive: True
1 day, 14:48:57.540243 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 14:48:57.806162 WARNING: dropped 3561 target PSMs due to missing features
1 day, 14:48:57.806324 WARNING: dropped 3554 decoy PSMs due to missing features
1 day, 14:48:58.465729 INFO: Estimating optimal hyperparameters - samples: 1,463,824, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 14:48:58.470058 INFO: Using random state 368128 for train-test-split
1 day, 14:49:34.845484 INFO: Test AUC: 0.549
1 day, 14:49:34.845700 INFO: Train AUC: 0.561
1 day, 14:49:34.845741 INFO: AUC difference: 2.22%
1 day, 14:49:35.698847 INFO: Resetting torch num_threads to 80
1 day, 14:49:35.731481 PROGRESS: === Extracted 1836896 precursors and 10550388 fragments ===
1 day, 14:49:35.732593 INFO: === FDR correction performed with classifier version 14 ===
1 day, 14:49:35.797382 PROGRESS: ============================= Precursor FDR =============================
1 day, 14:49:35.797723 PROGRESS: Total precursors accumulated: 363,022
1 day, 14:49:35.797805 PROGRESS: Target precursors: 205,799 (56.69%)
1 day, 14:49:35.797994 PROGRESS: Decoy precursors: 157,223 (43.31%)
1 day, 14:49:35.798071 PROGRESS: 
1 day, 14:49:35.798130 PROGRESS: Precursor Summary:
1 day, 14:49:35.801620 PROGRESS: Channel   0:	 0.050 FDR:   622; 0.010 FDR:   420; 0.001 FDR:   305
1 day, 14:49:35.801735 PROGRESS: 
1 day, 14:49:35.801808 PROGRESS: Protein Summary:
1 day, 14:49:35.804951 PROGRESS: Channel   0:	 0.050 FDR:   467; 0.010 FDR:   310; 0.001 FDR:   224
1 day, 14:49:35.805068 PROGRESS: =========================================================================
1 day, 14:49:35.832027 INFO: Target number of precursors reached.
1 day, 14:49:36.974359 INFO: fragments_df: keeping 5000 of 10550388 [sum(precursor_idx_mask)=11107 sum(mass_error_mask)=10550171 stop_rank=5000
1 day, 14:49:37.762888 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:49:37.891164 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:49:38.024636 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:49:38.155048 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:49:38.807469 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 14:49:38.807917 INFO: Using score_cutoff 28.091640004348758 (fac=0.99, q=1)
1 day, 14:49:38.808270 INFO: Updating optimization_manager: fwhm_rt             : 2.7101197242736816 -> 2.6747164726257324
1 day, 14:49:38.808357 INFO: Updating optimization_manager: fwhm_mobility       : 0.0060933781787753105 -> 0.005683623254299164
1 day, 14:49:38.808420 INFO: Updating optimization_manager: score_cutoff        : 29.932785351562497 -> 28.091640004348758
1 day, 14:49:38.808484 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:49:38.862153 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:49:39.127709 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:49:39.189809 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:49:39.703671 INFO: === checking if optimization conditions were reached ===
1 day, 14:49:39.703971 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 14:49:39.706405 INFO: Updating optimization_manager: rt_error            : 184.84240834373455 -> 149.81376151293014
1 day, 14:49:39.706549 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 149.8138.
1 day, 14:49:39.706633 INFO: ==============================================
1 day, 14:49:39.706715 INFO: Starting optimization step 4.
1 day, 14:49:39.706781 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 14:49:39.706848 INFO: Using python extraction backend
1 day, 14:49:39.706973 PROGRESS: Extracting batch of 407917 precursors
1 day, 14:49:39.707046 INFO: === Search parameters used ===
1 day, 14:49:39.707100 INFO: rt_error       : 149.81376151293014
1 day, 14:49:39.707149 INFO: mobility_error : 0.1
1 day, 14:49:39.707195 INFO: num_candidates : 3
1 day, 14:49:39.707240 INFO: ms1_error      : 15.0
1 day, 14:49:39.707285 INFO: ms2_error      : 15.0
1 day, 14:49:39.707328 INFO: fwhm_rt        : 2.6747164726257324
1 day, 14:49:39.707371 INFO: quant_window   : 3
1 day, 14:49:39.707414 INFO: ==============================================
1 day, 14:49:39.815216 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 14:49:39.815357 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 14:49:39.815407 INFO: FWHM in RT is 2.67 seconds, sigma is 0.45
1 day, 14:49:39.815433 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.08
1 day, 14:49:39.816166 INFO: Starting candidate selection
1 day, 14:51:43.642106 INFO: Starting candidate scoring
1 day, 14:51:54.926073 INFO: Finished candidate processing
1 day, 14:51:54.926372 INFO: Collecting candidate features
1 day, 14:51:56.628719 WARNING: intensity_correlation has 3536 NaNs ( 0.39 % out of 906890)
1 day, 14:51:56.629722 WARNING: height_correlation has 450 NaNs ( 0.05 % out of 906890)
1 day, 14:51:56.661923 INFO: Collecting fragment features
1 day, 14:51:57.131476 INFO: Finished candidate scoring
1 day, 14:51:57.757762 INFO: performing precursor FDR with 47 features
1 day, 14:51:57.757903 INFO: Decoy channel: -1
1 day, 14:51:57.757932 INFO: competitive: True
1 day, 14:51:57.978391 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 14:51:58.124888 WARNING: dropped 1899 target PSMs due to missing features
1 day, 14:51:58.125041 WARNING: dropped 1878 decoy PSMs due to missing features
1 day, 14:51:58.452908 INFO: Estimating optimal hyperparameters - samples: 722,490, batch_size: 2,959, learning_rate: 8.50e-04
1 day, 14:51:58.454465 INFO: Using random state 368128 for train-test-split
1 day, 14:52:19.230147 INFO: Test AUC: 0.546
1 day, 14:52:19.230348 INFO: Train AUC: 0.564
1 day, 14:52:19.230386 INFO: AUC difference: 3.25%
1 day, 14:52:19.768921 INFO: Resetting torch num_threads to 80
1 day, 14:52:19.786476 PROGRESS: === Extracted 906890 precursors and 5126731 fragments ===
1 day, 14:52:19.787355 INFO: === FDR correction performed with classifier version 14 ===
1 day, 14:52:19.821243 PROGRESS: ============================= Precursor FDR =============================
1 day, 14:52:19.821557 PROGRESS: Total precursors accumulated: 180,454
1 day, 14:52:19.821630 PROGRESS: Target precursors: 102,853 (57.00%)
1 day, 14:52:19.821691 PROGRESS: Decoy precursors: 77,601 (43.00%)
1 day, 14:52:19.821756 PROGRESS: 
1 day, 14:52:19.821809 PROGRESS: Precursor Summary:
1 day, 14:52:19.824121 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   240; 0.001 FDR:   193
1 day, 14:52:19.824230 PROGRESS: 
1 day, 14:52:19.824299 PROGRESS: Protein Summary:
1 day, 14:52:19.826487 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   203; 0.001 FDR:   162
1 day, 14:52:19.826590 PROGRESS: =========================================================================
1 day, 14:52:19.836718 INFO: Target number of precursors reached.
1 day, 14:52:20.399685 INFO: fragments_df: keeping 3558 of 5126731 [sum(precursor_idx_mask)=6079 sum(mass_error_mask)=5126595 stop_rank=3558
1 day, 14:52:21.165025 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:52:21.300615 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:52:21.423790 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:52:21.534225 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:52:21.963973 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 14:52:21.964436 INFO: Using score_cutoff 8.856752552747727 (fac=0.99, q=1)
1 day, 14:52:21.964792 INFO: Updating optimization_manager: fwhm_rt             : 2.6747164726257324 -> 2.68251895904541
1 day, 14:52:21.964888 INFO: Updating optimization_manager: fwhm_mobility       : 0.005683623254299164 -> 0.0052765896543860435
1 day, 14:52:21.964959 INFO: Updating optimization_manager: score_cutoff        : 28.091640004348758 -> 8.856752552747727
1 day, 14:52:21.965033 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:52:22.014644 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:52:22.271316 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:52:22.322929 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:52:22.825689 INFO: === checking if optimization conditions were reached ===
1 day, 14:52:22.826012 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 14:52:22.828341 INFO: Updating optimization_manager: rt_error            : 149.81376151293014 -> 120.09340215860688
1 day, 14:52:22.828484 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 120.0934.
1 day, 14:52:22.828569 INFO: ==============================================
1 day, 14:52:22.828655 INFO: Starting optimization step 5.
1 day, 14:52:22.828731 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 14:52:22.828809 INFO: Using python extraction backend
1 day, 14:52:22.828936 PROGRESS: Extracting batch of 407917 precursors
1 day, 14:52:22.829021 INFO: === Search parameters used ===
1 day, 14:52:22.829088 INFO: rt_error       : 120.09340215860688
1 day, 14:52:22.829150 INFO: mobility_error : 0.1
1 day, 14:52:22.829209 INFO: num_candidates : 3
1 day, 14:52:22.829271 INFO: ms1_error      : 15.0
1 day, 14:52:22.829327 INFO: ms2_error      : 15.0
1 day, 14:52:22.829386 INFO: fwhm_rt        : 2.68251895904541
1 day, 14:52:22.829441 INFO: quant_window   : 3
1 day, 14:52:22.829499 INFO: ==============================================
1 day, 14:52:22.936020 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 14:52:22.936169 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 14:52:22.936227 INFO: FWHM in RT is 2.68 seconds, sigma is 0.45
1 day, 14:52:22.936260 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.86
1 day, 14:52:22.937011 INFO: Starting candidate selection
1 day, 14:54:02.581404 INFO: Starting candidate scoring
1 day, 14:54:13.697453 INFO: Finished candidate processing
1 day, 14:54:13.697721 INFO: Collecting candidate features
1 day, 14:54:15.392169 WARNING: intensity_correlation has 4220 NaNs ( 0.48 % out of 876362)
1 day, 14:54:15.393149 WARNING: height_correlation has 586 NaNs ( 0.07 % out of 876362)
1 day, 14:54:15.424009 INFO: Collecting fragment features
1 day, 14:54:15.876894 INFO: Finished candidate scoring
1 day, 14:54:16.503106 INFO: performing precursor FDR with 47 features
1 day, 14:54:16.503309 INFO: Decoy channel: -1
1 day, 14:54:16.503342 INFO: competitive: True
1 day, 14:54:16.722440 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 14:54:16.859388 WARNING: dropped 2250 target PSMs due to missing features
1 day, 14:54:16.859559 WARNING: dropped 2267 decoy PSMs due to missing features
1 day, 14:54:17.153620 INFO: Estimating optimal hyperparameters - samples: 697,476, batch_size: 2,856, learning_rate: 8.35e-04
1 day, 14:54:17.155102 INFO: Using random state 368128 for train-test-split
1 day, 14:54:34.700891 INFO: Test AUC: 0.542
1 day, 14:54:34.701050 INFO: Train AUC: 0.565
1 day, 14:54:34.701090 INFO: AUC difference: 4.06%
1 day, 14:54:35.229178 INFO: Resetting torch num_threads to 80
1 day, 14:54:35.246318 PROGRESS: === Extracted 876362 precursors and 4736572 fragments ===
1 day, 14:54:35.247193 INFO: === FDR correction performed with classifier version 14 ===
1 day, 14:54:35.279289 PROGRESS: ============================= Precursor FDR =============================
1 day, 14:54:35.279603 PROGRESS: Total precursors accumulated: 179,160
1 day, 14:54:35.279690 PROGRESS: Target precursors: 101,701 (56.77%)
1 day, 14:54:35.279752 PROGRESS: Decoy precursors: 77,459 (43.23%)
1 day, 14:54:35.279805 PROGRESS: 
1 day, 14:54:35.279860 PROGRESS: Precursor Summary:
1 day, 14:54:35.282180 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:    12; 0.001 FDR:    12
1 day, 14:54:35.282290 PROGRESS: 
1 day, 14:54:35.282353 PROGRESS: Protein Summary:
1 day, 14:54:35.284420 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:    12; 0.001 FDR:    12
1 day, 14:54:35.284523 PROGRESS: =========================================================================
1 day, 14:54:35.291388 INFO: Target number of precursors not reached yet.
1 day, 14:54:36.034155 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:54:36.085155 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:54:36.346956 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:54:36.398087 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:54:36.900067 INFO: === skipping optimization until target number of precursors are found ===
1 day, 14:54:36.900383 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 14:54:36.900506 INFO: Starting optimization step 6.
1 day, 14:54:36.900589 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 14:54:36.900664 INFO: Using python extraction backend
1 day, 14:54:36.900789 PROGRESS: Extracting batch of 408390 precursors
1 day, 14:54:36.900894 INFO: === Search parameters used ===
1 day, 14:54:36.900957 INFO: rt_error       : 120.09340215860688
1 day, 14:54:36.901011 INFO: mobility_error : 0.1
1 day, 14:54:36.901070 INFO: num_candidates : 3
1 day, 14:54:36.901122 INFO: ms1_error      : 15.0
1 day, 14:54:36.901171 INFO: ms2_error      : 15.0
1 day, 14:54:36.901219 INFO: fwhm_rt        : 2.68251895904541
1 day, 14:54:36.901265 INFO: quant_window   : 3
1 day, 14:54:36.901314 INFO: ==============================================
1 day, 14:54:37.007345 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 14:54:37.007493 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 14:54:37.007540 INFO: FWHM in RT is 2.68 seconds, sigma is 0.45
1 day, 14:54:37.007565 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.86
1 day, 14:54:37.008326 INFO: Starting candidate selection
1 day, 14:56:15.041738 INFO: Starting candidate scoring
1 day, 14:56:25.996486 INFO: Finished candidate processing
1 day, 14:56:25.996954 INFO: Collecting candidate features
1 day, 14:56:27.667370 WARNING: intensity_correlation has 4241 NaNs ( 0.48 % out of 875347)
1 day, 14:56:27.668351 WARNING: height_correlation has 576 NaNs ( 0.07 % out of 875347)
1 day, 14:56:27.699375 INFO: Collecting fragment features
1 day, 14:56:28.197927 INFO: Finished candidate scoring
1 day, 14:56:29.238781 INFO: performing precursor FDR with 47 features
1 day, 14:56:29.238947 INFO: Decoy channel: -1
1 day, 14:56:29.238981 INFO: competitive: True
1 day, 14:56:29.887784 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 14:56:30.178801 WARNING: dropped 4510 target PSMs due to missing features
1 day, 14:56:30.178974 WARNING: dropped 4515 decoy PSMs due to missing features
1 day, 14:56:30.877430 INFO: Estimating optimal hyperparameters - samples: 1,394,147, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 14:56:30.880185 INFO: Using random state 368128 for train-test-split
1 day, 14:57:05.751834 INFO: Test AUC: 0.550
1 day, 14:57:05.751994 INFO: Train AUC: 0.560
1 day, 14:57:05.752033 INFO: AUC difference: 1.79%
1 day, 14:57:06.581019 INFO: Resetting torch num_threads to 80
1 day, 14:57:06.838526 PROGRESS: === Extracted 1751709 precursors and 9463978 fragments ===
1 day, 14:57:06.839674 INFO: === FDR correction performed with classifier version 14 ===
1 day, 14:57:06.900888 PROGRESS: ============================= Precursor FDR =============================
1 day, 14:57:06.901233 PROGRESS: Total precursors accumulated: 358,130
1 day, 14:57:06.901308 PROGRESS: Target precursors: 202,268 (56.48%)
1 day, 14:57:06.901374 PROGRESS: Decoy precursors: 155,862 (43.52%)
1 day, 14:57:06.901431 PROGRESS: 
1 day, 14:57:06.901488 PROGRESS: Precursor Summary:
1 day, 14:57:06.904916 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   394; 0.001 FDR:   173
1 day, 14:57:06.905034 PROGRESS: 
1 day, 14:57:06.905101 PROGRESS: Protein Summary:
1 day, 14:57:06.908223 PROGRESS: Channel   0:	 0.050 FDR:   453; 0.010 FDR:   294; 0.001 FDR:   135
1 day, 14:57:06.908338 PROGRESS: =========================================================================
1 day, 14:57:06.915529 INFO: Target number of precursors reached.
1 day, 14:57:08.002488 INFO: fragments_df: keeping 5000 of 9463978 [sum(precursor_idx_mask)=10503 sum(mass_error_mask)=9463765 stop_rank=5000
1 day, 14:57:09.171417 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:57:09.314972 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:57:09.461098 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:57:09.610785 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:57:10.326052 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 14:57:10.326506 INFO: Using score_cutoff 25.555728194618226 (fac=0.99, q=1)
1 day, 14:57:10.326859 INFO: Updating optimization_manager: fwhm_rt             : 2.68251895904541 -> 2.6713263988494873
1 day, 14:57:10.326948 INFO: Updating optimization_manager: fwhm_mobility       : 0.0052765896543860435 -> 0.005577614530920982
1 day, 14:57:10.327012 INFO: Updating optimization_manager: score_cutoff        : 8.856752552747727 -> 25.555728194618226
1 day, 14:57:10.327072 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 14:57:10.436021 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 14:57:10.972255 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 14:57:11.085917 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 14:57:12.109931 INFO: === checking if optimization conditions were reached ===
1 day, 14:57:12.110317 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 14:57:12.112671 INFO: Updating optimization_manager: rt_error            : 120.09340215860688 -> 109.08048799783728
1 day, 14:57:12.112836 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 109.0805.
1 day, 14:57:12.112919 INFO: ==============================================
1 day, 14:57:12.112997 INFO: Starting optimization step 7.
1 day, 14:57:12.113066 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 14:57:12.113136 INFO: Using python extraction backend
1 day, 14:57:12.113245 PROGRESS: Extracting batch of 816307 precursors
1 day, 14:57:12.113317 INFO: === Search parameters used ===
1 day, 14:57:12.113374 INFO: rt_error       : 109.08048799783728
1 day, 14:57:12.113429 INFO: mobility_error : 0.1
1 day, 14:57:12.113479 INFO: num_candidates : 3
1 day, 14:57:12.113528 INFO: ms1_error      : 15.0
1 day, 14:57:12.113576 INFO: ms2_error      : 15.0
1 day, 14:57:12.113625 INFO: fwhm_rt        : 2.6713263988494873
1 day, 14:57:12.113673 INFO: quant_window   : 3
1 day, 14:57:12.113721 INFO: ==============================================
1 day, 14:57:12.311234 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 14:57:12.311403 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 14:57:12.311450 INFO: FWHM in RT is 2.67 seconds, sigma is 0.45
1 day, 14:57:12.311477 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.02
1 day, 14:57:12.312264 INFO: Starting candidate selection
1 day, 15:00:20.571724 INFO: Starting candidate scoring
1 day, 15:00:43.070714 INFO: Finished candidate processing
1 day, 15:00:43.071125 INFO: Collecting candidate features
1 day, 15:00:47.152219 WARNING: intensity_correlation has 8622 NaNs ( 0.49 % out of 1748173)
1 day, 15:00:47.154118 WARNING: height_correlation has 1147 NaNs ( 0.07 % out of 1748173)
1 day, 15:00:47.217178 INFO: Collecting fragment features
1 day, 15:00:48.179126 INFO: Finished candidate scoring
1 day, 15:00:49.620100 INFO: performing precursor FDR with 47 features
1 day, 15:00:49.620248 INFO: Decoy channel: -1
1 day, 15:00:49.620277 INFO: competitive: True
1 day, 15:00:50.071156 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:00:50.350291 WARNING: dropped 4550 target PSMs due to missing features
1 day, 15:00:50.350459 WARNING: dropped 4635 decoy PSMs due to missing features
1 day, 15:00:51.394735 INFO: Estimating optimal hyperparameters - samples: 1,391,190, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 15:00:51.398848 INFO: Using random state 368128 for train-test-split
1 day, 15:01:30.833601 INFO: Test AUC: 0.545
1 day, 15:01:30.833782 INFO: Train AUC: 0.558
1 day, 15:01:30.833820 INFO: AUC difference: 2.30%
1 day, 15:01:31.611265 INFO: Resetting torch num_threads to 80
1 day, 15:01:31.644758 PROGRESS: === Extracted 1748173 precursors and 9427145 fragments ===
1 day, 15:01:31.645819 INFO: === FDR correction performed with classifier version 14 ===
1 day, 15:01:31.713832 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:01:31.714188 PROGRESS: Total precursors accumulated: 356,555
1 day, 15:01:31.714272 PROGRESS: Target precursors: 203,324 (57.02%)
1 day, 15:01:31.714337 PROGRESS: Decoy precursors: 153,231 (42.98%)
1 day, 15:01:31.714407 PROGRESS: 
1 day, 15:01:31.714462 PROGRESS: Precursor Summary:
1 day, 15:01:31.717851 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   428; 0.001 FDR:   187
1 day, 15:01:31.717980 PROGRESS: 
1 day, 15:01:31.718045 PROGRESS: Protein Summary:
1 day, 15:01:31.721209 PROGRESS: Channel   0:	 0.050 FDR:   451; 0.010 FDR:   315; 0.001 FDR:   138
1 day, 15:01:31.721315 PROGRESS: =========================================================================
1 day, 15:01:31.731975 INFO: Target number of precursors reached.
1 day, 15:01:32.736154 INFO: fragments_df: keeping 5000 of 9427145 [sum(precursor_idx_mask)=11055 sum(mass_error_mask)=9426922 stop_rank=5000
1 day, 15:01:33.534198 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:01:33.678400 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:01:33.828178 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:01:33.983778 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:01:34.697459 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 15:01:34.697927 INFO: Using score_cutoff 24.548505916786194 (fac=0.99, q=1)
1 day, 15:01:34.698268 INFO: Updating optimization_manager: fwhm_rt             : 2.6713263988494873 -> 2.7154486179351807
1 day, 15:01:34.698359 INFO: Updating optimization_manager: fwhm_mobility       : 0.005577614530920982 -> 0.005830679088830948
1 day, 15:01:34.698422 INFO: Updating optimization_manager: score_cutoff        : 25.555728194618226 -> 24.548505916786194
1 day, 15:01:34.698490 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:01:34.752281 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:01:35.009430 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:01:35.064130 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:01:35.572564 INFO: === checking if optimization conditions were reached ===
1 day, 15:01:35.572892 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 15:01:35.575275 INFO: Updating optimization_manager: rt_error            : 109.08048799783728 -> 114.36922539334796
1 day, 15:01:35.575422 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 114.3692.
1 day, 15:01:35.575507 INFO: ==============================================
1 day, 15:01:35.575594 INFO: Starting optimization step 8.
1 day, 15:01:35.575675 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 15:01:35.575751 INFO: Using python extraction backend
1 day, 15:01:35.575870 PROGRESS: Extracting batch of 407917 precursors
1 day, 15:01:35.575951 INFO: === Search parameters used ===
1 day, 15:01:35.576014 INFO: rt_error       : 114.36922539334796
1 day, 15:01:35.576073 INFO: mobility_error : 0.1
1 day, 15:01:35.576128 INFO: num_candidates : 3
1 day, 15:01:35.576182 INFO: ms1_error      : 15.0
1 day, 15:01:35.576235 INFO: ms2_error      : 15.0
1 day, 15:01:35.576287 INFO: fwhm_rt        : 2.7154486179351807
1 day, 15:01:35.576339 INFO: quant_window   : 3
1 day, 15:01:35.576400 INFO: ==============================================
1 day, 15:01:35.685683 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:01:35.685833 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:01:35.685899 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
1 day, 15:01:35.685932 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.16
1 day, 15:01:35.686642 INFO: Starting candidate selection
1 day, 15:03:17.242622 INFO: Starting candidate scoring
1 day, 15:03:28.236361 INFO: Finished candidate processing
1 day, 15:03:28.236627 INFO: Collecting candidate features
1 day, 15:03:30.460645 WARNING: intensity_correlation has 4027 NaNs ( 0.45 % out of 886056)
1 day, 15:03:30.461629 WARNING: height_correlation has 516 NaNs ( 0.06 % out of 886056)
1 day, 15:03:30.494311 INFO: Collecting fragment features
1 day, 15:03:30.974487 INFO: Finished candidate scoring
1 day, 15:03:31.674238 INFO: performing precursor FDR with 47 features
1 day, 15:03:31.674381 INFO: Decoy channel: -1
1 day, 15:03:31.674409 INFO: competitive: True
1 day, 15:03:31.910577 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:03:32.055496 WARNING: dropped 2157 target PSMs due to missing features
1 day, 15:03:32.055657 WARNING: dropped 2133 decoy PSMs due to missing features
1 day, 15:03:32.525505 INFO: Estimating optimal hyperparameters - samples: 705,412, batch_size: 2,889, learning_rate: 8.40e-04
1 day, 15:03:32.526938 INFO: Using random state 368128 for train-test-split
1 day, 15:03:53.853586 INFO: Test AUC: 0.543
1 day, 15:03:53.853736 INFO: Train AUC: 0.564
1 day, 15:03:53.853773 INFO: AUC difference: 3.78%
1 day, 15:03:54.384041 INFO: Resetting torch num_threads to 80
1 day, 15:03:54.402086 PROGRESS: === Extracted 886056 precursors and 4855073 fragments ===
1 day, 15:03:54.402927 INFO: === FDR correction performed with classifier version 14 ===
1 day, 15:03:54.437698 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:03:54.438076 PROGRESS: Total precursors accumulated: 178,982
1 day, 15:03:54.438155 PROGRESS: Target precursors: 101,676 (56.81%)
1 day, 15:03:54.438217 PROGRESS: Decoy precursors: 77,306 (43.19%)
1 day, 15:03:54.438272 PROGRESS: 
1 day, 15:03:54.438326 PROGRESS: Precursor Summary:
1 day, 15:03:54.440628 PROGRESS: Channel   0:	 0.050 FDR:   388; 0.010 FDR:   214; 0.001 FDR:   141
1 day, 15:03:54.440735 PROGRESS: 
1 day, 15:03:54.440800 PROGRESS: Protein Summary:
1 day, 15:03:54.442948 PROGRESS: Channel   0:	 0.050 FDR:   335; 0.010 FDR:   176; 0.001 FDR:   119
1 day, 15:03:54.443056 PROGRESS: =========================================================================
1 day, 15:03:54.459601 INFO: Target number of precursors reached.
1 day, 15:03:55.007688 INFO: fragments_df: keeping 3235 of 4855073 [sum(precursor_idx_mask)=5419 sum(mass_error_mask)=4854948 stop_rank=3235
1 day, 15:03:55.779489 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:03:55.909014 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:03:56.040916 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:03:56.174796 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:03:56.628171 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 15:03:56.628630 INFO: Using score_cutoff 7.098755003499984 (fac=0.99, q=1)
1 day, 15:03:56.628949 INFO: Updating optimization_manager: fwhm_rt             : 2.7154486179351807 -> 2.765960454940796
1 day, 15:03:56.629034 INFO: Updating optimization_manager: fwhm_mobility       : 0.005830679088830948 -> 0.005536109674721956
1 day, 15:03:56.629094 INFO: Updating optimization_manager: score_cutoff        : 24.548505916786194 -> 7.098755003499984
1 day, 15:03:56.629152 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:03:56.679718 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:03:56.936339 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:03:56.993176 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:03:57.484283 INFO: === checking if optimization conditions were reached ===
1 day, 15:03:57.484583 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 15:03:57.485919 INFO: Updating optimization_manager: rt_error            : 114.36922539334796 -> 109.08048799783728
1 day, 15:03:57.486090 INFO: Updating optimization_manager: classifier_version  : 14 -> 22
1 day, 15:03:57.486206 INFO: Updating optimization_manager: score_cutoff        : 7.098755003499984 -> 24.548505916786194
1 day, 15:03:57.486313 INFO: Updating optimization_manager: fwhm_rt             : 2.765960454940796 -> 2.7154486179351807
1 day, 15:03:57.486414 INFO: Updating optimization_manager: fwhm_mobility       : 0.005536109674721956 -> 0.005830679088830948
1 day, 15:03:57.486517 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 109.0805 found after 7 searches.
1 day, 15:03:57.486597 INFO: ==============================================
1 day, 15:03:57.486694 PROGRESS: Optimization finished for rt_error.
1 day, 15:03:58.089045 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:03:58.140373 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:03:58.397691 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:03:58.453803 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:03:58.946320 INFO: Starting optimization step 0.
1 day, 15:03:58.946621 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 15:03:58.946721 INFO: Using python extraction backend
1 day, 15:03:58.946845 PROGRESS: Extracting batch of 407917 precursors
1 day, 15:03:58.946931 INFO: === Search parameters used ===
1 day, 15:03:58.946993 INFO: rt_error       : 109.08048799783728
1 day, 15:03:58.947048 INFO: mobility_error : 0.1
1 day, 15:03:58.947109 INFO: num_candidates : 3
1 day, 15:03:58.947163 INFO: ms1_error      : 15.0
1 day, 15:03:58.947213 INFO: ms2_error      : 15.0
1 day, 15:03:58.947261 INFO: fwhm_rt        : 2.7154486179351807
1 day, 15:03:58.947312 INFO: quant_window   : 3
1 day, 15:03:58.947362 INFO: ==============================================
1 day, 15:03:59.066069 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:03:59.066218 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:03:59.066267 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
1 day, 15:03:59.066293 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.16
1 day, 15:03:59.067033 INFO: Starting candidate selection
1 day, 15:05:34.333080 INFO: Starting candidate scoring
1 day, 15:05:45.395530 INFO: Finished candidate processing
1 day, 15:05:45.395757 INFO: Collecting candidate features
1 day, 15:05:47.201502 WARNING: intensity_correlation has 4332 NaNs ( 0.50 % out of 866857)
1 day, 15:05:47.202506 WARNING: height_correlation has 594 NaNs ( 0.07 % out of 866857)
1 day, 15:05:47.234841 INFO: Collecting fragment features
1 day, 15:05:47.661998 INFO: Finished candidate scoring
1 day, 15:05:48.290694 INFO: performing precursor FDR with 47 features
1 day, 15:05:48.290832 INFO: Decoy channel: -1
1 day, 15:05:48.290859 INFO: competitive: True
1 day, 15:05:48.520313 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:05:48.654859 WARNING: dropped 2299 target PSMs due to missing features
1 day, 15:05:48.655020 WARNING: dropped 2337 decoy PSMs due to missing features
1 day, 15:05:48.944128 INFO: Estimating optimal hyperparameters - samples: 689,776, batch_size: 2,825, learning_rate: 8.30e-04
1 day, 15:05:48.945753 INFO: Using random state 490638 for train-test-split
1 day, 15:06:07.924552 INFO: Test AUC: 0.551
1 day, 15:06:07.924704 INFO: Train AUC: 0.571
1 day, 15:06:07.924742 INFO: AUC difference: 3.47%
1 day, 15:06:08.447641 INFO: Resetting torch num_threads to 80
1 day, 15:06:08.465554 PROGRESS: === Extracted 866857 precursors and 4655141 fragments ===
1 day, 15:06:08.466375 INFO: === FDR correction performed with classifier version 22 ===
1 day, 15:06:08.499069 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:06:08.499395 PROGRESS: Total precursors accumulated: 178,041
1 day, 15:06:08.499470 PROGRESS: Target precursors: 101,957 (57.27%)
1 day, 15:06:08.499529 PROGRESS: Decoy precursors: 76,084 (42.73%)
1 day, 15:06:08.499583 PROGRESS: 
1 day, 15:06:08.499636 PROGRESS: Precursor Summary:
1 day, 15:06:08.501927 PROGRESS: Channel   0:	 0.050 FDR:   509; 0.010 FDR:   281; 0.001 FDR:   224
1 day, 15:06:08.502037 PROGRESS: 
1 day, 15:06:08.502103 PROGRESS: Protein Summary:
1 day, 15:06:08.504278 PROGRESS: Channel   0:	 0.050 FDR:   443; 0.010 FDR:   237; 0.001 FDR:   183
1 day, 15:06:08.504379 PROGRESS: =========================================================================
1 day, 15:06:08.509737 INFO: Target number of precursors reached.
1 day, 15:06:09.005223 INFO: fragments_df: keeping 3976 of 4655141 [sum(precursor_idx_mask)=7126 sum(mass_error_mask)=4655002 stop_rank=3976
1 day, 15:06:09.628810 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:06:09.764688 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:06:09.907448 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:06:10.052118 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:06:10.605358 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 15:06:10.605819 INFO: Using score_cutoff 23.59278681564331 (fac=0.99, q=1)
1 day, 15:06:10.606158 INFO: Updating optimization_manager: fwhm_rt             : 2.7154486179351807 -> 2.624377727508545
1 day, 15:06:10.606251 INFO: Updating optimization_manager: fwhm_mobility       : 0.005830679088830948 -> 0.004825434647500515
1 day, 15:06:10.606320 INFO: Updating optimization_manager: score_cutoff        : 24.548505916786194 -> 23.59278681564331
1 day, 15:06:10.606387 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:06:10.659392 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:06:10.922348 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:06:10.986049 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:06:11.491861 INFO: === checking if optimization conditions were reached ===
1 day, 15:06:11.492175 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 15:06:11.494072 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06914107222034659
1 day, 15:06:11.494208 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0691.
1 day, 15:06:11.494290 INFO: ==============================================
1 day, 15:06:11.494373 INFO: Starting optimization step 1.
1 day, 15:06:11.494458 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 15:06:11.494531 INFO: Using python extraction backend
1 day, 15:06:11.494644 PROGRESS: Extracting batch of 407917 precursors
1 day, 15:06:11.494720 INFO: === Search parameters used ===
1 day, 15:06:11.494785 INFO: rt_error       : 109.08048799783728
1 day, 15:06:11.494838 INFO: mobility_error : 0.06914107222034659
1 day, 15:06:11.494889 INFO: num_candidates : 3
1 day, 15:06:11.494938 INFO: ms1_error      : 15.0
1 day, 15:06:11.494993 INFO: ms2_error      : 15.0
1 day, 15:06:11.495042 INFO: fwhm_rt        : 2.624377727508545
1 day, 15:06:11.495089 INFO: quant_window   : 3
1 day, 15:06:11.495134 INFO: ==============================================
1 day, 15:06:11.604553 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:06:11.604702 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:06:11.604751 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
1 day, 15:06:11.604776 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.62
1 day, 15:06:11.605502 INFO: Starting candidate selection
1 day, 15:07:18.003788 INFO: Starting candidate scoring
1 day, 15:07:28.408585 INFO: Finished candidate processing
1 day, 15:07:28.408861 INFO: Collecting candidate features
1 day, 15:07:29.972926 WARNING: intensity_correlation has 4456 NaNs ( 0.53 % out of 835476)
1 day, 15:07:29.973939 WARNING: height_correlation has 612 NaNs ( 0.07 % out of 835476)
1 day, 15:07:30.005405 INFO: Collecting fragment features
1 day, 15:07:30.425209 INFO: Finished candidate scoring
1 day, 15:07:31.050876 INFO: performing precursor FDR with 47 features
1 day, 15:07:31.051016 INFO: Decoy channel: -1
1 day, 15:07:31.051045 INFO: competitive: True
1 day, 15:07:31.272325 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:07:31.401599 WARNING: dropped 2419 target PSMs due to missing features
1 day, 15:07:31.401764 WARNING: dropped 2343 decoy PSMs due to missing features
1 day, 15:07:31.711591 INFO: Estimating optimal hyperparameters - samples: 664,571, batch_size: 2,722, learning_rate: 8.15e-04
1 day, 15:07:31.712996 INFO: Using random state 490638 for train-test-split
1 day, 15:07:50.501101 INFO: Test AUC: 0.551
1 day, 15:07:50.501268 INFO: Train AUC: 0.571
1 day, 15:07:50.501306 INFO: AUC difference: 3.62%
1 day, 15:07:51.003371 INFO: Resetting torch num_threads to 80
1 day, 15:07:51.020701 PROGRESS: === Extracted 835476 precursors and 4420226 fragments ===
1 day, 15:07:51.021488 INFO: === FDR correction performed with classifier version 22 ===
1 day, 15:07:51.054329 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:07:51.054665 PROGRESS: Total precursors accumulated: 172,963
1 day, 15:07:51.054739 PROGRESS: Target precursors: 99,289 (57.40%)
1 day, 15:07:51.054802 PROGRESS: Decoy precursors: 73,674 (42.60%)
1 day, 15:07:51.054856 PROGRESS: 
1 day, 15:07:51.054912 PROGRESS: Precursor Summary:
1 day, 15:07:51.057153 PROGRESS: Channel   0:	 0.050 FDR:   362; 0.010 FDR:     4; 0.001 FDR:     4
1 day, 15:07:51.057259 PROGRESS: 
1 day, 15:07:51.057323 PROGRESS: Protein Summary:
1 day, 15:07:51.059342 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:     4; 0.001 FDR:     4
1 day, 15:07:51.059454 PROGRESS: =========================================================================
1 day, 15:07:51.064725 INFO: Target number of precursors not reached yet.
1 day, 15:07:51.673572 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:07:51.727727 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:07:51.986328 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:07:52.050637 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:07:52.566458 INFO: === skipping optimization until target number of precursors are found ===
1 day, 15:07:52.566755 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 15:07:52.566885 INFO: Starting optimization step 2.
1 day, 15:07:52.566978 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 15:07:52.567054 INFO: Using python extraction backend
1 day, 15:07:52.567171 PROGRESS: Extracting batch of 408390 precursors
1 day, 15:07:52.567257 INFO: === Search parameters used ===
1 day, 15:07:52.567313 INFO: rt_error       : 109.08048799783728
1 day, 15:07:52.567363 INFO: mobility_error : 0.06914107222034659
1 day, 15:07:52.567411 INFO: num_candidates : 3
1 day, 15:07:52.567459 INFO: ms1_error      : 15.0
1 day, 15:07:52.567505 INFO: ms2_error      : 15.0
1 day, 15:07:52.567549 INFO: fwhm_rt        : 2.624377727508545
1 day, 15:07:52.567593 INFO: quant_window   : 3
1 day, 15:07:52.567637 INFO: ==============================================
1 day, 15:07:52.674824 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:07:52.674973 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:07:52.675019 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
1 day, 15:07:52.675044 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.62
1 day, 15:07:52.675784 INFO: Starting candidate selection
1 day, 15:08:59.164443 INFO: Starting candidate scoring
1 day, 15:09:09.132539 INFO: Finished candidate processing
1 day, 15:09:09.132768 INFO: Collecting candidate features
1 day, 15:09:10.772347 WARNING: intensity_correlation has 4590 NaNs ( 0.55 % out of 834271)
1 day, 15:09:10.773371 WARNING: height_correlation has 601 NaNs ( 0.07 % out of 834271)
1 day, 15:09:10.804756 INFO: Collecting fragment features
1 day, 15:09:11.243749 INFO: Finished candidate scoring
1 day, 15:09:12.209704 INFO: performing precursor FDR with 47 features
1 day, 15:09:12.209901 INFO: Decoy channel: -1
1 day, 15:09:12.209936 INFO: competitive: True
1 day, 15:09:12.940273 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:09:13.237487 WARNING: dropped 4847 target PSMs due to missing features
1 day, 15:09:13.237682 WARNING: dropped 4798 decoy PSMs due to missing features
1 day, 15:09:14.138113 INFO: Estimating optimal hyperparameters - samples: 1,328,081, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 15:09:14.140933 INFO: Using random state 490638 for train-test-split
1 day, 15:09:53.360760 INFO: Test AUC: 0.551
1 day, 15:09:53.360981 INFO: Train AUC: 0.565
1 day, 15:09:53.361024 INFO: AUC difference: 2.53%
1 day, 15:09:54.132271 INFO: Resetting torch num_threads to 80
1 day, 15:09:54.415100 PROGRESS: === Extracted 1669747 precursors and 8831843 fragments ===
1 day, 15:09:54.416291 INFO: === FDR correction performed with classifier version 22 ===
1 day, 15:09:54.489465 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:09:54.489833 PROGRESS: Total precursors accumulated: 345,773
1 day, 15:09:54.489935 PROGRESS: Target precursors: 196,549 (56.84%)
1 day, 15:09:54.490026 PROGRESS: Decoy precursors: 149,224 (43.16%)
1 day, 15:09:54.490091 PROGRESS: 
1 day, 15:09:54.490154 PROGRESS: Precursor Summary:
1 day, 15:09:54.493710 PROGRESS: Channel   0:	 0.050 FDR:   672; 0.010 FDR:   515; 0.001 FDR:   461
1 day, 15:09:54.493834 PROGRESS: 
1 day, 15:09:54.493928 PROGRESS: Protein Summary:
1 day, 15:09:54.497105 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   384; 0.001 FDR:   346
1 day, 15:09:54.497232 PROGRESS: =========================================================================
1 day, 15:09:54.504022 INFO: Target number of precursors reached.
1 day, 15:09:55.458232 INFO: fragments_df: keeping 5000 of 8831843 [sum(precursor_idx_mask)=13166 sum(mass_error_mask)=8831654 stop_rank=5000
1 day, 15:09:56.255233 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:09:56.391012 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:09:56.531983 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:09:56.667284 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:09:57.324408 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 15:09:57.324965 INFO: Using score_cutoff 20.778265351867674 (fac=0.99, q=1)
1 day, 15:09:57.325334 INFO: Updating optimization_manager: fwhm_rt             : 2.624377727508545 -> 2.6516294479370117
1 day, 15:09:57.325423 INFO: Updating optimization_manager: fwhm_mobility       : 0.004825434647500515 -> 0.005376193672418594
1 day, 15:09:57.325482 INFO: Updating optimization_manager: score_cutoff        : 23.59278681564331 -> 20.778265351867674
1 day, 15:09:57.325553 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:09:57.379600 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:09:57.640996 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:09:57.696114 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:09:58.191378 INFO: === checking if optimization conditions were reached ===
1 day, 15:09:58.191690 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 15:09:58.193996 INFO: Updating optimization_manager: mobility_error      : 0.06914107222034659 -> 0.06417409342808669
1 day, 15:09:58.194149 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0642.
1 day, 15:09:58.194229 INFO: ==============================================
1 day, 15:09:58.194306 INFO: Starting optimization step 3.
1 day, 15:09:58.194376 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 15:09:58.194445 INFO: Using python extraction backend
1 day, 15:09:58.194574 PROGRESS: Extracting batch of 407917 precursors
1 day, 15:09:58.194652 INFO: === Search parameters used ===
1 day, 15:09:58.194708 INFO: rt_error       : 109.08048799783728
1 day, 15:09:58.194758 INFO: mobility_error : 0.06417409342808669
1 day, 15:09:58.194806 INFO: num_candidates : 3
1 day, 15:09:58.194852 INFO: ms1_error      : 15.0
1 day, 15:09:58.194899 INFO: ms2_error      : 15.0
1 day, 15:09:58.194946 INFO: fwhm_rt        : 2.6516294479370117
1 day, 15:09:58.195004 INFO: quant_window   : 3
1 day, 15:09:58.195053 INFO: ==============================================
1 day, 15:09:58.324234 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:09:58.324395 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:09:58.324444 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
1 day, 15:09:58.324470 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.92
1 day, 15:09:58.325196 INFO: Starting candidate selection
1 day, 15:11:01.538188 INFO: Starting candidate scoring
1 day, 15:11:11.737812 INFO: Finished candidate processing
1 day, 15:11:11.737991 INFO: Collecting candidate features
1 day, 15:11:13.228939 WARNING: intensity_correlation has 4396 NaNs ( 0.53 % out of 836110)
1 day, 15:11:13.229901 WARNING: height_correlation has 583 NaNs ( 0.07 % out of 836110)
1 day, 15:11:13.260090 INFO: Collecting fragment features
1 day, 15:11:13.674620 INFO: Finished candidate scoring
1 day, 15:11:14.288663 INFO: performing precursor FDR with 47 features
1 day, 15:11:14.288802 INFO: Decoy channel: -1
1 day, 15:11:14.288831 INFO: competitive: True
1 day, 15:11:14.499094 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:11:14.630532 WARNING: dropped 2377 target PSMs due to missing features
1 day, 15:11:14.630692 WARNING: dropped 2321 decoy PSMs due to missing features
1 day, 15:11:14.936580 INFO: Estimating optimal hyperparameters - samples: 665,129, batch_size: 2,724, learning_rate: 8.15e-04
1 day, 15:11:14.937891 INFO: Using random state 490638 for train-test-split
1 day, 15:11:32.739027 INFO: Test AUC: 0.551
1 day, 15:11:32.739184 INFO: Train AUC: 0.570
1 day, 15:11:32.739219 INFO: AUC difference: 3.35%
1 day, 15:11:33.228266 INFO: Resetting torch num_threads to 80
1 day, 15:11:33.245644 PROGRESS: === Extracted 836110 precursors and 4464949 fragments ===
1 day, 15:11:33.246451 INFO: === FDR correction performed with classifier version 22 ===
1 day, 15:11:33.279068 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:11:33.279396 PROGRESS: Total precursors accumulated: 171,819
1 day, 15:11:33.279482 PROGRESS: Target precursors: 98,282 (57.20%)
1 day, 15:11:33.279543 PROGRESS: Decoy precursors: 73,537 (42.80%)
1 day, 15:11:33.279599 PROGRESS: 
1 day, 15:11:33.279650 PROGRESS: Precursor Summary:
1 day, 15:11:33.281889 PROGRESS: Channel   0:	 0.050 FDR:   402; 0.010 FDR:   253; 0.001 FDR:   137
1 day, 15:11:33.281992 PROGRESS: 
1 day, 15:11:33.282055 PROGRESS: Protein Summary:
1 day, 15:11:33.284137 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:   210; 0.001 FDR:   115
1 day, 15:11:33.284244 PROGRESS: =========================================================================
1 day, 15:11:33.294077 INFO: Target number of precursors reached.
1 day, 15:11:33.767791 INFO: fragments_df: keeping 3812 of 4464949 [sum(precursor_idx_mask)=6580 sum(mass_error_mask)=4464850 stop_rank=3812
1 day, 15:11:34.399047 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:11:34.532509 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:11:34.666065 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:11:34.804683 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:11:35.334702 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 15:11:35.335162 INFO: Using score_cutoff 25.58522730102539 (fac=0.99, q=1)
1 day, 15:11:35.335492 INFO: Updating optimization_manager: fwhm_rt             : 2.6516294479370117 -> 2.6941771507263184
1 day, 15:11:35.335576 INFO: Updating optimization_manager: fwhm_mobility       : 0.005376193672418594 -> 0.005147038958966732
1 day, 15:11:35.335636 INFO: Updating optimization_manager: score_cutoff        : 20.778265351867674 -> 25.58522730102539
1 day, 15:11:35.335695 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:11:35.390216 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:11:35.652068 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:11:35.717501 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:11:36.236133 INFO: === checking if optimization conditions were reached ===
1 day, 15:11:36.236415 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 15:11:36.237398 INFO: Updating optimization_manager: mobility_error      : 0.06417409342808669 -> 0.1
1 day, 15:11:36.237551 INFO: Updating optimization_manager: classifier_version  : 22 -> 24
1 day, 15:11:36.237658 INFO: Updating optimization_manager: score_cutoff        : 25.58522730102539 -> 23.59278681564331
1 day, 15:11:36.237759 INFO: Updating optimization_manager: fwhm_rt             : 2.6941771507263184 -> 2.624377727508545
1 day, 15:11:36.237856 INFO: Updating optimization_manager: fwhm_mobility       : 0.005147038958966732 -> 0.004825434647500515
1 day, 15:11:36.237971 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 15:11:36.238053 INFO: ==============================================
1 day, 15:11:36.238132 PROGRESS: Optimization finished for mobility_error.
1 day, 15:11:36.840498 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:11:36.895817 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:11:37.151447 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:11:37.211891 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:11:37.717347 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 15:11:37.717604 PROGRESS: ==============================================
1 day, 15:11:37.717689 PROGRESS: ms2_error      : 15.0000
1 day, 15:11:37.717754 PROGRESS: ms1_error      : 15.0000
1 day, 15:11:37.717816 PROGRESS: rt_error       : 109.0805
1 day, 15:11:37.717880 PROGRESS: mobility_error : 0.1000
1 day, 15:11:37.717936 PROGRESS: ==============================================
1 day, 15:11:37.725183 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 15:11:39.435507 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 15:11:47.405191 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 15:11:49.230698 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 15:12:04.708167 INFO: Using python extraction backend
1 day, 15:12:04.708624 PROGRESS: Extracting batch of 12210649 precursors
1 day, 15:12:04.708733 INFO: === Search parameters used ===
1 day, 15:12:04.708807 INFO: rt_error       : 109.08048799783728
1 day, 15:12:04.708863 INFO: mobility_error : 0.1
1 day, 15:12:04.708914 INFO: num_candidates : 3
1 day, 15:12:04.708962 INFO: ms1_error      : 15.0
1 day, 15:12:04.709009 INFO: ms2_error      : 15.0
1 day, 15:12:04.709055 INFO: fwhm_rt        : 2.624377727508545
1 day, 15:12:04.709102 INFO: quant_window   : 3
1 day, 15:12:04.709148 INFO: ==============================================
1 day, 15:12:06.796540 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:12:06.796694 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:12:06.796742 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
1 day, 15:12:06.796769 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.62
1 day, 15:12:06.797616 INFO: Starting candidate selection
1 day, 15:56:07.436928 INFO: Removed 27265453 precursors with score below cutoff 23.59278681564331
1 day, 15:56:10.876414 INFO: Starting candidate scoring
1 day, 15:57:13.767977 INFO: Finished candidate processing
1 day, 15:57:13.768387 INFO: Collecting candidate features
1 day, 15:57:28.203921 WARNING: intensity_correlation has 3053 NaNs ( 0.06 % out of 4925364)
1 day, 15:57:28.208405 WARNING: height_correlation has 177 NaNs ( 0.00 % out of 4925364)
1 day, 15:57:28.375292 INFO: Collecting fragment features
1 day, 15:57:31.762734 INFO: Finished candidate scoring
1 day, 15:57:35.585662 INFO: === Performing FDR correction with classifier version 24 ===
1 day, 15:57:35.586315 INFO: performing precursor FDR with 47 features
1 day, 15:57:35.586359 INFO: Decoy channel: -1
1 day, 15:57:35.586390 INFO: competitive: True
1 day, 15:57:36.941376 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:57:37.593257 WARNING: dropped 1661 target PSMs due to missing features
1 day, 15:57:37.593441 WARNING: dropped 1511 decoy PSMs due to missing features
1 day, 15:57:39.572021 INFO: Estimating optimal hyperparameters - samples: 3,937,753, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 15:57:39.580312 INFO: Using random state 948685 for train-test-split
1 day, 15:59:20.300646 INFO: Test AUC: 0.549
1 day, 15:59:20.300916 INFO: Train AUC: 0.554
1 day, 15:59:20.300958 INFO: AUC difference: 0.92%
1 day, 15:59:22.085664 INFO: Resetting torch num_threads to 80
1 day, 15:59:22.203720 INFO: Removing fragments below FDR threshold
1 day, 15:59:22.542771 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:59:22.543047 PROGRESS: Total precursors accumulated: 8,655
1 day, 15:59:22.543126 PROGRESS: Target precursors: 8,570 (99.02%)
1 day, 15:59:22.543189 PROGRESS: Decoy precursors: 85 (0.98%)
1 day, 15:59:22.543246 PROGRESS: 
1 day, 15:59:22.543299 PROGRESS: Precursor Summary:
1 day, 15:59:22.547352 PROGRESS: Channel   0:	 0.050 FDR: 8,570; 0.010 FDR: 8,570; 0.001 FDR: 6,176
1 day, 15:59:22.547506 PROGRESS: 
1 day, 15:59:22.547575 PROGRESS: Protein Summary:
1 day, 15:59:22.551849 PROGRESS: Channel   0:	 0.050 FDR: 2,067; 0.010 FDR: 2,067; 0.001 FDR: 1,462
1 day, 15:59:22.551960 PROGRESS: =========================================================================
1 day, 15:59:22.625579 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R1/psm.parquet
1 day, 15:59:22.681599 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R1/frag.parquet
1 day, 15:59:22.718429 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R1
1 day, 15:59:23.058781 PROGRESS: Loading raw file 8/12: B9_G_DIA_nLC_tTOF_R2 
1 day, 15:59:23.058969 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
1 day, 15:59:23.059048 INFO: Creating folder plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R2/figures
1 day, 15:59:23.059236 INFO: Initializing TimingManager
1 day, 15:59:23.059783 INFO: Initializing RawFileManager
1 day, 15:59:23.059911 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:23.059981 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:23.060033 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:23.238224 INFO: Reading 22,624 frames with 313,858,254 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:28.643306 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d...
1 day, 15:59:28.645312 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:28.648180 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:28.648636 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:28.649462 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:28.651865 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:28.674432 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:28.674780 INFO: Indexing quadrupole dimension
1 day, 15:59:28.761703 INFO: Transposing detector events
1 day, 15:59:30.376503 INFO: Finished transposing data
1 day, 15:59:30.376705 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
1 day, 15:59:30.377283 INFO: RT (min)            : 0.0 - 40.0
1 day, 15:59:30.377382 INFO: RT duration (sec)   : 2399.9
1 day, 15:59:30.377447 INFO: RT duration (min)   : 40.0
1 day, 15:59:30.377502 INFO: Cycle len (scans)   : 12
1 day, 15:59:30.377559 INFO: Cycle len (sec)     : 1.27
1 day, 15:59:30.377610 INFO: Number of cycles    : 1885
1 day, 15:59:30.377668 INFO: MS2 range (m/z)     : 374.4 - 1151.9
1 day, 15:59:30.377737 INFO: Creating DIA data object took: 7.317849159240723
1 day, 15:59:32.026076 INFO: Initializing CalibrationManager
1 day, 15:59:32.026411 INFO: Setting up calibration estimators ..
1 day, 15:59:32.026484 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 15:59:32.026582 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 15:59:32.026672 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 15:59:32.026742 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 15:59:32.026818 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1 day, 15:59:32.026881 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
1 day, 15:59:32.026936 INFO: Done setting up calibration estimators.
1 day, 15:59:32.027077 INFO: Initializing OptimizationManager
1 day, 15:59:32.027179 INFO: initial parameter: ms1_error = 30
1 day, 15:59:32.027237 INFO: initial parameter: ms2_error = 30
1 day, 15:59:32.027288 INFO: initial parameter: rt_error = 1199.9678125
1 day, 15:59:32.027341 INFO: initial parameter: mobility_error = 0.1
1 day, 15:59:32.027385 INFO: initial parameter: num_candidates = 1
1 day, 15:59:32.027428 INFO: initial parameter: fwhm_rt = 5
1 day, 15:59:32.027472 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 15:59:32.027513 INFO: initial parameter: score_cutoff = 0
1 day, 15:59:32.027554 INFO: initial parameter: classifier_version = -1
1 day, 15:59:32.027627 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R2
1 day, 15:59:32.027850 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 15:59:32.027885 INFO: Initializing FDRManager
1 day, 15:59:32.027933 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 15:59:33.091378 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
1 day, 15:59:33.766260 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 15:59:33.766706 INFO: Updating optimization_manager: rt_error            : 1199.9678125 -> 1199.9678125
1 day, 15:59:33.766815 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 15:59:33.767003 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 15:59:33.767099 PROGRESS: Starting initial search for precursors.
1 day, 15:59:33.767187 INFO: Starting optimization step 0.
1 day, 15:59:33.767251 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 15:59:33.767328 INFO: Using python extraction backend
1 day, 15:59:33.767480 PROGRESS: Extracting batch of 395 precursors
1 day, 15:59:33.767553 INFO: === Search parameters used ===
1 day, 15:59:33.767604 INFO: rt_error       : 1199.9678125
1 day, 15:59:33.767655 INFO: mobility_error : 0.1
1 day, 15:59:33.767701 INFO: num_candidates : 1
1 day, 15:59:33.767747 INFO: ms1_error      : 30
1 day, 15:59:33.767795 INFO: ms2_error      : 30
1 day, 15:59:33.767840 INFO: fwhm_rt        : 5
1 day, 15:59:33.767884 INFO: quant_window   : 3
1 day, 15:59:33.767928 INFO: ==============================================
1 day, 15:59:33.768756 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:59:33.768804 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:59:33.768846 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 15:59:33.768869 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 15:59:33.769790 INFO: Starting candidate selection
1 day, 15:59:35.649835 INFO: Starting candidate scoring
1 day, 15:59:35.690453 INFO: Finished candidate processing
1 day, 15:59:35.690533 INFO: Collecting candidate features
1 day, 15:59:35.700585 INFO: Collecting fragment features
1 day, 15:59:35.702869 INFO: Finished candidate scoring
1 day, 15:59:35.703821 INFO: performing precursor FDR with 47 features
1 day, 15:59:35.703867 INFO: Decoy channel: -1
1 day, 15:59:35.703893 INFO: competitive: True
1 day, 15:59:35.705159 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:59:35.707120 INFO: Estimating optimal hyperparameters - samples: 272, batch_size: 128, learning_rate: 1.77e-04
1 day, 15:59:35.707896 INFO: Using random state 625957 for train-test-split
1 day, 15:59:35.731762 INFO: Test AUC: 0.506
1 day, 15:59:35.731862 INFO: Train AUC: 0.512
1 day, 15:59:35.731897 INFO: AUC difference: 1.23%
1 day, 15:59:35.983444 INFO: Resetting torch num_threads to 80
1 day, 15:59:35.983930 PROGRESS: === Extracted 341 precursors and 2794 fragments ===
1 day, 15:59:35.984382 INFO: === FDR correction performed with classifier version -1 ===
1 day, 15:59:35.984924 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:59:35.985021 PROGRESS: Total precursors accumulated: 173
1 day, 15:59:35.985085 PROGRESS: Target precursors: 84 (48.55%)
1 day, 15:59:35.985140 PROGRESS: Decoy precursors: 89 (51.45%)
1 day, 15:59:35.985190 PROGRESS: 
1 day, 15:59:35.985237 PROGRESS: Precursor Summary:
1 day, 15:59:35.986196 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 15:59:35.986297 PROGRESS: 
1 day, 15:59:35.986358 PROGRESS: Protein Summary:
1 day, 15:59:35.987394 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 15:59:35.987486 PROGRESS: =========================================================================
1 day, 15:59:35.987596 INFO: Target number of precursors not reached yet.
1 day, 15:59:36.049565 INFO: Starting optimization step 1.
1 day, 15:59:36.049786 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 15:59:36.049886 INFO: Using python extraction backend
1 day, 15:59:36.050006 PROGRESS: Extracting batch of 796 precursors
1 day, 15:59:36.050082 INFO: === Search parameters used ===
1 day, 15:59:36.050136 INFO: rt_error       : 1199.9678125
1 day, 15:59:36.050186 INFO: mobility_error : 0.1
1 day, 15:59:36.050233 INFO: num_candidates : 1
1 day, 15:59:36.050282 INFO: ms1_error      : 30
1 day, 15:59:36.050330 INFO: ms2_error      : 30
1 day, 15:59:36.050375 INFO: fwhm_rt        : 5
1 day, 15:59:36.050418 INFO: quant_window   : 3
1 day, 15:59:36.050463 INFO: ==============================================
1 day, 15:59:36.051172 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:59:36.051221 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:59:36.051254 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 15:59:36.051278 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 15:59:36.051965 INFO: Starting candidate selection
1 day, 15:59:38.764391 INFO: Starting candidate scoring
1 day, 15:59:38.805158 INFO: Finished candidate processing
1 day, 15:59:38.805254 INFO: Collecting candidate features
1 day, 15:59:38.815974 INFO: Collecting fragment features
1 day, 15:59:38.818423 INFO: Finished candidate scoring
1 day, 15:59:38.821575 INFO: performing precursor FDR with 47 features
1 day, 15:59:38.821643 INFO: Decoy channel: -1
1 day, 15:59:38.821688 INFO: competitive: True
1 day, 15:59:38.824765 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:59:38.826651 INFO: Estimating optimal hyperparameters - samples: 846, batch_size: 128, learning_rate: 1.77e-04
1 day, 15:59:38.826746 INFO: Using random state 570270 for train-test-split
1 day, 15:59:38.903973 INFO: Test AUC: 0.478
1 day, 15:59:38.904073 INFO: Train AUC: 0.603
1 day, 15:59:38.904109 INFO: AUC difference: 20.84%
1 day, 15:59:38.904135 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 15:59:39.143261 INFO: Resetting torch num_threads to 80
1 day, 15:59:39.144557 PROGRESS: === Extracted 1058 precursors and 8785 fragments ===
1 day, 15:59:39.144994 INFO: === FDR correction performed with classifier version -1 ===
1 day, 15:59:39.145588 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:59:39.145688 PROGRESS: Total precursors accumulated: 539
1 day, 15:59:39.145758 PROGRESS: Target precursors: 323 (59.93%)
1 day, 15:59:39.145826 PROGRESS: Decoy precursors: 216 (40.07%)
1 day, 15:59:39.145895 PROGRESS: 
1 day, 15:59:39.145950 PROGRESS: Precursor Summary:
1 day, 15:59:39.146902 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
1 day, 15:59:39.146997 PROGRESS: 
1 day, 15:59:39.147059 PROGRESS: Protein Summary:
1 day, 15:59:39.148107 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
1 day, 15:59:39.148200 PROGRESS: =========================================================================
1 day, 15:59:39.148360 INFO: Target number of precursors not reached yet.
1 day, 15:59:39.214004 INFO: Starting optimization step 2.
1 day, 15:59:39.214237 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 15:59:39.214325 INFO: Using python extraction backend
1 day, 15:59:39.214437 PROGRESS: Extracting batch of 1598 precursors
1 day, 15:59:39.214518 INFO: === Search parameters used ===
1 day, 15:59:39.214575 INFO: rt_error       : 1199.9678125
1 day, 15:59:39.214626 INFO: mobility_error : 0.1
1 day, 15:59:39.214678 INFO: num_candidates : 1
1 day, 15:59:39.214727 INFO: ms1_error      : 30
1 day, 15:59:39.214788 INFO: ms2_error      : 30
1 day, 15:59:39.214835 INFO: fwhm_rt        : 5
1 day, 15:59:39.214882 INFO: quant_window   : 3
1 day, 15:59:39.214928 INFO: ==============================================
1 day, 15:59:39.215748 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:59:39.215796 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:59:39.215828 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 15:59:39.215853 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 15:59:39.216615 INFO: Starting candidate selection
1 day, 15:59:44.357795 INFO: Starting candidate scoring
1 day, 15:59:44.421286 INFO: Finished candidate processing
1 day, 15:59:44.421384 INFO: Collecting candidate features
1 day, 15:59:44.429821 WARNING: intensity_correlation has 1 NaNs ( 0.07 % out of 1422)
1 day, 15:59:44.433609 INFO: Collecting fragment features
1 day, 15:59:44.436475 INFO: Finished candidate scoring
1 day, 15:59:44.439619 INFO: performing precursor FDR with 47 features
1 day, 15:59:44.439678 INFO: Decoy channel: -1
1 day, 15:59:44.439708 INFO: competitive: True
1 day, 15:59:44.443108 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:59:44.444465 WARNING: dropped 1 target PSMs due to missing features
1 day, 15:59:44.445422 INFO: Estimating optimal hyperparameters - samples: 1,983, batch_size: 128, learning_rate: 1.77e-04
1 day, 15:59:44.445508 INFO: Using random state 867070 for train-test-split
1 day, 15:59:44.665552 INFO: Test AUC: 0.515
1 day, 15:59:44.665660 INFO: Train AUC: 0.613
1 day, 15:59:44.665694 INFO: AUC difference: 16.02%
1 day, 15:59:44.665720 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 15:59:44.907146 INFO: Resetting torch num_threads to 80
1 day, 15:59:44.908959 PROGRESS: === Extracted 2480 precursors and 20616 fragments ===
1 day, 15:59:44.909427 INFO: === FDR correction performed with classifier version -1 ===
1 day, 15:59:44.910109 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:59:44.910212 PROGRESS: Total precursors accumulated: 1,263
1 day, 15:59:44.910280 PROGRESS: Target precursors: 731 (57.88%)
1 day, 15:59:44.910339 PROGRESS: Decoy precursors: 532 (42.12%)
1 day, 15:59:44.910393 PROGRESS: 
1 day, 15:59:44.910444 PROGRESS: Precursor Summary:
1 day, 15:59:44.911392 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 15:59:44.911486 PROGRESS: 
1 day, 15:59:44.911549 PROGRESS: Protein Summary:
1 day, 15:59:44.912584 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 15:59:44.912685 PROGRESS: =========================================================================
1 day, 15:59:44.912851 INFO: Target number of precursors not reached yet.
1 day, 15:59:44.982075 INFO: Starting optimization step 3.
1 day, 15:59:44.982309 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 15:59:44.982402 INFO: Using python extraction backend
1 day, 15:59:44.982521 PROGRESS: Extracting batch of 3192 precursors
1 day, 15:59:44.982601 INFO: === Search parameters used ===
1 day, 15:59:44.982660 INFO: rt_error       : 1199.9678125
1 day, 15:59:44.982712 INFO: mobility_error : 0.1
1 day, 15:59:44.982771 INFO: num_candidates : 1
1 day, 15:59:44.982822 INFO: ms1_error      : 30
1 day, 15:59:44.982870 INFO: ms2_error      : 30
1 day, 15:59:44.982917 INFO: fwhm_rt        : 5
1 day, 15:59:44.982963 INFO: quant_window   : 3
1 day, 15:59:44.983011 INFO: ==============================================
1 day, 15:59:44.984055 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:59:44.984107 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:59:44.984143 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 15:59:44.984169 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 15:59:44.985029 INFO: Starting candidate selection
1 day, 15:59:54.011207 INFO: Starting candidate scoring
1 day, 15:59:54.098814 INFO: Finished candidate processing
1 day, 15:59:54.098927 INFO: Collecting candidate features
1 day, 15:59:54.109549 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 2870)
1 day, 15:59:54.113448 INFO: Collecting fragment features
1 day, 15:59:54.117259 INFO: Finished candidate scoring
1 day, 15:59:54.121641 INFO: performing precursor FDR with 47 features
1 day, 15:59:54.121699 INFO: Decoy channel: -1
1 day, 15:59:54.121727 INFO: competitive: True
1 day, 15:59:54.125945 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 15:59:54.127596 WARNING: dropped 2 target PSMs due to missing features
1 day, 15:59:54.128883 INFO: Estimating optimal hyperparameters - samples: 4,278, batch_size: 128, learning_rate: 1.77e-04
1 day, 15:59:54.128976 INFO: Using random state 82091 for train-test-split
1 day, 15:59:54.536115 INFO: Test AUC: 0.524
1 day, 15:59:54.536213 INFO: Train AUC: 0.594
1 day, 15:59:54.536245 INFO: AUC difference: 11.86%
1 day, 15:59:54.536269 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 15:59:54.776605 INFO: Resetting torch num_threads to 80
1 day, 15:59:54.779006 PROGRESS: === Extracted 5350 precursors and 44666 fragments ===
1 day, 15:59:54.779444 INFO: === FDR correction performed with classifier version -1 ===
1 day, 15:59:54.780263 PROGRESS: ============================= Precursor FDR =============================
1 day, 15:59:54.780363 PROGRESS: Total precursors accumulated: 2,719
1 day, 15:59:54.780431 PROGRESS: Target precursors: 1,591 (58.51%)
1 day, 15:59:54.780489 PROGRESS: Decoy precursors: 1,128 (41.49%)
1 day, 15:59:54.780542 PROGRESS: 
1 day, 15:59:54.780594 PROGRESS: Precursor Summary:
1 day, 15:59:54.781559 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 15:59:54.781652 PROGRESS: 
1 day, 15:59:54.781713 PROGRESS: Protein Summary:
1 day, 15:59:54.782767 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 15:59:54.782863 PROGRESS: =========================================================================
1 day, 15:59:54.783038 INFO: Target number of precursors not reached yet.
1 day, 15:59:54.856976 INFO: Starting optimization step 4.
1 day, 15:59:54.857235 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 15:59:54.857320 INFO: Using python extraction backend
1 day, 15:59:54.857441 PROGRESS: Extracting batch of 6381 precursors
1 day, 15:59:54.857520 INFO: === Search parameters used ===
1 day, 15:59:54.857576 INFO: rt_error       : 1199.9678125
1 day, 15:59:54.857626 INFO: mobility_error : 0.1
1 day, 15:59:54.857676 INFO: num_candidates : 1
1 day, 15:59:54.857725 INFO: ms1_error      : 30
1 day, 15:59:54.857772 INFO: ms2_error      : 30
1 day, 15:59:54.857818 INFO: fwhm_rt        : 5
1 day, 15:59:54.857874 INFO: quant_window   : 3
1 day, 15:59:54.857926 INFO: ==============================================
1 day, 15:59:54.859376 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 15:59:54.859428 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 15:59:54.859459 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 15:59:54.859486 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 15:59:54.860235 INFO: Starting candidate selection
1 day, 16:00:11.489793 INFO: Starting candidate scoring
1 day, 16:00:11.653078 INFO: Finished candidate processing
1 day, 16:00:11.653240 INFO: Collecting candidate features
1 day, 16:00:11.676410 WARNING: intensity_correlation has 4 NaNs ( 0.07 % out of 5724)
1 day, 16:00:11.676764 WARNING: height_correlation has 1 NaNs ( 0.02 % out of 5724)
1 day, 16:00:11.683367 INFO: Collecting fragment features
1 day, 16:00:11.693463 INFO: Finished candidate scoring
1 day, 16:00:11.703096 INFO: performing precursor FDR with 47 features
1 day, 16:00:11.703215 INFO: Decoy channel: -1
1 day, 16:00:11.703245 INFO: competitive: True
1 day, 16:00:11.709328 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 16:00:11.712208 WARNING: dropped 4 target PSMs due to missing features
1 day, 16:00:11.712275 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 16:00:11.714536 INFO: Estimating optimal hyperparameters - samples: 8,853, batch_size: 128, learning_rate: 1.77e-04
1 day, 16:00:11.714639 INFO: Using random state 295828 for train-test-split
1 day, 16:00:12.775973 INFO: Test AUC: 0.537
1 day, 16:00:12.776098 INFO: Train AUC: 0.595
1 day, 16:00:12.776130 INFO: AUC difference: 9.74%
1 day, 16:00:12.776154 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 16:00:13.019980 INFO: Resetting torch num_threads to 80
1 day, 16:00:13.023584 PROGRESS: === Extracted 11074 precursors and 91959 fragments ===
1 day, 16:00:13.024056 INFO: === FDR correction performed with classifier version -1 ===
1 day, 16:00:13.025290 PROGRESS: ============================= Precursor FDR =============================
1 day, 16:00:13.025390 PROGRESS: Total precursors accumulated: 5,628
1 day, 16:00:13.025462 PROGRESS: Target precursors: 3,322 (59.03%)
1 day, 16:00:13.025522 PROGRESS: Decoy precursors: 2,306 (40.97%)
1 day, 16:00:13.025575 PROGRESS: 
1 day, 16:00:13.025626 PROGRESS: Precursor Summary:
1 day, 16:00:13.026638 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 16:00:13.026738 PROGRESS: 
1 day, 16:00:13.026806 PROGRESS: Protein Summary:
1 day, 16:00:13.027899 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 16:00:13.027989 PROGRESS: =========================================================================
1 day, 16:00:13.028191 INFO: Target number of precursors not reached yet.
1 day, 16:00:13.164027 INFO: Starting optimization step 5.
1 day, 16:00:13.164279 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1 day, 16:00:13.164361 INFO: Using python extraction backend
1 day, 16:00:13.164471 PROGRESS: Extracting batch of 12763 precursors
1 day, 16:00:13.164546 INFO: === Search parameters used ===
1 day, 16:00:13.164598 INFO: rt_error       : 1199.9678125
1 day, 16:00:13.164646 INFO: mobility_error : 0.1
1 day, 16:00:13.164691 INFO: num_candidates : 1
1 day, 16:00:13.164736 INFO: ms1_error      : 30
1 day, 16:00:13.164780 INFO: ms2_error      : 30
1 day, 16:00:13.164823 INFO: fwhm_rt        : 5
1 day, 16:00:13.164865 INFO: quant_window   : 3
1 day, 16:00:13.164908 INFO: ==============================================
1 day, 16:00:13.167584 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 16:00:13.167639 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 16:00:13.167669 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 16:00:13.167691 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 16:00:13.168386 INFO: Starting candidate selection
1 day, 16:00:44.586053 INFO: Starting candidate scoring
1 day, 16:00:44.828130 INFO: Finished candidate processing
1 day, 16:00:44.828241 INFO: Collecting candidate features
1 day, 16:00:44.852718 WARNING: intensity_correlation has 5 NaNs ( 0.04 % out of 11460)
1 day, 16:00:44.853053 WARNING: height_correlation has 1 NaNs ( 0.01 % out of 11460)
1 day, 16:00:44.857423 INFO: Collecting fragment features
1 day, 16:00:44.867768 INFO: Finished candidate scoring
1 day, 16:00:44.891595 INFO: performing precursor FDR with 47 features
1 day, 16:00:44.891767 INFO: Decoy channel: -1
1 day, 16:00:44.891797 INFO: competitive: True
1 day, 16:00:44.902655 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 16:00:44.907856 WARNING: dropped 5 target PSMs due to missing features
1 day, 16:00:44.907970 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 16:00:44.911723 INFO: Estimating optimal hyperparameters - samples: 18,017, batch_size: 128, learning_rate: 1.77e-04
1 day, 16:00:44.911891 INFO: Using random state 448881 for train-test-split
1 day, 16:00:47.214700 INFO: Test AUC: 0.543
1 day, 16:00:47.214865 INFO: Train AUC: 0.602
1 day, 16:00:47.214902 INFO: AUC difference: 9.68%
1 day, 16:00:47.214931 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 16:00:47.479136 INFO: Resetting torch num_threads to 80
1 day, 16:00:47.485535 PROGRESS: === Extracted 22534 precursors and 187097 fragments ===
1 day, 16:00:47.486275 INFO: === FDR correction performed with classifier version -1 ===
1 day, 16:00:47.488393 PROGRESS: ============================= Precursor FDR =============================
1 day, 16:00:47.488518 PROGRESS: Total precursors accumulated: 11,444
1 day, 16:00:47.488599 PROGRESS: Target precursors: 7,062 (61.71%)
1 day, 16:00:47.488660 PROGRESS: Decoy precursors: 4,382 (38.29%)
1 day, 16:00:47.488717 PROGRESS: 
1 day, 16:00:47.488769 PROGRESS: Precursor Summary:
1 day, 16:00:47.489835 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
1 day, 16:00:47.489947 PROGRESS: 
1 day, 16:00:47.490010 PROGRESS: Protein Summary:
1 day, 16:00:47.491140 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
1 day, 16:00:47.491233 PROGRESS: =========================================================================
1 day, 16:00:47.491866 INFO: Target number of precursors not reached yet.
1 day, 16:00:48.024273 INFO: Starting optimization step 6.
1 day, 16:00:48.024616 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1 day, 16:00:48.024713 INFO: Using python extraction backend
1 day, 16:00:48.024855 PROGRESS: Extracting batch of 25523 precursors
1 day, 16:00:48.024937 INFO: === Search parameters used ===
1 day, 16:00:48.024995 INFO: rt_error       : 1199.9678125
1 day, 16:00:48.025047 INFO: mobility_error : 0.1
1 day, 16:00:48.025097 INFO: num_candidates : 1
1 day, 16:00:48.025145 INFO: ms1_error      : 30
1 day, 16:00:48.025191 INFO: ms2_error      : 30
1 day, 16:00:48.025236 INFO: fwhm_rt        : 5
1 day, 16:00:48.025281 INFO: quant_window   : 3
1 day, 16:00:48.025339 INFO: ==============================================
1 day, 16:00:48.033274 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 16:00:48.033372 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 16:00:48.033406 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 16:00:48.033435 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 16:00:48.034403 INFO: Starting candidate selection
1 day, 16:01:48.375447 INFO: Starting candidate scoring
1 day, 16:01:48.785751 INFO: Finished candidate processing
1 day, 16:01:48.785854 INFO: Collecting candidate features
1 day, 16:01:48.831699 WARNING: intensity_correlation has 9 NaNs ( 0.04 % out of 22854)
1 day, 16:01:48.831993 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 22854)
1 day, 16:01:48.836514 INFO: Collecting fragment features
1 day, 16:01:48.852274 INFO: Finished candidate scoring
1 day, 16:01:48.879186 INFO: performing precursor FDR with 47 features
1 day, 16:01:48.879350 INFO: Decoy channel: -1
1 day, 16:01:48.879385 INFO: competitive: True
1 day, 16:01:48.901776 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 16:01:48.913316 WARNING: dropped 11 target PSMs due to missing features
1 day, 16:01:48.913471 WARNING: dropped 10 decoy PSMs due to missing features
1 day, 16:01:48.921754 INFO: Estimating optimal hyperparameters - samples: 36,293, batch_size: 148, learning_rate: 1.90e-04
1 day, 16:01:48.922014 INFO: Using random state 180430 for train-test-split
1 day, 16:01:53.144236 INFO: Test AUC: 0.548
1 day, 16:01:53.144380 INFO: Train AUC: 0.598
1 day, 16:01:53.144419 INFO: AUC difference: 8.39%
1 day, 16:01:53.144447 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 16:01:53.406626 INFO: Resetting torch num_threads to 80
1 day, 16:01:53.418035 PROGRESS: === Extracted 45388 precursors and 377307 fragments ===
1 day, 16:01:53.418894 INFO: === FDR correction performed with classifier version -1 ===
1 day, 16:01:53.424039 PROGRESS: ============================= Precursor FDR =============================
1 day, 16:01:53.424186 PROGRESS: Total precursors accumulated: 23,064
1 day, 16:01:53.424259 PROGRESS: Target precursors: 14,253 (61.80%)
1 day, 16:01:53.424322 PROGRESS: Decoy precursors: 8,811 (38.20%)
1 day, 16:01:53.424380 PROGRESS: 
1 day, 16:01:53.424434 PROGRESS: Precursor Summary:
1 day, 16:01:53.425543 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 16:01:53.425666 PROGRESS: 
1 day, 16:01:53.425729 PROGRESS: Protein Summary:
1 day, 16:01:53.426894 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 16:01:53.426993 PROGRESS: =========================================================================
1 day, 16:01:53.427491 INFO: Target number of precursors not reached yet.
1 day, 16:01:54.038851 INFO: Starting optimization step 7.
1 day, 16:01:54.039186 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1 day, 16:01:54.039275 INFO: Using python extraction backend
1 day, 16:01:54.039414 PROGRESS: Extracting batch of 51061 precursors
1 day, 16:01:54.039498 INFO: === Search parameters used ===
1 day, 16:01:54.039556 INFO: rt_error       : 1199.9678125
1 day, 16:01:54.039623 INFO: mobility_error : 0.1
1 day, 16:01:54.039674 INFO: num_candidates : 1
1 day, 16:01:54.039720 INFO: ms1_error      : 30
1 day, 16:01:54.039765 INFO: ms2_error      : 30
1 day, 16:01:54.039808 INFO: fwhm_rt        : 5
1 day, 16:01:54.039851 INFO: quant_window   : 3
1 day, 16:01:54.039898 INFO: ==============================================
1 day, 16:01:54.056124 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 16:01:54.056279 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 16:01:54.056317 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 16:01:54.056341 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 16:01:54.057411 INFO: Starting candidate selection
1 day, 16:03:52.344539 INFO: Starting candidate scoring
1 day, 16:03:53.059906 INFO: Finished candidate processing
1 day, 16:03:53.060099 INFO: Collecting candidate features
1 day, 16:03:53.137437 WARNING: intensity_correlation has 10 NaNs ( 0.02 % out of 45673)
1 day, 16:03:53.143011 INFO: Collecting fragment features
1 day, 16:03:53.169676 INFO: Finished candidate scoring
1 day, 16:03:53.219530 INFO: performing precursor FDR with 47 features
1 day, 16:03:53.219687 INFO: Decoy channel: -1
1 day, 16:03:53.219717 INFO: competitive: True
1 day, 16:03:53.258395 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 16:03:53.277114 WARNING: dropped 17 target PSMs due to missing features
1 day, 16:03:53.277254 WARNING: dropped 14 decoy PSMs due to missing features
1 day, 16:03:53.292070 INFO: Estimating optimal hyperparameters - samples: 72,824, batch_size: 298, learning_rate: 2.70e-04
1 day, 16:03:53.292396 INFO: Using random state 914427 for train-test-split
1 day, 16:03:58.490821 INFO: Test AUC: 0.549
1 day, 16:03:58.490946 INFO: Train AUC: 0.594
1 day, 16:03:58.490980 INFO: AUC difference: 7.57%
1 day, 16:03:58.491006 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 16:03:58.760839 INFO: Resetting torch num_threads to 80
1 day, 16:03:58.780325 PROGRESS: === Extracted 91061 precursors and 756127 fragments ===
1 day, 16:03:58.781056 INFO: === FDR correction performed with classifier version -1 ===
1 day, 16:03:58.791234 PROGRESS: ============================= Precursor FDR =============================
1 day, 16:03:58.791410 PROGRESS: Total precursors accumulated: 46,258
1 day, 16:03:58.791482 PROGRESS: Target precursors: 28,242 (61.05%)
1 day, 16:03:58.791543 PROGRESS: Decoy precursors: 18,016 (38.95%)
1 day, 16:03:58.791600 PROGRESS: 
1 day, 16:03:58.791652 PROGRESS: Precursor Summary:
1 day, 16:03:58.792955 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 16:03:58.793054 PROGRESS: 
1 day, 16:03:58.793118 PROGRESS: Protein Summary:
1 day, 16:03:58.794406 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 16:03:58.794507 PROGRESS: =========================================================================
1 day, 16:03:58.795483 INFO: Target number of precursors not reached yet.
1 day, 16:03:59.162083 INFO: Starting optimization step 8.
1 day, 16:03:59.162394 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1 day, 16:03:59.162497 INFO: Using python extraction backend
1 day, 16:03:59.162647 PROGRESS: Extracting batch of 102076 precursors
1 day, 16:03:59.162731 INFO: === Search parameters used ===
1 day, 16:03:59.162787 INFO: rt_error       : 1199.9678125
1 day, 16:03:59.162837 INFO: mobility_error : 0.1
1 day, 16:03:59.162885 INFO: num_candidates : 1
1 day, 16:03:59.162930 INFO: ms1_error      : 30
1 day, 16:03:59.162976 INFO: ms2_error      : 30
1 day, 16:03:59.163021 INFO: fwhm_rt        : 5
1 day, 16:03:59.163067 INFO: quant_window   : 3
1 day, 16:03:59.163112 INFO: ==============================================
1 day, 16:03:59.189537 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 16:03:59.189676 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 16:03:59.189708 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 16:03:59.189735 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 16:03:59.190682 INFO: Starting candidate selection
1 day, 16:07:52.765679 INFO: Starting candidate scoring
1 day, 16:07:54.073727 INFO: Finished candidate processing
1 day, 16:07:54.074117 INFO: Collecting candidate features
1 day, 16:07:54.254766 WARNING: intensity_correlation has 29 NaNs ( 0.03 % out of 91350)
1 day, 16:07:54.255104 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 91350)
1 day, 16:07:54.261962 INFO: Collecting fragment features
1 day, 16:07:54.320901 INFO: Finished candidate scoring
1 day, 16:07:54.423163 INFO: performing precursor FDR with 47 features
1 day, 16:07:54.423326 INFO: Decoy channel: -1
1 day, 16:07:54.423356 INFO: competitive: True
1 day, 16:07:54.502799 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 16:07:54.539160 WARNING: dropped 35 target PSMs due to missing features
1 day, 16:07:54.539311 WARNING: dropped 26 decoy PSMs due to missing features
1 day, 16:07:54.593926 INFO: Estimating optimal hyperparameters - samples: 145,880, batch_size: 597, learning_rate: 3.82e-04
1 day, 16:07:54.594426 INFO: Using random state 419672 for train-test-split
1 day, 16:08:01.653894 INFO: Test AUC: 0.548
1 day, 16:08:01.654035 INFO: Train AUC: 0.582
1 day, 16:08:01.654068 INFO: AUC difference: 5.72%
1 day, 16:08:01.654094 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 16:08:01.947092 INFO: Resetting torch num_threads to 80
1 day, 16:08:01.982736 PROGRESS: === Extracted 182411 precursors and 1516779 fragments ===
1 day, 16:08:01.983633 INFO: === FDR correction performed with classifier version -1 ===
1 day, 16:08:02.002096 PROGRESS: ============================= Precursor FDR =============================
1 day, 16:08:02.002398 PROGRESS: Total precursors accumulated: 92,688
1 day, 16:08:02.002486 PROGRESS: Target precursors: 56,116 (60.54%)
1 day, 16:08:02.002550 PROGRESS: Decoy precursors: 36,572 (39.46%)
1 day, 16:08:02.002608 PROGRESS: 
1 day, 16:08:02.002662 PROGRESS: Precursor Summary:
1 day, 16:08:02.004312 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 16:08:02.004426 PROGRESS: 
1 day, 16:08:02.004492 PROGRESS: Protein Summary:
1 day, 16:08:02.006066 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 16:08:02.006180 PROGRESS: =========================================================================
1 day, 16:08:02.007804 INFO: Target number of precursors not reached yet.
1 day, 16:08:02.959876 INFO: Starting optimization step 9.
1 day, 16:08:02.960224 PROGRESS: === Extracting elution groups 102200 to 204600 ===
1 day, 16:08:02.960322 INFO: Using python extraction backend
1 day, 16:08:02.960464 PROGRESS: Extracting batch of 204132 precursors
1 day, 16:08:02.960551 INFO: === Search parameters used ===
1 day, 16:08:02.960608 INFO: rt_error       : 1199.9678125
1 day, 16:08:02.960670 INFO: mobility_error : 0.1
1 day, 16:08:02.960719 INFO: num_candidates : 1
1 day, 16:08:02.960768 INFO: ms1_error      : 30
1 day, 16:08:02.960817 INFO: ms2_error      : 30
1 day, 16:08:02.960864 INFO: fwhm_rt        : 5
1 day, 16:08:02.960912 INFO: quant_window   : 3
1 day, 16:08:02.960958 INFO: ==============================================
1 day, 16:08:03.013312 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 16:08:03.013459 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 16:08:03.013492 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 16:08:03.013515 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 16:08:03.014492 INFO: Starting candidate selection
1 day, 16:15:56.070174 INFO: Starting candidate scoring
1 day, 16:15:58.763056 INFO: Finished candidate processing
1 day, 16:15:58.763261 INFO: Collecting candidate features
1 day, 16:15:59.268240 WARNING: intensity_correlation has 50 NaNs ( 0.03 % out of 182919)
1 day, 16:15:59.268718 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 182919)
1 day, 16:15:59.279248 INFO: Collecting fragment features
1 day, 16:15:59.423800 INFO: Finished candidate scoring
1 day, 16:15:59.681711 INFO: performing precursor FDR with 47 features
1 day, 16:15:59.681916 INFO: Decoy channel: -1
1 day, 16:15:59.681949 INFO: competitive: True
1 day, 16:15:59.875385 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 16:15:59.961057 WARNING: dropped 59 target PSMs due to missing features
1 day, 16:15:59.961244 WARNING: dropped 55 decoy PSMs due to missing features
1 day, 16:16:00.149021 INFO: Estimating optimal hyperparameters - samples: 292,172, batch_size: 1,196, learning_rate: 5.40e-04
1 day, 16:16:00.149837 INFO: Using random state 231820 for train-test-split
1 day, 16:16:12.150674 INFO: Test AUC: 0.541
1 day, 16:16:12.150870 INFO: Train AUC: 0.581
1 day, 16:16:12.150909 INFO: AUC difference: 6.83%
1 day, 16:16:12.150934 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 16:16:12.528546 INFO: Resetting torch num_threads to 80
1 day, 16:16:12.617158 PROGRESS: === Extracted 365330 precursors and 3037550 fragments ===
1 day, 16:16:12.618420 INFO: === FDR correction performed with classifier version -1 ===
1 day, 16:16:12.658723 PROGRESS: ============================= Precursor FDR =============================
1 day, 16:16:12.659086 PROGRESS: Total precursors accumulated: 185,648
1 day, 16:16:12.659165 PROGRESS: Target precursors: 108,888 (58.65%)
1 day, 16:16:12.659227 PROGRESS: Decoy precursors: 76,760 (41.35%)
1 day, 16:16:12.659283 PROGRESS: 
1 day, 16:16:12.659337 PROGRESS: Precursor Summary:
1 day, 16:16:12.661617 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 16:16:12.661721 PROGRESS: 
1 day, 16:16:12.661784 PROGRESS: Protein Summary:
1 day, 16:16:12.663799 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 16:16:12.663921 PROGRESS: =========================================================================
1 day, 16:16:12.671598 INFO: Target number of precursors not reached yet.
1 day, 16:16:14.232073 INFO: Starting optimization step 10.
1 day, 16:16:14.232430 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 16:16:14.232579 INFO: Using python extraction backend
1 day, 16:16:14.232748 PROGRESS: Extracting batch of 408390 precursors
1 day, 16:16:14.232841 INFO: === Search parameters used ===
1 day, 16:16:14.232899 INFO: rt_error       : 1199.9678125
1 day, 16:16:14.232952 INFO: mobility_error : 0.1
1 day, 16:16:14.233001 INFO: num_candidates : 1
1 day, 16:16:14.233051 INFO: ms1_error      : 30
1 day, 16:16:14.233099 INFO: ms2_error      : 30
1 day, 16:16:14.233146 INFO: fwhm_rt        : 5
1 day, 16:16:14.233218 INFO: quant_window   : 3
1 day, 16:16:14.233268 INFO: ==============================================
1 day, 16:16:14.362698 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 16:16:14.362868 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 16:16:14.362913 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 16:16:14.362939 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 16:16:14.364155 INFO: Starting candidate selection
1 day, 16:31:33.227743 INFO: Starting candidate scoring
1 day, 16:31:38.354097 INFO: Finished candidate processing
1 day, 16:31:38.354421 INFO: Collecting candidate features
1 day, 16:31:39.290671 WARNING: intensity_correlation has 110 NaNs ( 0.03 % out of 364995)
1 day, 16:31:39.291286 WARNING: height_correlation has 13 NaNs ( 0.00 % out of 364995)
1 day, 16:31:39.307512 INFO: Collecting fragment features
1 day, 16:31:39.549768 INFO: Finished candidate scoring
1 day, 16:31:40.067790 INFO: performing precursor FDR with 47 features
1 day, 16:31:40.067948 INFO: Decoy channel: -1
1 day, 16:31:40.067976 INFO: competitive: True
1 day, 16:31:40.353875 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 16:31:40.479899 WARNING: dropped 110 target PSMs due to missing features
1 day, 16:31:40.480060 WARNING: dropped 122 decoy PSMs due to missing features
1 day, 16:31:40.861809 INFO: Estimating optimal hyperparameters - samples: 584,074, batch_size: 2,392, learning_rate: 7.64e-04
1 day, 16:31:40.862974 INFO: Using random state 959021 for train-test-split
1 day, 16:31:56.500363 INFO: Test AUC: 0.545
1 day, 16:31:56.500520 INFO: Train AUC: 0.567
1 day, 16:31:56.500562 INFO: AUC difference: 3.75%
1 day, 16:31:59.701488 INFO: Resetting torch num_threads to 80
1 day, 16:31:59.821508 PROGRESS: === Extracted 730325 precursors and 6072136 fragments ===
1 day, 16:31:59.822647 INFO: === FDR correction performed with classifier version -1 ===
1 day, 16:31:59.882400 PROGRESS: ============================= Precursor FDR =============================
1 day, 16:31:59.882742 PROGRESS: Total precursors accumulated: 371,099
1 day, 16:31:59.882816 PROGRESS: Target precursors: 213,694 (57.58%)
1 day, 16:31:59.882877 PROGRESS: Decoy precursors: 157,405 (42.42%)
1 day, 16:31:59.882931 PROGRESS: 
1 day, 16:31:59.882981 PROGRESS: Precursor Summary:
1 day, 16:31:59.886413 PROGRESS: Channel   0:	 0.050 FDR:   255; 0.010 FDR:   116; 0.001 FDR:    87
1 day, 16:31:59.886526 PROGRESS: 
1 day, 16:31:59.886590 PROGRESS: Protein Summary:
1 day, 16:31:59.889583 PROGRESS: Channel   0:	 0.050 FDR:   193; 0.010 FDR:    89; 0.001 FDR:    67
1 day, 16:31:59.889690 PROGRESS: =========================================================================
1 day, 16:31:59.895110 INFO: Target number of precursors not reached yet.
1 day, 16:32:01.904717 INFO: Starting optimization step 11.
1 day, 16:32:01.905023 PROGRESS: === Extracting elution groups 409400 to 819000 ===
1 day, 16:32:01.905120 INFO: Using python extraction backend
1 day, 16:32:01.905252 PROGRESS: Extracting batch of 816689 precursors
1 day, 16:32:01.905338 INFO: === Search parameters used ===
1 day, 16:32:01.905406 INFO: rt_error       : 1199.9678125
1 day, 16:32:01.905460 INFO: mobility_error : 0.1
1 day, 16:32:01.905511 INFO: num_candidates : 1
1 day, 16:32:01.905560 INFO: ms1_error      : 30
1 day, 16:32:01.905607 INFO: ms2_error      : 30
1 day, 16:32:01.905652 INFO: fwhm_rt        : 5
1 day, 16:32:01.905698 INFO: quant_window   : 3
1 day, 16:32:01.905743 INFO: ==============================================
1 day, 16:32:02.103421 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 16:32:02.103566 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 16:32:02.103604 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 16:32:02.103631 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 16:32:02.104770 INFO: Starting candidate selection
1 day, 17:02:08.962445 INFO: Starting candidate scoring
1 day, 17:02:18.876823 INFO: Finished candidate processing
1 day, 17:02:18.876946 INFO: Collecting candidate features
1 day, 17:02:20.770523 WARNING: intensity_correlation has 242 NaNs ( 0.03 % out of 731234)
1 day, 17:02:20.771512 WARNING: height_correlation has 18 NaNs ( 0.00 % out of 731234)
1 day, 17:02:20.798142 INFO: Collecting fragment features
1 day, 17:02:21.482969 INFO: Finished candidate scoring
1 day, 17:02:22.544363 INFO: performing precursor FDR with 47 features
1 day, 17:02:22.544528 INFO: Decoy channel: -1
1 day, 17:02:22.544558 INFO: competitive: True
1 day, 17:02:23.275252 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:02:23.530671 WARNING: dropped 219 target PSMs due to missing features
1 day, 17:02:23.530857 WARNING: dropped 268 decoy PSMs due to missing features
1 day, 17:02:24.626167 INFO: Estimating optimal hyperparameters - samples: 1,168,857, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 17:02:24.628789 INFO: Using random state 41898 for train-test-split
1 day, 17:02:56.163899 INFO: Test AUC: 0.545
1 day, 17:02:56.164206 INFO: Train AUC: 0.561
1 day, 17:02:56.164260 INFO: AUC difference: 2.85%
1 day, 17:02:56.929941 INFO: Resetting torch num_threads to 80
1 day, 17:02:57.368636 PROGRESS: === Extracted 1461559 precursors and 12148103 fragments ===
1 day, 17:02:57.370517 INFO: === FDR correction performed with classifier version -1 ===
1 day, 17:02:57.527719 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:02:57.528101 PROGRESS: Total precursors accumulated: 742,623
1 day, 17:02:57.528208 PROGRESS: Target precursors: 421,243 (56.72%)
1 day, 17:02:57.528270 PROGRESS: Decoy precursors: 321,380 (43.28%)
1 day, 17:02:57.528325 PROGRESS: 
1 day, 17:02:57.528377 PROGRESS: Precursor Summary:
1 day, 17:02:57.534854 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:   180; 0.001 FDR:     1
1 day, 17:02:57.535022 PROGRESS: 
1 day, 17:02:57.535091 PROGRESS: Protein Summary:
1 day, 17:02:57.540157 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   127; 0.001 FDR:     1
1 day, 17:02:57.540278 PROGRESS: =========================================================================
1 day, 17:02:57.560685 INFO: Target number of precursors not reached yet.
1 day, 17:03:00.432907 INFO: Starting optimization step 12.
1 day, 17:03:00.433249 PROGRESS: === Extracting elution groups 819000 to 1638200 ===
1 day, 17:03:00.433434 INFO: Using python extraction backend
1 day, 17:03:00.433660 PROGRESS: Extracting batch of 1633286 precursors
1 day, 17:03:00.433756 INFO: === Search parameters used ===
1 day, 17:03:00.433815 INFO: rt_error       : 1199.9678125
1 day, 17:03:00.433880 INFO: mobility_error : 0.1
1 day, 17:03:00.433936 INFO: num_candidates : 1
1 day, 17:03:00.433990 INFO: ms1_error      : 30
1 day, 17:03:00.434040 INFO: ms2_error      : 30
1 day, 17:03:00.434089 INFO: fwhm_rt        : 5
1 day, 17:03:00.434137 INFO: quant_window   : 3
1 day, 17:03:00.434186 INFO: ==============================================
1 day, 17:03:00.930450 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 17:03:00.930613 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 17:03:00.930666 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 17:03:00.930698 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 17:03:00.931971 INFO: Starting candidate selection
1 day, 18:04:42.274408 INFO: Starting candidate scoring
1 day, 18:05:01.734126 INFO: Finished candidate processing
1 day, 18:05:01.734356 INFO: Collecting candidate features
1 day, 18:05:05.536624 WARNING: intensity_correlation has 407 NaNs ( 0.03 % out of 1461582)
1 day, 18:05:05.538364 WARNING: height_correlation has 33 NaNs ( 0.00 % out of 1461582)
1 day, 18:05:05.588118 INFO: Collecting fragment features
1 day, 18:05:06.668294 INFO: Finished candidate scoring
1 day, 18:05:08.778461 INFO: performing precursor FDR with 47 features
1 day, 18:05:08.778619 INFO: Decoy channel: -1
1 day, 18:05:08.778654 INFO: competitive: True
1 day, 18:05:09.857750 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 18:05:10.339886 WARNING: dropped 410 target PSMs due to missing features
1 day, 18:05:10.340052 WARNING: dropped 506 decoy PSMs due to missing features
1 day, 18:05:12.474967 INFO: Estimating optimal hyperparameters - samples: 2,337,780, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 18:05:12.480654 INFO: Using random state 184888 for train-test-split
1 day, 18:06:17.900781 INFO: Test AUC: 0.559
1 day, 18:06:17.900969 INFO: Train AUC: 0.567
1 day, 18:06:17.901007 INFO: AUC difference: 1.40%
1 day, 18:06:19.107585 INFO: Resetting torch num_threads to 80
1 day, 18:06:21.471534 PROGRESS: === Extracted 2923141 precursors and 24295548 fragments ===
1 day, 18:06:21.473756 INFO: === FDR correction performed with classifier version -1 ===
1 day, 18:06:21.702884 PROGRESS: ============================= Precursor FDR =============================
1 day, 18:06:21.703219 PROGRESS: Total precursors accumulated: 1,485,382
1 day, 18:06:21.703309 PROGRESS: Target precursors: 853,064 (57.43%)
1 day, 18:06:21.703375 PROGRESS: Decoy precursors: 632,318 (42.57%)
1 day, 18:06:21.703432 PROGRESS: 
1 day, 18:06:21.703484 PROGRESS: Precursor Summary:
1 day, 18:06:21.713782 PROGRESS: Channel   0:	 0.050 FDR: 1,422; 0.010 FDR: 1,039; 0.001 FDR:   506
1 day, 18:06:21.713979 PROGRESS: 
1 day, 18:06:21.714064 PROGRESS: Protein Summary:
1 day, 18:06:21.723081 PROGRESS: Channel   0:	 0.050 FDR:   732; 0.010 FDR:   503; 0.001 FDR:   270
1 day, 18:06:21.723247 PROGRESS: =========================================================================
1 day, 18:06:21.741786 INFO: Target number of precursors reached.
1 day, 18:06:24.593535 INFO: fragments_df: keeping 5000 of 24295548 [sum(precursor_idx_mask)=11187 sum(mass_error_mask)=24295445 stop_rank=5000
1 day, 18:06:26.510821 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 18:06:26.707481 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 18:06:26.905927 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 18:06:27.082507 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 18:06:27.741482 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 18:06:27.741981 INFO: Using score_cutoff 37.788553255462645 (fac=0.99, q=1)
1 day, 18:06:27.742407 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.8084516525268555
1 day, 18:06:27.742500 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007926305755972862
1 day, 18:06:27.742566 INFO: Updating optimization_manager: score_cutoff        : 0 -> 37.788553255462645
1 day, 18:06:27.742647 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 18:06:27.843111 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 18:06:28.370730 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 18:06:28.474521 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 18:06:29.421985 INFO: Updating optimization_manager: classifier_version  : -1 -> 12
1 day, 18:06:29.422286 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 18:06:29.422460 INFO: Starting optimization step 13.
1 day, 18:06:29.422542 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 18:06:29.422669 INFO: Using python extraction backend
1 day, 18:06:29.422875 PROGRESS: Extracting batch of 816307 precursors
1 day, 18:06:29.422969 INFO: === Search parameters used ===
1 day, 18:06:29.423036 INFO: rt_error       : 1199.9678125
1 day, 18:06:29.423090 INFO: mobility_error : 0.1
1 day, 18:06:29.423141 INFO: num_candidates : 3
1 day, 18:06:29.423191 INFO: ms1_error      : 30
1 day, 18:06:29.423240 INFO: ms2_error      : 30
1 day, 18:06:29.423290 INFO: fwhm_rt        : 2.8084516525268555
1 day, 18:06:29.423339 INFO: quant_window   : 3
1 day, 18:06:29.423386 INFO: ==============================================
1 day, 18:06:29.631383 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 18:06:29.631541 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 18:06:29.631627 INFO: FWHM in RT is 2.81 seconds, sigma is 0.47
1 day, 18:06:29.631657 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.30
1 day, 18:06:29.632523 INFO: Starting candidate selection
1 day, 18:39:40.048859 INFO: Starting candidate scoring
1 day, 18:40:07.313788 INFO: Finished candidate processing
1 day, 18:40:07.314079 INFO: Collecting candidate features
1 day, 18:40:11.422419 WARNING: intensity_correlation has 732 NaNs ( 0.03 % out of 2096139)
1 day, 18:40:11.424496 WARNING: height_correlation has 50 NaNs ( 0.00 % out of 2096139)
1 day, 18:40:11.495789 INFO: Collecting fragment features
1 day, 18:40:12.719443 INFO: Finished candidate scoring
1 day, 18:40:13.956615 INFO: performing precursor FDR with 47 features
1 day, 18:40:13.956763 INFO: Decoy channel: -1
1 day, 18:40:13.956794 INFO: competitive: True
1 day, 18:40:14.428313 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 18:40:14.726420 WARNING: dropped 361 target PSMs due to missing features
1 day, 18:40:14.726596 WARNING: dropped 399 decoy PSMs due to missing features
1 day, 18:40:16.050282 INFO: Estimating optimal hyperparameters - samples: 1,676,303, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 18:40:16.054182 INFO: Using random state 953537 for train-test-split
1 day, 18:40:57.392641 INFO: Test AUC: 0.559
1 day, 18:40:57.392839 INFO: Train AUC: 0.573
1 day, 18:40:57.392875 INFO: AUC difference: 2.38%
1 day, 18:40:58.340381 INFO: Resetting torch num_threads to 80
1 day, 18:40:58.376379 PROGRESS: === Extracted 2096139 precursors and 16992861 fragments ===
1 day, 18:40:58.377502 INFO: === FDR correction performed with classifier version 12 ===
1 day, 18:40:58.439153 PROGRESS: ============================= Precursor FDR =============================
1 day, 18:40:58.439480 PROGRESS: Total precursors accumulated: 373,981
1 day, 18:40:58.439556 PROGRESS: Target precursors: 220,733 (59.02%)
1 day, 18:40:58.439637 PROGRESS: Decoy precursors: 153,248 (40.98%)
1 day, 18:40:58.439693 PROGRESS: 
1 day, 18:40:58.439746 PROGRESS: Precursor Summary:
1 day, 18:40:58.443222 PROGRESS: Channel   0:	 0.050 FDR:   373; 0.010 FDR:   252; 0.001 FDR:   216
1 day, 18:40:58.443337 PROGRESS: 
1 day, 18:40:58.443408 PROGRESS: Protein Summary:
1 day, 18:40:58.446540 PROGRESS: Channel   0:	 0.050 FDR:   288; 0.010 FDR:   189; 0.001 FDR:   165
1 day, 18:40:58.446661 PROGRESS: =========================================================================
1 day, 18:40:58.503972 INFO: Target number of precursors reached.
1 day, 18:41:00.366978 INFO: fragments_df: keeping 4914 of 16992861 [sum(precursor_idx_mask)=7440 sum(mass_error_mask)=16992796 stop_rank=4914
1 day, 18:41:02.729298 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 18:41:02.874832 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 18:41:03.010977 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 18:41:03.151010 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 18:41:03.862871 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 18:41:03.863347 INFO: Using score_cutoff 39.79447515678405 (fac=0.99, q=1)
1 day, 18:41:03.863725 INFO: Updating optimization_manager: fwhm_rt             : 2.8084516525268555 -> 2.902155876159668
1 day, 18:41:03.863817 INFO: Updating optimization_manager: fwhm_mobility       : 0.007926305755972862 -> 0.00813729502260685
1 day, 18:41:03.863880 INFO: Updating optimization_manager: score_cutoff        : 37.788553255462645 -> 39.79447515678405
1 day, 18:41:03.863963 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 18:41:03.968889 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 18:41:04.499846 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 18:41:04.601531 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 18:41:05.609999 INFO: === checking if optimization conditions were reached ===
1 day, 18:41:05.612456 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.079614112763583
1 day, 18:41:05.612628 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
1 day, 18:41:05.612711 PROGRESS: ❌ ms2_error      : 17.0796 > 15.0000 or insufficient steps taken.
1 day, 18:41:05.613837 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 18:41:05.613962 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
1 day, 18:41:05.614038 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 18:41:05.614109 INFO: ==============================================
1 day, 18:41:05.614193 INFO: Starting optimization step 14.
1 day, 18:41:05.614284 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 18:41:05.614364 INFO: Using python extraction backend
1 day, 18:41:05.614488 PROGRESS: Extracting batch of 816307 precursors
1 day, 18:41:05.614567 INFO: === Search parameters used ===
1 day, 18:41:05.614622 INFO: rt_error       : 1199.9678125
1 day, 18:41:05.614672 INFO: mobility_error : 0.1
1 day, 18:41:05.614719 INFO: num_candidates : 3
1 day, 18:41:05.614766 INFO: ms1_error      : 15.0
1 day, 18:41:05.614819 INFO: ms2_error      : 17.079614112763583
1 day, 18:41:05.614868 INFO: fwhm_rt        : 2.902155876159668
1 day, 18:41:05.614916 INFO: quant_window   : 3
1 day, 18:41:05.614961 INFO: ==============================================
1 day, 18:41:05.816988 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 18:41:05.817142 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 18:41:05.817209 INFO: FWHM in RT is 2.90 seconds, sigma is 0.48
1 day, 18:41:05.817237 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.41
1 day, 18:41:05.818171 INFO: Starting candidate selection
1 day, 19:10:48.828163 INFO: Starting candidate scoring
1 day, 19:11:13.198056 INFO: Finished candidate processing
1 day, 19:11:13.198460 INFO: Collecting candidate features
1 day, 19:11:17.140443 WARNING: intensity_correlation has 1932 NaNs ( 0.09 % out of 2056900)
1 day, 19:11:17.142537 WARNING: height_correlation has 150 NaNs ( 0.01 % out of 2056900)
1 day, 19:11:17.211213 INFO: Collecting fragment features
1 day, 19:11:18.297900 INFO: Finished candidate scoring
1 day, 19:11:19.665211 INFO: performing precursor FDR with 47 features
1 day, 19:11:19.665365 INFO: Decoy channel: -1
1 day, 19:11:19.665409 INFO: competitive: True
1 day, 19:11:20.150693 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:11:20.444385 WARNING: dropped 1016 target PSMs due to missing features
1 day, 19:11:20.444560 WARNING: dropped 1020 decoy PSMs due to missing features
1 day, 19:11:21.154123 INFO: Estimating optimal hyperparameters - samples: 1,643,891, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 19:11:21.159048 INFO: Using random state 147700 for train-test-split
1 day, 19:12:06.527055 INFO: Test AUC: 0.558
1 day, 19:12:06.527243 INFO: Train AUC: 0.569
1 day, 19:12:06.527281 INFO: AUC difference: 1.99%
1 day, 19:12:07.457734 INFO: Resetting torch num_threads to 80
1 day, 19:12:07.493585 PROGRESS: === Extracted 2056900 precursors and 14680388 fragments ===
1 day, 19:12:07.494813 INFO: === FDR correction performed with classifier version 13 ===
1 day, 19:12:07.555447 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:12:07.555778 PROGRESS: Total precursors accumulated: 372,801
1 day, 19:12:07.555858 PROGRESS: Target precursors: 217,090 (58.23%)
1 day, 19:12:07.555922 PROGRESS: Decoy precursors: 155,711 (41.77%)
1 day, 19:12:07.555978 PROGRESS: 
1 day, 19:12:07.556032 PROGRESS: Precursor Summary:
1 day, 19:12:07.559747 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   335; 0.001 FDR:   301
1 day, 19:12:07.559897 PROGRESS: 
1 day, 19:12:07.559966 PROGRESS: Protein Summary:
1 day, 19:12:07.563213 PROGRESS: Channel   0:	 0.050 FDR:   417; 0.010 FDR:   251; 0.001 FDR:   225
1 day, 19:12:07.563322 PROGRESS: =========================================================================
1 day, 19:12:07.577611 INFO: Target number of precursors reached.
1 day, 19:12:09.178647 INFO: fragments_df: keeping 5000 of 14680388 [sum(precursor_idx_mask)=9313 sum(mass_error_mask)=14680194 stop_rank=5000
1 day, 19:12:10.606964 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:12:10.748592 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:12:10.897097 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:12:11.044206 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:12:11.768402 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 19:12:11.768870 INFO: Using score_cutoff 30.409554470443727 (fac=0.99, q=1)
1 day, 19:12:11.769234 INFO: Updating optimization_manager: fwhm_rt             : 2.902155876159668 -> 2.6981875896453857
1 day, 19:12:11.769322 INFO: Updating optimization_manager: fwhm_mobility       : 0.00813729502260685 -> 0.006368431728333235
1 day, 19:12:11.769383 INFO: Updating optimization_manager: score_cutoff        : 39.79447515678405 -> 30.409554470443727
1 day, 19:12:11.769450 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:12:11.878093 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:12:12.413641 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:12:12.522673 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:12:13.551867 INFO: === checking if optimization conditions were reached ===
1 day, 19:12:13.554324 INFO: Updating optimization_manager: ms2_error           : 17.079614112763583 -> 15.0
1 day, 19:12:13.554501 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
1 day, 19:12:13.554589 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 19:12:13.555726 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 19:12:13.555838 INFO: Updating optimization_manager: classifier_version  : 14 -> 14
1 day, 19:12:13.555909 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 19:12:13.555989 INFO: ==============================================
1 day, 19:12:13.556070 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 19:12:14.533226 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:12:14.642689 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:12:15.177607 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:12:15.282473 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:12:16.307478 INFO: Starting optimization step 0.
1 day, 19:12:16.307787 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 19:12:16.307895 INFO: Using python extraction backend
1 day, 19:12:16.308072 PROGRESS: Extracting batch of 816307 precursors
1 day, 19:12:16.308171 INFO: === Search parameters used ===
1 day, 19:12:16.308242 INFO: rt_error       : 1199.9678125
1 day, 19:12:16.308304 INFO: mobility_error : 0.1
1 day, 19:12:16.308362 INFO: num_candidates : 3
1 day, 19:12:16.308422 INFO: ms1_error      : 15.0
1 day, 19:12:16.308476 INFO: ms2_error      : 15.0
1 day, 19:12:16.308530 INFO: fwhm_rt        : 2.6981875896453857
1 day, 19:12:16.308583 INFO: quant_window   : 3
1 day, 19:12:16.308637 INFO: ==============================================
1 day, 19:12:16.509951 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 19:12:16.510123 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 19:12:16.510194 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
1 day, 19:12:16.510228 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.45
1 day, 19:12:16.511074 INFO: Starting candidate selection
1 day, 19:42:15.636367 INFO: Starting candidate scoring
1 day, 19:42:39.614141 INFO: Finished candidate processing
1 day, 19:42:39.614457 INFO: Collecting candidate features
1 day, 19:42:45.162466 WARNING: intensity_correlation has 2440 NaNs ( 0.12 % out of 2038084)
1 day, 19:42:45.164752 WARNING: height_correlation has 159 NaNs ( 0.01 % out of 2038084)
1 day, 19:42:45.241931 INFO: Collecting fragment features
1 day, 19:42:46.472628 INFO: Finished candidate scoring
1 day, 19:42:47.932395 INFO: performing precursor FDR with 47 features
1 day, 19:42:47.932548 INFO: Decoy channel: -1
1 day, 19:42:47.932580 INFO: competitive: True
1 day, 19:42:48.408130 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:42:48.698016 WARNING: dropped 1240 target PSMs due to missing features
1 day, 19:42:48.698189 WARNING: dropped 1305 decoy PSMs due to missing features
1 day, 19:42:49.953114 INFO: Estimating optimal hyperparameters - samples: 1,628,431, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 19:42:49.957860 INFO: Using random state 918345 for train-test-split
1 day, 19:43:31.325832 INFO: Test AUC: 0.560
1 day, 19:43:31.326040 INFO: Train AUC: 0.573
1 day, 19:43:31.326078 INFO: AUC difference: 2.13%
1 day, 19:43:32.234190 INFO: Resetting torch num_threads to 80
1 day, 19:43:32.270985 PROGRESS: === Extracted 2038084 precursors and 13939964 fragments ===
1 day, 19:43:32.272161 INFO: === FDR correction performed with classifier version 14 ===
1 day, 19:43:32.332318 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:43:32.332652 PROGRESS: Total precursors accumulated: 372,516
1 day, 19:43:32.332733 PROGRESS: Target precursors: 217,732 (58.45%)
1 day, 19:43:32.332793 PROGRESS: Decoy precursors: 154,784 (41.55%)
1 day, 19:43:32.332880 PROGRESS: 
1 day, 19:43:32.332936 PROGRESS: Precursor Summary:
1 day, 19:43:32.336698 PROGRESS: Channel   0:	 0.050 FDR:   549; 0.010 FDR:   412; 0.001 FDR:   273
1 day, 19:43:32.336838 PROGRESS: 
1 day, 19:43:32.336906 PROGRESS: Protein Summary:
1 day, 19:43:32.340110 PROGRESS: Channel   0:	 0.050 FDR:   424; 0.010 FDR:   305; 0.001 FDR:   203
1 day, 19:43:32.340220 PROGRESS: =========================================================================
1 day, 19:43:32.350531 INFO: Target number of precursors reached.
1 day, 19:43:33.883743 INFO: fragments_df: keeping 5000 of 13939964 [sum(precursor_idx_mask)=11179 sum(mass_error_mask)=13939803 stop_rank=5000
1 day, 19:43:34.998174 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:43:35.135710 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:43:35.266138 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:43:35.393335 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:43:36.053589 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 19:43:36.054089 INFO: Using score_cutoff 25.209196962547303 (fac=0.99, q=1)
1 day, 19:43:36.054455 INFO: Updating optimization_manager: fwhm_rt             : 2.6981875896453857 -> 2.612621784210205
1 day, 19:43:36.054555 INFO: Updating optimization_manager: fwhm_mobility       : 0.006368431728333235 -> 0.005979595705866814
1 day, 19:43:36.054622 INFO: Updating optimization_manager: score_cutoff        : 30.409554470443727 -> 25.209196962547303
1 day, 19:43:36.054689 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:43:36.105577 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:43:36.360186 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:43:36.417046 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:43:36.950206 INFO: === checking if optimization conditions were reached ===
1 day, 19:43:36.950557 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 19:43:36.952935 INFO: Updating optimization_manager: rt_error            : 1199.9678125 -> 544.7886970503621
1 day, 19:43:36.953074 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 544.7887.
1 day, 19:43:36.953154 INFO: ==============================================
1 day, 19:43:36.953239 INFO: Starting optimization step 1.
1 day, 19:43:36.953312 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 19:43:36.953396 INFO: Using python extraction backend
1 day, 19:43:36.953533 PROGRESS: Extracting batch of 407917 precursors
1 day, 19:43:36.953616 INFO: === Search parameters used ===
1 day, 19:43:36.953677 INFO: rt_error       : 544.7886970503621
1 day, 19:43:36.953732 INFO: mobility_error : 0.1
1 day, 19:43:36.953786 INFO: num_candidates : 3
1 day, 19:43:36.953851 INFO: ms1_error      : 15.0
1 day, 19:43:36.953918 INFO: ms2_error      : 15.0
1 day, 19:43:36.953968 INFO: fwhm_rt        : 2.612621784210205
1 day, 19:43:36.954018 INFO: quant_window   : 3
1 day, 19:43:36.954066 INFO: ==============================================
1 day, 19:43:37.058726 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 19:43:37.058907 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 19:43:37.058967 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
1 day, 19:43:37.058999 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.24
1 day, 19:43:37.059882 INFO: Starting candidate selection
1 day, 19:50:54.894251 INFO: Starting candidate scoring
1 day, 19:51:06.736788 INFO: Finished candidate processing
1 day, 19:51:06.737033 INFO: Collecting candidate features
1 day, 19:51:08.659585 WARNING: intensity_correlation has 1872 NaNs ( 0.19 % out of 988521)
1 day, 19:51:08.660662 WARNING: height_correlation has 118 NaNs ( 0.01 % out of 988521)
1 day, 19:51:08.695835 INFO: Collecting fragment features
1 day, 19:51:09.252655 INFO: Finished candidate scoring
1 day, 19:51:09.962648 INFO: performing precursor FDR with 47 features
1 day, 19:51:09.962797 INFO: Decoy channel: -1
1 day, 19:51:09.962826 INFO: competitive: True
1 day, 19:51:10.205524 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:51:10.358179 WARNING: dropped 971 target PSMs due to missing features
1 day, 19:51:10.358343 WARNING: dropped 975 decoy PSMs due to missing features
1 day, 19:51:10.692208 INFO: Estimating optimal hyperparameters - samples: 789,260, batch_size: 3,232, learning_rate: 8.88e-04
1 day, 19:51:10.694476 INFO: Using random state 918345 for train-test-split
1 day, 19:51:31.222975 INFO: Test AUC: 0.554
1 day, 19:51:31.223182 INFO: Train AUC: 0.575
1 day, 19:51:31.223220 INFO: AUC difference: 3.79%
1 day, 19:51:31.815540 INFO: Resetting torch num_threads to 80
1 day, 19:51:31.833320 PROGRESS: === Extracted 988521 precursors and 6403449 fragments ===
1 day, 19:51:31.834184 INFO: === FDR correction performed with classifier version 14 ===
1 day, 19:51:31.864095 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:51:31.864388 PROGRESS: Total precursors accumulated: 184,577
1 day, 19:51:31.864464 PROGRESS: Target precursors: 108,058 (58.54%)
1 day, 19:51:31.864525 PROGRESS: Decoy precursors: 76,519 (41.46%)
1 day, 19:51:31.864581 PROGRESS: 
1 day, 19:51:31.864634 PROGRESS: Precursor Summary:
1 day, 19:51:31.866982 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   205; 0.001 FDR:   179
1 day, 19:51:31.867095 PROGRESS: 
1 day, 19:51:31.867165 PROGRESS: Protein Summary:
1 day, 19:51:31.869348 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   176; 0.001 FDR:   154
1 day, 19:51:31.869458 PROGRESS: =========================================================================
1 day, 19:51:31.907446 INFO: Target number of precursors reached.
1 day, 19:51:32.593318 INFO: fragments_df: keeping 3542 of 6403449 [sum(precursor_idx_mask)=5638 sum(mass_error_mask)=6403370 stop_rank=3542
1 day, 19:51:33.630890 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:51:33.765955 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:51:33.896878 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:51:34.033847 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:51:34.526716 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 19:51:34.527214 INFO: Using score_cutoff 24.52590063858032 (fac=0.99, q=1)
1 day, 19:51:34.527567 INFO: Updating optimization_manager: fwhm_rt             : 2.612621784210205 -> 2.681373119354248
1 day, 19:51:34.527659 INFO: Updating optimization_manager: fwhm_mobility       : 0.005979595705866814 -> 0.005673648323863745
1 day, 19:51:34.527724 INFO: Updating optimization_manager: score_cutoff        : 25.209196962547303 -> 24.52590063858032
1 day, 19:51:34.527789 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:51:34.580149 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:51:34.838059 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:51:34.896819 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:51:35.401969 INFO: === checking if optimization conditions were reached ===
1 day, 19:51:35.402312 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 19:51:35.404603 INFO: Updating optimization_manager: rt_error            : 544.7886970503621 -> 264.9260580201012
1 day, 19:51:35.404745 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 264.9261.
1 day, 19:51:35.404822 INFO: ==============================================
1 day, 19:51:35.404906 INFO: Starting optimization step 2.
1 day, 19:51:35.404984 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 19:51:35.405064 INFO: Using python extraction backend
1 day, 19:51:35.405188 PROGRESS: Extracting batch of 407917 precursors
1 day, 19:51:35.405270 INFO: === Search parameters used ===
1 day, 19:51:35.405330 INFO: rt_error       : 264.9260580201012
1 day, 19:51:35.405379 INFO: mobility_error : 0.1
1 day, 19:51:35.405427 INFO: num_candidates : 3
1 day, 19:51:35.405473 INFO: ms1_error      : 15.0
1 day, 19:51:35.405519 INFO: ms2_error      : 15.0
1 day, 19:51:35.405565 INFO: fwhm_rt        : 2.681373119354248
1 day, 19:51:35.405609 INFO: quant_window   : 3
1 day, 19:51:35.405654 INFO: ==============================================
1 day, 19:51:35.511273 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 19:51:35.511423 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 19:51:35.511479 INFO: FWHM in RT is 2.68 seconds, sigma is 0.45
1 day, 19:51:35.511504 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.07
1 day, 19:51:35.512293 INFO: Starting candidate selection
1 day, 19:55:18.720195 INFO: Starting candidate scoring
1 day, 19:55:30.207307 INFO: Finished candidate processing
1 day, 19:55:30.207553 INFO: Collecting candidate features
1 day, 19:55:31.983065 WARNING: intensity_correlation has 2701 NaNs ( 0.28 % out of 948594)
1 day, 19:55:31.984114 WARNING: height_correlation has 280 NaNs ( 0.03 % out of 948594)
1 day, 19:55:32.019202 INFO: Collecting fragment features
1 day, 19:55:32.535871 INFO: Finished candidate scoring
1 day, 19:55:33.163126 INFO: performing precursor FDR with 47 features
1 day, 19:55:33.163270 INFO: Decoy channel: -1
1 day, 19:55:33.163303 INFO: competitive: True
1 day, 19:55:33.406561 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:55:33.558566 WARNING: dropped 1440 target PSMs due to missing features
1 day, 19:55:33.558744 WARNING: dropped 1395 decoy PSMs due to missing features
1 day, 19:55:33.929103 INFO: Estimating optimal hyperparameters - samples: 756,607, batch_size: 3,099, learning_rate: 8.70e-04
1 day, 19:55:33.930811 INFO: Using random state 918345 for train-test-split
1 day, 19:55:56.454700 INFO: Test AUC: 0.548
1 day, 19:55:56.454878 INFO: Train AUC: 0.570
1 day, 19:55:56.454915 INFO: AUC difference: 3.71%
1 day, 19:55:57.018857 INFO: Resetting torch num_threads to 80
1 day, 19:55:57.037197 PROGRESS: === Extracted 948594 precursors and 5631460 fragments ===
1 day, 19:55:57.038048 INFO: === FDR correction performed with classifier version 14 ===
1 day, 19:55:57.070116 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:55:57.070469 PROGRESS: Total precursors accumulated: 183,297
1 day, 19:55:57.070544 PROGRESS: Target precursors: 105,529 (57.57%)
1 day, 19:55:57.070605 PROGRESS: Decoy precursors: 77,768 (42.43%)
1 day, 19:55:57.070660 PROGRESS: 
1 day, 19:55:57.070715 PROGRESS: Precursor Summary:
1 day, 19:55:57.073146 PROGRESS: Channel   0:	 0.050 FDR:   387; 0.010 FDR:   236; 0.001 FDR:   113
1 day, 19:55:57.073272 PROGRESS: 
1 day, 19:55:57.073337 PROGRESS: Protein Summary:
1 day, 19:55:57.075524 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   197; 0.001 FDR:   103
1 day, 19:55:57.075640 PROGRESS: =========================================================================
1 day, 19:55:57.080887 INFO: Target number of precursors reached.
1 day, 19:55:57.695664 INFO: fragments_df: keeping 3805 of 5631460 [sum(precursor_idx_mask)=6278 sum(mass_error_mask)=5631367 stop_rank=3805
1 day, 19:55:58.730400 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:55:58.870686 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:55:59.005054 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:55:59.146224 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:55:59.687514 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 19:55:59.688001 INFO: Using score_cutoff 23.058522116661074 (fac=0.99, q=1)
1 day, 19:55:59.688336 INFO: Updating optimization_manager: fwhm_rt             : 2.681373119354248 -> 2.628012180328369
1 day, 19:55:59.688423 INFO: Updating optimization_manager: fwhm_mobility       : 0.005673648323863745 -> 0.005505276843905449
1 day, 19:55:59.688482 INFO: Updating optimization_manager: score_cutoff        : 24.52590063858032 -> 23.058522116661074
1 day, 19:55:59.688546 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:55:59.740131 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:56:00.000504 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:56:00.060868 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:56:00.565196 INFO: === checking if optimization conditions were reached ===
1 day, 19:56:00.565504 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 19:56:00.567863 INFO: Updating optimization_manager: rt_error            : 264.9260580201012 -> 201.3076300016275
1 day, 19:56:00.568005 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 201.3076.
1 day, 19:56:00.568085 INFO: ==============================================
1 day, 19:56:00.568172 INFO: Starting optimization step 3.
1 day, 19:56:00.568248 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 19:56:00.568317 INFO: Using python extraction backend
1 day, 19:56:00.568434 PROGRESS: Extracting batch of 407917 precursors
1 day, 19:56:00.568512 INFO: === Search parameters used ===
1 day, 19:56:00.568570 INFO: rt_error       : 201.3076300016275
1 day, 19:56:00.568622 INFO: mobility_error : 0.1
1 day, 19:56:00.568674 INFO: num_candidates : 3
1 day, 19:56:00.568722 INFO: ms1_error      : 15.0
1 day, 19:56:00.568770 INFO: ms2_error      : 15.0
1 day, 19:56:00.568818 INFO: fwhm_rt        : 2.628012180328369
1 day, 19:56:00.568865 INFO: quant_window   : 3
1 day, 19:56:00.568912 INFO: ==============================================
1 day, 19:56:00.678408 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 19:56:00.678560 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 19:56:00.678608 INFO: FWHM in RT is 2.63 seconds, sigma is 0.44
1 day, 19:56:00.678639 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.98
1 day, 19:56:00.679384 INFO: Starting candidate selection
1 day, 19:58:51.264233 INFO: Starting candidate scoring
1 day, 19:59:02.524121 INFO: Finished candidate processing
1 day, 19:59:02.524316 INFO: Collecting candidate features
1 day, 19:59:04.241645 WARNING: intensity_correlation has 3219 NaNs ( 0.35 % out of 919590)
1 day, 19:59:04.242675 WARNING: height_correlation has 348 NaNs ( 0.04 % out of 919590)
1 day, 19:59:04.275507 INFO: Collecting fragment features
1 day, 19:59:04.769422 INFO: Finished candidate scoring
1 day, 19:59:05.409825 INFO: performing precursor FDR with 47 features
1 day, 19:59:05.409989 INFO: Decoy channel: -1
1 day, 19:59:05.410018 INFO: competitive: True
1 day, 19:59:05.645310 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:59:05.792839 WARNING: dropped 1731 target PSMs due to missing features
1 day, 19:59:05.793004 WARNING: dropped 1643 decoy PSMs due to missing features
1 day, 19:59:06.095454 INFO: Estimating optimal hyperparameters - samples: 732,972, batch_size: 3,002, learning_rate: 8.56e-04
1 day, 19:59:06.096800 INFO: Using random state 918345 for train-test-split
1 day, 19:59:26.292822 INFO: Test AUC: 0.546
1 day, 19:59:26.293037 INFO: Train AUC: 0.566
1 day, 19:59:26.293074 INFO: AUC difference: 3.55%
1 day, 19:59:26.857797 INFO: Resetting torch num_threads to 80
1 day, 19:59:26.875729 PROGRESS: === Extracted 919590 precursors and 5257995 fragments ===
1 day, 19:59:26.876590 INFO: === FDR correction performed with classifier version 14 ===
1 day, 19:59:26.907298 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:59:26.907578 PROGRESS: Total precursors accumulated: 181,366
1 day, 19:59:26.907653 PROGRESS: Target precursors: 104,131 (57.41%)
1 day, 19:59:26.907713 PROGRESS: Decoy precursors: 77,235 (42.59%)
1 day, 19:59:26.907766 PROGRESS: 
1 day, 19:59:26.907818 PROGRESS: Precursor Summary:
1 day, 19:59:26.910136 PROGRESS: Channel   0:	 0.050 FDR:   371; 0.010 FDR:   265; 0.001 FDR:   208
1 day, 19:59:26.910247 PROGRESS: 
1 day, 19:59:26.910312 PROGRESS: Protein Summary:
1 day, 19:59:26.912453 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   225; 0.001 FDR:   172
1 day, 19:59:26.912556 PROGRESS: =========================================================================
1 day, 19:59:26.917558 INFO: Target number of precursors reached.
1 day, 19:59:27.497008 INFO: fragments_df: keeping 4164 of 5257995 [sum(precursor_idx_mask)=6841 sum(mass_error_mask)=5257920 stop_rank=4164
1 day, 19:59:28.532809 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:59:28.675322 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:59:28.814892 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:59:28.958330 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:59:29.513881 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 19:59:29.514363 INFO: Using score_cutoff 23.278173362731934 (fac=0.99, q=1)
1 day, 19:59:29.514706 INFO: Updating optimization_manager: fwhm_rt             : 2.628012180328369 -> 2.6850008964538574
1 day, 19:59:29.514802 INFO: Updating optimization_manager: fwhm_mobility       : 0.005505276843905449 -> 0.00574040412902832
1 day, 19:59:29.514867 INFO: Updating optimization_manager: score_cutoff        : 23.058522116661074 -> 23.278173362731934
1 day, 19:59:29.514935 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 19:59:29.566901 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 19:59:29.823426 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 19:59:29.881403 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 19:59:30.394180 INFO: === checking if optimization conditions were reached ===
1 day, 19:59:30.394468 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 19:59:30.396873 INFO: Updating optimization_manager: rt_error            : 201.3076300016275 -> 190.83953179580507
1 day, 19:59:30.397009 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 190.8395.
1 day, 19:59:30.397088 INFO: ==============================================
1 day, 19:59:30.397171 INFO: Starting optimization step 4.
1 day, 19:59:30.397241 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 19:59:30.397315 INFO: Using python extraction backend
1 day, 19:59:30.397431 PROGRESS: Extracting batch of 407917 precursors
1 day, 19:59:30.397505 INFO: === Search parameters used ===
1 day, 19:59:30.397562 INFO: rt_error       : 190.83953179580507
1 day, 19:59:30.397612 INFO: mobility_error : 0.1
1 day, 19:59:30.397661 INFO: num_candidates : 3
1 day, 19:59:30.397713 INFO: ms1_error      : 15.0
1 day, 19:59:30.397774 INFO: ms2_error      : 15.0
1 day, 19:59:30.397823 INFO: fwhm_rt        : 2.6850008964538574
1 day, 19:59:30.397889 INFO: quant_window   : 3
1 day, 19:59:30.397945 INFO: ==============================================
1 day, 19:59:30.508433 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 19:59:30.508583 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 19:59:30.508646 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
1 day, 19:59:30.508673 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.11
1 day, 19:59:30.509365 INFO: Starting candidate selection
1 day, 20:02:11.927166 INFO: Starting candidate scoring
1 day, 20:02:23.105657 INFO: Finished candidate processing
1 day, 20:02:23.106066 INFO: Collecting candidate features
1 day, 20:02:24.867432 WARNING: intensity_correlation has 3333 NaNs ( 0.36 % out of 917058)
1 day, 20:02:24.868482 WARNING: height_correlation has 352 NaNs ( 0.04 % out of 917058)
1 day, 20:02:24.900921 INFO: Collecting fragment features
1 day, 20:02:25.399851 INFO: Finished candidate scoring
1 day, 20:02:26.000542 INFO: performing precursor FDR with 47 features
1 day, 20:02:26.000690 INFO: Decoy channel: -1
1 day, 20:02:26.000722 INFO: competitive: True
1 day, 20:02:26.228980 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:02:26.373390 WARNING: dropped 1745 target PSMs due to missing features
1 day, 20:02:26.373567 WARNING: dropped 1733 decoy PSMs due to missing features
1 day, 20:02:26.684602 INFO: Estimating optimal hyperparameters - samples: 730,864, batch_size: 2,993, learning_rate: 8.55e-04
1 day, 20:02:26.686118 INFO: Using random state 918345 for train-test-split
1 day, 20:02:48.112317 INFO: Test AUC: 0.550
1 day, 20:02:48.112497 INFO: Train AUC: 0.567
1 day, 20:02:48.112536 INFO: AUC difference: 3.02%
1 day, 20:02:48.639404 INFO: Resetting torch num_threads to 80
1 day, 20:02:48.657121 PROGRESS: === Extracted 917058 precursors and 5217739 fragments ===
1 day, 20:02:48.658046 INFO: === FDR correction performed with classifier version 14 ===
1 day, 20:02:48.688198 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:02:48.688513 PROGRESS: Total precursors accumulated: 181,275
1 day, 20:02:48.688588 PROGRESS: Target precursors: 103,462 (57.07%)
1 day, 20:02:48.688652 PROGRESS: Decoy precursors: 77,813 (42.93%)
1 day, 20:02:48.688707 PROGRESS: 
1 day, 20:02:48.688760 PROGRESS: Precursor Summary:
1 day, 20:02:48.690969 PROGRESS: Channel   0:	 0.050 FDR:   212; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 20:02:48.691079 PROGRESS: 
1 day, 20:02:48.691144 PROGRESS: Protein Summary:
1 day, 20:02:48.693185 PROGRESS: Channel   0:	 0.050 FDR:   178; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 20:02:48.693288 PROGRESS: =========================================================================
1 day, 20:02:48.698390 INFO: Target number of precursors not reached yet.
1 day, 20:02:49.748803 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:02:49.801421 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:02:50.063558 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:02:50.121181 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:02:50.613025 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:02:50.613334 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 20:02:50.613457 INFO: Starting optimization step 5.
1 day, 20:02:50.613536 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 20:02:50.613612 INFO: Using python extraction backend
1 day, 20:02:50.613732 PROGRESS: Extracting batch of 408390 precursors
1 day, 20:02:50.613818 INFO: === Search parameters used ===
1 day, 20:02:50.613893 INFO: rt_error       : 190.83953179580507
1 day, 20:02:50.613954 INFO: mobility_error : 0.1
1 day, 20:02:50.614007 INFO: num_candidates : 3
1 day, 20:02:50.614056 INFO: ms1_error      : 15.0
1 day, 20:02:50.614106 INFO: ms2_error      : 15.0
1 day, 20:02:50.614157 INFO: fwhm_rt        : 2.6850008964538574
1 day, 20:02:50.614211 INFO: quant_window   : 3
1 day, 20:02:50.614260 INFO: ==============================================
1 day, 20:02:50.724363 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 20:02:50.724523 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 20:02:50.724586 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
1 day, 20:02:50.724616 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.11
1 day, 20:02:50.725386 INFO: Starting candidate selection
1 day, 20:05:35.879564 INFO: Starting candidate scoring
1 day, 20:05:47.011256 INFO: Finished candidate processing
1 day, 20:05:47.011891 INFO: Collecting candidate features
1 day, 20:05:48.840188 WARNING: intensity_correlation has 3150 NaNs ( 0.34 % out of 916591)
1 day, 20:05:48.841203 WARNING: height_correlation has 328 NaNs ( 0.04 % out of 916591)
1 day, 20:05:48.873351 INFO: Collecting fragment features
1 day, 20:05:49.345365 INFO: Finished candidate scoring
1 day, 20:05:50.391834 INFO: performing precursor FDR with 47 features
1 day, 20:05:50.392009 INFO: Decoy channel: -1
1 day, 20:05:50.392060 INFO: competitive: True
1 day, 20:05:51.101608 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:05:51.373823 WARNING: dropped 3396 target PSMs due to missing features
1 day, 20:05:51.374005 WARNING: dropped 3380 decoy PSMs due to missing features
1 day, 20:05:52.139144 INFO: Estimating optimal hyperparameters - samples: 1,461,498, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 20:05:52.142339 INFO: Using random state 918345 for train-test-split
1 day, 20:06:29.280823 INFO: Test AUC: 0.549
1 day, 20:06:29.281013 INFO: Train AUC: 0.561
1 day, 20:06:29.281052 INFO: AUC difference: 2.06%
1 day, 20:06:30.150073 INFO: Resetting torch num_threads to 80
1 day, 20:06:30.413474 PROGRESS: === Extracted 1833649 precursors and 10431441 fragments ===
1 day, 20:06:30.414633 INFO: === FDR correction performed with classifier version 14 ===
1 day, 20:06:30.473634 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:06:30.473997 PROGRESS: Total precursors accumulated: 362,315
1 day, 20:06:30.474104 PROGRESS: Target precursors: 205,489 (56.72%)
1 day, 20:06:30.474168 PROGRESS: Decoy precursors: 156,826 (43.28%)
1 day, 20:06:30.474223 PROGRESS: 
1 day, 20:06:30.474276 PROGRESS: Precursor Summary:
1 day, 20:06:30.477908 PROGRESS: Channel   0:	 0.050 FDR:   650; 0.010 FDR:   364; 0.001 FDR:    29
1 day, 20:06:30.478043 PROGRESS: 
1 day, 20:06:30.478107 PROGRESS: Protein Summary:
1 day, 20:06:30.481187 PROGRESS: Channel   0:	 0.050 FDR:   508; 0.010 FDR:   269; 0.001 FDR:    28
1 day, 20:06:30.481293 PROGRESS: =========================================================================
1 day, 20:06:30.488150 INFO: Target number of precursors reached.
1 day, 20:06:31.692318 INFO: fragments_df: keeping 5000 of 10431441 [sum(precursor_idx_mask)=9742 sum(mass_error_mask)=10431264 stop_rank=5000
1 day, 20:06:33.122261 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:06:33.249020 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:06:33.383492 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:06:33.531137 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:06:34.244459 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:06:34.244940 INFO: Using score_cutoff 21.590608438682555 (fac=0.99, q=1)
1 day, 20:06:34.245280 INFO: Updating optimization_manager: fwhm_rt             : 2.6850008964538574 -> 2.6337437629699707
1 day, 20:06:34.245369 INFO: Updating optimization_manager: fwhm_mobility       : 0.00574040412902832 -> 0.005969944875687361
1 day, 20:06:34.245434 INFO: Updating optimization_manager: score_cutoff        : 23.278173362731934 -> 21.590608438682555
1 day, 20:06:34.245511 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:06:34.351284 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:06:34.876797 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:06:34.982718 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:06:35.979501 INFO: === checking if optimization conditions were reached ===
1 day, 20:06:35.979810 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 20:06:35.981348 INFO: Updating optimization_manager: rt_error            : 190.83953179580507 -> 201.3076300016275
1 day, 20:06:35.981517 INFO: Updating optimization_manager: classifier_version  : 14 -> 18
1 day, 20:06:35.981629 INFO: Updating optimization_manager: score_cutoff        : 21.590608438682555 -> 23.278173362731934
1 day, 20:06:35.981728 INFO: Updating optimization_manager: fwhm_rt             : 2.6337437629699707 -> 2.6850008964538574
1 day, 20:06:35.981827 INFO: Updating optimization_manager: fwhm_mobility       : 0.005969944875687361 -> 0.00574040412902832
1 day, 20:06:35.981940 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 201.3076 found after 5 searches.
1 day, 20:06:35.982017 INFO: ==============================================
1 day, 20:06:35.982096 PROGRESS: Optimization finished for rt_error.
1 day, 20:06:36.613059 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:06:36.665302 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:06:36.918495 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:06:36.977885 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:06:37.457040 INFO: Starting optimization step 0.
1 day, 20:06:37.457324 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 20:06:37.457414 INFO: Using python extraction backend
1 day, 20:06:37.457582 PROGRESS: Extracting batch of 407917 precursors
1 day, 20:06:37.457678 INFO: === Search parameters used ===
1 day, 20:06:37.457744 INFO: rt_error       : 201.3076300016275
1 day, 20:06:37.457797 INFO: mobility_error : 0.1
1 day, 20:06:37.457847 INFO: num_candidates : 3
1 day, 20:06:37.457911 INFO: ms1_error      : 15.0
1 day, 20:06:37.457960 INFO: ms2_error      : 15.0
1 day, 20:06:37.458008 INFO: fwhm_rt        : 2.6850008964538574
1 day, 20:06:37.458078 INFO: quant_window   : 3
1 day, 20:06:37.458131 INFO: ==============================================
1 day, 20:06:37.571085 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 20:06:37.571242 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 20:06:37.571293 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
1 day, 20:06:37.571321 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.11
1 day, 20:06:37.572063 INFO: Starting candidate selection
1 day, 20:09:26.073797 INFO: Starting candidate scoring
1 day, 20:09:37.126294 INFO: Finished candidate processing
1 day, 20:09:37.126546 INFO: Collecting candidate features
1 day, 20:09:38.998059 WARNING: intensity_correlation has 3263 NaNs ( 0.35 % out of 920103)
1 day, 20:09:38.999178 WARNING: height_correlation has 334 NaNs ( 0.04 % out of 920103)
1 day, 20:09:39.031422 INFO: Collecting fragment features
1 day, 20:09:39.508703 INFO: Finished candidate scoring
1 day, 20:09:40.139476 INFO: performing precursor FDR with 47 features
1 day, 20:09:40.139621 INFO: Decoy channel: -1
1 day, 20:09:40.139652 INFO: competitive: True
1 day, 20:09:40.363592 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:09:40.501140 WARNING: dropped 1729 target PSMs due to missing features
1 day, 20:09:40.501305 WARNING: dropped 1679 decoy PSMs due to missing features
1 day, 20:09:40.790309 INFO: Estimating optimal hyperparameters - samples: 733,356, batch_size: 3,003, learning_rate: 8.56e-04
1 day, 20:09:40.791901 INFO: Using random state 691184 for train-test-split
1 day, 20:10:02.185101 INFO: Test AUC: 0.555
1 day, 20:10:02.185270 INFO: Train AUC: 0.574
1 day, 20:10:02.185307 INFO: AUC difference: 3.44%
1 day, 20:10:02.736003 INFO: Resetting torch num_threads to 80
1 day, 20:10:02.753583 PROGRESS: === Extracted 920103 precursors and 5261400 fragments ===
1 day, 20:10:02.754446 INFO: === FDR correction performed with classifier version 18 ===
1 day, 20:10:02.784159 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:02.784429 PROGRESS: Total precursors accumulated: 181,403
1 day, 20:10:02.784521 PROGRESS: Target precursors: 104,866 (57.81%)
1 day, 20:10:02.784588 PROGRESS: Decoy precursors: 76,537 (42.19%)
1 day, 20:10:02.784643 PROGRESS: 
1 day, 20:10:02.784696 PROGRESS: Precursor Summary:
1 day, 20:10:02.786873 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:     6; 0.001 FDR:     6
1 day, 20:10:02.786994 PROGRESS: 
1 day, 20:10:02.787065 PROGRESS: Protein Summary:
1 day, 20:10:02.789132 PROGRESS: Channel   0:	 0.050 FDR:   271; 0.010 FDR:     6; 0.001 FDR:     6
1 day, 20:10:02.789233 PROGRESS: =========================================================================
1 day, 20:10:02.798945 INFO: Target number of precursors not reached yet.
1 day, 20:10:03.810633 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:10:03.871166 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:10:04.131972 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:10:04.189182 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:10:04.711244 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:10:04.711583 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 20:10:04.711713 INFO: Starting optimization step 1.
1 day, 20:10:04.711797 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 20:10:04.711870 INFO: Using python extraction backend
1 day, 20:10:04.711996 PROGRESS: Extracting batch of 408390 precursors
1 day, 20:10:04.712089 INFO: === Search parameters used ===
1 day, 20:10:04.712153 INFO: rt_error       : 201.3076300016275
1 day, 20:10:04.712207 INFO: mobility_error : 0.1
1 day, 20:10:04.712260 INFO: num_candidates : 3
1 day, 20:10:04.712331 INFO: ms1_error      : 15.0
1 day, 20:10:04.712383 INFO: ms2_error      : 15.0
1 day, 20:10:04.712430 INFO: fwhm_rt        : 2.6850008964538574
1 day, 20:10:04.712479 INFO: quant_window   : 3
1 day, 20:10:04.712527 INFO: ==============================================
1 day, 20:10:04.820084 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 20:10:04.820231 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 20:10:04.820282 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
1 day, 20:10:04.820308 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.11
1 day, 20:10:04.821099 INFO: Starting candidate selection
1 day, 20:12:48.361580 INFO: Starting candidate scoring
1 day, 20:12:59.581373 INFO: Finished candidate processing
1 day, 20:12:59.581595 INFO: Collecting candidate features
1 day, 20:13:01.344043 WARNING: intensity_correlation has 3036 NaNs ( 0.33 % out of 919318)
1 day, 20:13:01.345049 WARNING: height_correlation has 330 NaNs ( 0.04 % out of 919318)
1 day, 20:13:01.377342 INFO: Collecting fragment features
1 day, 20:13:01.866592 INFO: Finished candidate scoring
1 day, 20:13:03.074396 INFO: performing precursor FDR with 47 features
1 day, 20:13:03.074568 INFO: Decoy channel: -1
1 day, 20:13:03.074599 INFO: competitive: True
1 day, 20:13:03.746310 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:13:04.008217 WARNING: dropped 3323 target PSMs due to missing features
1 day, 20:13:04.008388 WARNING: dropped 3276 decoy PSMs due to missing features
1 day, 20:13:04.729031 INFO: Estimating optimal hyperparameters - samples: 1,466,257, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 20:13:04.731656 INFO: Using random state 691184 for train-test-split
1 day, 20:13:41.466796 INFO: Test AUC: 0.551
1 day, 20:13:41.467018 INFO: Train AUC: 0.564
1 day, 20:13:41.467057 INFO: AUC difference: 2.30%
1 day, 20:13:42.287878 INFO: Resetting torch num_threads to 80
1 day, 20:13:42.536958 PROGRESS: === Extracted 1839421 precursors and 10516233 fragments ===
1 day, 20:13:42.538170 INFO: === FDR correction performed with classifier version 18 ===
1 day, 20:13:42.596632 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:13:42.596960 PROGRESS: Total precursors accumulated: 362,557
1 day, 20:13:42.597066 PROGRESS: Target precursors: 206,238 (56.88%)
1 day, 20:13:42.597129 PROGRESS: Decoy precursors: 156,319 (43.12%)
1 day, 20:13:42.597184 PROGRESS: 
1 day, 20:13:42.597235 PROGRESS: Precursor Summary:
1 day, 20:13:42.600819 PROGRESS: Channel   0:	 0.050 FDR:   691; 0.010 FDR:   547; 0.001 FDR:   415
1 day, 20:13:42.600957 PROGRESS: 
1 day, 20:13:42.601023 PROGRESS: Protein Summary:
1 day, 20:13:42.604233 PROGRESS: Channel   0:	 0.050 FDR:   548; 0.010 FDR:   419; 0.001 FDR:   312
1 day, 20:13:42.604338 PROGRESS: =========================================================================
1 day, 20:13:42.609274 INFO: Target number of precursors reached.
1 day, 20:13:43.766273 INFO: fragments_df: keeping 5000 of 10516233 [sum(precursor_idx_mask)=14132 sum(mass_error_mask)=10516070 stop_rank=5000
1 day, 20:13:44.830599 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:13:44.983119 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:13:45.144628 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:13:45.303250 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:13:46.019884 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:13:46.020361 INFO: Using score_cutoff 22.460447955322266 (fac=0.99, q=1)
1 day, 20:13:46.020719 INFO: Updating optimization_manager: fwhm_rt             : 2.6850008964538574 -> 2.616802930831909
1 day, 20:13:46.020809 INFO: Updating optimization_manager: fwhm_mobility       : 0.00574040412902832 -> 0.00538262166082859
1 day, 20:13:46.020871 INFO: Updating optimization_manager: score_cutoff        : 23.278173362731934 -> 22.460447955322266
1 day, 20:13:46.020933 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:13:46.072441 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:13:46.325908 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:13:46.381506 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:13:46.889542 INFO: === checking if optimization conditions were reached ===
1 day, 20:13:46.889839 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:13:46.891931 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.08508560312872664
1 day, 20:13:46.892065 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0851.
1 day, 20:13:46.892143 INFO: ==============================================
1 day, 20:13:46.892223 INFO: Starting optimization step 2.
1 day, 20:13:46.892309 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 20:13:46.892380 INFO: Using python extraction backend
1 day, 20:13:46.892488 PROGRESS: Extracting batch of 407917 precursors
1 day, 20:13:46.892562 INFO: === Search parameters used ===
1 day, 20:13:46.892619 INFO: rt_error       : 201.3076300016275
1 day, 20:13:46.892671 INFO: mobility_error : 0.08508560312872664
1 day, 20:13:46.892720 INFO: num_candidates : 3
1 day, 20:13:46.892770 INFO: ms1_error      : 15.0
1 day, 20:13:46.892820 INFO: ms2_error      : 15.0
1 day, 20:13:46.892870 INFO: fwhm_rt        : 2.616802930831909
1 day, 20:13:46.892920 INFO: quant_window   : 3
1 day, 20:13:46.892968 INFO: ==============================================
1 day, 20:13:47.002164 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 20:13:47.002319 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 20:13:47.002365 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
1 day, 20:13:47.002393 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.92
1 day, 20:13:47.003170 INFO: Starting candidate selection
1 day, 20:16:09.377731 INFO: Starting candidate scoring
1 day, 20:16:20.391027 INFO: Finished candidate processing
1 day, 20:16:20.391424 INFO: Collecting candidate features
1 day, 20:16:22.220522 WARNING: intensity_correlation has 3284 NaNs ( 0.36 % out of 902351)
1 day, 20:16:22.221529 WARNING: height_correlation has 339 NaNs ( 0.04 % out of 902351)
1 day, 20:16:22.252984 INFO: Collecting fragment features
1 day, 20:16:22.717825 INFO: Finished candidate scoring
1 day, 20:16:23.312839 INFO: performing precursor FDR with 47 features
1 day, 20:16:23.312991 INFO: Decoy channel: -1
1 day, 20:16:23.313019 INFO: competitive: True
1 day, 20:16:23.525034 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:16:23.660185 WARNING: dropped 1728 target PSMs due to missing features
1 day, 20:16:23.660356 WARNING: dropped 1699 decoy PSMs due to missing features
1 day, 20:16:23.960184 INFO: Estimating optimal hyperparameters - samples: 719,139, batch_size: 2,945, learning_rate: 8.48e-04
1 day, 20:16:23.962073 INFO: Using random state 691184 for train-test-split
1 day, 20:16:43.256471 INFO: Test AUC: 0.557
1 day, 20:16:43.256644 INFO: Train AUC: 0.574
1 day, 20:16:43.256681 INFO: AUC difference: 3.00%
1 day, 20:16:43.795642 INFO: Resetting torch num_threads to 80
1 day, 20:16:43.813098 PROGRESS: === Extracted 902351 precursors and 5135271 fragments ===
1 day, 20:16:43.813980 INFO: === FDR correction performed with classifier version 18 ===
1 day, 20:16:43.843176 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:16:43.843459 PROGRESS: Total precursors accumulated: 178,687
1 day, 20:16:43.843533 PROGRESS: Target precursors: 103,028 (57.66%)
1 day, 20:16:43.843592 PROGRESS: Decoy precursors: 75,659 (42.34%)
1 day, 20:16:43.843646 PROGRESS: 
1 day, 20:16:43.843701 PROGRESS: Precursor Summary:
1 day, 20:16:43.845903 PROGRESS: Channel   0:	 0.050 FDR:   392; 0.010 FDR:   185; 0.001 FDR:   103
1 day, 20:16:43.846011 PROGRESS: 
1 day, 20:16:43.846091 PROGRESS: Protein Summary:
1 day, 20:16:43.848207 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   156; 0.001 FDR:    93
1 day, 20:16:43.848310 PROGRESS: =========================================================================
1 day, 20:16:43.857950 INFO: Target number of precursors not reached yet.
1 day, 20:16:44.862426 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:16:44.914267 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:16:45.172104 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:16:45.225619 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:16:45.726789 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:16:45.727113 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 20:16:45.727231 INFO: Starting optimization step 3.
1 day, 20:16:45.727313 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 20:16:45.727382 INFO: Using python extraction backend
1 day, 20:16:45.727501 PROGRESS: Extracting batch of 408390 precursors
1 day, 20:16:45.727585 INFO: === Search parameters used ===
1 day, 20:16:45.727643 INFO: rt_error       : 201.3076300016275
1 day, 20:16:45.727698 INFO: mobility_error : 0.08508560312872664
1 day, 20:16:45.727783 INFO: num_candidates : 3
1 day, 20:16:45.727836 INFO: ms1_error      : 15.0
1 day, 20:16:45.727885 INFO: ms2_error      : 15.0
1 day, 20:16:45.727948 INFO: fwhm_rt        : 2.616802930831909
1 day, 20:16:45.727999 INFO: quant_window   : 3
1 day, 20:16:45.728047 INFO: ==============================================
1 day, 20:16:45.836806 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 20:16:45.836964 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 20:16:45.837016 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
1 day, 20:16:45.837043 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.92
1 day, 20:16:45.837794 INFO: Starting candidate selection
1 day, 20:19:14.515855 INFO: Starting candidate scoring
1 day, 20:19:25.492691 INFO: Finished candidate processing
1 day, 20:19:25.492933 INFO: Collecting candidate features
1 day, 20:19:27.074111 WARNING: intensity_correlation has 3100 NaNs ( 0.34 % out of 901653)
1 day, 20:19:27.075213 WARNING: height_correlation has 336 NaNs ( 0.04 % out of 901653)
1 day, 20:19:27.109098 INFO: Collecting fragment features
1 day, 20:19:27.565834 INFO: Finished candidate scoring
1 day, 20:19:28.663299 INFO: performing precursor FDR with 47 features
1 day, 20:19:28.663462 INFO: Decoy channel: -1
1 day, 20:19:28.663491 INFO: competitive: True
1 day, 20:19:29.346243 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:19:29.595533 WARNING: dropped 3334 target PSMs due to missing features
1 day, 20:19:29.595707 WARNING: dropped 3338 decoy PSMs due to missing features
1 day, 20:19:30.208589 INFO: Estimating optimal hyperparameters - samples: 1,437,865, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 20:19:30.211655 INFO: Using random state 691184 for train-test-split
1 day, 20:20:05.476806 INFO: Test AUC: 0.551
1 day, 20:20:05.476995 INFO: Train AUC: 0.565
1 day, 20:20:05.477032 INFO: AUC difference: 2.43%
1 day, 20:20:06.295291 INFO: Resetting torch num_threads to 80
1 day, 20:20:06.537555 PROGRESS: === Extracted 1804004 precursors and 10264564 fragments ===
1 day, 20:20:06.538707 INFO: === FDR correction performed with classifier version 18 ===
1 day, 20:20:06.598462 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:20:06.598805 PROGRESS: Total precursors accumulated: 357,187
1 day, 20:20:06.598884 PROGRESS: Target precursors: 203,478 (56.97%)
1 day, 20:20:06.598947 PROGRESS: Decoy precursors: 153,709 (43.03%)
1 day, 20:20:06.599003 PROGRESS: 
1 day, 20:20:06.599073 PROGRESS: Precursor Summary:
1 day, 20:20:06.602402 PROGRESS: Channel   0:	 0.050 FDR:   692; 0.010 FDR:   502; 0.001 FDR:   321
1 day, 20:20:06.602516 PROGRESS: 
1 day, 20:20:06.602585 PROGRESS: Protein Summary:
1 day, 20:20:06.605686 PROGRESS: Channel   0:	 0.050 FDR:   551; 0.010 FDR:   381; 0.001 FDR:   240
1 day, 20:20:06.605796 PROGRESS: =========================================================================
1 day, 20:20:06.610726 INFO: Target number of precursors reached.
1 day, 20:20:07.773665 INFO: fragments_df: keeping 5000 of 10264564 [sum(precursor_idx_mask)=12767 sum(mass_error_mask)=10264393 stop_rank=5000
1 day, 20:20:08.813157 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:08.938064 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:09.078717 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:09.212606 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:09.859890 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:20:09.860359 INFO: Using score_cutoff 21.850621339416502 (fac=0.99, q=1)
1 day, 20:20:09.860710 INFO: Updating optimization_manager: fwhm_rt             : 2.616802930831909 -> 2.6038661003112793
1 day, 20:20:09.860800 INFO: Updating optimization_manager: fwhm_mobility       : 0.00538262166082859 -> 0.005790237337350845
1 day, 20:20:09.860862 INFO: Updating optimization_manager: score_cutoff        : 22.460447955322266 -> 21.850621339416502
1 day, 20:20:09.860929 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:09.911334 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:10.166397 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:10.218641 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:10.700206 INFO: === checking if optimization conditions were reached ===
1 day, 20:20:10.700501 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:20:10.702535 INFO: Updating optimization_manager: mobility_error      : 0.08508560312872664 -> 0.07453467773209588
1 day, 20:20:10.702675 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0745.
1 day, 20:20:10.702754 INFO: ==============================================
1 day, 20:20:10.702834 INFO: Starting optimization step 4.
1 day, 20:20:10.702924 PROGRESS: === Extracting elution groups 0 to 204600 ===
1 day, 20:20:10.702992 INFO: Using python extraction backend
1 day, 20:20:10.703115 PROGRESS: Extracting batch of 407917 precursors
1 day, 20:20:10.703195 INFO: === Search parameters used ===
1 day, 20:20:10.703252 INFO: rt_error       : 201.3076300016275
1 day, 20:20:10.703302 INFO: mobility_error : 0.07453467773209588
1 day, 20:20:10.703350 INFO: num_candidates : 3
1 day, 20:20:10.703397 INFO: ms1_error      : 15.0
1 day, 20:20:10.703442 INFO: ms2_error      : 15.0
1 day, 20:20:10.703487 INFO: fwhm_rt        : 2.6038661003112793
1 day, 20:20:10.703531 INFO: quant_window   : 3
1 day, 20:20:10.703575 INFO: ==============================================
1 day, 20:20:10.809835 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 20:20:10.810101 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 20:20:10.810155 INFO: FWHM in RT is 2.60 seconds, sigma is 0.43
1 day, 20:20:10.810181 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.14
1 day, 20:20:10.810957 INFO: Starting candidate selection
1 day, 20:22:13.823911 INFO: Starting candidate scoring
1 day, 20:22:25.281055 INFO: Finished candidate processing
1 day, 20:22:25.281239 INFO: Collecting candidate features
1 day, 20:22:27.111874 WARNING: intensity_correlation has 3398 NaNs ( 0.38 % out of 886492)
1 day, 20:22:27.112883 WARNING: height_correlation has 349 NaNs ( 0.04 % out of 886492)
1 day, 20:22:27.144360 INFO: Collecting fragment features
1 day, 20:22:27.605424 INFO: Finished candidate scoring
1 day, 20:22:28.443494 INFO: performing precursor FDR with 47 features
1 day, 20:22:28.443652 INFO: Decoy channel: -1
1 day, 20:22:28.443682 INFO: competitive: True
1 day, 20:22:28.670615 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:28.808675 WARNING: dropped 1795 target PSMs due to missing features
1 day, 20:22:28.808855 WARNING: dropped 1748 decoy PSMs due to missing features
1 day, 20:22:29.107308 INFO: Estimating optimal hyperparameters - samples: 706,359, batch_size: 2,893, learning_rate: 8.40e-04
1 day, 20:22:29.109025 INFO: Using random state 691184 for train-test-split
1 day, 20:22:48.719851 INFO: Test AUC: 0.553
1 day, 20:22:48.720021 INFO: Train AUC: 0.574
1 day, 20:22:48.720057 INFO: AUC difference: 3.63%
1 day, 20:22:49.260937 INFO: Resetting torch num_threads to 80
1 day, 20:22:49.278190 PROGRESS: === Extracted 886492 precursors and 5022925 fragments ===
1 day, 20:22:49.279113 INFO: === FDR correction performed with classifier version 18 ===
1 day, 20:22:49.310703 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:49.311006 PROGRESS: Total precursors accumulated: 176,016
1 day, 20:22:49.311085 PROGRESS: Target precursors: 101,833 (57.85%)
1 day, 20:22:49.311147 PROGRESS: Decoy precursors: 74,183 (42.15%)
1 day, 20:22:49.311205 PROGRESS: 
1 day, 20:22:49.311261 PROGRESS: Precursor Summary:
1 day, 20:22:49.313474 PROGRESS: Channel   0:	 0.050 FDR:   392; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:22:49.313615 PROGRESS: 
1 day, 20:22:49.313681 PROGRESS: Protein Summary:
1 day, 20:22:49.315758 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:22:49.315873 PROGRESS: =========================================================================
1 day, 20:22:49.325788 INFO: Target number of precursors not reached yet.
1 day, 20:22:50.360526 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:50.416404 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:50.680174 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:50.736647 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:51.273617 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:22:51.273935 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 20:22:51.274069 INFO: Starting optimization step 5.
1 day, 20:22:51.274193 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 20:22:51.274279 INFO: Using python extraction backend
1 day, 20:22:51.274411 PROGRESS: Extracting batch of 408390 precursors
1 day, 20:22:51.274506 INFO: === Search parameters used ===
1 day, 20:22:51.274573 INFO: rt_error       : 201.3076300016275
1 day, 20:22:51.274637 INFO: mobility_error : 0.07453467773209588
1 day, 20:22:51.274695 INFO: num_candidates : 3
1 day, 20:22:51.274754 INFO: ms1_error      : 15.0
1 day, 20:22:51.274809 INFO: ms2_error      : 15.0
1 day, 20:22:51.274867 INFO: fwhm_rt        : 2.6038661003112793
1 day, 20:22:51.274922 INFO: quant_window   : 3
1 day, 20:22:51.274987 INFO: ==============================================
1 day, 20:22:51.389770 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 20:22:51.389954 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 20:22:51.390013 INFO: FWHM in RT is 2.60 seconds, sigma is 0.43
1 day, 20:22:51.390048 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.14
1 day, 20:22:51.390858 INFO: Starting candidate selection
1 day, 20:24:54.394860 INFO: Starting candidate scoring
1 day, 20:25:05.177824 INFO: Finished candidate processing
1 day, 20:25:05.178319 INFO: Collecting candidate features
1 day, 20:25:06.711977 WARNING: intensity_correlation has 3153 NaNs ( 0.36 % out of 885809)
1 day, 20:25:06.713071 WARNING: height_correlation has 337 NaNs ( 0.04 % out of 885809)
1 day, 20:25:06.747256 INFO: Collecting fragment features
1 day, 20:25:07.201719 INFO: Finished candidate scoring
1 day, 20:25:08.165772 INFO: performing precursor FDR with 47 features
1 day, 20:25:08.165972 INFO: Decoy channel: -1
1 day, 20:25:08.166009 INFO: competitive: True
1 day, 20:25:08.815462 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:25:09.083928 WARNING: dropped 3427 target PSMs due to missing features
1 day, 20:25:09.084123 WARNING: dropped 3420 decoy PSMs due to missing features
1 day, 20:25:09.689061 INFO: Estimating optimal hyperparameters - samples: 1,412,363, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 20:25:09.693420 INFO: Using random state 691184 for train-test-split
1 day, 20:25:46.199188 INFO: Test AUC: 0.551
1 day, 20:25:46.199373 INFO: Train AUC: 0.564
1 day, 20:25:46.199410 INFO: AUC difference: 2.26%
1 day, 20:25:47.034661 INFO: Resetting torch num_threads to 80
1 day, 20:25:47.358159 PROGRESS: === Extracted 1772301 precursors and 10039929 fragments ===
1 day, 20:25:47.359291 INFO: === FDR correction performed with classifier version 18 ===
1 day, 20:25:47.417040 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:25:47.417390 PROGRESS: Total precursors accumulated: 351,791
1 day, 20:25:47.417463 PROGRESS: Target precursors: 200,088 (56.88%)
1 day, 20:25:47.417523 PROGRESS: Decoy precursors: 151,703 (43.12%)
1 day, 20:25:47.417576 PROGRESS: 
1 day, 20:25:47.417629 PROGRESS: Precursor Summary:
1 day, 20:25:47.420908 PROGRESS: Channel   0:	 0.050 FDR:   730; 0.010 FDR:   508; 0.001 FDR:   414
1 day, 20:25:47.421020 PROGRESS: 
1 day, 20:25:47.421085 PROGRESS: Protein Summary:
1 day, 20:25:47.424193 PROGRESS: Channel   0:	 0.050 FDR:   590; 0.010 FDR:   385; 0.001 FDR:   305
1 day, 20:25:47.424303 PROGRESS: =========================================================================
1 day, 20:25:47.429186 INFO: Target number of precursors reached.
1 day, 20:25:48.569209 INFO: fragments_df: keeping 5000 of 10039929 [sum(precursor_idx_mask)=12998 sum(mass_error_mask)=10039760 stop_rank=5000
1 day, 20:25:49.228753 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:25:49.387351 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:25:49.528039 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:25:49.660283 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:25:50.310330 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:25:50.310831 INFO: Using score_cutoff 21.8643658864975 (fac=0.99, q=1)
1 day, 20:25:50.311192 INFO: Updating optimization_manager: fwhm_rt             : 2.6038661003112793 -> 2.618699312210083
1 day, 20:25:50.311285 INFO: Updating optimization_manager: fwhm_mobility       : 0.005790237337350845 -> 0.005671042948961258
1 day, 20:25:50.311350 INFO: Updating optimization_manager: score_cutoff        : 21.850621339416502 -> 21.8643658864975
1 day, 20:25:50.311426 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:25:50.363207 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:25:50.620973 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:25:50.675443 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:25:51.191818 INFO: === checking if optimization conditions were reached ===
1 day, 20:25:51.192130 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:25:51.193250 INFO: Updating optimization_manager: mobility_error      : 0.07453467773209588 -> 0.1
1 day, 20:25:51.193415 INFO: Updating optimization_manager: classifier_version  : 18 -> 22
1 day, 20:25:51.193524 INFO: Updating optimization_manager: score_cutoff        : 21.8643658864975 -> 22.460447955322266
1 day, 20:25:51.193622 INFO: Updating optimization_manager: fwhm_rt             : 2.618699312210083 -> 2.616802930831909
1 day, 20:25:51.193719 INFO: Updating optimization_manager: fwhm_mobility       : 0.005671042948961258 -> 0.00538262166082859
1 day, 20:25:51.193814 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 20:25:51.193916 INFO: ==============================================
1 day, 20:25:51.194004 PROGRESS: Optimization finished for mobility_error.
1 day, 20:25:51.812625 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:25:51.865618 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:25:52.120892 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:25:52.175459 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:25:52.691070 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:25:52.691391 PROGRESS: ==============================================
1 day, 20:25:52.691494 PROGRESS: ms2_error      : 15.0000
1 day, 20:25:52.691565 PROGRESS: ms1_error      : 15.0000
1 day, 20:25:52.691632 PROGRESS: rt_error       : 201.3076
1 day, 20:25:52.691696 PROGRESS: mobility_error : 0.1000
1 day, 20:25:52.691751 PROGRESS: ==============================================
1 day, 20:25:52.703210 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:25:54.388792 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:26:02.164973 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:26:03.958790 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:26:19.497560 INFO: Using python extraction backend
1 day, 20:26:19.498043 PROGRESS: Extracting batch of 12210649 precursors
1 day, 20:26:19.498145 INFO: === Search parameters used ===
1 day, 20:26:19.498222 INFO: rt_error       : 201.3076300016275
1 day, 20:26:19.498282 INFO: mobility_error : 0.1
1 day, 20:26:19.498338 INFO: num_candidates : 3
1 day, 20:26:19.498388 INFO: ms1_error      : 15.0
1 day, 20:26:19.498436 INFO: ms2_error      : 15.0
1 day, 20:26:19.498484 INFO: fwhm_rt        : 2.616802930831909
1 day, 20:26:19.498532 INFO: quant_window   : 3
1 day, 20:26:19.498582 INFO: ==============================================
1 day, 20:26:21.614777 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 20:26:21.614950 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 20:26:21.615000 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
1 day, 20:26:21.615028 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.92
1 day, 20:26:21.616224 INFO: Starting candidate selection
1 day, 21:48:03.219465 INFO: Removed 23521809 precursors with score below cutoff 22.460447955322266
1 day, 21:48:06.600351 INFO: Starting candidate scoring
1 day, 21:49:52.520767 INFO: Finished candidate processing
1 day, 21:49:52.520941 INFO: Collecting candidate features
1 day, 21:50:07.827858 WARNING: intensity_correlation has 6256 NaNs ( 0.07 % out of 8570798)
1 day, 21:50:07.835865 WARNING: height_correlation has 358 NaNs ( 0.00 % out of 8570798)
1 day, 21:50:08.132867 INFO: Collecting fragment features
1 day, 21:50:13.844212 INFO: Finished candidate scoring
1 day, 21:50:19.195176 INFO: === Performing FDR correction with classifier version 22 ===
1 day, 21:50:19.195786 INFO: performing precursor FDR with 47 features
1 day, 21:50:19.195830 INFO: Decoy channel: -1
1 day, 21:50:19.195862 INFO: competitive: True
1 day, 21:50:21.033843 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 21:50:22.137558 WARNING: dropped 3409 target PSMs due to missing features
1 day, 21:50:22.137733 WARNING: dropped 3078 decoy PSMs due to missing features
1 day, 21:50:25.646927 INFO: Estimating optimal hyperparameters - samples: 6,851,448, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 21:50:25.666133 INFO: Using random state 671367 for train-test-split
1 day, 21:53:37.060570 INFO: Test AUC: 0.551
1 day, 21:53:37.060753 INFO: Train AUC: 0.554
1 day, 21:53:37.060792 INFO: AUC difference: 0.60%
1 day, 21:53:39.709195 INFO: Resetting torch num_threads to 80
1 day, 21:53:39.881293 INFO: Removing fragments below FDR threshold
1 day, 21:53:40.419294 PROGRESS: ============================= Precursor FDR =============================
1 day, 21:53:40.419577 PROGRESS: Total precursors accumulated: 8,730
1 day, 21:53:40.419667 PROGRESS: Target precursors: 8,644 (99.01%)
1 day, 21:53:40.419738 PROGRESS: Decoy precursors: 86 (0.99%)
1 day, 21:53:40.419799 PROGRESS: 
1 day, 21:53:40.419857 PROGRESS: Precursor Summary:
1 day, 21:53:40.423610 PROGRESS: Channel   0:	 0.050 FDR: 8,644; 0.010 FDR: 8,644; 0.001 FDR: 6,300
1 day, 21:53:40.423762 PROGRESS: 
1 day, 21:53:40.423832 PROGRESS: Protein Summary:
1 day, 21:53:40.428047 PROGRESS: Channel   0:	 0.050 FDR: 2,035; 0.010 FDR: 2,035; 0.001 FDR: 1,508
1 day, 21:53:40.428160 PROGRESS: =========================================================================
1 day, 21:53:40.534257 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R2/psm.parquet
1 day, 21:53:40.607603 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R2/frag.parquet
1 day, 21:53:40.644752 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R2
1 day, 21:53:41.364160 PROGRESS: Loading raw file 9/12: B9_G_DIA_nLC_tTOF_R3 
1 day, 21:53:41.364335 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
1 day, 21:53:41.364428 INFO: Creating folder plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R3/figures
1 day, 21:53:41.364632 INFO: Initializing TimingManager
1 day, 21:53:41.365206 INFO: Initializing RawFileManager
1 day, 21:53:41.365325 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:41.365402 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:41.365451 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:41.499758 INFO: Reading 22,622 frames with 373,160,144 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:46.922834 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d...
1 day, 21:53:46.924461 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:46.926704 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:46.927032 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:46.927632 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:46.929436 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:46.945080 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:46.950085 INFO: Indexing quadrupole dimension
1 day, 21:53:47.047626 INFO: Transposing detector events
1 day, 21:53:48.859735 INFO: Finished transposing data
1 day, 21:53:48.859936 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
1 day, 21:53:48.860484 INFO: RT (min)            : 0.0 - 40.0
1 day, 21:53:48.860578 INFO: RT duration (sec)   : 2399.9
1 day, 21:53:48.860639 INFO: RT duration (min)   : 40.0
1 day, 21:53:48.860696 INFO: Cycle len (scans)   : 12
1 day, 21:53:48.860747 INFO: Cycle len (sec)     : 1.27
1 day, 21:53:48.860797 INFO: Number of cycles    : 1885
1 day, 21:53:48.860857 INFO: MS2 range (m/z)     : 374.4 - 1151.9
1 day, 21:53:48.860919 INFO: Creating DIA data object took: 7.49560284614563
1 day, 21:53:50.388978 INFO: Initializing CalibrationManager
1 day, 21:53:50.389306 INFO: Setting up calibration estimators ..
1 day, 21:53:50.389389 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 21:53:50.389483 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 21:53:50.389587 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 21:53:50.389658 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 21:53:50.389732 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1 day, 21:53:50.389797 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
1 day, 21:53:50.389855 INFO: Done setting up calibration estimators.
1 day, 21:53:50.390030 INFO: Initializing OptimizationManager
1 day, 21:53:50.390148 INFO: initial parameter: ms1_error = 30
1 day, 21:53:50.390216 INFO: initial parameter: ms2_error = 30
1 day, 21:53:50.390277 INFO: initial parameter: rt_error = 1199.951535
1 day, 21:53:50.390336 INFO: initial parameter: mobility_error = 0.1
1 day, 21:53:50.390393 INFO: initial parameter: num_candidates = 1
1 day, 21:53:50.390449 INFO: initial parameter: fwhm_rt = 5
1 day, 21:53:50.390505 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 21:53:50.390563 INFO: initial parameter: score_cutoff = 0
1 day, 21:53:50.390615 INFO: initial parameter: classifier_version = -1
1 day, 21:53:50.390697 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R3
1 day, 21:53:50.390889 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 21:53:50.390930 INFO: Initializing FDRManager
1 day, 21:53:50.390985 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 21:53:51.464081 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
1 day, 21:53:52.195125 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 21:53:52.195717 INFO: Updating optimization_manager: rt_error            : 1199.951535 -> 1199.951535
1 day, 21:53:52.195837 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 21:53:52.196026 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 21:53:52.196131 PROGRESS: Starting initial search for precursors.
1 day, 21:53:52.196234 INFO: Starting optimization step 0.
1 day, 21:53:52.196307 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 21:53:52.196380 INFO: Using python extraction backend
1 day, 21:53:52.196497 PROGRESS: Extracting batch of 395 precursors
1 day, 21:53:52.196568 INFO: === Search parameters used ===
1 day, 21:53:52.196621 INFO: rt_error       : 1199.951535
1 day, 21:53:52.196669 INFO: mobility_error : 0.1
1 day, 21:53:52.196717 INFO: num_candidates : 1
1 day, 21:53:52.196763 INFO: ms1_error      : 30
1 day, 21:53:52.196807 INFO: ms2_error      : 30
1 day, 21:53:52.196853 INFO: fwhm_rt        : 5
1 day, 21:53:52.196897 INFO: quant_window   : 3
1 day, 21:53:52.196942 INFO: ==============================================
1 day, 21:53:52.197657 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 21:53:52.197706 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 21:53:52.197747 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 21:53:52.197772 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 21:53:52.198703 INFO: Starting candidate selection
1 day, 21:53:53.998243 INFO: Starting candidate scoring
1 day, 21:53:54.037615 INFO: Finished candidate processing
1 day, 21:53:54.037705 INFO: Collecting candidate features
1 day, 21:53:54.047445 INFO: Collecting fragment features
1 day, 21:53:54.049679 INFO: Finished candidate scoring
1 day, 21:53:54.050684 INFO: performing precursor FDR with 47 features
1 day, 21:53:54.050734 INFO: Decoy channel: -1
1 day, 21:53:54.050762 INFO: competitive: True
1 day, 21:53:54.051946 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 21:53:54.053619 INFO: Estimating optimal hyperparameters - samples: 276, batch_size: 128, learning_rate: 1.77e-04
1 day, 21:53:54.054419 INFO: Using random state 691924 for train-test-split
1 day, 21:53:54.077593 INFO: Test AUC: 0.444
1 day, 21:53:54.077668 INFO: Train AUC: 0.577
1 day, 21:53:54.077700 INFO: AUC difference: 22.93%
1 day, 21:53:54.077724 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 21:53:54.317471 INFO: Resetting torch num_threads to 80
1 day, 21:53:54.317974 PROGRESS: === Extracted 345 precursors and 2813 fragments ===
1 day, 21:53:54.318439 INFO: === FDR correction performed with classifier version -1 ===
1 day, 21:53:54.318989 PROGRESS: ============================= Precursor FDR =============================
1 day, 21:53:54.319083 PROGRESS: Total precursors accumulated: 174
1 day, 21:53:54.319151 PROGRESS: Target precursors: 88 (50.57%)
1 day, 21:53:54.319208 PROGRESS: Decoy precursors: 86 (49.43%)
1 day, 21:53:54.319261 PROGRESS: 
1 day, 21:53:54.319310 PROGRESS: Precursor Summary:
1 day, 21:53:54.320250 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 21:53:54.320343 PROGRESS: 
1 day, 21:53:54.320405 PROGRESS: Protein Summary:
1 day, 21:53:54.321425 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 21:53:54.321516 PROGRESS: =========================================================================
1 day, 21:53:54.321629 INFO: Target number of precursors not reached yet.
1 day, 21:53:54.383142 INFO: Starting optimization step 1.
1 day, 21:53:54.383382 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 21:53:54.383467 INFO: Using python extraction backend
1 day, 21:53:54.383594 PROGRESS: Extracting batch of 796 precursors
1 day, 21:53:54.383672 INFO: === Search parameters used ===
1 day, 21:53:54.383730 INFO: rt_error       : 1199.951535
1 day, 21:53:54.383782 INFO: mobility_error : 0.1
1 day, 21:53:54.383832 INFO: num_candidates : 1
1 day, 21:53:54.383884 INFO: ms1_error      : 30
1 day, 21:53:54.383932 INFO: ms2_error      : 30
1 day, 21:53:54.384012 INFO: fwhm_rt        : 5
1 day, 21:53:54.384063 INFO: quant_window   : 3
1 day, 21:53:54.384109 INFO: ==============================================
1 day, 21:53:54.384796 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 21:53:54.384847 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 21:53:54.384889 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 21:53:54.384917 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 21:53:54.385797 INFO: Starting candidate selection
1 day, 21:53:57.220829 INFO: Starting candidate scoring
1 day, 21:53:57.262597 INFO: Finished candidate processing
1 day, 21:53:57.262697 INFO: Collecting candidate features
1 day, 21:53:57.273423 INFO: Collecting fragment features
1 day, 21:53:57.275876 INFO: Finished candidate scoring
1 day, 21:53:57.278191 INFO: performing precursor FDR with 47 features
1 day, 21:53:57.278250 INFO: Decoy channel: -1
1 day, 21:53:57.278279 INFO: competitive: True
1 day, 21:53:57.281240 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 21:53:57.283062 INFO: Estimating optimal hyperparameters - samples: 852, batch_size: 128, learning_rate: 1.77e-04
1 day, 21:53:57.283151 INFO: Using random state 597936 for train-test-split
1 day, 21:53:57.360616 INFO: Test AUC: 0.497
1 day, 21:53:57.360722 INFO: Train AUC: 0.617
1 day, 21:53:57.360758 INFO: AUC difference: 19.37%
1 day, 21:53:57.360784 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 21:53:57.601364 INFO: Resetting torch num_threads to 80
1 day, 21:53:57.602683 PROGRESS: === Extracted 1066 precursors and 8952 fragments ===
1 day, 21:53:57.603144 INFO: === FDR correction performed with classifier version -1 ===
1 day, 21:53:57.603721 PROGRESS: ============================= Precursor FDR =============================
1 day, 21:53:57.603821 PROGRESS: Total precursors accumulated: 542
1 day, 21:53:57.603890 PROGRESS: Target precursors: 321 (59.23%)
1 day, 21:53:57.603957 PROGRESS: Decoy precursors: 221 (40.77%)
1 day, 21:53:57.604012 PROGRESS: 
1 day, 21:53:57.604064 PROGRESS: Precursor Summary:
1 day, 21:53:57.605006 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 21:53:57.605100 PROGRESS: 
1 day, 21:53:57.605162 PROGRESS: Protein Summary:
1 day, 21:53:57.606205 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 21:53:57.606304 PROGRESS: =========================================================================
1 day, 21:53:57.606464 INFO: Target number of precursors not reached yet.
1 day, 21:53:57.671258 INFO: Starting optimization step 2.
1 day, 21:53:57.671510 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 21:53:57.671594 INFO: Using python extraction backend
1 day, 21:53:57.671709 PROGRESS: Extracting batch of 1598 precursors
1 day, 21:53:57.671784 INFO: === Search parameters used ===
1 day, 21:53:57.671840 INFO: rt_error       : 1199.951535
1 day, 21:53:57.671891 INFO: mobility_error : 0.1
1 day, 21:53:57.671941 INFO: num_candidates : 1
1 day, 21:53:57.671988 INFO: ms1_error      : 30
1 day, 21:53:57.672034 INFO: ms2_error      : 30
1 day, 21:53:57.672083 INFO: fwhm_rt        : 5
1 day, 21:53:57.672131 INFO: quant_window   : 3
1 day, 21:53:57.672180 INFO: ==============================================
1 day, 21:53:57.672992 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 21:53:57.673044 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 21:53:57.673076 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 21:53:57.673103 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 21:53:57.674017 INFO: Starting candidate selection
1 day, 21:54:02.623464 INFO: Starting candidate scoring
1 day, 21:54:02.679246 INFO: Finished candidate processing
1 day, 21:54:02.679354 INFO: Collecting candidate features
1 day, 21:54:02.691658 INFO: Collecting fragment features
1 day, 21:54:02.694641 INFO: Finished candidate scoring
1 day, 21:54:02.698024 INFO: performing precursor FDR with 47 features
1 day, 21:54:02.698086 INFO: Decoy channel: -1
1 day, 21:54:02.698114 INFO: competitive: True
1 day, 21:54:02.702336 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 21:54:02.704556 INFO: Estimating optimal hyperparameters - samples: 1,998, batch_size: 128, learning_rate: 1.77e-04
1 day, 21:54:02.704663 INFO: Using random state 951022 for train-test-split
1 day, 21:54:02.918519 INFO: Test AUC: 0.565
1 day, 21:54:02.918626 INFO: Train AUC: 0.614
1 day, 21:54:02.918660 INFO: AUC difference: 8.03%
1 day, 21:54:02.918683 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 21:54:03.158081 INFO: Resetting torch num_threads to 80
1 day, 21:54:03.159848 PROGRESS: === Extracted 2498 precursors and 20883 fragments ===
1 day, 21:54:03.160306 INFO: === FDR correction performed with classifier version -1 ===
1 day, 21:54:03.160984 PROGRESS: ============================= Precursor FDR =============================
1 day, 21:54:03.161082 PROGRESS: Total precursors accumulated: 1,268
1 day, 21:54:03.161149 PROGRESS: Target precursors: 800 (63.09%)
1 day, 21:54:03.161207 PROGRESS: Decoy precursors: 468 (36.91%)
1 day, 21:54:03.161262 PROGRESS: 
1 day, 21:54:03.161314 PROGRESS: Precursor Summary:
1 day, 21:54:03.162258 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 21:54:03.162357 PROGRESS: 
1 day, 21:54:03.162421 PROGRESS: Protein Summary:
1 day, 21:54:03.163443 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 21:54:03.163536 PROGRESS: =========================================================================
1 day, 21:54:03.163708 INFO: Target number of precursors not reached yet.
1 day, 21:54:03.232685 INFO: Starting optimization step 3.
1 day, 21:54:03.232919 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 21:54:03.233004 INFO: Using python extraction backend
1 day, 21:54:03.233118 PROGRESS: Extracting batch of 3192 precursors
1 day, 21:54:03.233196 INFO: === Search parameters used ===
1 day, 21:54:03.233253 INFO: rt_error       : 1199.951535
1 day, 21:54:03.233306 INFO: mobility_error : 0.1
1 day, 21:54:03.233368 INFO: num_candidates : 1
1 day, 21:54:03.233420 INFO: ms1_error      : 30
1 day, 21:54:03.233467 INFO: ms2_error      : 30
1 day, 21:54:03.233512 INFO: fwhm_rt        : 5
1 day, 21:54:03.233558 INFO: quant_window   : 3
1 day, 21:54:03.233604 INFO: ==============================================
1 day, 21:54:03.234640 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 21:54:03.234695 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 21:54:03.234730 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 21:54:03.234754 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 21:54:03.235590 INFO: Starting candidate selection
1 day, 21:54:12.584198 INFO: Starting candidate scoring
1 day, 21:54:12.678702 INFO: Finished candidate processing
1 day, 21:54:12.678822 INFO: Collecting candidate features
1 day, 21:54:12.693044 INFO: Collecting fragment features
1 day, 21:54:12.696874 INFO: Finished candidate scoring
1 day, 21:54:12.701266 INFO: performing precursor FDR with 47 features
1 day, 21:54:12.701330 INFO: Decoy channel: -1
1 day, 21:54:12.701358 INFO: competitive: True
1 day, 21:54:12.705693 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 21:54:12.708399 INFO: Estimating optimal hyperparameters - samples: 4,308, batch_size: 128, learning_rate: 1.77e-04
1 day, 21:54:12.708494 INFO: Using random state 183262 for train-test-split
1 day, 21:54:13.196396 INFO: Test AUC: 0.555
1 day, 21:54:13.196517 INFO: Train AUC: 0.614
1 day, 21:54:13.196555 INFO: AUC difference: 9.59%
1 day, 21:54:13.196584 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 21:54:13.435493 INFO: Resetting torch num_threads to 80
1 day, 21:54:13.437930 PROGRESS: === Extracted 5385 precursors and 45240 fragments ===
1 day, 21:54:13.438394 INFO: === FDR correction performed with classifier version -1 ===
1 day, 21:54:13.439236 PROGRESS: ============================= Precursor FDR =============================
1 day, 21:54:13.439337 PROGRESS: Total precursors accumulated: 2,729
1 day, 21:54:13.439406 PROGRESS: Target precursors: 1,690 (61.93%)
1 day, 21:54:13.439467 PROGRESS: Decoy precursors: 1,039 (38.07%)
1 day, 21:54:13.439523 PROGRESS: 
1 day, 21:54:13.439586 PROGRESS: Precursor Summary:
1 day, 21:54:13.440540 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 21:54:13.440634 PROGRESS: 
1 day, 21:54:13.440696 PROGRESS: Protein Summary:
1 day, 21:54:13.441718 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 21:54:13.441816 PROGRESS: =========================================================================
1 day, 21:54:13.442002 INFO: Target number of precursors not reached yet.
1 day, 21:54:13.515649 INFO: Starting optimization step 4.
1 day, 21:54:13.515929 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 21:54:13.516014 INFO: Using python extraction backend
1 day, 21:54:13.516124 PROGRESS: Extracting batch of 6381 precursors
1 day, 21:54:13.516198 INFO: === Search parameters used ===
1 day, 21:54:13.516252 INFO: rt_error       : 1199.951535
1 day, 21:54:13.516302 INFO: mobility_error : 0.1
1 day, 21:54:13.516361 INFO: num_candidates : 1
1 day, 21:54:13.516410 INFO: ms1_error      : 30
1 day, 21:54:13.516456 INFO: ms2_error      : 30
1 day, 21:54:13.516503 INFO: fwhm_rt        : 5
1 day, 21:54:13.516548 INFO: quant_window   : 3
1 day, 21:54:13.516592 INFO: ==============================================
1 day, 21:54:13.518044 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 21:54:13.518101 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 21:54:13.518134 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 21:54:13.518159 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 21:54:13.519013 INFO: Starting candidate selection
1 day, 21:54:30.576220 INFO: Starting candidate scoring
1 day, 21:54:30.735646 INFO: Finished candidate processing
1 day, 21:54:30.735771 INFO: Collecting candidate features
1 day, 21:54:30.754666 WARNING: intensity_correlation has 2 NaNs ( 0.03 % out of 5746)
1 day, 21:54:30.758680 INFO: Collecting fragment features
1 day, 21:54:30.763995 INFO: Finished candidate scoring
1 day, 21:54:30.771757 INFO: performing precursor FDR with 47 features
1 day, 21:54:30.771860 INFO: Decoy channel: -1
1 day, 21:54:30.771892 INFO: competitive: True
1 day, 21:54:30.777907 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 21:54:30.780659 WARNING: dropped 1 target PSMs due to missing features
1 day, 21:54:30.780725 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 21:54:30.782684 INFO: Estimating optimal hyperparameters - samples: 8,903, batch_size: 128, learning_rate: 1.77e-04
1 day, 21:54:30.782789 INFO: Using random state 363754 for train-test-split
1 day, 21:54:31.918178 INFO: Test AUC: 0.532
1 day, 21:54:31.918325 INFO: Train AUC: 0.622
1 day, 21:54:31.918361 INFO: AUC difference: 14.50%
1 day, 21:54:31.918387 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 21:54:32.166127 INFO: Resetting torch num_threads to 80
1 day, 21:54:32.170092 PROGRESS: === Extracted 11131 precursors and 93135 fragments ===
1 day, 21:54:32.170630 INFO: === FDR correction performed with classifier version -1 ===
1 day, 21:54:32.171892 PROGRESS: ============================= Precursor FDR =============================
1 day, 21:54:32.171999 PROGRESS: Total precursors accumulated: 5,654
1 day, 21:54:32.172070 PROGRESS: Target precursors: 3,600 (63.67%)
1 day, 21:54:32.172131 PROGRESS: Decoy precursors: 2,054 (36.33%)
1 day, 21:54:32.172188 PROGRESS: 
1 day, 21:54:32.172240 PROGRESS: Precursor Summary:
1 day, 21:54:32.173248 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
1 day, 21:54:32.173347 PROGRESS: 
1 day, 21:54:32.173416 PROGRESS: Protein Summary:
1 day, 21:54:32.174515 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
1 day, 21:54:32.174619 PROGRESS: =========================================================================
1 day, 21:54:32.174878 INFO: Target number of precursors not reached yet.
1 day, 21:54:32.264834 INFO: Starting optimization step 5.
1 day, 21:54:32.265135 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1 day, 21:54:32.265363 INFO: Using python extraction backend
1 day, 21:54:32.265495 PROGRESS: Extracting batch of 12763 precursors
1 day, 21:54:32.265575 INFO: === Search parameters used ===
1 day, 21:54:32.265630 INFO: rt_error       : 1199.951535
1 day, 21:54:32.265681 INFO: mobility_error : 0.1
1 day, 21:54:32.265729 INFO: num_candidates : 1
1 day, 21:54:32.265777 INFO: ms1_error      : 30
1 day, 21:54:32.265823 INFO: ms2_error      : 30
1 day, 21:54:32.265900 INFO: fwhm_rt        : 5
1 day, 21:54:32.265962 INFO: quant_window   : 3
1 day, 21:54:32.266010 INFO: ==============================================
1 day, 21:54:32.269117 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 21:54:32.269173 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 21:54:32.269204 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 21:54:32.269228 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 21:54:32.270092 INFO: Starting candidate selection
1 day, 21:55:03.970211 INFO: Starting candidate scoring
1 day, 21:55:04.230356 INFO: Finished candidate processing
1 day, 21:55:04.230470 INFO: Collecting candidate features
1 day, 21:55:04.254922 WARNING: intensity_correlation has 4 NaNs ( 0.03 % out of 11491)
1 day, 21:55:04.255152 WARNING: height_correlation has 1 NaNs ( 0.01 % out of 11491)
1 day, 21:55:04.260163 INFO: Collecting fragment features
1 day, 21:55:04.268884 INFO: Finished candidate scoring
1 day, 21:55:04.282706 INFO: performing precursor FDR with 47 features
1 day, 21:55:04.282856 INFO: Decoy channel: -1
1 day, 21:55:04.282886 INFO: competitive: True
1 day, 21:55:04.292580 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 21:55:04.297098 WARNING: dropped 5 target PSMs due to missing features
1 day, 21:55:04.297192 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 21:55:04.300923 INFO: Estimating optimal hyperparameters - samples: 18,092, batch_size: 128, learning_rate: 1.77e-04
1 day, 21:55:04.301065 INFO: Using random state 150909 for train-test-split
1 day, 21:55:06.306202 INFO: Test AUC: 0.552
1 day, 21:55:06.306347 INFO: Train AUC: 0.609
1 day, 21:55:06.306381 INFO: AUC difference: 9.36%
1 day, 21:55:06.306407 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 21:55:06.560925 INFO: Resetting torch num_threads to 80
1 day, 21:55:06.566459 PROGRESS: === Extracted 22622 precursors and 189445 fragments ===
1 day, 21:55:06.567111 INFO: === FDR correction performed with classifier version -1 ===
1 day, 21:55:06.569049 PROGRESS: ============================= Precursor FDR =============================
1 day, 21:55:06.569171 PROGRESS: Total precursors accumulated: 11,485
1 day, 21:55:06.569263 PROGRESS: Target precursors: 7,300 (63.56%)
1 day, 21:55:06.569336 PROGRESS: Decoy precursors: 4,185 (36.44%)
1 day, 21:55:06.569398 PROGRESS: 
1 day, 21:55:06.569459 PROGRESS: Precursor Summary:
1 day, 21:55:06.570560 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 21:55:06.570670 PROGRESS: 
1 day, 21:55:06.570742 PROGRESS: Protein Summary:
1 day, 21:55:06.571881 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 21:55:06.571983 PROGRESS: =========================================================================
1 day, 21:55:06.572261 INFO: Target number of precursors not reached yet.
1 day, 21:55:06.671329 INFO: Starting optimization step 6.
1 day, 21:55:06.671644 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1 day, 21:55:06.671754 INFO: Using python extraction backend
1 day, 21:55:06.671888 PROGRESS: Extracting batch of 25523 precursors
1 day, 21:55:06.671976 INFO: === Search parameters used ===
1 day, 21:55:06.672042 INFO: rt_error       : 1199.951535
1 day, 21:55:06.672104 INFO: mobility_error : 0.1
1 day, 21:55:06.672162 INFO: num_candidates : 1
1 day, 21:55:06.672218 INFO: ms1_error      : 30
1 day, 21:55:06.672274 INFO: ms2_error      : 30
1 day, 21:55:06.672328 INFO: fwhm_rt        : 5
1 day, 21:55:06.672382 INFO: quant_window   : 3
1 day, 21:55:06.672453 INFO: ==============================================
1 day, 21:55:06.678551 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 21:55:06.678635 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 21:55:06.678670 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 21:55:06.678699 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 21:55:06.679525 INFO: Starting candidate selection
1 day, 21:56:07.398351 INFO: Starting candidate scoring
1 day, 21:56:07.816345 INFO: Finished candidate processing
1 day, 21:56:07.816461 INFO: Collecting candidate features
1 day, 21:56:07.855885 WARNING: intensity_correlation has 4 NaNs ( 0.02 % out of 22952)
1 day, 21:56:07.860550 INFO: Collecting fragment features
1 day, 21:56:07.876445 INFO: Finished candidate scoring
1 day, 21:56:07.902225 INFO: performing precursor FDR with 47 features
1 day, 21:56:07.902375 INFO: Decoy channel: -1
1 day, 21:56:07.902405 INFO: competitive: True
1 day, 21:56:07.920703 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 21:56:07.929935 WARNING: dropped 7 target PSMs due to missing features
1 day, 21:56:07.930070 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 21:56:07.937413 INFO: Estimating optimal hyperparameters - samples: 36,450, batch_size: 149, learning_rate: 1.91e-04
1 day, 21:56:07.937620 INFO: Using random state 403352 for train-test-split
1 day, 21:56:11.890486 INFO: Test AUC: 0.552
1 day, 21:56:11.890633 INFO: Train AUC: 0.604
1 day, 21:56:11.890668 INFO: AUC difference: 8.66%
1 day, 21:56:11.890692 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 21:56:12.147961 INFO: Resetting torch num_threads to 80
1 day, 21:56:12.156842 PROGRESS: === Extracted 45574 precursors and 382384 fragments ===
1 day, 21:56:12.157531 INFO: === FDR correction performed with classifier version -1 ===
1 day, 21:56:12.161797 PROGRESS: ============================= Precursor FDR =============================
1 day, 21:56:12.161967 PROGRESS: Total precursors accumulated: 23,132
1 day, 21:56:12.162041 PROGRESS: Target precursors: 14,595 (63.09%)
1 day, 21:56:12.162101 PROGRESS: Decoy precursors: 8,537 (36.91%)
1 day, 21:56:12.162155 PROGRESS: 
1 day, 21:56:12.162207 PROGRESS: Precursor Summary:
1 day, 21:56:12.163336 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1 day, 21:56:12.163435 PROGRESS: 
1 day, 21:56:12.163498 PROGRESS: Protein Summary:
1 day, 21:56:12.164678 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1 day, 21:56:12.164775 PROGRESS: =========================================================================
1 day, 21:56:12.165174 INFO: Target number of precursors not reached yet.
1 day, 21:56:12.301467 INFO: Starting optimization step 7.
1 day, 21:56:12.301766 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1 day, 21:56:12.301851 INFO: Using python extraction backend
1 day, 21:56:12.301982 PROGRESS: Extracting batch of 51061 precursors
1 day, 21:56:12.302065 INFO: === Search parameters used ===
1 day, 21:56:12.302123 INFO: rt_error       : 1199.951535
1 day, 21:56:12.302191 INFO: mobility_error : 0.1
1 day, 21:56:12.302243 INFO: num_candidates : 1
1 day, 21:56:12.302292 INFO: ms1_error      : 30
1 day, 21:56:12.302338 INFO: ms2_error      : 30
1 day, 21:56:12.302384 INFO: fwhm_rt        : 5
1 day, 21:56:12.302429 INFO: quant_window   : 3
1 day, 21:56:12.302475 INFO: ==============================================
1 day, 21:56:12.315994 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 21:56:12.316126 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 21:56:12.316159 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 21:56:12.316183 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 21:56:12.317280 INFO: Starting candidate selection
1 day, 21:58:10.470916 INFO: Starting candidate scoring
1 day, 21:58:11.244455 INFO: Finished candidate processing
1 day, 21:58:11.244577 INFO: Collecting candidate features
1 day, 21:58:11.323660 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 45868)
1 day, 21:58:11.323998 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 45868)
1 day, 21:58:11.329345 INFO: Collecting fragment features
1 day, 21:58:11.356485 INFO: Finished candidate scoring
1 day, 21:58:11.409031 INFO: performing precursor FDR with 47 features
1 day, 21:58:11.409195 INFO: Decoy channel: -1
1 day, 21:58:11.409224 INFO: competitive: True
1 day, 21:58:11.447751 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 21:58:11.467092 WARNING: dropped 10 target PSMs due to missing features
1 day, 21:58:11.467245 WARNING: dropped 10 decoy PSMs due to missing features
1 day, 21:58:11.485976 INFO: Estimating optimal hyperparameters - samples: 73,137, batch_size: 299, learning_rate: 2.70e-04
1 day, 21:58:11.486281 INFO: Using random state 936015 for train-test-split
1 day, 21:58:16.960898 INFO: Test AUC: 0.547
1 day, 21:58:16.961055 INFO: Train AUC: 0.605
1 day, 21:58:16.961091 INFO: AUC difference: 9.50%
1 day, 21:58:16.961117 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 21:58:17.236803 INFO: Resetting torch num_threads to 80
1 day, 21:58:17.254866 PROGRESS: === Extracted 91442 precursors and 767357 fragments ===
1 day, 21:58:17.255606 INFO: === FDR correction performed with classifier version -1 ===
1 day, 21:58:17.265294 PROGRESS: ============================= Precursor FDR =============================
1 day, 21:58:17.265479 PROGRESS: Total precursors accumulated: 46,380
1 day, 21:58:17.265551 PROGRESS: Target precursors: 28,143 (60.68%)
1 day, 21:58:17.265610 PROGRESS: Decoy precursors: 18,237 (39.32%)
1 day, 21:58:17.265664 PROGRESS: 
1 day, 21:58:17.265716 PROGRESS: Precursor Summary:
1 day, 21:58:17.267050 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
1 day, 21:58:17.267154 PROGRESS: 
1 day, 21:58:17.267218 PROGRESS: Protein Summary:
1 day, 21:58:17.268533 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
1 day, 21:58:17.268628 PROGRESS: =========================================================================
1 day, 21:58:17.269427 INFO: Target number of precursors not reached yet.
1 day, 21:58:17.480986 INFO: Starting optimization step 8.
1 day, 21:58:17.481305 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1 day, 21:58:17.481395 INFO: Using python extraction backend
1 day, 21:58:17.481529 PROGRESS: Extracting batch of 102076 precursors
1 day, 21:58:17.481608 INFO: === Search parameters used ===
1 day, 21:58:17.481666 INFO: rt_error       : 1199.951535
1 day, 21:58:17.481717 INFO: mobility_error : 0.1
1 day, 21:58:17.481766 INFO: num_candidates : 1
1 day, 21:58:17.481816 INFO: ms1_error      : 30
1 day, 21:58:17.481862 INFO: ms2_error      : 30
1 day, 21:58:17.481956 INFO: fwhm_rt        : 5
1 day, 21:58:17.482002 INFO: quant_window   : 3
1 day, 21:58:17.482048 INFO: ==============================================
1 day, 21:58:17.507904 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 21:58:17.508050 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 21:58:17.508082 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 21:58:17.508107 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 21:58:17.509010 INFO: Starting candidate selection
1 day, 22:02:16.567054 INFO: Starting candidate scoring
1 day, 22:02:17.990381 INFO: Finished candidate processing
1 day, 22:02:17.990573 INFO: Collecting candidate features
1 day, 22:02:18.168423 WARNING: intensity_correlation has 27 NaNs ( 0.03 % out of 91759)
1 day, 22:02:18.168792 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 91759)
1 day, 22:02:18.175611 INFO: Collecting fragment features
1 day, 22:02:18.235871 INFO: Finished candidate scoring
1 day, 22:02:18.328377 INFO: performing precursor FDR with 47 features
1 day, 22:02:18.328540 INFO: Decoy channel: -1
1 day, 22:02:18.328570 INFO: competitive: True
1 day, 22:02:18.401137 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 22:02:18.434922 WARNING: dropped 24 target PSMs due to missing features
1 day, 22:02:18.435099 WARNING: dropped 24 decoy PSMs due to missing features
1 day, 22:02:18.483430 INFO: Estimating optimal hyperparameters - samples: 146,522, batch_size: 600, learning_rate: 3.83e-04
1 day, 22:02:18.483903 INFO: Using random state 9642 for train-test-split
1 day, 22:02:25.247626 INFO: Test AUC: 0.544
1 day, 22:02:25.247776 INFO: Train AUC: 0.598
1 day, 22:02:25.247814 INFO: AUC difference: 8.99%
1 day, 22:02:25.247840 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 22:02:25.547381 INFO: Resetting torch num_threads to 80
1 day, 22:02:25.580932 PROGRESS: === Extracted 183201 precursors and 1539090 fragments ===
1 day, 22:02:25.581774 INFO: === FDR correction performed with classifier version -1 ===
1 day, 22:02:25.599020 PROGRESS: ============================= Precursor FDR =============================
1 day, 22:02:25.599329 PROGRESS: Total precursors accumulated: 92,936
1 day, 22:02:25.599401 PROGRESS: Target precursors: 55,078 (59.26%)
1 day, 22:02:25.599464 PROGRESS: Decoy precursors: 37,858 (40.74%)
1 day, 22:02:25.599519 PROGRESS: 
1 day, 22:02:25.599573 PROGRESS: Precursor Summary:
1 day, 22:02:25.601134 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 22:02:25.601258 PROGRESS: 
1 day, 22:02:25.601324 PROGRESS: Protein Summary:
1 day, 22:02:25.602813 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 22:02:25.602917 PROGRESS: =========================================================================
1 day, 22:02:25.604345 INFO: Target number of precursors not reached yet.
1 day, 22:02:25.952417 INFO: Starting optimization step 9.
1 day, 22:02:25.952744 PROGRESS: === Extracting elution groups 102200 to 204600 ===
1 day, 22:02:25.952834 INFO: Using python extraction backend
1 day, 22:02:25.952962 PROGRESS: Extracting batch of 204132 precursors
1 day, 22:02:25.953044 INFO: === Search parameters used ===
1 day, 22:02:25.953102 INFO: rt_error       : 1199.951535
1 day, 22:02:25.953152 INFO: mobility_error : 0.1
1 day, 22:02:25.953202 INFO: num_candidates : 1
1 day, 22:02:25.953251 INFO: ms1_error      : 30
1 day, 22:02:25.953300 INFO: ms2_error      : 30
1 day, 22:02:25.953349 INFO: fwhm_rt        : 5
1 day, 22:02:25.953397 INFO: quant_window   : 3
1 day, 22:02:25.953447 INFO: ==============================================
1 day, 22:02:26.005285 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 22:02:26.005444 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 22:02:26.005479 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 22:02:26.005503 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 22:02:26.006697 INFO: Starting candidate selection
1 day, 22:10:09.412581 INFO: Starting candidate scoring
1 day, 22:10:12.086021 INFO: Finished candidate processing
1 day, 22:10:12.086362 INFO: Collecting candidate features
1 day, 22:10:12.470163 WARNING: intensity_correlation has 50 NaNs ( 0.03 % out of 183750)
1 day, 22:10:12.470594 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 183750)
1 day, 22:10:12.480399 INFO: Collecting fragment features
1 day, 22:10:12.599521 INFO: Finished candidate scoring
1 day, 22:10:12.784049 INFO: performing precursor FDR with 47 features
1 day, 22:10:12.784219 INFO: Decoy channel: -1
1 day, 22:10:12.784252 INFO: competitive: True
1 day, 22:10:12.924244 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 22:10:12.989852 WARNING: dropped 43 target PSMs due to missing features
1 day, 22:10:12.990042 WARNING: dropped 59 decoy PSMs due to missing features
1 day, 22:10:13.103758 INFO: Estimating optimal hyperparameters - samples: 293,479, batch_size: 1,202, learning_rate: 5.42e-04
1 day, 22:10:13.104509 INFO: Using random state 738490 for train-test-split
1 day, 22:10:23.529765 INFO: Test AUC: 0.547
1 day, 22:10:23.529947 INFO: Train AUC: 0.583
1 day, 22:10:23.529983 INFO: AUC difference: 6.18%
1 day, 22:10:23.530011 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 22:10:23.899288 INFO: Resetting torch num_threads to 80
1 day, 22:10:23.965433 PROGRESS: === Extracted 366951 precursors and 3082514 fragments ===
1 day, 22:10:23.966484 INFO: === FDR correction performed with classifier version -1 ===
1 day, 22:10:23.997507 PROGRESS: ============================= Precursor FDR =============================
1 day, 22:10:23.997833 PROGRESS: Total precursors accumulated: 186,162
1 day, 22:10:23.997955 PROGRESS: Target precursors: 108,740 (58.41%)
1 day, 22:10:23.998036 PROGRESS: Decoy precursors: 77,422 (41.59%)
1 day, 22:10:23.998091 PROGRESS: 
1 day, 22:10:23.998142 PROGRESS: Precursor Summary:
1 day, 22:10:24.000381 PROGRESS: Channel   0:	 0.050 FDR:    82; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 22:10:24.000482 PROGRESS: 
1 day, 22:10:24.000543 PROGRESS: Protein Summary:
1 day, 22:10:24.002577 PROGRESS: Channel   0:	 0.050 FDR:    74; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 22:10:24.002688 PROGRESS: =========================================================================
1 day, 22:10:24.005451 INFO: Target number of precursors not reached yet.
1 day, 22:10:24.618096 INFO: Starting optimization step 10.
1 day, 22:10:24.618427 PROGRESS: === Extracting elution groups 204600 to 409400 ===
1 day, 22:10:24.618538 INFO: Using python extraction backend
1 day, 22:10:24.618683 PROGRESS: Extracting batch of 408390 precursors
1 day, 22:10:24.618769 INFO: === Search parameters used ===
1 day, 22:10:24.618828 INFO: rt_error       : 1199.951535
1 day, 22:10:24.618881 INFO: mobility_error : 0.1
1 day, 22:10:24.618933 INFO: num_candidates : 1
1 day, 22:10:24.618983 INFO: ms1_error      : 30
1 day, 22:10:24.619031 INFO: ms2_error      : 30
1 day, 22:10:24.619078 INFO: fwhm_rt        : 5
1 day, 22:10:24.619141 INFO: quant_window   : 3
1 day, 22:10:24.619189 INFO: ==============================================
1 day, 22:10:24.722240 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 22:10:24.722394 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 22:10:24.722432 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 22:10:24.722460 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 22:10:24.723578 INFO: Starting candidate selection
1 day, 22:25:48.229142 INFO: Starting candidate scoring
1 day, 22:25:53.523021 INFO: Finished candidate processing
1 day, 22:25:53.523369 INFO: Collecting candidate features
1 day, 22:25:54.321196 WARNING: intensity_correlation has 85 NaNs ( 0.02 % out of 366286)
1 day, 22:25:54.321820 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 366286)
1 day, 22:25:54.337145 INFO: Collecting fragment features
1 day, 22:25:54.629480 INFO: Finished candidate scoring
1 day, 22:25:55.129531 INFO: performing precursor FDR with 47 features
1 day, 22:25:55.129691 INFO: Decoy channel: -1
1 day, 22:25:55.129725 INFO: competitive: True
1 day, 22:25:55.455955 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 22:25:55.581789 WARNING: dropped 84 target PSMs due to missing features
1 day, 22:25:55.581965 WARNING: dropped 107 decoy PSMs due to missing features
1 day, 22:25:56.046240 INFO: Estimating optimal hyperparameters - samples: 586,436, batch_size: 2,402, learning_rate: 7.66e-04
1 day, 22:25:56.047745 INFO: Using random state 618703 for train-test-split
1 day, 22:26:13.894603 INFO: Test AUC: 0.545
1 day, 22:26:13.894907 INFO: Train AUC: 0.569
1 day, 22:26:13.894947 INFO: AUC difference: 4.13%
1 day, 22:26:14.371062 INFO: Resetting torch num_threads to 80
1 day, 22:26:14.612009 PROGRESS: === Extracted 733237 precursors and 6159095 fragments ===
1 day, 22:26:14.613211 INFO: === FDR correction performed with classifier version -1 ===
1 day, 22:26:14.671171 PROGRESS: ============================= Precursor FDR =============================
1 day, 22:26:14.671496 PROGRESS: Total precursors accumulated: 372,046
1 day, 22:26:14.671574 PROGRESS: Target precursors: 213,459 (57.37%)
1 day, 22:26:14.671637 PROGRESS: Decoy precursors: 158,587 (42.63%)
1 day, 22:26:14.671693 PROGRESS: 
1 day, 22:26:14.671751 PROGRESS: Precursor Summary:
1 day, 22:26:14.675579 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   176; 0.001 FDR:     1
1 day, 22:26:14.675697 PROGRESS: 
1 day, 22:26:14.675766 PROGRESS: Protein Summary:
1 day, 22:26:14.679100 PROGRESS: Channel   0:	 0.050 FDR:   220; 0.010 FDR:   138; 0.001 FDR:     1
1 day, 22:26:14.679216 PROGRESS: =========================================================================
1 day, 22:26:14.685247 INFO: Target number of precursors not reached yet.
1 day, 22:26:16.829002 INFO: Starting optimization step 11.
1 day, 22:26:16.829312 PROGRESS: === Extracting elution groups 409400 to 819000 ===
1 day, 22:26:16.829457 INFO: Using python extraction backend
1 day, 22:26:16.829638 PROGRESS: Extracting batch of 816689 precursors
1 day, 22:26:16.829730 INFO: === Search parameters used ===
1 day, 22:26:16.829808 INFO: rt_error       : 1199.951535
1 day, 22:26:16.829873 INFO: mobility_error : 0.1
1 day, 22:26:16.829931 INFO: num_candidates : 1
1 day, 22:26:16.829981 INFO: ms1_error      : 30
1 day, 22:26:16.830028 INFO: ms2_error      : 30
1 day, 22:26:16.830073 INFO: fwhm_rt        : 5
1 day, 22:26:16.830117 INFO: quant_window   : 3
1 day, 22:26:16.830162 INFO: ==============================================
1 day, 22:26:17.042995 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 22:26:17.043140 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 22:26:17.043185 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
1 day, 22:26:17.043211 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
1 day, 22:26:17.044250 INFO: Starting candidate selection
1 day, 22:56:41.891631 INFO: Starting candidate scoring
1 day, 22:56:51.845210 INFO: Finished candidate processing
1 day, 22:56:51.845331 INFO: Collecting candidate features
1 day, 22:56:53.657560 WARNING: intensity_correlation has 185 NaNs ( 0.03 % out of 734102)
1 day, 22:56:53.658461 WARNING: height_correlation has 17 NaNs ( 0.00 % out of 734102)
1 day, 22:56:53.684731 INFO: Collecting fragment features
1 day, 22:56:54.155204 INFO: Finished candidate scoring
1 day, 22:56:55.122608 INFO: performing precursor FDR with 47 features
1 day, 22:56:55.122771 INFO: Decoy channel: -1
1 day, 22:56:55.122801 INFO: competitive: True
1 day, 22:56:55.712413 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 22:56:55.936727 WARNING: dropped 169 target PSMs due to missing features
1 day, 22:56:55.936898 WARNING: dropped 217 decoy PSMs due to missing features
1 day, 22:56:57.037466 INFO: Estimating optimal hyperparameters - samples: 1,173,562, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 22:56:57.040525 INFO: Using random state 254038 for train-test-split
1 day, 22:57:28.715123 INFO: Test AUC: 0.548
1 day, 22:57:28.715388 INFO: Train AUC: 0.563
1 day, 22:57:28.715426 INFO: AUC difference: 2.72%
1 day, 22:57:29.469293 INFO: Resetting torch num_threads to 80
1 day, 22:57:29.902401 PROGRESS: === Extracted 1467339 precursors and 12323315 fragments ===
1 day, 22:57:29.903929 INFO: === FDR correction performed with classifier version -1 ===
1 day, 22:57:30.024067 PROGRESS: ============================= Precursor FDR =============================
1 day, 22:57:30.024409 PROGRESS: Total precursors accumulated: 744,489
1 day, 22:57:30.024494 PROGRESS: Target precursors: 423,604 (56.90%)
1 day, 22:57:30.024557 PROGRESS: Decoy precursors: 320,885 (43.10%)
1 day, 22:57:30.024613 PROGRESS: 
1 day, 22:57:30.024666 PROGRESS: Precursor Summary:
1 day, 22:57:30.030698 PROGRESS: Channel   0:	 0.050 FDR:   603; 0.010 FDR:   443; 0.001 FDR:   106
1 day, 22:57:30.030849 PROGRESS: 
1 day, 22:57:30.030918 PROGRESS: Protein Summary:
1 day, 22:57:30.035891 PROGRESS: Channel   0:	 0.050 FDR:   404; 0.010 FDR:   291; 0.001 FDR:    84
1 day, 22:57:30.036009 PROGRESS: =========================================================================
1 day, 22:57:30.050084 INFO: Target number of precursors reached.
1 day, 22:57:31.394945 INFO: fragments_df: keeping 4134 of 12323315 [sum(precursor_idx_mask)=4786 sum(mass_error_mask)=12323259 stop_rank=4134
1 day, 22:57:33.162516 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 22:57:33.324064 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 22:57:33.474296 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 22:57:33.628162 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 22:57:34.201382 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 22:57:34.201851 INFO: Using score_cutoff 42.057906049346926 (fac=0.99, q=1)
1 day, 22:57:34.202223 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.9712514877319336
1 day, 22:57:34.202314 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007997134700417519
1 day, 22:57:34.202378 INFO: Updating optimization_manager: score_cutoff        : 0 -> 42.057906049346926
1 day, 22:57:34.202446 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 22:57:34.305237 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 22:57:34.833188 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 22:57:34.938079 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 22:57:36.005099 INFO: Updating optimization_manager: classifier_version  : -1 -> 11
1 day, 22:57:36.005420 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 22:57:36.005555 INFO: Starting optimization step 12.
1 day, 22:57:36.005638 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 22:57:36.005746 INFO: Using python extraction backend
1 day, 22:57:36.005935 PROGRESS: Extracting batch of 816307 precursors
1 day, 22:57:36.006026 INFO: === Search parameters used ===
1 day, 22:57:36.006084 INFO: rt_error       : 1199.951535
1 day, 22:57:36.006139 INFO: mobility_error : 0.1
1 day, 22:57:36.006189 INFO: num_candidates : 3
1 day, 22:57:36.006238 INFO: ms1_error      : 30
1 day, 22:57:36.006285 INFO: ms2_error      : 30
1 day, 22:57:36.006330 INFO: fwhm_rt        : 2.9712514877319336
1 day, 22:57:36.006376 INFO: quant_window   : 3
1 day, 22:57:36.006423 INFO: ==============================================
1 day, 22:57:36.237572 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 22:57:36.237724 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 22:57:36.237785 INFO: FWHM in RT is 2.97 seconds, sigma is 0.50
1 day, 22:57:36.237813 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.33
1 day, 22:57:36.238704 INFO: Starting candidate selection
1 day, 23:30:10.440286 INFO: Starting candidate scoring
1 day, 23:30:38.105654 INFO: Finished candidate processing
1 day, 23:30:38.105913 INFO: Collecting candidate features
1 day, 23:30:41.979419 WARNING: intensity_correlation has 641 NaNs ( 0.03 % out of 2103176)
1 day, 23:30:41.981504 WARNING: height_correlation has 55 NaNs ( 0.00 % out of 2103176)
1 day, 23:30:42.050264 INFO: Collecting fragment features
1 day, 23:30:43.312656 INFO: Finished candidate scoring
1 day, 23:30:44.760865 INFO: performing precursor FDR with 47 features
1 day, 23:30:44.761020 INFO: Decoy channel: -1
1 day, 23:30:44.761053 INFO: competitive: True
1 day, 23:30:45.234228 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 23:30:45.532696 WARNING: dropped 283 target PSMs due to missing features
1 day, 23:30:45.532870 WARNING: dropped 397 decoy PSMs due to missing features
1 day, 23:30:46.299074 INFO: Estimating optimal hyperparameters - samples: 1,681,996, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 23:30:46.304464 INFO: Using random state 910005 for train-test-split
1 day, 23:31:31.099808 INFO: Test AUC: 0.556
1 day, 23:31:31.100001 INFO: Train AUC: 0.567
1 day, 23:31:31.100040 INFO: AUC difference: 2.00%
1 day, 23:31:32.032409 INFO: Resetting torch num_threads to 80
1 day, 23:31:32.069040 PROGRESS: === Extracted 2103176 precursors and 17266888 fragments ===
1 day, 23:31:32.070115 INFO: === FDR correction performed with classifier version 11 ===
1 day, 23:31:32.136674 PROGRESS: ============================= Precursor FDR =============================
1 day, 23:31:32.136994 PROGRESS: Total precursors accumulated: 374,577
1 day, 23:31:32.137072 PROGRESS: Target precursors: 219,532 (58.61%)
1 day, 23:31:32.137131 PROGRESS: Decoy precursors: 155,045 (41.39%)
1 day, 23:31:32.137184 PROGRESS: 
1 day, 23:31:32.137236 PROGRESS: Precursor Summary:
1 day, 23:31:32.140778 PROGRESS: Channel   0:	 0.050 FDR:   406; 0.010 FDR:   323; 0.001 FDR:     0
1 day, 23:31:32.140916 PROGRESS: 
1 day, 23:31:32.140982 PROGRESS: Protein Summary:
1 day, 23:31:32.144192 PROGRESS: Channel   0:	 0.050 FDR:   314; 0.010 FDR:   246; 0.001 FDR:     0
1 day, 23:31:32.144306 PROGRESS: =========================================================================
1 day, 23:31:32.163167 INFO: Target number of precursors reached.
1 day, 23:31:33.970785 INFO: fragments_df: keeping 5000 of 17266888 [sum(precursor_idx_mask)=9191 sum(mass_error_mask)=17266816 stop_rank=5000
1 day, 23:31:35.574162 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 23:31:35.687125 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 23:31:35.804248 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 23:31:35.926408 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 23:31:36.579533 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 23:31:36.580003 INFO: Using score_cutoff 35.52517277984619 (fac=0.99, q=1)
1 day, 23:31:36.580354 INFO: Updating optimization_manager: fwhm_rt             : 2.9712514877319336 -> 2.9541449546813965
1 day, 23:31:36.580444 INFO: Updating optimization_manager: fwhm_mobility       : 0.007997134700417519 -> 0.007962065748870373
1 day, 23:31:36.580509 INFO: Updating optimization_manager: score_cutoff        : 42.057906049346926 -> 35.52517277984619
1 day, 23:31:36.580576 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 23:31:36.683789 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 23:31:37.209471 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 23:31:37.312650 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 23:31:38.279388 INFO: === checking if optimization conditions were reached ===
1 day, 23:31:38.281714 INFO: Updating optimization_manager: ms2_error           : 30 -> 16.988990919194578
1 day, 23:31:38.281948 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1 day, 23:31:38.282041 PROGRESS: ❌ ms2_error      : 16.9890 > 15.0000 or insufficient steps taken.
1 day, 23:31:38.283162 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 23:31:38.283285 INFO: Updating optimization_manager: classifier_version  : 12 -> 12
1 day, 23:31:38.283363 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 23:31:38.283427 INFO: ==============================================
1 day, 23:31:38.283503 INFO: Starting optimization step 13.
1 day, 23:31:38.283568 PROGRESS: === Extracting elution groups 0 to 409400 ===
1 day, 23:31:38.283633 INFO: Using python extraction backend
1 day, 23:31:38.283744 PROGRESS: Extracting batch of 816307 precursors
1 day, 23:31:38.283820 INFO: === Search parameters used ===
1 day, 23:31:38.283880 INFO: rt_error       : 1199.951535
1 day, 23:31:38.283930 INFO: mobility_error : 0.1
1 day, 23:31:38.283979 INFO: num_candidates : 3
1 day, 23:31:38.284027 INFO: ms1_error      : 15.0
1 day, 23:31:38.284075 INFO: ms2_error      : 16.988990919194578
1 day, 23:31:38.284123 INFO: fwhm_rt        : 2.9541449546813965
1 day, 23:31:38.284170 INFO: quant_window   : 3
1 day, 23:31:38.284216 INFO: ==============================================
1 day, 23:31:38.482904 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
1 day, 23:31:38.483069 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
1 day, 23:31:38.483121 INFO: FWHM in RT is 2.95 seconds, sigma is 0.49
1 day, 23:31:38.483148 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.32
1 day, 23:31:38.484012 INFO: Starting candidate selection
2 days, 0:03:06.368634 INFO: Starting candidate scoring
2 days, 0:03:32.525516 INFO: Finished candidate processing
2 days, 0:03:32.525809 INFO: Collecting candidate features
2 days, 0:03:36.304208 WARNING: intensity_correlation has 2044 NaNs ( 0.10 % out of 2073174)
2 days, 0:03:36.306195 WARNING: height_correlation has 130 NaNs ( 0.01 % out of 2073174)
2 days, 0:03:36.374282 INFO: Collecting fragment features
2 days, 0:03:37.397508 INFO: Finished candidate scoring
2 days, 0:03:38.793173 INFO: performing precursor FDR with 47 features
2 days, 0:03:38.793316 INFO: Decoy channel: -1
2 days, 0:03:38.793345 INFO: competitive: True
2 days, 0:03:39.296992 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 0:03:39.602936 WARNING: dropped 1033 target PSMs due to missing features
2 days, 0:03:39.603101 WARNING: dropped 1104 decoy PSMs due to missing features
2 days, 0:03:40.547459 INFO: Estimating optimal hyperparameters - samples: 1,656,829, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 0:03:40.551421 INFO: Using random state 217527 for train-test-split
2 days, 0:04:23.199789 INFO: Test AUC: 0.559
2 days, 0:04:23.200028 INFO: Train AUC: 0.567
2 days, 0:04:23.200065 INFO: AUC difference: 1.50%
2 days, 0:04:24.133461 INFO: Resetting torch num_threads to 80
2 days, 0:04:24.169317 PROGRESS: === Extracted 2073174 precursors and 14836848 fragments ===
2 days, 0:04:24.170479 INFO: === FDR correction performed with classifier version 12 ===
2 days, 0:04:24.230319 PROGRESS: ============================= Precursor FDR =============================
2 days, 0:04:24.230659 PROGRESS: Total precursors accumulated: 374,574
2 days, 0:04:24.230731 PROGRESS: Target precursors: 217,815 (58.15%)
2 days, 0:04:24.230790 PROGRESS: Decoy precursors: 156,759 (41.85%)
2 days, 0:04:24.230843 PROGRESS: 
2 days, 0:04:24.230896 PROGRESS: Precursor Summary:
2 days, 0:04:24.234236 PROGRESS: Channel   0:	 0.050 FDR:   562; 0.010 FDR:   419; 0.001 FDR:   359
2 days, 0:04:24.234357 PROGRESS: 
2 days, 0:04:24.234425 PROGRESS: Protein Summary:
2 days, 0:04:24.237557 PROGRESS: Channel   0:	 0.050 FDR:   436; 0.010 FDR:   307; 0.001 FDR:   267
2 days, 0:04:24.237661 PROGRESS: =========================================================================
2 days, 0:04:24.247516 INFO: Target number of precursors reached.
2 days, 0:04:25.820833 INFO: fragments_df: keeping 5000 of 14836848 [sum(precursor_idx_mask)=11522 sum(mass_error_mask)=14836697 stop_rank=5000
2 days, 0:04:27.015607 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:04:27.164598 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:04:27.316917 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:04:27.466035 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:04:28.186369 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 0:04:28.186841 INFO: Using score_cutoff 31.092466738128664 (fac=0.99, q=1)
2 days, 0:04:28.187205 INFO: Updating optimization_manager: fwhm_rt             : 2.9541449546813965 -> 2.798157215118408
2 days, 0:04:28.187293 INFO: Updating optimization_manager: fwhm_mobility       : 0.007962065748870373 -> 0.006450008135288954
2 days, 0:04:28.187356 INFO: Updating optimization_manager: score_cutoff        : 35.52517277984619 -> 31.092466738128664
2 days, 0:04:28.187422 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:04:28.237542 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:04:28.493553 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:04:28.546268 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:04:29.026939 INFO: === checking if optimization conditions were reached ===
2 days, 0:04:29.029262 INFO: Updating optimization_manager: ms2_error           : 16.988990919194578 -> 15.0
2 days, 0:04:29.029424 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
2 days, 0:04:29.029504 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 0:04:29.030674 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 0:04:29.030784 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
2 days, 0:04:29.030851 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 0:04:29.030910 INFO: ==============================================
2 days, 0:04:29.030985 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 0:04:29.607198 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:04:29.658609 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:04:29.909711 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:04:29.961820 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:04:30.436905 INFO: Starting optimization step 0.
2 days, 0:04:30.437193 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 0:04:30.437294 INFO: Using python extraction backend
2 days, 0:04:30.437434 PROGRESS: Extracting batch of 407917 precursors
2 days, 0:04:30.437519 INFO: === Search parameters used ===
2 days, 0:04:30.437577 INFO: rt_error       : 1199.951535
2 days, 0:04:30.437629 INFO: mobility_error : 0.1
2 days, 0:04:30.437677 INFO: num_candidates : 3
2 days, 0:04:30.437724 INFO: ms1_error      : 15.0
2 days, 0:04:30.437769 INFO: ms2_error      : 15.0
2 days, 0:04:30.437813 INFO: fwhm_rt        : 2.798157215118408
2 days, 0:04:30.437856 INFO: quant_window   : 3
2 days, 0:04:30.437927 INFO: ==============================================
2 days, 0:04:30.540624 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 0:04:30.540779 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 0:04:30.540836 INFO: FWHM in RT is 2.80 seconds, sigma is 0.47
2 days, 0:04:30.540863 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.50
2 days, 0:04:30.541591 INFO: Starting candidate selection
2 days, 0:20:57.781566 INFO: Starting candidate scoring
2 days, 0:21:09.764143 INFO: Finished candidate processing
2 days, 0:21:09.764397 INFO: Collecting candidate features
2 days, 0:21:11.820532 WARNING: intensity_correlation has 1056 NaNs ( 0.10 % out of 1026255)
2 days, 0:21:11.821807 WARNING: height_correlation has 72 NaNs ( 0.01 % out of 1026255)
2 days, 0:21:11.860852 INFO: Collecting fragment features
2 days, 0:21:12.441318 INFO: Finished candidate scoring
2 days, 0:21:13.051271 INFO: performing precursor FDR with 47 features
2 days, 0:21:13.051421 INFO: Decoy channel: -1
2 days, 0:21:13.051473 INFO: competitive: True
2 days, 0:21:13.310142 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 0:21:13.464519 WARNING: dropped 505 target PSMs due to missing features
2 days, 0:21:13.464691 WARNING: dropped 603 decoy PSMs due to missing features
2 days, 0:21:13.936024 INFO: Estimating optimal hyperparameters - samples: 820,117, batch_size: 3,359, learning_rate: 9.06e-04
2 days, 0:21:13.938330 INFO: Using random state 367219 for train-test-split
2 days, 0:21:37.179943 INFO: Test AUC: 0.554
2 days, 0:21:37.180117 INFO: Train AUC: 0.574
2 days, 0:21:37.180354 INFO: AUC difference: 3.39%
2 days, 0:21:37.766163 INFO: Resetting torch num_threads to 80
2 days, 0:21:37.785262 PROGRESS: === Extracted 1026255 precursors and 7147485 fragments ===
2 days, 0:21:37.786131 INFO: === FDR correction performed with classifier version 13 ===
2 days, 0:21:37.817482 PROGRESS: ============================= Precursor FDR =============================
2 days, 0:21:37.817768 PROGRESS: Total precursors accumulated: 186,639
2 days, 0:21:37.817841 PROGRESS: Target precursors: 109,930 (58.90%)
2 days, 0:21:37.817922 PROGRESS: Decoy precursors: 76,709 (41.10%)
2 days, 0:21:37.817979 PROGRESS: 
2 days, 0:21:37.818047 PROGRESS: Precursor Summary:
2 days, 0:21:37.820379 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   204; 0.001 FDR:    98
2 days, 0:21:37.820483 PROGRESS: 
2 days, 0:21:37.820547 PROGRESS: Protein Summary:
2 days, 0:21:37.822684 PROGRESS: Channel   0:	 0.050 FDR:   309; 0.010 FDR:   170; 0.001 FDR:    80
2 days, 0:21:37.822804 PROGRESS: =========================================================================
2 days, 0:21:37.832616 INFO: Target number of precursors reached.
2 days, 0:21:38.618249 INFO: fragments_df: keeping 3431 of 7147485 [sum(precursor_idx_mask)=5627 sum(mass_error_mask)=7147446 stop_rank=3431
2 days, 0:21:39.764379 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:21:39.897222 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:21:40.021446 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:21:40.139227 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:21:40.559999 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 0:21:40.560468 INFO: Using score_cutoff 28.294202379226686 (fac=0.99, q=1)
2 days, 0:21:40.560814 INFO: Updating optimization_manager: fwhm_rt             : 2.798157215118408 -> 2.8403635025024414
2 days, 0:21:40.560905 INFO: Updating optimization_manager: fwhm_mobility       : 0.006450008135288954 -> 0.0064637018367648125
2 days, 0:21:40.560970 INFO: Updating optimization_manager: score_cutoff        : 31.092466738128664 -> 28.294202379226686
2 days, 0:21:40.561039 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:21:40.613398 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:21:40.870351 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:21:40.930755 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:21:41.442681 INFO: === checking if optimization conditions were reached ===
2 days, 0:21:41.442980 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 0:21:41.445022 INFO: Updating optimization_manager: rt_error            : 1199.951535 -> 631.8974069473824
2 days, 0:21:41.445152 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 631.8974.
2 days, 0:21:41.445229 INFO: ==============================================
2 days, 0:21:41.445306 INFO: Starting optimization step 1.
2 days, 0:21:41.445379 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 0:21:41.445449 INFO: Using python extraction backend
2 days, 0:21:41.445566 PROGRESS: Extracting batch of 407917 precursors
2 days, 0:21:41.445640 INFO: === Search parameters used ===
2 days, 0:21:41.445703 INFO: rt_error       : 631.8974069473824
2 days, 0:21:41.445754 INFO: mobility_error : 0.1
2 days, 0:21:41.445803 INFO: num_candidates : 3
2 days, 0:21:41.445850 INFO: ms1_error      : 15.0
2 days, 0:21:41.445924 INFO: ms2_error      : 15.0
2 days, 0:21:41.445987 INFO: fwhm_rt        : 2.8403635025024414
2 days, 0:21:41.446033 INFO: quant_window   : 3
2 days, 0:21:41.446078 INFO: ==============================================
2 days, 0:21:41.548202 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 0:21:41.548353 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 0:21:41.548402 INFO: FWHM in RT is 2.84 seconds, sigma is 0.47
2 days, 0:21:41.548429 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.50
2 days, 0:21:41.549269 INFO: Starting candidate selection
2 days, 0:31:47.621491 INFO: Starting candidate scoring
2 days, 0:31:59.986185 INFO: Finished candidate processing
2 days, 0:31:59.986504 INFO: Collecting candidate features
2 days, 0:32:02.230749 WARNING: intensity_correlation has 1542 NaNs ( 0.15 % out of 1009075)
2 days, 0:32:02.231947 WARNING: height_correlation has 114 NaNs ( 0.01 % out of 1009075)
2 days, 0:32:02.269927 INFO: Collecting fragment features
2 days, 0:32:02.943343 INFO: Finished candidate scoring
2 days, 0:32:03.696562 INFO: performing precursor FDR with 47 features
2 days, 0:32:03.696711 INFO: Decoy channel: -1
2 days, 0:32:03.696745 INFO: competitive: True
2 days, 0:32:03.981277 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 0:32:04.142604 WARNING: dropped 791 target PSMs due to missing features
2 days, 0:32:04.142794 WARNING: dropped 821 decoy PSMs due to missing features
2 days, 0:32:04.778232 INFO: Estimating optimal hyperparameters - samples: 805,970, batch_size: 3,301, learning_rate: 8.98e-04
2 days, 0:32:04.780343 INFO: Using random state 367219 for train-test-split
2 days, 0:32:27.597493 INFO: Test AUC: 0.554
2 days, 0:32:27.597671 INFO: Train AUC: 0.572
2 days, 0:32:27.597708 INFO: AUC difference: 3.05%
2 days, 0:32:28.164456 INFO: Resetting torch num_threads to 80
2 days, 0:32:28.183000 PROGRESS: === Extracted 1009075 precursors and 6754178 fragments ===
2 days, 0:32:28.183930 INFO: === FDR correction performed with classifier version 13 ===
2 days, 0:32:28.213787 PROGRESS: ============================= Precursor FDR =============================
2 days, 0:32:28.214095 PROGRESS: Total precursors accumulated: 186,401
2 days, 0:32:28.214169 PROGRESS: Target precursors: 108,406 (58.16%)
2 days, 0:32:28.214231 PROGRESS: Decoy precursors: 77,995 (41.84%)
2 days, 0:32:28.214286 PROGRESS: 
2 days, 0:32:28.214338 PROGRESS: Precursor Summary:
2 days, 0:32:28.216560 PROGRESS: Channel   0:	 0.050 FDR:   289; 0.010 FDR:   165; 0.001 FDR:    87
2 days, 0:32:28.216675 PROGRESS: 
2 days, 0:32:28.216751 PROGRESS: Protein Summary:
2 days, 0:32:28.218865 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:   139; 0.001 FDR:    74
2 days, 0:32:28.218974 PROGRESS: =========================================================================
2 days, 0:32:28.230324 INFO: Target number of precursors not reached yet.
2 days, 0:32:29.367690 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:32:29.420757 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:32:29.682198 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:32:29.742449 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:32:30.241934 INFO: === skipping optimization until target number of precursors are found ===
2 days, 0:32:30.242266 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 0:32:30.242401 INFO: Starting optimization step 2.
2 days, 0:32:30.242501 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 0:32:30.242584 INFO: Using python extraction backend
2 days, 0:32:30.242714 PROGRESS: Extracting batch of 408390 precursors
2 days, 0:32:30.242802 INFO: === Search parameters used ===
2 days, 0:32:30.242861 INFO: rt_error       : 631.8974069473824
2 days, 0:32:30.242913 INFO: mobility_error : 0.1
2 days, 0:32:30.242965 INFO: num_candidates : 3
2 days, 0:32:30.243016 INFO: ms1_error      : 15.0
2 days, 0:32:30.243068 INFO: ms2_error      : 15.0
2 days, 0:32:30.243116 INFO: fwhm_rt        : 2.8403635025024414
2 days, 0:32:30.243166 INFO: quant_window   : 3
2 days, 0:32:30.243216 INFO: ==============================================
2 days, 0:32:30.346476 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 0:32:30.346632 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 0:32:30.346684 INFO: FWHM in RT is 2.84 seconds, sigma is 0.47
2 days, 0:32:30.346710 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.50
2 days, 0:32:30.347615 INFO: Starting candidate selection
2 days, 0:41:18.604189 INFO: Starting candidate scoring
2 days, 0:41:30.616058 INFO: Finished candidate processing
2 days, 0:41:30.616552 INFO: Collecting candidate features
2 days, 0:41:32.740040 WARNING: intensity_correlation has 1644 NaNs ( 0.16 % out of 1007484)
2 days, 0:41:32.741146 WARNING: height_correlation has 128 NaNs ( 0.01 % out of 1007484)
2 days, 0:41:32.776348 INFO: Collecting fragment features
2 days, 0:41:33.317180 INFO: Finished candidate scoring
2 days, 0:41:34.606175 INFO: performing precursor FDR with 47 features
2 days, 0:41:34.606342 INFO: Decoy channel: -1
2 days, 0:41:34.606373 INFO: competitive: True
2 days, 0:41:35.368723 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 0:41:35.655851 WARNING: dropped 1654 target PSMs due to missing features
2 days, 0:41:35.656039 WARNING: dropped 1687 decoy PSMs due to missing features
2 days, 0:41:36.344938 INFO: Estimating optimal hyperparameters - samples: 1,610,574, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 0:41:36.348650 INFO: Using random state 367219 for train-test-split
2 days, 0:42:15.768155 INFO: Test AUC: 0.554
2 days, 0:42:15.768395 INFO: Train AUC: 0.566
2 days, 0:42:15.768436 INFO: AUC difference: 2.14%
2 days, 0:42:16.684964 INFO: Resetting torch num_threads to 80
2 days, 0:42:16.932989 PROGRESS: === Extracted 2016559 precursors and 13500641 fragments ===
2 days, 0:42:16.934201 INFO: === FDR correction performed with classifier version 13 ===
2 days, 0:42:16.995703 PROGRESS: ============================= Precursor FDR =============================
2 days, 0:42:16.996039 PROGRESS: Total precursors accumulated: 372,499
2 days, 0:42:16.996114 PROGRESS: Target precursors: 214,815 (57.67%)
2 days, 0:42:16.996176 PROGRESS: Decoy precursors: 157,684 (42.33%)
2 days, 0:42:16.996230 PROGRESS: 
2 days, 0:42:16.996284 PROGRESS: Precursor Summary:
2 days, 0:42:16.999664 PROGRESS: Channel   0:	 0.050 FDR:   631; 0.010 FDR:   419; 0.001 FDR:   372
2 days, 0:42:16.999799 PROGRESS: 
2 days, 0:42:16.999867 PROGRESS: Protein Summary:
2 days, 0:42:17.003038 PROGRESS: Channel   0:	 0.050 FDR:   490; 0.010 FDR:   309; 0.001 FDR:   272
2 days, 0:42:17.003145 PROGRESS: =========================================================================
2 days, 0:42:17.008232 INFO: Target number of precursors reached.
2 days, 0:42:18.488881 INFO: fragments_df: keeping 5000 of 13500641 [sum(precursor_idx_mask)=11480 sum(mass_error_mask)=13500533 stop_rank=5000
2 days, 0:42:19.653998 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:42:19.799982 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:42:19.926851 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:42:20.051636 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:42:20.703408 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 0:42:20.703870 INFO: Using score_cutoff 26.370374184036255 (fac=0.99, q=1)
2 days, 0:42:20.704219 INFO: Updating optimization_manager: fwhm_rt             : 2.8403635025024414 -> 2.778052568435669
2 days, 0:42:20.704306 INFO: Updating optimization_manager: fwhm_mobility       : 0.0064637018367648125 -> 0.006325735244899988
2 days, 0:42:20.704367 INFO: Updating optimization_manager: score_cutoff        : 28.294202379226686 -> 26.370374184036255
2 days, 0:42:20.704430 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:42:20.754935 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:42:21.007657 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:42:21.063065 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:42:21.555598 INFO: === checking if optimization conditions were reached ===
2 days, 0:42:21.555911 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 0:42:21.558191 INFO: Updating optimization_manager: rt_error            : 631.8974069473824 -> 388.981281077612
2 days, 0:42:21.558325 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 388.9813.
2 days, 0:42:21.558403 INFO: ==============================================
2 days, 0:42:21.558483 INFO: Starting optimization step 3.
2 days, 0:42:21.558559 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 0:42:21.558627 INFO: Using python extraction backend
2 days, 0:42:21.558746 PROGRESS: Extracting batch of 407917 precursors
2 days, 0:42:21.558822 INFO: === Search parameters used ===
2 days, 0:42:21.558879 INFO: rt_error       : 388.981281077612
2 days, 0:42:21.558931 INFO: mobility_error : 0.1
2 days, 0:42:21.558981 INFO: num_candidates : 3
2 days, 0:42:21.559031 INFO: ms1_error      : 15.0
2 days, 0:42:21.559079 INFO: ms2_error      : 15.0
2 days, 0:42:21.559151 INFO: fwhm_rt        : 2.778052568435669
2 days, 0:42:21.559200 INFO: quant_window   : 3
2 days, 0:42:21.559248 INFO: ==============================================
2 days, 0:42:21.668685 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 0:42:21.668841 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 0:42:21.668889 INFO: FWHM in RT is 2.78 seconds, sigma is 0.46
2 days, 0:42:21.668913 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.43
2 days, 0:42:21.669697 INFO: Starting candidate selection
2 days, 0:48:42.710901 INFO: Starting candidate scoring
2 days, 0:48:54.421495 INFO: Finished candidate processing
2 days, 0:48:54.421780 INFO: Collecting candidate features
2 days, 0:48:56.389024 WARNING: intensity_correlation has 1976 NaNs ( 0.20 % out of 975497)
2 days, 0:48:56.390105 WARNING: height_correlation has 171 NaNs ( 0.02 % out of 975497)
2 days, 0:48:56.424904 INFO: Collecting fragment features
2 days, 0:48:56.982374 INFO: Finished candidate scoring
2 days, 0:48:57.739129 INFO: performing precursor FDR with 47 features
2 days, 0:48:57.739275 INFO: Decoy channel: -1
2 days, 0:48:57.739305 INFO: competitive: True
2 days, 0:48:57.981555 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 0:48:58.127268 WARNING: dropped 1014 target PSMs due to missing features
2 days, 0:48:58.127430 WARNING: dropped 1053 decoy PSMs due to missing features
2 days, 0:48:58.480784 INFO: Estimating optimal hyperparameters - samples: 778,744, batch_size: 3,189, learning_rate: 8.82e-04
2 days, 0:48:58.482147 INFO: Using random state 367219 for train-test-split
2 days, 0:49:20.384500 INFO: Test AUC: 0.548
2 days, 0:49:20.384731 INFO: Train AUC: 0.568
2 days, 0:49:20.384771 INFO: AUC difference: 3.59%
2 days, 0:49:20.960906 INFO: Resetting torch num_threads to 80
2 days, 0:49:20.979115 PROGRESS: === Extracted 975497 precursors and 6136393 fragments ===
2 days, 0:49:20.980005 INFO: === FDR correction performed with classifier version 13 ===
2 days, 0:49:21.009584 PROGRESS: ============================= Precursor FDR =============================
2 days, 0:49:21.009873 PROGRESS: Total precursors accumulated: 184,527
2 days, 0:49:21.009953 PROGRESS: Target precursors: 106,266 (57.59%)
2 days, 0:49:21.010012 PROGRESS: Decoy precursors: 78,261 (42.41%)
2 days, 0:49:21.010065 PROGRESS: 
2 days, 0:49:21.010116 PROGRESS: Precursor Summary:
2 days, 0:49:21.012362 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   249; 0.001 FDR:   212
2 days, 0:49:21.012474 PROGRESS: 
2 days, 0:49:21.012536 PROGRESS: Protein Summary:
2 days, 0:49:21.014748 PROGRESS: Channel   0:	 0.050 FDR:   283; 0.010 FDR:   202; 0.001 FDR:   173
2 days, 0:49:21.014855 PROGRESS: =========================================================================
2 days, 0:49:21.034696 INFO: Target number of precursors reached.
2 days, 0:49:21.685685 INFO: fragments_df: keeping 3974 of 6136393 [sum(precursor_idx_mask)=6766 sum(mass_error_mask)=6136353 stop_rank=3974
2 days, 0:49:22.840471 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:49:22.972403 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:49:23.105230 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:49:23.236378 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:49:23.791946 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 0:49:23.792409 INFO: Using score_cutoff 28.662892520141604 (fac=0.99, q=1)
2 days, 0:49:23.792767 INFO: Updating optimization_manager: fwhm_rt             : 2.778052568435669 -> 2.6458072662353516
2 days, 0:49:23.792865 INFO: Updating optimization_manager: fwhm_mobility       : 0.006325735244899988 -> 0.005864297971129417
2 days, 0:49:23.792934 INFO: Updating optimization_manager: score_cutoff        : 26.370374184036255 -> 28.662892520141604
2 days, 0:49:23.793000 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:49:23.847803 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:49:24.104277 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:49:24.165467 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:49:24.655090 INFO: === checking if optimization conditions were reached ===
2 days, 0:49:24.655402 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 0:49:24.657704 INFO: Updating optimization_manager: rt_error            : 388.981281077612 -> 289.5612155201539
2 days, 0:49:24.657844 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 289.5612.
2 days, 0:49:24.657940 INFO: ==============================================
2 days, 0:49:24.658021 INFO: Starting optimization step 4.
2 days, 0:49:24.658086 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 0:49:24.658150 INFO: Using python extraction backend
2 days, 0:49:24.658273 PROGRESS: Extracting batch of 407917 precursors
2 days, 0:49:24.658351 INFO: === Search parameters used ===
2 days, 0:49:24.658407 INFO: rt_error       : 289.5612155201539
2 days, 0:49:24.658458 INFO: mobility_error : 0.1
2 days, 0:49:24.658505 INFO: num_candidates : 3
2 days, 0:49:24.658552 INFO: ms1_error      : 15.0
2 days, 0:49:24.658624 INFO: ms2_error      : 15.0
2 days, 0:49:24.658674 INFO: fwhm_rt        : 2.6458072662353516
2 days, 0:49:24.658722 INFO: quant_window   : 3
2 days, 0:49:24.658772 INFO: ==============================================
2 days, 0:49:24.760478 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 0:49:24.760632 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 0:49:24.760682 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
2 days, 0:49:24.760709 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.18
2 days, 0:49:24.761473 INFO: Starting candidate selection
2 days, 0:53:42.067978 INFO: Starting candidate scoring
2 days, 0:53:53.628667 INFO: Finished candidate processing
2 days, 0:53:53.628849 INFO: Collecting candidate features
2 days, 0:53:55.502968 WARNING: intensity_correlation has 2293 NaNs ( 0.24 % out of 954651)
2 days, 0:53:55.504180 WARNING: height_correlation has 223 NaNs ( 0.02 % out of 954651)
2 days, 0:53:55.540073 INFO: Collecting fragment features
2 days, 0:53:56.056900 INFO: Finished candidate scoring
2 days, 0:53:56.633989 INFO: performing precursor FDR with 47 features
2 days, 0:53:56.634137 INFO: Decoy channel: -1
2 days, 0:53:56.634169 INFO: competitive: True
2 days, 0:53:56.869405 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 0:53:57.010848 WARNING: dropped 1186 target PSMs due to missing features
2 days, 0:53:57.011016 WARNING: dropped 1224 decoy PSMs due to missing features
2 days, 0:53:57.599902 INFO: Estimating optimal hyperparameters - samples: 761,792, batch_size: 3,120, learning_rate: 8.73e-04
2 days, 0:53:57.601982 INFO: Using random state 367219 for train-test-split
2 days, 0:54:16.571145 INFO: Test AUC: 0.545
2 days, 0:54:16.571322 INFO: Train AUC: 0.565
2 days, 0:54:16.571359 INFO: AUC difference: 3.56%
2 days, 0:54:17.130032 INFO: Resetting torch num_threads to 80
2 days, 0:54:17.148093 PROGRESS: === Extracted 954651 precursors and 5809007 fragments ===
2 days, 0:54:17.149038 INFO: === FDR correction performed with classifier version 13 ===
2 days, 0:54:17.180572 PROGRESS: ============================= Precursor FDR =============================
2 days, 0:54:17.180926 PROGRESS: Total precursors accumulated: 183,426
2 days, 0:54:17.181001 PROGRESS: Target precursors: 104,922 (57.20%)
2 days, 0:54:17.181063 PROGRESS: Decoy precursors: 78,504 (42.80%)
2 days, 0:54:17.181118 PROGRESS: 
2 days, 0:54:17.181172 PROGRESS: Precursor Summary:
2 days, 0:54:17.183531 PROGRESS: Channel   0:	 0.050 FDR:   367; 0.010 FDR:   186; 0.001 FDR:   146
2 days, 0:54:17.183640 PROGRESS: 
2 days, 0:54:17.183703 PROGRESS: Protein Summary:
2 days, 0:54:17.185832 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   154; 0.001 FDR:   121
2 days, 0:54:17.185944 PROGRESS: =========================================================================
2 days, 0:54:17.190972 INFO: Target number of precursors not reached yet.
2 days, 0:54:18.333956 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:54:18.388325 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:54:18.640641 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:54:18.700317 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:54:19.167322 INFO: === skipping optimization until target number of precursors are found ===
2 days, 0:54:19.167640 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 0:54:19.167791 INFO: Starting optimization step 5.
2 days, 0:54:19.167896 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 0:54:19.167993 INFO: Using python extraction backend
2 days, 0:54:19.168157 PROGRESS: Extracting batch of 408390 precursors
2 days, 0:54:19.168276 INFO: === Search parameters used ===
2 days, 0:54:19.168369 INFO: rt_error       : 289.5612155201539
2 days, 0:54:19.168454 INFO: mobility_error : 0.1
2 days, 0:54:19.168536 INFO: num_candidates : 3
2 days, 0:54:19.168617 INFO: ms1_error      : 15.0
2 days, 0:54:19.168698 INFO: ms2_error      : 15.0
2 days, 0:54:19.168773 INFO: fwhm_rt        : 2.6458072662353516
2 days, 0:54:19.168844 INFO: quant_window   : 3
2 days, 0:54:19.168921 INFO: ==============================================
2 days, 0:54:19.271551 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 0:54:19.271700 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 0:54:19.271761 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
2 days, 0:54:19.271799 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.18
2 days, 0:54:19.272657 INFO: Starting candidate selection
2 days, 0:58:36.118111 INFO: Starting candidate scoring
2 days, 0:58:47.416815 INFO: Finished candidate processing
2 days, 0:58:47.417060 INFO: Collecting candidate features
2 days, 0:58:49.373115 WARNING: intensity_correlation has 2382 NaNs ( 0.25 % out of 953871)
2 days, 0:58:49.374187 WARNING: height_correlation has 244 NaNs ( 0.03 % out of 953871)
2 days, 0:58:49.408403 INFO: Collecting fragment features
2 days, 0:58:49.950541 INFO: Finished candidate scoring
2 days, 0:58:54.675164 INFO: performing precursor FDR with 47 features
2 days, 0:58:54.675338 INFO: Decoy channel: -1
2 days, 0:58:54.675369 INFO: competitive: True
2 days, 0:58:55.443271 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 0:58:55.716659 WARNING: dropped 2443 target PSMs due to missing features
2 days, 0:58:55.716834 WARNING: dropped 2468 decoy PSMs due to missing features
2 days, 0:58:56.362736 INFO: Estimating optimal hyperparameters - samples: 1,522,888, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 0:58:56.366782 INFO: Using random state 367219 for train-test-split
2 days, 0:59:34.785986 INFO: Test AUC: 0.550
2 days, 0:59:34.786152 INFO: Train AUC: 0.560
2 days, 0:59:34.786189 INFO: AUC difference: 1.93%
2 days, 0:59:35.667161 INFO: Resetting torch num_threads to 80
2 days, 0:59:35.927604 PROGRESS: === Extracted 1908522 precursors and 11615331 fragments ===
2 days, 0:59:35.928718 INFO: === FDR correction performed with classifier version 13 ===
2 days, 0:59:35.985878 PROGRESS: ============================= Precursor FDR =============================
2 days, 0:59:35.986211 PROGRESS: Total precursors accumulated: 366,585
2 days, 0:59:35.986313 PROGRESS: Target precursors: 208,379 (56.84%)
2 days, 0:59:35.986377 PROGRESS: Decoy precursors: 158,206 (43.16%)
2 days, 0:59:35.986431 PROGRESS: 
2 days, 0:59:35.986481 PROGRESS: Precursor Summary:
2 days, 0:59:35.990162 PROGRESS: Channel   0:	 0.050 FDR:   675; 0.010 FDR:   551; 0.001 FDR:   395
2 days, 0:59:35.990305 PROGRESS: 
2 days, 0:59:35.990369 PROGRESS: Protein Summary:
2 days, 0:59:35.993595 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:   422; 0.001 FDR:   293
2 days, 0:59:35.993701 PROGRESS: =========================================================================
2 days, 0:59:35.998661 INFO: Target number of precursors reached.
2 days, 0:59:37.297383 INFO: fragments_df: keeping 5000 of 11615331 [sum(precursor_idx_mask)=14599 sum(mass_error_mask)=11615208 stop_rank=5000
2 days, 0:59:38.469706 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:59:38.626666 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:59:38.791351 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:59:38.954697 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:59:39.682400 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 0:59:39.682869 INFO: Using score_cutoff 23.87625354766846 (fac=0.99, q=1)
2 days, 0:59:39.683190 INFO: Updating optimization_manager: fwhm_rt             : 2.6458072662353516 -> 2.6967389583587646
2 days, 0:59:39.683277 INFO: Updating optimization_manager: fwhm_mobility       : 0.005864297971129417 -> 0.0055794925428926945
2 days, 0:59:39.683336 INFO: Updating optimization_manager: score_cutoff        : 28.662892520141604 -> 23.87625354766846
2 days, 0:59:39.683403 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 0:59:39.733260 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 0:59:39.986937 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 0:59:40.039093 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 0:59:40.559090 INFO: === checking if optimization conditions were reached ===
2 days, 0:59:40.559387 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 0:59:40.561887 INFO: Updating optimization_manager: rt_error            : 289.5612155201539 -> 242.04338658001987
2 days, 0:59:40.562044 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 242.0434.
2 days, 0:59:40.562120 INFO: ==============================================
2 days, 0:59:40.562200 INFO: Starting optimization step 6.
2 days, 0:59:40.562265 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 0:59:40.562329 INFO: Using python extraction backend
2 days, 0:59:40.562434 PROGRESS: Extracting batch of 407917 precursors
2 days, 0:59:40.562508 INFO: === Search parameters used ===
2 days, 0:59:40.562564 INFO: rt_error       : 242.04338658001987
2 days, 0:59:40.562614 INFO: mobility_error : 0.1
2 days, 0:59:40.562663 INFO: num_candidates : 3
2 days, 0:59:40.562710 INFO: ms1_error      : 15.0
2 days, 0:59:40.562756 INFO: ms2_error      : 15.0
2 days, 0:59:40.562801 INFO: fwhm_rt        : 2.6967389583587646
2 days, 0:59:40.562864 INFO: quant_window   : 3
2 days, 0:59:40.562912 INFO: ==============================================
2 days, 0:59:40.672267 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 0:59:40.672426 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 0:59:40.672476 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
2 days, 0:59:40.672502 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.02
2 days, 0:59:40.673348 INFO: Starting candidate selection
2 days, 1:03:06.687092 INFO: Starting candidate scoring
2 days, 1:03:19.422645 INFO: Finished candidate processing
2 days, 1:03:19.422926 INFO: Collecting candidate features
2 days, 1:03:21.306564 WARNING: intensity_correlation has 2550 NaNs ( 0.27 % out of 941753)
2 days, 1:03:21.307694 WARNING: height_correlation has 249 NaNs ( 0.03 % out of 941753)
2 days, 1:03:21.343282 INFO: Collecting fragment features
2 days, 1:03:21.897313 INFO: Finished candidate scoring
2 days, 1:03:22.614298 INFO: performing precursor FDR with 47 features
2 days, 1:03:22.614448 INFO: Decoy channel: -1
2 days, 1:03:22.614478 INFO: competitive: True
2 days, 1:03:22.860933 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:03:23.012323 WARNING: dropped 1331 target PSMs due to missing features
2 days, 1:03:23.012495 WARNING: dropped 1339 decoy PSMs due to missing features
2 days, 1:03:23.670874 INFO: Estimating optimal hyperparameters - samples: 751,266, batch_size: 3,077, learning_rate: 8.67e-04
2 days, 1:03:23.674718 INFO: Using random state 367219 for train-test-split
2 days, 1:03:45.203427 INFO: Test AUC: 0.548
2 days, 1:03:45.203600 INFO: Train AUC: 0.565
2 days, 1:03:45.203636 INFO: AUC difference: 3.15%
2 days, 1:03:45.756290 INFO: Resetting torch num_threads to 80
2 days, 1:03:45.774080 PROGRESS: === Extracted 941753 precursors and 5613440 fragments ===
2 days, 1:03:45.774980 INFO: === FDR correction performed with classifier version 13 ===
2 days, 1:03:45.804620 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:03:45.804913 PROGRESS: Total precursors accumulated: 182,725
2 days, 1:03:45.804989 PROGRESS: Target precursors: 104,107 (56.97%)
2 days, 1:03:45.805053 PROGRESS: Decoy precursors: 78,618 (43.03%)
2 days, 1:03:45.805107 PROGRESS: 
2 days, 1:03:45.805161 PROGRESS: Precursor Summary:
2 days, 1:03:45.807429 PROGRESS: Channel   0:	 0.050 FDR:   317; 0.010 FDR:    13; 0.001 FDR:    13
2 days, 1:03:45.807539 PROGRESS: 
2 days, 1:03:45.807605 PROGRESS: Protein Summary:
2 days, 1:03:45.809684 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:    12; 0.001 FDR:    12
2 days, 1:03:45.809788 PROGRESS: =========================================================================
2 days, 1:03:45.820673 INFO: Target number of precursors not reached yet.
2 days, 1:03:46.952268 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:03:47.001575 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:03:47.250959 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:03:47.304273 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:03:47.788064 INFO: === skipping optimization until target number of precursors are found ===
2 days, 1:03:47.788363 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 1:03:47.788481 INFO: Starting optimization step 7.
2 days, 1:03:47.788560 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 1:03:47.788637 INFO: Using python extraction backend
2 days, 1:03:47.788760 PROGRESS: Extracting batch of 408390 precursors
2 days, 1:03:47.788848 INFO: === Search parameters used ===
2 days, 1:03:47.788912 INFO: rt_error       : 242.04338658001987
2 days, 1:03:47.788966 INFO: mobility_error : 0.1
2 days, 1:03:47.789016 INFO: num_candidates : 3
2 days, 1:03:47.789065 INFO: ms1_error      : 15.0
2 days, 1:03:47.789115 INFO: ms2_error      : 15.0
2 days, 1:03:47.789163 INFO: fwhm_rt        : 2.6967389583587646
2 days, 1:03:47.789212 INFO: quant_window   : 3
2 days, 1:03:47.789258 INFO: ==============================================
2 days, 1:03:47.889954 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:03:47.890110 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:03:47.890162 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
2 days, 1:03:47.890190 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.02
2 days, 1:03:47.891046 INFO: Starting candidate selection
2 days, 1:07:09.106452 INFO: Starting candidate scoring
2 days, 1:07:20.655725 INFO: Finished candidate processing
2 days, 1:07:20.656098 INFO: Collecting candidate features
2 days, 1:07:22.608242 WARNING: intensity_correlation has 2574 NaNs ( 0.27 % out of 940576)
2 days, 1:07:22.609394 WARNING: height_correlation has 296 NaNs ( 0.03 % out of 940576)
2 days, 1:07:22.645097 INFO: Collecting fragment features
2 days, 1:07:23.104827 INFO: Finished candidate scoring
2 days, 1:07:24.190007 INFO: performing precursor FDR with 47 features
2 days, 1:07:24.190171 INFO: Decoy channel: -1
2 days, 1:07:24.190225 INFO: competitive: True
2 days, 1:07:24.905401 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:07:25.169573 WARNING: dropped 2739 target PSMs due to missing features
2 days, 1:07:25.169740 WARNING: dropped 2640 decoy PSMs due to missing features
2 days, 1:07:25.832826 INFO: Estimating optimal hyperparameters - samples: 1,501,560, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 1:07:25.836631 INFO: Using random state 367219 for train-test-split
2 days, 1:08:08.476977 INFO: Test AUC: 0.549
2 days, 1:08:08.477155 INFO: Train AUC: 0.560
2 days, 1:08:08.477193 INFO: AUC difference: 2.08%
2 days, 1:08:09.352733 INFO: Resetting torch num_threads to 80
2 days, 1:08:09.673146 PROGRESS: === Extracted 1882329 precursors and 11221054 fragments ===
2 days, 1:08:09.674269 INFO: === FDR correction performed with classifier version 13 ===
2 days, 1:08:09.731842 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:08:09.732166 PROGRESS: Total precursors accumulated: 365,124
2 days, 1:08:09.732246 PROGRESS: Target precursors: 206,969 (56.68%)
2 days, 1:08:09.732309 PROGRESS: Decoy precursors: 158,155 (43.32%)
2 days, 1:08:09.732383 PROGRESS: 
2 days, 1:08:09.732440 PROGRESS: Precursor Summary:
2 days, 1:08:09.736101 PROGRESS: Channel   0:	 0.050 FDR:   715; 0.010 FDR:   514; 0.001 FDR:   466
2 days, 1:08:09.736247 PROGRESS: 
2 days, 1:08:09.736323 PROGRESS: Protein Summary:
2 days, 1:08:09.739626 PROGRESS: Channel   0:	 0.050 FDR:   556; 0.010 FDR:   387; 0.001 FDR:   347
2 days, 1:08:09.739747 PROGRESS: =========================================================================
2 days, 1:08:09.744667 INFO: Target number of precursors reached.
2 days, 1:08:10.985564 INFO: fragments_df: keeping 5000 of 11221054 [sum(precursor_idx_mask)=13632 sum(mass_error_mask)=11220925 stop_rank=5000
2 days, 1:08:12.143705 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:08:12.301567 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:08:12.458488 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:08:12.618522 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:08:13.345040 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:08:13.345508 INFO: Using score_cutoff 24.43395368614197 (fac=0.99, q=1)
2 days, 1:08:13.345874 INFO: Updating optimization_manager: fwhm_rt             : 2.6967389583587646 -> 2.66841197013855
2 days, 1:08:13.345966 INFO: Updating optimization_manager: fwhm_mobility       : 0.0055794925428926945 -> 0.005655982997268438
2 days, 1:08:13.346029 INFO: Updating optimization_manager: score_cutoff        : 23.87625354766846 -> 24.43395368614197
2 days, 1:08:13.346090 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:08:13.397982 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:08:13.652280 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:08:13.706887 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:08:14.193852 INFO: === checking if optimization conditions were reached ===
2 days, 1:08:14.194150 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 1:08:14.196644 INFO: Updating optimization_manager: rt_error            : 242.04338658001987 -> 189.96405029649327
2 days, 1:08:14.196797 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 189.9641.
2 days, 1:08:14.196879 INFO: ==============================================
2 days, 1:08:14.196960 INFO: Starting optimization step 8.
2 days, 1:08:14.197028 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 1:08:14.197096 INFO: Using python extraction backend
2 days, 1:08:14.197204 PROGRESS: Extracting batch of 407917 precursors
2 days, 1:08:14.197278 INFO: === Search parameters used ===
2 days, 1:08:14.197338 INFO: rt_error       : 189.96405029649327
2 days, 1:08:14.197392 INFO: mobility_error : 0.1
2 days, 1:08:14.197444 INFO: num_candidates : 3
2 days, 1:08:14.197495 INFO: ms1_error      : 15.0
2 days, 1:08:14.197544 INFO: ms2_error      : 15.0
2 days, 1:08:14.197593 INFO: fwhm_rt        : 2.66841197013855
2 days, 1:08:14.197642 INFO: quant_window   : 3
2 days, 1:08:14.197713 INFO: ==============================================
2 days, 1:08:14.315768 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:08:14.315934 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:08:14.315984 INFO: FWHM in RT is 2.67 seconds, sigma is 0.45
2 days, 1:08:14.316009 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.07
2 days, 1:08:14.316833 INFO: Starting candidate selection
2 days, 1:10:59.966467 INFO: Starting candidate scoring
2 days, 1:11:11.675933 INFO: Finished candidate processing
2 days, 1:11:11.676166 INFO: Collecting candidate features
2 days, 1:11:13.527114 WARNING: intensity_correlation has 2769 NaNs ( 0.30 % out of 929237)
2 days, 1:11:13.528251 WARNING: height_correlation has 269 NaNs ( 0.03 % out of 929237)
2 days, 1:11:13.564350 INFO: Collecting fragment features
2 days, 1:11:14.052058 INFO: Finished candidate scoring
2 days, 1:11:14.627907 INFO: performing precursor FDR with 47 features
2 days, 1:11:14.628054 INFO: Decoy channel: -1
2 days, 1:11:14.628085 INFO: competitive: True
2 days, 1:11:14.861958 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:11:14.999624 WARNING: dropped 1465 target PSMs due to missing features
2 days, 1:11:14.999789 WARNING: dropped 1434 decoy PSMs due to missing features
2 days, 1:11:15.314953 INFO: Estimating optimal hyperparameters - samples: 741,070, batch_size: 3,035, learning_rate: 8.61e-04
2 days, 1:11:15.316919 INFO: Using random state 367219 for train-test-split
2 days, 1:11:39.403958 INFO: Test AUC: 0.544
2 days, 1:11:39.404127 INFO: Train AUC: 0.566
2 days, 1:11:39.404164 INFO: AUC difference: 3.94%
2 days, 1:11:39.952338 INFO: Resetting torch num_threads to 80
2 days, 1:11:39.969797 PROGRESS: === Extracted 929237 precursors and 5443487 fragments ===
2 days, 1:11:39.970798 INFO: === FDR correction performed with classifier version 13 ===
2 days, 1:11:40.003965 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:11:40.004320 PROGRESS: Total precursors accumulated: 181,719
2 days, 1:11:40.004393 PROGRESS: Target precursors: 103,326 (56.86%)
2 days, 1:11:40.004454 PROGRESS: Decoy precursors: 78,393 (43.14%)
2 days, 1:11:40.004509 PROGRESS: 
2 days, 1:11:40.004563 PROGRESS: Precursor Summary:
2 days, 1:11:40.006858 PROGRESS: Channel   0:	 0.050 FDR:   315; 0.010 FDR:     4; 0.001 FDR:     4
2 days, 1:11:40.006965 PROGRESS: 
2 days, 1:11:40.007030 PROGRESS: Protein Summary:
2 days, 1:11:40.009083 PROGRESS: Channel   0:	 0.050 FDR:   262; 0.010 FDR:     4; 0.001 FDR:     4
2 days, 1:11:40.009189 PROGRESS: =========================================================================
2 days, 1:11:40.018559 INFO: Target number of precursors not reached yet.
2 days, 1:11:41.141055 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:11:41.193222 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:11:41.448015 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:11:41.502286 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:11:41.987611 INFO: === skipping optimization until target number of precursors are found ===
2 days, 1:11:41.987916 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 1:11:41.988051 INFO: Starting optimization step 9.
2 days, 1:11:41.988131 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 1:11:41.988203 INFO: Using python extraction backend
2 days, 1:11:41.988323 PROGRESS: Extracting batch of 408390 precursors
2 days, 1:11:41.988408 INFO: === Search parameters used ===
2 days, 1:11:41.988468 INFO: rt_error       : 189.96405029649327
2 days, 1:11:41.988520 INFO: mobility_error : 0.1
2 days, 1:11:41.988571 INFO: num_candidates : 3
2 days, 1:11:41.988621 INFO: ms1_error      : 15.0
2 days, 1:11:41.988670 INFO: ms2_error      : 15.0
2 days, 1:11:41.988717 INFO: fwhm_rt        : 2.66841197013855
2 days, 1:11:41.988765 INFO: quant_window   : 3
2 days, 1:11:41.988821 INFO: ==============================================
2 days, 1:11:42.090132 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:11:42.090283 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:11:42.090330 INFO: FWHM in RT is 2.67 seconds, sigma is 0.45
2 days, 1:11:42.090355 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.07
2 days, 1:11:42.091143 INFO: Starting candidate selection
2 days, 1:14:28.288739 INFO: Starting candidate scoring
2 days, 1:14:39.694058 INFO: Finished candidate processing
2 days, 1:14:39.694328 INFO: Collecting candidate features
2 days, 1:14:41.682659 WARNING: intensity_correlation has 2831 NaNs ( 0.30 % out of 928496)
2 days, 1:14:41.683681 WARNING: height_correlation has 326 NaNs ( 0.04 % out of 928496)
2 days, 1:14:41.716048 INFO: Collecting fragment features
2 days, 1:14:42.197352 INFO: Finished candidate scoring
2 days, 1:14:43.333268 INFO: performing precursor FDR with 47 features
2 days, 1:14:43.333428 INFO: Decoy channel: -1
2 days, 1:14:43.333459 INFO: competitive: True
2 days, 1:14:44.092938 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:14:44.374025 WARNING: dropped 3012 target PSMs due to missing features
2 days, 1:14:44.374193 WARNING: dropped 2866 decoy PSMs due to missing features
2 days, 1:14:45.268711 INFO: Estimating optimal hyperparameters - samples: 1,481,484, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 1:14:45.271415 INFO: Using random state 367219 for train-test-split
2 days, 1:15:27.553983 INFO: Test AUC: 0.547
2 days, 1:15:27.554174 INFO: Train AUC: 0.560
2 days, 1:15:27.554215 INFO: AUC difference: 2.26%
2 days, 1:15:28.423592 INFO: Resetting torch num_threads to 80
2 days, 1:15:28.655940 PROGRESS: === Extracted 1857733 precursors and 10881143 fragments ===
2 days, 1:15:28.657011 INFO: === FDR correction performed with classifier version 13 ===
2 days, 1:15:28.719041 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:15:28.719354 PROGRESS: Total precursors accumulated: 363,147
2 days, 1:15:28.719437 PROGRESS: Target precursors: 204,662 (56.36%)
2 days, 1:15:28.719500 PROGRESS: Decoy precursors: 158,485 (43.64%)
2 days, 1:15:28.719560 PROGRESS: 
2 days, 1:15:28.719615 PROGRESS: Precursor Summary:
2 days, 1:15:28.723439 PROGRESS: Channel   0:	 0.050 FDR:   666; 0.010 FDR:   543; 0.001 FDR:   437
2 days, 1:15:28.723586 PROGRESS: 
2 days, 1:15:28.723653 PROGRESS: Protein Summary:
2 days, 1:15:28.727024 PROGRESS: Channel   0:	 0.050 FDR:   515; 0.010 FDR:   410; 0.001 FDR:   333
2 days, 1:15:28.727156 PROGRESS: =========================================================================
2 days, 1:15:28.732157 INFO: Target number of precursors reached.
2 days, 1:15:29.935098 INFO: fragments_df: keeping 5000 of 10881143 [sum(precursor_idx_mask)=14309 sum(mass_error_mask)=10880991 stop_rank=5000
2 days, 1:15:31.085383 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:15:31.218539 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:15:31.357833 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:15:31.494208 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:15:32.155614 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:15:32.156104 INFO: Using score_cutoff 12.412073280143739 (fac=0.99, q=1)
2 days, 1:15:32.156451 INFO: Updating optimization_manager: fwhm_rt             : 2.66841197013855 -> 2.6566779613494873
2 days, 1:15:32.156546 INFO: Updating optimization_manager: fwhm_mobility       : 0.005655982997268438 -> 0.005387671757489443
2 days, 1:15:32.156612 INFO: Updating optimization_manager: score_cutoff        : 24.43395368614197 -> 12.412073280143739
2 days, 1:15:32.156683 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:15:32.207962 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:15:32.460970 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:15:32.515240 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:15:33.001858 INFO: === checking if optimization conditions were reached ===
2 days, 1:15:33.002169 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 1:15:33.004683 INFO: Updating optimization_manager: rt_error            : 189.96405029649327 -> 158.8279872241982
2 days, 1:15:33.004846 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 158.8280.
2 days, 1:15:33.004923 INFO: ==============================================
2 days, 1:15:33.004999 INFO: Starting optimization step 10.
2 days, 1:15:33.005065 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 1:15:33.005134 INFO: Using python extraction backend
2 days, 1:15:33.005246 PROGRESS: Extracting batch of 407917 precursors
2 days, 1:15:33.005318 INFO: === Search parameters used ===
2 days, 1:15:33.005374 INFO: rt_error       : 158.8279872241982
2 days, 1:15:33.005425 INFO: mobility_error : 0.1
2 days, 1:15:33.005474 INFO: num_candidates : 3
2 days, 1:15:33.005520 INFO: ms1_error      : 15.0
2 days, 1:15:33.005565 INFO: ms2_error      : 15.0
2 days, 1:15:33.005610 INFO: fwhm_rt        : 2.6566779613494873
2 days, 1:15:33.005655 INFO: quant_window   : 3
2 days, 1:15:33.005699 INFO: ==============================================
2 days, 1:15:33.105203 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:15:33.105358 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:15:33.105406 INFO: FWHM in RT is 2.66 seconds, sigma is 0.44
2 days, 1:15:33.105432 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.92
2 days, 1:15:33.106220 INFO: Starting candidate selection
2 days, 1:17:45.177250 INFO: Starting candidate scoring
2 days, 1:17:56.558918 INFO: Finished candidate processing
2 days, 1:17:56.559077 INFO: Collecting candidate features
2 days, 1:17:58.364262 WARNING: intensity_correlation has 3137 NaNs ( 0.34 % out of 920680)
2 days, 1:17:58.365325 WARNING: height_correlation has 304 NaNs ( 0.03 % out of 920680)
2 days, 1:17:58.398213 INFO: Collecting fragment features
2 days, 1:17:58.895691 INFO: Finished candidate scoring
2 days, 1:17:59.482446 INFO: performing precursor FDR with 47 features
2 days, 1:17:59.482593 INFO: Decoy channel: -1
2 days, 1:17:59.482622 INFO: competitive: True
2 days, 1:17:59.697465 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:17:59.831369 WARNING: dropped 1650 target PSMs due to missing features
2 days, 1:17:59.831538 WARNING: dropped 1621 decoy PSMs due to missing features
2 days, 1:18:00.133788 INFO: Estimating optimal hyperparameters - samples: 733,927, batch_size: 3,006, learning_rate: 8.57e-04
2 days, 1:18:00.135243 INFO: Using random state 367219 for train-test-split
2 days, 1:18:23.200776 INFO: Test AUC: 0.541
2 days, 1:18:23.200954 INFO: Train AUC: 0.559
2 days, 1:18:23.200991 INFO: AUC difference: 3.31%
2 days, 1:18:23.745777 INFO: Resetting torch num_threads to 80
2 days, 1:18:23.763012 PROGRESS: === Extracted 920680 precursors and 5296963 fragments ===
2 days, 1:18:23.763965 INFO: === FDR correction performed with classifier version 13 ===
2 days, 1:18:23.793703 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:18:23.794042 PROGRESS: Total precursors accumulated: 181,598
2 days, 1:18:23.794118 PROGRESS: Target precursors: 102,516 (56.45%)
2 days, 1:18:23.794182 PROGRESS: Decoy precursors: 79,082 (43.55%)
2 days, 1:18:23.794238 PROGRESS: 
2 days, 1:18:23.794291 PROGRESS: Precursor Summary:
2 days, 1:18:23.796670 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   237; 0.001 FDR:   218
2 days, 1:18:23.796774 PROGRESS: 
2 days, 1:18:23.796840 PROGRESS: Protein Summary:
2 days, 1:18:23.799043 PROGRESS: Channel   0:	 0.050 FDR:   286; 0.010 FDR:   193; 0.001 FDR:   178
2 days, 1:18:23.799166 PROGRESS: =========================================================================
2 days, 1:18:23.812358 INFO: Target number of precursors reached.
2 days, 1:18:24.376027 INFO: fragments_df: keeping 3826 of 5296963 [sum(precursor_idx_mask)=6225 sum(mass_error_mask)=5296884 stop_rank=3826
2 days, 1:18:25.527105 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:18:25.644456 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:18:25.757101 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:18:25.884458 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:18:26.418030 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:18:26.418497 INFO: Using score_cutoff 29.15378876953125 (fac=0.99, q=1)
2 days, 1:18:26.418844 INFO: Updating optimization_manager: fwhm_rt             : 2.6566779613494873 -> 2.583367347717285
2 days, 1:18:26.418929 INFO: Updating optimization_manager: fwhm_mobility       : 0.005387671757489443 -> 0.006142349448055029
2 days, 1:18:26.418989 INFO: Updating optimization_manager: score_cutoff        : 12.412073280143739 -> 29.15378876953125
2 days, 1:18:26.419047 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:18:26.471932 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:18:26.728652 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:18:26.787874 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:18:27.288867 INFO: === checking if optimization conditions were reached ===
2 days, 1:18:27.289175 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 1:18:27.291477 INFO: Updating optimization_manager: rt_error            : 158.8279872241982 -> 118.21079483693433
2 days, 1:18:27.291625 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 118.2108.
2 days, 1:18:27.291705 INFO: ==============================================
2 days, 1:18:27.291785 INFO: Starting optimization step 11.
2 days, 1:18:27.291855 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 1:18:27.291923 INFO: Using python extraction backend
2 days, 1:18:27.292033 PROGRESS: Extracting batch of 407917 precursors
2 days, 1:18:27.292108 INFO: === Search parameters used ===
2 days, 1:18:27.292171 INFO: rt_error       : 118.21079483693433
2 days, 1:18:27.292223 INFO: mobility_error : 0.1
2 days, 1:18:27.292291 INFO: num_candidates : 3
2 days, 1:18:27.292343 INFO: ms1_error      : 15.0
2 days, 1:18:27.292391 INFO: ms2_error      : 15.0
2 days, 1:18:27.292438 INFO: fwhm_rt        : 2.583367347717285
2 days, 1:18:27.292484 INFO: quant_window   : 3
2 days, 1:18:27.292528 INFO: ==============================================
2 days, 1:18:27.392810 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:18:27.392970 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:18:27.393018 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 1:18:27.393044 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.33
2 days, 1:18:27.393803 INFO: Starting candidate selection
2 days, 1:20:05.200467 INFO: Starting candidate scoring
2 days, 1:20:16.401881 INFO: Finished candidate processing
2 days, 1:20:16.402134 INFO: Collecting candidate features
2 days, 1:20:18.141494 WARNING: intensity_correlation has 3649 NaNs ( 0.41 % out of 898770)
2 days, 1:20:18.142514 WARNING: height_correlation has 406 NaNs ( 0.05 % out of 898770)
2 days, 1:20:18.174102 INFO: Collecting fragment features
2 days, 1:20:18.639858 INFO: Finished candidate scoring
2 days, 1:20:19.201569 INFO: performing precursor FDR with 47 features
2 days, 1:20:19.201718 INFO: Decoy channel: -1
2 days, 1:20:19.201748 INFO: competitive: True
2 days, 1:20:19.411551 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:20:19.550263 WARNING: dropped 1919 target PSMs due to missing features
2 days, 1:20:19.550429 WARNING: dropped 1921 decoy PSMs due to missing features
2 days, 1:20:19.849573 INFO: Estimating optimal hyperparameters - samples: 715,944, batch_size: 2,932, learning_rate: 8.46e-04
2 days, 1:20:19.851152 INFO: Using random state 367219 for train-test-split
2 days, 1:20:39.028923 INFO: Test AUC: 0.544
2 days, 1:20:39.029086 INFO: Train AUC: 0.565
2 days, 1:20:39.029124 INFO: AUC difference: 3.78%
2 days, 1:20:39.554154 INFO: Resetting torch num_threads to 80
2 days, 1:20:39.570907 PROGRESS: === Extracted 898770 precursors and 5032559 fragments ===
2 days, 1:20:39.571796 INFO: === FDR correction performed with classifier version 13 ===
2 days, 1:20:39.602808 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:20:39.603107 PROGRESS: Total precursors accumulated: 179,630
2 days, 1:20:39.603182 PROGRESS: Target precursors: 102,263 (56.93%)
2 days, 1:20:39.603246 PROGRESS: Decoy precursors: 77,367 (43.07%)
2 days, 1:20:39.603304 PROGRESS: 
2 days, 1:20:39.603361 PROGRESS: Precursor Summary:
2 days, 1:20:39.605752 PROGRESS: Channel   0:	 0.050 FDR:   402; 0.010 FDR:   277; 0.001 FDR:   235
2 days, 1:20:39.605876 PROGRESS: 
2 days, 1:20:39.605948 PROGRESS: Protein Summary:
2 days, 1:20:39.608176 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   229; 0.001 FDR:   197
2 days, 1:20:39.608281 PROGRESS: =========================================================================
2 days, 1:20:39.615034 INFO: Target number of precursors reached.
2 days, 1:20:40.163170 INFO: fragments_df: keeping 4123 of 5032559 [sum(precursor_idx_mask)=7183 sum(mass_error_mask)=5032467 stop_rank=4123
2 days, 1:20:41.304636 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:20:41.435630 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:20:41.573205 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:20:41.711242 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:20:42.299217 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:20:42.299694 INFO: Using score_cutoff 24.597327138519287 (fac=0.99, q=1)
2 days, 1:20:42.300029 INFO: Updating optimization_manager: fwhm_rt             : 2.583367347717285 -> 2.6185426712036133
2 days, 1:20:42.300119 INFO: Updating optimization_manager: fwhm_mobility       : 0.006142349448055029 -> 0.005284134764224291
2 days, 1:20:42.300183 INFO: Updating optimization_manager: score_cutoff        : 29.15378876953125 -> 24.597327138519287
2 days, 1:20:42.300245 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:20:42.350837 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:20:42.606939 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:20:42.665171 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:20:43.163711 INFO: === checking if optimization conditions were reached ===
2 days, 1:20:43.164037 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 1:20:43.166343 INFO: Updating optimization_manager: rt_error            : 118.21079483693433 -> 110.06374854592511
2 days, 1:20:43.166489 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 110.0637.
2 days, 1:20:43.166568 INFO: ==============================================
2 days, 1:20:43.166668 INFO: Starting optimization step 12.
2 days, 1:20:43.166742 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 1:20:43.166809 INFO: Using python extraction backend
2 days, 1:20:43.166916 PROGRESS: Extracting batch of 407917 precursors
2 days, 1:20:43.166989 INFO: === Search parameters used ===
2 days, 1:20:43.167046 INFO: rt_error       : 110.06374854592511
2 days, 1:20:43.167097 INFO: mobility_error : 0.1
2 days, 1:20:43.167145 INFO: num_candidates : 3
2 days, 1:20:43.167193 INFO: ms1_error      : 15.0
2 days, 1:20:43.167239 INFO: ms2_error      : 15.0
2 days, 1:20:43.167285 INFO: fwhm_rt        : 2.6185426712036133
2 days, 1:20:43.167331 INFO: quant_window   : 3
2 days, 1:20:43.167376 INFO: ==============================================
2 days, 1:20:43.265373 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:20:43.265533 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:20:43.265582 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 1:20:43.265608 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.86
2 days, 1:20:43.266338 INFO: Starting candidate selection
2 days, 1:22:33.793136 INFO: Starting candidate scoring
2 days, 1:22:45.853688 INFO: Finished candidate processing
2 days, 1:22:45.853887 INFO: Collecting candidate features
2 days, 1:22:47.834851 WARNING: intensity_correlation has 3804 NaNs ( 0.43 % out of 885068)
2 days, 1:22:47.835921 WARNING: height_correlation has 438 NaNs ( 0.05 % out of 885068)
2 days, 1:22:47.870223 INFO: Collecting fragment features
2 days, 1:22:48.325745 INFO: Finished candidate scoring
2 days, 1:22:48.897835 INFO: performing precursor FDR with 47 features
2 days, 1:22:48.897994 INFO: Decoy channel: -1
2 days, 1:22:48.898022 INFO: competitive: True
2 days, 1:22:49.104553 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:22:49.233501 WARNING: dropped 2021 target PSMs due to missing features
2 days, 1:22:49.233667 WARNING: dropped 1986 decoy PSMs due to missing features
2 days, 1:22:49.524653 INFO: Estimating optimal hyperparameters - samples: 704,848, batch_size: 2,887, learning_rate: 8.40e-04
2 days, 1:22:49.526448 INFO: Using random state 367219 for train-test-split
2 days, 1:23:08.505945 INFO: Test AUC: 0.542
2 days, 1:23:08.506124 INFO: Train AUC: 0.564
2 days, 1:23:08.506161 INFO: AUC difference: 3.89%
2 days, 1:23:09.040483 INFO: Resetting torch num_threads to 80
2 days, 1:23:09.057119 PROGRESS: === Extracted 885068 precursors and 4874223 fragments ===
2 days, 1:23:09.057975 INFO: === FDR correction performed with classifier version 13 ===
2 days, 1:23:09.087131 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:23:09.087437 PROGRESS: Total precursors accumulated: 178,653
2 days, 1:23:09.087511 PROGRESS: Target precursors: 101,197 (56.64%)
2 days, 1:23:09.087573 PROGRESS: Decoy precursors: 77,456 (43.36%)
2 days, 1:23:09.087628 PROGRESS: 
2 days, 1:23:09.087681 PROGRESS: Precursor Summary:
2 days, 1:23:09.089965 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   248; 0.001 FDR:   212
2 days, 1:23:09.090099 PROGRESS: 
2 days, 1:23:09.090167 PROGRESS: Protein Summary:
2 days, 1:23:09.092312 PROGRESS: Channel   0:	 0.050 FDR:   279; 0.010 FDR:   204; 0.001 FDR:   176
2 days, 1:23:09.092418 PROGRESS: =========================================================================
2 days, 1:23:09.097034 INFO: Target number of precursors reached.
2 days, 1:23:09.626313 INFO: fragments_df: keeping 3755 of 4874223 [sum(precursor_idx_mask)=6265 sum(mass_error_mask)=4874123 stop_rank=3755
2 days, 1:23:10.767599 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:23:10.878396 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:23:10.997154 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:23:11.107314 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:23:11.560746 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:23:11.561223 INFO: Using score_cutoff 23.253838084602357 (fac=0.99, q=1)
2 days, 1:23:11.561559 INFO: Updating optimization_manager: fwhm_rt             : 2.6185426712036133 -> 2.63114595413208
2 days, 1:23:11.561651 INFO: Updating optimization_manager: fwhm_mobility       : 0.005284134764224291 -> 0.005631627514958382
2 days, 1:23:11.561716 INFO: Updating optimization_manager: score_cutoff        : 24.597327138519287 -> 23.253838084602357
2 days, 1:23:11.561779 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:23:11.615086 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:23:11.873737 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:23:11.931180 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:23:12.439049 INFO: === checking if optimization conditions were reached ===
2 days, 1:23:12.439404 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2 days, 1:23:12.441734 INFO: Updating optimization_manager: rt_error            : 110.06374854592511 -> 103.6300953955836
2 days, 1:23:12.441890 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 103.6301.
2 days, 1:23:12.441998 INFO: ==============================================
2 days, 1:23:12.442103 INFO: Starting optimization step 13.
2 days, 1:23:12.442191 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 1:23:12.442283 INFO: Using python extraction backend
2 days, 1:23:12.442418 PROGRESS: Extracting batch of 407917 precursors
2 days, 1:23:12.442511 INFO: === Search parameters used ===
2 days, 1:23:12.442590 INFO: rt_error       : 103.6300953955836
2 days, 1:23:12.442663 INFO: mobility_error : 0.1
2 days, 1:23:12.442734 INFO: num_candidates : 3
2 days, 1:23:12.442804 INFO: ms1_error      : 15.0
2 days, 1:23:12.442874 INFO: ms2_error      : 15.0
2 days, 1:23:12.442941 INFO: fwhm_rt        : 2.63114595413208
2 days, 1:23:12.443010 INFO: quant_window   : 3
2 days, 1:23:12.443078 INFO: ==============================================
2 days, 1:23:12.543090 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:23:12.543251 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:23:12.543308 INFO: FWHM in RT is 2.63 seconds, sigma is 0.44
2 days, 1:23:12.543339 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.05
2 days, 1:23:12.544148 INFO: Starting candidate selection
2 days, 1:24:46.395202 INFO: Starting candidate scoring
2 days, 1:24:56.875117 INFO: Finished candidate processing
2 days, 1:24:56.875554 INFO: Collecting candidate features
2 days, 1:24:59.065698 WARNING: intensity_correlation has 3874 NaNs ( 0.44 % out of 877522)
2 days, 1:24:59.066797 WARNING: height_correlation has 450 NaNs ( 0.05 % out of 877522)
2 days, 1:24:59.101635 INFO: Collecting fragment features
2 days, 1:24:59.612260 INFO: Finished candidate scoring
2 days, 1:25:00.330858 INFO: performing precursor FDR with 47 features
2 days, 1:25:00.331012 INFO: Decoy channel: -1
2 days, 1:25:00.331044 INFO: competitive: True
2 days, 1:25:00.641474 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:25:00.827466 WARNING: dropped 2018 target PSMs due to missing features
2 days, 1:25:00.827641 WARNING: dropped 2065 decoy PSMs due to missing features
2 days, 1:25:01.449053 INFO: Estimating optimal hyperparameters - samples: 698,751, batch_size: 2,862, learning_rate: 8.36e-04
2 days, 1:25:01.450804 INFO: Using random state 367219 for train-test-split
2 days, 1:25:23.532801 INFO: Test AUC: 0.545
2 days, 1:25:23.532970 INFO: Train AUC: 0.563
2 days, 1:25:23.533009 INFO: AUC difference: 3.28%
2 days, 1:25:24.073558 INFO: Resetting torch num_threads to 80
2 days, 1:25:24.099542 PROGRESS: === Extracted 877522 precursors and 4817249 fragments ===
2 days, 1:25:24.100562 INFO: === FDR correction performed with classifier version 13 ===
2 days, 1:25:24.143476 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:25:24.143805 PROGRESS: Total precursors accumulated: 177,977
2 days, 1:25:24.143886 PROGRESS: Target precursors: 100,721 (56.59%)
2 days, 1:25:24.143945 PROGRESS: Decoy precursors: 77,256 (43.41%)
2 days, 1:25:24.143997 PROGRESS: 
2 days, 1:25:24.144050 PROGRESS: Precursor Summary:
2 days, 1:25:24.146553 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   256; 0.001 FDR:   220
2 days, 1:25:24.146662 PROGRESS: 
2 days, 1:25:24.146725 PROGRESS: Protein Summary:
2 days, 1:25:24.148927 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   211; 0.001 FDR:   179
2 days, 1:25:24.149029 PROGRESS: =========================================================================
2 days, 1:25:24.156841 INFO: Target number of precursors reached.
2 days, 1:25:24.679348 INFO: fragments_df: keeping 3903 of 4817249 [sum(precursor_idx_mask)=6522 sum(mass_error_mask)=4817141 stop_rank=3903
2 days, 1:25:26.159977 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:25:26.281440 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:25:26.398318 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:25:26.519552 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:25:27.002344 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:25:27.002864 INFO: Using score_cutoff 22.821236552238467 (fac=0.99, q=1)
2 days, 1:25:27.003222 INFO: Updating optimization_manager: fwhm_rt             : 2.63114595413208 -> 2.6225287914276123
2 days, 1:25:27.003320 INFO: Updating optimization_manager: fwhm_mobility       : 0.005631627514958382 -> 0.005587823688983917
2 days, 1:25:27.003386 INFO: Updating optimization_manager: score_cutoff        : 23.253838084602357 -> 22.821236552238467
2 days, 1:25:27.003452 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:25:27.054715 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:25:27.320718 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:25:27.380738 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:25:27.927016 INFO: === checking if optimization conditions were reached ===
2 days, 1:25:27.927357 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
2 days, 1:25:27.929948 INFO: Updating optimization_manager: rt_error            : 103.6300953955836 -> 103.22601237515559
2 days, 1:25:27.930102 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 103.2260.
2 days, 1:25:27.930188 INFO: ==============================================
2 days, 1:25:27.930270 INFO: Starting optimization step 14.
2 days, 1:25:27.930343 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 1:25:27.930417 INFO: Using python extraction backend
2 days, 1:25:27.930547 PROGRESS: Extracting batch of 407917 precursors
2 days, 1:25:27.930624 INFO: === Search parameters used ===
2 days, 1:25:27.930686 INFO: rt_error       : 103.22601237515559
2 days, 1:25:27.930739 INFO: mobility_error : 0.1
2 days, 1:25:27.930789 INFO: num_candidates : 3
2 days, 1:25:27.930851 INFO: ms1_error      : 15.0
2 days, 1:25:27.930904 INFO: ms2_error      : 15.0
2 days, 1:25:27.930954 INFO: fwhm_rt        : 2.6225287914276123
2 days, 1:25:27.931002 INFO: quant_window   : 3
2 days, 1:25:27.931050 INFO: ==============================================
2 days, 1:25:28.068579 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:25:28.068742 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:25:28.068799 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 1:25:28.068827 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.03
2 days, 1:25:28.069651 INFO: Starting candidate selection
2 days, 1:27:01.609294 INFO: Starting candidate scoring
2 days, 1:27:12.472402 INFO: Finished candidate processing
2 days, 1:27:12.472663 INFO: Collecting candidate features
2 days, 1:27:14.132571 WARNING: intensity_correlation has 3842 NaNs ( 0.44 % out of 876645)
2 days, 1:27:14.133570 WARNING: height_correlation has 440 NaNs ( 0.05 % out of 876645)
2 days, 1:27:14.164809 INFO: Collecting fragment features
2 days, 1:27:14.603222 INFO: Finished candidate scoring
2 days, 1:27:15.193291 INFO: performing precursor FDR with 47 features
2 days, 1:27:15.193442 INFO: Decoy channel: -1
2 days, 1:27:15.193470 INFO: competitive: True
2 days, 1:27:15.395535 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:27:15.522817 WARNING: dropped 1992 target PSMs due to missing features
2 days, 1:27:15.522984 WARNING: dropped 2054 decoy PSMs due to missing features
2 days, 1:27:15.810816 INFO: Estimating optimal hyperparameters - samples: 698,079, batch_size: 2,859, learning_rate: 8.35e-04
2 days, 1:27:15.812190 INFO: Using random state 367219 for train-test-split
2 days, 1:27:37.880137 INFO: Test AUC: 0.543
2 days, 1:27:37.880323 INFO: Train AUC: 0.564
2 days, 1:27:37.880370 INFO: AUC difference: 3.68%
2 days, 1:27:38.438887 INFO: Resetting torch num_threads to 80
2 days, 1:27:38.464973 PROGRESS: === Extracted 876645 precursors and 4818081 fragments ===
2 days, 1:27:38.465966 INFO: === FDR correction performed with classifier version 13 ===
2 days, 1:27:38.506586 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:27:38.506936 PROGRESS: Total precursors accumulated: 177,630
2 days, 1:27:38.507022 PROGRESS: Target precursors: 100,614 (56.64%)
2 days, 1:27:38.507094 PROGRESS: Decoy precursors: 77,016 (43.36%)
2 days, 1:27:38.507163 PROGRESS: 
2 days, 1:27:38.507228 PROGRESS: Precursor Summary:
2 days, 1:27:38.509659 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   226; 0.001 FDR:   184
2 days, 1:27:38.509776 PROGRESS: 
2 days, 1:27:38.509853 PROGRESS: Protein Summary:
2 days, 1:27:38.512081 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   187; 0.001 FDR:   156
2 days, 1:27:38.512191 PROGRESS: =========================================================================
2 days, 1:27:38.522518 INFO: Target number of precursors reached.
2 days, 1:27:39.059284 INFO: fragments_df: keeping 3494 of 4818081 [sum(precursor_idx_mask)=5742 sum(mass_error_mask)=4817974 stop_rank=3494
2 days, 1:27:40.561798 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:27:40.681148 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:27:40.802956 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:27:40.914678 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:27:41.345411 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:27:41.345975 INFO: Using score_cutoff 23.8797874546051 (fac=0.99, q=1)
2 days, 1:27:41.346327 INFO: Updating optimization_manager: fwhm_rt             : 2.6225287914276123 -> 2.6727051734924316
2 days, 1:27:41.346422 INFO: Updating optimization_manager: fwhm_mobility       : 0.005587823688983917 -> 0.006015990395098925
2 days, 1:27:41.346491 INFO: Updating optimization_manager: score_cutoff        : 22.821236552238467 -> 23.8797874546051
2 days, 1:27:41.346561 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:27:41.398803 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:27:41.658039 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:27:41.718158 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:27:42.283833 INFO: === checking if optimization conditions were reached ===
2 days, 1:27:42.284165 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
2 days, 1:27:42.285685 INFO: Updating optimization_manager: rt_error            : 103.22601237515559 -> 103.6300953955836
2 days, 1:27:42.285857 INFO: Updating optimization_manager: classifier_version  : 13 -> 27
2 days, 1:27:42.285995 INFO: Updating optimization_manager: score_cutoff        : 23.8797874546051 -> 22.821236552238467
2 days, 1:27:42.286102 INFO: Updating optimization_manager: fwhm_rt             : 2.6727051734924316 -> 2.6225287914276123
2 days, 1:27:42.286218 INFO: Updating optimization_manager: fwhm_mobility       : 0.006015990395098925 -> 0.005587823688983917
2 days, 1:27:42.286322 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 103.6301 found after 11 searches.
2 days, 1:27:42.286405 INFO: ==============================================
2 days, 1:27:42.286487 PROGRESS: Optimization finished for rt_error.
2 days, 1:27:43.067200 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:27:43.120896 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:27:43.382533 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:27:43.441921 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:27:43.984660 INFO: Starting optimization step 0.
2 days, 1:27:43.984985 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 1:27:43.985090 INFO: Using python extraction backend
2 days, 1:27:43.985239 PROGRESS: Extracting batch of 407917 precursors
2 days, 1:27:43.985332 INFO: === Search parameters used ===
2 days, 1:27:43.985397 INFO: rt_error       : 103.6300953955836
2 days, 1:27:43.985452 INFO: mobility_error : 0.1
2 days, 1:27:43.985507 INFO: num_candidates : 3
2 days, 1:27:43.985561 INFO: ms1_error      : 15.0
2 days, 1:27:43.985613 INFO: ms2_error      : 15.0
2 days, 1:27:43.985663 INFO: fwhm_rt        : 2.6225287914276123
2 days, 1:27:43.985714 INFO: quant_window   : 3
2 days, 1:27:43.985776 INFO: ==============================================
2 days, 1:27:44.123283 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:27:44.123447 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:27:44.123502 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 1:27:44.123530 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.03
2 days, 1:27:44.124333 INFO: Starting candidate selection
2 days, 1:29:18.585544 INFO: Starting candidate scoring
2 days, 1:29:30.088953 INFO: Finished candidate processing
2 days, 1:29:30.089212 INFO: Collecting candidate features
2 days, 1:29:32.250330 WARNING: intensity_correlation has 3884 NaNs ( 0.44 % out of 880448)
2 days, 1:29:32.251415 WARNING: height_correlation has 447 NaNs ( 0.05 % out of 880448)
2 days, 1:29:32.287351 INFO: Collecting fragment features
2 days, 1:29:32.792016 INFO: Finished candidate scoring
2 days, 1:29:33.527909 INFO: performing precursor FDR with 47 features
2 days, 1:29:33.528067 INFO: Decoy channel: -1
2 days, 1:29:33.528096 INFO: competitive: True
2 days, 1:29:33.830637 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:29:34.014750 WARNING: dropped 2022 target PSMs due to missing features
2 days, 1:29:34.014931 WARNING: dropped 2069 decoy PSMs due to missing features
2 days, 1:29:34.441942 INFO: Estimating optimal hyperparameters - samples: 701,085, batch_size: 2,871, learning_rate: 8.37e-04
2 days, 1:29:34.443449 INFO: Using random state 42609 for train-test-split
2 days, 1:29:57.033004 INFO: Test AUC: 0.550
2 days, 1:29:57.033177 INFO: Train AUC: 0.571
2 days, 1:29:57.033214 INFO: AUC difference: 3.68%
2 days, 1:29:57.569742 INFO: Resetting torch num_threads to 80
2 days, 1:29:57.595876 PROGRESS: === Extracted 880448 precursors and 4830829 fragments ===
2 days, 1:29:57.596879 INFO: === FDR correction performed with classifier version 27 ===
2 days, 1:29:57.636487 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:29:57.636834 PROGRESS: Total precursors accumulated: 178,569
2 days, 1:29:57.636910 PROGRESS: Target precursors: 102,931 (57.64%)
2 days, 1:29:57.636970 PROGRESS: Decoy precursors: 75,638 (42.36%)
2 days, 1:29:57.637024 PROGRESS: 
2 days, 1:29:57.637076 PROGRESS: Precursor Summary:
2 days, 1:29:57.639457 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   284; 0.001 FDR:   193
2 days, 1:29:57.639575 PROGRESS: 
2 days, 1:29:57.639641 PROGRESS: Protein Summary:
2 days, 1:29:57.641796 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   233; 0.001 FDR:   157
2 days, 1:29:57.641909 PROGRESS: =========================================================================
2 days, 1:29:57.649427 INFO: Target number of precursors reached.
2 days, 1:29:58.163124 INFO: fragments_df: keeping 4238 of 4830829 [sum(precursor_idx_mask)=7271 sum(mass_error_mask)=4830714 stop_rank=4238
2 days, 1:29:59.633082 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:29:59.748062 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:29:59.864647 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:29:59.976936 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:30:00.509273 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:30:00.509804 INFO: Using score_cutoff 23.519288424682617 (fac=0.99, q=1)
2 days, 1:30:00.510166 INFO: Updating optimization_manager: fwhm_rt             : 2.6225287914276123 -> 2.610778331756592
2 days, 1:30:00.510257 INFO: Updating optimization_manager: fwhm_mobility       : 0.005587823688983917 -> 0.005311479791998863
2 days, 1:30:00.510319 INFO: Updating optimization_manager: score_cutoff        : 22.821236552238467 -> 23.519288424682617
2 days, 1:30:00.510381 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:30:00.563613 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:30:00.830321 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:30:00.888998 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:30:01.433702 INFO: === checking if optimization conditions were reached ===
2 days, 1:30:01.434082 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 1:30:01.436239 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0735955586176307
2 days, 1:30:01.436387 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0736.
2 days, 1:30:01.436475 INFO: ==============================================
2 days, 1:30:01.436565 INFO: Starting optimization step 1.
2 days, 1:30:01.436644 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 1:30:01.436727 INFO: Using python extraction backend
2 days, 1:30:01.436856 PROGRESS: Extracting batch of 407917 precursors
2 days, 1:30:01.436938 INFO: === Search parameters used ===
2 days, 1:30:01.437015 INFO: rt_error       : 103.6300953955836
2 days, 1:30:01.437078 INFO: mobility_error : 0.0735955586176307
2 days, 1:30:01.437136 INFO: num_candidates : 3
2 days, 1:30:01.437195 INFO: ms1_error      : 15.0
2 days, 1:30:01.437249 INFO: ms2_error      : 15.0
2 days, 1:30:01.437303 INFO: fwhm_rt        : 2.610778331756592
2 days, 1:30:01.437357 INFO: quant_window   : 3
2 days, 1:30:01.437411 INFO: ==============================================
2 days, 1:30:01.575835 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:30:01.576006 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:30:01.576064 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
2 days, 1:30:01.576093 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.88
2 days, 1:30:01.576881 INFO: Starting candidate selection
2 days, 1:31:12.882605 INFO: Starting candidate scoring
2 days, 1:31:23.713003 INFO: Finished candidate processing
2 days, 1:31:23.713175 INFO: Collecting candidate features
2 days, 1:31:25.329090 WARNING: intensity_correlation has 4032 NaNs ( 0.47 % out of 850880)
2 days, 1:31:25.330146 WARNING: height_correlation has 474 NaNs ( 0.06 % out of 850880)
2 days, 1:31:25.362786 INFO: Collecting fragment features
2 days, 1:31:25.806623 INFO: Finished candidate scoring
2 days, 1:31:26.387439 INFO: performing precursor FDR with 47 features
2 days, 1:31:26.387594 INFO: Decoy channel: -1
2 days, 1:31:26.387625 INFO: competitive: True
2 days, 1:31:26.592119 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:31:26.717668 WARNING: dropped 2099 target PSMs due to missing features
2 days, 1:31:26.717840 WARNING: dropped 2166 decoy PSMs due to missing features
2 days, 1:31:27.003005 INFO: Estimating optimal hyperparameters - samples: 677,292, batch_size: 2,774, learning_rate: 8.23e-04
2 days, 1:31:27.004484 INFO: Using random state 42609 for train-test-split
2 days, 1:31:46.435674 INFO: Test AUC: 0.550
2 days, 1:31:46.435844 INFO: Train AUC: 0.569
2 days, 1:31:46.435880 INFO: AUC difference: 3.47%
2 days, 1:31:46.969009 INFO: Resetting torch num_threads to 80
2 days, 1:31:46.993612 PROGRESS: === Extracted 850880 precursors and 4610831 fragments ===
2 days, 1:31:46.994505 INFO: === FDR correction performed with classifier version 27 ===
2 days, 1:31:47.043186 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:31:47.043516 PROGRESS: Total precursors accumulated: 174,254
2 days, 1:31:47.043588 PROGRESS: Target precursors: 100,091 (57.44%)
2 days, 1:31:47.043648 PROGRESS: Decoy precursors: 74,163 (42.56%)
2 days, 1:31:47.043700 PROGRESS: 
2 days, 1:31:47.043753 PROGRESS: Precursor Summary:
2 days, 1:31:47.046157 PROGRESS: Channel   0:	 0.050 FDR:   408; 0.010 FDR:   258; 0.001 FDR:   207
2 days, 1:31:47.046271 PROGRESS: 
2 days, 1:31:47.046335 PROGRESS: Protein Summary:
2 days, 1:31:47.048469 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   213; 0.001 FDR:   171
2 days, 1:31:47.048570 PROGRESS: =========================================================================
2 days, 1:31:47.058459 INFO: Target number of precursors reached.
2 days, 1:31:47.561263 INFO: fragments_df: keeping 3898 of 4610831 [sum(precursor_idx_mask)=6514 sum(mass_error_mask)=4610711 stop_rank=3898
2 days, 1:31:49.070081 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:31:49.183398 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:31:49.296713 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:31:49.410426 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:31:49.888961 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:31:49.889475 INFO: Using score_cutoff 10.126341367149353 (fac=0.99, q=1)
2 days, 1:31:49.889809 INFO: Updating optimization_manager: fwhm_rt             : 2.610778331756592 -> 2.612431049346924
2 days, 1:31:49.889905 INFO: Updating optimization_manager: fwhm_mobility       : 0.005311479791998863 -> 0.005531782284379005
2 days, 1:31:49.889968 INFO: Updating optimization_manager: score_cutoff        : 23.519288424682617 -> 10.126341367149353
2 days, 1:31:49.890027 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:31:49.938945 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:31:50.204060 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:31:50.267282 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:31:50.808059 INFO: === checking if optimization conditions were reached ===
2 days, 1:31:50.808388 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 1:31:50.810644 INFO: Updating optimization_manager: mobility_error      : 0.0735955586176307 -> 0.06438609337452318
2 days, 1:31:50.810803 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0644.
2 days, 1:31:50.810882 INFO: ==============================================
2 days, 1:31:50.810961 INFO: Starting optimization step 2.
2 days, 1:31:50.811026 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 1:31:50.811095 INFO: Using python extraction backend
2 days, 1:31:50.811211 PROGRESS: Extracting batch of 407917 precursors
2 days, 1:31:50.811282 INFO: === Search parameters used ===
2 days, 1:31:50.811333 INFO: rt_error       : 103.6300953955836
2 days, 1:31:50.811381 INFO: mobility_error : 0.06438609337452318
2 days, 1:31:50.811427 INFO: num_candidates : 3
2 days, 1:31:50.811472 INFO: ms1_error      : 15.0
2 days, 1:31:50.811517 INFO: ms2_error      : 15.0
2 days, 1:31:50.811564 INFO: fwhm_rt        : 2.612431049346924
2 days, 1:31:50.811611 INFO: quant_window   : 3
2 days, 1:31:50.811658 INFO: ==============================================
2 days, 1:31:50.929626 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:31:50.929803 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:31:50.929860 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
2 days, 1:31:50.929909 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.00
2 days, 1:31:50.930719 INFO: Starting candidate selection
2 days, 1:32:55.389632 INFO: Starting candidate scoring
2 days, 1:33:06.557704 INFO: Finished candidate processing
2 days, 1:33:06.557999 INFO: Collecting candidate features
2 days, 1:33:08.640996 WARNING: intensity_correlation has 3989 NaNs ( 0.47 % out of 847669)
2 days, 1:33:08.641985 WARNING: height_correlation has 418 NaNs ( 0.05 % out of 847669)
2 days, 1:33:08.672304 INFO: Collecting fragment features
2 days, 1:33:09.136425 INFO: Finished candidate scoring
2 days, 1:33:09.836315 INFO: performing precursor FDR with 47 features
2 days, 1:33:09.836466 INFO: Decoy channel: -1
2 days, 1:33:09.836495 INFO: competitive: True
2 days, 1:33:10.115871 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 1:33:10.289993 WARNING: dropped 2073 target PSMs due to missing features
2 days, 1:33:10.290243 WARNING: dropped 2112 decoy PSMs due to missing features
2 days, 1:33:10.838630 INFO: Estimating optimal hyperparameters - samples: 674,787, batch_size: 2,763, learning_rate: 8.21e-04
2 days, 1:33:10.840062 INFO: Using random state 42609 for train-test-split
2 days, 1:33:32.396524 INFO: Test AUC: 0.553
2 days, 1:33:32.396688 INFO: Train AUC: 0.572
2 days, 1:33:32.396726 INFO: AUC difference: 3.34%
2 days, 1:33:32.926318 INFO: Resetting torch num_threads to 80
2 days, 1:33:32.955665 PROGRESS: === Extracted 847669 precursors and 4596063 fragments ===
2 days, 1:33:32.956589 INFO: === FDR correction performed with classifier version 27 ===
2 days, 1:33:32.995554 PROGRESS: ============================= Precursor FDR =============================
2 days, 1:33:32.995888 PROGRESS: Total precursors accumulated: 172,889
2 days, 1:33:32.995963 PROGRESS: Target precursors: 99,547 (57.58%)
2 days, 1:33:32.996024 PROGRESS: Decoy precursors: 73,342 (42.42%)
2 days, 1:33:32.996090 PROGRESS: 
2 days, 1:33:32.996145 PROGRESS: Precursor Summary:
2 days, 1:33:32.998451 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   239; 0.001 FDR:   205
2 days, 1:33:32.998559 PROGRESS: 
2 days, 1:33:32.998626 PROGRESS: Protein Summary:
2 days, 1:33:33.000741 PROGRESS: Channel   0:	 0.050 FDR:   297; 0.010 FDR:   196; 0.001 FDR:   169
2 days, 1:33:33.000846 PROGRESS: =========================================================================
2 days, 1:33:33.008180 INFO: Target number of precursors reached.
2 days, 1:33:33.525788 INFO: fragments_df: keeping 3596 of 4596063 [sum(precursor_idx_mask)=5983 sum(mass_error_mask)=4595953 stop_rank=3596
2 days, 1:33:35.036309 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:33:35.146472 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:33:35.257747 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:33:35.364036 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:33:35.809132 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 1:33:35.809645 INFO: Using score_cutoff 18.152576633262633 (fac=0.99, q=1)
2 days, 1:33:35.809987 INFO: Updating optimization_manager: fwhm_rt             : 2.612431049346924 -> 2.6185426712036133
2 days, 1:33:35.810081 INFO: Updating optimization_manager: fwhm_mobility       : 0.005531782284379005 -> 0.005616947542876005
2 days, 1:33:35.810144 INFO: Updating optimization_manager: score_cutoff        : 10.126341367149353 -> 18.152576633262633
2 days, 1:33:35.810211 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:33:35.864047 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:33:36.134784 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:33:36.205066 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:33:36.780232 INFO: === checking if optimization conditions were reached ===
2 days, 1:33:36.780556 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 1:33:36.781667 INFO: Updating optimization_manager: mobility_error      : 0.06438609337452318 -> 0.1
2 days, 1:33:36.781831 INFO: Updating optimization_manager: classifier_version  : 27 -> 29
2 days, 1:33:36.781963 INFO: Updating optimization_manager: score_cutoff        : 18.152576633262633 -> 23.519288424682617
2 days, 1:33:36.782084 INFO: Updating optimization_manager: fwhm_rt             : 2.6185426712036133 -> 2.610778331756592
2 days, 1:33:36.782181 INFO: Updating optimization_manager: fwhm_mobility       : 0.005616947542876005 -> 0.005311479791998863
2 days, 1:33:36.782275 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
2 days, 1:33:36.782345 INFO: ==============================================
2 days, 1:33:36.782422 PROGRESS: Optimization finished for mobility_error.
2 days, 1:33:37.689736 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:33:37.744292 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:33:38.012946 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:33:38.074548 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:33:38.624552 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 1:33:38.624874 PROGRESS: ==============================================
2 days, 1:33:38.624970 PROGRESS: ms2_error      : 15.0000
2 days, 1:33:38.625033 PROGRESS: ms1_error      : 15.0000
2 days, 1:33:38.625091 PROGRESS: rt_error       : 103.6301
2 days, 1:33:38.625141 PROGRESS: mobility_error : 0.1000
2 days, 1:33:38.625189 PROGRESS: ==============================================
2 days, 1:33:38.634811 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 1:33:40.498848 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 1:33:48.817371 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 1:33:50.626910 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 1:34:09.015285 INFO: Using python extraction backend
2 days, 1:34:09.015791 PROGRESS: Extracting batch of 12210649 precursors
2 days, 1:34:09.015907 INFO: === Search parameters used ===
2 days, 1:34:09.015973 INFO: rt_error       : 103.6300953955836
2 days, 1:34:09.016032 INFO: mobility_error : 0.1
2 days, 1:34:09.016087 INFO: num_candidates : 3
2 days, 1:34:09.016139 INFO: ms1_error      : 15.0
2 days, 1:34:09.016188 INFO: ms2_error      : 15.0
2 days, 1:34:09.016238 INFO: fwhm_rt        : 2.610778331756592
2 days, 1:34:09.016287 INFO: quant_window   : 3
2 days, 1:34:09.016335 INFO: ==============================================
2 days, 1:34:12.196433 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 1:34:12.196609 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 1:34:12.196661 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
2 days, 1:34:12.196689 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.88
2 days, 1:34:12.223194 INFO: Starting candidate selection
2 days, 2:20:26.104100 INFO: Removed 26787233 precursors with score below cutoff 23.519288424682617
2 days, 2:20:29.386744 INFO: Starting candidate scoring
2 days, 2:21:36.819174 INFO: Finished candidate processing
2 days, 2:21:36.819437 INFO: Collecting candidate features
2 days, 2:21:47.732060 WARNING: intensity_correlation has 3178 NaNs ( 0.06 % out of 5374644)
2 days, 2:21:47.737077 WARNING: height_correlation has 190 NaNs ( 0.00 % out of 5374644)
2 days, 2:21:47.918264 INFO: Collecting fragment features
2 days, 2:21:52.029958 INFO: Finished candidate scoring
2 days, 2:21:55.938628 INFO: === Performing FDR correction with classifier version 29 ===
2 days, 2:21:55.939323 INFO: performing precursor FDR with 47 features
2 days, 2:21:55.939366 INFO: Decoy channel: -1
2 days, 2:21:55.939400 INFO: competitive: True
2 days, 2:21:57.460038 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:21:58.233879 WARNING: dropped 1728 target PSMs due to missing features
2 days, 2:21:58.234068 WARNING: dropped 1581 decoy PSMs due to missing features
2 days, 2:22:01.975396 INFO: Estimating optimal hyperparameters - samples: 4,297,068, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 2:22:01.985209 INFO: Using random state 334355 for train-test-split
2 days, 2:23:57.959267 INFO: Test AUC: 0.549
2 days, 2:23:57.959472 INFO: Train AUC: 0.554
2 days, 2:23:57.959511 INFO: AUC difference: 0.92%
2 days, 2:23:59.887422 INFO: Resetting torch num_threads to 80
2 days, 2:24:00.015724 INFO: Removing fragments below FDR threshold
2 days, 2:24:00.416814 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:24:00.417110 PROGRESS: Total precursors accumulated: 9,014
2 days, 2:24:00.417181 PROGRESS: Target precursors: 8,925 (99.01%)
2 days, 2:24:00.417240 PROGRESS: Decoy precursors: 89 (0.99%)
2 days, 2:24:00.417295 PROGRESS: 
2 days, 2:24:00.417347 PROGRESS: Precursor Summary:
2 days, 2:24:00.421062 PROGRESS: Channel   0:	 0.050 FDR: 8,925; 0.010 FDR: 8,925; 0.001 FDR: 6,812
2 days, 2:24:00.421186 PROGRESS: 
2 days, 2:24:00.421250 PROGRESS: Protein Summary:
2 days, 2:24:00.425619 PROGRESS: Channel   0:	 0.050 FDR: 2,145; 0.010 FDR: 2,145; 0.001 FDR: 1,673
2 days, 2:24:00.425751 PROGRESS: =========================================================================
2 days, 2:24:00.502598 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R3/psm.parquet
2 days, 2:24:00.559197 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R3/frag.parquet
2 days, 2:24:00.601938 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R3
2 days, 2:24:01.500518 PROGRESS: Loading raw file 10/12: B9_G_DIA_nLC_tTOF_R4 
2 days, 2:24:01.500702 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
2 days, 2:24:01.500788 INFO: Creating folder plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R4/figures
2 days, 2:24:01.500994 INFO: Initializing TimingManager
2 days, 2:24:01.501558 INFO: Initializing RawFileManager
2 days, 2:24:01.501669 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:01.501734 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:01.501778 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:01.665396 INFO: Reading 22,623 frames with 398,008,957 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:06.447157 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d...
2 days, 2:24:06.449306 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:06.452004 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:06.452364 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:06.452994 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:06.455202 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:06.478103 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:06.478393 INFO: Indexing quadrupole dimension
2 days, 2:24:06.614044 INFO: Transposing detector events
2 days, 2:24:09.082161 INFO: Finished transposing data
2 days, 2:24:09.082339 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 2:24:09.082950 INFO: RT (min)            : 0.0 - 40.0
2 days, 2:24:09.083003 INFO: RT duration (sec)   : 2399.9
2 days, 2:24:09.083035 INFO: RT duration (min)   : 40.0
2 days, 2:24:09.083068 INFO: Cycle len (scans)   : 12
2 days, 2:24:09.083095 INFO: Cycle len (sec)     : 1.27
2 days, 2:24:09.083123 INFO: Number of cycles    : 1885
2 days, 2:24:09.083151 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 2:24:09.083203 INFO: Creating DIA data object took: 7.581526279449463
2 days, 2:24:10.828658 INFO: Initializing CalibrationManager
2 days, 2:24:10.829014 INFO: Setting up calibration estimators ..
2 days, 2:24:10.829103 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 2:24:10.829213 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 2:24:10.829315 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 2:24:10.829391 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 2:24:10.829467 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 2:24:10.829543 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 2:24:10.829600 INFO: Done setting up calibration estimators.
2 days, 2:24:10.829725 INFO: Initializing OptimizationManager
2 days, 2:24:10.829832 INFO: initial parameter: ms1_error = 30
2 days, 2:24:10.829898 INFO: initial parameter: ms2_error = 30
2 days, 2:24:10.829955 INFO: initial parameter: rt_error = 1199.9630585
2 days, 2:24:10.830004 INFO: initial parameter: mobility_error = 0.1
2 days, 2:24:10.830048 INFO: initial parameter: num_candidates = 1
2 days, 2:24:10.830092 INFO: initial parameter: fwhm_rt = 5
2 days, 2:24:10.830136 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 2:24:10.830184 INFO: initial parameter: score_cutoff = 0
2 days, 2:24:10.830227 INFO: initial parameter: classifier_version = -1
2 days, 2:24:10.830302 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R4
2 days, 2:24:10.830515 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 2:24:10.830551 INFO: Initializing FDRManager
2 days, 2:24:10.830587 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 2:24:11.927928 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
2 days, 2:24:12.656398 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 2:24:12.656881 INFO: Updating optimization_manager: rt_error            : 1199.9630585 -> 1199.9630585
2 days, 2:24:12.656995 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 2:24:12.657184 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 2:24:12.657287 PROGRESS: Starting initial search for precursors.
2 days, 2:24:12.657377 INFO: Starting optimization step 0.
2 days, 2:24:12.657448 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 2:24:12.657520 INFO: Using python extraction backend
2 days, 2:24:12.657633 PROGRESS: Extracting batch of 395 precursors
2 days, 2:24:12.657703 INFO: === Search parameters used ===
2 days, 2:24:12.657759 INFO: rt_error       : 1199.9630585
2 days, 2:24:12.657817 INFO: mobility_error : 0.1
2 days, 2:24:12.657873 INFO: num_candidates : 1
2 days, 2:24:12.657928 INFO: ms1_error      : 30
2 days, 2:24:12.657977 INFO: ms2_error      : 30
2 days, 2:24:12.658023 INFO: fwhm_rt        : 5
2 days, 2:24:12.658068 INFO: quant_window   : 3
2 days, 2:24:12.658113 INFO: ==============================================
2 days, 2:24:12.658861 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:24:12.658910 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:24:12.658949 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:24:12.658973 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:24:12.662307 INFO: Starting candidate selection
2 days, 2:24:14.900667 INFO: Starting candidate scoring
2 days, 2:24:14.946486 INFO: Finished candidate processing
2 days, 2:24:14.946592 INFO: Collecting candidate features
2 days, 2:24:14.957068 INFO: Collecting fragment features
2 days, 2:24:14.959420 INFO: Finished candidate scoring
2 days, 2:24:14.960384 INFO: performing precursor FDR with 47 features
2 days, 2:24:14.960431 INFO: Decoy channel: -1
2 days, 2:24:14.960457 INFO: competitive: True
2 days, 2:24:14.961655 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:24:14.963577 INFO: Estimating optimal hyperparameters - samples: 275, batch_size: 128, learning_rate: 1.77e-04
2 days, 2:24:14.964386 INFO: Using random state 811769 for train-test-split
2 days, 2:24:14.989428 INFO: Test AUC: 0.381
2 days, 2:24:14.989520 INFO: Train AUC: 0.520
2 days, 2:24:14.989553 INFO: AUC difference: 26.71%
2 days, 2:24:14.989577 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:24:15.234939 INFO: Resetting torch num_threads to 80
2 days, 2:24:15.235457 PROGRESS: === Extracted 344 precursors and 2841 fragments ===
2 days, 2:24:15.235946 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:24:15.236515 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:24:15.236611 PROGRESS: Total precursors accumulated: 174
2 days, 2:24:15.236679 PROGRESS: Target precursors: 92 (52.87%)
2 days, 2:24:15.236739 PROGRESS: Decoy precursors: 82 (47.13%)
2 days, 2:24:15.236793 PROGRESS: 
2 days, 2:24:15.236846 PROGRESS: Precursor Summary:
2 days, 2:24:15.237796 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 2:24:15.237898 PROGRESS: 
2 days, 2:24:15.237965 PROGRESS: Protein Summary:
2 days, 2:24:15.239000 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 2:24:15.239092 PROGRESS: =========================================================================
2 days, 2:24:15.239209 INFO: Target number of precursors not reached yet.
2 days, 2:24:15.303096 INFO: Starting optimization step 1.
2 days, 2:24:15.303335 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 2:24:15.303419 INFO: Using python extraction backend
2 days, 2:24:15.303540 PROGRESS: Extracting batch of 796 precursors
2 days, 2:24:15.303616 INFO: === Search parameters used ===
2 days, 2:24:15.303670 INFO: rt_error       : 1199.9630585
2 days, 2:24:15.303720 INFO: mobility_error : 0.1
2 days, 2:24:15.303766 INFO: num_candidates : 1
2 days, 2:24:15.303814 INFO: ms1_error      : 30
2 days, 2:24:15.303858 INFO: ms2_error      : 30
2 days, 2:24:15.303903 INFO: fwhm_rt        : 5
2 days, 2:24:15.303949 INFO: quant_window   : 3
2 days, 2:24:15.303993 INFO: ==============================================
2 days, 2:24:15.304720 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:24:15.304771 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:24:15.304801 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:24:15.304826 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:24:15.310164 INFO: Starting candidate selection
2 days, 2:24:19.649080 INFO: Starting candidate scoring
2 days, 2:24:19.699542 INFO: Finished candidate processing
2 days, 2:24:19.699677 INFO: Collecting candidate features
2 days, 2:24:19.713812 INFO: Collecting fragment features
2 days, 2:24:19.716877 INFO: Finished candidate scoring
2 days, 2:24:19.720838 INFO: performing precursor FDR with 47 features
2 days, 2:24:19.720906 INFO: Decoy channel: -1
2 days, 2:24:19.720938 INFO: competitive: True
2 days, 2:24:19.724276 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:24:19.726177 INFO: Estimating optimal hyperparameters - samples: 852, batch_size: 128, learning_rate: 1.77e-04
2 days, 2:24:19.726269 INFO: Using random state 199606 for train-test-split
2 days, 2:24:19.810568 INFO: Test AUC: 0.500
2 days, 2:24:19.810682 INFO: Train AUC: 0.596
2 days, 2:24:19.810716 INFO: AUC difference: 16.09%
2 days, 2:24:19.810742 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:24:20.055198 INFO: Resetting torch num_threads to 80
2 days, 2:24:20.056572 PROGRESS: === Extracted 1065 precursors and 9034 fragments ===
2 days, 2:24:20.057051 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:24:20.057664 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:24:20.057757 PROGRESS: Total precursors accumulated: 542
2 days, 2:24:20.057825 PROGRESS: Target precursors: 316 (58.30%)
2 days, 2:24:20.057905 PROGRESS: Decoy precursors: 226 (41.70%)
2 days, 2:24:20.057964 PROGRESS: 
2 days, 2:24:20.058013 PROGRESS: Precursor Summary:
2 days, 2:24:20.059003 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2 days, 2:24:20.059098 PROGRESS: 
2 days, 2:24:20.059157 PROGRESS: Protein Summary:
2 days, 2:24:20.060216 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2 days, 2:24:20.060308 PROGRESS: =========================================================================
2 days, 2:24:20.060458 INFO: Target number of precursors not reached yet.
2 days, 2:24:20.129477 INFO: Starting optimization step 2.
2 days, 2:24:20.129734 PROGRESS: === Extracting elution groups 600 to 1400 ===
2 days, 2:24:20.129816 INFO: Using python extraction backend
2 days, 2:24:20.129937 PROGRESS: Extracting batch of 1598 precursors
2 days, 2:24:20.130020 INFO: === Search parameters used ===
2 days, 2:24:20.130076 INFO: rt_error       : 1199.9630585
2 days, 2:24:20.130124 INFO: mobility_error : 0.1
2 days, 2:24:20.130171 INFO: num_candidates : 1
2 days, 2:24:20.130217 INFO: ms1_error      : 30
2 days, 2:24:20.130266 INFO: ms2_error      : 30
2 days, 2:24:20.130311 INFO: fwhm_rt        : 5
2 days, 2:24:20.130355 INFO: quant_window   : 3
2 days, 2:24:20.130399 INFO: ==============================================
2 days, 2:24:20.131288 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:24:20.131336 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:24:20.131365 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:24:20.131388 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:24:20.142911 INFO: Starting candidate selection
2 days, 2:24:27.479223 INFO: Starting candidate scoring
2 days, 2:24:27.552624 INFO: Finished candidate processing
2 days, 2:24:27.552751 INFO: Collecting candidate features
2 days, 2:24:27.567997 INFO: Collecting fragment features
2 days, 2:24:27.571689 INFO: Finished candidate scoring
2 days, 2:24:27.575840 INFO: performing precursor FDR with 47 features
2 days, 2:24:27.575920 INFO: Decoy channel: -1
2 days, 2:24:27.575953 INFO: competitive: True
2 days, 2:24:27.580318 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:24:27.583287 INFO: Estimating optimal hyperparameters - samples: 1,997, batch_size: 128, learning_rate: 1.77e-04
2 days, 2:24:27.583387 INFO: Using random state 78876 for train-test-split
2 days, 2:24:27.809698 INFO: Test AUC: 0.533
2 days, 2:24:27.809822 INFO: Train AUC: 0.592
2 days, 2:24:27.809874 INFO: AUC difference: 9.98%
2 days, 2:24:27.809905 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:24:28.079363 INFO: Resetting torch num_threads to 80
2 days, 2:24:28.081667 PROGRESS: === Extracted 2497 precursors and 21044 fragments ===
2 days, 2:24:28.082277 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:24:28.083124 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:24:28.083256 PROGRESS: Total precursors accumulated: 1,267
2 days, 2:24:28.083332 PROGRESS: Target precursors: 752 (59.35%)
2 days, 2:24:28.083400 PROGRESS: Decoy precursors: 515 (40.65%)
2 days, 2:24:28.083463 PROGRESS: 
2 days, 2:24:28.083523 PROGRESS: Precursor Summary:
2 days, 2:24:28.084692 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 2:24:28.084800 PROGRESS: 
2 days, 2:24:28.084872 PROGRESS: Protein Summary:
2 days, 2:24:28.086146 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 2:24:28.086260 PROGRESS: =========================================================================
2 days, 2:24:28.086486 INFO: Target number of precursors not reached yet.
2 days, 2:24:28.263343 INFO: Starting optimization step 3.
2 days, 2:24:28.263681 PROGRESS: === Extracting elution groups 1400 to 3000 ===
2 days, 2:24:28.263779 INFO: Using python extraction backend
2 days, 2:24:28.263922 PROGRESS: Extracting batch of 3192 precursors
2 days, 2:24:28.264013 INFO: === Search parameters used ===
2 days, 2:24:28.264079 INFO: rt_error       : 1199.9630585
2 days, 2:24:28.264148 INFO: mobility_error : 0.1
2 days, 2:24:28.264223 INFO: num_candidates : 1
2 days, 2:24:28.264283 INFO: ms1_error      : 30
2 days, 2:24:28.264338 INFO: ms2_error      : 30
2 days, 2:24:28.264394 INFO: fwhm_rt        : 5
2 days, 2:24:28.264447 INFO: quant_window   : 3
2 days, 2:24:28.264500 INFO: ==============================================
2 days, 2:24:28.266321 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:24:28.266384 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:24:28.266430 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:24:28.266460 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:24:28.270571 INFO: Starting candidate selection
2 days, 2:24:39.076791 INFO: Starting candidate scoring
2 days, 2:24:39.176323 INFO: Finished candidate processing
2 days, 2:24:39.176448 INFO: Collecting candidate features
2 days, 2:24:39.188888 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 2884)
2 days, 2:24:39.192781 INFO: Collecting fragment features
2 days, 2:24:39.196820 INFO: Finished candidate scoring
2 days, 2:24:39.206807 INFO: performing precursor FDR with 47 features
2 days, 2:24:39.206977 INFO: Decoy channel: -1
2 days, 2:24:39.207007 INFO: competitive: True
2 days, 2:24:39.215024 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:24:39.216939 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 2:24:39.219333 INFO: Estimating optimal hyperparameters - samples: 4,304, batch_size: 128, learning_rate: 1.77e-04
2 days, 2:24:39.219427 INFO: Using random state 236674 for train-test-split
2 days, 2:24:39.658865 INFO: Test AUC: 0.538
2 days, 2:24:39.658984 INFO: Train AUC: 0.590
2 days, 2:24:39.659018 INFO: AUC difference: 8.72%
2 days, 2:24:39.659042 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:24:39.895681 INFO: Resetting torch num_threads to 80
2 days, 2:24:39.898092 PROGRESS: === Extracted 5381 precursors and 45637 fragments ===
2 days, 2:24:39.898598 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:24:39.899429 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:24:39.899528 PROGRESS: Total precursors accumulated: 2,729
2 days, 2:24:39.899594 PROGRESS: Target precursors: 1,638 (60.02%)
2 days, 2:24:39.899652 PROGRESS: Decoy precursors: 1,091 (39.98%)
2 days, 2:24:39.899704 PROGRESS: 
2 days, 2:24:39.899754 PROGRESS: Precursor Summary:
2 days, 2:24:39.900731 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 2:24:39.900827 PROGRESS: 
2 days, 2:24:39.900888 PROGRESS: Protein Summary:
2 days, 2:24:39.901959 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 2:24:39.902056 PROGRESS: =========================================================================
2 days, 2:24:39.902258 INFO: Target number of precursors not reached yet.
2 days, 2:24:40.124837 INFO: Starting optimization step 4.
2 days, 2:24:40.125141 PROGRESS: === Extracting elution groups 3000 to 6200 ===
2 days, 2:24:40.125230 INFO: Using python extraction backend
2 days, 2:24:40.125357 PROGRESS: Extracting batch of 6381 precursors
2 days, 2:24:40.125435 INFO: === Search parameters used ===
2 days, 2:24:40.125492 INFO: rt_error       : 1199.9630585
2 days, 2:24:40.125541 INFO: mobility_error : 0.1
2 days, 2:24:40.125592 INFO: num_candidates : 1
2 days, 2:24:40.125640 INFO: ms1_error      : 30
2 days, 2:24:40.125688 INFO: ms2_error      : 30
2 days, 2:24:40.125734 INFO: fwhm_rt        : 5
2 days, 2:24:40.125788 INFO: quant_window   : 3
2 days, 2:24:40.125835 INFO: ==============================================
2 days, 2:24:40.127922 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:24:40.127975 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:24:40.128006 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:24:40.128030 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:24:40.128952 INFO: Starting candidate selection
2 days, 2:24:57.111055 INFO: Starting candidate scoring
2 days, 2:24:57.256954 INFO: Finished candidate processing
2 days, 2:24:57.257079 INFO: Collecting candidate features
2 days, 2:24:57.275600 WARNING: intensity_correlation has 1 NaNs ( 0.02 % out of 5741)
2 days, 2:24:57.279629 INFO: Collecting fragment features
2 days, 2:24:57.286219 INFO: Finished candidate scoring
2 days, 2:24:57.295327 INFO: performing precursor FDR with 47 features
2 days, 2:24:57.295433 INFO: Decoy channel: -1
2 days, 2:24:57.295463 INFO: competitive: True
2 days, 2:24:57.301081 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:24:57.304479 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 2:24:57.306619 INFO: Estimating optimal hyperparameters - samples: 8,896, batch_size: 128, learning_rate: 1.77e-04
2 days, 2:24:57.306725 INFO: Using random state 576003 for train-test-split
2 days, 2:24:58.305926 INFO: Test AUC: 0.541
2 days, 2:24:58.306047 INFO: Train AUC: 0.592
2 days, 2:24:58.306080 INFO: AUC difference: 8.61%
2 days, 2:24:58.306105 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:24:58.561015 INFO: Resetting torch num_threads to 80
2 days, 2:24:58.564894 PROGRESS: === Extracted 11122 precursors and 93906 fragments ===
2 days, 2:24:58.565473 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:24:58.566746 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:24:58.566855 PROGRESS: Total precursors accumulated: 5,653
2 days, 2:24:58.566940 PROGRESS: Target precursors: 3,313 (58.61%)
2 days, 2:24:58.567002 PROGRESS: Decoy precursors: 2,340 (41.39%)
2 days, 2:24:58.567057 PROGRESS: 
2 days, 2:24:58.567111 PROGRESS: Precursor Summary:
2 days, 2:24:58.568119 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2 days, 2:24:58.568218 PROGRESS: 
2 days, 2:24:58.568295 PROGRESS: Protein Summary:
2 days, 2:24:58.569375 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2 days, 2:24:58.569471 PROGRESS: =========================================================================
2 days, 2:24:58.569674 INFO: Target number of precursors not reached yet.
2 days, 2:24:58.888498 INFO: Starting optimization step 5.
2 days, 2:24:58.888802 PROGRESS: === Extracting elution groups 6200 to 12600 ===
2 days, 2:24:58.888889 INFO: Using python extraction backend
2 days, 2:24:58.889019 PROGRESS: Extracting batch of 12763 precursors
2 days, 2:24:58.889096 INFO: === Search parameters used ===
2 days, 2:24:58.889152 INFO: rt_error       : 1199.9630585
2 days, 2:24:58.889203 INFO: mobility_error : 0.1
2 days, 2:24:58.889253 INFO: num_candidates : 1
2 days, 2:24:58.889302 INFO: ms1_error      : 30
2 days, 2:24:58.889349 INFO: ms2_error      : 30
2 days, 2:24:58.889396 INFO: fwhm_rt        : 5
2 days, 2:24:58.889441 INFO: quant_window   : 3
2 days, 2:24:58.889485 INFO: ==============================================
2 days, 2:24:58.893197 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:24:58.893267 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:24:58.893300 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:24:58.893324 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:24:58.898072 INFO: Starting candidate selection
2 days, 2:25:33.137730 INFO: Starting candidate scoring
2 days, 2:25:33.401721 INFO: Finished candidate processing
2 days, 2:25:33.401883 INFO: Collecting candidate features
2 days, 2:25:33.448514 INFO: Collecting fragment features
2 days, 2:25:33.460973 INFO: Finished candidate scoring
2 days, 2:25:33.476761 INFO: performing precursor FDR with 47 features
2 days, 2:25:33.476925 INFO: Decoy channel: -1
2 days, 2:25:33.476961 INFO: competitive: True
2 days, 2:25:33.489336 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:25:33.493690 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 2:25:33.498201 INFO: Estimating optimal hyperparameters - samples: 18,108, batch_size: 128, learning_rate: 1.77e-04
2 days, 2:25:33.498373 INFO: Using random state 682567 for train-test-split
2 days, 2:25:35.887453 INFO: Test AUC: 0.539
2 days, 2:25:35.887598 INFO: Train AUC: 0.596
2 days, 2:25:35.887631 INFO: AUC difference: 9.55%
2 days, 2:25:35.887654 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:25:36.144415 INFO: Resetting torch num_threads to 80
2 days, 2:25:36.150847 PROGRESS: === Extracted 22637 precursors and 190900 fragments ===
2 days, 2:25:36.151517 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:25:36.154823 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:25:36.154951 PROGRESS: Total precursors accumulated: 11,494
2 days, 2:25:36.155027 PROGRESS: Target precursors: 6,828 (59.40%)
2 days, 2:25:36.155086 PROGRESS: Decoy precursors: 4,666 (40.60%)
2 days, 2:25:36.155137 PROGRESS: 
2 days, 2:25:36.155186 PROGRESS: Precursor Summary:
2 days, 2:25:36.156265 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
2 days, 2:25:36.156357 PROGRESS: 
2 days, 2:25:36.156416 PROGRESS: Protein Summary:
2 days, 2:25:36.157549 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
2 days, 2:25:36.157639 PROGRESS: =========================================================================
2 days, 2:25:36.157991 INFO: Target number of precursors not reached yet.
2 days, 2:25:36.425946 INFO: Starting optimization step 6.
2 days, 2:25:36.426262 PROGRESS: === Extracting elution groups 12600 to 25400 ===
2 days, 2:25:36.426357 INFO: Using python extraction backend
2 days, 2:25:36.426497 PROGRESS: Extracting batch of 25523 precursors
2 days, 2:25:36.426579 INFO: === Search parameters used ===
2 days, 2:25:36.426634 INFO: rt_error       : 1199.9630585
2 days, 2:25:36.426703 INFO: mobility_error : 0.1
2 days, 2:25:36.426754 INFO: num_candidates : 1
2 days, 2:25:36.426803 INFO: ms1_error      : 30
2 days, 2:25:36.426851 INFO: ms2_error      : 30
2 days, 2:25:36.426903 INFO: fwhm_rt        : 5
2 days, 2:25:36.426950 INFO: quant_window   : 3
2 days, 2:25:36.427004 INFO: ==============================================
2 days, 2:25:36.437043 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:25:36.437145 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:25:36.437180 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:25:36.437204 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:25:36.438341 INFO: Starting candidate selection
2 days, 2:26:35.866305 INFO: Starting candidate scoring
2 days, 2:26:36.283938 INFO: Finished candidate processing
2 days, 2:26:36.284057 INFO: Collecting candidate features
2 days, 2:26:36.328471 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 22972)
2 days, 2:26:36.333127 INFO: Collecting fragment features
2 days, 2:26:36.350871 INFO: Finished candidate scoring
2 days, 2:26:36.379813 INFO: performing precursor FDR with 47 features
2 days, 2:26:36.379981 INFO: Decoy channel: -1
2 days, 2:26:36.380012 INFO: competitive: True
2 days, 2:26:36.404966 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:26:36.416377 WARNING: dropped 2 target PSMs due to missing features
2 days, 2:26:36.416527 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 2:26:36.424173 INFO: Estimating optimal hyperparameters - samples: 36,484, batch_size: 149, learning_rate: 1.91e-04
2 days, 2:26:36.424415 INFO: Using random state 500262 for train-test-split
2 days, 2:26:40.449199 INFO: Test AUC: 0.544
2 days, 2:26:40.449359 INFO: Train AUC: 0.600
2 days, 2:26:40.449394 INFO: AUC difference: 9.24%
2 days, 2:26:40.449419 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:26:40.718849 INFO: Resetting torch num_threads to 80
2 days, 2:26:40.730074 PROGRESS: === Extracted 45609 precursors and 385378 fragments ===
2 days, 2:26:40.730853 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:26:40.736383 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:26:40.736538 PROGRESS: Total precursors accumulated: 23,160
2 days, 2:26:40.736608 PROGRESS: Target precursors: 13,822 (59.68%)
2 days, 2:26:40.736667 PROGRESS: Decoy precursors: 9,338 (40.32%)
2 days, 2:26:40.736719 PROGRESS: 
2 days, 2:26:40.736769 PROGRESS: Precursor Summary:
2 days, 2:26:40.737959 PROGRESS: Channel   0:	 0.050 FDR:    17; 0.010 FDR:    17; 0.001 FDR:    17
2 days, 2:26:40.738060 PROGRESS: 
2 days, 2:26:40.738121 PROGRESS: Protein Summary:
2 days, 2:26:40.739327 PROGRESS: Channel   0:	 0.050 FDR:    17; 0.010 FDR:    17; 0.001 FDR:    17
2 days, 2:26:40.739424 PROGRESS: =========================================================================
2 days, 2:26:40.739980 INFO: Target number of precursors not reached yet.
2 days, 2:26:41.080598 INFO: Starting optimization step 7.
2 days, 2:26:41.080912 PROGRESS: === Extracting elution groups 25400 to 51000 ===
2 days, 2:26:41.081009 INFO: Using python extraction backend
2 days, 2:26:41.081151 PROGRESS: Extracting batch of 51061 precursors
2 days, 2:26:41.081235 INFO: === Search parameters used ===
2 days, 2:26:41.081292 INFO: rt_error       : 1199.9630585
2 days, 2:26:41.081353 INFO: mobility_error : 0.1
2 days, 2:26:41.081402 INFO: num_candidates : 1
2 days, 2:26:41.081446 INFO: ms1_error      : 30
2 days, 2:26:41.081489 INFO: ms2_error      : 30
2 days, 2:26:41.081531 INFO: fwhm_rt        : 5
2 days, 2:26:41.081572 INFO: quant_window   : 3
2 days, 2:26:41.081615 INFO: ==============================================
2 days, 2:26:41.098928 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:26:41.099067 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:26:41.099108 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:26:41.099133 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:26:41.100033 INFO: Starting candidate selection
2 days, 2:28:39.960842 INFO: Starting candidate scoring
2 days, 2:28:40.728724 INFO: Finished candidate processing
2 days, 2:28:40.728909 INFO: Collecting candidate features
2 days, 2:28:40.830825 WARNING: intensity_correlation has 17 NaNs ( 0.04 % out of 45911)
2 days, 2:28:40.836302 INFO: Collecting fragment features
2 days, 2:28:40.862826 INFO: Finished candidate scoring
2 days, 2:28:40.910091 INFO: performing precursor FDR with 47 features
2 days, 2:28:40.910256 INFO: Decoy channel: -1
2 days, 2:28:40.910293 INFO: competitive: True
2 days, 2:28:40.948307 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:28:40.967937 WARNING: dropped 9 target PSMs due to missing features
2 days, 2:28:40.968102 WARNING: dropped 12 decoy PSMs due to missing features
2 days, 2:28:40.982793 INFO: Estimating optimal hyperparameters - samples: 73,199, batch_size: 299, learning_rate: 2.70e-04
2 days, 2:28:40.983115 INFO: Using random state 830250 for train-test-split
2 days, 2:28:45.978581 INFO: Test AUC: 0.543
2 days, 2:28:45.978745 INFO: Train AUC: 0.603
2 days, 2:28:45.978780 INFO: AUC difference: 9.94%
2 days, 2:28:45.978806 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:28:46.254434 INFO: Resetting torch num_threads to 80
2 days, 2:28:46.271501 PROGRESS: === Extracted 91520 precursors and 773383 fragments ===
2 days, 2:28:46.272306 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:28:46.281737 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:28:46.281929 PROGRESS: Total precursors accumulated: 46,428
2 days, 2:28:46.282010 PROGRESS: Target precursors: 27,803 (59.88%)
2 days, 2:28:46.282091 PROGRESS: Decoy precursors: 18,625 (40.12%)
2 days, 2:28:46.282148 PROGRESS: 
2 days, 2:28:46.282202 PROGRESS: Precursor Summary:
2 days, 2:28:46.283541 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
2 days, 2:28:46.283648 PROGRESS: 
2 days, 2:28:46.283710 PROGRESS: Protein Summary:
2 days, 2:28:46.285020 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
2 days, 2:28:46.285123 PROGRESS: =========================================================================
2 days, 2:28:46.286035 INFO: Target number of precursors not reached yet.
2 days, 2:28:46.684523 INFO: Starting optimization step 8.
2 days, 2:28:46.684815 PROGRESS: === Extracting elution groups 51000 to 102200 ===
2 days, 2:28:46.684909 INFO: Using python extraction backend
2 days, 2:28:46.685040 PROGRESS: Extracting batch of 102076 precursors
2 days, 2:28:46.685119 INFO: === Search parameters used ===
2 days, 2:28:46.685176 INFO: rt_error       : 1199.9630585
2 days, 2:28:46.685226 INFO: mobility_error : 0.1
2 days, 2:28:46.685275 INFO: num_candidates : 1
2 days, 2:28:46.685322 INFO: ms1_error      : 30
2 days, 2:28:46.685367 INFO: ms2_error      : 30
2 days, 2:28:46.685412 INFO: fwhm_rt        : 5
2 days, 2:28:46.685458 INFO: quant_window   : 3
2 days, 2:28:46.685501 INFO: ==============================================
2 days, 2:28:46.709945 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:28:46.710099 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:28:46.710131 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:28:46.710158 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:28:46.711014 INFO: Starting candidate selection
2 days, 2:32:45.382944 INFO: Starting candidate scoring
2 days, 2:32:46.883406 INFO: Finished candidate processing
2 days, 2:32:46.883583 INFO: Collecting candidate features
2 days, 2:32:47.096153 WARNING: intensity_correlation has 17 NaNs ( 0.02 % out of 91838)
2 days, 2:32:47.096880 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 91838)
2 days, 2:32:47.104158 INFO: Collecting fragment features
2 days, 2:32:47.162246 INFO: Finished candidate scoring
2 days, 2:32:47.285560 INFO: performing precursor FDR with 47 features
2 days, 2:32:47.285721 INFO: Decoy channel: -1
2 days, 2:32:47.285757 INFO: competitive: True
2 days, 2:32:47.389952 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:32:47.436034 WARNING: dropped 15 target PSMs due to missing features
2 days, 2:32:47.436179 WARNING: dropped 23 decoy PSMs due to missing features
2 days, 2:32:47.493891 INFO: Estimating optimal hyperparameters - samples: 146,656, batch_size: 600, learning_rate: 3.83e-04
2 days, 2:32:47.494339 INFO: Using random state 505018 for train-test-split
2 days, 2:32:54.881387 INFO: Test AUC: 0.539
2 days, 2:32:54.881548 INFO: Train AUC: 0.581
2 days, 2:32:54.881583 INFO: AUC difference: 7.22%
2 days, 2:32:54.881609 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:32:55.182330 INFO: Resetting torch num_threads to 80
2 days, 2:32:55.214993 PROGRESS: === Extracted 183358 precursors and 1550967 fragments ===
2 days, 2:32:55.215924 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:32:55.232440 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:32:55.232759 PROGRESS: Total precursors accumulated: 93,001
2 days, 2:32:55.232832 PROGRESS: Target precursors: 53,900 (57.96%)
2 days, 2:32:55.232897 PROGRESS: Decoy precursors: 39,101 (42.04%)
2 days, 2:32:55.232961 PROGRESS: 
2 days, 2:32:55.233019 PROGRESS: Precursor Summary:
2 days, 2:32:55.234668 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 2:32:55.234791 PROGRESS: 
2 days, 2:32:55.234856 PROGRESS: Protein Summary:
2 days, 2:32:55.236339 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 2:32:55.236444 PROGRESS: =========================================================================
2 days, 2:32:55.237968 INFO: Target number of precursors not reached yet.
2 days, 2:32:56.280968 INFO: Starting optimization step 9.
2 days, 2:32:56.281313 PROGRESS: === Extracting elution groups 102200 to 204600 ===
2 days, 2:32:56.281420 INFO: Using python extraction backend
2 days, 2:32:56.281565 PROGRESS: Extracting batch of 204132 precursors
2 days, 2:32:56.281650 INFO: === Search parameters used ===
2 days, 2:32:56.281709 INFO: rt_error       : 1199.9630585
2 days, 2:32:56.281761 INFO: mobility_error : 0.1
2 days, 2:32:56.281811 INFO: num_candidates : 1
2 days, 2:32:56.281862 INFO: ms1_error      : 30
2 days, 2:32:56.281939 INFO: ms2_error      : 30
2 days, 2:32:56.281993 INFO: fwhm_rt        : 5
2 days, 2:32:56.282040 INFO: quant_window   : 3
2 days, 2:32:56.282087 INFO: ==============================================
2 days, 2:32:56.334522 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:32:56.334688 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:32:56.334721 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:32:56.334746 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:32:56.335630 INFO: Starting candidate selection
2 days, 2:40:48.634277 INFO: Starting candidate scoring
2 days, 2:40:51.240735 INFO: Finished candidate processing
2 days, 2:40:51.241275 INFO: Collecting candidate features
2 days, 2:40:51.644129 WARNING: intensity_correlation has 43 NaNs ( 0.02 % out of 183895)
2 days, 2:40:51.644563 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 183895)
2 days, 2:40:51.654388 INFO: Collecting fragment features
2 days, 2:40:51.777604 INFO: Finished candidate scoring
2 days, 2:40:52.129903 INFO: performing precursor FDR with 47 features
2 days, 2:40:52.130075 INFO: Decoy channel: -1
2 days, 2:40:52.130105 INFO: competitive: True
2 days, 2:40:52.278942 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:40:52.346233 WARNING: dropped 31 target PSMs due to missing features
2 days, 2:40:52.346392 WARNING: dropped 55 decoy PSMs due to missing features
2 days, 2:40:52.505191 INFO: Estimating optimal hyperparameters - samples: 293,733, batch_size: 1,203, learning_rate: 5.42e-04
2 days, 2:40:52.505779 INFO: Using random state 490908 for train-test-split
2 days, 2:41:04.482746 INFO: Test AUC: 0.543
2 days, 2:41:04.482907 INFO: Train AUC: 0.573
2 days, 2:41:04.482943 INFO: AUC difference: 5.24%
2 days, 2:41:04.482969 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 2:41:04.852467 INFO: Resetting torch num_threads to 80
2 days, 2:41:04.916181 PROGRESS: === Extracted 367253 precursors and 3106030 fragments ===
2 days, 2:41:04.917159 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:41:04.947454 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:41:04.947792 PROGRESS: Total precursors accumulated: 186,282
2 days, 2:41:04.947870 PROGRESS: Target precursors: 107,230 (57.56%)
2 days, 2:41:04.947931 PROGRESS: Decoy precursors: 79,052 (42.44%)
2 days, 2:41:04.947989 PROGRESS: 
2 days, 2:41:04.948041 PROGRESS: Precursor Summary:
2 days, 2:41:04.950139 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 2:41:04.950248 PROGRESS: 
2 days, 2:41:04.950316 PROGRESS: Protein Summary:
2 days, 2:41:04.952223 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 2:41:04.952321 PROGRESS: =========================================================================
2 days, 2:41:04.956096 INFO: Target number of precursors not reached yet.
2 days, 2:41:06.240998 INFO: Starting optimization step 10.
2 days, 2:41:06.241306 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 2:41:06.241415 INFO: Using python extraction backend
2 days, 2:41:06.241578 PROGRESS: Extracting batch of 408390 precursors
2 days, 2:41:06.241668 INFO: === Search parameters used ===
2 days, 2:41:06.241724 INFO: rt_error       : 1199.9630585
2 days, 2:41:06.241773 INFO: mobility_error : 0.1
2 days, 2:41:06.241847 INFO: num_candidates : 1
2 days, 2:41:06.241910 INFO: ms1_error      : 30
2 days, 2:41:06.241959 INFO: ms2_error      : 30
2 days, 2:41:06.242004 INFO: fwhm_rt        : 5
2 days, 2:41:06.242053 INFO: quant_window   : 3
2 days, 2:41:06.242097 INFO: ==============================================
2 days, 2:41:06.340884 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:41:06.341041 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:41:06.341086 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:41:06.341113 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:41:06.342066 INFO: Starting candidate selection
2 days, 2:56:53.558992 INFO: Starting candidate scoring
2 days, 2:56:58.997064 INFO: Finished candidate processing
2 days, 2:56:58.997422 INFO: Collecting candidate features
2 days, 2:56:59.918435 WARNING: intensity_correlation has 107 NaNs ( 0.03 % out of 366840)
2 days, 2:56:59.919018 WARNING: height_correlation has 8 NaNs ( 0.00 % out of 366840)
2 days, 2:56:59.933857 INFO: Collecting fragment features
2 days, 2:57:00.205541 INFO: Finished candidate scoring
2 days, 2:57:00.829234 INFO: performing precursor FDR with 47 features
2 days, 2:57:00.829394 INFO: Decoy channel: -1
2 days, 2:57:00.829426 INFO: competitive: True
2 days, 2:57:01.189198 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 2:57:01.309684 WARNING: dropped 74 target PSMs due to missing features
2 days, 2:57:01.309851 WARNING: dropped 122 decoy PSMs due to missing features
2 days, 2:57:01.622157 INFO: Estimating optimal hyperparameters - samples: 587,117, batch_size: 2,404, learning_rate: 7.66e-04
2 days, 2:57:01.623211 INFO: Using random state 408348 for train-test-split
2 days, 2:57:18.059759 INFO: Test AUC: 0.540
2 days, 2:57:18.059930 INFO: Train AUC: 0.566
2 days, 2:57:18.059968 INFO: AUC difference: 4.67%
2 days, 2:57:18.550855 INFO: Resetting torch num_threads to 80
2 days, 2:57:18.711253 PROGRESS: === Extracted 734093 precursors and 6209074 fragments ===
2 days, 2:57:18.712341 INFO: === FDR correction performed with classifier version -1 ===
2 days, 2:57:18.770123 PROGRESS: ============================= Precursor FDR =============================
2 days, 2:57:18.770447 PROGRESS: Total precursors accumulated: 372,372
2 days, 2:57:18.770530 PROGRESS: Target precursors: 211,938 (56.92%)
2 days, 2:57:18.770594 PROGRESS: Decoy precursors: 160,434 (43.08%)
2 days, 2:57:18.770654 PROGRESS: 
2 days, 2:57:18.770708 PROGRESS: Precursor Summary:
2 days, 2:57:18.774339 PROGRESS: Channel   0:	 0.050 FDR:   247; 0.010 FDR:   150; 0.001 FDR:   128
2 days, 2:57:18.774487 PROGRESS: 
2 days, 2:57:18.774556 PROGRESS: Protein Summary:
2 days, 2:57:18.777893 PROGRESS: Channel   0:	 0.050 FDR:   199; 0.010 FDR:   123; 0.001 FDR:   104
2 days, 2:57:18.778020 PROGRESS: =========================================================================
2 days, 2:57:18.783150 INFO: Target number of precursors not reached yet.
2 days, 2:57:20.194129 INFO: Starting optimization step 11.
2 days, 2:57:20.194464 PROGRESS: === Extracting elution groups 409400 to 819000 ===
2 days, 2:57:20.194583 INFO: Using python extraction backend
2 days, 2:57:20.194753 PROGRESS: Extracting batch of 816689 precursors
2 days, 2:57:20.194863 INFO: === Search parameters used ===
2 days, 2:57:20.194944 INFO: rt_error       : 1199.9630585
2 days, 2:57:20.195007 INFO: mobility_error : 0.1
2 days, 2:57:20.195057 INFO: num_candidates : 1
2 days, 2:57:20.195103 INFO: ms1_error      : 30
2 days, 2:57:20.195151 INFO: ms2_error      : 30
2 days, 2:57:20.195197 INFO: fwhm_rt        : 5
2 days, 2:57:20.195248 INFO: quant_window   : 3
2 days, 2:57:20.195293 INFO: ==============================================
2 days, 2:57:20.525742 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 2:57:20.525911 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 2:57:20.525964 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 2:57:20.525997 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 2:57:20.527055 INFO: Starting candidate selection
2 days, 3:27:06.074394 INFO: Starting candidate scoring
2 days, 3:27:16.247230 INFO: Finished candidate processing
2 days, 3:27:16.247414 INFO: Collecting candidate features
2 days, 3:27:18.084072 WARNING: intensity_correlation has 178 NaNs ( 0.02 % out of 735067)
2 days, 3:27:18.084939 WARNING: height_correlation has 7 NaNs ( 0.00 % out of 735067)
2 days, 3:27:18.109914 INFO: Collecting fragment features
2 days, 3:27:18.638520 INFO: Finished candidate scoring
2 days, 3:27:19.499446 INFO: performing precursor FDR with 47 features
2 days, 3:27:19.499607 INFO: Decoy channel: -1
2 days, 3:27:19.499645 INFO: competitive: True
2 days, 3:27:20.176907 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 3:27:20.428197 WARNING: dropped 171 target PSMs due to missing features
2 days, 3:27:20.428377 WARNING: dropped 209 decoy PSMs due to missing features
2 days, 3:27:21.247819 INFO: Estimating optimal hyperparameters - samples: 1,175,024, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 3:27:21.250075 INFO: Using random state 862000 for train-test-split
2 days, 3:27:50.780151 INFO: Test AUC: 0.546
2 days, 3:27:50.780387 INFO: Train AUC: 0.559
2 days, 3:27:50.780428 INFO: AUC difference: 2.30%
2 days, 3:27:51.541381 INFO: Resetting torch num_threads to 80
2 days, 3:27:52.041496 PROGRESS: === Extracted 1469160 precursors and 12424157 fragments ===
2 days, 3:27:52.043207 INFO: === FDR correction performed with classifier version -1 ===
2 days, 3:27:52.168301 PROGRESS: ============================= Precursor FDR =============================
2 days, 3:27:52.168656 PROGRESS: Total precursors accumulated: 745,135
2 days, 3:27:52.168742 PROGRESS: Target precursors: 421,679 (56.59%)
2 days, 3:27:52.168810 PROGRESS: Decoy precursors: 323,456 (43.41%)
2 days, 3:27:52.168871 PROGRESS: 
2 days, 3:27:52.168928 PROGRESS: Precursor Summary:
2 days, 3:27:52.175161 PROGRESS: Channel   0:	 0.050 FDR:   562; 0.010 FDR:   303; 0.001 FDR:   187
2 days, 3:27:52.175327 PROGRESS: 
2 days, 3:27:52.175398 PROGRESS: Protein Summary:
2 days, 3:27:52.180501 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   196; 0.001 FDR:   129
2 days, 3:27:52.180618 PROGRESS: =========================================================================
2 days, 3:27:52.191051 INFO: Target number of precursors reached.
2 days, 3:27:53.601807 INFO: fragments_df: keeping 3069 of 12424157 [sum(precursor_idx_mask)=3326 sum(mass_error_mask)=12423979 stop_rank=3069
2 days, 3:27:55.787028 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 3:27:55.930691 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 3:27:56.078545 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 3:27:56.224335 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 3:27:56.663285 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 3:27:56.663740 INFO: Using score_cutoff 45.76803059921264 (fac=0.99, q=1)
2 days, 3:27:56.664091 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0449769496917725
2 days, 3:27:56.664180 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.00913533940911293
2 days, 3:27:56.664242 INFO: Updating optimization_manager: score_cutoff        : 0 -> 45.76803059921264
2 days, 3:27:56.664310 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 3:27:56.886833 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 3:27:57.981279 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 3:27:58.223242 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 3:28:00.491533 INFO: Updating optimization_manager: classifier_version  : -1 -> 11
2 days, 3:28:00.491881 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 3:28:00.492032 INFO: Starting optimization step 12.
2 days, 3:28:00.492121 PROGRESS: === Extracting elution groups 0 to 819000 ===
2 days, 3:28:00.492235 INFO: Using python extraction backend
2 days, 3:28:00.492386 PROGRESS: Extracting batch of 1632996 precursors
2 days, 3:28:00.492476 INFO: === Search parameters used ===
2 days, 3:28:00.492545 INFO: rt_error       : 1199.9630585
2 days, 3:28:00.492623 INFO: mobility_error : 0.1
2 days, 3:28:00.492682 INFO: num_candidates : 3
2 days, 3:28:00.492738 INFO: ms1_error      : 30
2 days, 3:28:00.492795 INFO: ms2_error      : 30
2 days, 3:28:00.492852 INFO: fwhm_rt        : 3.0449769496917725
2 days, 3:28:00.492909 INFO: quant_window   : 3
2 days, 3:28:00.492965 INFO: ==============================================
2 days, 3:28:01.137351 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 3:28:01.137508 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 3:28:01.137566 INFO: FWHM in RT is 3.04 seconds, sigma is 0.51
2 days, 3:28:01.137598 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.95
2 days, 3:28:01.142453 INFO: Starting candidate selection
2 days, 4:37:56.121132 INFO: Starting candidate scoring
2 days, 4:38:51.045844 INFO: Finished candidate processing
2 days, 4:38:51.046273 INFO: Collecting candidate features
2 days, 4:38:59.246294 WARNING: intensity_correlation has 1241 NaNs ( 0.03 % out of 4221256)
2 days, 4:38:59.250215 WARNING: height_correlation has 94 NaNs ( 0.00 % out of 4221256)
2 days, 4:38:59.390275 INFO: Collecting fragment features
2 days, 4:39:01.865312 INFO: Finished candidate scoring
2 days, 4:39:04.478441 INFO: performing precursor FDR with 47 features
2 days, 4:39:04.478602 INFO: Decoy channel: -1
2 days, 4:39:04.478636 INFO: competitive: True
2 days, 4:39:05.421494 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 4:39:06.039703 WARNING: dropped 568 target PSMs due to missing features
2 days, 4:39:06.039880 WARNING: dropped 725 decoy PSMs due to missing features
2 days, 4:39:08.016267 INFO: Estimating optimal hyperparameters - samples: 3,375,970, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 4:39:08.037334 INFO: Using random state 686477 for train-test-split
2 days, 4:40:28.433484 INFO: Test AUC: 0.562
2 days, 4:40:28.433681 INFO: Train AUC: 0.567
2 days, 4:40:28.433719 INFO: AUC difference: 0.72%
2 days, 4:40:29.955124 INFO: Resetting torch num_threads to 80
2 days, 4:40:30.024792 PROGRESS: === Extracted 4221256 precursors and 34994709 fragments ===
2 days, 4:40:30.026540 INFO: === FDR correction performed with classifier version 11 ===
2 days, 4:40:30.142392 PROGRESS: ============================= Precursor FDR =============================
2 days, 4:40:30.142738 PROGRESS: Total precursors accumulated: 750,433
2 days, 4:40:30.142817 PROGRESS: Target precursors: 437,563 (58.31%)
2 days, 4:40:30.142879 PROGRESS: Decoy precursors: 312,870 (41.69%)
2 days, 4:40:30.142934 PROGRESS: 
2 days, 4:40:30.142992 PROGRESS: Precursor Summary:
2 days, 4:40:30.148839 PROGRESS: Channel   0:	 0.050 FDR:   495; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 4:40:30.149012 PROGRESS: 
2 days, 4:40:30.149080 PROGRESS: Protein Summary:
2 days, 4:40:30.153859 PROGRESS: Channel   0:	 0.050 FDR:   329; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 4:40:30.153995 PROGRESS: =========================================================================
2 days, 4:40:30.180527 INFO: Target number of precursors not reached yet.
2 days, 4:40:32.219135 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 4:40:32.439462 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 4:40:33.506679 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 4:40:33.732766 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 4:40:35.689534 INFO: === skipping optimization until target number of precursors are found ===
2 days, 4:40:35.689860 INFO: Starting optimization step 13.
2 days, 4:40:35.689970 PROGRESS: === Extracting elution groups 819000 to 1638200 ===
2 days, 4:40:35.690053 INFO: Using python extraction backend
2 days, 4:40:35.690178 PROGRESS: Extracting batch of 1633286 precursors
2 days, 4:40:35.690295 INFO: === Search parameters used ===
2 days, 4:40:35.690357 INFO: rt_error       : 1199.9630585
2 days, 4:40:35.690410 INFO: mobility_error : 0.1
2 days, 4:40:35.690463 INFO: num_candidates : 3
2 days, 4:40:35.690511 INFO: ms1_error      : 30
2 days, 4:40:35.690558 INFO: ms2_error      : 30
2 days, 4:40:35.690603 INFO: fwhm_rt        : 3.0449769496917725
2 days, 4:40:35.690650 INFO: quant_window   : 3
2 days, 4:40:35.690695 INFO: ==============================================
2 days, 4:40:36.069393 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 4:40:36.069544 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 4:40:36.069594 INFO: FWHM in RT is 3.04 seconds, sigma is 0.51
2 days, 4:40:36.069619 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.95
2 days, 4:40:36.070522 INFO: Starting candidate selection
2 days, 5:47:27.509305 INFO: Starting candidate scoring
2 days, 5:48:30.867904 INFO: Finished candidate processing
2 days, 5:48:30.868263 INFO: Collecting candidate features
2 days, 5:48:38.898978 WARNING: intensity_correlation has 1238 NaNs ( 0.03 % out of 4221184)
2 days, 5:48:38.902997 WARNING: height_correlation has 92 NaNs ( 0.00 % out of 4221184)
2 days, 5:48:39.046759 INFO: Collecting fragment features
2 days, 5:48:41.661734 INFO: Finished candidate scoring
2 days, 5:48:46.540085 INFO: performing precursor FDR with 47 features
2 days, 5:48:46.540243 INFO: Decoy channel: -1
2 days, 5:48:46.540278 INFO: competitive: True
2 days, 5:48:49.419664 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 5:48:50.680930 WARNING: dropped 1155 target PSMs due to missing features
2 days, 5:48:50.681102 WARNING: dropped 1431 decoy PSMs due to missing features
2 days, 5:48:53.899577 INFO: Estimating optimal hyperparameters - samples: 6,751,883, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 5:48:53.913030 INFO: Using random state 686477 for train-test-split
2 days, 5:51:36.031244 INFO: Test AUC: 0.566
2 days, 5:51:36.031430 INFO: Train AUC: 0.569
2 days, 5:51:36.031468 INFO: AUC difference: 0.41%
2 days, 5:51:38.483755 INFO: Resetting torch num_threads to 80
2 days, 5:51:40.151464 PROGRESS: === Extracted 8442440 precursors and 69983580 fragments ===
2 days, 5:51:40.153765 INFO: === FDR correction performed with classifier version 11 ===
2 days, 5:51:40.384058 PROGRESS: ============================= Precursor FDR =============================
2 days, 5:51:40.384416 PROGRESS: Total precursors accumulated: 1,501,028
2 days, 5:51:40.384501 PROGRESS: Target precursors: 877,133 (58.44%)
2 days, 5:51:40.384564 PROGRESS: Decoy precursors: 623,895 (41.56%)
2 days, 5:51:40.384619 PROGRESS: 
2 days, 5:51:40.384671 PROGRESS: Precursor Summary:
2 days, 5:51:40.394852 PROGRESS: Channel   0:	 0.050 FDR: 1,570; 0.010 FDR: 1,038; 0.001 FDR:   465
2 days, 5:51:40.395052 PROGRESS: 
2 days, 5:51:40.395148 PROGRESS: Protein Summary:
2 days, 5:51:40.404543 PROGRESS: Channel   0:	 0.050 FDR:   816; 0.010 FDR:   514; 0.001 FDR:   271
2 days, 5:51:40.404758 PROGRESS: =========================================================================
2 days, 5:51:40.433376 INFO: Target number of precursors reached.
2 days, 5:51:48.054109 INFO: fragments_df: keeping 5000 of 69983580 [sum(precursor_idx_mask)=30349 sum(mass_error_mask)=69982831 stop_rank=5000
2 days, 5:51:49.581315 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 5:51:49.779368 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 5:51:49.977832 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 5:51:50.177742 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 5:51:50.898512 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 5:51:50.899051 INFO: Using score_cutoff 37.13001763801575 (fac=0.99, q=1)
2 days, 5:51:50.899459 INFO: Updating optimization_manager: fwhm_rt             : 3.0449769496917725 -> 3.0432167053222656
2 days, 5:51:50.899562 INFO: Updating optimization_manager: fwhm_mobility       : 0.00913533940911293 -> 0.007836779579520226
2 days, 5:51:50.899655 INFO: Updating optimization_manager: score_cutoff        : 45.76803059921264 -> 37.13001763801575
2 days, 5:51:50.899745 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 5:51:51.000033 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 5:51:51.530141 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 5:51:51.647212 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 5:51:52.597229 INFO: === checking if optimization conditions were reached ===
2 days, 5:51:52.599558 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
2 days, 5:51:52.599733 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
2 days, 5:51:52.599811 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 5:51:52.601005 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 5:51:52.601111 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
2 days, 5:51:52.601184 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 5:51:52.601245 INFO: ==============================================
2 days, 5:51:52.601321 INFO: Starting optimization step 14.
2 days, 5:51:52.601386 PROGRESS: === Extracting elution groups 0 to 409400 ===
2 days, 5:51:52.601478 INFO: Using python extraction backend
2 days, 5:51:52.601606 PROGRESS: Extracting batch of 816307 precursors
2 days, 5:51:52.601678 INFO: === Search parameters used ===
2 days, 5:51:52.601732 INFO: rt_error       : 1199.9630585
2 days, 5:51:52.601779 INFO: mobility_error : 0.1
2 days, 5:51:52.601825 INFO: num_candidates : 3
2 days, 5:51:52.601887 INFO: ms1_error      : 15.0
2 days, 5:51:52.601942 INFO: ms2_error      : 15.0
2 days, 5:51:52.601987 INFO: fwhm_rt        : 3.0432167053222656
2 days, 5:51:52.602032 INFO: quant_window   : 3
2 days, 5:51:52.602074 INFO: ==============================================
2 days, 5:51:52.805005 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 5:51:52.805167 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 5:51:52.805225 INFO: FWHM in RT is 3.04 seconds, sigma is 0.51
2 days, 5:51:52.805251 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.25
2 days, 5:51:52.812382 INFO: Starting candidate selection
2 days, 6:29:03.568132 INFO: Starting candidate scoring
2 days, 6:29:26.806721 INFO: Finished candidate processing
2 days, 6:29:26.806983 INFO: Collecting candidate features
2 days, 6:29:30.725492 WARNING: intensity_correlation has 2149 NaNs ( 0.10 % out of 2057059)
2 days, 6:29:30.727467 WARNING: height_correlation has 152 NaNs ( 0.01 % out of 2057059)
2 days, 6:29:30.795274 INFO: Collecting fragment features
2 days, 6:29:31.965126 INFO: Finished candidate scoring
2 days, 6:29:33.335693 INFO: performing precursor FDR with 47 features
2 days, 6:29:33.335843 INFO: Decoy channel: -1
2 days, 6:29:33.335875 INFO: competitive: True
2 days, 6:29:33.787455 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 6:29:34.072410 WARNING: dropped 1102 target PSMs due to missing features
2 days, 6:29:34.072584 WARNING: dropped 1142 decoy PSMs due to missing features
2 days, 6:29:34.809438 INFO: Estimating optimal hyperparameters - samples: 1,643,852, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 6:29:34.818568 INFO: Using random state 404067 for train-test-split
2 days, 6:30:15.527311 INFO: Test AUC: 0.563
2 days, 6:30:15.527531 INFO: Train AUC: 0.572
2 days, 6:30:15.527572 INFO: AUC difference: 1.69%
2 days, 6:30:16.405694 INFO: Resetting torch num_threads to 80
2 days, 6:30:16.441269 PROGRESS: === Extracted 2057059 precursors and 14558703 fragments ===
2 days, 6:30:16.442393 INFO: === FDR correction performed with classifier version 13 ===
2 days, 6:30:16.502990 PROGRESS: ============================= Precursor FDR =============================
2 days, 6:30:16.503335 PROGRESS: Total precursors accumulated: 373,057
2 days, 6:30:16.503431 PROGRESS: Target precursors: 218,859 (58.67%)
2 days, 6:30:16.503490 PROGRESS: Decoy precursors: 154,198 (41.33%)
2 days, 6:30:16.503542 PROGRESS: 
2 days, 6:30:16.503593 PROGRESS: Precursor Summary:
2 days, 6:30:16.507074 PROGRESS: Channel   0:	 0.050 FDR:   570; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 6:30:16.507223 PROGRESS: 
2 days, 6:30:16.507287 PROGRESS: Protein Summary:
2 days, 6:30:16.510421 PROGRESS: Channel   0:	 0.050 FDR:   442; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 6:30:16.510526 PROGRESS: =========================================================================
2 days, 6:30:16.565022 INFO: Target number of precursors not reached yet.
2 days, 6:30:17.884912 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 6:30:17.990682 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 6:30:18.514439 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 6:30:18.619467 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 6:30:19.558162 INFO: === skipping optimization until target number of precursors are found ===
2 days, 6:30:19.558491 INFO: Starting optimization step 15.
2 days, 6:30:19.558580 PROGRESS: === Extracting elution groups 409400 to 819000 ===
2 days, 6:30:19.558662 INFO: Using python extraction backend
2 days, 6:30:19.558785 PROGRESS: Extracting batch of 816689 precursors
2 days, 6:30:19.558865 INFO: === Search parameters used ===
2 days, 6:30:19.558921 INFO: rt_error       : 1199.9630585
2 days, 6:30:19.558970 INFO: mobility_error : 0.1
2 days, 6:30:19.559017 INFO: num_candidates : 3
2 days, 6:30:19.559062 INFO: ms1_error      : 15.0
2 days, 6:30:19.559104 INFO: ms2_error      : 15.0
2 days, 6:30:19.559148 INFO: fwhm_rt        : 3.0432167053222656
2 days, 6:30:19.559190 INFO: quant_window   : 3
2 days, 6:30:19.559232 INFO: ==============================================
2 days, 6:30:19.747974 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 6:30:19.748127 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 6:30:19.748177 INFO: FWHM in RT is 3.04 seconds, sigma is 0.51
2 days, 6:30:19.748204 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.25
2 days, 6:30:19.749114 INFO: Starting candidate selection
2 days, 7:08:14.671086 INFO: Starting candidate scoring
2 days, 7:08:38.097896 INFO: Finished candidate processing
2 days, 7:08:38.098340 INFO: Collecting candidate features
2 days, 7:08:42.157459 WARNING: intensity_correlation has 1978 NaNs ( 0.10 % out of 2059880)
2 days, 7:08:42.159574 WARNING: height_correlation has 135 NaNs ( 0.01 % out of 2059880)
2 days, 7:08:42.228742 INFO: Collecting fragment features
2 days, 7:08:43.296095 INFO: Finished candidate scoring
2 days, 7:08:45.384321 INFO: performing precursor FDR with 47 features
2 days, 7:08:45.384489 INFO: Decoy channel: -1
2 days, 7:08:45.384522 INFO: competitive: True
2 days, 7:08:46.881480 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 7:08:47.458539 WARNING: dropped 2120 target PSMs due to missing features
2 days, 7:08:47.458710 WARNING: dropped 2196 decoy PSMs due to missing features
2 days, 7:08:49.234670 INFO: Estimating optimal hyperparameters - samples: 3,290,098, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 7:08:49.240632 INFO: Using random state 404067 for train-test-split
2 days, 7:10:08.676333 INFO: Test AUC: 0.563
2 days, 7:10:08.676528 INFO: Train AUC: 0.567
2 days, 7:10:08.676568 INFO: AUC difference: 0.81%
2 days, 7:10:10.124743 INFO: Resetting torch num_threads to 80
2 days, 7:10:10.734262 PROGRESS: === Extracted 4116939 precursors and 29127733 fragments ===
2 days, 7:10:10.735705 INFO: === FDR correction performed with classifier version 13 ===
2 days, 7:10:10.894449 PROGRESS: ============================= Precursor FDR =============================
2 days, 7:10:10.894800 PROGRESS: Total precursors accumulated: 746,564
2 days, 7:10:10.894895 PROGRESS: Target precursors: 434,302 (58.17%)
2 days, 7:10:10.894957 PROGRESS: Decoy precursors: 312,262 (41.83%)
2 days, 7:10:10.895032 PROGRESS: 
2 days, 7:10:10.895084 PROGRESS: Precursor Summary:
2 days, 7:10:10.900624 PROGRESS: Channel   0:	 0.050 FDR:   934; 0.010 FDR:   316; 0.001 FDR:   135
2 days, 7:10:10.900780 PROGRESS: 
2 days, 7:10:10.900858 PROGRESS: Protein Summary:
2 days, 7:10:10.905774 PROGRESS: Channel   0:	 0.050 FDR:   600; 0.010 FDR:   210; 0.001 FDR:    88
2 days, 7:10:10.905892 PROGRESS: =========================================================================
2 days, 7:10:10.919889 INFO: Target number of precursors reached.
2 days, 7:10:13.979487 INFO: fragments_df: keeping 5000 of 29127733 [sum(precursor_idx_mask)=9613 sum(mass_error_mask)=29127329 stop_rank=5000
2 days, 7:10:15.974236 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 7:10:16.113094 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 7:10:16.255915 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 7:10:16.398643 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 7:10:17.109207 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 7:10:17.109700 INFO: Using score_cutoff 46.52450587463379 (fac=0.99, q=1)
2 days, 7:10:17.110058 INFO: Updating optimization_manager: fwhm_rt             : 3.0432167053222656 -> 3.164046287536621
2 days, 7:10:17.110146 INFO: Updating optimization_manager: fwhm_mobility       : 0.007836779579520226 -> 0.008485810831189156
2 days, 7:10:17.110206 INFO: Updating optimization_manager: score_cutoff        : 37.13001763801575 -> 46.52450587463379
2 days, 7:10:17.110271 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 7:10:17.337728 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 7:10:18.422568 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 7:10:18.643495 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 7:10:20.507965 INFO: === checking if optimization conditions were reached ===
2 days, 7:10:20.510305 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
2 days, 7:10:20.510472 INFO: Updating optimization_manager: classifier_version  : 13 -> 15
2 days, 7:10:20.510545 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 7:10:20.511647 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 7:10:20.511760 INFO: Updating optimization_manager: classifier_version  : 15 -> 15
2 days, 7:10:20.511828 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 7:10:20.511890 INFO: ==============================================
2 days, 7:10:20.511966 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 7:10:22.125482 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 7:10:22.369921 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 7:10:23.464597 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 7:10:23.683074 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 7:10:25.536690 INFO: Starting optimization step 0.
2 days, 7:10:25.537006 PROGRESS: === Extracting elution groups 0 to 819000 ===
2 days, 7:10:25.537117 INFO: Using python extraction backend
2 days, 7:10:25.537265 PROGRESS: Extracting batch of 1632996 precursors
2 days, 7:10:25.537368 INFO: === Search parameters used ===
2 days, 7:10:25.537450 INFO: rt_error       : 1199.9630585
2 days, 7:10:25.537521 INFO: mobility_error : 0.1
2 days, 7:10:25.537587 INFO: num_candidates : 3
2 days, 7:10:25.537651 INFO: ms1_error      : 15.0
2 days, 7:10:25.537716 INFO: ms2_error      : 15.0
2 days, 7:10:25.537778 INFO: fwhm_rt        : 3.164046287536621
2 days, 7:10:25.537839 INFO: quant_window   : 3
2 days, 7:10:25.537916 INFO: ==============================================
2 days, 7:10:25.907402 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 7:10:25.907574 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 7:10:25.907635 INFO: FWHM in RT is 3.16 seconds, sigma is 0.53
2 days, 7:10:25.907691 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.60
2 days, 7:10:25.908558 INFO: Starting candidate selection
2 days, 8:25:21.364562 INFO: Starting candidate scoring
2 days, 8:26:11.562797 INFO: Finished candidate processing
2 days, 8:26:11.562975 INFO: Collecting candidate features
2 days, 8:26:19.814289 WARNING: intensity_correlation has 4140 NaNs ( 0.10 % out of 4124587)
2 days, 8:26:19.818294 WARNING: height_correlation has 283 NaNs ( 0.01 % out of 4124587)
2 days, 8:26:19.960226 INFO: Collecting fragment features
2 days, 8:26:22.410238 INFO: Finished candidate scoring
2 days, 8:26:25.277847 INFO: performing precursor FDR with 47 features
2 days, 8:26:25.277992 INFO: Decoy channel: -1
2 days, 8:26:25.278023 INFO: competitive: True
2 days, 8:26:26.283873 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:26:26.923509 WARNING: dropped 2116 target PSMs due to missing features
2 days, 8:26:26.923681 WARNING: dropped 2214 decoy PSMs due to missing features
2 days, 8:26:28.649541 INFO: Estimating optimal hyperparameters - samples: 3,296,205, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 8:26:28.657404 INFO: Using random state 409743 for train-test-split
2 days, 8:27:57.109889 INFO: Test AUC: 0.568
2 days, 8:27:57.110054 INFO: Train AUC: 0.572
2 days, 8:27:57.110095 INFO: AUC difference: 0.81%
2 days, 8:27:58.685413 INFO: Resetting torch num_threads to 80
2 days, 8:27:58.781006 PROGRESS: === Extracted 4124587 precursors and 29269186 fragments ===
2 days, 8:27:58.782447 INFO: === FDR correction performed with classifier version 15 ===
2 days, 8:27:58.907053 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:27:58.907364 PROGRESS: Total precursors accumulated: 747,070
2 days, 8:27:58.907444 PROGRESS: Target precursors: 438,512 (58.70%)
2 days, 8:27:58.907509 PROGRESS: Decoy precursors: 308,558 (41.30%)
2 days, 8:27:58.907577 PROGRESS: 
2 days, 8:27:58.907631 PROGRESS: Precursor Summary:
2 days, 8:27:58.913388 PROGRESS: Channel   0:	 0.050 FDR: 1,091; 0.010 FDR:   617; 0.001 FDR:   331
2 days, 8:27:58.913530 PROGRESS: 
2 days, 8:27:58.913603 PROGRESS: Protein Summary:
2 days, 8:27:58.918990 PROGRESS: Channel   0:	 0.050 FDR:   702; 0.010 FDR:   384; 0.001 FDR:   226
2 days, 8:27:58.919142 PROGRESS: =========================================================================
2 days, 8:27:58.948039 INFO: Target number of precursors reached.
2 days, 8:28:02.132603 INFO: fragments_df: keeping 5000 of 29269186 [sum(precursor_idx_mask)=17562 sum(mass_error_mask)=29268755 stop_rank=5000
2 days, 8:28:03.830781 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:28:04.042891 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:28:04.251962 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:28:04.447413 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:28:05.166707 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 8:28:05.167151 INFO: Using score_cutoff 22.855853073120116 (fac=0.99, q=1)
2 days, 8:28:05.167511 INFO: Updating optimization_manager: fwhm_rt             : 3.164046287536621 -> 2.8775393962860107
2 days, 8:28:05.167600 INFO: Updating optimization_manager: fwhm_mobility       : 0.008485810831189156 -> 0.006781857926398516
2 days, 8:28:05.167663 INFO: Updating optimization_manager: score_cutoff        : 46.52450587463379 -> 22.855853073120116
2 days, 8:28:05.167734 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:28:05.277239 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:28:05.831706 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:28:05.950001 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:28:06.994882 INFO: === checking if optimization conditions were reached ===
2 days, 8:28:06.995131 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 8:28:06.997493 INFO: Updating optimization_manager: rt_error            : 1199.9630585 -> 211.1601315529245
2 days, 8:28:06.997633 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 211.1601.
2 days, 8:28:06.997708 INFO: ==============================================
2 days, 8:28:06.997788 INFO: Starting optimization step 1.
2 days, 8:28:06.997854 PROGRESS: === Extracting elution groups 0 to 409400 ===
2 days, 8:28:06.997949 INFO: Using python extraction backend
2 days, 8:28:06.998080 PROGRESS: Extracting batch of 816307 precursors
2 days, 8:28:06.998155 INFO: === Search parameters used ===
2 days, 8:28:06.998208 INFO: rt_error       : 211.1601315529245
2 days, 8:28:06.998260 INFO: mobility_error : 0.1
2 days, 8:28:06.998307 INFO: num_candidates : 3
2 days, 8:28:06.998353 INFO: ms1_error      : 15.0
2 days, 8:28:06.998398 INFO: ms2_error      : 15.0
2 days, 8:28:06.998443 INFO: fwhm_rt        : 2.8775393962860107
2 days, 8:28:06.998488 INFO: quant_window   : 3
2 days, 8:28:06.998542 INFO: ==============================================
2 days, 8:28:07.202887 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:28:07.203025 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:28:07.203081 INFO: FWHM in RT is 2.88 seconds, sigma is 0.48
2 days, 8:28:07.203107 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.68
2 days, 8:28:07.214097 INFO: Starting candidate selection
2 days, 8:35:20.716771 INFO: Starting candidate scoring
2 days, 8:35:43.999552 INFO: Finished candidate processing
2 days, 8:35:43.999758 INFO: Collecting candidate features
2 days, 8:35:47.642155 WARNING: intensity_correlation has 5280 NaNs ( 0.28 % out of 1885843)
2 days, 8:35:47.643955 WARNING: height_correlation has 514 NaNs ( 0.03 % out of 1885843)
2 days, 8:35:47.706520 INFO: Collecting fragment features
2 days, 8:35:48.800176 INFO: Finished candidate scoring
2 days, 8:35:50.336325 INFO: performing precursor FDR with 47 features
2 days, 8:35:50.336478 INFO: Decoy channel: -1
2 days, 8:35:50.336506 INFO: competitive: True
2 days, 8:35:50.783405 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:35:51.051103 WARNING: dropped 2779 target PSMs due to missing features
2 days, 8:35:51.051268 WARNING: dropped 2764 decoy PSMs due to missing features
2 days, 8:35:51.770946 INFO: Estimating optimal hyperparameters - samples: 1,504,240, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 8:35:51.779169 INFO: Using random state 409743 for train-test-split
2 days, 8:36:28.572794 INFO: Test AUC: 0.554
2 days, 8:36:28.572968 INFO: Train AUC: 0.562
2 days, 8:36:28.573006 INFO: AUC difference: 1.48%
2 days, 8:36:29.426989 INFO: Resetting torch num_threads to 80
2 days, 8:36:29.460145 PROGRESS: === Extracted 1885843 precursors and 11320150 fragments ===
2 days, 8:36:29.461295 INFO: === FDR correction performed with classifier version 15 ===
2 days, 8:36:29.519642 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:36:29.519990 PROGRESS: Total precursors accumulated: 365,790
2 days, 8:36:29.520065 PROGRESS: Target precursors: 208,767 (57.07%)
2 days, 8:36:29.520126 PROGRESS: Decoy precursors: 157,023 (42.93%)
2 days, 8:36:29.520181 PROGRESS: 
2 days, 8:36:29.520232 PROGRESS: Precursor Summary:
2 days, 8:36:29.523583 PROGRESS: Channel   0:	 0.050 FDR:   714; 0.010 FDR:   533; 0.001 FDR:   402
2 days, 8:36:29.523696 PROGRESS: 
2 days, 8:36:29.523765 PROGRESS: Protein Summary:
2 days, 8:36:29.526949 PROGRESS: Channel   0:	 0.050 FDR:   548; 0.010 FDR:   397; 0.001 FDR:   298
2 days, 8:36:29.527060 PROGRESS: =========================================================================
2 days, 8:36:29.546495 INFO: Target number of precursors reached.
2 days, 8:36:30.760257 INFO: fragments_df: keeping 5000 of 11320150 [sum(precursor_idx_mask)=14259 sum(mass_error_mask)=11319849 stop_rank=5000
2 days, 8:36:31.740364 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:36:31.871956 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:36:32.033533 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:36:32.191768 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:36:32.908356 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 8:36:32.908836 INFO: Using score_cutoff 25.947382914733886 (fac=0.99, q=1)
2 days, 8:36:32.909184 INFO: Updating optimization_manager: fwhm_rt             : 2.8775393962860107 -> 2.7513132095336914
2 days, 8:36:32.909265 INFO: Updating optimization_manager: fwhm_mobility       : 0.006781857926398516 -> 0.005723860580474138
2 days, 8:36:32.909323 INFO: Updating optimization_manager: score_cutoff        : 22.855853073120116 -> 25.947382914733886
2 days, 8:36:32.909379 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:36:32.969877 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:36:33.222940 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:36:33.278118 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:36:33.775612 INFO: === checking if optimization conditions were reached ===
2 days, 8:36:33.775918 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 8:36:33.778243 INFO: Updating optimization_manager: rt_error            : 211.1601315529245 -> 182.84898220997968
2 days, 8:36:33.778384 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 182.8490.
2 days, 8:36:33.778458 INFO: ==============================================
2 days, 8:36:33.778535 INFO: Starting optimization step 2.
2 days, 8:36:33.778599 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 8:36:33.778662 INFO: Using python extraction backend
2 days, 8:36:33.778768 PROGRESS: Extracting batch of 407917 precursors
2 days, 8:36:33.778836 INFO: === Search parameters used ===
2 days, 8:36:33.778913 INFO: rt_error       : 182.84898220997968
2 days, 8:36:33.778962 INFO: mobility_error : 0.1
2 days, 8:36:33.779008 INFO: num_candidates : 3
2 days, 8:36:33.779053 INFO: ms1_error      : 15.0
2 days, 8:36:33.779096 INFO: ms2_error      : 15.0
2 days, 8:36:33.779140 INFO: fwhm_rt        : 2.7513132095336914
2 days, 8:36:33.779186 INFO: quant_window   : 3
2 days, 8:36:33.779231 INFO: ==============================================
2 days, 8:36:33.884197 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:36:33.884353 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:36:33.884398 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
2 days, 8:36:33.884423 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.10
2 days, 8:36:33.885299 INFO: Starting candidate selection
2 days, 8:39:37.580058 INFO: Starting candidate scoring
2 days, 8:39:49.008416 INFO: Finished candidate processing
2 days, 8:39:49.008596 INFO: Collecting candidate features
2 days, 8:39:50.793275 WARNING: intensity_correlation has 2898 NaNs ( 0.31 % out of 930229)
2 days, 8:39:50.794356 WARNING: height_correlation has 288 NaNs ( 0.03 % out of 930229)
2 days, 8:39:50.827105 INFO: Collecting fragment features
2 days, 8:39:51.391967 INFO: Finished candidate scoring
2 days, 8:39:52.086901 INFO: performing precursor FDR with 47 features
2 days, 8:39:52.087056 INFO: Decoy channel: -1
2 days, 8:39:52.087086 INFO: competitive: True
2 days, 8:39:52.306401 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:39:52.443579 WARNING: dropped 1567 target PSMs due to missing features
2 days, 8:39:52.443753 WARNING: dropped 1470 decoy PSMs due to missing features
2 days, 8:39:52.757936 INFO: Estimating optimal hyperparameters - samples: 741,753, batch_size: 3,038, learning_rate: 8.61e-04
2 days, 8:39:52.759914 INFO: Using random state 409743 for train-test-split
2 days, 8:40:11.590323 INFO: Test AUC: 0.554
2 days, 8:40:11.590484 INFO: Train AUC: 0.566
2 days, 8:40:11.590521 INFO: AUC difference: 2.21%
2 days, 8:40:12.113019 INFO: Resetting torch num_threads to 80
2 days, 8:40:12.130482 PROGRESS: === Extracted 930229 precursors and 5476080 fragments ===
2 days, 8:40:12.131350 INFO: === FDR correction performed with classifier version 15 ===
2 days, 8:40:12.160715 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:40:12.161014 PROGRESS: Total precursors accumulated: 182,127
2 days, 8:40:12.161087 PROGRESS: Target precursors: 103,987 (57.10%)
2 days, 8:40:12.161147 PROGRESS: Decoy precursors: 78,140 (42.90%)
2 days, 8:40:12.161209 PROGRESS: 
2 days, 8:40:12.161262 PROGRESS: Precursor Summary:
2 days, 8:40:12.163540 PROGRESS: Channel   0:	 0.050 FDR:   451; 0.010 FDR:   273; 0.001 FDR:   160
2 days, 8:40:12.163649 PROGRESS: 
2 days, 8:40:12.163712 PROGRESS: Protein Summary:
2 days, 8:40:12.165881 PROGRESS: Channel   0:	 0.050 FDR:   382; 0.010 FDR:   225; 0.001 FDR:   131
2 days, 8:40:12.165983 PROGRESS: =========================================================================
2 days, 8:40:12.179614 INFO: Target number of precursors reached.
2 days, 8:40:12.770324 INFO: fragments_df: keeping 4137 of 5476080 [sum(precursor_idx_mask)=7143 sum(mass_error_mask)=5475958 stop_rank=4137
2 days, 8:40:13.708269 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:40:13.843325 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:40:13.981236 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:40:14.122373 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:40:14.694756 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 8:40:14.695227 INFO: Using score_cutoff 23.539154438781736 (fac=0.99, q=1)
2 days, 8:40:14.695571 INFO: Updating optimization_manager: fwhm_rt             : 2.7513132095336914 -> 2.7513132095336914
2 days, 8:40:14.695659 INFO: Updating optimization_manager: fwhm_mobility       : 0.005723860580474138 -> 0.005262887571007013
2 days, 8:40:14.695720 INFO: Updating optimization_manager: score_cutoff        : 25.947382914733886 -> 23.539154438781736
2 days, 8:40:14.695783 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:40:14.744624 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:40:15.000802 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:40:15.056426 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:40:15.546977 INFO: === checking if optimization conditions were reached ===
2 days, 8:40:15.547287 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 8:40:15.549611 INFO: Updating optimization_manager: rt_error            : 182.84898220997968 -> 143.00877364175335
2 days, 8:40:15.549775 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 143.0088.
2 days, 8:40:15.549883 INFO: ==============================================
2 days, 8:40:15.549983 INFO: Starting optimization step 3.
2 days, 8:40:15.550065 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 8:40:15.550145 INFO: Using python extraction backend
2 days, 8:40:15.550271 PROGRESS: Extracting batch of 407917 precursors
2 days, 8:40:15.550365 INFO: === Search parameters used ===
2 days, 8:40:15.550435 INFO: rt_error       : 143.00877364175335
2 days, 8:40:15.550498 INFO: mobility_error : 0.1
2 days, 8:40:15.550559 INFO: num_candidates : 3
2 days, 8:40:15.550619 INFO: ms1_error      : 15.0
2 days, 8:40:15.550679 INFO: ms2_error      : 15.0
2 days, 8:40:15.550738 INFO: fwhm_rt        : 2.7513132095336914
2 days, 8:40:15.550797 INFO: quant_window   : 3
2 days, 8:40:15.550857 INFO: ==============================================
2 days, 8:40:15.649387 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:40:15.649551 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:40:15.649601 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
2 days, 8:40:15.649627 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.85
2 days, 8:40:15.650511 INFO: Starting candidate selection
2 days, 8:43:11.624549 INFO: Starting candidate scoring
2 days, 8:43:23.299891 INFO: Finished candidate processing
2 days, 8:43:23.300278 INFO: Collecting candidate features
2 days, 8:43:25.030998 WARNING: intensity_correlation has 3297 NaNs ( 0.36 % out of 908990)
2 days, 8:43:25.032022 WARNING: height_correlation has 344 NaNs ( 0.04 % out of 908990)
2 days, 8:43:25.064200 INFO: Collecting fragment features
2 days, 8:43:25.546177 INFO: Finished candidate scoring
2 days, 8:43:26.150325 INFO: performing precursor FDR with 47 features
2 days, 8:43:26.150474 INFO: Decoy channel: -1
2 days, 8:43:26.150525 INFO: competitive: True
2 days, 8:43:26.365558 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:43:26.501401 WARNING: dropped 1759 target PSMs due to missing features
2 days, 8:43:26.501557 WARNING: dropped 1692 decoy PSMs due to missing features
2 days, 8:43:26.809458 INFO: Estimating optimal hyperparameters - samples: 724,431, batch_size: 2,967, learning_rate: 8.51e-04
2 days, 8:43:26.811459 INFO: Using random state 409743 for train-test-split
2 days, 8:43:44.733940 INFO: Test AUC: 0.549
2 days, 8:43:44.734108 INFO: Train AUC: 0.565
2 days, 8:43:44.734147 INFO: AUC difference: 2.79%
2 days, 8:43:45.257286 INFO: Resetting torch num_threads to 80
2 days, 8:43:45.274541 PROGRESS: === Extracted 908990 precursors and 5213189 fragments ===
2 days, 8:43:45.275414 INFO: === FDR correction performed with classifier version 15 ===
2 days, 8:43:45.304864 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:43:45.305184 PROGRESS: Total precursors accumulated: 180,317
2 days, 8:43:45.305257 PROGRESS: Target precursors: 102,843 (57.03%)
2 days, 8:43:45.305329 PROGRESS: Decoy precursors: 77,474 (42.97%)
2 days, 8:43:45.305406 PROGRESS: 
2 days, 8:43:45.305459 PROGRESS: Precursor Summary:
2 days, 8:43:45.307713 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   160; 0.001 FDR:   126
2 days, 8:43:45.307817 PROGRESS: 
2 days, 8:43:45.307880 PROGRESS: Protein Summary:
2 days, 8:43:45.310008 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   132; 0.001 FDR:   109
2 days, 8:43:45.310112 PROGRESS: =========================================================================
2 days, 8:43:45.314879 INFO: Target number of precursors not reached yet.
2 days, 8:43:46.220657 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:43:46.269081 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:43:46.527384 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:43:46.584225 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:43:47.084195 INFO: === skipping optimization until target number of precursors are found ===
2 days, 8:43:47.084523 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 8:43:47.084640 INFO: Starting optimization step 4.
2 days, 8:43:47.084720 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 8:43:47.084791 INFO: Using python extraction backend
2 days, 8:43:47.084911 PROGRESS: Extracting batch of 408390 precursors
2 days, 8:43:47.084996 INFO: === Search parameters used ===
2 days, 8:43:47.085056 INFO: rt_error       : 143.00877364175335
2 days, 8:43:47.085108 INFO: mobility_error : 0.1
2 days, 8:43:47.085173 INFO: num_candidates : 3
2 days, 8:43:47.085224 INFO: ms1_error      : 15.0
2 days, 8:43:47.085274 INFO: ms2_error      : 15.0
2 days, 8:43:47.085322 INFO: fwhm_rt        : 2.7513132095336914
2 days, 8:43:47.085368 INFO: quant_window   : 3
2 days, 8:43:47.085414 INFO: ==============================================
2 days, 8:43:47.185016 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:43:47.185170 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:43:47.185222 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
2 days, 8:43:47.185251 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.85
2 days, 8:43:47.187177 INFO: Starting candidate selection
2 days, 8:46:17.924055 INFO: Starting candidate scoring
2 days, 8:46:29.443116 INFO: Finished candidate processing
2 days, 8:46:29.443306 INFO: Collecting candidate features
2 days, 8:46:31.197826 WARNING: intensity_correlation has 3178 NaNs ( 0.35 % out of 907413)
2 days, 8:46:31.198850 WARNING: height_correlation has 364 NaNs ( 0.04 % out of 907413)
2 days, 8:46:31.230919 INFO: Collecting fragment features
2 days, 8:46:31.680972 INFO: Finished candidate scoring
2 days, 8:46:32.717493 INFO: performing precursor FDR with 47 features
2 days, 8:46:32.717741 INFO: Decoy channel: -1
2 days, 8:46:32.717775 INFO: competitive: True
2 days, 8:46:33.430717 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:46:33.693480 WARNING: dropped 3453 target PSMs due to missing features
2 days, 8:46:33.693658 WARNING: dropped 3350 decoy PSMs due to missing features
2 days, 8:46:34.501922 INFO: Estimating optimal hyperparameters - samples: 1,447,680, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 8:46:34.504557 INFO: Using random state 409743 for train-test-split
2 days, 8:47:09.649851 INFO: Test AUC: 0.552
2 days, 8:47:09.650063 INFO: Train AUC: 0.561
2 days, 8:47:09.650102 INFO: AUC difference: 1.61%
2 days, 8:47:10.488306 INFO: Resetting torch num_threads to 80
2 days, 8:47:10.699589 PROGRESS: === Extracted 1816403 precursors and 10414808 fragments ===
2 days, 8:47:10.700696 INFO: === FDR correction performed with classifier version 15 ===
2 days, 8:47:10.757524 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:47:10.757854 PROGRESS: Total precursors accumulated: 360,357
2 days, 8:47:10.757948 PROGRESS: Target precursors: 203,847 (56.57%)
2 days, 8:47:10.758006 PROGRESS: Decoy precursors: 156,510 (43.43%)
2 days, 8:47:10.758057 PROGRESS: 
2 days, 8:47:10.758107 PROGRESS: Precursor Summary:
2 days, 8:47:10.761468 PROGRESS: Channel   0:	 0.050 FDR:   752; 0.010 FDR:   545; 0.001 FDR:   212
2 days, 8:47:10.761590 PROGRESS: 
2 days, 8:47:10.761653 PROGRESS: Protein Summary:
2 days, 8:47:10.764792 PROGRESS: Channel   0:	 0.050 FDR:   577; 0.010 FDR:   400; 0.001 FDR:   162
2 days, 8:47:10.764898 PROGRESS: =========================================================================
2 days, 8:47:10.769804 INFO: Target number of precursors reached.
2 days, 8:47:11.880702 INFO: fragments_df: keeping 5000 of 10414808 [sum(precursor_idx_mask)=14472 sum(mass_error_mask)=10414554 stop_rank=5000
2 days, 8:47:12.829265 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:47:12.980664 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:47:13.138179 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:47:13.293182 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:47:14.008937 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 8:47:14.009418 INFO: Using score_cutoff 23.31426101989746 (fac=0.99, q=1)
2 days, 8:47:14.009764 INFO: Updating optimization_manager: fwhm_rt             : 2.7513132095336914 -> 2.7384541034698486
2 days, 8:47:14.009848 INFO: Updating optimization_manager: fwhm_mobility       : 0.005262887571007013 -> 0.005593164823949337
2 days, 8:47:14.009924 INFO: Updating optimization_manager: score_cutoff        : 23.539154438781736 -> 23.31426101989746
2 days, 8:47:14.009991 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:47:14.060309 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:47:14.319132 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:47:14.375380 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:47:14.890754 INFO: === checking if optimization conditions were reached ===
2 days, 8:47:14.891054 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 8:47:14.893496 INFO: Updating optimization_manager: rt_error            : 143.00877364175335 -> 130.4448822170309
2 days, 8:47:14.893673 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 130.4449.
2 days, 8:47:14.893751 INFO: ==============================================
2 days, 8:47:14.893836 INFO: Starting optimization step 5.
2 days, 8:47:14.893928 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 8:47:14.893998 INFO: Using python extraction backend
2 days, 8:47:14.894103 PROGRESS: Extracting batch of 407917 precursors
2 days, 8:47:14.894175 INFO: === Search parameters used ===
2 days, 8:47:14.894230 INFO: rt_error       : 130.4448822170309
2 days, 8:47:14.894277 INFO: mobility_error : 0.1
2 days, 8:47:14.894324 INFO: num_candidates : 3
2 days, 8:47:14.894369 INFO: ms1_error      : 15.0
2 days, 8:47:14.894413 INFO: ms2_error      : 15.0
2 days, 8:47:14.894456 INFO: fwhm_rt        : 2.7384541034698486
2 days, 8:47:14.894499 INFO: quant_window   : 3
2 days, 8:47:14.894541 INFO: ==============================================
2 days, 8:47:14.993744 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:47:14.993902 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:47:14.993952 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
2 days, 8:47:14.993978 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.03
2 days, 8:47:14.994758 INFO: Starting candidate selection
2 days, 8:49:30.670337 INFO: Starting candidate scoring
2 days, 8:49:42.063189 INFO: Finished candidate processing
2 days, 8:49:42.063575 INFO: Collecting candidate features
2 days, 8:49:43.787453 WARNING: intensity_correlation has 3606 NaNs ( 0.40 % out of 899659)
2 days, 8:49:43.788497 WARNING: height_correlation has 375 NaNs ( 0.04 % out of 899659)
2 days, 8:49:43.820554 INFO: Collecting fragment features
2 days, 8:49:44.284904 INFO: Finished candidate scoring
2 days, 8:49:44.877397 INFO: performing precursor FDR with 47 features
2 days, 8:49:44.877540 INFO: Decoy channel: -1
2 days, 8:49:44.877573 INFO: competitive: True
2 days, 8:49:45.083364 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:49:45.213427 WARNING: dropped 1903 target PSMs due to missing features
2 days, 8:49:45.213584 WARNING: dropped 1861 decoy PSMs due to missing features
2 days, 8:49:45.508745 INFO: Estimating optimal hyperparameters - samples: 716,716, batch_size: 2,935, learning_rate: 8.46e-04
2 days, 8:49:45.510208 INFO: Using random state 409743 for train-test-split
2 days, 8:50:03.716281 INFO: Test AUC: 0.548
2 days, 8:50:03.716457 INFO: Train AUC: 0.566
2 days, 8:50:03.716494 INFO: AUC difference: 3.14%
2 days, 8:50:04.219390 INFO: Resetting torch num_threads to 80
2 days, 8:50:04.236508 PROGRESS: === Extracted 899659 precursors and 5083886 fragments ===
2 days, 8:50:04.237348 INFO: === FDR correction performed with classifier version 15 ===
2 days, 8:50:04.267722 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:50:04.268046 PROGRESS: Total precursors accumulated: 179,810
2 days, 8:50:04.268118 PROGRESS: Target precursors: 102,476 (56.99%)
2 days, 8:50:04.268177 PROGRESS: Decoy precursors: 77,334 (43.01%)
2 days, 8:50:04.268231 PROGRESS: 
2 days, 8:50:04.268286 PROGRESS: Precursor Summary:
2 days, 8:50:04.270914 PROGRESS: Channel   0:	 0.050 FDR:   478; 0.010 FDR:   201; 0.001 FDR:   118
2 days, 8:50:04.271025 PROGRESS: 
2 days, 8:50:04.271089 PROGRESS: Protein Summary:
2 days, 8:50:04.273238 PROGRESS: Channel   0:	 0.050 FDR:   408; 0.010 FDR:   169; 0.001 FDR:    99
2 days, 8:50:04.273345 PROGRESS: =========================================================================
2 days, 8:50:04.286919 INFO: Target number of precursors reached.
2 days, 8:50:04.824143 INFO: fragments_df: keeping 3305 of 5083886 [sum(precursor_idx_mask)=5358 sum(mass_error_mask)=5083788 stop_rank=3305
2 days, 8:50:05.749785 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:50:05.861399 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:50:05.968653 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:50:06.077173 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:50:06.476664 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 8:50:06.477133 INFO: Using score_cutoff 28.635158214569092 (fac=0.99, q=1)
2 days, 8:50:06.477454 INFO: Updating optimization_manager: fwhm_rt             : 2.7384541034698486 -> 2.9442317485809326
2 days, 8:50:06.477539 INFO: Updating optimization_manager: fwhm_mobility       : 0.005593164823949337 -> 0.006143044214695692
2 days, 8:50:06.477598 INFO: Updating optimization_manager: score_cutoff        : 23.31426101989746 -> 28.635158214569092
2 days, 8:50:06.477662 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:50:06.529167 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:50:06.787807 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:50:06.851958 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:50:07.347735 INFO: === checking if optimization conditions were reached ===
2 days, 8:50:07.348039 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 8:50:07.349364 INFO: Updating optimization_manager: rt_error            : 130.4448822170309 -> 143.00877364175335
2 days, 8:50:07.349537 INFO: Updating optimization_manager: classifier_version  : 15 -> 20
2 days, 8:50:07.349649 INFO: Updating optimization_manager: score_cutoff        : 28.635158214569092 -> 23.31426101989746
2 days, 8:50:07.349750 INFO: Updating optimization_manager: fwhm_rt             : 2.9442317485809326 -> 2.7384541034698486
2 days, 8:50:07.349847 INFO: Updating optimization_manager: fwhm_mobility       : 0.006143044214695692 -> 0.005593164823949337
2 days, 8:50:07.349959 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 143.0088 found after 5 searches.
2 days, 8:50:07.350035 INFO: ==============================================
2 days, 8:50:07.350113 PROGRESS: Optimization finished for rt_error.
2 days, 8:50:07.918953 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:50:07.970877 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:50:08.222416 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:50:08.281189 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:50:08.771530 INFO: Starting optimization step 0.
2 days, 8:50:08.771824 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 8:50:08.771917 INFO: Using python extraction backend
2 days, 8:50:08.772044 PROGRESS: Extracting batch of 407917 precursors
2 days, 8:50:08.772146 INFO: === Search parameters used ===
2 days, 8:50:08.772209 INFO: rt_error       : 143.00877364175335
2 days, 8:50:08.772265 INFO: mobility_error : 0.1
2 days, 8:50:08.772317 INFO: num_candidates : 3
2 days, 8:50:08.772368 INFO: ms1_error      : 15.0
2 days, 8:50:08.772416 INFO: ms2_error      : 15.0
2 days, 8:50:08.772463 INFO: fwhm_rt        : 2.7384541034698486
2 days, 8:50:08.772510 INFO: quant_window   : 3
2 days, 8:50:08.772556 INFO: ==============================================
2 days, 8:50:08.871667 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:50:08.871826 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:50:08.871876 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
2 days, 8:50:08.871902 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.03
2 days, 8:50:08.872665 INFO: Starting candidate selection
2 days, 8:52:37.588541 INFO: Starting candidate scoring
2 days, 8:52:48.926936 INFO: Finished candidate processing
2 days, 8:52:48.927241 INFO: Collecting candidate features
2 days, 8:52:50.692920 WARNING: intensity_correlation has 3359 NaNs ( 0.37 % out of 907093)
2 days, 8:52:50.693951 WARNING: height_correlation has 350 NaNs ( 0.04 % out of 907093)
2 days, 8:52:50.726174 INFO: Collecting fragment features
2 days, 8:52:51.204412 INFO: Finished candidate scoring
2 days, 8:52:51.799723 INFO: performing precursor FDR with 47 features
2 days, 8:52:51.799882 INFO: Decoy channel: -1
2 days, 8:52:51.799910 INFO: competitive: True
2 days, 8:52:52.010981 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:52:52.144362 WARNING: dropped 1775 target PSMs due to missing features
2 days, 8:52:52.144521 WARNING: dropped 1742 decoy PSMs due to missing features
2 days, 8:52:52.453396 INFO: Estimating optimal hyperparameters - samples: 722,860, batch_size: 2,960, learning_rate: 8.50e-04
2 days, 8:52:52.455168 INFO: Using random state 104437 for train-test-split
2 days, 8:53:09.740936 INFO: Test AUC: 0.552
2 days, 8:53:09.741114 INFO: Train AUC: 0.572
2 days, 8:53:09.741150 INFO: AUC difference: 3.44%
2 days, 8:53:10.273380 INFO: Resetting torch num_threads to 80
2 days, 8:53:10.291059 PROGRESS: === Extracted 907093 precursors and 5198701 fragments ===
2 days, 8:53:10.291898 INFO: === FDR correction performed with classifier version 20 ===
2 days, 8:53:10.323029 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:53:10.323348 PROGRESS: Total precursors accumulated: 180,128
2 days, 8:53:10.323425 PROGRESS: Target precursors: 103,470 (57.44%)
2 days, 8:53:10.323488 PROGRESS: Decoy precursors: 76,658 (42.56%)
2 days, 8:53:10.323543 PROGRESS: 
2 days, 8:53:10.323596 PROGRESS: Precursor Summary:
2 days, 8:53:10.326204 PROGRESS: Channel   0:	 0.050 FDR:   494; 0.010 FDR:   217; 0.001 FDR:   164
2 days, 8:53:10.326320 PROGRESS: 
2 days, 8:53:10.326389 PROGRESS: Protein Summary:
2 days, 8:53:10.328571 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   183; 0.001 FDR:   139
2 days, 8:53:10.328691 PROGRESS: =========================================================================
2 days, 8:53:10.335694 INFO: Target number of precursors reached.
2 days, 8:53:10.875794 INFO: fragments_df: keeping 3446 of 5198701 [sum(precursor_idx_mask)=5735 sum(mass_error_mask)=5198591 stop_rank=3446
2 days, 8:53:11.819243 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:53:11.952400 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:53:12.083485 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:53:12.218271 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:53:12.702033 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 8:53:12.702526 INFO: Using score_cutoff 29.169572483825682 (fac=0.99, q=1)
2 days, 8:53:12.702877 INFO: Updating optimization_manager: fwhm_rt             : 2.7384541034698486 -> 2.842787265777588
2 days, 8:53:12.702965 INFO: Updating optimization_manager: fwhm_mobility       : 0.005593164823949337 -> 0.005958479829132557
2 days, 8:53:12.703027 INFO: Updating optimization_manager: score_cutoff        : 23.31426101989746 -> 29.169572483825682
2 days, 8:53:12.703089 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:53:12.757102 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:53:13.015172 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:53:13.079178 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:53:13.585605 INFO: === checking if optimization conditions were reached ===
2 days, 8:53:13.585956 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 8:53:13.587998 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.042401155517698866
2 days, 8:53:13.588150 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0424.
2 days, 8:53:13.588227 INFO: ==============================================
2 days, 8:53:13.588307 INFO: Starting optimization step 1.
2 days, 8:53:13.588372 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 8:53:13.588436 INFO: Using python extraction backend
2 days, 8:53:13.588544 PROGRESS: Extracting batch of 407917 precursors
2 days, 8:53:13.588622 INFO: === Search parameters used ===
2 days, 8:53:13.588674 INFO: rt_error       : 143.00877364175335
2 days, 8:53:13.588720 INFO: mobility_error : 0.042401155517698866
2 days, 8:53:13.588764 INFO: num_candidates : 3
2 days, 8:53:13.588810 INFO: ms1_error      : 15.0
2 days, 8:53:13.588854 INFO: ms2_error      : 15.0
2 days, 8:53:13.588898 INFO: fwhm_rt        : 2.842787265777588
2 days, 8:53:13.588941 INFO: quant_window   : 3
2 days, 8:53:13.588984 INFO: ==============================================
2 days, 8:53:13.693716 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:53:13.693887 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:53:13.693939 INFO: FWHM in RT is 2.84 seconds, sigma is 0.47
2 days, 8:53:13.693964 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.23
2 days, 8:53:13.694891 INFO: Starting candidate selection
2 days, 8:54:13.210783 INFO: Starting candidate scoring
2 days, 8:54:23.915790 INFO: Finished candidate processing
2 days, 8:54:23.915986 INFO: Collecting candidate features
2 days, 8:54:25.540293 WARNING: intensity_correlation has 3831 NaNs ( 0.47 % out of 821829)
2 days, 8:54:25.541239 WARNING: height_correlation has 403 NaNs ( 0.05 % out of 821829)
2 days, 8:54:25.570638 INFO: Collecting fragment features
2 days, 8:54:25.965623 INFO: Finished candidate scoring
2 days, 8:54:26.520862 INFO: performing precursor FDR with 47 features
2 days, 8:54:26.521008 INFO: Decoy channel: -1
2 days, 8:54:26.521038 INFO: competitive: True
2 days, 8:54:26.711895 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:54:26.831823 WARNING: dropped 2051 target PSMs due to missing features
2 days, 8:54:26.831988 WARNING: dropped 1984 decoy PSMs due to missing features
2 days, 8:54:27.097421 INFO: Estimating optimal hyperparameters - samples: 654,235, batch_size: 2,679, learning_rate: 8.09e-04
2 days, 8:54:27.098673 INFO: Using random state 104437 for train-test-split
2 days, 8:54:44.064066 INFO: Test AUC: 0.555
2 days, 8:54:44.064239 INFO: Train AUC: 0.575
2 days, 8:54:44.064277 INFO: AUC difference: 3.43%
2 days, 8:54:44.553582 INFO: Resetting torch num_threads to 80
2 days, 8:54:44.569533 PROGRESS: === Extracted 821829 precursors and 4490614 fragments ===
2 days, 8:54:44.570408 INFO: === FDR correction performed with classifier version 20 ===
2 days, 8:54:44.598439 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:54:44.598784 PROGRESS: Total precursors accumulated: 167,886
2 days, 8:54:44.598857 PROGRESS: Target precursors: 97,240 (57.92%)
2 days, 8:54:44.598937 PROGRESS: Decoy precursors: 70,646 (42.08%)
2 days, 8:54:44.598993 PROGRESS: 
2 days, 8:54:44.599045 PROGRESS: Precursor Summary:
2 days, 8:54:44.601402 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   364; 0.001 FDR:   160
2 days, 8:54:44.601507 PROGRESS: 
2 days, 8:54:44.601571 PROGRESS: Protein Summary:
2 days, 8:54:44.603689 PROGRESS: Channel   0:	 0.050 FDR:   363; 0.010 FDR:   302; 0.001 FDR:   135
2 days, 8:54:44.603796 PROGRESS: =========================================================================
2 days, 8:54:44.608971 INFO: Target number of precursors reached.
2 days, 8:54:45.100350 INFO: fragments_df: keeping 4792 of 4490614 [sum(precursor_idx_mask)=9049 sum(mass_error_mask)=4490483 stop_rank=4792
2 days, 8:54:46.030285 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:54:46.173340 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:54:46.318882 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:54:46.464082 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:54:47.144386 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 8:54:47.144881 INFO: Using score_cutoff 21.00392871494293 (fac=0.99, q=1)
2 days, 8:54:47.145219 INFO: Updating optimization_manager: fwhm_rt             : 2.842787265777588 -> 2.718057632446289
2 days, 8:54:47.145308 INFO: Updating optimization_manager: fwhm_mobility       : 0.005958479829132557 -> 0.004760817624628544
2 days, 8:54:47.145378 INFO: Updating optimization_manager: score_cutoff        : 29.169572483825682 -> 21.00392871494293
2 days, 8:54:47.145440 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:54:47.193957 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:54:47.451206 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:54:47.508303 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:54:47.984526 INFO: === checking if optimization conditions were reached ===
2 days, 8:54:47.984826 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 8:54:47.986895 INFO: Updating optimization_manager: mobility_error      : 0.042401155517698866 -> 0.03992889543543356
2 days, 8:54:47.987033 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0399.
2 days, 8:54:47.987107 INFO: ==============================================
2 days, 8:54:47.987180 INFO: Starting optimization step 2.
2 days, 8:54:47.987243 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 8:54:47.987308 INFO: Using python extraction backend
2 days, 8:54:47.987412 PROGRESS: Extracting batch of 407917 precursors
2 days, 8:54:47.987479 INFO: === Search parameters used ===
2 days, 8:54:47.987543 INFO: rt_error       : 143.00877364175335
2 days, 8:54:47.987590 INFO: mobility_error : 0.03992889543543356
2 days, 8:54:47.987635 INFO: num_candidates : 3
2 days, 8:54:47.987679 INFO: ms1_error      : 15.0
2 days, 8:54:47.987721 INFO: ms2_error      : 15.0
2 days, 8:54:47.987763 INFO: fwhm_rt        : 2.718057632446289
2 days, 8:54:47.987806 INFO: quant_window   : 3
2 days, 8:54:47.987866 INFO: ==============================================
2 days, 8:54:48.086539 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:54:48.086690 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:54:48.086735 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
2 days, 8:54:48.086758 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.58
2 days, 8:54:48.087577 INFO: Starting candidate selection
2 days, 8:55:47.819009 INFO: Starting candidate scoring
2 days, 8:55:58.337854 INFO: Finished candidate processing
2 days, 8:55:58.338057 INFO: Collecting candidate features
2 days, 8:55:59.878236 WARNING: intensity_correlation has 3890 NaNs ( 0.48 % out of 809459)
2 days, 8:55:59.879199 WARNING: height_correlation has 443 NaNs ( 0.05 % out of 809459)
2 days, 8:55:59.907954 INFO: Collecting fragment features
2 days, 8:56:00.300569 INFO: Finished candidate scoring
2 days, 8:56:00.852365 INFO: performing precursor FDR with 47 features
2 days, 8:56:00.852515 INFO: Decoy channel: -1
2 days, 8:56:00.852552 INFO: competitive: True
2 days, 8:56:01.042617 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:56:01.163136 WARNING: dropped 2047 target PSMs due to missing features
2 days, 8:56:01.163313 WARNING: dropped 2064 decoy PSMs due to missing features
2 days, 8:56:01.425940 INFO: Estimating optimal hyperparameters - samples: 644,278, batch_size: 2,638, learning_rate: 8.03e-04
2 days, 8:56:01.427520 INFO: Using random state 104437 for train-test-split
2 days, 8:56:17.966585 INFO: Test AUC: 0.557
2 days, 8:56:17.966755 INFO: Train AUC: 0.573
2 days, 8:56:17.966791 INFO: AUC difference: 2.65%
2 days, 8:56:18.471026 INFO: Resetting torch num_threads to 80
2 days, 8:56:18.486472 PROGRESS: === Extracted 809459 precursors and 4383265 fragments ===
2 days, 8:56:18.487308 INFO: === FDR correction performed with classifier version 20 ===
2 days, 8:56:18.515175 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:56:18.515513 PROGRESS: Total precursors accumulated: 166,523
2 days, 8:56:18.515584 PROGRESS: Target precursors: 95,749 (57.50%)
2 days, 8:56:18.515643 PROGRESS: Decoy precursors: 70,774 (42.50%)
2 days, 8:56:18.515730 PROGRESS: 
2 days, 8:56:18.515782 PROGRESS: Precursor Summary:
2 days, 8:56:18.518400 PROGRESS: Channel   0:	 0.050 FDR:   463; 0.010 FDR:   256; 0.001 FDR:   166
2 days, 8:56:18.518507 PROGRESS: 
2 days, 8:56:18.518572 PROGRESS: Protein Summary:
2 days, 8:56:18.520670 PROGRESS: Channel   0:	 0.050 FDR:   398; 0.010 FDR:   212; 0.001 FDR:   139
2 days, 8:56:18.520769 PROGRESS: =========================================================================
2 days, 8:56:18.527194 INFO: Target number of precursors reached.
2 days, 8:56:19.005617 INFO: fragments_df: keeping 3883 of 4383265 [sum(precursor_idx_mask)=6691 sum(mass_error_mask)=4383147 stop_rank=3883
2 days, 8:56:19.929125 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:56:20.063298 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:56:20.196947 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:56:20.331914 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:56:20.865627 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 8:56:20.866123 INFO: Using score_cutoff 23.46954561138153 (fac=0.99, q=1)
2 days, 8:56:20.866458 INFO: Updating optimization_manager: fwhm_rt             : 2.718057632446289 -> 2.820718288421631
2 days, 8:56:20.866543 INFO: Updating optimization_manager: fwhm_mobility       : 0.004760817624628544 -> 0.005759671330451965
2 days, 8:56:20.866603 INFO: Updating optimization_manager: score_cutoff        : 21.00392871494293 -> 23.46954561138153
2 days, 8:56:20.866665 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:56:20.918963 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:56:21.178988 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:56:21.241345 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:56:21.736840 INFO: === checking if optimization conditions were reached ===
2 days, 8:56:21.737146 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 8:56:21.739345 INFO: Updating optimization_manager: mobility_error      : 0.03992889543543356 -> 0.03770004422350258
2 days, 8:56:21.739520 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0377.
2 days, 8:56:21.739599 INFO: ==============================================
2 days, 8:56:21.739681 INFO: Starting optimization step 3.
2 days, 8:56:21.739747 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 8:56:21.739812 INFO: Using python extraction backend
2 days, 8:56:21.739919 PROGRESS: Extracting batch of 407917 precursors
2 days, 8:56:21.740005 INFO: === Search parameters used ===
2 days, 8:56:21.740064 INFO: rt_error       : 143.00877364175335
2 days, 8:56:21.740114 INFO: mobility_error : 0.03770004422350258
2 days, 8:56:21.740165 INFO: num_candidates : 3
2 days, 8:56:21.740213 INFO: ms1_error      : 15.0
2 days, 8:56:21.740263 INFO: ms2_error      : 15.0
2 days, 8:56:21.740310 INFO: fwhm_rt        : 2.820718288421631
2 days, 8:56:21.740359 INFO: quant_window   : 3
2 days, 8:56:21.740407 INFO: ==============================================
2 days, 8:56:21.839803 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:56:21.839961 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:56:21.840008 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
2 days, 8:56:21.840034 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.12
2 days, 8:56:21.840814 INFO: Starting candidate selection
2 days, 8:57:17.187931 INFO: Starting candidate scoring
2 days, 8:57:27.320242 INFO: Finished candidate processing
2 days, 8:57:27.320403 INFO: Collecting candidate features
2 days, 8:57:28.637524 WARNING: intensity_correlation has 3787 NaNs ( 0.47 % out of 811970)
2 days, 8:57:28.638476 WARNING: height_correlation has 402 NaNs ( 0.05 % out of 811970)
2 days, 8:57:28.667287 INFO: Collecting fragment features
2 days, 8:57:29.052817 INFO: Finished candidate scoring
2 days, 8:57:29.628282 INFO: performing precursor FDR with 47 features
2 days, 8:57:29.628431 INFO: Decoy channel: -1
2 days, 8:57:29.628459 INFO: competitive: True
2 days, 8:57:29.816007 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:57:29.934284 WARNING: dropped 2025 target PSMs due to missing features
2 days, 8:57:29.934449 WARNING: dropped 1977 decoy PSMs due to missing features
2 days, 8:57:30.193689 INFO: Estimating optimal hyperparameters - samples: 646,374, batch_size: 2,647, learning_rate: 8.04e-04
2 days, 8:57:30.194980 INFO: Using random state 104437 for train-test-split
2 days, 8:57:46.549427 INFO: Test AUC: 0.555
2 days, 8:57:46.549594 INFO: Train AUC: 0.574
2 days, 8:57:46.549632 INFO: AUC difference: 3.39%
2 days, 8:57:47.051249 INFO: Resetting torch num_threads to 80
2 days, 8:57:47.067119 PROGRESS: === Extracted 811970 precursors and 4419870 fragments ===
2 days, 8:57:47.068015 INFO: === FDR correction performed with classifier version 20 ===
2 days, 8:57:47.095650 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:57:47.095943 PROGRESS: Total precursors accumulated: 166,029
2 days, 8:57:47.096026 PROGRESS: Target precursors: 96,424 (58.08%)
2 days, 8:57:47.096097 PROGRESS: Decoy precursors: 69,605 (41.92%)
2 days, 8:57:47.096191 PROGRESS: 
2 days, 8:57:47.096259 PROGRESS: Precursor Summary:
2 days, 8:57:47.098843 PROGRESS: Channel   0:	 0.050 FDR:   487; 0.010 FDR:   348; 0.001 FDR:   109
2 days, 8:57:47.098958 PROGRESS: 
2 days, 8:57:47.099027 PROGRESS: Protein Summary:
2 days, 8:57:47.101162 PROGRESS: Channel   0:	 0.050 FDR:   415; 0.010 FDR:   293; 0.001 FDR:    97
2 days, 8:57:47.101271 PROGRESS: =========================================================================
2 days, 8:57:47.105841 INFO: Target number of precursors reached.
2 days, 8:57:47.589325 INFO: fragments_df: keeping 4668 of 4419870 [sum(precursor_idx_mask)=8634 sum(mass_error_mask)=4419742 stop_rank=4668
2 days, 8:57:48.177880 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:57:51.938726 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:57:52.085718 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:57:52.229836 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:57:52.895273 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 8:57:52.895770 INFO: Using score_cutoff 21.500218973350524 (fac=0.99, q=1)
2 days, 8:57:52.896104 INFO: Updating optimization_manager: fwhm_rt             : 2.820718288421631 -> 2.8215103149414062
2 days, 8:57:52.896192 INFO: Updating optimization_manager: fwhm_mobility       : 0.005759671330451965 -> 0.0049444157630205154
2 days, 8:57:52.896255 INFO: Updating optimization_manager: score_cutoff        : 23.46954561138153 -> 21.500218973350524
2 days, 8:57:52.896317 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:57:52.948157 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:57:53.203758 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:57:53.263179 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:57:53.766835 INFO: === checking if optimization conditions were reached ===
2 days, 8:57:53.767158 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
2 days, 8:57:53.769358 INFO: Updating optimization_manager: mobility_error      : 0.03770004422350258 -> 0.036681317139044246
2 days, 8:57:53.769520 PROGRESS: ❌ mobility_error : optimization incomplete after 4 search(es). Will search with parameter 0.0367.
2 days, 8:57:53.769598 INFO: ==============================================
2 days, 8:57:53.769683 INFO: Starting optimization step 4.
2 days, 8:57:53.769753 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 8:57:53.769820 INFO: Using python extraction backend
2 days, 8:57:53.769982 PROGRESS: Extracting batch of 407917 precursors
2 days, 8:57:53.770071 INFO: === Search parameters used ===
2 days, 8:57:53.770129 INFO: rt_error       : 143.00877364175335
2 days, 8:57:53.770178 INFO: mobility_error : 0.036681317139044246
2 days, 8:57:53.770224 INFO: num_candidates : 3
2 days, 8:57:53.770270 INFO: ms1_error      : 15.0
2 days, 8:57:53.770315 INFO: ms2_error      : 15.0
2 days, 8:57:53.770362 INFO: fwhm_rt        : 2.8215103149414062
2 days, 8:57:53.770407 INFO: quant_window   : 3
2 days, 8:57:53.770451 INFO: ==============================================
2 days, 8:57:53.869487 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:57:53.869642 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:57:53.869687 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
2 days, 8:57:53.869712 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.68
2 days, 8:57:53.870867 INFO: Starting candidate selection
2 days, 8:58:46.189406 INFO: Starting candidate scoring
2 days, 8:58:56.724945 INFO: Finished candidate processing
2 days, 8:58:56.725141 INFO: Collecting candidate features
2 days, 8:58:59.258998 WARNING: intensity_correlation has 3987 NaNs ( 0.50 % out of 794544)
2 days, 8:58:59.259920 WARNING: height_correlation has 433 NaNs ( 0.05 % out of 794544)
2 days, 8:58:59.290152 INFO: Collecting fragment features
2 days, 8:58:59.788356 INFO: Finished candidate scoring
2 days, 8:59:00.536602 INFO: performing precursor FDR with 47 features
2 days, 8:59:00.536752 INFO: Decoy channel: -1
2 days, 8:59:00.536784 INFO: competitive: True
2 days, 8:59:00.737429 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 8:59:00.857670 WARNING: dropped 2129 target PSMs due to missing features
2 days, 8:59:00.857840 WARNING: dropped 2071 decoy PSMs due to missing features
2 days, 8:59:01.392958 INFO: Estimating optimal hyperparameters - samples: 632,275, batch_size: 2,589, learning_rate: 7.95e-04
2 days, 8:59:01.394377 INFO: Using random state 104437 for train-test-split
2 days, 8:59:17.725198 INFO: Test AUC: 0.556
2 days, 8:59:17.725373 INFO: Train AUC: 0.574
2 days, 8:59:17.725409 INFO: AUC difference: 3.06%
2 days, 8:59:18.225647 INFO: Resetting torch num_threads to 80
2 days, 8:59:18.241115 PROGRESS: === Extracted 794544 precursors and 4266534 fragments ===
2 days, 8:59:18.241995 INFO: === FDR correction performed with classifier version 20 ===
2 days, 8:59:18.268624 PROGRESS: ============================= Precursor FDR =============================
2 days, 8:59:18.268882 PROGRESS: Total precursors accumulated: 164,292
2 days, 8:59:18.268954 PROGRESS: Target precursors: 95,400 (58.07%)
2 days, 8:59:18.269013 PROGRESS: Decoy precursors: 68,892 (41.93%)
2 days, 8:59:18.269086 PROGRESS: 
2 days, 8:59:18.269141 PROGRESS: Precursor Summary:
2 days, 8:59:18.271647 PROGRESS: Channel   0:	 0.050 FDR:   423; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 8:59:18.271757 PROGRESS: 
2 days, 8:59:18.271820 PROGRESS: Protein Summary:
2 days, 8:59:18.273843 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 8:59:18.273957 PROGRESS: =========================================================================
2 days, 8:59:18.280315 INFO: Target number of precursors not reached yet.
2 days, 8:59:19.206741 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 8:59:19.261843 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 8:59:19.522129 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 8:59:19.582972 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 8:59:20.082350 INFO: === skipping optimization until target number of precursors are found ===
2 days, 8:59:20.082672 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 8:59:20.082788 INFO: Starting optimization step 5.
2 days, 8:59:20.082865 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 8:59:20.082942 INFO: Using python extraction backend
2 days, 8:59:20.083059 PROGRESS: Extracting batch of 408390 precursors
2 days, 8:59:20.083160 INFO: === Search parameters used ===
2 days, 8:59:20.083214 INFO: rt_error       : 143.00877364175335
2 days, 8:59:20.083268 INFO: mobility_error : 0.036681317139044246
2 days, 8:59:20.083318 INFO: num_candidates : 3
2 days, 8:59:20.083364 INFO: ms1_error      : 15.0
2 days, 8:59:20.083408 INFO: ms2_error      : 15.0
2 days, 8:59:20.083451 INFO: fwhm_rt        : 2.8215103149414062
2 days, 8:59:20.083504 INFO: quant_window   : 3
2 days, 8:59:20.083548 INFO: ==============================================
2 days, 8:59:20.184038 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 8:59:20.184201 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 8:59:20.184245 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
2 days, 8:59:20.184269 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.68
2 days, 8:59:20.185428 INFO: Starting candidate selection
2 days, 9:00:11.346981 INFO: Starting candidate scoring
2 days, 9:00:21.952849 INFO: Finished candidate processing
2 days, 9:00:21.953048 INFO: Collecting candidate features
2 days, 9:00:23.929519 WARNING: intensity_correlation has 4047 NaNs ( 0.51 % out of 794101)
2 days, 9:00:23.930450 WARNING: height_correlation has 468 NaNs ( 0.06 % out of 794101)
2 days, 9:00:23.959021 INFO: Collecting fragment features
2 days, 9:00:24.423315 INFO: Finished candidate scoring
2 days, 9:00:25.503456 INFO: performing precursor FDR with 47 features
2 days, 9:00:25.503619 INFO: Decoy channel: -1
2 days, 9:00:25.503654 INFO: competitive: True
2 days, 9:00:26.117736 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:00:26.339641 WARNING: dropped 4235 target PSMs due to missing features
2 days, 9:00:26.339802 WARNING: dropped 4225 decoy PSMs due to missing features
2 days, 9:00:26.994564 INFO: Estimating optimal hyperparameters - samples: 1,264,148, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 9:00:26.996793 INFO: Using random state 104437 for train-test-split
2 days, 9:00:58.095729 INFO: Test AUC: 0.558
2 days, 9:00:58.095909 INFO: Train AUC: 0.570
2 days, 9:00:58.095951 INFO: AUC difference: 2.00%
2 days, 9:00:58.861051 INFO: Resetting torch num_threads to 80
2 days, 9:00:59.044940 PROGRESS: === Extracted 1588645 precursors and 8528637 fragments ===
2 days, 9:00:59.046017 INFO: === FDR correction performed with classifier version 20 ===
2 days, 9:00:59.101551 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:00:59.101921 PROGRESS: Total precursors accumulated: 328,258
2 days, 9:00:59.102008 PROGRESS: Target precursors: 188,594 (57.45%)
2 days, 9:00:59.102069 PROGRESS: Decoy precursors: 139,664 (42.55%)
2 days, 9:00:59.102122 PROGRESS: 
2 days, 9:00:59.102173 PROGRESS: Precursor Summary:
2 days, 9:00:59.105889 PROGRESS: Channel   0:	 0.050 FDR:   666; 0.010 FDR:   378; 0.001 FDR:    82
2 days, 9:00:59.106044 PROGRESS: 
2 days, 9:00:59.106111 PROGRESS: Protein Summary:
2 days, 9:00:59.109223 PROGRESS: Channel   0:	 0.050 FDR:   517; 0.010 FDR:   284; 0.001 FDR:    72
2 days, 9:00:59.109333 PROGRESS: =========================================================================
2 days, 9:00:59.115670 INFO: Target number of precursors reached.
2 days, 9:01:00.095680 INFO: fragments_df: keeping 5000 of 8528637 [sum(precursor_idx_mask)=10142 sum(mass_error_mask)=8528379 stop_rank=5000
2 days, 9:01:01.430849 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 9:01:01.607956 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 9:01:01.755950 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 9:01:01.901419 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 9:01:02.625557 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 9:01:02.626071 INFO: Using score_cutoff 24.167300873565676 (fac=0.99, q=1)
2 days, 9:01:02.626451 INFO: Updating optimization_manager: fwhm_rt             : 2.8215103149414062 -> 2.813343048095703
2 days, 9:01:02.626554 INFO: Updating optimization_manager: fwhm_mobility       : 0.0049444157630205154 -> 0.005871294531971216
2 days, 9:01:02.626642 INFO: Updating optimization_manager: score_cutoff        : 21.500218973350524 -> 24.167300873565676
2 days, 9:01:02.626724 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 9:01:02.731738 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 9:01:03.252874 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 9:01:03.359443 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 9:01:04.357406 INFO: === checking if optimization conditions were reached ===
2 days, 9:01:04.357715 PROGRESS: === Optimization of mobility_error has been performed 5 time(s); minimum number is 2 ===
2 days, 9:01:04.358792 INFO: Updating optimization_manager: mobility_error      : 0.036681317139044246 -> 0.042401155517698866
2 days, 9:01:04.358959 INFO: Updating optimization_manager: classifier_version  : 20 -> 23
2 days, 9:01:04.359088 INFO: Updating optimization_manager: score_cutoff        : 24.167300873565676 -> 21.00392871494293
2 days, 9:01:04.359188 INFO: Updating optimization_manager: fwhm_rt             : 2.813343048095703 -> 2.718057632446289
2 days, 9:01:04.359280 INFO: Updating optimization_manager: fwhm_mobility       : 0.005871294531971216 -> 0.004760817624628544
2 days, 9:01:04.359371 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0424 found after 5 searches.
2 days, 9:01:04.359440 INFO: ==============================================
2 days, 9:01:04.359513 PROGRESS: Optimization finished for mobility_error.
2 days, 9:01:04.943590 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 9:01:04.996333 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 9:01:05.254483 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 9:01:05.311831 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 9:01:05.809175 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 9:01:05.809469 PROGRESS: ==============================================
2 days, 9:01:05.809545 PROGRESS: ms2_error      : 15.0000
2 days, 9:01:05.809608 PROGRESS: ms1_error      : 15.0000
2 days, 9:01:05.809664 PROGRESS: rt_error       : 143.0088
2 days, 9:01:05.809717 PROGRESS: mobility_error : 0.0424
2 days, 9:01:05.809764 PROGRESS: ==============================================
2 days, 9:01:05.820013 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 9:01:07.350441 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 9:01:14.948893 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 9:01:16.446427 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 9:01:31.503728 INFO: Using python extraction backend
2 days, 9:01:31.504199 PROGRESS: Extracting batch of 12210649 precursors
2 days, 9:01:31.504298 INFO: === Search parameters used ===
2 days, 9:01:31.504361 INFO: rt_error       : 143.00877364175335
2 days, 9:01:31.504417 INFO: mobility_error : 0.042401155517698866
2 days, 9:01:31.504469 INFO: num_candidates : 3
2 days, 9:01:31.504519 INFO: ms1_error      : 15.0
2 days, 9:01:31.504565 INFO: ms2_error      : 15.0
2 days, 9:01:31.504613 INFO: fwhm_rt        : 2.718057632446289
2 days, 9:01:31.504658 INFO: quant_window   : 3
2 days, 9:01:31.504704 INFO: ==============================================
2 days, 9:01:33.514237 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:01:33.514401 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:01:33.514447 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
2 days, 9:01:33.514475 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.58
2 days, 9:01:33.515484 INFO: Starting candidate selection
2 days, 9:31:04.396912 INFO: Removed 23265211 precursors with score below cutoff 21.00392871494293
2 days, 9:31:07.595436 INFO: Starting candidate scoring
2 days, 9:32:38.882398 INFO: Finished candidate processing
2 days, 9:32:38.882672 INFO: Collecting candidate features
2 days, 9:32:52.583033 WARNING: intensity_correlation has 8203 NaNs ( 0.11 % out of 7436784)
2 days, 9:32:52.589821 WARNING: height_correlation has 397 NaNs ( 0.01 % out of 7436784)
2 days, 9:32:52.841376 INFO: Collecting fragment features
2 days, 9:32:57.886706 INFO: Finished candidate scoring
2 days, 9:33:02.205144 INFO: === Performing FDR correction with classifier version 23 ===
2 days, 9:33:02.206660 INFO: performing precursor FDR with 47 features
2 days, 9:33:02.206714 INFO: Decoy channel: -1
2 days, 9:33:02.206754 INFO: competitive: True
2 days, 9:33:03.932305 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:33:04.888928 WARNING: dropped 4448 target PSMs due to missing features
2 days, 9:33:04.889108 WARNING: dropped 4010 decoy PSMs due to missing features
2 days, 9:33:07.896671 INFO: Estimating optimal hyperparameters - samples: 5,942,660, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 9:33:07.931042 INFO: Using random state 186798 for train-test-split
2 days, 9:35:35.553533 INFO: Test AUC: 0.559
2 days, 9:35:35.553738 INFO: Train AUC: 0.563
2 days, 9:35:35.553776 INFO: AUC difference: 0.59%
2 days, 9:35:37.971251 INFO: Resetting torch num_threads to 80
2 days, 9:35:38.123460 INFO: Removing fragments below FDR threshold
2 days, 9:35:38.523587 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:35:38.523886 PROGRESS: Total precursors accumulated: 8,910
2 days, 9:35:38.523957 PROGRESS: Target precursors: 8,822 (99.01%)
2 days, 9:35:38.524016 PROGRESS: Decoy precursors: 88 (0.99%)
2 days, 9:35:38.524069 PROGRESS: 
2 days, 9:35:38.524121 PROGRESS: Precursor Summary:
2 days, 9:35:38.527575 PROGRESS: Channel   0:	 0.050 FDR: 8,822; 0.010 FDR: 8,822; 0.001 FDR: 4,845
2 days, 9:35:38.527695 PROGRESS: 
2 days, 9:35:38.527762 PROGRESS: Protein Summary:
2 days, 9:35:38.531954 PROGRESS: Channel   0:	 0.050 FDR: 2,143; 0.010 FDR: 2,143; 0.001 FDR: 1,248
2 days, 9:35:38.532066 PROGRESS: =========================================================================
2 days, 9:35:38.801094 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R4/psm.parquet
2 days, 9:35:38.860830 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R4/frag.parquet
2 days, 9:35:38.897824 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R4
2 days, 9:35:39.367685 PROGRESS: Loading raw file 11/12: B9_G_DIA_nLC_tTOF_R5 
2 days, 9:35:39.367855 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
2 days, 9:35:39.367939 INFO: Creating folder plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R5/figures
2 days, 9:35:39.368131 INFO: Initializing TimingManager
2 days, 9:35:39.368815 INFO: Initializing RawFileManager
2 days, 9:35:39.368922 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:39.368986 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:39.369028 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:39.505954 INFO: Reading 22,623 frames with 399,194,214 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:44.777264 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d...
2 days, 9:35:44.790124 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:44.792759 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:44.793229 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:44.794031 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:44.796344 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:44.810099 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:44.810414 INFO: Indexing quadrupole dimension
2 days, 9:35:44.966103 INFO: Transposing detector events
2 days, 9:35:46.555712 INFO: Finished transposing data
2 days, 9:35:46.555908 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 9:35:46.556493 INFO: RT (min)            : 0.0 - 40.0
2 days, 9:35:46.556595 INFO: RT duration (sec)   : 2400.0
2 days, 9:35:46.556653 INFO: RT duration (min)   : 40.0
2 days, 9:35:46.556700 INFO: Cycle len (scans)   : 12
2 days, 9:35:46.556747 INFO: Cycle len (sec)     : 1.27
2 days, 9:35:46.556792 INFO: Number of cycles    : 1885
2 days, 9:35:46.556838 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 9:35:46.556892 INFO: Creating DIA data object took: 7.187974214553833
2 days, 9:35:48.634901 INFO: Initializing CalibrationManager
2 days, 9:35:48.635235 INFO: Setting up calibration estimators ..
2 days, 9:35:48.635309 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 9:35:48.635397 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 9:35:48.635472 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 9:35:48.635533 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 9:35:48.635601 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 9:35:48.635665 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 9:35:48.635717 INFO: Done setting up calibration estimators.
2 days, 9:35:48.635839 INFO: Initializing OptimizationManager
2 days, 9:35:48.635935 INFO: initial parameter: ms1_error = 30
2 days, 9:35:48.635984 INFO: initial parameter: ms2_error = 30
2 days, 9:35:48.636032 INFO: initial parameter: rt_error = 1199.9910355
2 days, 9:35:48.636077 INFO: initial parameter: mobility_error = 0.1
2 days, 9:35:48.636121 INFO: initial parameter: num_candidates = 1
2 days, 9:35:48.636165 INFO: initial parameter: fwhm_rt = 5
2 days, 9:35:48.636208 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 9:35:48.636250 INFO: initial parameter: score_cutoff = 0
2 days, 9:35:48.636293 INFO: initial parameter: classifier_version = -1
2 days, 9:35:48.636368 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R5
2 days, 9:35:48.636537 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 9:35:48.636571 INFO: Initializing FDRManager
2 days, 9:35:48.636611 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 9:35:50.575534 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
2 days, 9:35:51.656692 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 9:35:51.657159 INFO: Updating optimization_manager: rt_error            : 1199.9910355 -> 1199.9910355
2 days, 9:35:51.657305 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 9:35:51.657537 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 9:35:51.657655 PROGRESS: Starting initial search for precursors.
2 days, 9:35:51.657773 INFO: Starting optimization step 0.
2 days, 9:35:51.657877 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 9:35:51.657998 INFO: Using python extraction backend
2 days, 9:35:51.658158 PROGRESS: Extracting batch of 395 precursors
2 days, 9:35:51.658249 INFO: === Search parameters used ===
2 days, 9:35:51.658325 INFO: rt_error       : 1199.9910355
2 days, 9:35:51.658394 INFO: mobility_error : 0.1
2 days, 9:35:51.658459 INFO: num_candidates : 1
2 days, 9:35:51.658520 INFO: ms1_error      : 30
2 days, 9:35:51.658581 INFO: ms2_error      : 30
2 days, 9:35:51.658641 INFO: fwhm_rt        : 5
2 days, 9:35:51.658700 INFO: quant_window   : 3
2 days, 9:35:51.658759 INFO: ==============================================
2 days, 9:35:51.659603 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:35:51.659654 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:35:51.659706 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:35:51.659741 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:35:51.660692 INFO: Starting candidate selection
2 days, 9:35:53.495404 INFO: Starting candidate scoring
2 days, 9:35:53.535226 INFO: Finished candidate processing
2 days, 9:35:53.535324 INFO: Collecting candidate features
2 days, 9:35:53.545295 INFO: Collecting fragment features
2 days, 9:35:53.547648 INFO: Finished candidate scoring
2 days, 9:35:53.548573 INFO: performing precursor FDR with 47 features
2 days, 9:35:53.548617 INFO: Decoy channel: -1
2 days, 9:35:53.548642 INFO: competitive: True
2 days, 9:35:53.549848 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:35:53.551588 INFO: Estimating optimal hyperparameters - samples: 274, batch_size: 128, learning_rate: 1.77e-04
2 days, 9:35:53.552380 INFO: Using random state 177313 for train-test-split
2 days, 9:35:53.572678 INFO: Test AUC: 0.439
2 days, 9:35:53.572748 INFO: Train AUC: 0.552
2 days, 9:35:53.572780 INFO: AUC difference: 20.44%
2 days, 9:35:53.572803 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 9:35:53.810169 INFO: Resetting torch num_threads to 80
2 days, 9:35:53.810662 PROGRESS: === Extracted 343 precursors and 2839 fragments ===
2 days, 9:35:53.811110 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:35:53.811722 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:35:53.811821 PROGRESS: Total precursors accumulated: 173
2 days, 9:35:53.811886 PROGRESS: Target precursors: 96 (55.49%)
2 days, 9:35:53.811942 PROGRESS: Decoy precursors: 77 (44.51%)
2 days, 9:35:53.811993 PROGRESS: 
2 days, 9:35:53.812045 PROGRESS: Precursor Summary:
2 days, 9:35:53.813001 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 9:35:53.813093 PROGRESS: 
2 days, 9:35:53.813152 PROGRESS: Protein Summary:
2 days, 9:35:53.814209 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 9:35:53.814308 PROGRESS: =========================================================================
2 days, 9:35:53.814419 INFO: Target number of precursors not reached yet.
2 days, 9:35:53.876064 INFO: Starting optimization step 1.
2 days, 9:35:53.876292 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 9:35:53.876374 INFO: Using python extraction backend
2 days, 9:35:53.876483 PROGRESS: Extracting batch of 796 precursors
2 days, 9:35:53.876556 INFO: === Search parameters used ===
2 days, 9:35:53.876609 INFO: rt_error       : 1199.9910355
2 days, 9:35:53.876659 INFO: mobility_error : 0.1
2 days, 9:35:53.876709 INFO: num_candidates : 1
2 days, 9:35:53.876756 INFO: ms1_error      : 30
2 days, 9:35:53.876803 INFO: ms2_error      : 30
2 days, 9:35:53.876852 INFO: fwhm_rt        : 5
2 days, 9:35:53.876898 INFO: quant_window   : 3
2 days, 9:35:53.876946 INFO: ==============================================
2 days, 9:35:53.877664 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:35:53.877715 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:35:53.877746 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:35:53.877772 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:35:53.878878 INFO: Starting candidate selection
2 days, 9:35:56.993359 INFO: Starting candidate scoring
2 days, 9:35:57.035737 INFO: Finished candidate processing
2 days, 9:35:57.035850 INFO: Collecting candidate features
2 days, 9:35:57.047118 INFO: Collecting fragment features
2 days, 9:35:57.049741 INFO: Finished candidate scoring
2 days, 9:35:57.052165 INFO: performing precursor FDR with 47 features
2 days, 9:35:57.052226 INFO: Decoy channel: -1
2 days, 9:35:57.052257 INFO: competitive: True
2 days, 9:35:57.055353 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:35:57.057242 INFO: Estimating optimal hyperparameters - samples: 848, batch_size: 128, learning_rate: 1.77e-04
2 days, 9:35:57.057342 INFO: Using random state 958563 for train-test-split
2 days, 9:35:57.118836 INFO: Test AUC: 0.551
2 days, 9:35:57.118940 INFO: Train AUC: 0.583
2 days, 9:35:57.118980 INFO: AUC difference: 5.53%
2 days, 9:35:57.119014 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 9:35:57.360856 INFO: Resetting torch num_threads to 80
2 days, 9:35:57.362245 PROGRESS: === Extracted 1061 precursors and 8997 fragments ===
2 days, 9:35:57.362703 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:35:57.363303 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:35:57.363406 PROGRESS: Total precursors accumulated: 540
2 days, 9:35:57.363479 PROGRESS: Target precursors: 328 (60.74%)
2 days, 9:35:57.363550 PROGRESS: Decoy precursors: 212 (39.26%)
2 days, 9:35:57.363612 PROGRESS: 
2 days, 9:35:57.363670 PROGRESS: Precursor Summary:
2 days, 9:35:57.364627 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 9:35:57.364724 PROGRESS: 
2 days, 9:35:57.364790 PROGRESS: Protein Summary:
2 days, 9:35:57.365829 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 9:35:57.365940 PROGRESS: =========================================================================
2 days, 9:35:57.366085 INFO: Target number of precursors not reached yet.
2 days, 9:35:57.431273 INFO: Starting optimization step 2.
2 days, 9:35:57.431534 PROGRESS: === Extracting elution groups 600 to 1400 ===
2 days, 9:35:57.431625 INFO: Using python extraction backend
2 days, 9:35:57.431745 PROGRESS: Extracting batch of 1598 precursors
2 days, 9:35:57.431827 INFO: === Search parameters used ===
2 days, 9:35:57.431889 INFO: rt_error       : 1199.9910355
2 days, 9:35:57.431946 INFO: mobility_error : 0.1
2 days, 9:35:57.432003 INFO: num_candidates : 1
2 days, 9:35:57.432058 INFO: ms1_error      : 30
2 days, 9:35:57.432112 INFO: ms2_error      : 30
2 days, 9:35:57.432165 INFO: fwhm_rt        : 5
2 days, 9:35:57.432218 INFO: quant_window   : 3
2 days, 9:35:57.432272 INFO: ==============================================
2 days, 9:35:57.433118 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:35:57.433191 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:35:57.433227 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:35:57.433256 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:35:57.434469 INFO: Starting candidate selection
2 days, 9:36:02.670248 INFO: Starting candidate scoring
2 days, 9:36:02.726660 INFO: Finished candidate processing
2 days, 9:36:02.726772 INFO: Collecting candidate features
2 days, 9:36:02.735139 WARNING: intensity_correlation has 1 NaNs ( 0.07 % out of 1429)
2 days, 9:36:02.738914 INFO: Collecting fragment features
2 days, 9:36:02.741885 INFO: Finished candidate scoring
2 days, 9:36:02.745308 INFO: performing precursor FDR with 47 features
2 days, 9:36:02.745363 INFO: Decoy channel: -1
2 days, 9:36:02.745393 INFO: competitive: True
2 days, 9:36:02.748759 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:36:02.750141 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 9:36:02.751210 INFO: Estimating optimal hyperparameters - samples: 1,991, batch_size: 128, learning_rate: 1.77e-04
2 days, 9:36:02.751314 INFO: Using random state 37404 for train-test-split
2 days, 9:36:02.905811 INFO: Test AUC: 0.584
2 days, 9:36:02.905951 INFO: Train AUC: 0.598
2 days, 9:36:02.905985 INFO: AUC difference: 2.39%
2 days, 9:36:03.148280 INFO: Resetting torch num_threads to 80
2 days, 9:36:03.150069 PROGRESS: === Extracted 2490 precursors and 21046 fragments ===
2 days, 9:36:03.150533 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:36:03.151230 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:36:03.151328 PROGRESS: Total precursors accumulated: 1,268
2 days, 9:36:03.151396 PROGRESS: Target precursors: 781 (61.59%)
2 days, 9:36:03.151452 PROGRESS: Decoy precursors: 487 (38.41%)
2 days, 9:36:03.151504 PROGRESS: 
2 days, 9:36:03.151552 PROGRESS: Precursor Summary:
2 days, 9:36:03.152514 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 9:36:03.152605 PROGRESS: 
2 days, 9:36:03.152665 PROGRESS: Protein Summary:
2 days, 9:36:03.153722 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 9:36:03.153813 PROGRESS: =========================================================================
2 days, 9:36:03.153976 INFO: Target number of precursors not reached yet.
2 days, 9:36:03.222207 INFO: Starting optimization step 3.
2 days, 9:36:03.222473 PROGRESS: === Extracting elution groups 1400 to 3000 ===
2 days, 9:36:03.222556 INFO: Using python extraction backend
2 days, 9:36:03.222668 PROGRESS: Extracting batch of 3192 precursors
2 days, 9:36:03.222744 INFO: === Search parameters used ===
2 days, 9:36:03.222799 INFO: rt_error       : 1199.9910355
2 days, 9:36:03.222848 INFO: mobility_error : 0.1
2 days, 9:36:03.222914 INFO: num_candidates : 1
2 days, 9:36:03.222963 INFO: ms1_error      : 30
2 days, 9:36:03.223008 INFO: ms2_error      : 30
2 days, 9:36:03.223052 INFO: fwhm_rt        : 5
2 days, 9:36:03.223096 INFO: quant_window   : 3
2 days, 9:36:03.223139 INFO: ==============================================
2 days, 9:36:03.224165 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:36:03.224215 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:36:03.224245 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:36:03.224268 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:36:03.225391 INFO: Starting candidate selection
2 days, 9:36:13.575601 INFO: Starting candidate scoring
2 days, 9:36:13.661241 INFO: Finished candidate processing
2 days, 9:36:13.661390 INFO: Collecting candidate features
2 days, 9:36:13.680773 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 2881)
2 days, 9:36:13.685682 INFO: Collecting fragment features
2 days, 9:36:13.690359 INFO: Finished candidate scoring
2 days, 9:36:13.698429 INFO: performing precursor FDR with 47 features
2 days, 9:36:13.698547 INFO: Decoy channel: -1
2 days, 9:36:13.698583 INFO: competitive: True
2 days, 9:36:13.705047 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:36:13.707528 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 9:36:13.709246 INFO: Estimating optimal hyperparameters - samples: 4,295, batch_size: 128, learning_rate: 1.77e-04
2 days, 9:36:13.709382 INFO: Using random state 987367 for train-test-split
2 days, 9:36:14.263580 INFO: Test AUC: 0.542
2 days, 9:36:14.263726 INFO: Train AUC: 0.595
2 days, 9:36:14.263760 INFO: AUC difference: 8.98%
2 days, 9:36:14.263786 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 9:36:14.500850 INFO: Resetting torch num_threads to 80
2 days, 9:36:14.503240 PROGRESS: === Extracted 5371 precursors and 45567 fragments ===
2 days, 9:36:14.503695 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:36:14.504573 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:36:14.504677 PROGRESS: Total precursors accumulated: 2,728
2 days, 9:36:14.504744 PROGRESS: Target precursors: 1,635 (59.93%)
2 days, 9:36:14.504809 PROGRESS: Decoy precursors: 1,093 (40.07%)
2 days, 9:36:14.504861 PROGRESS: 
2 days, 9:36:14.504912 PROGRESS: Precursor Summary:
2 days, 9:36:14.505913 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 9:36:14.506011 PROGRESS: 
2 days, 9:36:14.506070 PROGRESS: Protein Summary:
2 days, 9:36:14.507124 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 9:36:14.507220 PROGRESS: =========================================================================
2 days, 9:36:14.507386 INFO: Target number of precursors not reached yet.
2 days, 9:36:14.580571 INFO: Starting optimization step 4.
2 days, 9:36:14.580865 PROGRESS: === Extracting elution groups 3000 to 6200 ===
2 days, 9:36:14.580951 INFO: Using python extraction backend
2 days, 9:36:14.581063 PROGRESS: Extracting batch of 6381 precursors
2 days, 9:36:14.581138 INFO: === Search parameters used ===
2 days, 9:36:14.581192 INFO: rt_error       : 1199.9910355
2 days, 9:36:14.581240 INFO: mobility_error : 0.1
2 days, 9:36:14.581287 INFO: num_candidates : 1
2 days, 9:36:14.581332 INFO: ms1_error      : 30
2 days, 9:36:14.581377 INFO: ms2_error      : 30
2 days, 9:36:14.581423 INFO: fwhm_rt        : 5
2 days, 9:36:14.581469 INFO: quant_window   : 3
2 days, 9:36:14.581515 INFO: ==============================================
2 days, 9:36:14.582988 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:36:14.583041 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:36:14.583071 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:36:14.583095 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:36:14.584282 INFO: Starting candidate selection
2 days, 9:36:34.340186 INFO: Starting candidate scoring
2 days, 9:36:34.494842 INFO: Finished candidate processing
2 days, 9:36:34.494961 INFO: Collecting candidate features
2 days, 9:36:34.510657 WARNING: intensity_correlation has 1 NaNs ( 0.02 % out of 5756)
2 days, 9:36:34.514666 INFO: Collecting fragment features
2 days, 9:36:34.520658 INFO: Finished candidate scoring
2 days, 9:36:34.529703 INFO: performing precursor FDR with 47 features
2 days, 9:36:34.529807 INFO: Decoy channel: -1
2 days, 9:36:34.529835 INFO: competitive: True
2 days, 9:36:34.536996 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:36:34.539777 WARNING: dropped 1 target PSMs due to missing features
2 days, 9:36:34.539841 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 9:36:34.541812 INFO: Estimating optimal hyperparameters - samples: 8,899, batch_size: 128, learning_rate: 1.77e-04
2 days, 9:36:34.541928 INFO: Using random state 19020 for train-test-split
2 days, 9:36:35.502366 INFO: Test AUC: 0.525
2 days, 9:36:35.502495 INFO: Train AUC: 0.587
2 days, 9:36:35.502530 INFO: AUC difference: 10.60%
2 days, 9:36:35.502554 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 9:36:35.759852 INFO: Resetting torch num_threads to 80
2 days, 9:36:35.763308 PROGRESS: === Extracted 11127 precursors and 94026 fragments ===
2 days, 9:36:35.763803 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:36:35.765166 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:36:35.765271 PROGRESS: Total precursors accumulated: 5,649
2 days, 9:36:35.765342 PROGRESS: Target precursors: 3,323 (58.82%)
2 days, 9:36:35.765404 PROGRESS: Decoy precursors: 2,326 (41.18%)
2 days, 9:36:35.765461 PROGRESS: 
2 days, 9:36:35.765514 PROGRESS: Precursor Summary:
2 days, 9:36:35.766555 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2 days, 9:36:35.766671 PROGRESS: 
2 days, 9:36:35.766761 PROGRESS: Protein Summary:
2 days, 9:36:35.767907 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2 days, 9:36:35.768023 PROGRESS: =========================================================================
2 days, 9:36:35.768293 INFO: Target number of precursors not reached yet.
2 days, 9:36:36.046989 INFO: Starting optimization step 5.
2 days, 9:36:36.047330 PROGRESS: === Extracting elution groups 6200 to 12600 ===
2 days, 9:36:36.047435 INFO: Using python extraction backend
2 days, 9:36:36.047580 PROGRESS: Extracting batch of 12763 precursors
2 days, 9:36:36.047679 INFO: === Search parameters used ===
2 days, 9:36:36.047758 INFO: rt_error       : 1199.9910355
2 days, 9:36:36.047834 INFO: mobility_error : 0.1
2 days, 9:36:36.047906 INFO: num_candidates : 1
2 days, 9:36:36.047975 INFO: ms1_error      : 30
2 days, 9:36:36.048045 INFO: ms2_error      : 30
2 days, 9:36:36.048114 INFO: fwhm_rt        : 5
2 days, 9:36:36.048180 INFO: quant_window   : 3
2 days, 9:36:36.048246 INFO: ==============================================
2 days, 9:36:36.051809 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:36:36.051872 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:36:36.051917 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:36:36.051947 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:36:36.052889 INFO: Starting candidate selection
2 days, 9:37:13.330398 INFO: Starting candidate scoring
2 days, 9:37:13.578966 INFO: Finished candidate processing
2 days, 9:37:13.579284 INFO: Collecting candidate features
2 days, 9:37:13.602381 WARNING: intensity_correlation has 3 NaNs ( 0.03 % out of 11494)
2 days, 9:37:13.606580 INFO: Collecting fragment features
2 days, 9:37:13.616513 INFO: Finished candidate scoring
2 days, 9:37:13.631785 INFO: performing precursor FDR with 47 features
2 days, 9:37:13.631925 INFO: Decoy channel: -1
2 days, 9:37:13.631956 INFO: competitive: True
2 days, 9:37:13.642537 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:37:13.647222 WARNING: dropped 3 target PSMs due to missing features
2 days, 9:37:13.647319 WARNING: dropped 3 decoy PSMs due to missing features
2 days, 9:37:13.650672 INFO: Estimating optimal hyperparameters - samples: 18,092, batch_size: 128, learning_rate: 1.77e-04
2 days, 9:37:13.650815 INFO: Using random state 618556 for train-test-split
2 days, 9:37:15.525356 INFO: Test AUC: 0.539
2 days, 9:37:15.525505 INFO: Train AUC: 0.591
2 days, 9:37:15.525539 INFO: AUC difference: 8.82%
2 days, 9:37:15.525564 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 9:37:15.778518 INFO: Resetting torch num_threads to 80
2 days, 9:37:15.783703 PROGRESS: === Extracted 22621 precursors and 190805 fragments ===
2 days, 9:37:15.784299 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:37:15.786386 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:37:15.786517 PROGRESS: Total precursors accumulated: 11,482
2 days, 9:37:15.786598 PROGRESS: Target precursors: 6,783 (59.08%)
2 days, 9:37:15.786658 PROGRESS: Decoy precursors: 4,699 (40.92%)
2 days, 9:37:15.786710 PROGRESS: 
2 days, 9:37:15.786760 PROGRESS: Precursor Summary:
2 days, 9:37:15.787813 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
2 days, 9:37:15.787910 PROGRESS: 
2 days, 9:37:15.787973 PROGRESS: Protein Summary:
2 days, 9:37:15.789102 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
2 days, 9:37:15.789197 PROGRESS: =========================================================================
2 days, 9:37:15.789471 INFO: Target number of precursors not reached yet.
2 days, 9:37:16.157329 INFO: Starting optimization step 6.
2 days, 9:37:16.157633 PROGRESS: === Extracting elution groups 12600 to 25400 ===
2 days, 9:37:16.157726 INFO: Using python extraction backend
2 days, 9:37:16.157857 PROGRESS: Extracting batch of 25523 precursors
2 days, 9:37:16.157952 INFO: === Search parameters used ===
2 days, 9:37:16.158007 INFO: rt_error       : 1199.9910355
2 days, 9:37:16.158057 INFO: mobility_error : 0.1
2 days, 9:37:16.158105 INFO: num_candidates : 1
2 days, 9:37:16.158152 INFO: ms1_error      : 30
2 days, 9:37:16.158197 INFO: ms2_error      : 30
2 days, 9:37:16.158242 INFO: fwhm_rt        : 5
2 days, 9:37:16.158286 INFO: quant_window   : 3
2 days, 9:37:16.158350 INFO: ==============================================
2 days, 9:37:16.164699 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:37:16.164778 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:37:16.164810 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:37:16.164834 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:37:16.165947 INFO: Starting candidate selection
2 days, 9:38:28.519038 INFO: Starting candidate scoring
2 days, 9:38:28.944123 INFO: Finished candidate processing
2 days, 9:38:28.944267 INFO: Collecting candidate features
2 days, 9:38:28.984816 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 22963)
2 days, 9:38:28.985103 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 22963)
2 days, 9:38:28.989503 INFO: Collecting fragment features
2 days, 9:38:29.004794 INFO: Finished candidate scoring
2 days, 9:38:29.030683 INFO: performing precursor FDR with 47 features
2 days, 9:38:29.030841 INFO: Decoy channel: -1
2 days, 9:38:29.030871 INFO: competitive: True
2 days, 9:38:29.049688 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:38:29.058872 WARNING: dropped 5 target PSMs due to missing features
2 days, 9:38:29.059011 WARNING: dropped 5 decoy PSMs due to missing features
2 days, 9:38:29.065426 INFO: Estimating optimal hyperparameters - samples: 36,459, batch_size: 149, learning_rate: 1.91e-04
2 days, 9:38:29.065638 INFO: Using random state 675941 for train-test-split
2 days, 9:38:32.612575 INFO: Test AUC: 0.545
2 days, 9:38:32.612709 INFO: Train AUC: 0.602
2 days, 9:38:32.612747 INFO: AUC difference: 9.53%
2 days, 9:38:32.612773 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 9:38:32.875901 INFO: Resetting torch num_threads to 80
2 days, 9:38:32.885653 PROGRESS: === Extracted 45584 precursors and 385054 fragments ===
2 days, 9:38:32.886348 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:38:32.890704 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:38:32.890843 PROGRESS: Total precursors accumulated: 23,135
2 days, 9:38:32.890926 PROGRESS: Target precursors: 13,809 (59.69%)
2 days, 9:38:32.890986 PROGRESS: Decoy precursors: 9,326 (40.31%)
2 days, 9:38:32.891040 PROGRESS: 
2 days, 9:38:32.891091 PROGRESS: Precursor Summary:
2 days, 9:38:32.892214 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 9:38:32.892311 PROGRESS: 
2 days, 9:38:32.892374 PROGRESS: Protein Summary:
2 days, 9:38:32.893523 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 9:38:32.893619 PROGRESS: =========================================================================
2 days, 9:38:32.894027 INFO: Target number of precursors not reached yet.
2 days, 9:38:33.244906 INFO: Starting optimization step 7.
2 days, 9:38:33.245214 PROGRESS: === Extracting elution groups 25400 to 51000 ===
2 days, 9:38:33.245302 INFO: Using python extraction backend
2 days, 9:38:33.245431 PROGRESS: Extracting batch of 51061 precursors
2 days, 9:38:33.245514 INFO: === Search parameters used ===
2 days, 9:38:33.245572 INFO: rt_error       : 1199.9910355
2 days, 9:38:33.245638 INFO: mobility_error : 0.1
2 days, 9:38:33.245689 INFO: num_candidates : 1
2 days, 9:38:33.245736 INFO: ms1_error      : 30
2 days, 9:38:33.245784 INFO: ms2_error      : 30
2 days, 9:38:33.245831 INFO: fwhm_rt        : 5
2 days, 9:38:33.245889 INFO: quant_window   : 3
2 days, 9:38:33.245941 INFO: ==============================================
2 days, 9:38:33.258661 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:38:33.258801 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:38:33.258837 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:38:33.258865 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:38:33.260587 INFO: Starting candidate selection
2 days, 9:40:55.964194 INFO: Starting candidate scoring
2 days, 9:40:56.789602 INFO: Finished candidate processing
2 days, 9:40:56.789742 INFO: Collecting candidate features
2 days, 9:40:56.882319 WARNING: intensity_correlation has 11 NaNs ( 0.02 % out of 45855)
2 days, 9:40:56.888126 INFO: Collecting fragment features
2 days, 9:40:56.917094 INFO: Finished candidate scoring
2 days, 9:40:56.972252 INFO: performing precursor FDR with 47 features
2 days, 9:40:56.972416 INFO: Decoy channel: -1
2 days, 9:40:56.972447 INFO: competitive: True
2 days, 9:40:57.010568 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:40:57.029799 WARNING: dropped 11 target PSMs due to missing features
2 days, 9:40:57.029958 WARNING: dropped 10 decoy PSMs due to missing features
2 days, 9:40:57.042347 INFO: Estimating optimal hyperparameters - samples: 73,134, batch_size: 299, learning_rate: 2.70e-04
2 days, 9:40:57.042677 INFO: Using random state 270188 for train-test-split
2 days, 9:41:02.032334 INFO: Test AUC: 0.545
2 days, 9:41:02.032660 INFO: Train AUC: 0.599
2 days, 9:41:02.032698 INFO: AUC difference: 8.98%
2 days, 9:41:02.032722 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 9:41:02.315723 INFO: Resetting torch num_threads to 80
2 days, 9:41:02.334292 PROGRESS: === Extracted 91439 precursors and 772794 fragments ===
2 days, 9:41:02.335136 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:41:02.344178 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:41:02.344381 PROGRESS: Total precursors accumulated: 46,381
2 days, 9:41:02.344455 PROGRESS: Target precursors: 27,598 (59.50%)
2 days, 9:41:02.344515 PROGRESS: Decoy precursors: 18,783 (40.50%)
2 days, 9:41:02.344568 PROGRESS: 
2 days, 9:41:02.344620 PROGRESS: Precursor Summary:
2 days, 9:41:02.346037 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2 days, 9:41:02.346149 PROGRESS: 
2 days, 9:41:02.346215 PROGRESS: Protein Summary:
2 days, 9:41:02.347648 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2 days, 9:41:02.347748 PROGRESS: =========================================================================
2 days, 9:41:02.348824 INFO: Target number of precursors not reached yet.
2 days, 9:41:03.129440 INFO: Starting optimization step 8.
2 days, 9:41:03.129731 PROGRESS: === Extracting elution groups 51000 to 102200 ===
2 days, 9:41:03.129845 INFO: Using python extraction backend
2 days, 9:41:03.129998 PROGRESS: Extracting batch of 102076 precursors
2 days, 9:41:03.130081 INFO: === Search parameters used ===
2 days, 9:41:03.130139 INFO: rt_error       : 1199.9910355
2 days, 9:41:03.130191 INFO: mobility_error : 0.1
2 days, 9:41:03.130241 INFO: num_candidates : 1
2 days, 9:41:03.130289 INFO: ms1_error      : 30
2 days, 9:41:03.130338 INFO: ms2_error      : 30
2 days, 9:41:03.130385 INFO: fwhm_rt        : 5
2 days, 9:41:03.130435 INFO: quant_window   : 3
2 days, 9:41:03.130481 INFO: ==============================================
2 days, 9:41:03.156453 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:41:03.156608 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:41:03.156641 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:41:03.156668 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:41:03.158331 INFO: Starting candidate selection
2 days, 9:45:47.241908 INFO: Starting candidate scoring
2 days, 9:45:48.747499 INFO: Finished candidate processing
2 days, 9:45:48.747653 INFO: Collecting candidate features
2 days, 9:45:48.960237 WARNING: intensity_correlation has 22 NaNs ( 0.02 % out of 91744)
2 days, 9:45:48.960603 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 91744)
2 days, 9:45:48.967743 INFO: Collecting fragment features
2 days, 9:45:49.024671 INFO: Finished candidate scoring
2 days, 9:45:49.148303 INFO: performing precursor FDR with 47 features
2 days, 9:45:49.148470 INFO: Decoy channel: -1
2 days, 9:45:49.148508 INFO: competitive: True
2 days, 9:45:49.223413 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:45:49.257324 WARNING: dropped 20 target PSMs due to missing features
2 days, 9:45:49.257512 WARNING: dropped 24 decoy PSMs due to missing features
2 days, 9:45:49.306898 INFO: Estimating optimal hyperparameters - samples: 146,511, batch_size: 600, learning_rate: 3.83e-04
2 days, 9:45:49.307317 INFO: Using random state 701147 for train-test-split
2 days, 9:45:55.564234 INFO: Test AUC: 0.546
2 days, 9:45:55.564463 INFO: Train AUC: 0.588
2 days, 9:45:55.564501 INFO: AUC difference: 7.24%
2 days, 9:45:55.564526 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 9:45:55.876123 INFO: Resetting torch num_threads to 80
2 days, 9:45:55.910325 PROGRESS: === Extracted 183183 precursors and 1549346 fragments ===
2 days, 9:45:55.911212 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:45:55.928674 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:45:55.928980 PROGRESS: Total precursors accumulated: 92,925
2 days, 9:45:55.929092 PROGRESS: Target precursors: 54,595 (58.75%)
2 days, 9:45:55.929163 PROGRESS: Decoy precursors: 38,330 (41.25%)
2 days, 9:45:55.929218 PROGRESS: 
2 days, 9:45:55.929275 PROGRESS: Precursor Summary:
2 days, 9:45:55.930971 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2 days, 9:45:55.931092 PROGRESS: 
2 days, 9:45:55.931158 PROGRESS: Protein Summary:
2 days, 9:45:55.932759 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2 days, 9:45:55.932867 PROGRESS: =========================================================================
2 days, 9:45:55.936550 INFO: Target number of precursors not reached yet.
2 days, 9:45:56.844087 INFO: Starting optimization step 9.
2 days, 9:45:56.844395 PROGRESS: === Extracting elution groups 102200 to 204600 ===
2 days, 9:45:56.844504 INFO: Using python extraction backend
2 days, 9:45:56.844650 PROGRESS: Extracting batch of 204132 precursors
2 days, 9:45:56.844737 INFO: === Search parameters used ===
2 days, 9:45:56.844800 INFO: rt_error       : 1199.9910355
2 days, 9:45:56.844853 INFO: mobility_error : 0.1
2 days, 9:45:56.844904 INFO: num_candidates : 1
2 days, 9:45:56.844956 INFO: ms1_error      : 30
2 days, 9:45:56.845004 INFO: ms2_error      : 30
2 days, 9:45:56.845050 INFO: fwhm_rt        : 5
2 days, 9:45:56.845095 INFO: quant_window   : 3
2 days, 9:45:56.845140 INFO: ==============================================
2 days, 9:45:56.896869 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:45:56.897024 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:45:56.897060 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:45:56.897085 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:45:56.898192 INFO: Starting candidate selection
2 days, 9:55:18.297243 INFO: Starting candidate scoring
2 days, 9:55:21.242625 INFO: Finished candidate processing
2 days, 9:55:21.243117 INFO: Collecting candidate features
2 days, 9:55:21.913784 WARNING: intensity_correlation has 38 NaNs ( 0.02 % out of 183794)
2 days, 9:55:21.914404 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 183794)
2 days, 9:55:21.932456 INFO: Collecting fragment features
2 days, 9:55:22.100393 INFO: Finished candidate scoring
2 days, 9:55:22.364663 INFO: performing precursor FDR with 47 features
2 days, 9:55:22.364837 INFO: Decoy channel: -1
2 days, 9:55:22.364871 INFO: competitive: True
2 days, 9:55:22.530379 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 9:55:22.596463 WARNING: dropped 32 target PSMs due to missing features
2 days, 9:55:22.596641 WARNING: dropped 51 decoy PSMs due to missing features
2 days, 9:55:22.721444 INFO: Estimating optimal hyperparameters - samples: 293,515, batch_size: 1,202, learning_rate: 5.42e-04
2 days, 9:55:22.722010 INFO: Using random state 780300 for train-test-split
2 days, 9:55:32.368372 INFO: Test AUC: 0.543
2 days, 9:55:32.368543 INFO: Train AUC: 0.582
2 days, 9:55:32.368578 INFO: AUC difference: 6.65%
2 days, 9:55:32.368604 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 9:55:32.744273 INFO: Resetting torch num_threads to 80
2 days, 9:55:32.811076 PROGRESS: === Extracted 366977 precursors and 3103108 fragments ===
2 days, 9:55:32.812078 INFO: === FDR correction performed with classifier version -1 ===
2 days, 9:55:32.845059 PROGRESS: ============================= Precursor FDR =============================
2 days, 9:55:32.845413 PROGRESS: Total precursors accumulated: 186,133
2 days, 9:55:32.845485 PROGRESS: Target precursors: 108,392 (58.23%)
2 days, 9:55:32.845551 PROGRESS: Decoy precursors: 77,741 (41.77%)
2 days, 9:55:32.845602 PROGRESS: 
2 days, 9:55:32.845653 PROGRESS: Precursor Summary:
2 days, 9:55:32.847904 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
2 days, 9:55:32.848019 PROGRESS: 
2 days, 9:55:32.848082 PROGRESS: Protein Summary:
2 days, 9:55:32.850108 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
2 days, 9:55:32.850213 PROGRESS: =========================================================================
2 days, 9:55:32.854085 INFO: Target number of precursors not reached yet.
2 days, 9:55:34.006047 INFO: Starting optimization step 10.
2 days, 9:55:34.006401 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 9:55:34.006504 INFO: Using python extraction backend
2 days, 9:55:34.006641 PROGRESS: Extracting batch of 408390 precursors
2 days, 9:55:34.006724 INFO: === Search parameters used ===
2 days, 9:55:34.006782 INFO: rt_error       : 1199.9910355
2 days, 9:55:34.006833 INFO: mobility_error : 0.1
2 days, 9:55:34.006879 INFO: num_candidates : 1
2 days, 9:55:34.006927 INFO: ms1_error      : 30
2 days, 9:55:34.006972 INFO: ms2_error      : 30
2 days, 9:55:34.007016 INFO: fwhm_rt        : 5
2 days, 9:55:34.007076 INFO: quant_window   : 3
2 days, 9:55:34.007121 INFO: ==============================================
2 days, 9:55:34.102792 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 9:55:34.102938 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 9:55:34.102972 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 9:55:34.102998 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 9:55:34.104069 INFO: Starting candidate selection
2 days, 10:14:18.617328 INFO: Starting candidate scoring
2 days, 10:14:24.300672 INFO: Finished candidate processing
2 days, 10:14:24.300814 INFO: Collecting candidate features
2 days, 10:14:25.162588 WARNING: intensity_correlation has 88 NaNs ( 0.02 % out of 366515)
2 days, 10:14:25.163223 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 366515)
2 days, 10:14:25.178075 INFO: Collecting fragment features
2 days, 10:14:25.421805 INFO: Finished candidate scoring
2 days, 10:14:25.868471 INFO: performing precursor FDR with 47 features
2 days, 10:14:25.868651 INFO: Decoy channel: -1
2 days, 10:14:25.868682 INFO: competitive: True
2 days, 10:14:26.168162 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 10:14:26.298420 WARNING: dropped 79 target PSMs due to missing features
2 days, 10:14:26.298920 WARNING: dropped 97 decoy PSMs due to missing features
2 days, 10:14:26.599786 INFO: Estimating optimal hyperparameters - samples: 586,652, batch_size: 2,402, learning_rate: 7.66e-04
2 days, 10:14:26.600840 INFO: Using random state 204557 for train-test-split
2 days, 10:14:42.217122 INFO: Test AUC: 0.543
2 days, 10:14:42.217300 INFO: Train AUC: 0.564
2 days, 10:14:42.217338 INFO: AUC difference: 3.70%
2 days, 10:14:42.709001 INFO: Resetting torch num_threads to 80
2 days, 10:14:42.823157 PROGRESS: === Extracted 733492 precursors and 6201953 fragments ===
2 days, 10:14:42.824435 INFO: === FDR correction performed with classifier version -1 ===
2 days, 10:14:42.884856 PROGRESS: ============================= Precursor FDR =============================
2 days, 10:14:42.885203 PROGRESS: Total precursors accumulated: 372,059
2 days, 10:14:42.885283 PROGRESS: Target precursors: 212,153 (57.02%)
2 days, 10:14:42.885345 PROGRESS: Decoy precursors: 159,906 (42.98%)
2 days, 10:14:42.885397 PROGRESS: 
2 days, 10:14:42.885469 PROGRESS: Precursor Summary:
2 days, 10:14:42.889054 PROGRESS: Channel   0:	 0.050 FDR:   104; 0.010 FDR:     2; 0.001 FDR:     2
2 days, 10:14:42.889202 PROGRESS: 
2 days, 10:14:42.889267 PROGRESS: Protein Summary:
2 days, 10:14:42.892318 PROGRESS: Channel   0:	 0.050 FDR:    87; 0.010 FDR:     2; 0.001 FDR:     2
2 days, 10:14:42.892424 PROGRESS: =========================================================================
2 days, 10:14:42.899827 INFO: Target number of precursors not reached yet.
2 days, 10:14:44.412010 INFO: Starting optimization step 11.
2 days, 10:14:44.412361 PROGRESS: === Extracting elution groups 409400 to 819000 ===
2 days, 10:14:44.412501 INFO: Using python extraction backend
2 days, 10:14:44.412655 PROGRESS: Extracting batch of 816689 precursors
2 days, 10:14:44.412740 INFO: === Search parameters used ===
2 days, 10:14:44.412823 INFO: rt_error       : 1199.9910355
2 days, 10:14:44.412875 INFO: mobility_error : 0.1
2 days, 10:14:44.412922 INFO: num_candidates : 1
2 days, 10:14:44.412968 INFO: ms1_error      : 30
2 days, 10:14:44.413013 INFO: ms2_error      : 30
2 days, 10:14:44.413056 INFO: fwhm_rt        : 5
2 days, 10:14:44.413100 INFO: quant_window   : 3
2 days, 10:14:44.413151 INFO: ==============================================
2 days, 10:14:44.597223 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 10:14:44.597367 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 10:14:44.597402 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 10:14:44.597429 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 10:14:44.598613 INFO: Starting candidate selection
2 days, 10:51:49.245761 INFO: Starting candidate scoring
2 days, 10:52:00.953718 INFO: Finished candidate processing
2 days, 10:52:00.954203 INFO: Collecting candidate features
2 days, 10:52:02.994369 WARNING: intensity_correlation has 179 NaNs ( 0.02 % out of 734356)
2 days, 10:52:02.995276 WARNING: height_correlation has 19 NaNs ( 0.00 % out of 734356)
2 days, 10:52:03.020544 INFO: Collecting fragment features
2 days, 10:52:03.458265 INFO: Finished candidate scoring
2 days, 10:52:04.345526 INFO: performing precursor FDR with 47 features
2 days, 10:52:04.345705 INFO: Decoy channel: -1
2 days, 10:52:04.345737 INFO: competitive: True
2 days, 10:52:04.869962 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 10:52:05.101202 WARNING: dropped 172 target PSMs due to missing features
2 days, 10:52:05.101379 WARNING: dropped 194 decoy PSMs due to missing features
2 days, 10:52:05.738412 INFO: Estimating optimal hyperparameters - samples: 1,173,985, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 10:52:05.740532 INFO: Using random state 40307 for train-test-split
2 days, 10:52:36.596275 INFO: Test AUC: 0.546
2 days, 10:52:36.596471 INFO: Train AUC: 0.560
2 days, 10:52:36.596507 INFO: AUC difference: 2.41%
2 days, 10:52:37.337971 INFO: Resetting torch num_threads to 80
2 days, 10:52:37.571170 PROGRESS: === Extracted 1467848 precursors and 12411019 fragments ===
2 days, 10:52:37.572732 INFO: === FDR correction performed with classifier version -1 ===
2 days, 10:52:37.687314 PROGRESS: ============================= Precursor FDR =============================
2 days, 10:52:37.687657 PROGRESS: Total precursors accumulated: 744,461
2 days, 10:52:37.687739 PROGRESS: Target precursors: 423,751 (56.92%)
2 days, 10:52:37.687802 PROGRESS: Decoy precursors: 320,710 (43.08%)
2 days, 10:52:37.687856 PROGRESS: 
2 days, 10:52:37.687907 PROGRESS: Precursor Summary:
2 days, 10:52:37.693851 PROGRESS: Channel   0:	 0.050 FDR:   564; 0.010 FDR:   354; 0.001 FDR:     2
2 days, 10:52:37.694036 PROGRESS: 
2 days, 10:52:37.694129 PROGRESS: Protein Summary:
2 days, 10:52:37.699085 PROGRESS: Channel   0:	 0.050 FDR:   391; 0.010 FDR:   248; 0.001 FDR:     2
2 days, 10:52:37.699204 PROGRESS: =========================================================================
2 days, 10:52:37.713433 INFO: Target number of precursors reached.
2 days, 10:52:39.113708 INFO: fragments_df: keeping 3436 of 12411019 [sum(precursor_idx_mask)=3876 sum(mass_error_mask)=12410988 stop_rank=3436
2 days, 10:52:41.258499 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 10:52:41.376187 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 10:52:41.503384 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 10:52:41.627458 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 10:52:42.041481 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 10:52:42.041983 INFO: Using score_cutoff 23.695028190994265 (fac=0.99, q=1)
2 days, 10:52:42.042344 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.075864791870117
2 days, 10:52:42.042429 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008495261892676353
2 days, 10:52:42.042487 INFO: Updating optimization_manager: score_cutoff        : 0 -> 23.695028190994265
2 days, 10:52:42.042551 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 10:52:42.266980 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 10:52:43.319160 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 10:52:43.550784 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 10:52:45.523199 INFO: Updating optimization_manager: classifier_version  : -1 -> 11
2 days, 10:52:45.523538 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 10:52:45.523686 INFO: Starting optimization step 12.
2 days, 10:52:45.523760 PROGRESS: === Extracting elution groups 0 to 819000 ===
2 days, 10:52:45.523863 INFO: Using python extraction backend
2 days, 10:52:45.524013 PROGRESS: Extracting batch of 1632996 precursors
2 days, 10:52:45.524099 INFO: === Search parameters used ===
2 days, 10:52:45.524156 INFO: rt_error       : 1199.9910355
2 days, 10:52:45.524208 INFO: mobility_error : 0.1
2 days, 10:52:45.524257 INFO: num_candidates : 3
2 days, 10:52:45.524306 INFO: ms1_error      : 30
2 days, 10:52:45.524352 INFO: ms2_error      : 30
2 days, 10:52:45.524398 INFO: fwhm_rt        : 3.075864791870117
2 days, 10:52:45.524445 INFO: quant_window   : 3
2 days, 10:52:45.524491 INFO: ==============================================
2 days, 10:52:45.904790 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 10:52:45.904951 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 10:52:45.905012 INFO: FWHM in RT is 3.08 seconds, sigma is 0.51
2 days, 10:52:45.905039 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.60
2 days, 10:52:45.905918 INFO: Starting candidate selection
2 days, 12:16:07.160569 INFO: Starting candidate scoring
2 days, 12:17:10.920587 INFO: Finished candidate processing
2 days, 12:17:10.921129 INFO: Collecting candidate features
2 days, 12:17:18.721937 WARNING: intensity_correlation has 1157 NaNs ( 0.03 % out of 4215039)
2 days, 12:17:18.725967 WARNING: height_correlation has 95 NaNs ( 0.00 % out of 4215039)
2 days, 12:17:18.867612 INFO: Collecting fragment features
2 days, 12:17:21.366732 INFO: Finished candidate scoring
2 days, 12:17:24.073274 INFO: performing precursor FDR with 47 features
2 days, 12:17:24.073436 INFO: Decoy channel: -1
2 days, 12:17:24.073471 INFO: competitive: True
2 days, 12:17:24.996124 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 12:17:25.570683 WARNING: dropped 569 target PSMs due to missing features
2 days, 12:17:25.570853 WARNING: dropped 643 decoy PSMs due to missing features
2 days, 12:17:27.211576 INFO: Estimating optimal hyperparameters - samples: 3,371,061, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 12:17:27.218756 INFO: Using random state 594604 for train-test-split
2 days, 12:18:46.892387 INFO: Test AUC: 0.562
2 days, 12:18:46.892590 INFO: Train AUC: 0.568
2 days, 12:18:46.892628 INFO: AUC difference: 1.08%
2 days, 12:18:48.367730 INFO: Resetting torch num_threads to 80
2 days, 12:18:48.437391 PROGRESS: === Extracted 4215039 precursors and 34883118 fragments ===
2 days, 12:18:48.438979 INFO: === FDR correction performed with classifier version 11 ===
2 days, 12:18:48.559377 PROGRESS: ============================= Precursor FDR =============================
2 days, 12:18:48.559729 PROGRESS: Total precursors accumulated: 750,121
2 days, 12:18:48.559811 PROGRESS: Target precursors: 438,740 (58.49%)
2 days, 12:18:48.559870 PROGRESS: Decoy precursors: 311,381 (41.51%)
2 days, 12:18:48.559924 PROGRESS: 
2 days, 12:18:48.559975 PROGRESS: Precursor Summary:
2 days, 12:18:48.565707 PROGRESS: Channel   0:	 0.050 FDR:   524; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 12:18:48.565886 PROGRESS: 
2 days, 12:18:48.565955 PROGRESS: Protein Summary:
2 days, 12:18:48.570884 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 12:18:48.570993 PROGRESS: =========================================================================
2 days, 12:18:48.598222 INFO: Target number of precursors not reached yet.
2 days, 12:18:50.774893 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 12:18:50.989961 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 12:18:52.045990 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 12:18:52.256884 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 12:18:54.346023 INFO: === skipping optimization until target number of precursors are found ===
2 days, 12:18:54.346379 INFO: Starting optimization step 13.
2 days, 12:18:54.346474 PROGRESS: === Extracting elution groups 819000 to 1638200 ===
2 days, 12:18:54.346557 INFO: Using python extraction backend
2 days, 12:18:54.346683 PROGRESS: Extracting batch of 1633286 precursors
2 days, 12:18:54.346766 INFO: === Search parameters used ===
2 days, 12:18:54.346817 INFO: rt_error       : 1199.9910355
2 days, 12:18:54.346867 INFO: mobility_error : 0.1
2 days, 12:18:54.346914 INFO: num_candidates : 3
2 days, 12:18:54.346960 INFO: ms1_error      : 30
2 days, 12:18:54.347005 INFO: ms2_error      : 30
2 days, 12:18:54.347050 INFO: fwhm_rt        : 3.075864791870117
2 days, 12:18:54.347094 INFO: quant_window   : 3
2 days, 12:18:54.347138 INFO: ==============================================
2 days, 12:18:54.724439 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 12:18:54.724599 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 12:18:54.724648 INFO: FWHM in RT is 3.08 seconds, sigma is 0.51
2 days, 12:18:54.724676 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.60
2 days, 12:18:54.726147 INFO: Starting candidate selection
2 days, 13:43:42.950534 INFO: Starting candidate scoring
2 days, 13:44:46.168006 INFO: Finished candidate processing
2 days, 13:44:46.168413 INFO: Collecting candidate features
2 days, 13:44:53.855023 WARNING: intensity_correlation has 1150 NaNs ( 0.03 % out of 4214892)
2 days, 13:44:53.858903 WARNING: height_correlation has 95 NaNs ( 0.00 % out of 4214892)
2 days, 13:44:54.003722 INFO: Collecting fragment features
2 days, 13:44:56.717100 INFO: Finished candidate scoring
2 days, 13:45:00.843598 INFO: performing precursor FDR with 47 features
2 days, 13:45:00.843782 INFO: Decoy channel: -1
2 days, 13:45:00.843816 INFO: competitive: True
2 days, 13:45:03.654030 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 13:45:04.960289 WARNING: dropped 1139 target PSMs due to missing features
2 days, 13:45:04.960567 WARNING: dropped 1287 decoy PSMs due to missing features
2 days, 13:45:08.192602 INFO: Estimating optimal hyperparameters - samples: 6,742,004, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 13:45:08.207428 INFO: Using random state 594604 for train-test-split
2 days, 13:47:40.775990 INFO: Test AUC: 0.567
2 days, 13:47:40.776175 INFO: Train AUC: 0.569
2 days, 13:47:40.776214 INFO: AUC difference: 0.46%
2 days, 13:47:43.313476 INFO: Resetting torch num_threads to 80
2 days, 13:47:44.792032 PROGRESS: === Extracted 8429931 precursors and 69758067 fragments ===
2 days, 13:47:44.794266 INFO: === FDR correction performed with classifier version 11 ===
2 days, 13:47:45.061728 PROGRESS: ============================= Precursor FDR =============================
2 days, 13:47:45.062094 PROGRESS: Total precursors accumulated: 1,500,428
2 days, 13:47:45.062171 PROGRESS: Target precursors: 885,181 (59.00%)
2 days, 13:47:45.062231 PROGRESS: Decoy precursors: 615,247 (41.00%)
2 days, 13:47:45.062284 PROGRESS: 
2 days, 13:47:45.062339 PROGRESS: Precursor Summary:
2 days, 13:47:45.072207 PROGRESS: Channel   0:	 0.050 FDR: 1,568; 0.010 FDR: 1,127; 0.001 FDR:   557
2 days, 13:47:45.072397 PROGRESS: 
2 days, 13:47:45.072465 PROGRESS: Protein Summary:
2 days, 13:47:45.081636 PROGRESS: Channel   0:	 0.050 FDR:   799; 0.010 FDR:   543; 0.001 FDR:   295
2 days, 13:47:45.081808 PROGRESS: =========================================================================
2 days, 13:47:45.110051 INFO: Target number of precursors reached.
2 days, 13:47:52.766490 INFO: fragments_df: keeping 5000 of 69758067 [sum(precursor_idx_mask)=33001 sum(mass_error_mask)=69757934 stop_rank=5000
2 days, 13:47:54.526741 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 13:47:54.737149 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 13:47:54.953272 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 13:47:55.164526 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 13:47:55.886912 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 13:47:55.887398 INFO: Using score_cutoff 36.86192527999878 (fac=0.99, q=1)
2 days, 13:47:55.887775 INFO: Updating optimization_manager: fwhm_rt             : 3.075864791870117 -> 3.0309805870056152
2 days, 13:47:55.887861 INFO: Updating optimization_manager: fwhm_mobility       : 0.008495261892676353 -> 0.008078166283667088
2 days, 13:47:55.887923 INFO: Updating optimization_manager: score_cutoff        : 23.695028190994265 -> 36.86192527999878
2 days, 13:47:55.887988 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 13:47:55.990959 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 13:47:56.537053 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 13:47:56.645740 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 13:47:57.655676 INFO: === checking if optimization conditions were reached ===
2 days, 13:47:57.658192 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
2 days, 13:47:57.658363 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
2 days, 13:47:57.658443 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 13:47:57.659687 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 13:47:57.659802 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
2 days, 13:47:57.659882 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 13:47:57.659946 INFO: ==============================================
2 days, 13:47:57.660032 INFO: Starting optimization step 14.
2 days, 13:47:57.660102 PROGRESS: === Extracting elution groups 0 to 409400 ===
2 days, 13:47:57.660184 INFO: Using python extraction backend
2 days, 13:47:57.660333 PROGRESS: Extracting batch of 816307 precursors
2 days, 13:47:57.660412 INFO: === Search parameters used ===
2 days, 13:47:57.660467 INFO: rt_error       : 1199.9910355
2 days, 13:47:57.660516 INFO: mobility_error : 0.1
2 days, 13:47:57.660565 INFO: num_candidates : 3
2 days, 13:47:57.660614 INFO: ms1_error      : 15.0
2 days, 13:47:57.660662 INFO: ms2_error      : 15.0
2 days, 13:47:57.660709 INFO: fwhm_rt        : 3.0309805870056152
2 days, 13:47:57.660757 INFO: quant_window   : 3
2 days, 13:47:57.660803 INFO: ==============================================
2 days, 13:47:57.882167 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 13:47:57.882313 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 13:47:57.882374 INFO: FWHM in RT is 3.03 seconds, sigma is 0.51
2 days, 13:47:57.882429 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.38
2 days, 13:47:57.883343 INFO: Starting candidate selection
2 days, 14:25:12.346228 INFO: Starting candidate scoring
2 days, 14:25:35.766864 INFO: Finished candidate processing
2 days, 14:25:35.767313 INFO: Collecting candidate features
2 days, 14:25:39.864654 WARNING: intensity_correlation has 2085 NaNs ( 0.10 % out of 2057226)
2 days, 14:25:39.866762 WARNING: height_correlation has 108 NaNs ( 0.01 % out of 2057226)
2 days, 14:25:39.934777 INFO: Collecting fragment features
2 days, 14:25:40.970759 INFO: Finished candidate scoring
2 days, 14:25:42.113499 INFO: performing precursor FDR with 47 features
2 days, 14:25:42.113639 INFO: Decoy channel: -1
2 days, 14:25:42.113677 INFO: competitive: True
2 days, 14:25:42.584066 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 14:25:42.874422 WARNING: dropped 1041 target PSMs due to missing features
2 days, 14:25:42.874613 WARNING: dropped 1110 decoy PSMs due to missing features
2 days, 14:25:43.639996 INFO: Estimating optimal hyperparameters - samples: 1,644,060, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 14:25:43.643533 INFO: Using random state 996617 for train-test-split
2 days, 14:26:22.307332 INFO: Test AUC: 0.561
2 days, 14:26:22.307520 INFO: Train AUC: 0.570
2 days, 14:26:22.307558 INFO: AUC difference: 1.51%
2 days, 14:26:23.186908 INFO: Resetting torch num_threads to 80
2 days, 14:26:23.223028 PROGRESS: === Extracted 2057226 precursors and 14593839 fragments ===
2 days, 14:26:23.224195 INFO: === FDR correction performed with classifier version 13 ===
2 days, 14:26:23.282703 PROGRESS: ============================= Precursor FDR =============================
2 days, 14:26:23.283045 PROGRESS: Total precursors accumulated: 373,028
2 days, 14:26:23.283132 PROGRESS: Target precursors: 218,273 (58.51%)
2 days, 14:26:23.283196 PROGRESS: Decoy precursors: 154,755 (41.49%)
2 days, 14:26:23.283255 PROGRESS: 
2 days, 14:26:23.283308 PROGRESS: Precursor Summary:
2 days, 14:26:23.286916 PROGRESS: Channel   0:	 0.050 FDR:   557; 0.010 FDR:   463; 0.001 FDR:   342
2 days, 14:26:23.287060 PROGRESS: 
2 days, 14:26:23.287136 PROGRESS: Protein Summary:
2 days, 14:26:23.290370 PROGRESS: Channel   0:	 0.050 FDR:   424; 0.010 FDR:   345; 0.001 FDR:   262
2 days, 14:26:23.290479 PROGRESS: =========================================================================
2 days, 14:26:23.350078 INFO: Target number of precursors reached.
2 days, 14:26:24.911495 INFO: fragments_df: keeping 5000 of 14593839 [sum(precursor_idx_mask)=12716 sum(mass_error_mask)=14593759 stop_rank=5000
2 days, 14:26:26.120913 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 14:26:26.272866 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 14:26:26.426689 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 14:26:26.585516 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 14:26:27.303242 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 14:26:27.303735 INFO: Using score_cutoff 27.552084943771362 (fac=0.99, q=1)
2 days, 14:26:27.304106 INFO: Updating optimization_manager: fwhm_rt             : 3.0309805870056152 -> 2.8199450969696045
2 days, 14:26:27.304199 INFO: Updating optimization_manager: fwhm_mobility       : 0.008078166283667088 -> 0.006096608471125364
2 days, 14:26:27.304271 INFO: Updating optimization_manager: score_cutoff        : 36.86192527999878 -> 27.552084943771362
2 days, 14:26:27.304348 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 14:26:27.354253 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 14:26:27.617081 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 14:26:27.673721 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 14:26:28.152651 INFO: === checking if optimization conditions were reached ===
2 days, 14:26:28.155030 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
2 days, 14:26:28.155208 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
2 days, 14:26:28.155286 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 14:26:28.156415 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 14:26:28.156516 INFO: Updating optimization_manager: classifier_version  : 14 -> 14
2 days, 14:26:28.156581 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 14:26:28.156638 INFO: ==============================================
2 days, 14:26:28.156714 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 14:26:28.722717 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 14:26:28.771554 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 14:26:29.027641 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 14:26:29.084217 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 14:26:29.585302 INFO: Starting optimization step 0.
2 days, 14:26:29.585579 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 14:26:29.585684 INFO: Using python extraction backend
2 days, 14:26:29.585856 PROGRESS: Extracting batch of 407917 precursors
2 days, 14:26:29.585963 INFO: === Search parameters used ===
2 days, 14:26:29.586022 INFO: rt_error       : 1199.9910355
2 days, 14:26:29.586071 INFO: mobility_error : 0.1
2 days, 14:26:29.586119 INFO: num_candidates : 3
2 days, 14:26:29.586163 INFO: ms1_error      : 15.0
2 days, 14:26:29.586221 INFO: ms2_error      : 15.0
2 days, 14:26:29.586266 INFO: fwhm_rt        : 2.8199450969696045
2 days, 14:26:29.586312 INFO: quant_window   : 3
2 days, 14:26:29.586357 INFO: ==============================================
2 days, 14:26:29.685455 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 14:26:29.685617 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 14:26:29.685676 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
2 days, 14:26:29.685703 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.30
2 days, 14:26:29.686656 INFO: Starting candidate selection
2 days, 14:45:43.790382 INFO: Starting candidate scoring
2 days, 14:45:55.323707 INFO: Finished candidate processing
2 days, 14:45:55.323856 INFO: Collecting candidate features
2 days, 14:45:57.223980 WARNING: intensity_correlation has 1042 NaNs ( 0.10 % out of 1026945)
2 days, 14:45:57.225120 WARNING: height_correlation has 61 NaNs ( 0.01 % out of 1026945)
2 days, 14:45:57.261045 INFO: Collecting fragment features
2 days, 14:45:57.854715 INFO: Finished candidate scoring
2 days, 14:45:58.398265 INFO: performing precursor FDR with 47 features
2 days, 14:45:58.398407 INFO: Decoy channel: -1
2 days, 14:45:58.398437 INFO: competitive: True
2 days, 14:45:58.633769 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 14:45:58.781755 WARNING: dropped 518 target PSMs due to missing features
2 days, 14:45:58.781943 WARNING: dropped 558 decoy PSMs due to missing features
2 days, 14:45:59.135850 INFO: Estimating optimal hyperparameters - samples: 820,695, batch_size: 3,361, learning_rate: 9.06e-04
2 days, 14:45:59.138978 INFO: Using random state 21930 for train-test-split
2 days, 14:46:18.898745 INFO: Test AUC: 0.565
2 days, 14:46:18.898926 INFO: Train AUC: 0.582
2 days, 14:46:18.898963 INFO: AUC difference: 3.03%
2 days, 14:46:19.463810 INFO: Resetting torch num_threads to 80
2 days, 14:46:19.483484 PROGRESS: === Extracted 1026945 precursors and 7213369 fragments ===
2 days, 14:46:19.484418 INFO: === FDR correction performed with classifier version 14 ===
2 days, 14:46:19.516566 PROGRESS: ============================= Precursor FDR =============================
2 days, 14:46:19.516901 PROGRESS: Total precursors accumulated: 186,737
2 days, 14:46:19.516973 PROGRESS: Target precursors: 111,061 (59.47%)
2 days, 14:46:19.517033 PROGRESS: Decoy precursors: 75,676 (40.53%)
2 days, 14:46:19.517087 PROGRESS: 
2 days, 14:46:19.517137 PROGRESS: Precursor Summary:
2 days, 14:46:19.519502 PROGRESS: Channel   0:	 0.050 FDR:   282; 0.010 FDR:   231; 0.001 FDR:    56
2 days, 14:46:19.519624 PROGRESS: 
2 days, 14:46:19.519699 PROGRESS: Protein Summary:
2 days, 14:46:19.521891 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:   198; 0.001 FDR:    48
2 days, 14:46:19.521996 PROGRESS: =========================================================================
2 days, 14:46:19.560090 INFO: Target number of precursors reached.
2 days, 14:46:20.330430 INFO: fragments_df: keeping 3888 of 7213369 [sum(precursor_idx_mask)=6412 sum(mass_error_mask)=7213307 stop_rank=3888
2 days, 14:46:21.857758 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 14:46:22.000908 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 14:46:22.140297 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 14:46:22.270076 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 14:46:22.821601 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 14:46:22.822083 INFO: Using score_cutoff 31.231111490249635 (fac=0.99, q=1)
2 days, 14:46:22.822433 INFO: Updating optimization_manager: fwhm_rt             : 2.8199450969696045 -> 2.9151391983032227
2 days, 14:46:22.822517 INFO: Updating optimization_manager: fwhm_mobility       : 0.006096608471125364 -> 0.006167470011860132
2 days, 14:46:22.822574 INFO: Updating optimization_manager: score_cutoff        : 27.552084943771362 -> 31.231111490249635
2 days, 14:46:22.822634 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 14:46:22.874269 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 14:46:23.130824 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 14:46:23.193550 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 14:46:23.728112 INFO: === checking if optimization conditions were reached ===
2 days, 14:46:23.728435 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 14:46:23.730558 INFO: Updating optimization_manager: rt_error            : 1199.9910355 -> 707.9892221623327
2 days, 14:46:23.730705 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 707.9892.
2 days, 14:46:23.730781 INFO: ==============================================
2 days, 14:46:23.730860 INFO: Starting optimization step 1.
2 days, 14:46:23.730926 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 14:46:23.731018 INFO: Using python extraction backend
2 days, 14:46:23.731139 PROGRESS: Extracting batch of 407917 precursors
2 days, 14:46:23.731216 INFO: === Search parameters used ===
2 days, 14:46:23.731272 INFO: rt_error       : 707.9892221623327
2 days, 14:46:23.731320 INFO: mobility_error : 0.1
2 days, 14:46:23.731382 INFO: num_candidates : 3
2 days, 14:46:23.731432 INFO: ms1_error      : 15.0
2 days, 14:46:23.731478 INFO: ms2_error      : 15.0
2 days, 14:46:23.731522 INFO: fwhm_rt        : 2.9151391983032227
2 days, 14:46:23.731567 INFO: quant_window   : 3
2 days, 14:46:23.731610 INFO: ==============================================
2 days, 14:46:23.840370 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 14:46:23.840526 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 14:46:23.840583 INFO: FWHM in RT is 2.92 seconds, sigma is 0.49
2 days, 14:46:23.840609 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.34
2 days, 14:46:23.842129 INFO: Starting candidate selection
2 days, 14:58:37.751794 INFO: Starting candidate scoring
2 days, 14:58:49.589558 INFO: Finished candidate processing
2 days, 14:58:49.589862 INFO: Collecting candidate features
2 days, 14:58:51.465668 WARNING: intensity_correlation has 1262 NaNs ( 0.13 % out of 1008864)
2 days, 14:58:51.466796 WARNING: height_correlation has 74 NaNs ( 0.01 % out of 1008864)
2 days, 14:58:51.502110 INFO: Collecting fragment features
2 days, 14:58:52.047218 INFO: Finished candidate scoring
2 days, 14:58:52.765766 INFO: performing precursor FDR with 47 features
2 days, 14:58:52.765957 INFO: Decoy channel: -1
2 days, 14:58:52.765988 INFO: competitive: True
2 days, 14:58:53.022736 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 14:58:53.170288 WARNING: dropped 669 target PSMs due to missing features
2 days, 14:58:53.170479 WARNING: dropped 632 decoy PSMs due to missing features
2 days, 14:58:53.525254 INFO: Estimating optimal hyperparameters - samples: 806,050, batch_size: 3,301, learning_rate: 8.98e-04
2 days, 14:58:53.526699 INFO: Using random state 21930 for train-test-split
2 days, 14:59:12.213430 INFO: Test AUC: 0.561
2 days, 14:59:12.213586 INFO: Train AUC: 0.579
2 days, 14:59:12.213631 INFO: AUC difference: 3.04%
2 days, 14:59:12.766177 INFO: Resetting torch num_threads to 80
2 days, 14:59:12.784924 PROGRESS: === Extracted 1008864 precursors and 6955797 fragments ===
2 days, 14:59:12.785846 INFO: === FDR correction performed with classifier version 14 ===
2 days, 14:59:12.815529 PROGRESS: ============================= Precursor FDR =============================
2 days, 14:59:12.815824 PROGRESS: Total precursors accumulated: 185,300
2 days, 14:59:12.815896 PROGRESS: Target precursors: 109,193 (58.93%)
2 days, 14:59:12.815955 PROGRESS: Decoy precursors: 76,107 (41.07%)
2 days, 14:59:12.816008 PROGRESS: 
2 days, 14:59:12.816058 PROGRESS: Precursor Summary:
2 days, 14:59:12.818352 PROGRESS: Channel   0:	 0.050 FDR:   310; 0.010 FDR:   209; 0.001 FDR:   179
2 days, 14:59:12.818460 PROGRESS: 
2 days, 14:59:12.818527 PROGRESS: Protein Summary:
2 days, 14:59:12.820695 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:   178; 0.001 FDR:   150
2 days, 14:59:12.820794 PROGRESS: =========================================================================
2 days, 14:59:12.828011 INFO: Target number of precursors reached.
2 days, 14:59:13.539558 INFO: fragments_df: keeping 3636 of 6955797 [sum(precursor_idx_mask)=5907 sum(mass_error_mask)=6955715 stop_rank=3636
2 days, 14:59:14.709808 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 14:59:14.851188 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 14:59:14.983700 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 14:59:15.115138 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 14:59:15.629725 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 14:59:15.630233 INFO: Using score_cutoff 33.348301968383794 (fac=0.99, q=1)
2 days, 14:59:15.630573 INFO: Updating optimization_manager: fwhm_rt             : 2.9151391983032227 -> 2.8326642513275146
2 days, 14:59:15.630659 INFO: Updating optimization_manager: fwhm_mobility       : 0.006167470011860132 -> 0.005863726604729891
2 days, 14:59:15.630721 INFO: Updating optimization_manager: score_cutoff        : 31.231111490249635 -> 33.348301968383794
2 days, 14:59:15.630787 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 14:59:15.683064 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 14:59:15.938576 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 14:59:15.998261 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 14:59:16.475034 INFO: === checking if optimization conditions were reached ===
2 days, 14:59:16.475446 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 14:59:16.477813 INFO: Updating optimization_manager: rt_error            : 707.9892221623327 -> 332.02237800846416
2 days, 14:59:16.477977 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 332.0224.
2 days, 14:59:16.478077 INFO: ==============================================
2 days, 14:59:16.478180 INFO: Starting optimization step 2.
2 days, 14:59:16.478265 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 14:59:16.478367 INFO: Using python extraction backend
2 days, 14:59:16.478516 PROGRESS: Extracting batch of 407917 precursors
2 days, 14:59:16.478606 INFO: === Search parameters used ===
2 days, 14:59:16.478688 INFO: rt_error       : 332.02237800846416
2 days, 14:59:16.478751 INFO: mobility_error : 0.1
2 days, 14:59:16.478812 INFO: num_candidates : 3
2 days, 14:59:16.478872 INFO: ms1_error      : 15.0
2 days, 14:59:16.478931 INFO: ms2_error      : 15.0
2 days, 14:59:16.478990 INFO: fwhm_rt        : 2.8326642513275146
2 days, 14:59:16.479048 INFO: quant_window   : 3
2 days, 14:59:16.479106 INFO: ==============================================
2 days, 14:59:16.583464 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 14:59:16.583638 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 14:59:16.583709 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
2 days, 14:59:16.583744 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.18
2 days, 14:59:16.584730 INFO: Starting candidate selection
2 days, 15:05:01.250579 INFO: Starting candidate scoring
2 days, 15:05:12.964566 INFO: Finished candidate processing
2 days, 15:05:12.964737 INFO: Collecting candidate features
2 days, 15:05:14.872950 WARNING: intensity_correlation has 2093 NaNs ( 0.22 % out of 968440)
2 days, 15:05:14.874101 WARNING: height_correlation has 179 NaNs ( 0.02 % out of 968440)
2 days, 15:05:14.908118 INFO: Collecting fragment features
2 days, 15:05:15.543181 INFO: Finished candidate scoring
2 days, 15:05:16.132184 INFO: performing precursor FDR with 47 features
2 days, 15:05:16.132337 INFO: Decoy channel: -1
2 days, 15:05:16.132370 INFO: competitive: True
2 days, 15:05:16.360367 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:05:16.499320 WARNING: dropped 1051 target PSMs due to missing features
2 days, 15:05:16.499479 WARNING: dropped 1129 decoy PSMs due to missing features
2 days, 15:05:16.823280 INFO: Estimating optimal hyperparameters - samples: 773,008, batch_size: 3,166, learning_rate: 8.79e-04
2 days, 15:05:16.824961 INFO: Using random state 21930 for train-test-split
2 days, 15:05:35.362116 INFO: Test AUC: 0.556
2 days, 15:05:35.362530 INFO: Train AUC: 0.570
2 days, 15:05:35.362572 INFO: AUC difference: 2.54%
2 days, 15:05:35.905110 INFO: Resetting torch num_threads to 80
2 days, 15:05:35.923168 PROGRESS: === Extracted 968440 precursors and 6069545 fragments ===
2 days, 15:05:35.924066 INFO: === FDR correction performed with classifier version 14 ===
2 days, 15:05:35.953181 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:05:35.953484 PROGRESS: Total precursors accumulated: 184,274
2 days, 15:05:35.953556 PROGRESS: Target precursors: 106,477 (57.78%)
2 days, 15:05:35.953614 PROGRESS: Decoy precursors: 77,797 (42.22%)
2 days, 15:05:35.953672 PROGRESS: 
2 days, 15:05:35.953727 PROGRESS: Precursor Summary:
2 days, 15:05:35.956005 PROGRESS: Channel   0:	 0.050 FDR:   344; 0.010 FDR:   241; 0.001 FDR:   179
2 days, 15:05:35.956110 PROGRESS: 
2 days, 15:05:35.956172 PROGRESS: Protein Summary:
2 days, 15:05:35.958351 PROGRESS: Channel   0:	 0.050 FDR:   291; 0.010 FDR:   203; 0.001 FDR:   151
2 days, 15:05:35.958452 PROGRESS: =========================================================================
2 days, 15:05:35.966045 INFO: Target number of precursors reached.
2 days, 15:05:36.617724 INFO: fragments_df: keeping 3913 of 6069545 [sum(precursor_idx_mask)=6656 sum(mass_error_mask)=6069498 stop_rank=3913
2 days, 15:05:37.777718 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:05:37.915820 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:05:38.050917 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:05:38.187848 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:05:38.699956 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:05:38.700397 INFO: Using score_cutoff 27.29775297546387 (fac=0.99, q=1)
2 days, 15:05:38.700777 INFO: Updating optimization_manager: fwhm_rt             : 2.8326642513275146 -> 2.9092166423797607
2 days, 15:05:38.700866 INFO: Updating optimization_manager: fwhm_mobility       : 0.005863726604729891 -> 0.006037131883203983
2 days, 15:05:38.700938 INFO: Updating optimization_manager: score_cutoff        : 33.348301968383794 -> 27.29775297546387
2 days, 15:05:38.701003 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:05:38.752047 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:05:39.004074 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:05:39.056811 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:05:39.587660 INFO: === checking if optimization conditions were reached ===
2 days, 15:05:39.587908 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 15:05:39.590130 INFO: Updating optimization_manager: rt_error            : 332.02237800846416 -> 270.1599259490893
2 days, 15:05:39.590268 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 270.1599.
2 days, 15:05:39.590344 INFO: ==============================================
2 days, 15:05:39.590422 INFO: Starting optimization step 3.
2 days, 15:05:39.590487 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:05:39.590550 INFO: Using python extraction backend
2 days, 15:05:39.590665 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:05:39.590736 INFO: === Search parameters used ===
2 days, 15:05:39.590788 INFO: rt_error       : 270.1599259490893
2 days, 15:05:39.590835 INFO: mobility_error : 0.1
2 days, 15:05:39.590881 INFO: num_candidates : 3
2 days, 15:05:39.590925 INFO: ms1_error      : 15.0
2 days, 15:05:39.590968 INFO: ms2_error      : 15.0
2 days, 15:05:39.591022 INFO: fwhm_rt        : 2.9092166423797607
2 days, 15:05:39.591070 INFO: quant_window   : 3
2 days, 15:05:39.591115 INFO: ==============================================
2 days, 15:05:39.688831 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:05:39.688981 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:05:39.689031 INFO: FWHM in RT is 2.91 seconds, sigma is 0.49
2 days, 15:05:39.689055 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.27
2 days, 15:05:39.690364 INFO: Starting candidate selection
2 days, 15:10:12.335034 INFO: Starting candidate scoring
2 days, 15:10:24.098496 INFO: Finished candidate processing
2 days, 15:10:24.098885 INFO: Collecting candidate features
2 days, 15:10:25.985737 WARNING: intensity_correlation has 2278 NaNs ( 0.24 % out of 956689)
2 days, 15:10:25.986823 WARNING: height_correlation has 226 NaNs ( 0.02 % out of 956689)
2 days, 15:10:26.021100 INFO: Collecting fragment features
2 days, 15:10:26.631006 INFO: Finished candidate scoring
2 days, 15:10:27.388468 INFO: performing precursor FDR with 47 features
2 days, 15:10:27.388615 INFO: Decoy channel: -1
2 days, 15:10:27.388645 INFO: competitive: True
2 days, 15:10:27.611555 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:10:27.752704 WARNING: dropped 1189 target PSMs due to missing features
2 days, 15:10:27.752855 WARNING: dropped 1188 decoy PSMs due to missing features
2 days, 15:10:28.075593 INFO: Estimating optimal hyperparameters - samples: 763,449, batch_size: 3,127, learning_rate: 8.74e-04
2 days, 15:10:28.079398 INFO: Using random state 21930 for train-test-split
2 days, 15:10:47.801049 INFO: Test AUC: 0.551
2 days, 15:10:47.801212 INFO: Train AUC: 0.570
2 days, 15:10:47.801251 INFO: AUC difference: 3.24%
2 days, 15:10:48.357887 INFO: Resetting torch num_threads to 80
2 days, 15:10:48.375705 PROGRESS: === Extracted 956689 precursors and 5875205 fragments ===
2 days, 15:10:48.376581 INFO: === FDR correction performed with classifier version 14 ===
2 days, 15:10:48.406281 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:10:48.406553 PROGRESS: Total precursors accumulated: 183,680
2 days, 15:10:48.406629 PROGRESS: Target precursors: 106,214 (57.83%)
2 days, 15:10:48.406693 PROGRESS: Decoy precursors: 77,466 (42.17%)
2 days, 15:10:48.406764 PROGRESS: 
2 days, 15:10:48.406816 PROGRESS: Precursor Summary:
2 days, 15:10:48.409238 PROGRESS: Channel   0:	 0.050 FDR:   375; 0.010 FDR:   309; 0.001 FDR:   149
2 days, 15:10:48.409365 PROGRESS: 
2 days, 15:10:48.409430 PROGRESS: Protein Summary:
2 days, 15:10:48.411653 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   263; 0.001 FDR:   125
2 days, 15:10:48.411757 PROGRESS: =========================================================================
2 days, 15:10:48.416662 INFO: Target number of precursors reached.
2 days, 15:10:49.053280 INFO: fragments_df: keeping 4769 of 5875205 [sum(precursor_idx_mask)=8307 sum(mass_error_mask)=5875159 stop_rank=4769
2 days, 15:10:50.225979 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:10:50.370287 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:10:50.506224 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:10:50.652122 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:10:51.326377 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:10:51.326829 INFO: Using score_cutoff 23.61705923309326 (fac=0.99, q=1)
2 days, 15:10:51.327168 INFO: Updating optimization_manager: fwhm_rt             : 2.9092166423797607 -> 2.840768337249756
2 days, 15:10:51.327258 INFO: Updating optimization_manager: fwhm_mobility       : 0.006037131883203983 -> 0.00548138190060854
2 days, 15:10:51.327325 INFO: Updating optimization_manager: score_cutoff        : 27.29775297546387 -> 23.61705923309326
2 days, 15:10:51.327393 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:10:51.377612 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:10:51.633972 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:10:51.689142 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:10:52.178056 INFO: === checking if optimization conditions were reached ===
2 days, 15:10:52.178352 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 15:10:52.180627 INFO: Updating optimization_manager: rt_error            : 270.1599259490893 -> 228.8744765650413
2 days, 15:10:52.180770 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 228.8745.
2 days, 15:10:52.180849 INFO: ==============================================
2 days, 15:10:52.180935 INFO: Starting optimization step 4.
2 days, 15:10:52.181010 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:10:52.181082 INFO: Using python extraction backend
2 days, 15:10:52.181222 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:10:52.181301 INFO: === Search parameters used ===
2 days, 15:10:52.181360 INFO: rt_error       : 228.8744765650413
2 days, 15:10:52.181411 INFO: mobility_error : 0.1
2 days, 15:10:52.181463 INFO: num_candidates : 3
2 days, 15:10:52.181510 INFO: ms1_error      : 15.0
2 days, 15:10:52.181557 INFO: ms2_error      : 15.0
2 days, 15:10:52.181604 INFO: fwhm_rt        : 2.840768337249756
2 days, 15:10:52.181651 INFO: quant_window   : 3
2 days, 15:10:52.181698 INFO: ==============================================
2 days, 15:10:52.296807 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:10:52.296962 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:10:52.297011 INFO: FWHM in RT is 2.84 seconds, sigma is 0.47
2 days, 15:10:52.297037 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.97
2 days, 15:10:52.297971 INFO: Starting candidate selection
2 days, 15:14:58.637937 INFO: Starting candidate scoring
2 days, 15:15:10.418085 INFO: Finished candidate processing
2 days, 15:15:10.418295 INFO: Collecting candidate features
2 days, 15:15:12.240355 WARNING: intensity_correlation has 2443 NaNs ( 0.26 % out of 937817)
2 days, 15:15:12.241403 WARNING: height_correlation has 283 NaNs ( 0.03 % out of 937817)
2 days, 15:15:12.274281 INFO: Collecting fragment features
2 days, 15:15:12.864221 INFO: Finished candidate scoring
2 days, 15:15:13.658203 INFO: performing precursor FDR with 47 features
2 days, 15:15:13.658363 INFO: Decoy channel: -1
2 days, 15:15:13.658393 INFO: competitive: True
2 days, 15:15:13.882338 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:15:14.026446 WARNING: dropped 1271 target PSMs due to missing features
2 days, 15:15:14.026615 WARNING: dropped 1295 decoy PSMs due to missing features
2 days, 15:15:14.344397 INFO: Estimating optimal hyperparameters - samples: 748,200, batch_size: 3,064, learning_rate: 8.65e-04
2 days, 15:15:14.345804 INFO: Using random state 21930 for train-test-split
2 days, 15:15:31.819330 INFO: Test AUC: 0.554
2 days, 15:15:31.819524 INFO: Train AUC: 0.567
2 days, 15:15:31.819564 INFO: AUC difference: 2.38%
2 days, 15:15:32.362997 INFO: Resetting torch num_threads to 80
2 days, 15:15:32.380631 PROGRESS: === Extracted 937817 precursors and 5648518 fragments ===
2 days, 15:15:32.381543 INFO: === FDR correction performed with classifier version 14 ===
2 days, 15:15:32.411105 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:15:32.411385 PROGRESS: Total precursors accumulated: 181,841
2 days, 15:15:32.411456 PROGRESS: Target precursors: 104,258 (57.33%)
2 days, 15:15:32.411514 PROGRESS: Decoy precursors: 77,583 (42.67%)
2 days, 15:15:32.411567 PROGRESS: 
2 days, 15:15:32.411619 PROGRESS: Precursor Summary:
2 days, 15:15:32.413904 PROGRESS: Channel   0:	 0.050 FDR:   425; 0.010 FDR:   221; 0.001 FDR:   154
2 days, 15:15:32.414017 PROGRESS: 
2 days, 15:15:32.414083 PROGRESS: Protein Summary:
2 days, 15:15:32.416259 PROGRESS: Channel   0:	 0.050 FDR:   363; 0.010 FDR:   191; 0.001 FDR:   129
2 days, 15:15:32.416357 PROGRESS: =========================================================================
2 days, 15:15:32.421400 INFO: Target number of precursors reached.
2 days, 15:15:33.024265 INFO: fragments_df: keeping 3716 of 5648518 [sum(precursor_idx_mask)=6174 sum(mass_error_mask)=5648467 stop_rank=3716
2 days, 15:15:34.199596 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:15:34.337815 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:15:34.472284 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:15:34.603711 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:15:35.120280 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:15:35.120766 INFO: Using score_cutoff 31.257241630554198 (fac=0.99, q=1)
2 days, 15:15:35.121122 INFO: Updating optimization_manager: fwhm_rt             : 2.840768337249756 -> 2.861379861831665
2 days, 15:15:35.121209 INFO: Updating optimization_manager: fwhm_mobility       : 0.00548138190060854 -> 0.005508085712790489
2 days, 15:15:35.121267 INFO: Updating optimization_manager: score_cutoff        : 23.61705923309326 -> 31.257241630554198
2 days, 15:15:35.121329 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:15:35.176254 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:15:35.432947 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:15:35.501975 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:15:36.001817 INFO: === checking if optimization conditions were reached ===
2 days, 15:15:36.002183 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 15:15:36.004619 INFO: Updating optimization_manager: rt_error            : 228.8744765650413 -> 134.1962804787242
2 days, 15:15:36.004765 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 134.1963.
2 days, 15:15:36.004854 INFO: ==============================================
2 days, 15:15:36.004949 INFO: Starting optimization step 5.
2 days, 15:15:36.005028 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:15:36.005110 INFO: Using python extraction backend
2 days, 15:15:36.005264 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:15:36.005356 INFO: === Search parameters used ===
2 days, 15:15:36.005422 INFO: rt_error       : 134.1962804787242
2 days, 15:15:36.005481 INFO: mobility_error : 0.1
2 days, 15:15:36.005538 INFO: num_candidates : 3
2 days, 15:15:36.005595 INFO: ms1_error      : 15.0
2 days, 15:15:36.005651 INFO: ms2_error      : 15.0
2 days, 15:15:36.005708 INFO: fwhm_rt        : 2.861379861831665
2 days, 15:15:36.005769 INFO: quant_window   : 3
2 days, 15:15:36.005824 INFO: ==============================================
2 days, 15:15:36.157975 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:15:36.158155 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:15:36.158208 INFO: FWHM in RT is 2.86 seconds, sigma is 0.48
2 days, 15:15:36.158239 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.99
2 days, 15:15:36.159181 INFO: Starting candidate selection
2 days, 15:18:01.362523 INFO: Starting candidate scoring
2 days, 15:18:12.991372 INFO: Finished candidate processing
2 days, 15:18:12.991554 INFO: Collecting candidate features
2 days, 15:18:14.767007 WARNING: intensity_correlation has 3314 NaNs ( 0.37 % out of 901070)
2 days, 15:18:14.768025 WARNING: height_correlation has 416 NaNs ( 0.05 % out of 901070)
2 days, 15:18:14.799666 INFO: Collecting fragment features
2 days, 15:18:15.274286 INFO: Finished candidate scoring
2 days, 15:18:15.810393 INFO: performing precursor FDR with 47 features
2 days, 15:18:15.810539 INFO: Decoy channel: -1
2 days, 15:18:15.810570 INFO: competitive: True
2 days, 15:18:16.021955 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:18:16.152066 WARNING: dropped 1792 target PSMs due to missing features
2 days, 15:18:16.152242 WARNING: dropped 1714 decoy PSMs due to missing features
2 days, 15:18:16.443107 INFO: Estimating optimal hyperparameters - samples: 718,051, batch_size: 2,941, learning_rate: 8.47e-04
2 days, 15:18:16.444491 INFO: Using random state 21930 for train-test-split
2 days, 15:18:33.843357 INFO: Test AUC: 0.552
2 days, 15:18:33.843521 INFO: Train AUC: 0.565
2 days, 15:18:33.843560 INFO: AUC difference: 2.22%
2 days, 15:18:34.367059 INFO: Resetting torch num_threads to 80
2 days, 15:18:34.384314 PROGRESS: === Extracted 901070 precursors and 5130842 fragments ===
2 days, 15:18:34.385180 INFO: === FDR correction performed with classifier version 14 ===
2 days, 15:18:34.414702 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:18:34.414990 PROGRESS: Total precursors accumulated: 179,871
2 days, 15:18:34.415077 PROGRESS: Target precursors: 102,135 (56.78%)
2 days, 15:18:34.415137 PROGRESS: Decoy precursors: 77,736 (43.22%)
2 days, 15:18:34.415189 PROGRESS: 
2 days, 15:18:34.415240 PROGRESS: Precursor Summary:
2 days, 15:18:34.417738 PROGRESS: Channel   0:	 0.050 FDR:   393; 0.010 FDR:   263; 0.001 FDR:   223
2 days, 15:18:34.417843 PROGRESS: 
2 days, 15:18:34.417923 PROGRESS: Protein Summary:
2 days, 15:18:34.420073 PROGRESS: Channel   0:	 0.050 FDR:   334; 0.010 FDR:   221; 0.001 FDR:   189
2 days, 15:18:34.420172 PROGRESS: =========================================================================
2 days, 15:18:34.425100 INFO: Target number of precursors reached.
2 days, 15:18:34.996466 INFO: fragments_df: keeping 4048 of 5130842 [sum(precursor_idx_mask)=6959 sum(mass_error_mask)=5130785 stop_rank=4048
2 days, 15:18:36.166272 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:18:36.311894 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:18:36.430937 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:18:36.546942 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:18:37.050571 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:18:37.051066 INFO: Using score_cutoff 27.44823313407898 (fac=0.99, q=1)
2 days, 15:18:37.051421 INFO: Updating optimization_manager: fwhm_rt             : 2.861379861831665 -> 2.7897017002105713
2 days, 15:18:37.051526 INFO: Updating optimization_manager: fwhm_mobility       : 0.005508085712790489 -> 0.005378279834985733
2 days, 15:18:37.051608 INFO: Updating optimization_manager: score_cutoff        : 31.257241630554198 -> 27.44823313407898
2 days, 15:18:37.051687 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:18:37.104155 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:18:37.362743 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:18:37.420237 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:18:37.918524 INFO: === checking if optimization conditions were reached ===
2 days, 15:18:37.918831 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 15:18:37.921125 INFO: Updating optimization_manager: rt_error            : 134.1962804787242 -> 121.97188025334697
2 days, 15:18:37.921262 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 121.9719.
2 days, 15:18:37.921335 INFO: ==============================================
2 days, 15:18:37.921408 INFO: Starting optimization step 6.
2 days, 15:18:37.921474 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:18:37.921536 INFO: Using python extraction backend
2 days, 15:18:37.921638 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:18:37.921708 INFO: === Search parameters used ===
2 days, 15:18:37.921759 INFO: rt_error       : 121.97188025334697
2 days, 15:18:37.921806 INFO: mobility_error : 0.1
2 days, 15:18:37.921852 INFO: num_candidates : 3
2 days, 15:18:37.921918 INFO: ms1_error      : 15.0
2 days, 15:18:37.921964 INFO: ms2_error      : 15.0
2 days, 15:18:37.922009 INFO: fwhm_rt        : 2.7897017002105713
2 days, 15:18:37.922069 INFO: quant_window   : 3
2 days, 15:18:37.922117 INFO: ==============================================
2 days, 15:18:38.018756 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:18:38.018909 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:18:38.018958 INFO: FWHM in RT is 2.79 seconds, sigma is 0.47
2 days, 15:18:38.018982 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.91
2 days, 15:18:38.019750 INFO: Starting candidate selection
2 days, 15:20:40.214735 INFO: Starting candidate scoring
2 days, 15:20:51.516580 INFO: Finished candidate processing
2 days, 15:20:51.516740 INFO: Collecting candidate features
2 days, 15:20:53.146016 WARNING: intensity_correlation has 3533 NaNs ( 0.40 % out of 888387)
2 days, 15:20:53.147104 WARNING: height_correlation has 437 NaNs ( 0.05 % out of 888387)
2 days, 15:20:53.178638 INFO: Collecting fragment features
2 days, 15:20:53.629607 INFO: Finished candidate scoring
2 days, 15:20:54.149881 INFO: performing precursor FDR with 47 features
2 days, 15:20:54.150025 INFO: Decoy channel: -1
2 days, 15:20:54.150080 INFO: competitive: True
2 days, 15:20:54.350630 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:20:54.478866 WARNING: dropped 1936 target PSMs due to missing features
2 days, 15:20:54.479044 WARNING: dropped 1815 decoy PSMs due to missing features
2 days, 15:20:54.767658 INFO: Estimating optimal hyperparameters - samples: 707,708, batch_size: 2,898, learning_rate: 8.41e-04
2 days, 15:20:54.768968 INFO: Using random state 21930 for train-test-split
2 days, 15:21:11.409890 INFO: Test AUC: 0.547
2 days, 15:21:11.410058 INFO: Train AUC: 0.563
2 days, 15:21:11.410096 INFO: AUC difference: 2.87%
2 days, 15:21:11.935446 INFO: Resetting torch num_threads to 80
2 days, 15:21:11.952173 PROGRESS: === Extracted 888387 precursors and 4997296 fragments ===
2 days, 15:21:11.953024 INFO: === FDR correction performed with classifier version 14 ===
2 days, 15:21:11.981442 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:21:11.981728 PROGRESS: Total precursors accumulated: 178,433
2 days, 15:21:11.981801 PROGRESS: Target precursors: 101,200 (56.72%)
2 days, 15:21:11.981907 PROGRESS: Decoy precursors: 77,233 (43.28%)
2 days, 15:21:11.981965 PROGRESS: 
2 days, 15:21:11.982017 PROGRESS: Precursor Summary:
2 days, 15:21:11.984274 PROGRESS: Channel   0:	 0.050 FDR:   388; 0.010 FDR:   230; 0.001 FDR:   208
2 days, 15:21:11.984382 PROGRESS: 
2 days, 15:21:11.984445 PROGRESS: Protein Summary:
2 days, 15:21:11.986602 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   194; 0.001 FDR:   175
2 days, 15:21:11.986712 PROGRESS: =========================================================================
2 days, 15:21:11.991428 INFO: Target number of precursors reached.
2 days, 15:21:12.538377 INFO: fragments_df: keeping 3691 of 4997296 [sum(precursor_idx_mask)=6193 sum(mass_error_mask)=4997244 stop_rank=3691
2 days, 15:21:13.683127 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:21:13.815550 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:21:13.947080 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:21:14.086214 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:21:14.606936 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:21:14.607412 INFO: Using score_cutoff 30.620954784965512 (fac=0.99, q=1)
2 days, 15:21:14.607738 INFO: Updating optimization_manager: fwhm_rt             : 2.7897017002105713 -> 2.8516550064086914
2 days, 15:21:14.607827 INFO: Updating optimization_manager: fwhm_mobility       : 0.005378279834985733 -> 0.005611849017441273
2 days, 15:21:14.607886 INFO: Updating optimization_manager: score_cutoff        : 27.44823313407898 -> 30.620954784965512
2 days, 15:21:14.607942 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:21:14.661200 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:21:14.919171 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:21:14.981385 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:21:15.469627 INFO: === checking if optimization conditions were reached ===
2 days, 15:21:15.469920 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 15:21:15.472256 INFO: Updating optimization_manager: rt_error            : 121.97188025334697 -> 114.89034896239625
2 days, 15:21:15.472389 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 114.8903.
2 days, 15:21:15.472463 INFO: ==============================================
2 days, 15:21:15.472537 INFO: Starting optimization step 7.
2 days, 15:21:15.472602 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:21:15.472663 INFO: Using python extraction backend
2 days, 15:21:15.472764 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:21:15.472853 INFO: === Search parameters used ===
2 days, 15:21:15.472912 INFO: rt_error       : 114.89034896239625
2 days, 15:21:15.472961 INFO: mobility_error : 0.1
2 days, 15:21:15.473008 INFO: num_candidates : 3
2 days, 15:21:15.473054 INFO: ms1_error      : 15.0
2 days, 15:21:15.473099 INFO: ms2_error      : 15.0
2 days, 15:21:15.473144 INFO: fwhm_rt        : 2.8516550064086914
2 days, 15:21:15.473188 INFO: quant_window   : 3
2 days, 15:21:15.473231 INFO: ==============================================
2 days, 15:21:15.570360 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:21:15.570501 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:21:15.570549 INFO: FWHM in RT is 2.85 seconds, sigma is 0.48
2 days, 15:21:15.570574 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.04
2 days, 15:21:15.571427 INFO: Starting candidate selection
2 days, 15:23:17.847826 INFO: Starting candidate scoring
2 days, 15:23:29.244082 INFO: Finished candidate processing
2 days, 15:23:29.244288 INFO: Collecting candidate features
2 days, 15:23:32.030223 WARNING: intensity_correlation has 3605 NaNs ( 0.41 % out of 887793)
2 days, 15:23:32.031244 WARNING: height_correlation has 450 NaNs ( 0.05 % out of 887793)
2 days, 15:23:32.064039 INFO: Collecting fragment features
2 days, 15:23:32.605956 INFO: Finished candidate scoring
2 days, 15:23:33.382112 INFO: performing precursor FDR with 47 features
2 days, 15:23:33.382254 INFO: Decoy channel: -1
2 days, 15:23:33.382283 INFO: competitive: True
2 days, 15:23:33.617998 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:23:33.748371 WARNING: dropped 1925 target PSMs due to missing features
2 days, 15:23:33.748516 WARNING: dropped 1901 decoy PSMs due to missing features
2 days, 15:23:34.277549 INFO: Estimating optimal hyperparameters - samples: 707,173, batch_size: 2,896, learning_rate: 8.41e-04
2 days, 15:23:34.278953 INFO: Using random state 21930 for train-test-split
2 days, 15:23:50.923569 INFO: Test AUC: 0.550
2 days, 15:23:50.923730 INFO: Train AUC: 0.563
2 days, 15:23:50.923766 INFO: AUC difference: 2.25%
2 days, 15:23:51.442107 INFO: Resetting torch num_threads to 80
2 days, 15:23:51.472615 PROGRESS: === Extracted 887793 precursors and 4981361 fragments ===
2 days, 15:23:51.473487 INFO: === FDR correction performed with classifier version 14 ===
2 days, 15:23:51.503371 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:23:51.503642 PROGRESS: Total precursors accumulated: 178,660
2 days, 15:23:51.503717 PROGRESS: Target precursors: 101,509 (56.82%)
2 days, 15:23:51.503777 PROGRESS: Decoy precursors: 77,151 (43.18%)
2 days, 15:23:51.503829 PROGRESS: 
2 days, 15:23:51.503885 PROGRESS: Precursor Summary:
2 days, 15:23:51.506443 PROGRESS: Channel   0:	 0.050 FDR:   397; 0.010 FDR:   254; 0.001 FDR:   222
2 days, 15:23:51.506561 PROGRESS: 
2 days, 15:23:51.506627 PROGRESS: Protein Summary:
2 days, 15:23:51.508830 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   216; 0.001 FDR:   187
2 days, 15:23:51.508946 PROGRESS: =========================================================================
2 days, 15:23:51.516153 INFO: Target number of precursors reached.
2 days, 15:23:52.057993 INFO: fragments_df: keeping 3919 of 4981361 [sum(precursor_idx_mask)=6735 sum(mass_error_mask)=4981309 stop_rank=3919
2 days, 15:23:53.315171 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:23:53.448628 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:23:53.582339 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:23:53.716949 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:23:54.270888 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:23:54.271362 INFO: Using score_cutoff 26.86667788696289 (fac=0.99, q=1)
2 days, 15:23:54.271690 INFO: Updating optimization_manager: fwhm_rt             : 2.8516550064086914 -> 2.851456880569458
2 days, 15:23:54.271777 INFO: Updating optimization_manager: fwhm_mobility       : 0.005611849017441273 -> 0.005594657734036446
2 days, 15:23:54.271838 INFO: Updating optimization_manager: score_cutoff        : 30.620954784965512 -> 26.86667788696289
2 days, 15:23:54.271898 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:23:54.320047 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:23:54.577648 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:23:54.631105 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:23:55.113708 INFO: === checking if optimization conditions were reached ===
2 days, 15:23:55.114045 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 15:23:55.116374 INFO: Updating optimization_manager: rt_error            : 114.89034896239625 -> 115.7458079667977
2 days, 15:23:55.116538 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 115.7458.
2 days, 15:23:55.116642 INFO: ==============================================
2 days, 15:23:55.116751 INFO: Starting optimization step 8.
2 days, 15:23:55.116853 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:23:55.116960 INFO: Using python extraction backend
2 days, 15:23:55.117106 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:23:55.117197 INFO: === Search parameters used ===
2 days, 15:23:55.117273 INFO: rt_error       : 115.7458079667977
2 days, 15:23:55.117340 INFO: mobility_error : 0.1
2 days, 15:23:55.117407 INFO: num_candidates : 3
2 days, 15:23:55.117471 INFO: ms1_error      : 15.0
2 days, 15:23:55.117533 INFO: ms2_error      : 15.0
2 days, 15:23:55.117593 INFO: fwhm_rt        : 2.851456880569458
2 days, 15:23:55.117652 INFO: quant_window   : 3
2 days, 15:23:55.117712 INFO: ==============================================
2 days, 15:23:55.334893 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:23:55.335047 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:23:55.335108 INFO: FWHM in RT is 2.85 seconds, sigma is 0.48
2 days, 15:23:55.335140 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.03
2 days, 15:23:55.335931 INFO: Starting candidate selection
2 days, 15:25:55.719520 INFO: Starting candidate scoring
2 days, 15:26:07.008871 INFO: Finished candidate processing
2 days, 15:26:07.009081 INFO: Collecting candidate features
2 days, 15:26:08.704017 WARNING: intensity_correlation has 3482 NaNs ( 0.39 % out of 898381)
2 days, 15:26:08.705022 WARNING: height_correlation has 411 NaNs ( 0.05 % out of 898381)
2 days, 15:26:08.737413 INFO: Collecting fragment features
2 days, 15:26:09.204515 INFO: Finished candidate scoring
2 days, 15:26:09.752238 INFO: performing precursor FDR with 47 features
2 days, 15:26:09.752383 INFO: Decoy channel: -1
2 days, 15:26:09.752415 INFO: competitive: True
2 days, 15:26:09.965983 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:26:10.098209 WARNING: dropped 1891 target PSMs due to missing features
2 days, 15:26:10.098376 WARNING: dropped 1789 decoy PSMs due to missing features
2 days, 15:26:10.516462 INFO: Estimating optimal hyperparameters - samples: 715,760, batch_size: 2,931, learning_rate: 8.46e-04
2 days, 15:26:10.517822 INFO: Using random state 21930 for train-test-split
2 days, 15:26:28.029016 INFO: Test AUC: 0.548
2 days, 15:26:28.029212 INFO: Train AUC: 0.566
2 days, 15:26:28.029251 INFO: AUC difference: 3.14%
2 days, 15:26:28.537614 INFO: Resetting torch num_threads to 80
2 days, 15:26:28.554801 PROGRESS: === Extracted 898381 precursors and 5070658 fragments ===
2 days, 15:26:28.555657 INFO: === FDR correction performed with classifier version 14 ===
2 days, 15:26:28.584466 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:26:28.584742 PROGRESS: Total precursors accumulated: 179,658
2 days, 15:26:28.584816 PROGRESS: Target precursors: 102,084 (56.82%)
2 days, 15:26:28.584891 PROGRESS: Decoy precursors: 77,574 (43.18%)
2 days, 15:26:28.584947 PROGRESS: 
2 days, 15:26:28.584999 PROGRESS: Precursor Summary:
2 days, 15:26:28.587413 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   321; 0.001 FDR:   236
2 days, 15:26:28.587536 PROGRESS: 
2 days, 15:26:28.587602 PROGRESS: Protein Summary:
2 days, 15:26:28.589768 PROGRESS: Channel   0:	 0.050 FDR:   369; 0.010 FDR:   270; 0.001 FDR:   200
2 days, 15:26:28.589880 PROGRESS: =========================================================================
2 days, 15:26:28.594625 INFO: Target number of precursors reached.
2 days, 15:26:29.140771 INFO: fragments_df: keeping 4663 of 5070658 [sum(precursor_idx_mask)=8354 sum(mass_error_mask)=5070599 stop_rank=4663
2 days, 15:26:29.697640 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:26:29.844714 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:26:29.983709 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:26:30.123524 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:26:30.792736 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:26:30.793227 INFO: Using score_cutoff 25.079536869049072 (fac=0.99, q=1)
2 days, 15:26:30.793548 INFO: Updating optimization_manager: fwhm_rt             : 2.851456880569458 -> 2.8283615112304688
2 days, 15:26:30.793645 INFO: Updating optimization_manager: fwhm_mobility       : 0.005594657734036446 -> 0.005300937686115503
2 days, 15:26:30.793707 INFO: Updating optimization_manager: score_cutoff        : 26.86667788696289 -> 25.079536869049072
2 days, 15:26:30.793771 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:26:30.844253 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:26:31.100137 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:26:31.153267 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:26:31.651084 INFO: === checking if optimization conditions were reached ===
2 days, 15:26:31.651398 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2 days, 15:26:31.652781 INFO: Updating optimization_manager: rt_error            : 115.7458079667977 -> 115.7458079667977
2 days, 15:26:31.652945 INFO: Updating optimization_manager: classifier_version  : 14 -> 23
2 days, 15:26:31.653050 INFO: Updating optimization_manager: score_cutoff        : 25.079536869049072 -> 25.079536869049072
2 days, 15:26:31.653145 INFO: Updating optimization_manager: fwhm_rt             : 2.8283615112304688 -> 2.8283615112304688
2 days, 15:26:31.653236 INFO: Updating optimization_manager: fwhm_mobility       : 0.005300937686115503 -> 0.005300937686115503
2 days, 15:26:31.653330 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 115.7458 found after 9 searches.
2 days, 15:26:31.653399 INFO: ==============================================
2 days, 15:26:31.653472 PROGRESS: Optimization finished for rt_error.
2 days, 15:26:32.217146 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:26:32.268112 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:26:32.525378 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:26:32.578825 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:26:33.077773 INFO: Starting optimization step 0.
2 days, 15:26:33.078107 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:26:33.078215 INFO: Using python extraction backend
2 days, 15:26:33.078342 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:26:33.078424 INFO: === Search parameters used ===
2 days, 15:26:33.078481 INFO: rt_error       : 115.7458079667977
2 days, 15:26:33.078531 INFO: mobility_error : 0.1
2 days, 15:26:33.078577 INFO: num_candidates : 3
2 days, 15:26:33.078624 INFO: ms1_error      : 15.0
2 days, 15:26:33.078670 INFO: ms2_error      : 15.0
2 days, 15:26:33.078717 INFO: fwhm_rt        : 2.8283615112304688
2 days, 15:26:33.078762 INFO: quant_window   : 3
2 days, 15:26:33.078806 INFO: ==============================================
2 days, 15:26:33.180427 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:26:33.180578 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:26:33.180625 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
2 days, 15:26:33.180652 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.87
2 days, 15:26:33.181470 INFO: Starting candidate selection
2 days, 15:28:38.352577 INFO: Starting candidate scoring
2 days, 15:28:49.573021 INFO: Finished candidate processing
2 days, 15:28:49.573196 INFO: Collecting candidate features
2 days, 15:28:51.195592 WARNING: intensity_correlation has 3487 NaNs ( 0.39 % out of 896843)
2 days, 15:28:51.196626 WARNING: height_correlation has 412 NaNs ( 0.05 % out of 896843)
2 days, 15:28:51.229554 INFO: Collecting fragment features
2 days, 15:28:51.674621 INFO: Finished candidate scoring
2 days, 15:28:52.252247 INFO: performing precursor FDR with 47 features
2 days, 15:28:52.252390 INFO: Decoy channel: -1
2 days, 15:28:52.252420 INFO: competitive: True
2 days, 15:28:52.464564 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:28:52.596701 WARNING: dropped 1884 target PSMs due to missing features
2 days, 15:28:52.596853 WARNING: dropped 1802 decoy PSMs due to missing features
2 days, 15:28:53.003937 INFO: Estimating optimal hyperparameters - samples: 714,525, batch_size: 2,926, learning_rate: 8.45e-04
2 days, 15:28:53.005294 INFO: Using random state 861029 for train-test-split
2 days, 15:29:10.520017 INFO: Test AUC: 0.552
2 days, 15:29:10.520179 INFO: Train AUC: 0.575
2 days, 15:29:10.520219 INFO: AUC difference: 3.98%
2 days, 15:29:11.021957 INFO: Resetting torch num_threads to 80
2 days, 15:29:11.039534 PROGRESS: === Extracted 896843 precursors and 5063006 fragments ===
2 days, 15:29:11.040416 INFO: === FDR correction performed with classifier version 23 ===
2 days, 15:29:11.070623 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:29:11.070908 PROGRESS: Total precursors accumulated: 179,369
2 days, 15:29:11.070979 PROGRESS: Target precursors: 102,863 (57.35%)
2 days, 15:29:11.071039 PROGRESS: Decoy precursors: 76,506 (42.65%)
2 days, 15:29:11.071091 PROGRESS: 
2 days, 15:29:11.071143 PROGRESS: Precursor Summary:
2 days, 15:29:11.073434 PROGRESS: Channel   0:	 0.050 FDR:   448; 0.010 FDR:   339; 0.001 FDR:   294
2 days, 15:29:11.073560 PROGRESS: 
2 days, 15:29:11.073626 PROGRESS: Protein Summary:
2 days, 15:29:11.076008 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   286; 0.001 FDR:   250
2 days, 15:29:11.076112 PROGRESS: =========================================================================
2 days, 15:29:11.081264 INFO: Target number of precursors reached.
2 days, 15:29:11.636505 INFO: fragments_df: keeping 4866 of 5063006 [sum(precursor_idx_mask)=8768 sum(mass_error_mask)=5062950 stop_rank=4866
2 days, 15:29:12.217317 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:29:12.365129 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:29:12.505610 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:29:12.650674 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:29:13.366283 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:29:13.366774 INFO: Using score_cutoff 19.40573015098572 (fac=0.99, q=1)
2 days, 15:29:13.367113 INFO: Updating optimization_manager: fwhm_rt             : 2.8283615112304688 -> 2.6796932220458984
2 days, 15:29:13.367200 INFO: Updating optimization_manager: fwhm_mobility       : 0.005300937686115503 -> 0.0047226655296981335
2 days, 15:29:13.367260 INFO: Updating optimization_manager: score_cutoff        : 25.079536869049072 -> 19.40573015098572
2 days, 15:29:13.367322 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:29:13.417685 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:29:13.674706 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:29:13.728779 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:29:14.219719 INFO: === checking if optimization conditions were reached ===
2 days, 15:29:14.220014 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 15:29:14.222007 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0751604406881689
2 days, 15:29:14.222148 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0752.
2 days, 15:29:14.222225 INFO: ==============================================
2 days, 15:29:14.222303 INFO: Starting optimization step 1.
2 days, 15:29:14.222371 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:29:14.222435 INFO: Using python extraction backend
2 days, 15:29:14.222543 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:29:14.222614 INFO: === Search parameters used ===
2 days, 15:29:14.222672 INFO: rt_error       : 115.7458079667977
2 days, 15:29:14.222722 INFO: mobility_error : 0.0751604406881689
2 days, 15:29:14.222789 INFO: num_candidates : 3
2 days, 15:29:14.222836 INFO: ms1_error      : 15.0
2 days, 15:29:14.222881 INFO: ms2_error      : 15.0
2 days, 15:29:14.222924 INFO: fwhm_rt        : 2.6796932220458984
2 days, 15:29:14.222968 INFO: quant_window   : 3
2 days, 15:29:14.223012 INFO: ==============================================
2 days, 15:29:14.325407 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:29:14.325558 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:29:14.325609 INFO: FWHM in RT is 2.68 seconds, sigma is 0.45
2 days, 15:29:14.325634 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.56
2 days, 15:29:14.326590 INFO: Starting candidate selection
2 days, 15:30:45.314155 INFO: Starting candidate scoring
2 days, 15:30:56.553130 INFO: Finished candidate processing
2 days, 15:30:56.553300 INFO: Collecting candidate features
2 days, 15:30:58.367643 WARNING: intensity_correlation has 3671 NaNs ( 0.43 % out of 849573)
2 days, 15:30:58.368734 WARNING: height_correlation has 461 NaNs ( 0.05 % out of 849573)
2 days, 15:30:58.399346 INFO: Collecting fragment features
2 days, 15:30:58.816957 INFO: Finished candidate scoring
2 days, 15:30:59.496675 INFO: performing precursor FDR with 47 features
2 days, 15:30:59.496829 INFO: Decoy channel: -1
2 days, 15:30:59.496859 INFO: competitive: True
2 days, 15:30:59.699248 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:30:59.824196 WARNING: dropped 1967 target PSMs due to missing features
2 days, 15:30:59.824366 WARNING: dropped 1921 decoy PSMs due to missing features
2 days, 15:31:00.094140 INFO: Estimating optimal hyperparameters - samples: 676,548, batch_size: 2,771, learning_rate: 8.23e-04
2 days, 15:31:00.095439 INFO: Using random state 861029 for train-test-split
2 days, 15:31:16.598930 INFO: Test AUC: 0.555
2 days, 15:31:16.599099 INFO: Train AUC: 0.572
2 days, 15:31:16.599137 INFO: AUC difference: 2.93%
2 days, 15:31:17.108566 INFO: Resetting torch num_threads to 80
2 days, 15:31:17.125588 PROGRESS: === Extracted 849573 precursors and 4683925 fragments ===
2 days, 15:31:17.126493 INFO: === FDR correction performed with classifier version 23 ===
2 days, 15:31:17.153918 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:31:17.154204 PROGRESS: Total precursors accumulated: 173,025
2 days, 15:31:17.154290 PROGRESS: Target precursors: 99,190 (57.33%)
2 days, 15:31:17.154348 PROGRESS: Decoy precursors: 73,835 (42.67%)
2 days, 15:31:17.154400 PROGRESS: 
2 days, 15:31:17.154450 PROGRESS: Precursor Summary:
2 days, 15:31:17.156879 PROGRESS: Channel   0:	 0.050 FDR:   532; 0.010 FDR:   331; 0.001 FDR:   301
2 days, 15:31:17.157006 PROGRESS: 
2 days, 15:31:17.157070 PROGRESS: Protein Summary:
2 days, 15:31:17.159322 PROGRESS: Channel   0:	 0.050 FDR:   471; 0.010 FDR:   278; 0.001 FDR:   253
2 days, 15:31:17.159425 PROGRESS: =========================================================================
2 days, 15:31:17.166061 INFO: Target number of precursors reached.
2 days, 15:31:17.676389 INFO: fragments_df: keeping 4825 of 4683925 [sum(precursor_idx_mask)=8445 sum(mass_error_mask)=4683870 stop_rank=4825
2 days, 15:31:18.667549 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:31:18.824301 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:31:18.967380 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:31:19.111979 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:31:19.801001 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:31:19.801487 INFO: Using score_cutoff 24.220445320129397 (fac=0.99, q=1)
2 days, 15:31:19.801841 INFO: Updating optimization_manager: fwhm_rt             : 2.6796932220458984 -> 2.7305376529693604
2 days, 15:31:19.801948 INFO: Updating optimization_manager: fwhm_mobility       : 0.0047226655296981335 -> 0.00514757027849555
2 days, 15:31:19.802012 INFO: Updating optimization_manager: score_cutoff        : 19.40573015098572 -> 24.220445320129397
2 days, 15:31:19.802078 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:31:19.850282 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:31:20.109216 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:31:20.163549 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:31:20.640781 INFO: === checking if optimization conditions were reached ===
2 days, 15:31:20.641248 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 15:31:20.643452 INFO: Updating optimization_manager: mobility_error      : 0.0751604406881689 -> 0.053978458143341936
2 days, 15:31:20.643601 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0540.
2 days, 15:31:20.643706 INFO: ==============================================
2 days, 15:31:20.643817 INFO: Starting optimization step 2.
2 days, 15:31:20.643908 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:31:20.643997 INFO: Using python extraction backend
2 days, 15:31:20.644147 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:31:20.644248 INFO: === Search parameters used ===
2 days, 15:31:20.644328 INFO: rt_error       : 115.7458079667977
2 days, 15:31:20.644398 INFO: mobility_error : 0.053978458143341936
2 days, 15:31:20.644463 INFO: num_candidates : 3
2 days, 15:31:20.644527 INFO: ms1_error      : 15.0
2 days, 15:31:20.644608 INFO: ms2_error      : 15.0
2 days, 15:31:20.644672 INFO: fwhm_rt        : 2.7305376529693604
2 days, 15:31:20.644734 INFO: quant_window   : 3
2 days, 15:31:20.644795 INFO: ==============================================
2 days, 15:31:20.744891 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:31:20.745058 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:31:20.745113 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
2 days, 15:31:20.745145 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.79
2 days, 15:31:20.746048 INFO: Starting candidate selection
2 days, 15:32:26.334810 INFO: Starting candidate scoring
2 days, 15:32:36.961142 INFO: Finished candidate processing
2 days, 15:32:36.961396 INFO: Collecting candidate features
2 days, 15:32:38.596482 WARNING: intensity_correlation has 3849 NaNs ( 0.47 % out of 811293)
2 days, 15:32:38.597416 WARNING: height_correlation has 473 NaNs ( 0.06 % out of 811293)
2 days, 15:32:38.626462 INFO: Collecting fragment features
2 days, 15:32:39.024925 INFO: Finished candidate scoring
2 days, 15:32:39.561706 INFO: performing precursor FDR with 47 features
2 days, 15:32:39.561996 INFO: Decoy channel: -1
2 days, 15:32:39.562033 INFO: competitive: True
2 days, 15:32:39.750983 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:32:39.872539 WARNING: dropped 2082 target PSMs due to missing features
2 days, 15:32:39.872712 WARNING: dropped 1981 decoy PSMs due to missing features
2 days, 15:32:40.136210 INFO: Estimating optimal hyperparameters - samples: 645,784, batch_size: 2,645, learning_rate: 8.04e-04
2 days, 15:32:40.140052 INFO: Using random state 861029 for train-test-split
2 days, 15:32:56.450516 INFO: Test AUC: 0.551
2 days, 15:32:56.450665 INFO: Train AUC: 0.574
2 days, 15:32:56.450701 INFO: AUC difference: 4.06%
2 days, 15:32:56.953001 INFO: Resetting torch num_threads to 80
2 days, 15:32:56.968618 PROGRESS: === Extracted 811293 precursors and 4398802 fragments ===
2 days, 15:32:56.969426 INFO: === FDR correction performed with classifier version 23 ===
2 days, 15:32:56.996953 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:32:56.997252 PROGRESS: Total precursors accumulated: 167,026
2 days, 15:32:56.997325 PROGRESS: Target precursors: 95,890 (57.41%)
2 days, 15:32:56.997383 PROGRESS: Decoy precursors: 71,136 (42.59%)
2 days, 15:32:56.997436 PROGRESS: 
2 days, 15:32:56.997485 PROGRESS: Precursor Summary:
2 days, 15:32:56.999772 PROGRESS: Channel   0:	 0.050 FDR:   481; 0.010 FDR:   353; 0.001 FDR:   302
2 days, 15:32:56.999899 PROGRESS: 
2 days, 15:32:56.999961 PROGRESS: Protein Summary:
2 days, 15:32:57.002136 PROGRESS: Channel   0:	 0.050 FDR:   418; 0.010 FDR:   298; 0.001 FDR:   256
2 days, 15:32:57.002236 PROGRESS: =========================================================================
2 days, 15:32:57.008766 INFO: Target number of precursors reached.
2 days, 15:32:57.493644 INFO: fragments_df: keeping 4981 of 4398802 [sum(precursor_idx_mask)=9003 sum(mass_error_mask)=4398741 stop_rank=4981
2 days, 15:32:58.667393 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:32:58.815853 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:32:58.956674 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:32:59.092926 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:32:59.806798 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:32:59.807295 INFO: Using score_cutoff 22.389428340911866 (fac=0.99, q=1)
2 days, 15:32:59.807632 INFO: Updating optimization_manager: fwhm_rt             : 2.7305376529693604 -> 2.816084623336792
2 days, 15:32:59.807712 INFO: Updating optimization_manager: fwhm_mobility       : 0.00514757027849555 -> 0.0051683420315384865
2 days, 15:32:59.807768 INFO: Updating optimization_manager: score_cutoff        : 24.220445320129397 -> 22.389428340911866
2 days, 15:32:59.807823 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:32:59.861422 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:33:00.118234 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:33:00.171719 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:33:00.655105 INFO: === checking if optimization conditions were reached ===
2 days, 15:33:00.655412 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 15:33:00.657604 INFO: Updating optimization_manager: mobility_error      : 0.053978458143341936 -> 0.04553115433647938
2 days, 15:33:00.657733 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0455.
2 days, 15:33:00.657807 INFO: ==============================================
2 days, 15:33:00.657891 INFO: Starting optimization step 3.
2 days, 15:33:00.657965 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 15:33:00.658045 INFO: Using python extraction backend
2 days, 15:33:00.658151 PROGRESS: Extracting batch of 407917 precursors
2 days, 15:33:00.658219 INFO: === Search parameters used ===
2 days, 15:33:00.658271 INFO: rt_error       : 115.7458079667977
2 days, 15:33:00.658317 INFO: mobility_error : 0.04553115433647938
2 days, 15:33:00.658363 INFO: num_candidates : 3
2 days, 15:33:00.658408 INFO: ms1_error      : 15.0
2 days, 15:33:00.658452 INFO: ms2_error      : 15.0
2 days, 15:33:00.658494 INFO: fwhm_rt        : 2.816084623336792
2 days, 15:33:00.658538 INFO: quant_window   : 3
2 days, 15:33:00.658585 INFO: ==============================================
2 days, 15:33:00.758871 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:33:00.759028 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:33:00.759072 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
2 days, 15:33:00.759095 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.80
2 days, 15:33:00.759958 INFO: Starting candidate selection
2 days, 15:33:58.795485 INFO: Starting candidate scoring
2 days, 15:34:09.515751 INFO: Finished candidate processing
2 days, 15:34:09.516297 INFO: Collecting candidate features
2 days, 15:34:12.497577 WARNING: intensity_correlation has 4079 NaNs ( 0.51 % out of 796745)
2 days, 15:34:12.498527 WARNING: height_correlation has 497 NaNs ( 0.06 % out of 796745)
2 days, 15:34:12.531098 INFO: Collecting fragment features
2 days, 15:34:13.264310 INFO: Finished candidate scoring
2 days, 15:34:14.064310 INFO: performing precursor FDR with 47 features
2 days, 15:34:14.064470 INFO: Decoy channel: -1
2 days, 15:34:14.064499 INFO: competitive: True
2 days, 15:34:14.289162 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 15:34:14.409551 WARNING: dropped 2206 target PSMs due to missing features
2 days, 15:34:14.409711 WARNING: dropped 2108 decoy PSMs due to missing features
2 days, 15:34:14.870379 INFO: Estimating optimal hyperparameters - samples: 633,944, batch_size: 2,596, learning_rate: 7.96e-04
2 days, 15:34:14.871619 INFO: Using random state 861029 for train-test-split
2 days, 15:34:31.380790 INFO: Test AUC: 0.554
2 days, 15:34:31.380970 INFO: Train AUC: 0.573
2 days, 15:34:31.381007 INFO: AUC difference: 3.35%
2 days, 15:34:31.889833 INFO: Resetting torch num_threads to 80
2 days, 15:34:31.905122 PROGRESS: === Extracted 796745 precursors and 4266453 fragments ===
2 days, 15:34:31.905997 INFO: === FDR correction performed with classifier version 23 ===
2 days, 15:34:31.934944 PROGRESS: ============================= Precursor FDR =============================
2 days, 15:34:31.935205 PROGRESS: Total precursors accumulated: 165,298
2 days, 15:34:31.935276 PROGRESS: Target precursors: 95,287 (57.65%)
2 days, 15:34:31.935334 PROGRESS: Decoy precursors: 70,011 (42.35%)
2 days, 15:34:31.935399 PROGRESS: 
2 days, 15:34:31.935450 PROGRESS: Precursor Summary:
2 days, 15:34:31.937654 PROGRESS: Channel   0:	 0.050 FDR:   418; 0.010 FDR:   304; 0.001 FDR:   281
2 days, 15:34:31.937758 PROGRESS: 
2 days, 15:34:31.937837 PROGRESS: Protein Summary:
2 days, 15:34:31.939939 PROGRESS: Channel   0:	 0.050 FDR:   363; 0.010 FDR:   260; 0.001 FDR:   240
2 days, 15:34:31.940040 PROGRESS: =========================================================================
2 days, 15:34:31.946312 INFO: Target number of precursors reached.
2 days, 15:34:32.405845 INFO: fragments_df: keeping 4390 of 4266453 [sum(precursor_idx_mask)=7797 sum(mass_error_mask)=4266380 stop_rank=4390
2 days, 15:34:33.589024 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:34:33.714428 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:34:33.829524 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:34:33.938262 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:34:34.493325 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 15:34:34.493831 INFO: Using score_cutoff 22.685816785240174 (fac=0.99, q=1)
2 days, 15:34:34.494190 INFO: Updating optimization_manager: fwhm_rt             : 2.816084623336792 -> 2.7277274131774902
2 days, 15:34:34.494281 INFO: Updating optimization_manager: fwhm_mobility       : 0.0051683420315384865 -> 0.004984487313777208
2 days, 15:34:34.494342 INFO: Updating optimization_manager: score_cutoff        : 22.389428340911866 -> 22.685816785240174
2 days, 15:34:34.494403 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:34:34.545817 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:34:34.802192 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:34:34.857944 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:34:35.368836 INFO: === checking if optimization conditions were reached ===
2 days, 15:34:35.369166 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
2 days, 15:34:35.370262 INFO: Updating optimization_manager: mobility_error      : 0.04553115433647938 -> 0.053978458143341936
2 days, 15:34:35.370440 INFO: Updating optimization_manager: classifier_version  : 23 -> 26
2 days, 15:34:35.370563 INFO: Updating optimization_manager: score_cutoff        : 22.685816785240174 -> 22.389428340911866
2 days, 15:34:35.370666 INFO: Updating optimization_manager: fwhm_rt             : 2.7277274131774902 -> 2.816084623336792
2 days, 15:34:35.370763 INFO: Updating optimization_manager: fwhm_mobility       : 0.004984487313777208 -> 0.0051683420315384865
2 days, 15:34:35.370871 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0540 found after 4 searches.
2 days, 15:34:35.370942 INFO: ==============================================
2 days, 15:34:35.371014 PROGRESS: Optimization finished for mobility_error.
2 days, 15:34:35.938450 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:34:35.989941 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:34:36.246261 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:34:36.302092 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:34:36.795298 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 15:34:36.795597 PROGRESS: ==============================================
2 days, 15:34:36.795692 PROGRESS: ms2_error      : 15.0000
2 days, 15:34:36.795765 PROGRESS: ms1_error      : 15.0000
2 days, 15:34:36.795825 PROGRESS: rt_error       : 115.7458
2 days, 15:34:36.795897 PROGRESS: mobility_error : 0.0540
2 days, 15:34:36.795948 PROGRESS: ==============================================
2 days, 15:34:36.802468 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 15:34:38.383840 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 15:34:46.319423 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 15:34:47.752958 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 15:35:02.452655 INFO: Using python extraction backend
2 days, 15:35:02.453104 PROGRESS: Extracting batch of 12210649 precursors
2 days, 15:35:02.453203 INFO: === Search parameters used ===
2 days, 15:35:02.453269 INFO: rt_error       : 115.7458079667977
2 days, 15:35:02.453331 INFO: mobility_error : 0.053978458143341936
2 days, 15:35:02.453387 INFO: num_candidates : 3
2 days, 15:35:02.453441 INFO: ms1_error      : 15.0
2 days, 15:35:02.453496 INFO: ms2_error      : 15.0
2 days, 15:35:02.453548 INFO: fwhm_rt        : 2.816084623336792
2 days, 15:35:02.453599 INFO: quant_window   : 3
2 days, 15:35:02.453650 INFO: ==============================================
2 days, 15:35:04.846060 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 15:35:04.846232 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 15:35:04.846281 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
2 days, 15:35:04.846308 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.80
2 days, 15:35:04.847382 INFO: Starting candidate selection
2 days, 16:06:46.509437 INFO: Removed 25190425 precursors with score below cutoff 22.389428340911866
2 days, 16:06:50.282439 INFO: Starting candidate scoring
2 days, 16:08:03.436602 INFO: Finished candidate processing
2 days, 16:08:03.436878 INFO: Collecting candidate features
2 days, 16:08:14.943417 WARNING: intensity_correlation has 4696 NaNs ( 0.08 % out of 5978184)
2 days, 16:08:14.949022 WARNING: height_correlation has 225 NaNs ( 0.00 % out of 5978184)
2 days, 16:08:15.148456 INFO: Collecting fragment features
2 days, 16:08:19.325434 INFO: Finished candidate scoring
2 days, 16:08:22.988397 INFO: === Performing FDR correction with classifier version 26 ===
2 days, 16:08:22.988975 INFO: performing precursor FDR with 47 features
2 days, 16:08:22.989013 INFO: Decoy channel: -1
2 days, 16:08:22.989048 INFO: competitive: True
2 days, 16:08:24.380229 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:08:25.145805 WARNING: dropped 2572 target PSMs due to missing features
2 days, 16:08:25.145981 WARNING: dropped 2274 decoy PSMs due to missing features
2 days, 16:08:27.358078 INFO: Estimating optimal hyperparameters - samples: 4,778,670, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 16:08:27.368199 INFO: Using random state 907303 for train-test-split
2 days, 16:10:15.383354 INFO: Test AUC: 0.554
2 days, 16:10:15.383545 INFO: Train AUC: 0.558
2 days, 16:10:15.383582 INFO: AUC difference: 0.67%
2 days, 16:10:17.327562 INFO: Resetting torch num_threads to 80
2 days, 16:10:17.458766 INFO: Removing fragments below FDR threshold
2 days, 16:10:17.794695 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:10:17.794986 PROGRESS: Total precursors accumulated: 8,974
2 days, 16:10:17.795065 PROGRESS: Target precursors: 8,886 (99.02%)
2 days, 16:10:17.795120 PROGRESS: Decoy precursors: 88 (0.98%)
2 days, 16:10:17.795169 PROGRESS: 
2 days, 16:10:17.795216 PROGRESS: Precursor Summary:
2 days, 16:10:17.798965 PROGRESS: Channel   0:	 0.050 FDR: 8,886; 0.010 FDR: 8,886; 0.001 FDR: 5,707
2 days, 16:10:17.799107 PROGRESS: 
2 days, 16:10:17.799171 PROGRESS: Protein Summary:
2 days, 16:10:17.803377 PROGRESS: Channel   0:	 0.050 FDR: 2,235; 0.010 FDR: 2,235; 0.001 FDR: 1,512
2 days, 16:10:17.803487 PROGRESS: =========================================================================
2 days, 16:10:17.883601 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R5/psm.parquet
2 days, 16:10:17.942621 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R5/frag.parquet
2 days, 16:10:17.983064 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R5
2 days, 16:10:18.560211 PROGRESS: Loading raw file 12/12: B9_G_DIA_nLC_tTOF_R6 
2 days, 16:10:18.560378 INFO: Quantification results path: plasma_output/alphadia_2.1.0/library/quant
2 days, 16:10:18.560462 INFO: Creating folder plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R6/figures
2 days, 16:10:18.560663 INFO: Initializing TimingManager
2 days, 16:10:18.561168 INFO: Initializing RawFileManager
2 days, 16:10:18.561278 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:18.561342 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:18.561387 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:18.696393 INFO: Reading 22,623 frames with 408,184,843 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:23.819603 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d...
2 days, 16:10:23.821471 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:23.823987 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:23.824423 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:23.825134 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:23.827338 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:23.855785 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:23.856273 INFO: Indexing quadrupole dimension
2 days, 16:10:24.129141 INFO: Transposing detector events
2 days, 16:10:25.559453 INFO: Finished transposing data
2 days, 16:10:25.559660 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
2 days, 16:10:25.560174 INFO: RT (min)            : 0.0 - 40.0
2 days, 16:10:25.560273 INFO: RT duration (sec)   : 2400.0
2 days, 16:10:25.560335 INFO: RT duration (min)   : 40.0
2 days, 16:10:25.560396 INFO: Cycle len (scans)   : 12
2 days, 16:10:25.560453 INFO: Cycle len (sec)     : 1.27
2 days, 16:10:25.560506 INFO: Number of cycles    : 1885
2 days, 16:10:25.560557 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 16:10:25.560614 INFO: Creating DIA data object took: 6.999344110488892
2 days, 16:10:26.876539 INFO: Initializing CalibrationManager
2 days, 16:10:26.876892 INFO: Setting up calibration estimators ..
2 days, 16:10:26.876973 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 16:10:26.877069 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 16:10:26.877168 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 16:10:26.877234 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 16:10:26.877308 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 16:10:26.877373 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 16:10:26.877427 INFO: Done setting up calibration estimators.
2 days, 16:10:26.877556 INFO: Initializing OptimizationManager
2 days, 16:10:26.877662 INFO: initial parameter: ms1_error = 30
2 days, 16:10:26.877717 INFO: initial parameter: ms2_error = 30
2 days, 16:10:26.877769 INFO: initial parameter: rt_error = 1199.986106
2 days, 16:10:26.877818 INFO: initial parameter: mobility_error = 0.1
2 days, 16:10:26.877879 INFO: initial parameter: num_candidates = 1
2 days, 16:10:26.877939 INFO: initial parameter: fwhm_rt = 5
2 days, 16:10:26.877997 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 16:10:26.878044 INFO: initial parameter: score_cutoff = 0
2 days, 16:10:26.878091 INFO: initial parameter: classifier_version = -1
2 days, 16:10:26.878168 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R6
2 days, 16:10:26.878349 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 16:10:26.878385 INFO: Initializing FDRManager
2 days, 16:10:26.878427 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 16:10:27.914691 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
2 days, 16:10:28.544162 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 16:10:28.544606 INFO: Updating optimization_manager: rt_error            : 1199.986106 -> 1199.986106
2 days, 16:10:28.544713 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 16:10:28.544891 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 16:10:28.544984 PROGRESS: Starting initial search for precursors.
2 days, 16:10:28.545064 INFO: Starting optimization step 0.
2 days, 16:10:28.545129 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 16:10:28.545217 INFO: Using python extraction backend
2 days, 16:10:28.545331 PROGRESS: Extracting batch of 395 precursors
2 days, 16:10:28.545400 INFO: === Search parameters used ===
2 days, 16:10:28.545453 INFO: rt_error       : 1199.986106
2 days, 16:10:28.545501 INFO: mobility_error : 0.1
2 days, 16:10:28.545551 INFO: num_candidates : 1
2 days, 16:10:28.545596 INFO: ms1_error      : 30
2 days, 16:10:28.545643 INFO: ms2_error      : 30
2 days, 16:10:28.545689 INFO: fwhm_rt        : 5
2 days, 16:10:28.545732 INFO: quant_window   : 3
2 days, 16:10:28.545776 INFO: ==============================================
2 days, 16:10:28.546502 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:10:28.546554 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:10:28.546595 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:10:28.546618 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:10:28.547643 INFO: Starting candidate selection
2 days, 16:10:30.325046 INFO: Starting candidate scoring
2 days, 16:10:30.365109 INFO: Finished candidate processing
2 days, 16:10:30.365206 INFO: Collecting candidate features
2 days, 16:10:30.374913 INFO: Collecting fragment features
2 days, 16:10:30.377122 INFO: Finished candidate scoring
2 days, 16:10:30.377961 INFO: performing precursor FDR with 47 features
2 days, 16:10:30.378009 INFO: Decoy channel: -1
2 days, 16:10:30.378034 INFO: competitive: True
2 days, 16:10:30.379211 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:10:30.380811 INFO: Estimating optimal hyperparameters - samples: 274, batch_size: 128, learning_rate: 1.77e-04
2 days, 16:10:30.381543 INFO: Using random state 965167 for train-test-split
2 days, 16:10:30.400485 INFO: Test AUC: 0.496
2 days, 16:10:30.400560 INFO: Train AUC: 0.523
2 days, 16:10:30.400593 INFO: AUC difference: 5.26%
2 days, 16:10:30.400617 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:10:30.639982 INFO: Resetting torch num_threads to 80
2 days, 16:10:30.640424 PROGRESS: === Extracted 343 precursors and 2848 fragments ===
2 days, 16:10:30.640847 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:10:30.641392 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:10:30.641485 PROGRESS: Total precursors accumulated: 173
2 days, 16:10:30.641550 PROGRESS: Target precursors: 89 (51.45%)
2 days, 16:10:30.641613 PROGRESS: Decoy precursors: 84 (48.55%)
2 days, 16:10:30.641666 PROGRESS: 
2 days, 16:10:30.641717 PROGRESS: Precursor Summary:
2 days, 16:10:30.642681 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 16:10:30.642774 PROGRESS: 
2 days, 16:10:30.642834 PROGRESS: Protein Summary:
2 days, 16:10:30.643886 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 16:10:30.643976 PROGRESS: =========================================================================
2 days, 16:10:30.644080 INFO: Target number of precursors not reached yet.
2 days, 16:10:30.705069 INFO: Starting optimization step 1.
2 days, 16:10:30.705294 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 16:10:30.705375 INFO: Using python extraction backend
2 days, 16:10:30.705481 PROGRESS: Extracting batch of 796 precursors
2 days, 16:10:30.705557 INFO: === Search parameters used ===
2 days, 16:10:30.705613 INFO: rt_error       : 1199.986106
2 days, 16:10:30.705662 INFO: mobility_error : 0.1
2 days, 16:10:30.705708 INFO: num_candidates : 1
2 days, 16:10:30.705754 INFO: ms1_error      : 30
2 days, 16:10:30.705800 INFO: ms2_error      : 30
2 days, 16:10:30.705844 INFO: fwhm_rt        : 5
2 days, 16:10:30.705902 INFO: quant_window   : 3
2 days, 16:10:30.705951 INFO: ==============================================
2 days, 16:10:30.706614 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:10:30.706662 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:10:30.706694 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:10:30.706718 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:10:30.707608 INFO: Starting candidate selection
2 days, 16:10:33.678174 INFO: Starting candidate scoring
2 days, 16:10:33.718938 INFO: Finished candidate processing
2 days, 16:10:33.719039 INFO: Collecting candidate features
2 days, 16:10:33.729492 INFO: Collecting fragment features
2 days, 16:10:33.731876 INFO: Finished candidate scoring
2 days, 16:10:33.733955 INFO: performing precursor FDR with 47 features
2 days, 16:10:33.734008 INFO: Decoy channel: -1
2 days, 16:10:33.734035 INFO: competitive: True
2 days, 16:10:33.736897 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:10:33.738652 INFO: Estimating optimal hyperparameters - samples: 855, batch_size: 128, learning_rate: 1.77e-04
2 days, 16:10:33.738740 INFO: Using random state 693661 for train-test-split
2 days, 16:10:33.796996 INFO: Test AUC: 0.492
2 days, 16:10:33.797086 INFO: Train AUC: 0.607
2 days, 16:10:33.797116 INFO: AUC difference: 19.01%
2 days, 16:10:33.797138 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:10:34.029997 INFO: Resetting torch num_threads to 80
2 days, 16:10:34.031239 PROGRESS: === Extracted 1069 precursors and 9096 fragments ===
2 days, 16:10:34.031667 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:10:34.032261 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:10:34.032359 PROGRESS: Total precursors accumulated: 541
2 days, 16:10:34.032423 PROGRESS: Target precursors: 327 (60.44%)
2 days, 16:10:34.032487 PROGRESS: Decoy precursors: 214 (39.56%)
2 days, 16:10:34.032539 PROGRESS: 
2 days, 16:10:34.032587 PROGRESS: Precursor Summary:
2 days, 16:10:34.033539 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 16:10:34.033632 PROGRESS: 
2 days, 16:10:34.033689 PROGRESS: Protein Summary:
2 days, 16:10:34.034739 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 16:10:34.034839 PROGRESS: =========================================================================
2 days, 16:10:34.034986 INFO: Target number of precursors not reached yet.
2 days, 16:10:34.099580 INFO: Starting optimization step 2.
2 days, 16:10:34.099836 PROGRESS: === Extracting elution groups 600 to 1400 ===
2 days, 16:10:34.099917 INFO: Using python extraction backend
2 days, 16:10:34.100022 PROGRESS: Extracting batch of 1598 precursors
2 days, 16:10:34.100092 INFO: === Search parameters used ===
2 days, 16:10:34.100147 INFO: rt_error       : 1199.986106
2 days, 16:10:34.100194 INFO: mobility_error : 0.1
2 days, 16:10:34.100242 INFO: num_candidates : 1
2 days, 16:10:34.100287 INFO: ms1_error      : 30
2 days, 16:10:34.100331 INFO: ms2_error      : 30
2 days, 16:10:34.100374 INFO: fwhm_rt        : 5
2 days, 16:10:34.100416 INFO: quant_window   : 3
2 days, 16:10:34.100461 INFO: ==============================================
2 days, 16:10:34.101238 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:10:34.101287 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:10:34.101315 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:10:34.101338 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:10:34.102209 INFO: Starting candidate selection
2 days, 16:10:39.399231 INFO: Starting candidate scoring
2 days, 16:10:39.453399 INFO: Finished candidate processing
2 days, 16:10:39.453509 INFO: Collecting candidate features
2 days, 16:10:39.465210 INFO: Collecting fragment features
2 days, 16:10:39.468004 INFO: Finished candidate scoring
2 days, 16:10:39.471555 INFO: performing precursor FDR with 47 features
2 days, 16:10:39.471612 INFO: Decoy channel: -1
2 days, 16:10:39.471639 INFO: competitive: True
2 days, 16:10:39.474874 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:10:39.476893 INFO: Estimating optimal hyperparameters - samples: 2,001, batch_size: 128, learning_rate: 1.77e-04
2 days, 16:10:39.476978 INFO: Using random state 978197 for train-test-split
2 days, 16:10:39.671363 INFO: Test AUC: 0.525
2 days, 16:10:39.671467 INFO: Train AUC: 0.616
2 days, 16:10:39.671502 INFO: AUC difference: 14.70%
2 days, 16:10:39.671530 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:10:39.911379 INFO: Resetting torch num_threads to 80
2 days, 16:10:39.913059 PROGRESS: === Extracted 2502 precursors and 21217 fragments ===
2 days, 16:10:39.913502 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:10:39.914215 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:10:39.914315 PROGRESS: Total precursors accumulated: 1,268
2 days, 16:10:39.914383 PROGRESS: Target precursors: 768 (60.57%)
2 days, 16:10:39.914443 PROGRESS: Decoy precursors: 500 (39.43%)
2 days, 16:10:39.914497 PROGRESS: 
2 days, 16:10:39.914548 PROGRESS: Precursor Summary:
2 days, 16:10:39.915500 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 16:10:39.915593 PROGRESS: 
2 days, 16:10:39.915655 PROGRESS: Protein Summary:
2 days, 16:10:39.916681 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 16:10:39.916775 PROGRESS: =========================================================================
2 days, 16:10:39.916933 INFO: Target number of precursors not reached yet.
2 days, 16:10:40.002011 INFO: Starting optimization step 3.
2 days, 16:10:40.002256 PROGRESS: === Extracting elution groups 1400 to 3000 ===
2 days, 16:10:40.002338 INFO: Using python extraction backend
2 days, 16:10:40.002447 PROGRESS: Extracting batch of 3192 precursors
2 days, 16:10:40.002523 INFO: === Search parameters used ===
2 days, 16:10:40.002578 INFO: rt_error       : 1199.986106
2 days, 16:10:40.002629 INFO: mobility_error : 0.1
2 days, 16:10:40.002691 INFO: num_candidates : 1
2 days, 16:10:40.002742 INFO: ms1_error      : 30
2 days, 16:10:40.002789 INFO: ms2_error      : 30
2 days, 16:10:40.002833 INFO: fwhm_rt        : 5
2 days, 16:10:40.002880 INFO: quant_window   : 3
2 days, 16:10:40.002927 INFO: ==============================================
2 days, 16:10:40.004012 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:10:40.004062 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:10:40.004092 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:10:40.004117 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:10:40.004986 INFO: Starting candidate selection
2 days, 16:10:50.453217 INFO: Starting candidate scoring
2 days, 16:10:50.547216 INFO: Finished candidate processing
2 days, 16:10:50.547418 INFO: Collecting candidate features
2 days, 16:10:50.575799 INFO: Collecting fragment features
2 days, 16:10:50.580023 INFO: Finished candidate scoring
2 days, 16:10:50.584566 INFO: performing precursor FDR with 47 features
2 days, 16:10:50.584626 INFO: Decoy channel: -1
2 days, 16:10:50.584653 INFO: competitive: True
2 days, 16:10:50.588857 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:10:50.591452 INFO: Estimating optimal hyperparameters - samples: 4,308, batch_size: 128, learning_rate: 1.77e-04
2 days, 16:10:50.591545 INFO: Using random state 706741 for train-test-split
2 days, 16:10:50.986432 INFO: Test AUC: 0.546
2 days, 16:10:50.986542 INFO: Train AUC: 0.581
2 days, 16:10:50.986576 INFO: AUC difference: 5.86%
2 days, 16:10:50.986601 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:10:51.225421 INFO: Resetting torch num_threads to 80
2 days, 16:10:51.227711 PROGRESS: === Extracted 5386 precursors and 46022 fragments ===
2 days, 16:10:51.228146 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:10:51.228978 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:10:51.229081 PROGRESS: Total precursors accumulated: 2,729
2 days, 16:10:51.229148 PROGRESS: Target precursors: 1,587 (58.15%)
2 days, 16:10:51.229209 PROGRESS: Decoy precursors: 1,142 (41.85%)
2 days, 16:10:51.229267 PROGRESS: 
2 days, 16:10:51.229320 PROGRESS: Precursor Summary:
2 days, 16:10:51.230297 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 16:10:51.230398 PROGRESS: 
2 days, 16:10:51.230460 PROGRESS: Protein Summary:
2 days, 16:10:51.231483 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 16:10:51.231586 PROGRESS: =========================================================================
2 days, 16:10:51.231760 INFO: Target number of precursors not reached yet.
2 days, 16:10:51.329627 INFO: Starting optimization step 4.
2 days, 16:10:51.329905 PROGRESS: === Extracting elution groups 3000 to 6200 ===
2 days, 16:10:51.329994 INFO: Using python extraction backend
2 days, 16:10:51.330109 PROGRESS: Extracting batch of 6381 precursors
2 days, 16:10:51.330188 INFO: === Search parameters used ===
2 days, 16:10:51.330245 INFO: rt_error       : 1199.986106
2 days, 16:10:51.330297 INFO: mobility_error : 0.1
2 days, 16:10:51.330346 INFO: num_candidates : 1
2 days, 16:10:51.330394 INFO: ms1_error      : 30
2 days, 16:10:51.330441 INFO: ms2_error      : 30
2 days, 16:10:51.330488 INFO: fwhm_rt        : 5
2 days, 16:10:51.330534 INFO: quant_window   : 3
2 days, 16:10:51.330588 INFO: ==============================================
2 days, 16:10:51.332223 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:10:51.332274 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:10:51.332305 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:10:51.332329 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:10:51.333268 INFO: Starting candidate selection
2 days, 16:11:10.558963 INFO: Starting candidate scoring
2 days, 16:11:10.727789 INFO: Finished candidate processing
2 days, 16:11:10.727897 INFO: Collecting candidate features
2 days, 16:11:10.742813 WARNING: intensity_correlation has 1 NaNs ( 0.02 % out of 5737)
2 days, 16:11:10.746746 INFO: Collecting fragment features
2 days, 16:11:10.752220 INFO: Finished candidate scoring
2 days, 16:11:10.759515 INFO: performing precursor FDR with 47 features
2 days, 16:11:10.759611 INFO: Decoy channel: -1
2 days, 16:11:10.759639 INFO: competitive: True
2 days, 16:11:10.766179 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:11:10.768427 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 16:11:10.770309 INFO: Estimating optimal hyperparameters - samples: 8,897, batch_size: 128, learning_rate: 1.77e-04
2 days, 16:11:10.770409 INFO: Using random state 194003 for train-test-split
2 days, 16:11:11.696384 INFO: Test AUC: 0.518
2 days, 16:11:11.696505 INFO: Train AUC: 0.593
2 days, 16:11:11.696538 INFO: AUC difference: 12.60%
2 days, 16:11:11.696563 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:11:11.944961 INFO: Resetting torch num_threads to 80
2 days, 16:11:11.948320 PROGRESS: === Extracted 11123 precursors and 94786 fragments ===
2 days, 16:11:11.948801 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:11:11.950004 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:11:11.950113 PROGRESS: Total precursors accumulated: 5,646
2 days, 16:11:11.950184 PROGRESS: Target precursors: 3,322 (58.84%)
2 days, 16:11:11.950250 PROGRESS: Decoy precursors: 2,324 (41.16%)
2 days, 16:11:11.950306 PROGRESS: 
2 days, 16:11:11.950360 PROGRESS: Precursor Summary:
2 days, 16:11:11.951360 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
2 days, 16:11:11.951465 PROGRESS: 
2 days, 16:11:11.951540 PROGRESS: Protein Summary:
2 days, 16:11:11.952625 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
2 days, 16:11:11.952729 PROGRESS: =========================================================================
2 days, 16:11:11.952951 INFO: Target number of precursors not reached yet.
2 days, 16:11:12.116504 INFO: Starting optimization step 5.
2 days, 16:11:12.116771 PROGRESS: === Extracting elution groups 6200 to 12600 ===
2 days, 16:11:12.116856 INFO: Using python extraction backend
2 days, 16:11:12.116975 PROGRESS: Extracting batch of 12763 precursors
2 days, 16:11:12.117057 INFO: === Search parameters used ===
2 days, 16:11:12.117115 INFO: rt_error       : 1199.986106
2 days, 16:11:12.117168 INFO: mobility_error : 0.1
2 days, 16:11:12.117218 INFO: num_candidates : 1
2 days, 16:11:12.117269 INFO: ms1_error      : 30
2 days, 16:11:12.117317 INFO: ms2_error      : 30
2 days, 16:11:12.117366 INFO: fwhm_rt        : 5
2 days, 16:11:12.117413 INFO: quant_window   : 3
2 days, 16:11:12.117459 INFO: ==============================================
2 days, 16:11:12.120887 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:11:12.120953 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:11:12.120984 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:11:12.121009 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:11:12.121912 INFO: Starting candidate selection
2 days, 16:11:49.924873 INFO: Starting candidate scoring
2 days, 16:11:50.156933 INFO: Finished candidate processing
2 days, 16:11:50.157088 INFO: Collecting candidate features
2 days, 16:11:50.179959 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 11507)
2 days, 16:11:50.184083 INFO: Collecting fragment features
2 days, 16:11:50.195887 INFO: Finished candidate scoring
2 days, 16:11:50.210672 INFO: performing precursor FDR with 47 features
2 days, 16:11:50.210815 INFO: Decoy channel: -1
2 days, 16:11:50.210846 INFO: competitive: True
2 days, 16:11:50.220497 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:11:50.224767 WARNING: dropped 1 target PSMs due to missing features
2 days, 16:11:50.224859 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 16:11:50.228166 INFO: Estimating optimal hyperparameters - samples: 18,102, batch_size: 128, learning_rate: 1.77e-04
2 days, 16:11:50.228312 INFO: Using random state 207548 for train-test-split
2 days, 16:11:52.161643 INFO: Test AUC: 0.536
2 days, 16:11:52.161782 INFO: Train AUC: 0.604
2 days, 16:11:52.161816 INFO: AUC difference: 11.19%
2 days, 16:11:52.161839 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:11:52.416832 INFO: Resetting torch num_threads to 80
2 days, 16:11:52.421724 PROGRESS: === Extracted 22630 precursors and 192585 fragments ===
2 days, 16:11:52.422325 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:11:52.424382 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:11:52.424501 PROGRESS: Total precursors accumulated: 11,482
2 days, 16:11:52.424582 PROGRESS: Target precursors: 6,931 (60.36%)
2 days, 16:11:52.424640 PROGRESS: Decoy precursors: 4,551 (39.64%)
2 days, 16:11:52.424690 PROGRESS: 
2 days, 16:11:52.424739 PROGRESS: Precursor Summary:
2 days, 16:11:52.425784 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2 days, 16:11:52.425887 PROGRESS: 
2 days, 16:11:52.425951 PROGRESS: Protein Summary:
2 days, 16:11:52.427057 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2 days, 16:11:52.427148 PROGRESS: =========================================================================
2 days, 16:11:52.427478 INFO: Target number of precursors not reached yet.
2 days, 16:11:52.690300 INFO: Starting optimization step 6.
2 days, 16:11:52.690597 PROGRESS: === Extracting elution groups 12600 to 25400 ===
2 days, 16:11:52.690681 INFO: Using python extraction backend
2 days, 16:11:52.690797 PROGRESS: Extracting batch of 25523 precursors
2 days, 16:11:52.690875 INFO: === Search parameters used ===
2 days, 16:11:52.690928 INFO: rt_error       : 1199.986106
2 days, 16:11:52.690978 INFO: mobility_error : 0.1
2 days, 16:11:52.691031 INFO: num_candidates : 1
2 days, 16:11:52.691076 INFO: ms1_error      : 30
2 days, 16:11:52.691122 INFO: ms2_error      : 30
2 days, 16:11:52.691168 INFO: fwhm_rt        : 5
2 days, 16:11:52.691212 INFO: quant_window   : 3
2 days, 16:11:52.691271 INFO: ==============================================
2 days, 16:11:52.698335 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:11:52.698417 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:11:52.698449 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:11:52.698475 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:11:52.702170 INFO: Starting candidate selection
2 days, 16:13:05.877193 INFO: Starting candidate scoring
2 days, 16:13:06.278164 INFO: Finished candidate processing
2 days, 16:13:06.278332 INFO: Collecting candidate features
2 days, 16:13:06.318716 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 22963)
2 days, 16:13:06.318979 WARNING: height_correlation has 2 NaNs ( 0.01 % out of 22963)
2 days, 16:13:06.323367 INFO: Collecting fragment features
2 days, 16:13:06.338370 INFO: Finished candidate scoring
2 days, 16:13:06.361381 INFO: performing precursor FDR with 47 features
2 days, 16:13:06.361536 INFO: Decoy channel: -1
2 days, 16:13:06.361565 INFO: competitive: True
2 days, 16:13:06.379108 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:13:06.388475 WARNING: dropped 2 target PSMs due to missing features
2 days, 16:13:06.388635 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 16:13:06.394761 INFO: Estimating optimal hyperparameters - samples: 36,469, batch_size: 149, learning_rate: 1.91e-04
2 days, 16:13:06.394970 INFO: Using random state 673934 for train-test-split
2 days, 16:13:09.877309 INFO: Test AUC: 0.540
2 days, 16:13:09.877450 INFO: Train AUC: 0.605
2 days, 16:13:09.877482 INFO: AUC difference: 10.79%
2 days, 16:13:09.877504 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:13:10.142289 INFO: Resetting torch num_threads to 80
2 days, 16:13:10.150609 PROGRESS: === Extracted 45593 precursors and 388192 fragments ===
2 days, 16:13:10.151312 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:13:10.155548 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:13:10.155690 PROGRESS: Total precursors accumulated: 23,125
2 days, 16:13:10.155759 PROGRESS: Target precursors: 13,921 (60.20%)
2 days, 16:13:10.155817 PROGRESS: Decoy precursors: 9,204 (39.80%)
2 days, 16:13:10.155869 PROGRESS: 
2 days, 16:13:10.155919 PROGRESS: Precursor Summary:
2 days, 16:13:10.157040 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
2 days, 16:13:10.157142 PROGRESS: 
2 days, 16:13:10.157203 PROGRESS: Protein Summary:
2 days, 16:13:10.158406 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
2 days, 16:13:10.158504 PROGRESS: =========================================================================
2 days, 16:13:10.158978 INFO: Target number of precursors not reached yet.
2 days, 16:13:10.489558 INFO: Starting optimization step 7.
2 days, 16:13:10.489848 PROGRESS: === Extracting elution groups 25400 to 51000 ===
2 days, 16:13:10.489945 INFO: Using python extraction backend
2 days, 16:13:10.490092 PROGRESS: Extracting batch of 51061 precursors
2 days, 16:13:10.490169 INFO: === Search parameters used ===
2 days, 16:13:10.490223 INFO: rt_error       : 1199.986106
2 days, 16:13:10.490287 INFO: mobility_error : 0.1
2 days, 16:13:10.490337 INFO: num_candidates : 1
2 days, 16:13:10.490382 INFO: ms1_error      : 30
2 days, 16:13:10.490426 INFO: ms2_error      : 30
2 days, 16:13:10.490471 INFO: fwhm_rt        : 5
2 days, 16:13:10.490520 INFO: quant_window   : 3
2 days, 16:13:10.490563 INFO: ==============================================
2 days, 16:13:10.503498 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:13:10.503635 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:13:10.503668 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:13:10.503694 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:13:10.504548 INFO: Starting candidate selection
2 days, 16:15:35.193197 INFO: Starting candidate scoring
2 days, 16:15:35.988569 INFO: Finished candidate processing
2 days, 16:15:35.988688 INFO: Collecting candidate features
2 days, 16:15:36.066679 WARNING: intensity_correlation has 11 NaNs ( 0.02 % out of 45817)
2 days, 16:15:36.072182 INFO: Collecting fragment features
2 days, 16:15:36.099048 INFO: Finished candidate scoring
2 days, 16:15:36.151842 INFO: performing precursor FDR with 47 features
2 days, 16:15:36.152006 INFO: Decoy channel: -1
2 days, 16:15:36.152039 INFO: competitive: True
2 days, 16:15:36.187752 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:15:36.206008 WARNING: dropped 9 target PSMs due to missing features
2 days, 16:15:36.206147 WARNING: dropped 8 decoy PSMs due to missing features
2 days, 16:15:36.219513 INFO: Estimating optimal hyperparameters - samples: 73,114, batch_size: 299, learning_rate: 2.70e-04
2 days, 16:15:36.220144 INFO: Using random state 697870 for train-test-split
2 days, 16:15:40.814695 INFO: Test AUC: 0.540
2 days, 16:15:40.814844 INFO: Train AUC: 0.606
2 days, 16:15:40.814877 INFO: AUC difference: 10.89%
2 days, 16:15:40.814901 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:15:41.092684 INFO: Resetting torch num_threads to 80
2 days, 16:15:41.110649 PROGRESS: === Extracted 91410 precursors and 778803 fragments ===
2 days, 16:15:41.111374 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:15:41.121142 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:15:41.121304 PROGRESS: Total precursors accumulated: 46,351
2 days, 16:15:41.121376 PROGRESS: Target precursors: 27,706 (59.77%)
2 days, 16:15:41.121436 PROGRESS: Decoy precursors: 18,645 (40.23%)
2 days, 16:15:41.121488 PROGRESS: 
2 days, 16:15:41.121546 PROGRESS: Precursor Summary:
2 days, 16:15:41.122924 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
2 days, 16:15:41.123029 PROGRESS: 
2 days, 16:15:41.123092 PROGRESS: Protein Summary:
2 days, 16:15:41.124485 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
2 days, 16:15:41.124584 PROGRESS: =========================================================================
2 days, 16:15:41.125486 INFO: Target number of precursors not reached yet.
2 days, 16:15:41.695655 INFO: Starting optimization step 8.
2 days, 16:15:41.695975 PROGRESS: === Extracting elution groups 51000 to 102200 ===
2 days, 16:15:41.696066 INFO: Using python extraction backend
2 days, 16:15:41.696189 PROGRESS: Extracting batch of 102076 precursors
2 days, 16:15:41.696265 INFO: === Search parameters used ===
2 days, 16:15:41.696320 INFO: rt_error       : 1199.986106
2 days, 16:15:41.696368 INFO: mobility_error : 0.1
2 days, 16:15:41.696414 INFO: num_candidates : 1
2 days, 16:15:41.696458 INFO: ms1_error      : 30
2 days, 16:15:41.696504 INFO: ms2_error      : 30
2 days, 16:15:41.696547 INFO: fwhm_rt        : 5
2 days, 16:15:41.696590 INFO: quant_window   : 3
2 days, 16:15:41.696632 INFO: ==============================================
2 days, 16:15:41.722591 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:15:41.722739 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:15:41.722775 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:15:41.722799 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:15:41.723709 INFO: Starting candidate selection
2 days, 16:20:22.311192 INFO: Starting candidate scoring
2 days, 16:20:23.860984 INFO: Finished candidate processing
2 days, 16:20:23.861145 INFO: Collecting candidate features
2 days, 16:20:24.011035 WARNING: intensity_correlation has 25 NaNs ( 0.03 % out of 91766)
2 days, 16:20:24.011412 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 91766)
2 days, 16:20:24.018285 INFO: Collecting fragment features
2 days, 16:20:24.071940 INFO: Finished candidate scoring
2 days, 16:20:24.181267 INFO: performing precursor FDR with 47 features
2 days, 16:20:24.181607 INFO: Decoy channel: -1
2 days, 16:20:24.181651 INFO: competitive: True
2 days, 16:20:24.256439 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:20:24.291194 WARNING: dropped 23 target PSMs due to missing features
2 days, 16:20:24.291374 WARNING: dropped 21 decoy PSMs due to missing features
2 days, 16:20:24.334190 INFO: Estimating optimal hyperparameters - samples: 146,505, batch_size: 600, learning_rate: 3.83e-04
2 days, 16:20:24.334577 INFO: Using random state 109165 for train-test-split
2 days, 16:20:30.515099 INFO: Test AUC: 0.546
2 days, 16:20:30.515240 INFO: Train AUC: 0.596
2 days, 16:20:30.515275 INFO: AUC difference: 8.45%
2 days, 16:20:30.515300 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:20:30.822284 INFO: Resetting torch num_threads to 80
2 days, 16:20:30.854110 PROGRESS: === Extracted 183176 precursors and 1562874 fragments ===
2 days, 16:20:30.854982 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:20:30.872729 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:20:30.873008 PROGRESS: Total precursors accumulated: 92,867
2 days, 16:20:30.873085 PROGRESS: Target precursors: 55,212 (59.45%)
2 days, 16:20:30.873143 PROGRESS: Decoy precursors: 37,655 (40.55%)
2 days, 16:20:30.873195 PROGRESS: 
2 days, 16:20:30.873266 PROGRESS: Precursor Summary:
2 days, 16:20:30.875034 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
2 days, 16:20:30.875165 PROGRESS: 
2 days, 16:20:30.875227 PROGRESS: Protein Summary:
2 days, 16:20:30.876849 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
2 days, 16:20:30.876947 PROGRESS: =========================================================================
2 days, 16:20:30.879122 INFO: Target number of precursors not reached yet.
2 days, 16:20:31.633733 INFO: Starting optimization step 9.
2 days, 16:20:31.634037 PROGRESS: === Extracting elution groups 102200 to 204600 ===
2 days, 16:20:31.634153 INFO: Using python extraction backend
2 days, 16:20:31.634280 PROGRESS: Extracting batch of 204132 precursors
2 days, 16:20:31.634358 INFO: === Search parameters used ===
2 days, 16:20:31.634413 INFO: rt_error       : 1199.986106
2 days, 16:20:31.634461 INFO: mobility_error : 0.1
2 days, 16:20:31.634508 INFO: num_candidates : 1
2 days, 16:20:31.634555 INFO: ms1_error      : 30
2 days, 16:20:31.634599 INFO: ms2_error      : 30
2 days, 16:20:31.634642 INFO: fwhm_rt        : 5
2 days, 16:20:31.634684 INFO: quant_window   : 3
2 days, 16:20:31.634726 INFO: ==============================================
2 days, 16:20:31.685534 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:20:31.685681 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:20:31.685715 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:20:31.685739 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:20:31.688011 INFO: Starting candidate selection
2 days, 16:30:01.502831 INFO: Starting candidate scoring
2 days, 16:30:04.508865 INFO: Finished candidate processing
2 days, 16:30:04.509015 INFO: Collecting candidate features
2 days, 16:30:04.908529 WARNING: intensity_correlation has 45 NaNs ( 0.02 % out of 183734)
2 days, 16:30:04.908949 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 183734)
2 days, 16:30:04.919308 INFO: Collecting fragment features
2 days, 16:30:05.042378 INFO: Finished candidate scoring
2 days, 16:30:05.269559 INFO: performing precursor FDR with 47 features
2 days, 16:30:05.269709 INFO: Decoy channel: -1
2 days, 16:30:05.269737 INFO: competitive: True
2 days, 16:30:05.431200 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:30:05.494061 WARNING: dropped 36 target PSMs due to missing features
2 days, 16:30:05.494200 WARNING: dropped 56 decoy PSMs due to missing features
2 days, 16:30:05.619842 INFO: Estimating optimal hyperparameters - samples: 293,454, batch_size: 1,201, learning_rate: 5.41e-04
2 days, 16:30:05.620887 INFO: Using random state 451760 for train-test-split
2 days, 16:30:15.196168 INFO: Test AUC: 0.544
2 days, 16:30:15.196337 INFO: Train AUC: 0.585
2 days, 16:30:15.196373 INFO: AUC difference: 7.01%
2 days, 16:30:15.196397 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 16:30:15.563678 INFO: Resetting torch num_threads to 80
2 days, 16:30:15.631855 PROGRESS: === Extracted 366910 precursors and 3130888 fragments ===
2 days, 16:30:15.632812 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:30:15.663771 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:30:15.664080 PROGRESS: Total precursors accumulated: 186,020
2 days, 16:30:15.664172 PROGRESS: Target precursors: 108,721 (58.45%)
2 days, 16:30:15.664235 PROGRESS: Decoy precursors: 77,299 (41.55%)
2 days, 16:30:15.664289 PROGRESS: 
2 days, 16:30:15.664341 PROGRESS: Precursor Summary:
2 days, 16:30:15.666520 PROGRESS: Channel   0:	 0.050 FDR:    66; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 16:30:15.666625 PROGRESS: 
2 days, 16:30:15.666690 PROGRESS: Protein Summary:
2 days, 16:30:15.668692 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 16:30:15.668795 PROGRESS: =========================================================================
2 days, 16:30:15.672530 INFO: Target number of precursors not reached yet.
2 days, 16:30:16.673046 INFO: Starting optimization step 10.
2 days, 16:30:16.673353 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 16:30:16.673474 INFO: Using python extraction backend
2 days, 16:30:16.673645 PROGRESS: Extracting batch of 408390 precursors
2 days, 16:30:16.673737 INFO: === Search parameters used ===
2 days, 16:30:16.673794 INFO: rt_error       : 1199.986106
2 days, 16:30:16.673843 INFO: mobility_error : 0.1
2 days, 16:30:16.673909 INFO: num_candidates : 1
2 days, 16:30:16.673959 INFO: ms1_error      : 30
2 days, 16:30:16.674004 INFO: ms2_error      : 30
2 days, 16:30:16.674047 INFO: fwhm_rt        : 5
2 days, 16:30:16.674108 INFO: quant_window   : 3
2 days, 16:30:16.674154 INFO: ==============================================
2 days, 16:30:16.769068 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:30:16.769229 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:30:16.769265 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:30:16.769289 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:30:16.770356 INFO: Starting candidate selection
2 days, 16:49:07.188174 INFO: Starting candidate scoring
2 days, 16:49:13.131724 INFO: Finished candidate processing
2 days, 16:49:13.132178 INFO: Collecting candidate features
2 days, 16:49:14.019977 WARNING: intensity_correlation has 85 NaNs ( 0.02 % out of 366410)
2 days, 16:49:14.020576 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 366410)
2 days, 16:49:14.035142 INFO: Collecting fragment features
2 days, 16:49:14.261967 INFO: Finished candidate scoring
2 days, 16:49:14.802476 INFO: performing precursor FDR with 47 features
2 days, 16:49:14.802652 INFO: Decoy channel: -1
2 days, 16:49:14.802683 INFO: competitive: True
2 days, 16:49:15.097129 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 16:49:15.255275 WARNING: dropped 76 target PSMs due to missing features
2 days, 16:49:15.255450 WARNING: dropped 101 decoy PSMs due to missing features
2 days, 16:49:15.529902 INFO: Estimating optimal hyperparameters - samples: 586,514, batch_size: 2,402, learning_rate: 7.66e-04
2 days, 16:49:15.533576 INFO: Using random state 936133 for train-test-split
2 days, 16:49:30.824968 INFO: Test AUC: 0.543
2 days, 16:49:30.825360 INFO: Train AUC: 0.570
2 days, 16:49:30.825400 INFO: AUC difference: 4.66%
2 days, 16:49:31.306008 INFO: Resetting torch num_threads to 80
2 days, 16:49:31.646129 PROGRESS: === Extracted 733320 precursors and 6258218 fragments ===
2 days, 16:49:31.647276 INFO: === FDR correction performed with classifier version -1 ===
2 days, 16:49:31.707603 PROGRESS: ============================= Precursor FDR =============================
2 days, 16:49:31.707937 PROGRESS: Total precursors accumulated: 371,792
2 days, 16:49:31.708014 PROGRESS: Target precursors: 212,813 (57.24%)
2 days, 16:49:31.708077 PROGRESS: Decoy precursors: 158,979 (42.76%)
2 days, 16:49:31.708131 PROGRESS: 
2 days, 16:49:31.708185 PROGRESS: Precursor Summary:
2 days, 16:49:31.711646 PROGRESS: Channel   0:	 0.050 FDR:   255; 0.010 FDR:   134; 0.001 FDR:    21
2 days, 16:49:31.711786 PROGRESS: 
2 days, 16:49:31.711852 PROGRESS: Protein Summary:
2 days, 16:49:31.714984 PROGRESS: Channel   0:	 0.050 FDR:   204; 0.010 FDR:   105; 0.001 FDR:    21
2 days, 16:49:31.715100 PROGRESS: =========================================================================
2 days, 16:49:31.728412 INFO: Target number of precursors not reached yet.
2 days, 16:49:33.115831 INFO: Starting optimization step 11.
2 days, 16:49:33.116146 PROGRESS: === Extracting elution groups 409400 to 819000 ===
2 days, 16:49:33.116267 INFO: Using python extraction backend
2 days, 16:49:33.116413 PROGRESS: Extracting batch of 816689 precursors
2 days, 16:49:33.116498 INFO: === Search parameters used ===
2 days, 16:49:33.116572 INFO: rt_error       : 1199.986106
2 days, 16:49:33.116626 INFO: mobility_error : 0.1
2 days, 16:49:33.116676 INFO: num_candidates : 1
2 days, 16:49:33.116725 INFO: ms1_error      : 30
2 days, 16:49:33.116779 INFO: ms2_error      : 30
2 days, 16:49:33.116826 INFO: fwhm_rt        : 5
2 days, 16:49:33.116868 INFO: quant_window   : 3
2 days, 16:49:33.116913 INFO: ==============================================
2 days, 16:49:33.303230 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 16:49:33.303394 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 16:49:33.303435 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 16:49:33.303464 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 16:49:33.324656 INFO: Starting candidate selection
2 days, 17:26:48.929748 INFO: Starting candidate scoring
2 days, 17:27:00.909763 INFO: Finished candidate processing
2 days, 17:27:00.910023 INFO: Collecting candidate features
2 days, 17:27:02.734015 WARNING: intensity_correlation has 171 NaNs ( 0.02 % out of 734116)
2 days, 17:27:02.734900 WARNING: height_correlation has 8 NaNs ( 0.00 % out of 734116)
2 days, 17:27:02.759504 INFO: Collecting fragment features
2 days, 17:27:03.225921 INFO: Finished candidate scoring
2 days, 17:27:04.110270 INFO: performing precursor FDR with 47 features
2 days, 17:27:04.110539 INFO: Decoy channel: -1
2 days, 17:27:04.110581 INFO: competitive: True
2 days, 17:27:04.694736 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 17:27:04.925179 WARNING: dropped 160 target PSMs due to missing features
2 days, 17:27:04.925369 WARNING: dropped 194 decoy PSMs due to missing features
2 days, 17:27:05.534960 INFO: Estimating optimal hyperparameters - samples: 1,173,665, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 17:27:05.537218 INFO: Using random state 984943 for train-test-split
2 days, 17:27:31.901643 INFO: Test AUC: 0.546
2 days, 17:27:31.901828 INFO: Train AUC: 0.561
2 days, 17:27:31.901887 INFO: AUC difference: 2.66%
2 days, 17:27:32.619670 INFO: Resetting torch num_threads to 80
2 days, 17:27:32.830762 PROGRESS: === Extracted 1467436 precursors and 12518735 fragments ===
2 days, 17:27:32.832166 INFO: === FDR correction performed with classifier version -1 ===
2 days, 17:27:32.948787 PROGRESS: ============================= Precursor FDR =============================
2 days, 17:27:32.949107 PROGRESS: Total precursors accumulated: 743,928
2 days, 17:27:32.949187 PROGRESS: Target precursors: 422,166 (56.75%)
2 days, 17:27:32.949247 PROGRESS: Decoy precursors: 321,762 (43.25%)
2 days, 17:27:32.949301 PROGRESS: 
2 days, 17:27:32.949352 PROGRESS: Precursor Summary:
2 days, 17:27:32.955025 PROGRESS: Channel   0:	 0.050 FDR:   666; 0.010 FDR:   408; 0.001 FDR:     0
2 days, 17:27:32.955179 PROGRESS: 
2 days, 17:27:32.955245 PROGRESS: Protein Summary:
2 days, 17:27:32.960132 PROGRESS: Channel   0:	 0.050 FDR:   442; 0.010 FDR:   272; 0.001 FDR:     0
2 days, 17:27:32.960241 PROGRESS: =========================================================================
2 days, 17:27:32.970319 INFO: Target number of precursors reached.
2 days, 17:27:34.386216 INFO: fragments_df: keeping 3914 of 12518735 [sum(precursor_idx_mask)=4468 sum(mass_error_mask)=12518701 stop_rank=3914
2 days, 17:27:35.864501 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 17:27:35.995511 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 17:27:36.117833 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 17:27:36.258000 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 17:27:36.731423 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 17:27:36.731866 INFO: Using score_cutoff 42.10534745178222 (fac=0.99, q=1)
2 days, 17:27:36.732221 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1644349098205566
2 days, 17:27:36.732312 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008459225296974182
2 days, 17:27:36.732382 INFO: Updating optimization_manager: score_cutoff        : 0 -> 42.10534745178222
2 days, 17:27:36.732453 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 17:27:36.832982 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 17:27:37.348691 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 17:27:37.457810 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 17:27:38.394864 INFO: Updating optimization_manager: classifier_version  : -1 -> 11
2 days, 17:27:38.395189 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 17:27:38.395349 INFO: Starting optimization step 12.
2 days, 17:27:38.395453 PROGRESS: === Extracting elution groups 0 to 409400 ===
2 days, 17:27:38.395553 INFO: Using python extraction backend
2 days, 17:27:38.395723 PROGRESS: Extracting batch of 816307 precursors
2 days, 17:27:38.395827 INFO: === Search parameters used ===
2 days, 17:27:38.395906 INFO: rt_error       : 1199.986106
2 days, 17:27:38.395976 INFO: mobility_error : 0.1
2 days, 17:27:38.396042 INFO: num_candidates : 3
2 days, 17:27:38.396105 INFO: ms1_error      : 30
2 days, 17:27:38.396166 INFO: ms2_error      : 30
2 days, 17:27:38.396228 INFO: fwhm_rt        : 3.1644349098205566
2 days, 17:27:38.396290 INFO: quant_window   : 3
2 days, 17:27:38.396350 INFO: ==============================================
2 days, 17:27:38.590410 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 17:27:38.590544 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 17:27:38.590605 INFO: FWHM in RT is 3.16 seconds, sigma is 0.53
2 days, 17:27:38.590642 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.58
2 days, 17:27:38.591476 INFO: Starting candidate selection
2 days, 18:08:37.024039 INFO: Starting candidate scoring
2 days, 18:09:09.251870 INFO: Finished candidate processing
2 days, 18:09:09.252107 INFO: Collecting candidate features
2 days, 18:09:13.246685 WARNING: intensity_correlation has 550 NaNs ( 0.03 % out of 2104818)
2 days, 18:09:13.248881 WARNING: height_correlation has 40 NaNs ( 0.00 % out of 2104818)
2 days, 18:09:13.320519 INFO: Collecting fragment features
2 days, 18:09:14.481365 INFO: Finished candidate scoring
2 days, 18:09:15.592753 INFO: performing precursor FDR with 47 features
2 days, 18:09:15.592908 INFO: Decoy channel: -1
2 days, 18:09:15.592946 INFO: competitive: True
2 days, 18:09:16.064314 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 18:09:16.360457 WARNING: dropped 251 target PSMs due to missing features
2 days, 18:09:16.360628 WARNING: dropped 328 decoy PSMs due to missing features
2 days, 18:09:17.129129 INFO: Estimating optimal hyperparameters - samples: 1,683,391, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 18:09:17.132722 INFO: Using random state 252907 for train-test-split
2 days, 18:09:55.662144 INFO: Test AUC: 0.556
2 days, 18:09:55.662331 INFO: Train AUC: 0.566
2 days, 18:09:55.662366 INFO: AUC difference: 1.70%
2 days, 18:09:56.593173 INFO: Resetting torch num_threads to 80
2 days, 18:09:56.629831 PROGRESS: === Extracted 2104818 precursors and 17556174 fragments ===
2 days, 18:09:56.631006 INFO: === FDR correction performed with classifier version 11 ===
2 days, 18:09:56.689714 PROGRESS: ============================= Precursor FDR =============================
2 days, 18:09:56.690039 PROGRESS: Total precursors accumulated: 374,778
2 days, 18:09:56.690121 PROGRESS: Target precursors: 219,048 (58.45%)
2 days, 18:09:56.690181 PROGRESS: Decoy precursors: 155,730 (41.55%)
2 days, 18:09:56.690235 PROGRESS: 
2 days, 18:09:56.690289 PROGRESS: Precursor Summary:
2 days, 18:09:56.693708 PROGRESS: Channel   0:	 0.050 FDR:   408; 0.010 FDR:   288; 0.001 FDR:   231
2 days, 18:09:56.693848 PROGRESS: 
2 days, 18:09:56.694060 PROGRESS: Protein Summary:
2 days, 18:09:56.697279 PROGRESS: Channel   0:	 0.050 FDR:   320; 0.010 FDR:   220; 0.001 FDR:   180
2 days, 18:09:56.697384 PROGRESS: =========================================================================
2 days, 18:09:56.729047 INFO: Target number of precursors reached.
2 days, 18:09:58.585413 INFO: fragments_df: keeping 5000 of 17556174 [sum(precursor_idx_mask)=8641 sum(mass_error_mask)=17556103 stop_rank=5000
2 days, 18:10:00.033151 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 18:10:00.173999 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 18:10:00.309150 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 18:10:00.442274 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 18:10:01.164739 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 18:10:01.165194 INFO: Using score_cutoff 37.47138923377991 (fac=0.99, q=1)
2 days, 18:10:01.165545 INFO: Updating optimization_manager: fwhm_rt             : 3.1644349098205566 -> 3.0829579830169678
2 days, 18:10:01.165634 INFO: Updating optimization_manager: fwhm_mobility       : 0.008459225296974182 -> 0.007988717406988144
2 days, 18:10:01.165698 INFO: Updating optimization_manager: score_cutoff        : 42.10534745178222 -> 37.47138923377991
2 days, 18:10:01.165766 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 18:10:01.275238 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 18:10:01.796989 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 18:10:01.908898 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 18:10:02.912106 INFO: === checking if optimization conditions were reached ===
2 days, 18:10:02.914458 INFO: Updating optimization_manager: ms2_error           : 30 -> 16.064508446595344
2 days, 18:10:02.914651 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
2 days, 18:10:02.914731 PROGRESS: ❌ ms2_error      : 16.0645 > 15.0000 or insufficient steps taken.
2 days, 18:10:02.915844 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 18:10:02.915951 INFO: Updating optimization_manager: classifier_version  : 12 -> 12
2 days, 18:10:02.916025 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 18:10:02.916089 INFO: ==============================================
2 days, 18:10:02.916165 INFO: Starting optimization step 13.
2 days, 18:10:02.916235 PROGRESS: === Extracting elution groups 0 to 409400 ===
2 days, 18:10:02.916311 INFO: Using python extraction backend
2 days, 18:10:02.916436 PROGRESS: Extracting batch of 816307 precursors
2 days, 18:10:02.916513 INFO: === Search parameters used ===
2 days, 18:10:02.916568 INFO: rt_error       : 1199.986106
2 days, 18:10:02.916618 INFO: mobility_error : 0.1
2 days, 18:10:02.916665 INFO: num_candidates : 3
2 days, 18:10:02.916713 INFO: ms1_error      : 15.0
2 days, 18:10:02.916759 INFO: ms2_error      : 16.064508446595344
2 days, 18:10:02.916807 INFO: fwhm_rt        : 3.0829579830169678
2 days, 18:10:02.916853 INFO: quant_window   : 3
2 days, 18:10:02.916902 INFO: ==============================================
2 days, 18:10:03.109216 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 18:10:03.109380 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 18:10:03.109440 INFO: FWHM in RT is 3.08 seconds, sigma is 0.51
2 days, 18:10:03.109467 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.33
2 days, 18:10:03.110765 INFO: Starting candidate selection
2 days, 18:48:07.895917 INFO: Starting candidate scoring
2 days, 18:48:31.917836 INFO: Finished candidate processing
2 days, 18:48:31.918039 INFO: Collecting candidate features
2 days, 18:48:35.877725 WARNING: intensity_correlation has 1761 NaNs ( 0.08 % out of 2073944)
2 days, 18:48:35.879910 WARNING: height_correlation has 95 NaNs ( 0.00 % out of 2073944)
2 days, 18:48:35.948434 INFO: Collecting fragment features
2 days, 18:48:36.916508 INFO: Finished candidate scoring
2 days, 18:48:38.008895 INFO: performing precursor FDR with 47 features
2 days, 18:48:38.009040 INFO: Decoy channel: -1
2 days, 18:48:38.009080 INFO: competitive: True
2 days, 18:48:38.535013 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 18:48:38.823011 WARNING: dropped 891 target PSMs due to missing features
2 days, 18:48:38.823212 WARNING: dropped 929 decoy PSMs due to missing features
2 days, 18:48:39.595583 INFO: Estimating optimal hyperparameters - samples: 1,657,699, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 18:48:39.600076 INFO: Using random state 478415 for train-test-split
2 days, 18:49:20.809469 INFO: Test AUC: 0.557
2 days, 18:49:20.809641 INFO: Train AUC: 0.568
2 days, 18:49:20.809680 INFO: AUC difference: 1.93%
2 days, 18:49:21.680741 INFO: Resetting torch num_threads to 80
2 days, 18:49:21.716028 PROGRESS: === Extracted 2073944 precursors and 15112700 fragments ===
2 days, 18:49:21.717150 INFO: === FDR correction performed with classifier version 12 ===
2 days, 18:49:21.776430 PROGRESS: ============================= Precursor FDR =============================
2 days, 18:49:21.776740 PROGRESS: Total precursors accumulated: 374,384
2 days, 18:49:21.776820 PROGRESS: Target precursors: 218,084 (58.25%)
2 days, 18:49:21.776881 PROGRESS: Decoy precursors: 156,300 (41.75%)
2 days, 18:49:21.776933 PROGRESS: 
2 days, 18:49:21.776984 PROGRESS: Precursor Summary:
2 days, 18:49:21.780425 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   406; 0.001 FDR:   248
2 days, 18:49:21.780565 PROGRESS: 
2 days, 18:49:21.780638 PROGRESS: Protein Summary:
2 days, 18:49:21.784030 PROGRESS: Channel   0:	 0.050 FDR:   453; 0.010 FDR:   304; 0.001 FDR:   186
2 days, 18:49:21.784139 PROGRESS: =========================================================================
2 days, 18:49:21.798126 INFO: Target number of precursors reached.
2 days, 18:49:23.433318 INFO: fragments_df: keeping 5000 of 15112700 [sum(precursor_idx_mask)=11386 sum(mass_error_mask)=15112629 stop_rank=5000
2 days, 18:49:24.542514 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 18:49:24.694921 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 18:49:24.847120 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 18:49:24.992586 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 18:49:25.711763 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 18:49:25.712210 INFO: Using score_cutoff 29.878511867523194 (fac=0.99, q=1)
2 days, 18:49:25.712573 INFO: Updating optimization_manager: fwhm_rt             : 3.0829579830169678 -> 2.910709857940674
2 days, 18:49:25.712663 INFO: Updating optimization_manager: fwhm_mobility       : 0.007988717406988144 -> 0.006767905317246914
2 days, 18:49:25.712725 INFO: Updating optimization_manager: score_cutoff        : 37.47138923377991 -> 29.878511867523194
2 days, 18:49:25.712790 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 18:49:25.761549 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 18:49:26.018545 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 18:49:26.074265 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 18:49:26.575429 INFO: === checking if optimization conditions were reached ===
2 days, 18:49:26.577677 INFO: Updating optimization_manager: ms2_error           : 16.064508446595344 -> 15.0
2 days, 18:49:26.577831 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
2 days, 18:49:26.577925 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 18:49:26.579012 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 18:49:26.579118 INFO: Updating optimization_manager: classifier_version  : 13 -> 13
2 days, 18:49:26.579188 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 18:49:26.579250 INFO: ==============================================
2 days, 18:49:26.579329 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 18:49:27.130629 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 18:49:27.179861 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 18:49:27.436975 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 18:49:27.492712 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 18:49:27.996288 INFO: Starting optimization step 0.
2 days, 18:49:27.996578 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 18:49:27.996674 INFO: Using python extraction backend
2 days, 18:49:27.996813 PROGRESS: Extracting batch of 407917 precursors
2 days, 18:49:27.996896 INFO: === Search parameters used ===
2 days, 18:49:27.996955 INFO: rt_error       : 1199.986106
2 days, 18:49:27.997004 INFO: mobility_error : 0.1
2 days, 18:49:27.997053 INFO: num_candidates : 3
2 days, 18:49:27.997099 INFO: ms1_error      : 15.0
2 days, 18:49:27.997142 INFO: ms2_error      : 15.0
2 days, 18:49:27.997186 INFO: fwhm_rt        : 2.910709857940674
2 days, 18:49:27.997229 INFO: quant_window   : 3
2 days, 18:49:27.997271 INFO: ==============================================
2 days, 18:49:28.095968 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 18:49:28.096117 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 18:49:28.096175 INFO: FWHM in RT is 2.91 seconds, sigma is 0.49
2 days, 18:49:28.096199 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.67
2 days, 18:49:28.096968 INFO: Starting candidate selection
2 days, 19:08:25.702037 INFO: Starting candidate scoring
2 days, 19:08:37.401366 INFO: Finished candidate processing
2 days, 19:08:37.401550 INFO: Collecting candidate features
2 days, 19:08:39.327203 WARNING: intensity_correlation has 985 NaNs ( 0.10 % out of 1028442)
2 days, 19:08:39.328452 WARNING: height_correlation has 46 NaNs ( 0.00 % out of 1028442)
2 days, 19:08:39.364846 INFO: Collecting fragment features
2 days, 19:08:39.948471 INFO: Finished candidate scoring
2 days, 19:08:40.507341 INFO: performing precursor FDR with 47 features
2 days, 19:08:40.507490 INFO: Decoy channel: -1
2 days, 19:08:40.507523 INFO: competitive: True
2 days, 19:08:40.743063 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 19:08:40.893300 WARNING: dropped 486 target PSMs due to missing features
2 days, 19:08:40.893473 WARNING: dropped 528 decoy PSMs due to missing features
2 days, 19:08:41.285613 INFO: Estimating optimal hyperparameters - samples: 821,942, batch_size: 3,366, learning_rate: 9.07e-04
2 days, 19:08:41.287184 INFO: Using random state 589792 for train-test-split
2 days, 19:09:01.331781 INFO: Test AUC: 0.561
2 days, 19:09:01.331952 INFO: Train AUC: 0.577
2 days, 19:09:01.331989 INFO: AUC difference: 2.70%
2 days, 19:09:01.900915 INFO: Resetting torch num_threads to 80
2 days, 19:09:01.920556 PROGRESS: === Extracted 1028442 precursors and 7335023 fragments ===
2 days, 19:09:01.921422 INFO: === FDR correction performed with classifier version 13 ===
2 days, 19:09:01.952263 PROGRESS: ============================= Precursor FDR =============================
2 days, 19:09:01.952565 PROGRESS: Total precursors accumulated: 186,600
2 days, 19:09:01.952650 PROGRESS: Target precursors: 109,966 (58.93%)
2 days, 19:09:01.952711 PROGRESS: Decoy precursors: 76,634 (41.07%)
2 days, 19:09:01.952766 PROGRESS: 
2 days, 19:09:01.952819 PROGRESS: Precursor Summary:
2 days, 19:09:01.955059 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   223; 0.001 FDR:   172
2 days, 19:09:01.955167 PROGRESS: 
2 days, 19:09:01.955235 PROGRESS: Protein Summary:
2 days, 19:09:01.957365 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   187; 0.001 FDR:   145
2 days, 19:09:01.957466 PROGRESS: =========================================================================
2 days, 19:09:01.995756 INFO: Target number of precursors reached.
2 days, 19:09:02.782411 INFO: fragments_df: keeping 3797 of 7335023 [sum(precursor_idx_mask)=6249 sum(mass_error_mask)=7335006 stop_rank=3797
2 days, 19:09:03.882525 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:09:04.017238 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:09:08.242432 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:09:08.381749 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:09:08.922662 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 19:09:08.923135 INFO: Using score_cutoff 27.61165768318176 (fac=0.99, q=1)
2 days, 19:09:08.923442 INFO: Updating optimization_manager: fwhm_rt             : 2.910709857940674 -> 2.9594154357910156
2 days, 19:09:08.923528 INFO: Updating optimization_manager: fwhm_mobility       : 0.006767905317246914 -> 0.006354589480906725
2 days, 19:09:08.923588 INFO: Updating optimization_manager: score_cutoff        : 29.878511867523194 -> 27.61165768318176
2 days, 19:09:08.923646 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:09:08.975102 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:09:09.233883 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:09:09.288653 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:09:09.790521 INFO: === checking if optimization conditions were reached ===
2 days, 19:09:09.790855 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 19:09:09.792860 INFO: Updating optimization_manager: rt_error            : 1199.986106 -> 614.6278281638431
2 days, 19:09:09.792998 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 614.6278.
2 days, 19:09:09.793074 INFO: ==============================================
2 days, 19:09:09.793154 INFO: Starting optimization step 1.
2 days, 19:09:09.793224 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 19:09:09.793298 INFO: Using python extraction backend
2 days, 19:09:09.793406 PROGRESS: Extracting batch of 407917 precursors
2 days, 19:09:09.793479 INFO: === Search parameters used ===
2 days, 19:09:09.793537 INFO: rt_error       : 614.6278281638431
2 days, 19:09:09.793586 INFO: mobility_error : 0.1
2 days, 19:09:09.793635 INFO: num_candidates : 3
2 days, 19:09:09.793682 INFO: ms1_error      : 15.0
2 days, 19:09:09.793729 INFO: ms2_error      : 15.0
2 days, 19:09:09.793778 INFO: fwhm_rt        : 2.9594154357910156
2 days, 19:09:09.793826 INFO: quant_window   : 3
2 days, 19:09:09.793892 INFO: ==============================================
2 days, 19:09:09.902497 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 19:09:09.902662 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 19:09:09.902708 INFO: FWHM in RT is 2.96 seconds, sigma is 0.49
2 days, 19:09:09.902732 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.44
2 days, 19:09:09.903637 INFO: Starting candidate selection
2 days, 19:20:48.423690 INFO: Starting candidate scoring
2 days, 19:21:00.515615 INFO: Finished candidate processing
2 days, 19:21:00.515907 INFO: Collecting candidate features
2 days, 19:21:02.383155 WARNING: intensity_correlation has 1311 NaNs ( 0.13 % out of 1013245)
2 days, 19:21:02.384241 WARNING: height_correlation has 81 NaNs ( 0.01 % out of 1013245)
2 days, 19:21:02.419774 INFO: Collecting fragment features
2 days, 19:21:03.026277 INFO: Finished candidate scoring
2 days, 19:21:03.588874 INFO: performing precursor FDR with 47 features
2 days, 19:21:03.589024 INFO: Decoy channel: -1
2 days, 19:21:03.589060 INFO: competitive: True
2 days, 19:21:03.843447 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 19:21:03.988319 WARNING: dropped 641 target PSMs due to missing features
2 days, 19:21:03.988489 WARNING: dropped 724 decoy PSMs due to missing features
2 days, 19:21:04.335683 INFO: Estimating optimal hyperparameters - samples: 809,504, batch_size: 3,315, learning_rate: 9.00e-04
2 days, 19:21:04.337342 INFO: Using random state 589792 for train-test-split
2 days, 19:21:23.865219 INFO: Test AUC: 0.555
2 days, 19:21:23.865390 INFO: Train AUC: 0.575
2 days, 19:21:23.865427 INFO: AUC difference: 3.39%
2 days, 19:21:24.442678 INFO: Resetting torch num_threads to 80
2 days, 19:21:24.461659 PROGRESS: === Extracted 1013245 precursors and 7067445 fragments ===
2 days, 19:21:24.462586 INFO: === FDR correction performed with classifier version 13 ===
2 days, 19:21:24.492398 PROGRESS: ============================= Precursor FDR =============================
2 days, 19:21:24.492683 PROGRESS: Total precursors accumulated: 186,182
2 days, 19:21:24.492751 PROGRESS: Target precursors: 108,679 (58.37%)
2 days, 19:21:24.492804 PROGRESS: Decoy precursors: 77,503 (41.63%)
2 days, 19:21:24.492860 PROGRESS: 
2 days, 19:21:24.492908 PROGRESS: Precursor Summary:
2 days, 19:21:24.495177 PROGRESS: Channel   0:	 0.050 FDR:   294; 0.010 FDR:    53; 0.001 FDR:    53
2 days, 19:21:24.495282 PROGRESS: 
2 days, 19:21:24.495342 PROGRESS: Protein Summary:
2 days, 19:21:24.497457 PROGRESS: Channel   0:	 0.050 FDR:   252; 0.010 FDR:    49; 0.001 FDR:    49
2 days, 19:21:24.497553 PROGRESS: =========================================================================
2 days, 19:21:24.508238 INFO: Target number of precursors not reached yet.
2 days, 19:21:25.615611 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:21:25.667866 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:21:25.926348 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:21:25.976496 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:21:26.473548 INFO: === skipping optimization until target number of precursors are found ===
2 days, 19:21:26.474000 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 19:21:26.474165 INFO: Starting optimization step 2.
2 days, 19:21:26.474286 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 19:21:26.474391 INFO: Using python extraction backend
2 days, 19:21:26.474554 PROGRESS: Extracting batch of 408390 precursors
2 days, 19:21:26.474671 INFO: === Search parameters used ===
2 days, 19:21:26.474754 INFO: rt_error       : 614.6278281638431
2 days, 19:21:26.474830 INFO: mobility_error : 0.1
2 days, 19:21:26.474896 INFO: num_candidates : 3
2 days, 19:21:26.474957 INFO: ms1_error      : 15.0
2 days, 19:21:26.475016 INFO: ms2_error      : 15.0
2 days, 19:21:26.475073 INFO: fwhm_rt        : 2.9594154357910156
2 days, 19:21:26.475130 INFO: quant_window   : 3
2 days, 19:21:26.475190 INFO: ==============================================
2 days, 19:21:26.574170 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 19:21:26.574331 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 19:21:26.574399 INFO: FWHM in RT is 2.96 seconds, sigma is 0.49
2 days, 19:21:26.574435 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.44
2 days, 19:21:26.575405 INFO: Starting candidate selection
2 days, 19:33:12.333160 INFO: Starting candidate scoring
2 days, 19:33:24.140305 INFO: Finished candidate processing
2 days, 19:33:24.140558 INFO: Collecting candidate features
2 days, 19:33:26.054715 WARNING: intensity_correlation has 1411 NaNs ( 0.14 % out of 1011820)
2 days, 19:33:26.055831 WARNING: height_correlation has 73 NaNs ( 0.01 % out of 1011820)
2 days, 19:33:26.092433 INFO: Collecting fragment features
2 days, 19:33:26.695735 INFO: Finished candidate scoring
2 days, 19:33:28.003256 INFO: performing precursor FDR with 47 features
2 days, 19:33:28.003400 INFO: Decoy channel: -1
2 days, 19:33:28.003430 INFO: competitive: True
2 days, 19:33:28.827646 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 19:33:29.118478 WARNING: dropped 1329 target PSMs due to missing features
2 days, 19:33:29.118654 WARNING: dropped 1488 decoy PSMs due to missing features
2 days, 19:33:29.988535 INFO: Estimating optimal hyperparameters - samples: 1,617,798, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 19:33:29.991637 INFO: Using random state 589792 for train-test-split
2 days, 19:34:08.095933 INFO: Test AUC: 0.556
2 days, 19:34:08.096112 INFO: Train AUC: 0.568
2 days, 19:34:08.096149 INFO: AUC difference: 2.09%
2 days, 19:34:09.002198 INFO: Resetting torch num_threads to 80
2 days, 19:34:09.397276 PROGRESS: === Extracted 2025065 precursors and 14120993 fragments ===
2 days, 19:34:09.398371 INFO: === FDR correction performed with classifier version 13 ===
2 days, 19:34:09.456753 PROGRESS: ============================= Precursor FDR =============================
2 days, 19:34:09.457098 PROGRESS: Total precursors accumulated: 372,084
2 days, 19:34:09.457172 PROGRESS: Target precursors: 215,700 (57.97%)
2 days, 19:34:09.457234 PROGRESS: Decoy precursors: 156,384 (42.03%)
2 days, 19:34:09.457289 PROGRESS: 
2 days, 19:34:09.457341 PROGRESS: Precursor Summary:
2 days, 19:34:09.460885 PROGRESS: Channel   0:	 0.050 FDR:   648; 0.010 FDR:   475; 0.001 FDR:   338
2 days, 19:34:09.461023 PROGRESS: 
2 days, 19:34:09.461104 PROGRESS: Protein Summary:
2 days, 19:34:09.464369 PROGRESS: Channel   0:	 0.050 FDR:   513; 0.010 FDR:   358; 0.001 FDR:   256
2 days, 19:34:09.464482 PROGRESS: =========================================================================
2 days, 19:34:09.471772 INFO: Target number of precursors reached.
2 days, 19:34:10.970547 INFO: fragments_df: keeping 5000 of 14120993 [sum(precursor_idx_mask)=13018 sum(mass_error_mask)=14120899 stop_rank=5000
2 days, 19:34:12.056358 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:34:12.218811 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:34:12.378278 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:34:12.529676 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:34:13.255142 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 19:34:13.255601 INFO: Using score_cutoff 25.874624727630614 (fac=0.99, q=1)
2 days, 19:34:13.255946 INFO: Updating optimization_manager: fwhm_rt             : 2.9594154357910156 -> 2.8131988048553467
2 days, 19:34:13.256031 INFO: Updating optimization_manager: fwhm_mobility       : 0.006354589480906725 -> 0.006044815294444561
2 days, 19:34:13.256092 INFO: Updating optimization_manager: score_cutoff        : 27.61165768318176 -> 25.874624727630614
2 days, 19:34:13.256153 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:34:13.306375 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:34:13.563159 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:34:13.617887 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:34:14.110728 INFO: === checking if optimization conditions were reached ===
2 days, 19:34:14.111060 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 19:34:14.113444 INFO: Updating optimization_manager: rt_error            : 614.6278281638431 -> 492.4429618789062
2 days, 19:34:14.113591 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 492.4430.
2 days, 19:34:14.113669 INFO: ==============================================
2 days, 19:34:14.113747 INFO: Starting optimization step 3.
2 days, 19:34:14.113815 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 19:34:14.113891 INFO: Using python extraction backend
2 days, 19:34:14.114018 PROGRESS: Extracting batch of 407917 precursors
2 days, 19:34:14.114094 INFO: === Search parameters used ===
2 days, 19:34:14.114151 INFO: rt_error       : 492.4429618789062
2 days, 19:34:14.114202 INFO: mobility_error : 0.1
2 days, 19:34:14.114253 INFO: num_candidates : 3
2 days, 19:34:14.114302 INFO: ms1_error      : 15.0
2 days, 19:34:14.114351 INFO: ms2_error      : 15.0
2 days, 19:34:14.114399 INFO: fwhm_rt        : 2.8131988048553467
2 days, 19:34:14.114450 INFO: quant_window   : 3
2 days, 19:34:14.114501 INFO: ==============================================
2 days, 19:34:14.225748 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 19:34:14.225906 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 19:34:14.225959 INFO: FWHM in RT is 2.81 seconds, sigma is 0.47
2 days, 19:34:14.225985 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.28
2 days, 19:34:14.226957 INFO: Starting candidate selection
2 days, 19:42:50.259568 INFO: Starting candidate scoring
2 days, 19:43:02.898459 INFO: Finished candidate processing
2 days, 19:43:02.898734 INFO: Collecting candidate features
2 days, 19:43:04.778072 WARNING: intensity_correlation has 1607 NaNs ( 0.16 % out of 997909)
2 days, 19:43:04.779206 WARNING: height_correlation has 109 NaNs ( 0.01 % out of 997909)
2 days, 19:43:04.814389 INFO: Collecting fragment features
2 days, 19:43:05.405758 INFO: Finished candidate scoring
2 days, 19:43:06.301541 INFO: performing precursor FDR with 47 features
2 days, 19:43:06.301689 INFO: Decoy channel: -1
2 days, 19:43:06.301722 INFO: competitive: True
2 days, 19:43:06.545406 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 19:43:06.701655 WARNING: dropped 809 target PSMs due to missing features
2 days, 19:43:06.701824 WARNING: dropped 856 decoy PSMs due to missing features
2 days, 19:43:07.050014 INFO: Estimating optimal hyperparameters - samples: 796,995, batch_size: 3,264, learning_rate: 8.93e-04
2 days, 19:43:07.052211 INFO: Using random state 589792 for train-test-split
2 days, 19:43:28.546235 INFO: Test AUC: 0.546
2 days, 19:43:28.546408 INFO: Train AUC: 0.566
2 days, 19:43:28.546446 INFO: AUC difference: 3.56%
2 days, 19:43:29.114875 INFO: Resetting torch num_threads to 80
2 days, 19:43:29.134340 PROGRESS: === Extracted 997909 precursors and 6702749 fragments ===
2 days, 19:43:29.135338 INFO: === FDR correction performed with classifier version 13 ===
2 days, 19:43:29.166560 PROGRESS: ============================= Precursor FDR =============================
2 days, 19:43:29.166854 PROGRESS: Total precursors accumulated: 185,254
2 days, 19:43:29.166927 PROGRESS: Target precursors: 106,671 (57.58%)
2 days, 19:43:29.166989 PROGRESS: Decoy precursors: 78,583 (42.42%)
2 days, 19:43:29.167042 PROGRESS: 
2 days, 19:43:29.167094 PROGRESS: Precursor Summary:
2 days, 19:43:29.169548 PROGRESS: Channel   0:	 0.050 FDR:   364; 0.010 FDR:   291; 0.001 FDR:   265
2 days, 19:43:29.169656 PROGRESS: 
2 days, 19:43:29.169722 PROGRESS: Protein Summary:
2 days, 19:43:29.171939 PROGRESS: Channel   0:	 0.050 FDR:   315; 0.010 FDR:   246; 0.001 FDR:   222
2 days, 19:43:29.172073 PROGRESS: =========================================================================
2 days, 19:43:29.185923 INFO: Target number of precursors reached.
2 days, 19:43:29.907195 INFO: fragments_df: keeping 4558 of 6702749 [sum(precursor_idx_mask)=7776 sum(mass_error_mask)=6702712 stop_rank=4558
2 days, 19:43:31.029526 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:43:31.175857 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:43:31.319853 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:43:31.451213 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:43:32.104334 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 19:43:32.104836 INFO: Using score_cutoff 23.36382004737854 (fac=0.99, q=1)
2 days, 19:43:32.105185 INFO: Updating optimization_manager: fwhm_rt             : 2.8131988048553467 -> 2.8236992359161377
2 days, 19:43:32.105281 INFO: Updating optimization_manager: fwhm_mobility       : 0.006044815294444561 -> 0.005627322476357222
2 days, 19:43:32.105342 INFO: Updating optimization_manager: score_cutoff        : 25.874624727630614 -> 23.36382004737854
2 days, 19:43:32.105406 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:43:32.155778 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:43:32.413293 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:43:32.472592 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:43:33.009458 INFO: === checking if optimization conditions were reached ===
2 days, 19:43:33.009762 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 19:43:33.012208 INFO: Updating optimization_manager: rt_error            : 492.4429618789062 -> 456.573394131736
2 days, 19:43:33.012378 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 456.5734.
2 days, 19:43:33.012456 INFO: ==============================================
2 days, 19:43:33.012532 INFO: Starting optimization step 4.
2 days, 19:43:33.012598 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 19:43:33.012661 INFO: Using python extraction backend
2 days, 19:43:33.012774 PROGRESS: Extracting batch of 407917 precursors
2 days, 19:43:33.012845 INFO: === Search parameters used ===
2 days, 19:43:33.012897 INFO: rt_error       : 456.573394131736
2 days, 19:43:33.012946 INFO: mobility_error : 0.1
2 days, 19:43:33.012992 INFO: num_candidates : 3
2 days, 19:43:33.013037 INFO: ms1_error      : 15.0
2 days, 19:43:33.013088 INFO: ms2_error      : 15.0
2 days, 19:43:33.013140 INFO: fwhm_rt        : 2.8236992359161377
2 days, 19:43:33.013185 INFO: quant_window   : 3
2 days, 19:43:33.013228 INFO: ==============================================
2 days, 19:43:33.124042 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 19:43:33.124201 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 19:43:33.124250 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
2 days, 19:43:33.124274 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.05
2 days, 19:43:33.125373 INFO: Starting candidate selection
2 days, 19:51:17.114382 INFO: Starting candidate scoring
2 days, 19:51:29.965709 INFO: Finished candidate processing
2 days, 19:51:29.965899 INFO: Collecting candidate features
2 days, 19:51:31.935935 WARNING: intensity_correlation has 1594 NaNs ( 0.16 % out of 989402)
2 days, 19:51:31.937197 WARNING: height_correlation has 113 NaNs ( 0.01 % out of 989402)
2 days, 19:51:31.974535 INFO: Collecting fragment features
2 days, 19:51:32.509974 INFO: Finished candidate scoring
2 days, 19:51:33.124398 INFO: performing precursor FDR with 47 features
2 days, 19:51:33.124525 INFO: Decoy channel: -1
2 days, 19:51:33.124563 INFO: competitive: True
2 days, 19:51:33.379148 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 19:51:33.534578 WARNING: dropped 785 target PSMs due to missing features
2 days, 19:51:33.534725 WARNING: dropped 876 decoy PSMs due to missing features
2 days, 19:51:33.946645 INFO: Estimating optimal hyperparameters - samples: 790,192, batch_size: 3,236, learning_rate: 8.89e-04
2 days, 19:51:33.948420 INFO: Using random state 589792 for train-test-split
2 days, 19:51:54.329010 INFO: Test AUC: 0.551
2 days, 19:51:54.329148 INFO: Train AUC: 0.569
2 days, 19:51:54.329184 INFO: AUC difference: 3.19%
2 days, 19:51:54.962637 INFO: Resetting torch num_threads to 80
2 days, 19:51:54.983060 PROGRESS: === Extracted 989402 precursors and 6615223 fragments ===
2 days, 19:51:54.983891 INFO: === FDR correction performed with classifier version 13 ===
2 days, 19:51:55.019984 PROGRESS: ============================= Precursor FDR =============================
2 days, 19:51:55.020267 PROGRESS: Total precursors accumulated: 184,199
2 days, 19:51:55.020366 PROGRESS: Target precursors: 106,511 (57.82%)
2 days, 19:51:55.020440 PROGRESS: Decoy precursors: 77,688 (42.18%)
2 days, 19:51:55.020507 PROGRESS: 
2 days, 19:51:55.020572 PROGRESS: Precursor Summary:
2 days, 19:51:55.023412 PROGRESS: Channel   0:	 0.050 FDR:   349; 0.010 FDR:   242; 0.001 FDR:   185
2 days, 19:51:55.023561 PROGRESS: 
2 days, 19:51:55.023637 PROGRESS: Protein Summary:
2 days, 19:51:55.026034 PROGRESS: Channel   0:	 0.050 FDR:   297; 0.010 FDR:   207; 0.001 FDR:   157
2 days, 19:51:55.026148 PROGRESS: =========================================================================
2 days, 19:51:55.039701 INFO: Target number of precursors reached.
2 days, 19:51:55.799361 INFO: fragments_df: keeping 3916 of 6615223 [sum(precursor_idx_mask)=6485 sum(mass_error_mask)=6615174 stop_rank=3916
2 days, 19:51:56.872378 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:51:57.006710 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:51:57.173301 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:51:57.324530 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:51:57.962712 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 19:51:57.963174 INFO: Using score_cutoff 30.751695236206057 (fac=0.99, q=1)
2 days, 19:51:57.963515 INFO: Updating optimization_manager: fwhm_rt             : 2.8236992359161377 -> 2.835481643676758
2 days, 19:51:57.963598 INFO: Updating optimization_manager: fwhm_mobility       : 0.005627322476357222 -> 0.0058456771075725555
2 days, 19:51:57.963655 INFO: Updating optimization_manager: score_cutoff        : 23.36382004737854 -> 30.751695236206057
2 days, 19:51:57.963711 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:51:58.019487 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:51:58.289664 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:51:58.360988 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:51:58.887922 INFO: === checking if optimization conditions were reached ===
2 days, 19:51:58.888195 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 19:51:58.890588 INFO: Updating optimization_manager: rt_error            : 456.573394131736 -> 326.98038554720733
2 days, 19:51:58.890738 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 326.9804.
2 days, 19:51:58.890824 INFO: ==============================================
2 days, 19:51:58.890924 INFO: Starting optimization step 5.
2 days, 19:51:58.891011 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 19:51:58.891105 INFO: Using python extraction backend
2 days, 19:51:58.891238 PROGRESS: Extracting batch of 407917 precursors
2 days, 19:51:58.891324 INFO: === Search parameters used ===
2 days, 19:51:58.891392 INFO: rt_error       : 326.98038554720733
2 days, 19:51:58.891453 INFO: mobility_error : 0.1
2 days, 19:51:58.891514 INFO: num_candidates : 3
2 days, 19:51:58.891574 INFO: ms1_error      : 15.0
2 days, 19:51:58.891637 INFO: ms2_error      : 15.0
2 days, 19:51:58.891698 INFO: fwhm_rt        : 2.835481643676758
2 days, 19:51:58.891760 INFO: quant_window   : 3
2 days, 19:51:58.891824 INFO: ==============================================
2 days, 19:51:58.999085 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 19:51:58.999216 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 19:51:58.999274 INFO: FWHM in RT is 2.84 seconds, sigma is 0.47
2 days, 19:51:58.999308 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.17
2 days, 19:51:59.002764 INFO: Starting candidate selection
2 days, 19:58:00.635971 INFO: Starting candidate scoring
2 days, 19:58:12.486496 INFO: Finished candidate processing
2 days, 19:58:12.486724 INFO: Collecting candidate features
2 days, 19:58:14.290863 WARNING: intensity_correlation has 2028 NaNs ( 0.21 % out of 961498)
2 days, 19:58:14.291907 WARNING: height_correlation has 211 NaNs ( 0.02 % out of 961498)
2 days, 19:58:14.326291 INFO: Collecting fragment features
2 days, 19:58:14.835107 INFO: Finished candidate scoring
2 days, 19:58:15.386281 INFO: performing precursor FDR with 47 features
2 days, 19:58:15.386420 INFO: Decoy channel: -1
2 days, 19:58:15.386450 INFO: competitive: True
2 days, 19:58:15.606356 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 19:58:15.745272 WARNING: dropped 1056 target PSMs due to missing features
2 days, 19:58:15.745433 WARNING: dropped 1070 decoy PSMs due to missing features
2 days, 19:58:16.062523 INFO: Estimating optimal hyperparameters - samples: 767,497, batch_size: 3,143, learning_rate: 8.76e-04
2 days, 19:58:16.064019 INFO: Using random state 589792 for train-test-split
2 days, 19:58:35.025099 INFO: Test AUC: 0.548
2 days, 19:58:35.025308 INFO: Train AUC: 0.566
2 days, 19:58:35.025345 INFO: AUC difference: 3.11%
2 days, 19:58:35.579589 INFO: Resetting torch num_threads to 80
2 days, 19:58:35.598241 PROGRESS: === Extracted 961498 precursors and 6077548 fragments ===
2 days, 19:58:35.599076 INFO: === FDR correction performed with classifier version 13 ===
2 days, 19:58:35.627992 PROGRESS: ============================= Precursor FDR =============================
2 days, 19:58:35.628291 PROGRESS: Total precursors accumulated: 183,275
2 days, 19:58:35.628361 PROGRESS: Target precursors: 104,937 (57.26%)
2 days, 19:58:35.628419 PROGRESS: Decoy precursors: 78,338 (42.74%)
2 days, 19:58:35.628469 PROGRESS: 
2 days, 19:58:35.628519 PROGRESS: Precursor Summary:
2 days, 19:58:35.630872 PROGRESS: Channel   0:	 0.050 FDR:   382; 0.010 FDR:   303; 0.001 FDR:   250
2 days, 19:58:35.630986 PROGRESS: 
2 days, 19:58:35.631068 PROGRESS: Protein Summary:
2 days, 19:58:35.633271 PROGRESS: Channel   0:	 0.050 FDR:   335; 0.010 FDR:   260; 0.001 FDR:   213
2 days, 19:58:35.633370 PROGRESS: =========================================================================
2 days, 19:58:35.640502 INFO: Target number of precursors reached.
2 days, 19:58:36.318036 INFO: fragments_df: keeping 4724 of 6077548 [sum(precursor_idx_mask)=8232 sum(mass_error_mask)=6077513 stop_rank=4724
2 days, 19:58:37.366143 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:58:37.510559 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:58:37.648543 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:58:37.786238 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:58:38.468735 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 19:58:38.469211 INFO: Using score_cutoff 24.2470387676239 (fac=0.99, q=1)
2 days, 19:58:38.469546 INFO: Updating optimization_manager: fwhm_rt             : 2.835481643676758 -> 2.845781087875366
2 days, 19:58:38.469636 INFO: Updating optimization_manager: fwhm_mobility       : 0.0058456771075725555 -> 0.005626242142170668
2 days, 19:58:38.469699 INFO: Updating optimization_manager: score_cutoff        : 30.751695236206057 -> 24.2470387676239
2 days, 19:58:38.469761 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 19:58:38.519920 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 19:58:38.781104 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 19:58:38.844093 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 19:58:39.343398 INFO: === checking if optimization conditions were reached ===
2 days, 19:58:39.343744 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 19:58:39.346061 INFO: Updating optimization_manager: rt_error            : 326.98038554720733 -> 308.29858059432456
2 days, 19:58:39.346206 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 308.2986.
2 days, 19:58:39.346286 INFO: ==============================================
2 days, 19:58:39.346364 INFO: Starting optimization step 6.
2 days, 19:58:39.346431 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 19:58:39.346493 INFO: Using python extraction backend
2 days, 19:58:39.346596 PROGRESS: Extracting batch of 407917 precursors
2 days, 19:58:39.346683 INFO: === Search parameters used ===
2 days, 19:58:39.346738 INFO: rt_error       : 308.29858059432456
2 days, 19:58:39.346788 INFO: mobility_error : 0.1
2 days, 19:58:39.346839 INFO: num_candidates : 3
2 days, 19:58:39.346887 INFO: ms1_error      : 15.0
2 days, 19:58:39.346936 INFO: ms2_error      : 15.0
2 days, 19:58:39.346984 INFO: fwhm_rt        : 2.845781087875366
2 days, 19:58:39.347030 INFO: quant_window   : 3
2 days, 19:58:39.347076 INFO: ==============================================
2 days, 19:58:39.445942 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 19:58:39.446089 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 19:58:39.446134 INFO: FWHM in RT is 2.85 seconds, sigma is 0.47
2 days, 19:58:39.446161 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.05
2 days, 19:58:39.446964 INFO: Starting candidate selection
2 days, 20:04:13.430458 INFO: Starting candidate scoring
2 days, 20:04:25.116612 INFO: Finished candidate processing
2 days, 20:04:25.116770 INFO: Collecting candidate features
2 days, 20:04:26.897367 WARNING: intensity_correlation has 2175 NaNs ( 0.23 % out of 954146)
2 days, 20:04:26.898441 WARNING: height_correlation has 234 NaNs ( 0.02 % out of 954146)
2 days, 20:04:26.932498 INFO: Collecting fragment features
2 days, 20:04:27.448318 INFO: Finished candidate scoring
2 days, 20:04:28.186816 INFO: performing precursor FDR with 47 features
2 days, 20:04:28.186973 INFO: Decoy channel: -1
2 days, 20:04:28.187010 INFO: competitive: True
2 days, 20:04:28.415346 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:04:28.560081 WARNING: dropped 1133 target PSMs due to missing features
2 days, 20:04:28.560256 WARNING: dropped 1150 decoy PSMs due to missing features
2 days, 20:04:28.891566 INFO: Estimating optimal hyperparameters - samples: 761,490, batch_size: 3,119, learning_rate: 8.73e-04
2 days, 20:04:28.893126 INFO: Using random state 589792 for train-test-split
2 days, 20:04:47.557248 INFO: Test AUC: 0.548
2 days, 20:04:47.557425 INFO: Train AUC: 0.566
2 days, 20:04:47.557470 INFO: AUC difference: 3.17%
2 days, 20:04:48.103368 INFO: Resetting torch num_threads to 80
2 days, 20:04:48.122062 PROGRESS: === Extracted 954146 precursors and 5970495 fragments ===
2 days, 20:04:48.122915 INFO: === FDR correction performed with classifier version 13 ===
2 days, 20:04:48.152497 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:04:48.152768 PROGRESS: Total precursors accumulated: 182,649
2 days, 20:04:48.152849 PROGRESS: Target precursors: 104,192 (57.04%)
2 days, 20:04:48.152917 PROGRESS: Decoy precursors: 78,457 (42.96%)
2 days, 20:04:48.152982 PROGRESS: 
2 days, 20:04:48.153046 PROGRESS: Precursor Summary:
2 days, 20:04:48.155449 PROGRESS: Channel   0:	 0.050 FDR:   425; 0.010 FDR:   271; 0.001 FDR:     6
2 days, 20:04:48.155569 PROGRESS: 
2 days, 20:04:48.155644 PROGRESS: Protein Summary:
2 days, 20:04:48.157841 PROGRESS: Channel   0:	 0.050 FDR:   367; 0.010 FDR:   230; 0.001 FDR:     6
2 days, 20:04:48.157965 PROGRESS: =========================================================================
2 days, 20:04:48.165196 INFO: Target number of precursors reached.
2 days, 20:04:48.815194 INFO: fragments_df: keeping 4087 of 5970495 [sum(precursor_idx_mask)=7176 sum(mass_error_mask)=5970458 stop_rank=4087
2 days, 20:04:49.839774 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:04:49.977449 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:04:50.113488 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:04:50.249141 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:04:50.823896 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 20:04:50.824370 INFO: Using score_cutoff 7.842497918128967 (fac=0.99, q=1)
2 days, 20:04:50.824702 INFO: Updating optimization_manager: fwhm_rt             : 2.845781087875366 -> 2.9259421825408936
2 days, 20:04:50.824795 INFO: Updating optimization_manager: fwhm_mobility       : 0.005626242142170668 -> 0.005757707171142101
2 days, 20:04:50.824872 INFO: Updating optimization_manager: score_cutoff        : 24.2470387676239 -> 7.842497918128967
2 days, 20:04:50.824953 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:04:50.874748 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:04:51.130822 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:04:51.179162 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:04:51.687080 INFO: === checking if optimization conditions were reached ===
2 days, 20:04:51.687389 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 20:04:51.689710 INFO: Updating optimization_manager: rt_error            : 308.29858059432456 -> 288.6703715336644
2 days, 20:04:51.689842 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 288.6704.
2 days, 20:04:51.689967 INFO: ==============================================
2 days, 20:04:51.690055 INFO: Starting optimization step 7.
2 days, 20:04:51.690127 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 20:04:51.690198 INFO: Using python extraction backend
2 days, 20:04:51.690314 PROGRESS: Extracting batch of 407917 precursors
2 days, 20:04:51.690392 INFO: === Search parameters used ===
2 days, 20:04:51.690454 INFO: rt_error       : 288.6703715336644
2 days, 20:04:51.690515 INFO: mobility_error : 0.1
2 days, 20:04:51.690571 INFO: num_candidates : 3
2 days, 20:04:51.690624 INFO: ms1_error      : 15.0
2 days, 20:04:51.690676 INFO: ms2_error      : 15.0
2 days, 20:04:51.690735 INFO: fwhm_rt        : 2.9259421825408936
2 days, 20:04:51.690794 INFO: quant_window   : 3
2 days, 20:04:51.690846 INFO: ==============================================
2 days, 20:04:51.793156 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:04:51.793324 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:04:51.793386 INFO: FWHM in RT is 2.93 seconds, sigma is 0.49
2 days, 20:04:51.793420 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.12
2 days, 20:04:51.794587 INFO: Starting candidate selection
2 days, 20:10:38.589567 INFO: Starting candidate scoring
2 days, 20:10:50.744876 INFO: Finished candidate processing
2 days, 20:10:50.745210 INFO: Collecting candidate features
2 days, 20:10:52.461220 WARNING: intensity_correlation has 2106 NaNs ( 0.22 % out of 960637)
2 days, 20:10:52.462299 WARNING: height_correlation has 223 NaNs ( 0.02 % out of 960637)
2 days, 20:10:52.495875 INFO: Collecting fragment features
2 days, 20:10:52.981969 INFO: Finished candidate scoring
2 days, 20:10:53.523243 INFO: performing precursor FDR with 47 features
2 days, 20:10:53.523382 INFO: Decoy channel: -1
2 days, 20:10:53.523414 INFO: competitive: True
2 days, 20:10:53.742900 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:10:53.882162 WARNING: dropped 1089 target PSMs due to missing features
2 days, 20:10:53.882322 WARNING: dropped 1112 decoy PSMs due to missing features
2 days, 20:10:54.201153 INFO: Estimating optimal hyperparameters - samples: 766,748, batch_size: 3,140, learning_rate: 8.76e-04
2 days, 20:10:54.202624 INFO: Using random state 589792 for train-test-split
2 days, 20:11:13.091016 INFO: Test AUC: 0.549
2 days, 20:11:13.091183 INFO: Train AUC: 0.567
2 days, 20:11:13.091219 INFO: AUC difference: 3.19%
2 days, 20:11:13.645460 INFO: Resetting torch num_threads to 80
2 days, 20:11:13.663991 PROGRESS: === Extracted 960637 precursors and 6030838 fragments ===
2 days, 20:11:13.664833 INFO: === FDR correction performed with classifier version 13 ===
2 days, 20:11:13.694531 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:11:13.694795 PROGRESS: Total precursors accumulated: 183,450
2 days, 20:11:13.694870 PROGRESS: Target precursors: 105,330 (57.42%)
2 days, 20:11:13.694929 PROGRESS: Decoy precursors: 78,120 (42.58%)
2 days, 20:11:13.694983 PROGRESS: 
2 days, 20:11:13.695035 PROGRESS: Precursor Summary:
2 days, 20:11:13.697355 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   281; 0.001 FDR:   130
2 days, 20:11:13.697488 PROGRESS: 
2 days, 20:11:13.697552 PROGRESS: Protein Summary:
2 days, 20:11:13.699765 PROGRESS: Channel   0:	 0.050 FDR:   332; 0.010 FDR:   242; 0.001 FDR:   109
2 days, 20:11:13.699873 PROGRESS: =========================================================================
2 days, 20:11:13.706767 INFO: Target number of precursors reached.
2 days, 20:11:14.401438 INFO: fragments_df: keeping 4223 of 6030838 [sum(precursor_idx_mask)=7417 sum(mass_error_mask)=6030810 stop_rank=4223
2 days, 20:11:15.431245 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:11:15.575649 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:11:15.709545 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:11:15.850392 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:11:16.453476 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 20:11:16.453943 INFO: Using score_cutoff 8.852375696182252 (fac=0.99, q=1)
2 days, 20:11:16.454284 INFO: Updating optimization_manager: fwhm_rt             : 2.9259421825408936 -> 2.9308247566223145
2 days, 20:11:16.454368 INFO: Updating optimization_manager: fwhm_mobility       : 0.005757707171142101 -> 0.005947865545749664
2 days, 20:11:16.454425 INFO: Updating optimization_manager: score_cutoff        : 7.842497918128967 -> 8.852375696182252
2 days, 20:11:16.454484 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:11:16.504118 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:11:16.762477 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:11:16.813306 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:11:17.302379 INFO: === checking if optimization conditions were reached ===
2 days, 20:11:17.302691 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 20:11:17.304995 INFO: Updating optimization_manager: rt_error            : 288.6703715336644 -> 274.0348301631632
2 days, 20:11:17.305132 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 274.0348.
2 days, 20:11:17.305207 INFO: ==============================================
2 days, 20:11:17.305286 INFO: Starting optimization step 8.
2 days, 20:11:17.305353 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 20:11:17.305433 INFO: Using python extraction backend
2 days, 20:11:17.305544 PROGRESS: Extracting batch of 407917 precursors
2 days, 20:11:17.305620 INFO: === Search parameters used ===
2 days, 20:11:17.305676 INFO: rt_error       : 274.0348301631632
2 days, 20:11:17.305726 INFO: mobility_error : 0.1
2 days, 20:11:17.305778 INFO: num_candidates : 3
2 days, 20:11:17.305826 INFO: ms1_error      : 15.0
2 days, 20:11:17.305890 INFO: ms2_error      : 15.0
2 days, 20:11:17.305939 INFO: fwhm_rt        : 2.9308247566223145
2 days, 20:11:17.305987 INFO: quant_window   : 3
2 days, 20:11:17.306033 INFO: ==============================================
2 days, 20:11:17.405212 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:11:17.405348 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:11:17.405399 INFO: FWHM in RT is 2.93 seconds, sigma is 0.49
2 days, 20:11:17.405427 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.22
2 days, 20:11:17.406285 INFO: Starting candidate selection
2 days, 20:15:52.664581 INFO: Starting candidate scoring
2 days, 20:16:04.633574 INFO: Finished candidate processing
2 days, 20:16:04.633755 INFO: Collecting candidate features
2 days, 20:16:06.393842 WARNING: intensity_correlation has 2181 NaNs ( 0.23 % out of 956362)
2 days, 20:16:06.394906 WARNING: height_correlation has 258 NaNs ( 0.03 % out of 956362)
2 days, 20:16:06.428361 INFO: Collecting fragment features
2 days, 20:16:06.967227 INFO: Finished candidate scoring
2 days, 20:16:07.516185 INFO: performing precursor FDR with 47 features
2 days, 20:16:07.516320 INFO: Decoy channel: -1
2 days, 20:16:07.516349 INFO: competitive: True
2 days, 20:16:07.735852 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:16:07.877686 WARNING: dropped 1151 target PSMs due to missing features
2 days, 20:16:07.877842 WARNING: dropped 1142 decoy PSMs due to missing features
2 days, 20:16:08.209332 INFO: Estimating optimal hyperparameters - samples: 763,255, batch_size: 3,126, learning_rate: 8.74e-04
2 days, 20:16:08.210911 INFO: Using random state 589792 for train-test-split
2 days, 20:16:28.088163 INFO: Test AUC: 0.549
2 days, 20:16:28.088320 INFO: Train AUC: 0.564
2 days, 20:16:28.088373 INFO: AUC difference: 2.54%
2 days, 20:16:28.640603 INFO: Resetting torch num_threads to 80
2 days, 20:16:28.658765 PROGRESS: === Extracted 956362 precursors and 5992872 fragments ===
2 days, 20:16:28.659591 INFO: === FDR correction performed with classifier version 13 ===
2 days, 20:16:28.689146 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:16:28.689438 PROGRESS: Total precursors accumulated: 182,928
2 days, 20:16:28.689508 PROGRESS: Target precursors: 104,726 (57.25%)
2 days, 20:16:28.689575 PROGRESS: Decoy precursors: 78,202 (42.75%)
2 days, 20:16:28.689627 PROGRESS: 
2 days, 20:16:28.689677 PROGRESS: Precursor Summary:
2 days, 20:16:28.692009 PROGRESS: Channel   0:	 0.050 FDR:   329; 0.010 FDR:   218; 0.001 FDR:   143
2 days, 20:16:28.692116 PROGRESS: 
2 days, 20:16:28.692179 PROGRESS: Protein Summary:
2 days, 20:16:28.694364 PROGRESS: Channel   0:	 0.050 FDR:   279; 0.010 FDR:   184; 0.001 FDR:   122
2 days, 20:16:28.694467 PROGRESS: =========================================================================
2 days, 20:16:28.701296 INFO: Target number of precursors reached.
2 days, 20:16:29.350405 INFO: fragments_df: keeping 3614 of 5992872 [sum(precursor_idx_mask)=6052 sum(mass_error_mask)=5992827 stop_rank=3614
2 days, 20:16:30.435844 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:16:30.548648 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:16:30.658554 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:16:30.776141 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:16:31.285121 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 20:16:31.285591 INFO: Using score_cutoff 23.121337685394288 (fac=0.99, q=1)
2 days, 20:16:31.285933 INFO: Updating optimization_manager: fwhm_rt             : 2.9308247566223145 -> 3.026144504547119
2 days, 20:16:31.286031 INFO: Updating optimization_manager: fwhm_mobility       : 0.005947865545749664 -> 0.006554780527949333
2 days, 20:16:31.286112 INFO: Updating optimization_manager: score_cutoff        : 8.852375696182252 -> 23.121337685394288
2 days, 20:16:31.286189 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:16:31.336090 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:16:31.588349 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:16:31.641791 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:16:32.132131 INFO: === checking if optimization conditions were reached ===
2 days, 20:16:32.132422 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 20:16:32.134627 INFO: Updating optimization_manager: rt_error            : 274.0348301631632 -> 239.48220593682228
2 days, 20:16:32.134777 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 239.4822.
2 days, 20:16:32.134854 INFO: ==============================================
2 days, 20:16:32.134933 INFO: Starting optimization step 9.
2 days, 20:16:32.134994 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 20:16:32.135056 INFO: Using python extraction backend
2 days, 20:16:32.135163 PROGRESS: Extracting batch of 407917 precursors
2 days, 20:16:32.135231 INFO: === Search parameters used ===
2 days, 20:16:32.135308 INFO: rt_error       : 239.48220593682228
2 days, 20:16:32.135375 INFO: mobility_error : 0.1
2 days, 20:16:32.135440 INFO: num_candidates : 3
2 days, 20:16:32.135504 INFO: ms1_error      : 15.0
2 days, 20:16:32.135568 INFO: ms2_error      : 15.0
2 days, 20:16:32.135630 INFO: fwhm_rt        : 3.026144504547119
2 days, 20:16:32.135691 INFO: quant_window   : 3
2 days, 20:16:32.135750 INFO: ==============================================
2 days, 20:16:32.241419 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:16:32.241578 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:16:32.241661 INFO: FWHM in RT is 3.03 seconds, sigma is 0.50
2 days, 20:16:32.241691 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.55
2 days, 20:16:32.242517 INFO: Starting candidate selection
2 days, 20:20:35.533803 INFO: Starting candidate scoring
2 days, 20:20:47.380047 INFO: Finished candidate processing
2 days, 20:20:47.380606 INFO: Collecting candidate features
2 days, 20:20:49.513015 WARNING: intensity_correlation has 2278 NaNs ( 0.24 % out of 954312)
2 days, 20:20:49.514104 WARNING: height_correlation has 264 NaNs ( 0.03 % out of 954312)
2 days, 20:20:49.547796 INFO: Collecting fragment features
2 days, 20:20:50.102445 INFO: Finished candidate scoring
2 days, 20:20:50.637286 INFO: performing precursor FDR with 47 features
2 days, 20:20:50.637437 INFO: Decoy channel: -1
2 days, 20:20:50.637490 INFO: competitive: True
2 days, 20:20:50.855504 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:20:50.993925 WARNING: dropped 1177 target PSMs due to missing features
2 days, 20:20:50.994092 WARNING: dropped 1209 decoy PSMs due to missing features
2 days, 20:20:51.355102 INFO: Estimating optimal hyperparameters - samples: 761,540, batch_size: 3,119, learning_rate: 8.73e-04
2 days, 20:20:51.356566 INFO: Using random state 589792 for train-test-split
2 days, 20:21:09.580538 INFO: Test AUC: 0.547
2 days, 20:21:09.580714 INFO: Train AUC: 0.567
2 days, 20:21:09.580750 INFO: AUC difference: 3.50%
2 days, 20:21:10.134747 INFO: Resetting torch num_threads to 80
2 days, 20:21:10.152602 PROGRESS: === Extracted 954312 precursors and 5947170 fragments ===
2 days, 20:21:10.153497 INFO: === FDR correction performed with classifier version 13 ===
2 days, 20:21:10.182886 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:21:10.183212 PROGRESS: Total precursors accumulated: 183,002
2 days, 20:21:10.183301 PROGRESS: Target precursors: 105,112 (57.44%)
2 days, 20:21:10.183362 PROGRESS: Decoy precursors: 77,890 (42.56%)
2 days, 20:21:10.183414 PROGRESS: 
2 days, 20:21:10.183466 PROGRESS: Precursor Summary:
2 days, 20:21:10.185724 PROGRESS: Channel   0:	 0.050 FDR:   347; 0.010 FDR:   116; 0.001 FDR:   104
2 days, 20:21:10.185829 PROGRESS: 
2 days, 20:21:10.185903 PROGRESS: Protein Summary:
2 days, 20:21:10.188028 PROGRESS: Channel   0:	 0.050 FDR:   300; 0.010 FDR:   103; 0.001 FDR:    92
2 days, 20:21:10.188129 PROGRESS: =========================================================================
2 days, 20:21:10.194889 INFO: Target number of precursors not reached yet.
2 days, 20:21:11.207408 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:21:11.257762 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:21:11.511758 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:21:11.564959 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:21:12.054317 INFO: === skipping optimization until target number of precursors are found ===
2 days, 20:21:12.054631 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 20:21:12.054745 INFO: Starting optimization step 10.
2 days, 20:21:12.054821 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 20:21:12.054890 INFO: Using python extraction backend
2 days, 20:21:12.055007 PROGRESS: Extracting batch of 408390 precursors
2 days, 20:21:12.055107 INFO: === Search parameters used ===
2 days, 20:21:12.055165 INFO: rt_error       : 239.48220593682228
2 days, 20:21:12.055218 INFO: mobility_error : 0.1
2 days, 20:21:12.055269 INFO: num_candidates : 3
2 days, 20:21:12.055317 INFO: ms1_error      : 15.0
2 days, 20:21:12.055365 INFO: ms2_error      : 15.0
2 days, 20:21:12.055411 INFO: fwhm_rt        : 3.026144504547119
2 days, 20:21:12.055458 INFO: quant_window   : 3
2 days, 20:21:12.055504 INFO: ==============================================
2 days, 20:21:12.152525 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:21:12.152712 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:21:12.152760 INFO: FWHM in RT is 3.03 seconds, sigma is 0.50
2 days, 20:21:12.152784 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.55
2 days, 20:21:12.153624 INFO: Starting candidate selection
2 days, 20:25:15.907093 INFO: Starting candidate scoring
2 days, 20:25:27.994767 INFO: Finished candidate processing
2 days, 20:25:27.995358 INFO: Collecting candidate features
2 days, 20:25:29.786741 WARNING: intensity_correlation has 2356 NaNs ( 0.25 % out of 953108)
2 days, 20:25:29.787830 WARNING: height_correlation has 272 NaNs ( 0.03 % out of 953108)
2 days, 20:25:29.821480 INFO: Collecting fragment features
2 days, 20:25:30.342109 INFO: Finished candidate scoring
2 days, 20:25:31.549661 INFO: performing precursor FDR with 47 features
2 days, 20:25:31.549825 INFO: Decoy channel: -1
2 days, 20:25:31.549861 INFO: competitive: True
2 days, 20:25:32.249782 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:25:32.524359 WARNING: dropped 2420 target PSMs due to missing features
2 days, 20:25:32.524514 WARNING: dropped 2453 decoy PSMs due to missing features
2 days, 20:25:33.336244 INFO: Estimating optimal hyperparameters - samples: 1,522,037, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 20:25:33.339072 INFO: Using random state 589792 for train-test-split
2 days, 20:26:07.772487 INFO: Test AUC: 0.548
2 days, 20:26:07.772662 INFO: Train AUC: 0.561
2 days, 20:26:07.772700 INFO: AUC difference: 2.14%
2 days, 20:26:08.619703 INFO: Resetting torch num_threads to 80
2 days, 20:26:08.840940 PROGRESS: === Extracted 1907420 precursors and 11883569 fragments ===
2 days, 20:26:08.842081 INFO: === FDR correction performed with classifier version 13 ===
2 days, 20:26:08.901356 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:26:08.901661 PROGRESS: Total precursors accumulated: 365,725
2 days, 20:26:08.901741 PROGRESS: Target precursors: 206,830 (56.55%)
2 days, 20:26:08.901802 PROGRESS: Decoy precursors: 158,895 (43.45%)
2 days, 20:26:08.901857 PROGRESS: 
2 days, 20:26:08.901928 PROGRESS: Precursor Summary:
2 days, 20:26:08.905532 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   319; 0.001 FDR:   297
2 days, 20:26:08.905669 PROGRESS: 
2 days, 20:26:08.905734 PROGRESS: Protein Summary:
2 days, 20:26:08.908957 PROGRESS: Channel   0:	 0.050 FDR:   454; 0.010 FDR:   241; 0.001 FDR:   223
2 days, 20:26:08.909066 PROGRESS: =========================================================================
2 days, 20:26:08.916527 INFO: Target number of precursors reached.
2 days, 20:26:10.204420 INFO: fragments_df: keeping 5000 of 11883569 [sum(precursor_idx_mask)=8918 sum(mass_error_mask)=11883477 stop_rank=5000
2 days, 20:26:11.659574 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:26:11.803694 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:26:11.944237 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:26:12.088598 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:26:12.805242 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 20:26:12.805702 INFO: Using score_cutoff 11.05832039337158 (fac=0.99, q=1)
2 days, 20:26:12.806055 INFO: Updating optimization_manager: fwhm_rt             : 3.026144504547119 -> 2.9601781368255615
2 days, 20:26:12.806145 INFO: Updating optimization_manager: fwhm_mobility       : 0.006554780527949333 -> 0.0068600852973759174
2 days, 20:26:12.806208 INFO: Updating optimization_manager: score_cutoff        : 23.121337685394288 -> 11.05832039337158
2 days, 20:26:12.806268 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:26:12.909592 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:26:13.440891 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:26:13.544357 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:26:14.500736 INFO: === checking if optimization conditions were reached ===
2 days, 20:26:14.501054 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2 days, 20:26:14.502387 INFO: Updating optimization_manager: rt_error            : 239.48220593682228 -> 288.6703715336644
2 days, 20:26:14.502568 INFO: Updating optimization_manager: classifier_version  : 13 -> 21
2 days, 20:26:14.502679 INFO: Updating optimization_manager: score_cutoff        : 11.05832039337158 -> 8.852375696182252
2 days, 20:26:14.502778 INFO: Updating optimization_manager: fwhm_rt             : 2.9601781368255615 -> 2.9308247566223145
2 days, 20:26:14.502872 INFO: Updating optimization_manager: fwhm_mobility       : 0.0068600852973759174 -> 0.005947865545749664
2 days, 20:26:14.502965 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 288.6704 found after 9 searches.
2 days, 20:26:14.503036 INFO: ==============================================
2 days, 20:26:14.503113 PROGRESS: Optimization finished for rt_error.
2 days, 20:26:15.079066 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:26:15.131005 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:26:15.390295 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:26:15.443899 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:26:15.920856 INFO: Starting optimization step 0.
2 days, 20:26:15.921153 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 20:26:15.921239 INFO: Using python extraction backend
2 days, 20:26:15.921363 PROGRESS: Extracting batch of 407917 precursors
2 days, 20:26:15.921446 INFO: === Search parameters used ===
2 days, 20:26:15.921505 INFO: rt_error       : 288.6703715336644
2 days, 20:26:15.921554 INFO: mobility_error : 0.1
2 days, 20:26:15.921602 INFO: num_candidates : 3
2 days, 20:26:15.921667 INFO: ms1_error      : 15.0
2 days, 20:26:15.921716 INFO: ms2_error      : 15.0
2 days, 20:26:15.921762 INFO: fwhm_rt        : 2.9308247566223145
2 days, 20:26:15.921806 INFO: quant_window   : 3
2 days, 20:26:15.921849 INFO: ==============================================
2 days, 20:26:16.020350 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:26:16.020503 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:26:16.020549 INFO: FWHM in RT is 2.93 seconds, sigma is 0.49
2 days, 20:26:16.020576 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.22
2 days, 20:26:16.021432 INFO: Starting candidate selection
2 days, 20:31:35.154767 INFO: Starting candidate scoring
2 days, 20:31:46.989300 INFO: Finished candidate processing
2 days, 20:31:46.989549 INFO: Collecting candidate features
2 days, 20:31:48.801930 WARNING: intensity_correlation has 2167 NaNs ( 0.23 % out of 955147)
2 days, 20:31:48.803127 WARNING: height_correlation has 244 NaNs ( 0.03 % out of 955147)
2 days, 20:31:48.837650 INFO: Collecting fragment features
2 days, 20:31:49.381098 INFO: Finished candidate scoring
2 days, 20:31:49.939574 INFO: performing precursor FDR with 47 features
2 days, 20:31:49.939717 INFO: Decoy channel: -1
2 days, 20:31:49.939771 INFO: competitive: True
2 days, 20:31:50.160380 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:31:50.300347 WARNING: dropped 1146 target PSMs due to missing features
2 days, 20:31:50.300512 WARNING: dropped 1132 decoy PSMs due to missing features
2 days, 20:31:50.632356 INFO: Estimating optimal hyperparameters - samples: 762,295, batch_size: 3,122, learning_rate: 8.73e-04
2 days, 20:31:50.633833 INFO: Using random state 56762 for train-test-split
2 days, 20:32:08.798974 INFO: Test AUC: 0.551
2 days, 20:32:08.799136 INFO: Train AUC: 0.572
2 days, 20:32:08.799171 INFO: AUC difference: 3.65%
2 days, 20:32:09.355943 INFO: Resetting torch num_threads to 80
2 days, 20:32:09.374097 PROGRESS: === Extracted 955147 precursors and 5950305 fragments ===
2 days, 20:32:09.374971 INFO: === FDR correction performed with classifier version 21 ===
2 days, 20:32:09.404283 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:32:09.404584 PROGRESS: Total precursors accumulated: 183,238
2 days, 20:32:09.404668 PROGRESS: Target precursors: 105,547 (57.60%)
2 days, 20:32:09.404740 PROGRESS: Decoy precursors: 77,691 (42.40%)
2 days, 20:32:09.404804 PROGRESS: 
2 days, 20:32:09.404869 PROGRESS: Precursor Summary:
2 days, 20:32:09.407353 PROGRESS: Channel   0:	 0.050 FDR:   505; 0.010 FDR:   287; 0.001 FDR:   279
2 days, 20:32:09.407476 PROGRESS: 
2 days, 20:32:09.407549 PROGRESS: Protein Summary:
2 days, 20:32:09.409847 PROGRESS: Channel   0:	 0.050 FDR:   448; 0.010 FDR:   245; 0.001 FDR:   238
2 days, 20:32:09.409967 PROGRESS: =========================================================================
2 days, 20:32:09.419673 INFO: Target number of precursors reached.
2 days, 20:32:10.069596 INFO: fragments_df: keeping 4279 of 5950305 [sum(precursor_idx_mask)=7534 sum(mass_error_mask)=5950264 stop_rank=4279
2 days, 20:32:11.149798 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:32:11.282418 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:32:11.420511 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:32:11.563043 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:32:12.097991 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 20:32:12.098451 INFO: Using score_cutoff 23.605798542022704 (fac=0.99, q=1)
2 days, 20:32:12.098792 INFO: Updating optimization_manager: fwhm_rt             : 2.9308247566223145 -> 2.976619005203247
2 days, 20:32:12.098888 INFO: Updating optimization_manager: fwhm_mobility       : 0.005947865545749664 -> 0.006224067881703377
2 days, 20:32:12.098960 INFO: Updating optimization_manager: score_cutoff        : 8.852375696182252 -> 23.605798542022704
2 days, 20:32:12.099036 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:32:12.147861 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:32:12.403337 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:32:12.457497 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:32:12.962109 INFO: === checking if optimization conditions were reached ===
2 days, 20:32:12.962414 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 20:32:12.964232 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07517830290310788
2 days, 20:32:12.964370 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0752.
2 days, 20:32:12.964451 INFO: ==============================================
2 days, 20:32:12.964530 INFO: Starting optimization step 1.
2 days, 20:32:12.964620 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 20:32:12.964694 INFO: Using python extraction backend
2 days, 20:32:12.964807 PROGRESS: Extracting batch of 407917 precursors
2 days, 20:32:12.964883 INFO: === Search parameters used ===
2 days, 20:32:12.964944 INFO: rt_error       : 288.6703715336644
2 days, 20:32:12.964994 INFO: mobility_error : 0.07517830290310788
2 days, 20:32:12.965043 INFO: num_candidates : 3
2 days, 20:32:12.965090 INFO: ms1_error      : 15.0
2 days, 20:32:12.965138 INFO: ms2_error      : 15.0
2 days, 20:32:12.965185 INFO: fwhm_rt        : 2.976619005203247
2 days, 20:32:12.965232 INFO: quant_window   : 3
2 days, 20:32:12.965278 INFO: ==============================================
2 days, 20:32:13.061811 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:32:13.061977 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:32:13.062027 INFO: FWHM in RT is 2.98 seconds, sigma is 0.50
2 days, 20:32:13.062054 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.37
2 days, 20:32:13.063085 INFO: Starting candidate selection
2 days, 20:36:17.477697 INFO: Starting candidate scoring
2 days, 20:36:29.118464 INFO: Finished candidate processing
2 days, 20:36:29.118662 INFO: Collecting candidate features
2 days, 20:36:30.816415 WARNING: intensity_correlation has 2271 NaNs ( 0.24 % out of 931915)
2 days, 20:36:30.817431 WARNING: height_correlation has 247 NaNs ( 0.03 % out of 931915)
2 days, 20:36:30.850133 INFO: Collecting fragment features
2 days, 20:36:31.295569 INFO: Finished candidate scoring
2 days, 20:36:31.818890 INFO: performing precursor FDR with 47 features
2 days, 20:36:31.819030 INFO: Decoy channel: -1
2 days, 20:36:31.819058 INFO: competitive: True
2 days, 20:36:32.031671 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:36:32.165504 WARNING: dropped 1168 target PSMs due to missing features
2 days, 20:36:32.165650 WARNING: dropped 1209 decoy PSMs due to missing features
2 days, 20:36:32.476626 INFO: Estimating optimal hyperparameters - samples: 743,630, batch_size: 3,045, learning_rate: 8.62e-04
2 days, 20:36:32.478035 INFO: Using random state 56762 for train-test-split
2 days, 20:36:50.606258 INFO: Test AUC: 0.552
2 days, 20:36:50.606426 INFO: Train AUC: 0.572
2 days, 20:36:50.606463 INFO: AUC difference: 3.37%
2 days, 20:36:51.148306 INFO: Resetting torch num_threads to 80
2 days, 20:36:51.165862 PROGRESS: === Extracted 931915 precursors and 5782416 fragments ===
2 days, 20:36:51.166727 INFO: === FDR correction performed with classifier version 21 ===
2 days, 20:36:51.197180 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:36:51.197475 PROGRESS: Total precursors accumulated: 179,767
2 days, 20:36:51.197552 PROGRESS: Target precursors: 103,607 (57.63%)
2 days, 20:36:51.197622 PROGRESS: Decoy precursors: 76,160 (42.37%)
2 days, 20:36:51.197675 PROGRESS: 
2 days, 20:36:51.197727 PROGRESS: Precursor Summary:
2 days, 20:36:51.200097 PROGRESS: Channel   0:	 0.050 FDR:   420; 0.010 FDR:   166; 0.001 FDR:   134
2 days, 20:36:51.200224 PROGRESS: 
2 days, 20:36:51.200307 PROGRESS: Protein Summary:
2 days, 20:36:51.202612 PROGRESS: Channel   0:	 0.050 FDR:   370; 0.010 FDR:   139; 0.001 FDR:   112
2 days, 20:36:51.202720 PROGRESS: =========================================================================
2 days, 20:36:51.209548 INFO: Target number of precursors not reached yet.
2 days, 20:36:52.260270 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:36:52.309880 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:36:52.566037 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:36:52.620190 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:36:53.112564 INFO: === skipping optimization until target number of precursors are found ===
2 days, 20:36:53.112871 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 20:36:53.112988 INFO: Starting optimization step 2.
2 days, 20:36:53.113065 PROGRESS: === Extracting elution groups 204600 to 409400 ===
2 days, 20:36:53.113134 INFO: Using python extraction backend
2 days, 20:36:53.113251 PROGRESS: Extracting batch of 408390 precursors
2 days, 20:36:53.113331 INFO: === Search parameters used ===
2 days, 20:36:53.113390 INFO: rt_error       : 288.6703715336644
2 days, 20:36:53.113441 INFO: mobility_error : 0.07517830290310788
2 days, 20:36:53.113489 INFO: num_candidates : 3
2 days, 20:36:53.113540 INFO: ms1_error      : 15.0
2 days, 20:36:53.113586 INFO: ms2_error      : 15.0
2 days, 20:36:53.113648 INFO: fwhm_rt        : 2.976619005203247
2 days, 20:36:53.113695 INFO: quant_window   : 3
2 days, 20:36:53.113740 INFO: ==============================================
2 days, 20:36:53.210957 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:36:53.211101 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:36:53.211146 INFO: FWHM in RT is 2.98 seconds, sigma is 0.50
2 days, 20:36:53.211172 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.37
2 days, 20:36:53.211943 INFO: Starting candidate selection
2 days, 20:40:52.871044 INFO: Starting candidate scoring
2 days, 20:41:04.560910 INFO: Finished candidate processing
2 days, 20:41:04.561081 INFO: Collecting candidate features
2 days, 20:41:06.345393 WARNING: intensity_correlation has 2380 NaNs ( 0.26 % out of 931541)
2 days, 20:41:06.346442 WARNING: height_correlation has 285 NaNs ( 0.03 % out of 931541)
2 days, 20:41:06.378975 INFO: Collecting fragment features
2 days, 20:41:06.902907 INFO: Finished candidate scoring
2 days, 20:41:07.917847 INFO: performing precursor FDR with 47 features
2 days, 20:41:07.918024 INFO: Decoy channel: -1
2 days, 20:41:07.918053 INFO: competitive: True
2 days, 20:41:08.692312 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:41:08.975161 WARNING: dropped 2371 target PSMs due to missing features
2 days, 20:41:08.975323 WARNING: dropped 2535 decoy PSMs due to missing features
2 days, 20:41:09.769183 INFO: Estimating optimal hyperparameters - samples: 1,486,840, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 20:41:09.771852 INFO: Using random state 56762 for train-test-split
2 days, 20:41:43.573329 INFO: Test AUC: 0.551
2 days, 20:41:43.573493 INFO: Train AUC: 0.563
2 days, 20:41:43.573529 INFO: AUC difference: 2.12%
2 days, 20:41:44.391072 INFO: Resetting torch num_threads to 80
2 days, 20:41:44.648921 PROGRESS: === Extracted 1863456 precursors and 11559339 fragments ===
2 days, 20:41:44.649989 INFO: === FDR correction performed with classifier version 21 ===
2 days, 20:41:44.707146 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:41:44.707472 PROGRESS: Total precursors accumulated: 359,302
2 days, 20:41:44.707548 PROGRESS: Target precursors: 204,963 (57.04%)
2 days, 20:41:44.707607 PROGRESS: Decoy precursors: 154,339 (42.96%)
2 days, 20:41:44.707662 PROGRESS: 
2 days, 20:41:44.707715 PROGRESS: Precursor Summary:
2 days, 20:41:44.711220 PROGRESS: Channel   0:	 0.050 FDR:   643; 0.010 FDR:   465; 0.001 FDR:   427
2 days, 20:41:44.711360 PROGRESS: 
2 days, 20:41:44.711429 PROGRESS: Protein Summary:
2 days, 20:41:44.714631 PROGRESS: Channel   0:	 0.050 FDR:   505; 0.010 FDR:   351; 0.001 FDR:   323
2 days, 20:41:44.714741 PROGRESS: =========================================================================
2 days, 20:41:44.719592 INFO: Target number of precursors reached.
2 days, 20:41:46.009843 INFO: fragments_df: keeping 5000 of 11559339 [sum(precursor_idx_mask)=12916 sum(mass_error_mask)=11559231 stop_rank=5000
2 days, 20:41:47.033571 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:41:47.190072 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:41:47.343528 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:41:47.495194 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:41:48.212253 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 20:41:48.212705 INFO: Using score_cutoff 30.689880207824707 (fac=0.99, q=1)
2 days, 20:41:48.213047 INFO: Updating optimization_manager: fwhm_rt             : 2.976619005203247 -> 2.8534297943115234
2 days, 20:41:48.213132 INFO: Updating optimization_manager: fwhm_mobility       : 0.006224067881703377 -> 0.005953621584922075
2 days, 20:41:48.213193 INFO: Updating optimization_manager: score_cutoff        : 23.605798542022704 -> 30.689880207824707
2 days, 20:41:48.213253 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:41:48.262121 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:41:48.520458 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:41:48.576017 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:41:49.075567 INFO: === checking if optimization conditions were reached ===
2 days, 20:41:49.075861 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 20:41:49.077809 INFO: Updating optimization_manager: mobility_error      : 0.07517830290310788 -> 0.06393553427095688
2 days, 20:41:49.077969 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0639.
2 days, 20:41:49.078048 INFO: ==============================================
2 days, 20:41:49.078123 INFO: Starting optimization step 3.
2 days, 20:41:49.078187 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 20:41:49.078250 INFO: Using python extraction backend
2 days, 20:41:49.078365 PROGRESS: Extracting batch of 407917 precursors
2 days, 20:41:49.078439 INFO: === Search parameters used ===
2 days, 20:41:49.078493 INFO: rt_error       : 288.6703715336644
2 days, 20:41:49.078541 INFO: mobility_error : 0.06393553427095688
2 days, 20:41:49.078586 INFO: num_candidates : 3
2 days, 20:41:49.078631 INFO: ms1_error      : 15.0
2 days, 20:41:49.078676 INFO: ms2_error      : 15.0
2 days, 20:41:49.078719 INFO: fwhm_rt        : 2.8534297943115234
2 days, 20:41:49.078763 INFO: quant_window   : 3
2 days, 20:41:49.078812 INFO: ==============================================
2 days, 20:41:49.184039 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:41:49.184179 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:41:49.184223 INFO: FWHM in RT is 2.85 seconds, sigma is 0.48
2 days, 20:41:49.184248 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.23
2 days, 20:41:49.184983 INFO: Starting candidate selection
2 days, 20:46:06.380685 INFO: Starting candidate scoring
2 days, 20:46:21.516988 INFO: Finished candidate processing
2 days, 20:46:21.517240 INFO: Collecting candidate features
2 days, 20:46:23.722992 WARNING: intensity_correlation has 2495 NaNs ( 0.27 % out of 910132)
2 days, 20:46:23.724426 WARNING: height_correlation has 273 NaNs ( 0.03 % out of 910132)
2 days, 20:46:23.767113 INFO: Collecting fragment features
2 days, 20:46:24.364450 INFO: Finished candidate scoring
2 days, 20:46:24.928877 INFO: performing precursor FDR with 47 features
2 days, 20:46:24.929033 INFO: Decoy channel: -1
2 days, 20:46:24.929072 INFO: competitive: True
2 days, 20:46:25.196603 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:46:25.377666 WARNING: dropped 1308 target PSMs due to missing features
2 days, 20:46:25.377833 WARNING: dropped 1311 decoy PSMs due to missing features
2 days, 20:46:25.890758 INFO: Estimating optimal hyperparameters - samples: 726,010, batch_size: 2,973, learning_rate: 8.52e-04
2 days, 20:46:25.892222 INFO: Using random state 56762 for train-test-split
2 days, 20:46:40.022882 INFO: Test AUC: 0.554
2 days, 20:46:40.023066 INFO: Train AUC: 0.576
2 days, 20:46:40.023108 INFO: AUC difference: 3.79%
2 days, 20:46:40.682585 INFO: Resetting torch num_threads to 80
2 days, 20:46:40.710072 PROGRESS: === Extracted 910132 precursors and 5542743 fragments ===
2 days, 20:46:40.711030 INFO: === FDR correction performed with classifier version 21 ===
2 days, 20:46:40.749696 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:46:40.750040 PROGRESS: Total precursors accumulated: 177,177
2 days, 20:46:40.750131 PROGRESS: Target precursors: 102,392 (57.79%)
2 days, 20:46:40.750200 PROGRESS: Decoy precursors: 74,785 (42.21%)
2 days, 20:46:40.750262 PROGRESS: 
2 days, 20:46:40.750324 PROGRESS: Precursor Summary:
2 days, 20:46:40.753316 PROGRESS: Channel   0:	 0.050 FDR:   445; 0.010 FDR:   309; 0.001 FDR:   266
2 days, 20:46:40.753472 PROGRESS: 
2 days, 20:46:40.753549 PROGRESS: Protein Summary:
2 days, 20:46:40.756524 PROGRESS: Channel   0:	 0.050 FDR:   394; 0.010 FDR:   268; 0.001 FDR:   228
2 days, 20:46:40.756640 PROGRESS: =========================================================================
2 days, 20:46:40.782357 INFO: Target number of precursors reached.
2 days, 20:46:41.728429 INFO: fragments_df: keeping 4488 of 5542743 [sum(precursor_idx_mask)=8310 sum(mass_error_mask)=5542693 stop_rank=4488
2 days, 20:46:43.004563 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:46:43.239516 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:46:43.452226 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:46:43.615731 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:46:44.304698 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 20:46:44.305147 INFO: Using score_cutoff 19.047329598999024 (fac=0.99, q=1)
2 days, 20:46:44.305518 INFO: Updating optimization_manager: fwhm_rt             : 2.8534297943115234 -> 2.9794623851776123
2 days, 20:46:44.305620 INFO: Updating optimization_manager: fwhm_mobility       : 0.005953621584922075 -> 0.005983738228678703
2 days, 20:46:44.305703 INFO: Updating optimization_manager: score_cutoff        : 30.689880207824707 -> 19.047329598999024
2 days, 20:46:44.305786 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:46:44.361689 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:46:44.628922 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:46:44.693532 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:46:45.188813 INFO: === checking if optimization conditions were reached ===
2 days, 20:46:45.189104 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 20:46:45.191170 INFO: Updating optimization_manager: mobility_error      : 0.06393553427095688 -> 0.0582087615900455
2 days, 20:46:45.191305 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0582.
2 days, 20:46:45.191381 INFO: ==============================================
2 days, 20:46:45.191458 INFO: Starting optimization step 4.
2 days, 20:46:45.191531 PROGRESS: === Extracting elution groups 0 to 204600 ===
2 days, 20:46:45.191597 INFO: Using python extraction backend
2 days, 20:46:45.191705 PROGRESS: Extracting batch of 407917 precursors
2 days, 20:46:45.191780 INFO: === Search parameters used ===
2 days, 20:46:45.191833 INFO: rt_error       : 288.6703715336644
2 days, 20:46:45.191882 INFO: mobility_error : 0.0582087615900455
2 days, 20:46:45.191930 INFO: num_candidates : 3
2 days, 20:46:45.191977 INFO: ms1_error      : 15.0
2 days, 20:46:45.192023 INFO: ms2_error      : 15.0
2 days, 20:46:45.192070 INFO: fwhm_rt        : 2.9794623851776123
2 days, 20:46:45.192120 INFO: quant_window   : 3
2 days, 20:46:45.192169 INFO: ==============================================
2 days, 20:46:45.290730 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:46:45.290873 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:46:45.290924 INFO: FWHM in RT is 2.98 seconds, sigma is 0.50
2 days, 20:46:45.290950 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.24
2 days, 20:46:45.294747 INFO: Starting candidate selection
2 days, 20:51:29.869136 INFO: Starting candidate scoring
2 days, 20:51:44.245960 INFO: Finished candidate processing
2 days, 20:51:44.246205 INFO: Collecting candidate features
2 days, 20:51:46.087090 WARNING: intensity_correlation has 2382 NaNs ( 0.26 % out of 906734)
2 days, 20:51:46.088164 WARNING: height_correlation has 250 NaNs ( 0.03 % out of 906734)
2 days, 20:51:46.121326 INFO: Collecting fragment features
2 days, 20:51:46.617907 INFO: Finished candidate scoring
2 days, 20:51:47.386221 INFO: performing precursor FDR with 47 features
2 days, 20:51:47.386345 INFO: Decoy channel: -1
2 days, 20:51:47.386380 INFO: competitive: True
2 days, 20:51:47.638990 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 20:51:47.775011 WARNING: dropped 1215 target PSMs due to missing features
2 days, 20:51:47.775140 WARNING: dropped 1280 decoy PSMs due to missing features
2 days, 20:51:48.117575 INFO: Estimating optimal hyperparameters - samples: 723,391, batch_size: 2,963, learning_rate: 8.51e-04
2 days, 20:51:48.118901 INFO: Using random state 56762 for train-test-split
2 days, 20:52:06.281614 INFO: Test AUC: 0.552
2 days, 20:52:06.281767 INFO: Train AUC: 0.571
2 days, 20:52:06.281812 INFO: AUC difference: 3.21%
2 days, 20:52:06.903508 INFO: Resetting torch num_threads to 80
2 days, 20:52:06.931776 PROGRESS: === Extracted 906734 precursors and 5561003 fragments ===
2 days, 20:52:06.932832 INFO: === FDR correction performed with classifier version 21 ===
2 days, 20:52:06.978023 PROGRESS: ============================= Precursor FDR =============================
2 days, 20:52:06.978415 PROGRESS: Total precursors accumulated: 175,849
2 days, 20:52:06.978532 PROGRESS: Target precursors: 101,071 (57.48%)
2 days, 20:52:06.978616 PROGRESS: Decoy precursors: 74,778 (42.52%)
2 days, 20:52:06.978696 PROGRESS: 
2 days, 20:52:06.978779 PROGRESS: Precursor Summary:
2 days, 20:52:06.982640 PROGRESS: Channel   0:	 0.050 FDR:   455; 0.010 FDR:   230; 0.001 FDR:   194
2 days, 20:52:06.982799 PROGRESS: 
2 days, 20:52:06.982906 PROGRESS: Protein Summary:
2 days, 20:52:06.986743 PROGRESS: Channel   0:	 0.050 FDR:   401; 0.010 FDR:   200; 0.001 FDR:   167
2 days, 20:52:06.986882 PROGRESS: =========================================================================
2 days, 20:52:06.998987 INFO: Target number of precursors reached.
2 days, 20:52:07.671938 INFO: fragments_df: keeping 3583 of 5561003 [sum(precursor_idx_mask)=6251 sum(mass_error_mask)=5560969 stop_rank=3583
2 days, 20:52:08.905764 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:52:09.108991 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:52:09.263703 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:52:09.430685 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:52:10.076104 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 20:52:10.076598 INFO: Using score_cutoff 24.589261106872556 (fac=0.99, q=1)
2 days, 20:52:10.077000 INFO: Updating optimization_manager: fwhm_rt             : 2.9794623851776123 -> 2.9273252487182617
2 days, 20:52:10.077103 INFO: Updating optimization_manager: fwhm_mobility       : 0.005983738228678703 -> 0.006037475075572729
2 days, 20:52:10.077173 INFO: Updating optimization_manager: score_cutoff        : 19.047329598999024 -> 24.589261106872556
2 days, 20:52:10.077253 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:52:10.134408 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:52:10.408958 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:52:10.498036 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:52:11.060087 INFO: === checking if optimization conditions were reached ===
2 days, 20:52:11.060482 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
2 days, 20:52:11.061649 INFO: Updating optimization_manager: mobility_error      : 0.0582087615900455 -> 0.06393553427095688
2 days, 20:52:11.061820 INFO: Updating optimization_manager: classifier_version  : 21 -> 28
2 days, 20:52:11.061964 INFO: Updating optimization_manager: score_cutoff        : 24.589261106872556 -> 19.047329598999024
2 days, 20:52:11.062071 INFO: Updating optimization_manager: fwhm_rt             : 2.9273252487182617 -> 2.9794623851776123
2 days, 20:52:11.062163 INFO: Updating optimization_manager: fwhm_mobility       : 0.006037475075572729 -> 0.005983738228678703
2 days, 20:52:11.062258 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0639 found after 4 searches.
2 days, 20:52:11.062326 INFO: ==============================================
2 days, 20:52:11.062404 PROGRESS: Optimization finished for mobility_error.
2 days, 20:52:11.747788 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:52:11.813972 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:52:12.080412 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:52:12.187988 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:52:12.711421 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 20:52:12.711980 PROGRESS: ==============================================
2 days, 20:52:12.712423 PROGRESS: ms2_error      : 15.0000
2 days, 20:52:12.712637 PROGRESS: ms1_error      : 15.0000
2 days, 20:52:12.712835 PROGRESS: rt_error       : 288.6704
2 days, 20:52:12.712935 PROGRESS: mobility_error : 0.0639
2 days, 20:52:12.713022 PROGRESS: ==============================================
2 days, 20:52:12.719979 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 20:52:14.437110 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 20:52:22.743141 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 20:52:24.361495 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 20:52:41.388463 INFO: Using python extraction backend
2 days, 20:52:41.388908 PROGRESS: Extracting batch of 12210649 precursors
2 days, 20:52:41.389088 INFO: === Search parameters used ===
2 days, 20:52:41.389200 INFO: rt_error       : 288.6703715336644
2 days, 20:52:41.389291 INFO: mobility_error : 0.06393553427095688
2 days, 20:52:41.389374 INFO: num_candidates : 3
2 days, 20:52:41.389451 INFO: ms1_error      : 15.0
2 days, 20:52:41.389522 INFO: ms2_error      : 15.0
2 days, 20:52:41.389591 INFO: fwhm_rt        : 2.9794623851776123
2 days, 20:52:41.389661 INFO: quant_window   : 3
2 days, 20:52:41.389745 INFO: ==============================================
2 days, 20:52:44.070413 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 20:52:44.070570 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 20:52:44.070656 INFO: FWHM in RT is 2.98 seconds, sigma is 0.50
2 days, 20:52:44.070706 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.24
2 days, 20:52:44.086082 INFO: Starting candidate selection
2 days, 23:21:02.268874 INFO: Removed 15664568 precursors with score below cutoff 19.047329598999024
2 days, 23:21:05.958610 INFO: Starting candidate scoring
2 days, 23:25:10.358777 INFO: Finished candidate processing
2 days, 23:25:10.358999 INFO: Collecting candidate features
2 days, 23:26:32.112858 WARNING: intensity_correlation has 16995 NaNs ( 0.11 % out of 15551476)
2 days, 23:26:32.130120 WARNING: height_correlation has 803 NaNs ( 0.01 % out of 15551476)
2 days, 23:26:32.882002 INFO: Collecting fragment features
2 days, 23:26:44.322531 INFO: Finished candidate scoring
2 days, 23:26:56.517171 INFO: === Performing FDR correction with classifier version 28 ===
2 days, 23:26:56.517847 INFO: performing precursor FDR with 47 features
2 days, 23:26:56.517912 INFO: Decoy channel: -1
2 days, 23:26:56.517954 INFO: competitive: True
2 days, 23:27:00.964992 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:27:03.430750 WARNING: dropped 9045 target PSMs due to missing features
2 days, 23:27:03.430895 WARNING: dropped 8506 decoy PSMs due to missing features
2 days, 23:27:12.652989 INFO: Estimating optimal hyperparameters - samples: 12,427,140, batch_size: 4,096, learning_rate: 1.00e-03
2 days, 23:27:12.683851 INFO: Using random state 870240 for train-test-split
2 days, 23:36:03.063366 INFO: Test AUC: 0.553
2 days, 23:36:03.063717 INFO: Train AUC: 0.555
2 days, 23:36:03.063779 INFO: AUC difference: 0.37%
2 days, 23:36:07.214192 INFO: Resetting torch num_threads to 80
2 days, 23:36:07.552676 INFO: Removing fragments below FDR threshold
2 days, 23:36:08.759822 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:36:08.760084 PROGRESS: Total precursors accumulated: 8,898
2 days, 23:36:08.760205 PROGRESS: Target precursors: 8,810 (99.01%)
2 days, 23:36:08.760307 PROGRESS: Decoy precursors: 88 (0.99%)
2 days, 23:36:08.760403 PROGRESS: 
2 days, 23:36:08.760495 PROGRESS: Precursor Summary:
2 days, 23:36:08.765671 PROGRESS: Channel   0:	 0.050 FDR: 8,810; 0.010 FDR: 8,810; 0.001 FDR: 5,535
2 days, 23:36:08.765884 PROGRESS: 
2 days, 23:36:08.765995 PROGRESS: Protein Summary:
2 days, 23:36:08.772626 PROGRESS: Channel   0:	 0.050 FDR: 2,246; 0.010 FDR: 2,246; 0.001 FDR: 1,453
2 days, 23:36:08.772837 PROGRESS: =========================================================================
2 days, 23:36:09.023445 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R6/psm.parquet
2 days, 23:36:09.118662 INFO: Saving results to plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R6/frag.parquet
2 days, 23:36:09.177931 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R6
2 days, 23:36:43.940788 PROGRESS: Processing search outputs
2 days, 23:36:43.940941 PROGRESS: Performing protein grouping and FDR
2 days, 23:36:43.940998 INFO: Building output for A9_G_DIA_nLC_tTOF_R1
2 days, 23:36:44.000069 INFO: Building output for A9_G_DIA_nLC_tTOF_R2
2 days, 23:36:44.013649 INFO: Building output for A9_G_DIA_nLC_tTOF_R3
2 days, 23:36:44.024094 INFO: Building output for A9_G_DIA_nLC_tTOF_R4
2 days, 23:36:44.034008 INFO: Building output for A9_G_DIA_nLC_tTOF_R5
2 days, 23:36:44.045302 INFO: Building output for A9_G_DIA_nLC_tTOF_R6
2 days, 23:36:44.057829 INFO: Building output for B9_G_DIA_nLC_tTOF_R1
2 days, 23:36:44.070404 INFO: Building output for B9_G_DIA_nLC_tTOF_R2
2 days, 23:36:44.082612 INFO: Building output for B9_G_DIA_nLC_tTOF_R3
2 days, 23:36:44.094937 INFO: Building output for B9_G_DIA_nLC_tTOF_R4
2 days, 23:36:44.106177 INFO: Building output for B9_G_DIA_nLC_tTOF_R5
2 days, 23:36:44.116943 INFO: Building output for B9_G_DIA_nLC_tTOF_R6
2 days, 23:36:44.128688 INFO: Building combined output
2 days, 23:36:44.141286 INFO: Performing protein inference
2 days, 23:36:44.355860 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
2 days, 23:36:46.649737 INFO: Performing protein FDR
2 days, 23:36:49.875310 INFO: Normalizing q-values using 3,878 targets and 759 decoys
2 days, 23:36:49.877657 INFO: Test AUC: 0.803
2 days, 23:36:49.877786 INFO: Train AUC: 0.807
2 days, 23:36:49.877904 INFO: AUC difference: 0.55%
2 days, 23:36:50.348417 INFO: ================ Protein FDR =================
2 days, 23:36:50.348579 INFO: Unique protein groups in output
2 days, 23:36:50.348646 INFO:   1% protein FDR: 1,683
2 days, 23:36:50.348690 INFO: 
2 days, 23:36:50.348734 INFO: Unique precursor in output
2 days, 23:36:50.348780 INFO:   1% protein FDR: 13,761
2 days, 23:36:50.348823 INFO: ================================================
2 days, 23:36:50.362892 PROGRESS: Building search statistics
2 days, 23:36:50.385568 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R1/optimization_manager.pkl
2 days, 23:36:50.385750 INFO: Initializing OptimizationManager
2 days, 23:36:50.386042 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R1/calibration_manager.pkl
2 days, 23:36:50.386130 INFO: Initializing CalibrationManager
2 days, 23:36:50.386356 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R1/raw_file_manager.pkl
2 days, 23:36:50.386437 INFO: Initializing RawFileManager
2 days, 23:36:50.392268 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R2/optimization_manager.pkl
2 days, 23:36:50.392403 INFO: Initializing OptimizationManager
2 days, 23:36:50.392669 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R2/calibration_manager.pkl
2 days, 23:36:50.392779 INFO: Initializing CalibrationManager
2 days, 23:36:50.393039 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R2/raw_file_manager.pkl
2 days, 23:36:50.393144 INFO: Initializing RawFileManager
2 days, 23:36:50.398966 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R3/optimization_manager.pkl
2 days, 23:36:50.399101 INFO: Initializing OptimizationManager
2 days, 23:36:50.399364 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R3/calibration_manager.pkl
2 days, 23:36:50.399461 INFO: Initializing CalibrationManager
2 days, 23:36:50.399719 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R3/raw_file_manager.pkl
2 days, 23:36:50.399820 INFO: Initializing RawFileManager
2 days, 23:36:50.405407 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R4/optimization_manager.pkl
2 days, 23:36:50.405552 INFO: Initializing OptimizationManager
2 days, 23:36:50.405809 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R4/calibration_manager.pkl
2 days, 23:36:50.405917 INFO: Initializing CalibrationManager
2 days, 23:36:50.406167 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R4/raw_file_manager.pkl
2 days, 23:36:50.406270 INFO: Initializing RawFileManager
2 days, 23:36:50.414891 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R5/optimization_manager.pkl
2 days, 23:36:50.415080 INFO: Initializing OptimizationManager
2 days, 23:36:50.415390 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R5/calibration_manager.pkl
2 days, 23:36:50.415510 INFO: Initializing CalibrationManager
2 days, 23:36:50.415811 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R5/raw_file_manager.pkl
2 days, 23:36:50.415934 INFO: Initializing RawFileManager
2 days, 23:36:50.425888 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R6/optimization_manager.pkl
2 days, 23:36:50.426146 INFO: Initializing OptimizationManager
2 days, 23:36:50.426505 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R6/calibration_manager.pkl
2 days, 23:36:50.426645 INFO: Initializing CalibrationManager
2 days, 23:36:50.426985 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R6/raw_file_manager.pkl
2 days, 23:36:50.427130 INFO: Initializing RawFileManager
2 days, 23:36:50.437410 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R1/optimization_manager.pkl
2 days, 23:36:50.437609 INFO: Initializing OptimizationManager
2 days, 23:36:50.437960 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R1/calibration_manager.pkl
2 days, 23:36:50.438078 INFO: Initializing CalibrationManager
2 days, 23:36:50.438558 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R1/raw_file_manager.pkl
2 days, 23:36:50.438693 INFO: Initializing RawFileManager
2 days, 23:36:50.453855 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R2/optimization_manager.pkl
2 days, 23:36:50.454067 INFO: Initializing OptimizationManager
2 days, 23:36:50.454373 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R2/calibration_manager.pkl
2 days, 23:36:50.454480 INFO: Initializing CalibrationManager
2 days, 23:36:50.454766 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R2/raw_file_manager.pkl
2 days, 23:36:50.454880 INFO: Initializing RawFileManager
2 days, 23:36:50.461615 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R3/optimization_manager.pkl
2 days, 23:36:50.461755 INFO: Initializing OptimizationManager
2 days, 23:36:50.462038 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R3/calibration_manager.pkl
2 days, 23:36:50.462134 INFO: Initializing CalibrationManager
2 days, 23:36:50.462357 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R3/raw_file_manager.pkl
2 days, 23:36:50.462444 INFO: Initializing RawFileManager
2 days, 23:36:50.468381 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R4/optimization_manager.pkl
2 days, 23:36:50.468540 INFO: Initializing OptimizationManager
2 days, 23:36:50.468773 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R4/calibration_manager.pkl
2 days, 23:36:50.468863 INFO: Initializing CalibrationManager
2 days, 23:36:50.469069 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R4/raw_file_manager.pkl
2 days, 23:36:50.469158 INFO: Initializing RawFileManager
2 days, 23:36:50.474949 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R5/optimization_manager.pkl
2 days, 23:36:50.475081 INFO: Initializing OptimizationManager
2 days, 23:36:50.475308 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R5/calibration_manager.pkl
2 days, 23:36:50.475397 INFO: Initializing CalibrationManager
2 days, 23:36:50.475605 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R5/raw_file_manager.pkl
2 days, 23:36:50.475693 INFO: Initializing RawFileManager
2 days, 23:36:50.481607 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R6/optimization_manager.pkl
2 days, 23:36:50.481738 INFO: Initializing OptimizationManager
2 days, 23:36:50.481966 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R6/calibration_manager.pkl
2 days, 23:36:50.482056 INFO: Initializing CalibrationManager
2 days, 23:36:50.482253 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R6/raw_file_manager.pkl
2 days, 23:36:50.482342 INFO: Initializing RawFileManager
2 days, 23:36:50.483787 INFO: Writing stat output to disk
2 days, 23:36:50.483847 INFO: Saving plasma_output/alphadia_2.1.0/library/stat.tsv to disk
2 days, 23:36:50.487477 PROGRESS: Building internal statistics
2 days, 23:36:50.487691 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R1/timing_manager.pkl
2 days, 23:36:50.487737 INFO: Initializing TimingManager
2 days, 23:36:50.488016 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R2/timing_manager.pkl
2 days, 23:36:50.488063 INFO: Initializing TimingManager
2 days, 23:36:50.488285 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R3/timing_manager.pkl
2 days, 23:36:50.488328 INFO: Initializing TimingManager
2 days, 23:36:50.488538 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R4/timing_manager.pkl
2 days, 23:36:50.488582 INFO: Initializing TimingManager
2 days, 23:36:50.488791 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R5/timing_manager.pkl
2 days, 23:36:50.488834 INFO: Initializing TimingManager
2 days, 23:36:50.489038 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/A9_G_DIA_nLC_tTOF_R6/timing_manager.pkl
2 days, 23:36:50.489081 INFO: Initializing TimingManager
2 days, 23:36:50.489292 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R1/timing_manager.pkl
2 days, 23:36:50.489335 INFO: Initializing TimingManager
2 days, 23:36:50.489539 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R2/timing_manager.pkl
2 days, 23:36:50.489581 INFO: Initializing TimingManager
2 days, 23:36:50.489788 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R3/timing_manager.pkl
2 days, 23:36:50.489831 INFO: Initializing TimingManager
2 days, 23:36:50.490057 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R4/timing_manager.pkl
2 days, 23:36:50.490102 INFO: Initializing TimingManager
2 days, 23:36:50.490299 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R5/timing_manager.pkl
2 days, 23:36:50.490341 INFO: Initializing TimingManager
2 days, 23:36:50.490545 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/library/quant/B9_G_DIA_nLC_tTOF_R6/timing_manager.pkl
2 days, 23:36:50.490586 INFO: Initializing TimingManager
2 days, 23:36:50.491105 INFO: Writing internal output to disk
2 days, 23:36:50.491160 INFO: Saving plasma_output/alphadia_2.1.0/library/internal.tsv to disk
2 days, 23:36:50.509802 INFO: Performing label free quantification
2 days, 23:36:50.509959 INFO: Accumulating fragment data
2 days, 23:36:50.510015 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R1
2 days, 23:36:50.778554 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R2
2 days, 23:36:50.896406 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R3
2 days, 23:36:51.019248 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R4
2 days, 23:36:51.146392 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R5
2 days, 23:36:51.278990 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R6
2 days, 23:36:51.421510 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R1
2 days, 23:36:51.564505 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R2
2 days, 23:36:51.725893 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R3
2 days, 23:36:51.893207 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R4
2 days, 23:36:52.046093 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R5
2 days, 23:36:52.207184 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R6
2 days, 23:36:52.409251 INFO: Performing label free quantification on the precursor level
2 days, 23:36:52.409380 INFO: Filtering fragments by quality
2 days, 23:36:52.451057 INFO: Performing label-free quantification with directlfq normalization
2 days, 23:36:52.511777 INFO: Applying directLFQ normalization
2 days, 23:36:53.517560 INFO: 13761 lfq-groups total
2 days, 23:38:29.836003 INFO: using 80 processes
2 days, 23:38:29.898011 INFO: lfq-object 0
2 days, 23:38:29.956820 INFO: lfq-object 100
2 days, 23:38:30.011606 INFO: lfq-object 200
2 days, 23:38:30.060437 INFO: lfq-object 300
2 days, 23:38:30.097877 INFO: lfq-object 400
2 days, 23:38:30.173506 INFO: lfq-object 500
2 days, 23:38:30.241677 INFO: lfq-object 600
2 days, 23:38:30.317726 INFO: lfq-object 700
2 days, 23:38:30.331271 INFO: lfq-object 800
2 days, 23:38:30.414066 INFO: lfq-object 900
2 days, 23:38:30.486387 INFO: lfq-object 1000
2 days, 23:38:30.492116 INFO: lfq-object 1100
2 days, 23:38:30.572358 INFO: lfq-object 1200
2 days, 23:38:30.667472 INFO: lfq-object 1300
2 days, 23:38:30.756764 INFO: lfq-object 1400
2 days, 23:38:30.762350 INFO: lfq-object 1500
2 days, 23:38:30.856013 INFO: lfq-object 1600
2 days, 23:38:30.939235 INFO: lfq-object 1700
2 days, 23:38:31.019248 INFO: lfq-object 1800
2 days, 23:38:31.030585 INFO: lfq-object 1900
2 days, 23:38:31.102911 INFO: lfq-object 2000
2 days, 23:38:31.162451 INFO: lfq-object 2100
2 days, 23:38:31.167447 INFO: lfq-object 2200
2 days, 23:38:31.257208 INFO: lfq-object 2300
2 days, 23:38:31.309420 INFO: lfq-object 2400
2 days, 23:38:31.364374 INFO: lfq-object 2500
2 days, 23:38:31.385790 INFO: lfq-object 2600
2 days, 23:38:31.475900 INFO: lfq-object 2700
2 days, 23:38:31.538843 INFO: lfq-object 2800
2 days, 23:38:31.595027 INFO: lfq-object 2900
2 days, 23:38:31.611615 INFO: lfq-object 3000
2 days, 23:38:31.688959 INFO: lfq-object 3100
2 days, 23:38:31.776370 INFO: lfq-object 3200
2 days, 23:38:31.779499 INFO: lfq-object 3300
2 days, 23:38:31.862813 INFO: lfq-object 3400
2 days, 23:38:31.899254 INFO: lfq-object 3500
2 days, 23:38:31.966803 INFO: lfq-object 3600
2 days, 23:38:31.982766 INFO: lfq-object 3700
2 days, 23:38:32.051605 INFO: lfq-object 3800
2 days, 23:38:32.142455 INFO: lfq-object 3900
2 days, 23:38:32.196365 INFO: lfq-object 4100
2 days, 23:38:32.219374 INFO: lfq-object 4000
2 days, 23:38:32.305936 INFO: lfq-object 4200
2 days, 23:38:32.362381 INFO: lfq-object 4300
2 days, 23:38:32.372445 INFO: lfq-object 4400
2 days, 23:38:32.461858 INFO: lfq-object 4500
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2 days, 23:38:32.622164 INFO: lfq-object 4800
2 days, 23:38:32.690099 INFO: lfq-object 4900
2 days, 23:38:32.753242 INFO: lfq-object 5000
2 days, 23:38:32.854198 INFO: lfq-object 5100
2 days, 23:38:32.858691 INFO: lfq-object 5200
2 days, 23:38:32.937691 INFO: lfq-object 5300
2 days, 23:38:32.980709 INFO: lfq-object 5400
2 days, 23:38:33.020557 INFO: lfq-object 5500
2 days, 23:38:33.120689 INFO: lfq-object 5600
2 days, 23:38:33.189117 INFO: lfq-object 5700
2 days, 23:38:33.261995 INFO: lfq-object 5900
2 days, 23:38:33.275146 INFO: lfq-object 5800
2 days, 23:38:33.320680 INFO: lfq-object 6000
2 days, 23:38:33.409744 INFO: lfq-object 6100
2 days, 23:38:33.479670 INFO: lfq-object 6200
2 days, 23:38:33.508170 INFO: lfq-object 6300
2 days, 23:38:33.583819 INFO: lfq-object 6400
2 days, 23:38:33.654289 INFO: lfq-object 6600
2 days, 23:38:33.657247 INFO: lfq-object 6500
2 days, 23:38:33.729747 INFO: lfq-object 6700
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2 days, 23:38:33.982604 INFO: lfq-object 7100
2 days, 23:38:34.085503 INFO: lfq-object 7200
2 days, 23:38:34.149169 INFO: lfq-object 7400
2 days, 23:38:34.165727 INFO: lfq-object 7300
2 days, 23:38:34.235125 INFO: lfq-object 7500
2 days, 23:38:34.314171 INFO: lfq-object 7600
2 days, 23:38:34.335410 INFO: lfq-object 7700
2 days, 23:38:34.422535 INFO: lfq-object 7800
2 days, 23:38:34.493984 INFO: lfq-object 7900
2 days, 23:38:34.569745 INFO: lfq-object 8000
2 days, 23:38:41.598249 INFO: lfq-object 8100
2 days, 23:38:41.667294 INFO: lfq-object 8200
2 days, 23:38:41.759653 INFO: lfq-object 8300
2 days, 23:38:41.833312 INFO: lfq-object 8500
2 days, 23:38:41.836010 INFO: lfq-object 8400
2 days, 23:38:41.898428 INFO: lfq-object 8600
2 days, 23:38:41.971230 INFO: lfq-object 8700
2 days, 23:38:41.974750 INFO: lfq-object 8800
2 days, 23:38:42.070611 INFO: lfq-object 8900
2 days, 23:38:42.156926 INFO: lfq-object 9000
2 days, 23:38:42.224841 INFO: lfq-object 9100
2 days, 23:38:42.225266 INFO: lfq-object 9200
2 days, 23:38:42.316778 INFO: lfq-object 9300
2 days, 23:38:42.386635 INFO: lfq-object 9400
2 days, 23:38:42.457969 INFO: lfq-object 9500
2 days, 23:38:42.487509 INFO: lfq-object 9600
2 days, 23:38:42.563308 INFO: lfq-object 9700
2 days, 23:38:42.637061 INFO: lfq-object 9800
2 days, 23:38:42.650556 INFO: lfq-object 9900
2 days, 23:38:42.734855 INFO: lfq-object 10000
2 days, 23:38:42.786364 INFO: lfq-object 10100
2 days, 23:38:42.889510 INFO: lfq-object 10200
2 days, 23:38:42.893368 INFO: lfq-object 10300
2 days, 23:38:42.973860 INFO: lfq-object 10400
2 days, 23:38:43.081293 INFO: lfq-object 10500
2 days, 23:38:43.157776 INFO: lfq-object 10600
2 days, 23:38:43.171665 INFO: lfq-object 10700
2 days, 23:38:43.235708 INFO: lfq-object 10800
2 days, 23:38:43.342935 INFO: lfq-object 10900
2 days, 23:38:43.354981 INFO: lfq-object 11000
2 days, 23:38:43.452146 INFO: lfq-object 11100
2 days, 23:38:43.515028 INFO: lfq-object 11200
2 days, 23:38:43.577441 INFO: lfq-object 11300
2 days, 23:38:43.598834 INFO: lfq-object 11400
2 days, 23:38:43.670655 INFO: lfq-object 11500
2 days, 23:38:43.776315 INFO: lfq-object 11600
2 days, 23:38:43.855961 INFO: lfq-object 11700
2 days, 23:38:43.868762 INFO: lfq-object 11800
2 days, 23:38:43.956250 INFO: lfq-object 11900
2 days, 23:38:44.010819 INFO: lfq-object 12000
2 days, 23:38:44.040501 INFO: lfq-object 12100
2 days, 23:38:44.130252 INFO: lfq-object 12200
2 days, 23:38:44.196922 INFO: lfq-object 12300
2 days, 23:38:44.302694 INFO: lfq-object 12400
2 days, 23:38:44.323173 INFO: lfq-object 12500
2 days, 23:38:44.395745 INFO: lfq-object 12600
2 days, 23:38:44.449700 INFO: lfq-object 12700
2 days, 23:38:44.525565 INFO: lfq-object 12900
2 days, 23:38:44.561665 INFO: lfq-object 12800
2 days, 23:38:44.605445 INFO: lfq-object 13000
2 days, 23:38:44.661080 INFO: lfq-object 13100
2 days, 23:38:44.696232 INFO: lfq-object 13200
2 days, 23:38:44.768305 INFO: lfq-object 13300
2 days, 23:38:44.850420 INFO: lfq-object 13400
2 days, 23:38:44.897465 INFO: lfq-object 13500
2 days, 23:38:44.910423 INFO: lfq-object 13600
2 days, 23:38:44.986966 INFO: lfq-object 13700
2 days, 23:38:49.424005 INFO: Performing label free quantification on the peptide level
2 days, 23:38:49.424210 INFO: Filtering fragments by quality
2 days, 23:38:49.482190 INFO: Performing label-free quantification with directlfq normalization
2 days, 23:38:49.558109 INFO: Applying directLFQ normalization
2 days, 23:38:49.691576 INFO: 12848 lfq-groups total
2 days, 23:40:26.203672 INFO: using 80 processes
2 days, 23:40:26.285676 INFO: lfq-object 0
2 days, 23:40:26.350999 INFO: lfq-object 100
2 days, 23:40:26.430896 INFO: lfq-object 300
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2 days, 23:40:26.510871 INFO: lfq-object 400
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2 days, 23:40:26.658162 INFO: lfq-object 700
2 days, 23:40:26.666906 INFO: lfq-object 600
2 days, 23:40:26.737840 INFO: lfq-object 800
2 days, 23:40:26.818233 INFO: lfq-object 900
2 days, 23:40:26.853909 INFO: lfq-object 1000
2 days, 23:40:26.937222 INFO: lfq-object 1100
2 days, 23:40:26.985059 INFO: lfq-object 1200
2 days, 23:40:27.058474 INFO: lfq-object 1400
2 days, 23:40:27.075235 INFO: lfq-object 1300
2 days, 23:40:27.165859 INFO: lfq-object 1500
2 days, 23:40:27.177060 INFO: lfq-object 1600
2 days, 23:40:27.298025 INFO: lfq-object 1700
2 days, 23:40:27.365379 INFO: lfq-object 1800
2 days, 23:40:27.387731 INFO: lfq-object 1900
2 days, 23:40:27.495981 INFO: lfq-object 2000
2 days, 23:40:27.507604 INFO: lfq-object 2100
2 days, 23:40:27.576628 INFO: lfq-object 2200
2 days, 23:40:27.609670 INFO: lfq-object 2300
2 days, 23:40:27.711125 INFO: lfq-object 2400
2 days, 23:40:27.808640 INFO: lfq-object 2500
2 days, 23:40:27.834515 INFO: lfq-object 2600
2 days, 23:40:27.919103 INFO: lfq-object 2700
2 days, 23:40:27.941962 INFO: lfq-object 2800
2 days, 23:40:28.051252 INFO: lfq-object 2900
2 days, 23:40:28.091014 INFO: lfq-object 3000
2 days, 23:40:28.177187 INFO: lfq-object 3100
2 days, 23:40:28.206556 INFO: lfq-object 3200
2 days, 23:40:28.275141 INFO: lfq-object 3300
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2 days, 23:40:28.400692 INFO: lfq-object 3500
2 days, 23:40:28.506477 INFO: lfq-object 3600
2 days, 23:40:28.547148 INFO: lfq-object 3700
2 days, 23:40:28.624844 INFO: lfq-object 3800
2 days, 23:40:28.631676 INFO: lfq-object 3900
2 days, 23:40:28.729858 INFO: lfq-object 4000
2 days, 23:40:28.745459 INFO: lfq-object 4100
2 days, 23:40:28.819693 INFO: lfq-object 4200
2 days, 23:40:28.884419 INFO: lfq-object 4300
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2 days, 23:40:29.393029 INFO: lfq-object 5100
2 days, 23:40:29.395920 INFO: lfq-object 5000
2 days, 23:40:29.473590 INFO: lfq-object 5200
2 days, 23:40:29.534105 INFO: lfq-object 5300
2 days, 23:40:29.631114 INFO: lfq-object 5500
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2 days, 23:40:29.930726 INFO: lfq-object 6000
2 days, 23:40:30.031434 INFO: lfq-object 6200
2 days, 23:40:30.041766 INFO: lfq-object 6100
2 days, 23:40:30.111283 INFO: lfq-object 6300
2 days, 23:40:30.123921 INFO: lfq-object 6400
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2 days, 23:40:30.548968 INFO: lfq-object 7000
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2 days, 23:40:30.720897 INFO: lfq-object 7200
2 days, 23:40:30.752509 INFO: lfq-object 7300
2 days, 23:40:30.843738 INFO: lfq-object 7400
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2 days, 23:40:31.841182 INFO: lfq-object 9000
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2 days, 23:40:32.057240 INFO: lfq-object 9400
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2 days, 23:40:32.424829 INFO: lfq-object 10000
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2 days, 23:40:32.636346 INFO: lfq-object 10400
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2 days, 23:40:32.764679 INFO: lfq-object 10600
2 days, 23:40:32.863449 INFO: lfq-object 10700
2 days, 23:40:32.871466 INFO: lfq-object 10800
2 days, 23:40:32.932186 INFO: lfq-object 10900
2 days, 23:40:32.977694 INFO: lfq-object 11000
2 days, 23:40:33.053876 INFO: lfq-object 11100
2 days, 23:40:33.075051 INFO: lfq-object 11200
2 days, 23:40:33.163639 INFO: lfq-object 11300
2 days, 23:40:33.201760 INFO: lfq-object 11400
2 days, 23:40:33.289924 INFO: lfq-object 11500
2 days, 23:40:33.376801 INFO: lfq-object 11600
2 days, 23:40:33.383884 INFO: lfq-object 11700
2 days, 23:40:33.483565 INFO: lfq-object 11800
2 days, 23:40:33.515801 INFO: lfq-object 11900
2 days, 23:40:33.597246 INFO: lfq-object 12100
2 days, 23:40:33.600980 INFO: lfq-object 12000
2 days, 23:40:33.659457 INFO: lfq-object 12200
2 days, 23:40:33.690991 INFO: lfq-object 12300
2 days, 23:40:33.777968 INFO: lfq-object 12400
2 days, 23:40:33.850335 INFO: lfq-object 12500
2 days, 23:40:33.881170 INFO: lfq-object 12600
2 days, 23:40:33.987289 INFO: lfq-object 12800
2 days, 23:40:33.997936 INFO: lfq-object 12700
2 days, 23:40:38.322794 INFO: Performing label free quantification on the pg level
2 days, 23:40:38.323016 INFO: Filtering fragments by quality
2 days, 23:40:38.375433 INFO: Performing label-free quantification with directlfq normalization
2 days, 23:40:38.407969 INFO: Applying directLFQ normalization
2 days, 23:40:38.492121 INFO: 1683 lfq-groups total
2 days, 23:42:11.280190 INFO: using 80 processes
2 days, 23:42:11.304307 INFO: lfq-object 0
2 days, 23:42:11.412611 INFO: lfq-object 100
2 days, 23:42:11.487478 INFO: lfq-object 200
2 days, 23:42:11.585741 INFO: lfq-object 300
2 days, 23:42:11.714005 INFO: lfq-object 400
2 days, 23:42:11.786370 INFO: lfq-object 500
2 days, 23:42:11.865491 INFO: lfq-object 600
2 days, 23:42:11.972765 INFO: lfq-object 700
2 days, 23:42:12.072093 INFO: lfq-object 800
2 days, 23:42:12.142055 INFO: lfq-object 900
2 days, 23:42:12.227004 INFO: lfq-object 1000
2 days, 23:42:12.384415 INFO: lfq-object 1200
2 days, 23:42:12.472342 INFO: lfq-object 1300
2 days, 23:42:12.528898 INFO: lfq-object 1100
2 days, 23:42:12.540546 INFO: lfq-object 1400
2 days, 23:42:12.622974 INFO: lfq-object 1500
2 days, 23:42:12.706620 INFO: lfq-object 1600
2 days, 23:42:16.631809 INFO: Writing psm output to disk
2 days, 23:42:16.657557 INFO: Saving plasma_output/alphadia_2.1.0/library/precursors.parquet to disk
2 days, 23:42:16.851862 INFO: Writing precursor output to disk
2 days, 23:42:16.853683 INFO: Saving plasma_output/alphadia_2.1.0/library/precursor.matrix.parquet to disk
2 days, 23:42:16.875901 INFO: Writing peptide output to disk
2 days, 23:42:16.877132 INFO: Saving plasma_output/alphadia_2.1.0/library/peptide.matrix.parquet to disk
2 days, 23:42:16.898450 INFO: Writing pg output to disk
2 days, 23:42:16.899714 INFO: Saving plasma_output/alphadia_2.1.0/library/pg.matrix.parquet to disk
2 days, 23:42:16.925959 PROGRESS: Building MBR spectral library
2 days, 23:42:16.926191 INFO: Running MbrLibraryBuilder
2 days, 23:42:19.218257 INFO: MBR spectral library contains 13,761 precursors, 1,683 proteins
2 days, 23:42:19.218437 INFO: Writing MBR spectral library to disk
2 days, 23:42:20.054557 PROGRESS: =================== Search step 'library' finished ===================
2 days, 23:42:22.353006 INFO: =================== Running step 'mbr' ===================
2 days, 23:42:22.356131 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 15.0, 'target_ms2_tolerance': 15.0}})
2 days, 23:42:22.356355 INFO: loading default config from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/default.yaml
2 days, 23:42:22.370013 INFO: loading additional config provided via CLI
2 days, 23:42:22.370118 INFO: loading additional config provided via CLI parameters
2 days, 23:42:22.370565 INFO: Updating config with 'user defined'
2 days, 23:42:22.370640 WARNING: Key 'general.astral_ms1' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.370681 WARNING: Key 'general.mmap_detector_events' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.370794 WARNING: Key 'selection_config' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.370822 WARNING: Key 'scoring_config' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.370879 WARNING: Key 'fdr.enable_two_step_classifier' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.370907 WARNING: Key 'fdr.two_step_classifier_max_iterations' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.371024 INFO: Updating config with 'user defined (cli)'
2 days, 23:42:22.371077 INFO: loading default config from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/default_python.yaml
2 days, 23:42:22.371978 INFO: updating config with user defined values: [{'calibration': {'batch_size': 8000, 'optimization_lock_target': 200, 'min_steps': 2}, 'optimization': {'rt_error': {'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'maximal_decrease': 0.2, 'favour_narrower_optimum': True, 'maximum_decrease_from_maximum': 0.1}}}, {'version': 1, 'workflow_name': None, 'output_directory': None, 'library_path': None, 'raw_paths': ['/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d'], 'fasta_paths': [], 'quant_directory': None, 'general': {'thread_count': 80, 'transfer_step_enabled': False, 'mbr_step_enabled': True, 'reuse_calibration': False, 'reuse_quant': False, 'astral_ms1': False, 'log_level': 'INFO', 'mmap_detector_events': False, 'use_gpu': True, 'save_figures': True, 'save_library': True, 'save_flat_library': False, 'input_library_type': 'base', 'save_mbr_library': True, 'random_state': None}, 'library_prediction': {'enabled': False, 'enzyme': 'trypsin/p', 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M;Acetyl@Protein_N-term', 'max_var_mod_num': 1, 'missed_cleavages': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [400, 1000], 'fragment_mz': [50, 2000], 'nce': 25.0, 'fragment_types': ['b', 'y'], 'max_fragment_charge': 2, 'instrument': 'timsTOF', 'peptdeep_model_path': None, 'peptdeep_model_type': 'generic'}, 'custom_modifications': [{'name': 'Dimethyl:d12@K', 'composition': 'H(-2)2H(8)13C(2)'}, {'name': 'Dimethyl:d12@Any_N-term', 'composition': 'H(-2)2H(8)13C(2)'}, {'name': 'Dimethyl:d12@Protein_N-term', 'composition': 'H(-2)2H(8)13C(2)'}, {'name': 'mTRAQ:d12@K', 'composition': 'H(12)C(1)13C(10)15N(2)O(1)'}, {'name': 'mTRAQ:d12@Any_N-term', 'composition': 'H(12)C(1)13C(14)15N(2)O(1)'}, {'name': 'mTRAQ:d12@Protein_N-term', 'composition': 'H(12)C(1)13C(14)15N(2)O(1)'}, {'name': 'Label:13C(12)@K', 'composition': 'C(12)'}], 'search': {'extraction_backend': 'python', 'target_ms1_tolerance': 15, 'target_ms2_tolerance': 15, 'target_rt_tolerance': 0.0, 'target_mobility_tolerance': 0.0, 'quant_window': 3, 'target_num_candidates': 3, 'channel_filter': '', 'exclude_shared_ions': True, 'compete_for_fragments': True, 'quant_all': True, 'top_k_fragments_selection': 12, 'top_k_fragments_scoring': 12, 'min_fragment_intensity': 0.01, 'experimental_xic': True, 'optimized_peak_group_score': False}, 'calibration': {'batch_size': 200, 'optimization_lock_target': 200, 'max_steps': 20, 'min_steps': 2, 'max_skips': 1, 'max_fragments': 5000, 'min_correlation': 0.7}, 'search_initial': {'num_candidates': 1, 'ms1_tolerance': 30, 'ms2_tolerance': 30, 'mobility_tolerance': 0.1, 'rt_tolerance': 0.5}, 'selection_config': {'peak_len_rt': 10.0, 'sigma_scale_rt': 0.5, 'peak_len_mobility': 0.01, 'sigma_scale_mobility': 1.0, 'top_k_precursors': 3, 'kernel_size': 30, 'f_mobility': 1.0, 'f_rt': 0.99, 'center_fraction': 0.5, 'min_size_mobility': 8, 'min_size_rt': 3, 'max_size_mobility': 20, 'max_size_rt': 15, 'group_channels': False, 'use_weighted_score': True, 'join_close_candidates': False, 'join_close_candidates_scan_threshold': 0.6, 'join_close_candidates_cycle_threshold': 0.6}, 'scoring_config': {'score_grouped': False, 'top_k_isotopes': 3, 'reference_channel': -1, 'precursor_mz_tolerance': 10, 'fragment_mz_tolerance': 15}, 'library_multiplexing': {'enabled': False, 'input_channel': 0, 'multiplex_mapping': []}, 'multiplexing': {'enabled': False, 'target_channels': '4,8', 'decoy_channel': 12, 'reference_channel': 0, 'competitive_scoring': True}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins', 'inference_strategy': 'heuristic', 'competitive_scoring': True, 'keep_decoys': False, 'channel_wise_fdr': False, 'enable_two_step_classifier': False, 'two_step_classifier_max_iterations': 5, 'enable_nn_hyperparameter_tuning': True}, 'search_output': {'file_format': 'parquet', 'precursor_level_lfq': True, 'peptide_level_lfq': True, 'save_fragment_quant_matrix': False, 'min_k_fragments': 12, 'min_correlation': 0.9, 'num_samples_quadratic': 50, 'min_nonnan': 3}, 'optimization': {'order_of_optimization': None, 'ms2_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': True, 'maximal_decrease': 0.5, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.1}, 'ms1_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': False, 'maximal_decrease': 0.2, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.1}, 'mobility_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': False, 'maximal_decrease': 0.2, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.1}, 'rt_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': True, 'maximal_decrease': 0.2, 'favour_narrower_optimum': True, 'maximum_decrease_from_maximum': 0.1}}, 'optimization_manager': {'fwhm_rt': 5, 'fwhm_mobility': 0.01, 'score_cutoff': 0}, 'transfer_library': {'enabled': False, 'fragment_types': ['b', 'y'], 'max_charge': 2, 'top_k_samples': 3, 'norm_delta_max': True, 'precursor_correlation_cutoff': 0.5, 'fragment_correlation_ratio': 0.75}, 'transfer_learning': {'enabled': False, 'batch_size': 2000, 'max_lr': 0.0001, 'train_fraction': 0.7, 'validation_fraction': 0.2, 'test_fraction': 0.1, 'test_interval': 1, 'lr_patience': 3, 'epochs': 51, 'warmup_epochs': 5, 'nce': 25, 'instrument': 'Astral'}}, {'raw_paths': ['/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d', '/public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d', '/public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d'], 'library_path': '/home/robbe/ProteoBench_diaPASEF/plasma_output/alphadia_2.1.0/library/speclib.hdf', 'fasta_paths': ['./ProteoBenchFASTA_DDAQuantification.fasta']}, {'fasta_paths': [], 'fdr': {'inference_strategy': 'library'}, 'search': {'target_ms1_tolerance': 15.0, 'target_ms2_tolerance': 15.0}, 'quant_directory': None, 'library_prediction': {'enabled': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_path': 'plasma_output/alphadia_2.1.0/library/speclib.mbr.hdf', 'output_directory': 'plasma_output/alphadia_2.1.0'}]
2 days, 23:42:22.372297 INFO: Updating config with 'default_python'
2 days, 23:42:22.372353 INFO: Updating config with 'user defined'
2 days, 23:42:22.372396 WARNING: Key 'general.astral_ms1' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.372426 WARNING: Key 'general.mmap_detector_events' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.372500 WARNING: Key 'selection_config' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.372525 WARNING: Key 'scoring_config' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.372564 WARNING: Key 'fdr.enable_two_step_classifier' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.372586 WARNING: Key 'fdr.two_step_classifier_max_iterations' has been removed from AlphaDIA. Please update your config.yaml as this will be an error in future versions.
2 days, 23:42:22.372672 INFO: Updating config with 'user defined (cli)'
2 days, 23:42:22.372696 INFO: Updating config with 'multistep search'
2 days, 23:42:22.372748 INFO: [32;20m├──version: 1 [user defined, default: None][0m
2 days, 23:42:22.372778 INFO: ├──workflow_name: None
2 days, 23:42:22.372802 INFO: [32;20m├──output_directory: plasma_output/alphadia_2.1.0 [multistep search, default: None][0m
2 days, 23:42:22.372827 INFO: [32;20m├──library_path: plasma_output/alphadia_2.1.0/library/speclib.mbr.hdf [multistep search, default: None][0m
2 days, 23:42:22.372851 INFO: ├──raw_paths:
2 days, 23:42:22.372874 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d [user defined (cli), default: None][0m
2 days, 23:42:22.372897 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d [user defined (cli), default: None][0m
2 days, 23:42:22.372923 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d [user defined (cli), default: None][0m
2 days, 23:42:22.372947 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d [user defined (cli), default: None][0m
2 days, 23:42:22.372970 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d [user defined (cli), default: None][0m
2 days, 23:42:22.372998 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d [user defined (cli), default: None][0m
2 days, 23:42:22.373021 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d [user defined (cli), default: None][0m
2 days, 23:42:22.373045 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d [user defined (cli), default: None][0m
2 days, 23:42:22.373068 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d [user defined (cli), default: None][0m
2 days, 23:42:22.373090 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d [user defined (cli), default: None][0m
2 days, 23:42:22.373113 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d [user defined (cli), default: None][0m
2 days, 23:42:22.373134 INFO: │   [32;20m- /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d [user defined (cli), default: None][0m
2 days, 23:42:22.373157 INFO: ├──fasta_paths:
2 days, 23:42:22.373180 INFO: ├──quant_directory: None
2 days, 23:42:22.373203 INFO: ├──general
2 days, 23:42:22.373228 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
2 days, 23:42:22.373253 INFO: │   ├──transfer_step_enabled: False
2 days, 23:42:22.373277 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
2 days, 23:42:22.373301 INFO: │   ├──reuse_calibration: False
2 days, 23:42:22.373323 INFO: │   ├──reuse_quant: False
2 days, 23:42:22.373346 INFO: │   ├──log_level: INFO
2 days, 23:42:22.373371 INFO: │   ├──use_gpu: True
2 days, 23:42:22.373394 INFO: │   ├──save_figures: True
2 days, 23:42:22.373417 INFO: │   ├──save_library: True
2 days, 23:42:22.373439 INFO: │   ├──save_flat_library: False
2 days, 23:42:22.373461 INFO: │   ├──input_library_type: base
2 days, 23:42:22.373484 INFO: │   ├──save_mbr_library: True
2 days, 23:42:22.373506 INFO: │   └──random_state: None
2 days, 23:42:22.373529 INFO: ├──library_loading
2 days, 23:42:22.373553 INFO: │   └──drop_decoys: False
2 days, 23:42:22.373575 INFO: ├──library_prediction
2 days, 23:42:22.373598 INFO: │   ├──enabled: False
2 days, 23:42:22.373621 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
2 days, 23:42:22.373644 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
2 days, 23:42:22.373666 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
2 days, 23:42:22.373689 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
2 days, 23:42:22.373712 INFO: │   ├──missed_cleavages: 1
2 days, 23:42:22.373734 INFO: │   ├──precursor_len:
2 days, 23:42:22.373757 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
2 days, 23:42:22.373779 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
2 days, 23:42:22.373801 INFO: │   ├──precursor_charge:
2 days, 23:42:22.373824 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
2 days, 23:42:22.373847 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
2 days, 23:42:22.373883 INFO: │   ├──precursor_mz:
2 days, 23:42:22.373909 INFO: │   │   - 400
2 days, 23:42:22.373932 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
2 days, 23:42:22.373954 INFO: │   ├──fragment_mz:
2 days, 23:42:22.373976 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
2 days, 23:42:22.374003 INFO: │   │   - 2000
2 days, 23:42:22.374027 INFO: │   ├──nce: 25.0
2 days, 23:42:22.374048 INFO: │   ├──fragment_types:
2 days, 23:42:22.374070 INFO: │   │   - b
2 days, 23:42:22.374092 INFO: │   │   - y
2 days, 23:42:22.374114 INFO: │   ├──max_fragment_charge: 2
2 days, 23:42:22.374136 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
2 days, 23:42:22.374159 INFO: │   ├──peptdeep_model_path: None
2 days, 23:42:22.374181 INFO: │   ├──peptdeep_model_type: generic
2 days, 23:42:22.374204 INFO: │   ├──predict_charge: False
2 days, 23:42:22.374228 INFO: │   └──min_charge_probability: 0.1
2 days, 23:42:22.374250 INFO: ├──custom_modifications:
2 days, 23:42:22.374274 INFO: │   ├──name: Dimethyl:d12@K
2 days, 23:42:22.374296 INFO: │   └──composition: H(-2)2H(8)13C(2)
2 days, 23:42:22.374319 INFO: │   ├──name: Dimethyl:d12@Any_N-term
2 days, 23:42:22.374341 INFO: │   └──composition: H(-2)2H(8)13C(2)
2 days, 23:42:22.374363 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
2 days, 23:42:22.374385 INFO: │   └──composition: H(-2)2H(8)13C(2)
2 days, 23:42:22.374407 INFO: │   ├──name: mTRAQ:d12@K
2 days, 23:42:22.374429 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
2 days, 23:42:22.374451 INFO: │   ├──name: mTRAQ:d12@Any_N-term
2 days, 23:42:22.374474 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2 days, 23:42:22.374496 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
2 days, 23:42:22.374518 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2 days, 23:42:22.374540 INFO: │   ├──name: Label:13C(12)@K
2 days, 23:42:22.374563 INFO: │   └──composition: C(12)
2 days, 23:42:22.374585 INFO: ├──search
2 days, 23:42:22.374608 INFO: │   [32;20m├──extraction_backend: python [user defined, default: rust][0m
2 days, 23:42:22.374634 INFO: │   [32;20m├──target_ms1_tolerance: 15.0 [multistep search, default: 5][0m
2 days, 23:42:22.374658 INFO: │   [32;20m├──target_ms2_tolerance: 15.0 [multistep search, default: 10][0m
2 days, 23:42:22.374681 INFO: │   ├──target_rt_tolerance: 0.0
2 days, 23:42:22.374704 INFO: │   ├──target_mobility_tolerance: 0.0
2 days, 23:42:22.374727 INFO: │   ├──quant_window: 3
2 days, 23:42:22.374749 INFO: │   ├──target_num_candidates: 3
2 days, 23:42:22.374772 INFO: │   ├──channel_filter: 
2 days, 23:42:22.374795 INFO: │   ├──compete_for_fragments: True
2 days, 23:42:22.374817 INFO: │   ├──top_k_fragments_selection: 12
2 days, 23:42:22.374839 INFO: │   ├──top_k_fragments_scoring: 12
2 days, 23:42:22.374862 INFO: │   ├──min_fragment_intensity: 0.01
2 days, 23:42:22.374884 INFO: │   ├──optimized_peak_group_score: False
2 days, 23:42:22.374905 INFO: │   ├──exclude_shared_ions: True
2 days, 23:42:22.374927 INFO: │   ├──quant_all: True
2 days, 23:42:22.374948 INFO: │   └──experimental_xic: True
2 days, 23:42:22.374968 INFO: ├──calibration
2 days, 23:42:22.374990 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 1000][0m
2 days, 23:42:22.375011 INFO: │   [32;20m├──optimization_lock_target: 200 [user defined, default: 1000][0m
2 days, 23:42:22.375032 INFO: │   ├──max_steps: 20
2 days, 23:42:22.375053 INFO: │   [32;20m├──min_steps: 2 [user defined, default: 5][0m
2 days, 23:42:22.375074 INFO: │   ├──max_skips: 1
2 days, 23:42:22.375096 INFO: │   ├──max_fragments: 5000
2 days, 23:42:22.375118 INFO: │   └──min_correlation: 0.7
2 days, 23:42:22.375138 INFO: ├──search_initial
2 days, 23:42:22.375160 INFO: │   ├──num_candidates: 1
2 days, 23:42:22.375180 INFO: │   ├──ms1_tolerance: 30
2 days, 23:42:22.375201 INFO: │   ├──ms2_tolerance: 30
2 days, 23:42:22.375224 INFO: │   ├──mobility_tolerance: 0.1
2 days, 23:42:22.375247 INFO: │   └──rt_tolerance: 0.5
2 days, 23:42:22.375272 INFO: ├──library_multiplexing
2 days, 23:42:22.375295 INFO: │   ├──enabled: False
2 days, 23:42:22.375317 INFO: │   ├──input_channel: 0
2 days, 23:42:22.375339 INFO: │   └──multiplex_mapping:
2 days, 23:42:22.375361 INFO: ├──multiplexing
2 days, 23:42:22.375383 INFO: │   ├──enabled: False
2 days, 23:42:22.375406 INFO: │   ├──target_channels: 4,8
2 days, 23:42:22.375427 INFO: │   ├──decoy_channel: 12
2 days, 23:42:22.375448 INFO: │   ├──reference_channel: 0
2 days, 23:42:22.375469 INFO: │   └──competitive_scoring: True
2 days, 23:42:22.375489 INFO: ├──fdr
2 days, 23:42:22.375512 INFO: │   ├──fdr: 0.01
2 days, 23:42:22.375533 INFO: │   ├──group_level: proteins
2 days, 23:42:22.375554 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
2 days, 23:42:22.375575 INFO: │   ├──competitive_scoring: True
2 days, 23:42:22.375596 INFO: │   ├──keep_decoys: False
2 days, 23:42:22.375618 INFO: │   ├──keep_decoys_in_mbr_library: False
2 days, 23:42:22.375639 INFO: │   ├──channel_wise_fdr: False
2 days, 23:42:22.375660 INFO: │   └──enable_nn_hyperparameter_tuning: True
2 days, 23:42:22.375681 INFO: ├──search_output
2 days, 23:42:22.375702 INFO: │   ├──file_format: parquet
2 days, 23:42:22.375724 INFO: │   ├──precursor_level_lfq: True
2 days, 23:42:22.375744 INFO: │   ├──peptide_level_lfq: True
2 days, 23:42:22.375765 INFO: │   ├──save_fragment_quant_matrix: False
2 days, 23:42:22.375786 INFO: │   ├──min_k_fragments: 12
2 days, 23:42:22.375807 INFO: │   ├──min_correlation: 0.9
2 days, 23:42:22.375828 INFO: │   ├──num_samples_quadratic: 50
2 days, 23:42:22.375849 INFO: │   ├──min_nonnan: 3
2 days, 23:42:22.375870 INFO: │   ├──normalization_method: directlfq
2 days, 23:42:22.375891 INFO: │   └──normalize_directlfq: True
2 days, 23:42:22.375911 INFO: ├──optimization
2 days, 23:42:22.375932 INFO: │   ├──order_of_optimization: None
2 days, 23:42:22.375953 INFO: │   ├──ms2_error
2 days, 23:42:22.375975 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2 days, 23:42:22.375997 INFO: │   │   ├──targeted_update_factor: 1.0
2 days, 23:42:22.376018 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2 days, 23:42:22.376040 INFO: │   │   ├──automatic_update_factor: 1.1
2 days, 23:42:22.376062 INFO: │   │   ├──try_narrower_values: True
2 days, 23:42:22.376085 INFO: │   │   ├──maximal_decrease: 0.5
2 days, 23:42:22.376107 INFO: │   │   ├──favour_narrower_optimum: False
2 days, 23:42:22.376128 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2 days, 23:42:22.376149 INFO: │   ├──ms1_error
2 days, 23:42:22.376171 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2 days, 23:42:22.376193 INFO: │   │   ├──targeted_update_factor: 1.0
2 days, 23:42:22.376215 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2 days, 23:42:22.376236 INFO: │   │   ├──automatic_update_factor: 1.1
2 days, 23:42:22.376257 INFO: │   │   ├──try_narrower_values: False
2 days, 23:42:22.376278 INFO: │   │   ├──maximal_decrease: 0.2
2 days, 23:42:22.376300 INFO: │   │   ├──favour_narrower_optimum: False
2 days, 23:42:22.376322 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2 days, 23:42:22.376343 INFO: │   ├──mobility_error
2 days, 23:42:22.376365 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2 days, 23:42:22.376387 INFO: │   │   ├──targeted_update_factor: 1.0
2 days, 23:42:22.376410 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2 days, 23:42:22.376432 INFO: │   │   ├──automatic_update_factor: 1.1
2 days, 23:42:22.376453 INFO: │   │   ├──try_narrower_values: False
2 days, 23:42:22.376477 INFO: │   │   ├──maximal_decrease: 0.2
2 days, 23:42:22.376499 INFO: │   │   ├──favour_narrower_optimum: False
2 days, 23:42:22.376520 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2 days, 23:42:22.376541 INFO: │   └──rt_error
2 days, 23:42:22.376563 INFO: │       ├──targeted_update_percentile_range: 0.95
2 days, 23:42:22.376584 INFO: │       ├──targeted_update_factor: 1.0
2 days, 23:42:22.376610 INFO: │       [32;20m├──automatic_update_percentile_range: 0.99 [user defined, default: 0.999][0m
2 days, 23:42:22.376634 INFO: │       [32;20m├──automatic_update_factor: 1.1 [user defined, default: 1.5][0m
2 days, 23:42:22.376657 INFO: │       ├──try_narrower_values: True
2 days, 23:42:22.376680 INFO: │       [32;20m├──maximal_decrease: 0.2 [user defined, default: 0.1][0m
2 days, 23:42:22.376704 INFO: │       [32;20m├──favour_narrower_optimum: True [user defined, default: False][0m
2 days, 23:42:22.376728 INFO: │       [32;20m└──maximum_decrease_from_maximum: 0.1 [user defined, default: 0.5][0m
2 days, 23:42:22.376750 INFO: ├──optimization_manager
2 days, 23:42:22.376773 INFO: │   ├──fwhm_rt: 5
2 days, 23:42:22.376796 INFO: │   ├──fwhm_mobility: 0.01
2 days, 23:42:22.376819 INFO: │   └──score_cutoff: 0
2 days, 23:42:22.376841 INFO: ├──transfer_library
2 days, 23:42:22.376863 INFO: │   ├──enabled: False
2 days, 23:42:22.376885 INFO: │   ├──fragment_types:
2 days, 23:42:22.376907 INFO: │   │   - b
2 days, 23:42:22.376928 INFO: │   │   - y
2 days, 23:42:22.376951 INFO: │   ├──max_charge: 2
2 days, 23:42:22.376974 INFO: │   ├──top_k_samples: 3
2 days, 23:42:22.376997 INFO: │   ├──norm_delta_max: True
2 days, 23:42:22.377019 INFO: │   ├──precursor_correlation_cutoff: 0.5
2 days, 23:42:22.377042 INFO: │   └──fragment_correlation_ratio: 0.75
2 days, 23:42:22.377064 INFO: └──transfer_learning
2 days, 23:42:22.377087 INFO:     ├──enabled: False
2 days, 23:42:22.377109 INFO:     ├──batch_size: 2000
2 days, 23:42:22.377132 INFO:     ├──max_lr: 0.0001
2 days, 23:42:22.377154 INFO:     ├──train_fraction: 0.7
2 days, 23:42:22.377177 INFO:     ├──validation_fraction: 0.2
2 days, 23:42:22.377199 INFO:     ├──test_fraction: 0.1
2 days, 23:42:22.377221 INFO:     ├──test_interval: 1
2 days, 23:42:22.377243 INFO:     ├──lr_patience: 3
2 days, 23:42:22.377265 INFO:     ├──epochs: 51
2 days, 23:42:22.377287 INFO:     ├──warmup_epochs: 5
2 days, 23:42:22.377309 INFO:     ├──nce: 25
2 days, 23:42:22.377331 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
2 days, 23:42:22.383264 INFO: Registering 7 custom modifications
2 days, 23:42:22.405874 INFO: Searching 12 files:
2 days, 23:42:22.405964 INFO:   A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:22.405998 INFO:   A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:42:22.406029 INFO:   A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:42:22.406057 INFO:   A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:42:22.406083 INFO:   A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:42:22.406108 INFO:   A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:42:22.406134 INFO:   B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:22.406159 INFO:   B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:42:22.406184 INFO:   B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:42:22.406211 INFO:   B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:42:22.406237 INFO:   B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:42:22.406261 INFO:   B9_G_DIA_nLC_tTOF_R6.d
2 days, 23:42:22.406286 INFO: Using 0 fasta files:
2 days, 23:42:22.406311 INFO: Using library: plasma_output/alphadia_2.1.0/library/speclib.mbr.hdf
2 days, 23:42:22.406340 INFO: Saving output to: plasma_output/alphadia_2.1.0
2 days, 23:42:22.406377 PROGRESS: Loading spectral library
2 days, 23:42:22.406427 PROGRESS: Loading library (type: base) from disk..
2 days, 23:42:22.406474 INFO: Running DynamicLoader
2 days, 23:42:22.406551 INFO: Loading .hdf library from plasma_output/alphadia_2.1.0/library/speclib.mbr.hdf
2 days, 23:42:22.558132 INFO: Running PrecursorInitializer
2 days, 23:42:22.558467 INFO: Channel column already present, skipping initialization
2 days, 23:42:22.558514 INFO: Elution group indices already present, skipping initialization
2 days, 23:42:22.558551 INFO: Precursor indices already present, skipping initialization
2 days, 23:42:22.558583 INFO: Running AnnotateFasta
2 days, 23:42:22.560141 INFO: Running IsotopeGenerator
2 days, 23:42:22.560272 INFO: Isotope information already present, skipping isotope generation
2 days, 23:42:22.560313 INFO: Running RTNormalization
2 days, 23:42:22.561724 INFO: Saving library to plasma_output/alphadia_2.1.0/speclib.hdf
2 days, 23:42:22.748905 INFO: Running DecoyGenerator
2 days, 23:42:29.398086 INFO: Running FlattenLibrary
2 days, 23:42:30.587536 INFO: Running InitFlatColumns
2 days, 23:42:30.590723 INFO: Running LogFlatLibraryStats
2 days, 23:42:30.590809 INFO: ============ Library Stats ============
2 days, 23:42:30.590843 INFO: Number of precursors: 27,522
2 days, 23:42:30.601234 INFO: 	thereof targets:13,761
2 days, 23:42:30.601338 INFO: 	thereof decoys: 13,761
2 days, 23:42:30.601820 INFO: Number of elution groups: 13,761
2 days, 23:42:30.601879 INFO: 	average size: 2.00
2 days, 23:42:30.602651 INFO: Number of proteins: 1,683
2 days, 23:42:30.602946 INFO: Number of channels: 1 ([0])
2 days, 23:42:30.603029 INFO: Isotopes Distribution for 4 isotopes
2 days, 23:42:30.603059 INFO: =======================================
2 days, 23:42:30.603122 PROGRESS: =================== Starting Search Workflows for step mbr ===================
2 days, 23:42:30.603181 PROGRESS: Loading raw file 1/12: A9_G_DIA_nLC_tTOF_R1 
2 days, 23:42:30.603235 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:42:30.603286 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R1/figures
2 days, 23:42:30.603486 INFO: Initializing TimingManager
2 days, 23:42:30.603849 INFO: Initializing RawFileManager
2 days, 23:42:30.603961 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:30.604015 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:30.604058 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:30.840043 INFO: Reading 22,623 frames with 335,647,195 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:35.145073 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d...
2 days, 23:42:35.146541 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:35.155561 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:35.155883 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:35.156532 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:35.158555 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:35.182861 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:35.183263 INFO: Indexing quadrupole dimension
2 days, 23:42:35.310700 INFO: Transposing detector events
2 days, 23:42:37.066433 INFO: Finished transposing data
2 days, 23:42:37.066562 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
2 days, 23:42:37.067034 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:42:37.067087 INFO: RT duration (sec)   : 2399.9
2 days, 23:42:37.067120 INFO: RT duration (min)   : 40.0
2 days, 23:42:37.067152 INFO: Cycle len (scans)   : 12
2 days, 23:42:37.067180 INFO: Cycle len (sec)     : 1.27
2 days, 23:42:37.067207 INFO: Number of cycles    : 1885
2 days, 23:42:37.067237 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:42:37.067272 INFO: Creating DIA data object took: 6.46332311630249
2 days, 23:42:37.072465 INFO: Initializing CalibrationManager
2 days, 23:42:37.072715 INFO: Setting up calibration estimators ..
2 days, 23:42:37.072788 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:42:37.072876 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:42:37.072963 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:42:37.073035 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:42:37.073110 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:42:37.073177 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:42:37.073236 INFO: Done setting up calibration estimators.
2 days, 23:42:37.073347 INFO: Initializing OptimizationManager
2 days, 23:42:37.073453 INFO: initial parameter: ms1_error = 30
2 days, 23:42:37.073510 INFO: initial parameter: ms2_error = 30
2 days, 23:42:37.073566 INFO: initial parameter: rt_error = 1199.955978
2 days, 23:42:37.073628 INFO: initial parameter: mobility_error = 0.1
2 days, 23:42:37.073692 INFO: initial parameter: num_candidates = 1
2 days, 23:42:37.073745 INFO: initial parameter: fwhm_rt = 5
2 days, 23:42:37.073798 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:42:37.073852 INFO: initial parameter: score_cutoff = 0
2 days, 23:42:37.073929 INFO: initial parameter: classifier_version = -1
2 days, 23:42:37.074018 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R1
2 days, 23:42:37.074247 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:42:37.074286 INFO: Initializing FDRManager
2 days, 23:42:37.074333 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:42:37.082630 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:42:37.088350 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:42:37.088719 INFO: Updating optimization_manager: rt_error            : 1199.955978 -> 1199.955978
2 days, 23:42:37.088840 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:42:37.089043 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:42:37.089144 PROGRESS: Starting initial search for precursors.
2 days, 23:42:37.089236 INFO: Starting optimization step 0.
2 days, 23:42:37.089309 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:42:37.089394 INFO: Using python extraction backend
2 days, 23:42:37.089548 PROGRESS: Extracting batch of 399 precursors
2 days, 23:42:37.089627 INFO: === Search parameters used ===
2 days, 23:42:37.089687 INFO: rt_error       : 1199.955978
2 days, 23:42:37.089741 INFO: mobility_error : 0.1
2 days, 23:42:37.089796 INFO: num_candidates : 1
2 days, 23:42:37.089849 INFO: ms1_error      : 30
2 days, 23:42:37.089920 INFO: ms2_error      : 30
2 days, 23:42:37.089973 INFO: fwhm_rt        : 5
2 days, 23:42:37.090033 INFO: quant_window   : 3
2 days, 23:42:37.090085 INFO: ==============================================
2 days, 23:42:37.090930 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:42:37.090984 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:42:37.091026 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:42:37.091068 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:42:37.106021 INFO: Starting candidate selection
2 days, 23:42:41.153767 INFO: Starting candidate scoring
2 days, 23:42:41.198811 INFO: Finished candidate processing
2 days, 23:42:41.198915 INFO: Collecting candidate features
2 days, 23:42:41.211270 INFO: Collecting fragment features
2 days, 23:42:41.214220 INFO: Finished candidate scoring
2 days, 23:42:41.215472 INFO: performing precursor FDR with 47 features
2 days, 23:42:41.215527 INFO: Decoy channel: -1
2 days, 23:42:41.215558 INFO: competitive: True
2 days, 23:42:41.218511 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:42:41.220800 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:42:41.221766 INFO: Using random state 693220 for train-test-split
2 days, 23:42:41.248740 INFO: Test AUC: 0.511
2 days, 23:42:41.248826 INFO: Train AUC: 0.479
2 days, 23:42:41.248862 INFO: AUC difference: 6.60%
2 days, 23:42:41.248902 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:42:45.899071 INFO: Resetting torch num_threads to 80
2 days, 23:42:45.899704 PROGRESS: === Extracted 399 precursors and 3662 fragments ===
2 days, 23:42:45.900334 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:42:45.901071 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:42:45.901194 PROGRESS: Total precursors accumulated: 200
2 days, 23:42:45.901288 PROGRESS: Target precursors: 98 (49.00%)
2 days, 23:42:45.901373 PROGRESS: Decoy precursors: 102 (51.00%)
2 days, 23:42:45.901450 PROGRESS: 
2 days, 23:42:45.901526 PROGRESS: Precursor Summary:
2 days, 23:42:45.902684 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 23:42:45.902816 PROGRESS: 
2 days, 23:42:45.902905 PROGRESS: Protein Summary:
2 days, 23:42:45.904144 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 23:42:45.904279 PROGRESS: =========================================================================
2 days, 23:42:45.904441 INFO: Target number of precursors not reached yet.
2 days, 23:42:45.908257 INFO: Starting optimization step 1.
2 days, 23:42:45.908542 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:42:45.908650 INFO: Using python extraction backend
2 days, 23:42:45.908838 PROGRESS: Extracting batch of 798 precursors
2 days, 23:42:45.909115 INFO: === Search parameters used ===
2 days, 23:42:45.909242 INFO: rt_error       : 1199.955978
2 days, 23:42:45.909373 INFO: mobility_error : 0.1
2 days, 23:42:45.909497 INFO: num_candidates : 1
2 days, 23:42:45.909600 INFO: ms1_error      : 30
2 days, 23:42:45.909717 INFO: ms2_error      : 30
2 days, 23:42:45.909832 INFO: fwhm_rt        : 5
2 days, 23:42:45.910082 INFO: quant_window   : 3
2 days, 23:42:45.910161 INFO: ==============================================
2 days, 23:42:45.911108 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:42:45.911222 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:42:45.911305 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:42:45.911367 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:42:45.915311 INFO: Starting candidate selection
2 days, 23:42:51.415224 INFO: Starting candidate scoring
2 days, 23:42:51.476893 INFO: Finished candidate processing
2 days, 23:42:51.477096 INFO: Collecting candidate features
2 days, 23:42:51.498581 INFO: Collecting fragment features
2 days, 23:42:51.503541 INFO: Finished candidate scoring
2 days, 23:42:51.507980 INFO: performing precursor FDR with 47 features
2 days, 23:42:51.508069 INFO: Decoy channel: -1
2 days, 23:42:51.508111 INFO: competitive: True
2 days, 23:42:51.512496 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:42:51.514982 INFO: Estimating optimal hyperparameters - samples: 956, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:42:51.515119 INFO: Using random state 836306 for train-test-split
2 days, 23:42:51.591425 INFO: Test AUC: 0.734
2 days, 23:42:51.591526 INFO: Train AUC: 0.760
2 days, 23:42:51.591558 INFO: AUC difference: 3.41%
2 days, 23:42:51.860876 INFO: Resetting torch num_threads to 80
2 days, 23:42:51.862235 PROGRESS: === Extracted 1196 precursors and 11221 fragments ===
2 days, 23:42:51.862720 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:42:51.863386 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:42:51.863492 PROGRESS: Total precursors accumulated: 600
2 days, 23:42:51.863569 PROGRESS: Target precursors: 446 (74.33%)
2 days, 23:42:51.863644 PROGRESS: Decoy precursors: 154 (25.67%)
2 days, 23:42:51.863708 PROGRESS: 
2 days, 23:42:51.863766 PROGRESS: Precursor Summary:
2 days, 23:42:51.864931 PROGRESS: Channel   0:	 0.050 FDR:   281; 0.010 FDR:   229; 0.001 FDR:   147
2 days, 23:42:51.865031 PROGRESS: 
2 days, 23:42:51.865100 PROGRESS: Protein Summary:
2 days, 23:42:51.866357 PROGRESS: Channel   0:	 0.050 FDR:   206; 0.010 FDR:   164; 0.001 FDR:   102
2 days, 23:42:51.866458 PROGRESS: =========================================================================
2 days, 23:42:51.866690 INFO: Target number of precursors reached.
2 days, 23:42:51.869906 INFO: fragments_df: keeping 1935 of 11221 [sum(precursor_idx_mask)=2382 sum(mass_error_mask)=11221 stop_rank=1935
2 days, 23:42:51.873492 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:42:52.041399 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:42:52.185987 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:42:52.389119 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:42:52.741696 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:42:52.742312 INFO: Using score_cutoff 36.90545568695068 (fac=0.99, q=1)
2 days, 23:42:52.742809 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.8905673027038574
2 days, 23:42:52.742921 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.006969645153731108
2 days, 23:42:52.743005 INFO: Updating optimization_manager: score_cutoff        : 0 -> 36.90545568695068
2 days, 23:42:52.743083 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:42:52.744596 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:42:52.746538 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:42:52.747674 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:42:52.750263 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2 days, 23:42:52.750374 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:42:52.750468 INFO: Starting optimization step 2.
2 days, 23:42:52.750537 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:42:52.750606 INFO: Using python extraction backend
2 days, 23:42:52.750718 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:42:52.750788 INFO: === Search parameters used ===
2 days, 23:42:52.750841 INFO: rt_error       : 1199.955978
2 days, 23:42:52.750889 INFO: mobility_error : 0.1
2 days, 23:42:52.750933 INFO: num_candidates : 3
2 days, 23:42:52.750977 INFO: ms1_error      : 30
2 days, 23:42:52.751021 INFO: ms2_error      : 30
2 days, 23:42:52.751066 INFO: fwhm_rt        : 2.8905673027038574
2 days, 23:42:52.751109 INFO: quant_window   : 3
2 days, 23:42:52.751152 INFO: ==============================================
2 days, 23:42:52.752255 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:42:52.752305 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:42:52.752345 INFO: FWHM in RT is 2.89 seconds, sigma is 0.48
2 days, 23:42:52.752369 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.78
2 days, 23:42:52.760110 INFO: Starting candidate selection
2 days, 23:42:59.665600 INFO: Starting candidate scoring
2 days, 23:42:59.795066 INFO: Finished candidate processing
2 days, 23:42:59.795196 INFO: Collecting candidate features
2 days, 23:42:59.821298 INFO: Collecting fragment features
2 days, 23:42:59.828253 INFO: Finished candidate scoring
2 days, 23:42:59.832478 INFO: performing precursor FDR with 47 features
2 days, 23:42:59.832590 INFO: Decoy channel: -1
2 days, 23:42:59.832637 INFO: competitive: True
2 days, 23:42:59.837998 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:42:59.841384 INFO: Estimating optimal hyperparameters - samples: 2,744, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:42:59.841578 INFO: Using random state 875581 for train-test-split
2 days, 23:43:00.162591 INFO: Test AUC: 0.675
2 days, 23:43:00.162701 INFO: Train AUC: 0.686
2 days, 23:43:00.162743 INFO: AUC difference: 1.64%
2 days, 23:43:00.503475 INFO: Resetting torch num_threads to 80
2 days, 23:43:00.504223 PROGRESS: === Extracted 3431 precursors and 31096 fragments ===
2 days, 23:43:00.504689 INFO: === FDR correction performed with classifier version 1 ===
2 days, 23:43:00.505430 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:00.505560 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:00.505643 PROGRESS: Target precursors: 476 (79.33%)
2 days, 23:43:00.505712 PROGRESS: Decoy precursors: 124 (20.67%)
2 days, 23:43:00.505777 PROGRESS: 
2 days, 23:43:00.505839 PROGRESS: Precursor Summary:
2 days, 23:43:00.507517 PROGRESS: Channel   0:	 0.050 FDR:   332; 0.010 FDR:   281; 0.001 FDR:   255
2 days, 23:43:00.507640 PROGRESS: 
2 days, 23:43:00.507727 PROGRESS: Protein Summary:
2 days, 23:43:00.509663 PROGRESS: Channel   0:	 0.050 FDR:   249; 0.010 FDR:   205; 0.001 FDR:   185
2 days, 23:43:00.509789 PROGRESS: =========================================================================
2 days, 23:43:00.510025 INFO: Target number of precursors reached.
2 days, 23:43:00.520259 INFO: fragments_df: keeping 4855 of 31096 [sum(precursor_idx_mask)=7874 sum(mass_error_mask)=31096 stop_rank=4855
2 days, 23:43:00.525657 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:00.706680 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:00.931955 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:01.164308 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:01.970642 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:01.971117 INFO: Using score_cutoff 32.9027892036438 (fac=0.99, q=1)
2 days, 23:43:01.971498 INFO: Updating optimization_manager: fwhm_rt             : 2.8905673027038574 -> 2.8202431201934814
2 days, 23:43:01.971607 INFO: Updating optimization_manager: fwhm_mobility       : 0.006969645153731108 -> 0.006239886861294508
2 days, 23:43:01.971690 INFO: Updating optimization_manager: score_cutoff        : 36.90545568695068 -> 32.9027892036438
2 days, 23:43:01.971774 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:01.973007 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:01.974576 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:01.975492 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:01.977639 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:01.979517 INFO: Updating optimization_manager: ms2_error           : 30 -> 18.03127317255113
2 days, 23:43:01.979643 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2 days, 23:43:01.979734 PROGRESS: ❌ ms2_error      : 18.0313 > 15.0000 or insufficient steps taken.
2 days, 23:43:01.980803 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:43:01.980914 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
2 days, 23:43:01.980993 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:43:01.981064 INFO: ==============================================
2 days, 23:43:01.981175 INFO: Starting optimization step 3.
2 days, 23:43:01.981259 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:01.981340 INFO: Using python extraction backend
2 days, 23:43:01.981465 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:01.981551 INFO: === Search parameters used ===
2 days, 23:43:01.981620 INFO: rt_error       : 1199.955978
2 days, 23:43:01.981693 INFO: mobility_error : 0.1
2 days, 23:43:01.981759 INFO: num_candidates : 3
2 days, 23:43:01.981824 INFO: ms1_error      : 15.0
2 days, 23:43:01.981903 INFO: ms2_error      : 18.03127317255113
2 days, 23:43:01.981993 INFO: fwhm_rt        : 2.8202431201934814
2 days, 23:43:01.982063 INFO: quant_window   : 3
2 days, 23:43:01.982132 INFO: ==============================================
2 days, 23:43:01.983439 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:01.983515 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:01.983567 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
2 days, 23:43:01.983606 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.38
2 days, 23:43:01.994224 INFO: Starting candidate selection
2 days, 23:43:08.638948 INFO: Starting candidate scoring
2 days, 23:43:08.743137 INFO: Finished candidate processing
2 days, 23:43:08.743272 INFO: Collecting candidate features
2 days, 23:43:08.763301 INFO: Collecting fragment features
2 days, 23:43:08.769903 INFO: Finished candidate scoring
2 days, 23:43:08.774039 INFO: performing precursor FDR with 47 features
2 days, 23:43:08.774225 INFO: Decoy channel: -1
2 days, 23:43:08.774337 INFO: competitive: True
2 days, 23:43:08.779661 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:08.783506 INFO: Estimating optimal hyperparameters - samples: 2,751, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:08.783739 INFO: Using random state 357050 for train-test-split
2 days, 23:43:09.161174 INFO: Test AUC: 0.744
2 days, 23:43:09.161321 INFO: Train AUC: 0.726
2 days, 23:43:09.162340 INFO: AUC difference: 2.52%
2 days, 23:43:09.535468 INFO: Resetting torch num_threads to 80
2 days, 23:43:09.536162 PROGRESS: === Extracted 3439 precursors and 28274 fragments ===
2 days, 23:43:09.536622 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:43:09.537285 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:09.537397 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:09.537494 PROGRESS: Target precursors: 510 (85.00%)
2 days, 23:43:09.537580 PROGRESS: Decoy precursors: 90 (15.00%)
2 days, 23:43:09.537663 PROGRESS: 
2 days, 23:43:09.537745 PROGRESS: Precursor Summary:
2 days, 23:43:09.539007 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   364; 0.001 FDR:   334
2 days, 23:43:09.539129 PROGRESS: 
2 days, 23:43:09.539214 PROGRESS: Protein Summary:
2 days, 23:43:09.540660 PROGRESS: Channel   0:	 0.050 FDR:   317; 0.010 FDR:   272; 0.001 FDR:   250
2 days, 23:43:09.540779 PROGRESS: =========================================================================
2 days, 23:43:09.540950 INFO: Target number of precursors reached.
2 days, 23:43:09.548011 INFO: fragments_df: keeping 5000 of 28274 [sum(precursor_idx_mask)=9510 sum(mass_error_mask)=28267 stop_rank=5000
2 days, 23:43:09.551540 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:09.732821 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:09.886942 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:10.059567 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:10.891726 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:10.892213 INFO: Using score_cutoff 25.3377080783844 (fac=0.99, q=1)
2 days, 23:43:10.892558 INFO: Updating optimization_manager: fwhm_rt             : 2.8202431201934814 -> 2.659914493560791
2 days, 23:43:10.892649 INFO: Updating optimization_manager: fwhm_mobility       : 0.006239886861294508 -> 0.005217036232352257
2 days, 23:43:10.892725 INFO: Updating optimization_manager: score_cutoff        : 32.9027892036438 -> 25.3377080783844
2 days, 23:43:10.892791 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:10.893943 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:10.895424 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:10.896247 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:10.898338 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:10.900163 INFO: Updating optimization_manager: ms2_error           : 18.03127317255113 -> 15.0
2 days, 23:43:10.900281 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:43:10.900370 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:43:10.901417 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:43:10.901537 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:43:10.901625 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:43:10.901703 INFO: ==============================================
2 days, 23:43:10.901797 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:43:10.905243 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:10.906191 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:10.907598 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:10.908433 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:10.910459 INFO: Starting optimization step 0.
2 days, 23:43:10.910590 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:10.910699 INFO: Using python extraction backend
2 days, 23:43:10.910832 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:10.910936 INFO: === Search parameters used ===
2 days, 23:43:10.911020 INFO: rt_error       : 1199.955978
2 days, 23:43:10.911089 INFO: mobility_error : 0.1
2 days, 23:43:10.911160 INFO: num_candidates : 3
2 days, 23:43:10.911226 INFO: ms1_error      : 15.0
2 days, 23:43:10.911292 INFO: ms2_error      : 15.0
2 days, 23:43:10.911357 INFO: fwhm_rt        : 2.659914493560791
2 days, 23:43:10.911421 INFO: quant_window   : 3
2 days, 23:43:10.911485 INFO: ==============================================
2 days, 23:43:10.912379 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:10.912433 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:10.912487 INFO: FWHM in RT is 2.66 seconds, sigma is 0.44
2 days, 23:43:10.912522 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.83
2 days, 23:43:10.918434 INFO: Starting candidate selection
2 days, 23:43:20.056433 INFO: Starting candidate scoring
2 days, 23:43:20.164126 INFO: Finished candidate processing
2 days, 23:43:20.164264 INFO: Collecting candidate features
2 days, 23:43:20.188290 INFO: Collecting fragment features
2 days, 23:43:20.195670 INFO: Finished candidate scoring
2 days, 23:43:20.199416 INFO: performing precursor FDR with 47 features
2 days, 23:43:20.199519 INFO: Decoy channel: -1
2 days, 23:43:20.199568 INFO: competitive: True
2 days, 23:43:20.204834 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:20.208602 INFO: Estimating optimal hyperparameters - samples: 2,728, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:20.208757 INFO: Using random state 908305 for train-test-split
2 days, 23:43:20.587519 INFO: Test AUC: 0.758
2 days, 23:43:20.587657 INFO: Train AUC: 0.736
2 days, 23:43:20.587714 INFO: AUC difference: 3.01%
2 days, 23:43:20.894758 INFO: Resetting torch num_threads to 80
2 days, 23:43:20.895392 PROGRESS: === Extracted 3410 precursors and 26847 fragments ===
2 days, 23:43:20.895833 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:20.896461 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:20.896561 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:20.896644 PROGRESS: Target precursors: 519 (86.50%)
2 days, 23:43:20.896711 PROGRESS: Decoy precursors: 81 (13.50%)
2 days, 23:43:20.896775 PROGRESS: 
2 days, 23:43:20.896836 PROGRESS: Precursor Summary:
2 days, 23:43:20.898054 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   373; 0.001 FDR:   350
2 days, 23:43:20.898162 PROGRESS: 
2 days, 23:43:20.898235 PROGRESS: Protein Summary:
2 days, 23:43:20.899609 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   270; 0.001 FDR:   256
2 days, 23:43:20.899713 PROGRESS: =========================================================================
2 days, 23:43:20.899884 INFO: Target number of precursors reached.
2 days, 23:43:20.906042 INFO: fragments_df: keeping 5000 of 26847 [sum(precursor_idx_mask)=9494 sum(mass_error_mask)=26841 stop_rank=5000
2 days, 23:43:20.909576 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:21.088675 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:21.276053 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:21.470098 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:22.315986 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:22.316524 INFO: Using score_cutoff 24.81176442260742 (fac=0.99, q=1)
2 days, 23:43:22.316936 INFO: Updating optimization_manager: fwhm_rt             : 2.659914493560791 -> 2.6138617992401123
2 days, 23:43:22.317043 INFO: Updating optimization_manager: fwhm_mobility       : 0.005217036232352257 -> 0.004750261083245277
2 days, 23:43:22.317121 INFO: Updating optimization_manager: score_cutoff        : 25.3377080783844 -> 24.81176442260742
2 days, 23:43:22.317202 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:22.318435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:22.320002 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:22.320900 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:22.322991 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:22.323128 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:43:22.324836 INFO: Updating optimization_manager: rt_error            : 1199.955978 -> 242.6365249080548
2 days, 23:43:22.324948 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 242.6365.
2 days, 23:43:22.325028 INFO: ==============================================
2 days, 23:43:22.325113 INFO: Starting optimization step 1.
2 days, 23:43:22.325187 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:22.325258 INFO: Using python extraction backend
2 days, 23:43:22.325371 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:22.325448 INFO: === Search parameters used ===
2 days, 23:43:22.325519 INFO: rt_error       : 242.6365249080548
2 days, 23:43:22.325579 INFO: mobility_error : 0.1
2 days, 23:43:22.325638 INFO: num_candidates : 3
2 days, 23:43:22.325697 INFO: ms1_error      : 15.0
2 days, 23:43:22.325752 INFO: ms2_error      : 15.0
2 days, 23:43:22.325806 INFO: fwhm_rt        : 2.6138617992401123
2 days, 23:43:22.325860 INFO: quant_window   : 3
2 days, 23:43:22.325939 INFO: ==============================================
2 days, 23:43:22.326899 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:22.326956 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:22.327000 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
2 days, 23:43:22.327033 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.58
2 days, 23:43:22.330446 INFO: Starting candidate selection
2 days, 23:43:25.278018 INFO: Starting candidate scoring
2 days, 23:43:25.379721 INFO: Finished candidate processing
2 days, 23:43:25.379869 INFO: Collecting candidate features
2 days, 23:43:25.397457 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3372)
2 days, 23:43:25.405774 INFO: Collecting fragment features
2 days, 23:43:25.413477 INFO: Finished candidate scoring
2 days, 23:43:25.417355 INFO: performing precursor FDR with 47 features
2 days, 23:43:25.417468 INFO: Decoy channel: -1
2 days, 23:43:25.417508 INFO: competitive: True
2 days, 23:43:25.423276 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:25.425266 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:43:25.425340 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:43:25.426860 INFO: Estimating optimal hyperparameters - samples: 2,694, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:25.426990 INFO: Using random state 908305 for train-test-split
2 days, 23:43:25.833218 INFO: Test AUC: 0.761
2 days, 23:43:25.833360 INFO: Train AUC: 0.784
2 days, 23:43:25.833414 INFO: AUC difference: 2.97%
2 days, 23:43:26.225519 INFO: Resetting torch num_threads to 80
2 days, 23:43:26.226193 PROGRESS: === Extracted 3372 precursors and 25611 fragments ===
2 days, 23:43:26.226649 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:26.227268 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:26.227379 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:26.227478 PROGRESS: Target precursors: 550 (91.67%)
2 days, 23:43:26.227562 PROGRESS: Decoy precursors: 50 (8.33%)
2 days, 23:43:26.227640 PROGRESS: 
2 days, 23:43:26.227716 PROGRESS: Precursor Summary:
2 days, 23:43:26.228923 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   452; 0.001 FDR:   368
2 days, 23:43:26.229042 PROGRESS: 
2 days, 23:43:26.229132 PROGRESS: Protein Summary:
2 days, 23:43:26.230676 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   333; 0.001 FDR:   275
2 days, 23:43:26.230796 PROGRESS: =========================================================================
2 days, 23:43:26.230998 INFO: Target number of precursors reached.
2 days, 23:43:26.240729 INFO: fragments_df: keeping 5000 of 25611 [sum(precursor_idx_mask)=11142 sum(mass_error_mask)=25611 stop_rank=5000
2 days, 23:43:26.246260 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:26.423750 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:26.608341 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:26.856540 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:27.714884 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:27.715508 INFO: Using score_cutoff 20.318925881195067 (fac=0.99, q=1)
2 days, 23:43:27.716013 INFO: Updating optimization_manager: fwhm_rt             : 2.6138617992401123 -> 2.5502142906188965
2 days, 23:43:27.716129 INFO: Updating optimization_manager: fwhm_mobility       : 0.004750261083245277 -> 0.004292616620659828
2 days, 23:43:27.716220 INFO: Updating optimization_manager: score_cutoff        : 24.81176442260742 -> 20.318925881195067
2 days, 23:43:27.716314 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:27.717932 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:27.719835 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:27.721002 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:27.723579 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:27.723723 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:43:27.726352 INFO: Updating optimization_manager: rt_error            : 242.6365249080548 -> 199.72613158718724
2 days, 23:43:27.726490 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 199.7261.
2 days, 23:43:27.726606 INFO: ==============================================
2 days, 23:43:27.726722 INFO: Starting optimization step 2.
2 days, 23:43:27.726819 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:27.726924 INFO: Using python extraction backend
2 days, 23:43:27.727086 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:27.727204 INFO: === Search parameters used ===
2 days, 23:43:27.727298 INFO: rt_error       : 199.72613158718724
2 days, 23:43:27.727389 INFO: mobility_error : 0.1
2 days, 23:43:27.727474 INFO: num_candidates : 3
2 days, 23:43:27.727554 INFO: ms1_error      : 15.0
2 days, 23:43:27.727633 INFO: ms2_error      : 15.0
2 days, 23:43:27.727717 INFO: fwhm_rt        : 2.5502142906188965
2 days, 23:43:27.727811 INFO: quant_window   : 3
2 days, 23:43:27.727896 INFO: ==============================================
2 days, 23:43:27.729194 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:27.729266 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:27.729330 INFO: FWHM in RT is 2.55 seconds, sigma is 0.43
2 days, 23:43:27.729379 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.33
2 days, 23:43:27.734765 INFO: Starting candidate selection
2 days, 23:43:30.325552 INFO: Starting candidate scoring
2 days, 23:43:30.422286 INFO: Finished candidate processing
2 days, 23:43:30.422424 INFO: Collecting candidate features
2 days, 23:43:30.439104 WARNING: intensity_correlation has 5 NaNs ( 0.15 % out of 3362)
2 days, 23:43:30.444312 INFO: Collecting fragment features
2 days, 23:43:30.449444 INFO: Finished candidate scoring
2 days, 23:43:30.453254 INFO: performing precursor FDR with 47 features
2 days, 23:43:30.453368 INFO: Decoy channel: -1
2 days, 23:43:30.453445 INFO: competitive: True
2 days, 23:43:30.458787 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:30.461444 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:43:30.461639 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 23:43:30.463382 INFO: Estimating optimal hyperparameters - samples: 2,685, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:30.463515 INFO: Using random state 908305 for train-test-split
2 days, 23:43:30.815104 INFO: Test AUC: 0.764
2 days, 23:43:30.815231 INFO: Train AUC: 0.796
2 days, 23:43:30.815274 INFO: AUC difference: 4.03%
2 days, 23:43:31.162649 INFO: Resetting torch num_threads to 80
2 days, 23:43:31.163538 PROGRESS: === Extracted 3362 precursors and 25319 fragments ===
2 days, 23:43:31.164001 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:31.164657 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:31.164762 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:31.164844 PROGRESS: Target precursors: 548 (91.33%)
2 days, 23:43:31.164917 PROGRESS: Decoy precursors: 52 (8.67%)
2 days, 23:43:31.164986 PROGRESS: 
2 days, 23:43:31.165052 PROGRESS: Precursor Summary:
2 days, 23:43:31.166254 PROGRESS: Channel   0:	 0.050 FDR:   510; 0.010 FDR:   436; 0.001 FDR:   371
2 days, 23:43:31.166363 PROGRESS: 
2 days, 23:43:31.166439 PROGRESS: Protein Summary:
2 days, 23:43:31.167774 PROGRESS: Channel   0:	 0.050 FDR:   374; 0.010 FDR:   319; 0.001 FDR:   279
2 days, 23:43:31.167887 PROGRESS: =========================================================================
2 days, 23:43:31.168116 INFO: Target number of precursors reached.
2 days, 23:43:31.174924 INFO: fragments_df: keeping 5000 of 25319 [sum(precursor_idx_mask)=10737 sum(mass_error_mask)=25319 stop_rank=5000
2 days, 23:43:31.179267 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:31.339819 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:31.533376 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:31.761738 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:32.570830 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:32.571302 INFO: Using score_cutoff 20.33553598022461 (fac=0.99, q=1)
2 days, 23:43:32.571700 INFO: Updating optimization_manager: fwhm_rt             : 2.5502142906188965 -> 2.5515520572662354
2 days, 23:43:32.571805 INFO: Updating optimization_manager: fwhm_mobility       : 0.004292616620659828 -> 0.004276474472135305
2 days, 23:43:32.571894 INFO: Updating optimization_manager: score_cutoff        : 20.318925881195067 -> 20.33553598022461
2 days, 23:43:32.571975 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:32.573163 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:32.574752 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:32.575665 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:32.577791 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:32.577925 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:43:32.579894 INFO: Updating optimization_manager: rt_error            : 199.72613158718724 -> 45.434867343580706
2 days, 23:43:32.580015 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 45.4349.
2 days, 23:43:32.580098 INFO: ==============================================
2 days, 23:43:32.580190 INFO: Starting optimization step 3.
2 days, 23:43:32.580265 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:32.580338 INFO: Using python extraction backend
2 days, 23:43:32.580455 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:32.580537 INFO: === Search parameters used ===
2 days, 23:43:32.580599 INFO: rt_error       : 45.434867343580706
2 days, 23:43:32.580658 INFO: mobility_error : 0.1
2 days, 23:43:32.580716 INFO: num_candidates : 3
2 days, 23:43:32.580774 INFO: ms1_error      : 15.0
2 days, 23:43:32.580830 INFO: ms2_error      : 15.0
2 days, 23:43:32.580887 INFO: fwhm_rt        : 2.5515520572662354
2 days, 23:43:32.580944 INFO: quant_window   : 3
2 days, 23:43:32.580999 INFO: ==============================================
2 days, 23:43:32.582022 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:32.582086 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:32.582134 INFO: FWHM in RT is 2.55 seconds, sigma is 0.43
2 days, 23:43:32.582162 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.32
2 days, 23:43:32.586882 INFO: Starting candidate selection
2 days, 23:43:33.448498 INFO: Starting candidate scoring
2 days, 23:43:33.547265 INFO: Finished candidate processing
2 days, 23:43:33.547430 INFO: Collecting candidate features
2 days, 23:43:33.561114 WARNING: intensity_correlation has 7 NaNs ( 0.21 % out of 3265)
2 days, 23:43:33.561471 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3265)
2 days, 23:43:33.566747 INFO: Collecting fragment features
2 days, 23:43:33.571764 INFO: Finished candidate scoring
2 days, 23:43:33.574275 INFO: performing precursor FDR with 47 features
2 days, 23:43:33.574358 INFO: Decoy channel: -1
2 days, 23:43:33.574389 INFO: competitive: True
2 days, 23:43:33.578652 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:33.580630 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:43:33.580741 WARNING: dropped 6 decoy PSMs due to missing features
2 days, 23:43:33.582311 INFO: Estimating optimal hyperparameters - samples: 2,605, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:33.582460 INFO: Using random state 908305 for train-test-split
2 days, 23:43:33.926517 INFO: Test AUC: 0.798
2 days, 23:43:33.926665 INFO: Train AUC: 0.837
2 days, 23:43:33.926718 INFO: AUC difference: 4.70%
2 days, 23:43:34.282252 INFO: Resetting torch num_threads to 80
2 days, 23:43:34.283087 PROGRESS: === Extracted 3265 precursors and 23105 fragments ===
2 days, 23:43:34.283659 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:34.284667 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:34.284792 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:34.284896 PROGRESS: Target precursors: 580 (96.67%)
2 days, 23:43:34.284994 PROGRESS: Decoy precursors: 20 (3.33%)
2 days, 23:43:34.285086 PROGRESS: 
2 days, 23:43:34.285184 PROGRESS: Precursor Summary:
2 days, 23:43:34.287194 PROGRESS: Channel   0:	 0.050 FDR:   580; 0.010 FDR:   543; 0.001 FDR:   478
2 days, 23:43:34.287320 PROGRESS: 
2 days, 23:43:34.287419 PROGRESS: Protein Summary:
2 days, 23:43:34.289690 PROGRESS: Channel   0:	 0.050 FDR:   421; 0.010 FDR:   396; 0.001 FDR:   351
2 days, 23:43:34.289811 PROGRESS: =========================================================================
2 days, 23:43:34.290037 INFO: Target number of precursors reached.
2 days, 23:43:34.299443 INFO: fragments_df: keeping 5000 of 23105 [sum(precursor_idx_mask)=12786 sum(mass_error_mask)=23105 stop_rank=5000
2 days, 23:43:34.304380 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:34.570929 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:34.780826 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:34.967222 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:35.718170 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:35.718648 INFO: Using score_cutoff 16.973334925460815 (fac=0.99, q=1)
2 days, 23:43:35.719012 INFO: Updating optimization_manager: fwhm_rt             : 2.5515520572662354 -> 2.522803783416748
2 days, 23:43:35.719109 INFO: Updating optimization_manager: fwhm_mobility       : 0.004276474472135305 -> 0.0037947460077703
2 days, 23:43:35.719188 INFO: Updating optimization_manager: score_cutoff        : 20.33553598022461 -> 16.973334925460815
2 days, 23:43:35.719269 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:35.720416 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:35.721819 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:35.722706 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:35.725159 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:35.725286 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:43:35.728034 INFO: Updating optimization_manager: rt_error            : 45.434867343580706 -> 30.601685787055498
2 days, 23:43:35.728186 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 30.6017.
2 days, 23:43:35.728295 INFO: ==============================================
2 days, 23:43:35.728409 INFO: Starting optimization step 4.
2 days, 23:43:35.728511 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:35.728618 INFO: Using python extraction backend
2 days, 23:43:35.728768 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:35.728871 INFO: === Search parameters used ===
2 days, 23:43:35.728965 INFO: rt_error       : 30.601685787055498
2 days, 23:43:35.729057 INFO: mobility_error : 0.1
2 days, 23:43:35.729161 INFO: num_candidates : 3
2 days, 23:43:35.729246 INFO: ms1_error      : 15.0
2 days, 23:43:35.729325 INFO: ms2_error      : 15.0
2 days, 23:43:35.729408 INFO: fwhm_rt        : 2.522803783416748
2 days, 23:43:35.729491 INFO: quant_window   : 3
2 days, 23:43:35.729562 INFO: ==============================================
2 days, 23:43:35.730860 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:35.730935 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:35.730995 INFO: FWHM in RT is 2.52 seconds, sigma is 0.42
2 days, 23:43:35.731042 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.06
2 days, 23:43:35.742094 INFO: Starting candidate selection
2 days, 23:43:36.341177 INFO: Starting candidate scoring
2 days, 23:43:36.438248 INFO: Finished candidate processing
2 days, 23:43:36.438426 INFO: Collecting candidate features
2 days, 23:43:36.452014 WARNING: intensity_correlation has 10 NaNs ( 0.31 % out of 3210)
2 days, 23:43:36.452269 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3210)
2 days, 23:43:36.458632 INFO: Collecting fragment features
2 days, 23:43:36.464145 INFO: Finished candidate scoring
2 days, 23:43:36.466709 INFO: performing precursor FDR with 47 features
2 days, 23:43:36.466776 INFO: Decoy channel: -1
2 days, 23:43:36.466817 INFO: competitive: True
2 days, 23:43:36.470998 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:36.472964 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:43:36.473022 WARNING: dropped 8 decoy PSMs due to missing features
2 days, 23:43:36.474693 INFO: Estimating optimal hyperparameters - samples: 2,559, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:36.474793 INFO: Using random state 908305 for train-test-split
2 days, 23:43:36.777122 INFO: Test AUC: 0.856
2 days, 23:43:36.777246 INFO: Train AUC: 0.859
2 days, 23:43:36.777281 INFO: AUC difference: 0.36%
2 days, 23:43:37.079892 INFO: Resetting torch num_threads to 80
2 days, 23:43:37.080602 PROGRESS: === Extracted 3210 precursors and 22397 fragments ===
2 days, 23:43:37.081084 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:37.081808 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:37.081935 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:37.082015 PROGRESS: Target precursors: 579 (96.50%)
2 days, 23:43:37.082082 PROGRESS: Decoy precursors: 21 (3.50%)
2 days, 23:43:37.082143 PROGRESS: 
2 days, 23:43:37.082202 PROGRESS: Precursor Summary:
2 days, 23:43:37.083607 PROGRESS: Channel   0:	 0.050 FDR:   579; 0.010 FDR:   547; 0.001 FDR:   443
2 days, 23:43:37.083760 PROGRESS: 
2 days, 23:43:37.083870 PROGRESS: Protein Summary:
2 days, 23:43:37.085568 PROGRESS: Channel   0:	 0.050 FDR:   424; 0.010 FDR:   405; 0.001 FDR:   323
2 days, 23:43:37.085672 PROGRESS: =========================================================================
2 days, 23:43:37.085837 INFO: Target number of precursors reached.
2 days, 23:43:37.093955 INFO: fragments_df: keeping 5000 of 22397 [sum(precursor_idx_mask)=12920 sum(mass_error_mask)=22397 stop_rank=5000
2 days, 23:43:37.098027 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:37.316461 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:37.508930 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:37.768217 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:38.561730 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:38.562236 INFO: Using score_cutoff 16.701205321884157 (fac=0.99, q=1)
2 days, 23:43:38.562625 INFO: Updating optimization_manager: fwhm_rt             : 2.522803783416748 -> 2.4969682693481445
2 days, 23:43:38.562726 INFO: Updating optimization_manager: fwhm_mobility       : 0.0037947460077703 -> 0.003747704904526472
2 days, 23:43:38.562807 INFO: Updating optimization_manager: score_cutoff        : 16.973334925460815 -> 16.701205321884157
2 days, 23:43:38.562891 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:38.564059 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:38.565536 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:38.566409 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:38.568556 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:38.568676 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:43:38.570681 INFO: Updating optimization_manager: rt_error            : 30.601685787055498 -> 12.960346247076709
2 days, 23:43:38.570806 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 12.9603.
2 days, 23:43:38.570892 INFO: ==============================================
2 days, 23:43:38.570982 INFO: Starting optimization step 5.
2 days, 23:43:38.571072 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:38.571154 INFO: Using python extraction backend
2 days, 23:43:38.571276 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:38.571370 INFO: === Search parameters used ===
2 days, 23:43:38.571440 INFO: rt_error       : 12.960346247076709
2 days, 23:43:38.571507 INFO: mobility_error : 0.1
2 days, 23:43:38.571570 INFO: num_candidates : 3
2 days, 23:43:38.571630 INFO: ms1_error      : 15.0
2 days, 23:43:38.571692 INFO: ms2_error      : 15.0
2 days, 23:43:38.571753 INFO: fwhm_rt        : 2.4969682693481445
2 days, 23:43:38.571813 INFO: quant_window   : 3
2 days, 23:43:38.571873 INFO: ==============================================
2 days, 23:43:38.572788 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:38.572840 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:38.572890 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:43:38.572925 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.03
2 days, 23:43:38.579928 INFO: Starting candidate selection
2 days, 23:43:39.197245 INFO: Starting candidate scoring
2 days, 23:43:39.307165 INFO: Finished candidate processing
2 days, 23:43:39.307284 INFO: Collecting candidate features
2 days, 23:43:39.317336 WARNING: intensity_correlation has 19 NaNs ( 0.60 % out of 3173)
2 days, 23:43:39.317575 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3173)
2 days, 23:43:39.321527 INFO: Collecting fragment features
2 days, 23:43:39.325366 INFO: Finished candidate scoring
2 days, 23:43:39.327144 INFO: performing precursor FDR with 47 features
2 days, 23:43:39.327202 INFO: Decoy channel: -1
2 days, 23:43:39.327242 INFO: competitive: True
2 days, 23:43:39.330514 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:39.332217 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:43:39.332274 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:43:39.332328 WARNING: FDR calculation for 1663 target and 1490 decoy PSMs
2 days, 23:43:39.332362 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:43:39.333642 INFO: Estimating optimal hyperparameters - samples: 2,522, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:39.333743 INFO: Using random state 908305 for train-test-split
2 days, 23:43:39.530029 INFO: Test AUC: 0.848
2 days, 23:43:39.530145 INFO: Train AUC: 0.879
2 days, 23:43:39.530181 INFO: AUC difference: 3.50%
2 days, 23:43:39.825117 INFO: Resetting torch num_threads to 80
2 days, 23:43:39.825790 PROGRESS: === Extracted 3173 precursors and 21703 fragments ===
2 days, 23:43:39.826292 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:39.826928 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:39.827045 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:39.827140 PROGRESS: Target precursors: 585 (97.50%)
2 days, 23:43:39.827224 PROGRESS: Decoy precursors: 15 (2.50%)
2 days, 23:43:39.827303 PROGRESS: 
2 days, 23:43:39.827382 PROGRESS: Precursor Summary:
2 days, 23:43:39.828575 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   569; 0.001 FDR:   427
2 days, 23:43:39.828692 PROGRESS: 
2 days, 23:43:39.828776 PROGRESS: Protein Summary:
2 days, 23:43:39.830202 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   417; 0.001 FDR:   316
2 days, 23:43:39.830316 PROGRESS: =========================================================================
2 days, 23:43:39.830520 INFO: Target number of precursors reached.
2 days, 23:43:39.836960 INFO: fragments_df: keeping 5000 of 21703 [sum(precursor_idx_mask)=13204 sum(mass_error_mask)=21703 stop_rank=5000
2 days, 23:43:39.840513 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:40.080388 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:40.324606 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:40.538194 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:41.506279 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:41.506790 INFO: Using score_cutoff 14.205846770095826 (fac=0.99, q=1)
2 days, 23:43:41.507165 INFO: Updating optimization_manager: fwhm_rt             : 2.4969682693481445 -> 2.467947483062744
2 days, 23:43:41.507255 INFO: Updating optimization_manager: fwhm_mobility       : 0.003747704904526472 -> 0.0035973351914435625
2 days, 23:43:41.507324 INFO: Updating optimization_manager: score_cutoff        : 16.701205321884157 -> 14.205846770095826
2 days, 23:43:41.507392 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:41.508643 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:41.510157 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:41.511071 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:41.513255 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:41.513371 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 23:43:41.515567 INFO: Updating optimization_manager: rt_error            : 12.960346247076709 -> 10.86540921849913
2 days, 23:43:41.515689 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 10.8654.
2 days, 23:43:41.515768 INFO: ==============================================
2 days, 23:43:41.515850 INFO: Starting optimization step 6.
2 days, 23:43:41.515919 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:41.515990 INFO: Using python extraction backend
2 days, 23:43:41.516108 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:41.516185 INFO: === Search parameters used ===
2 days, 23:43:41.516254 INFO: rt_error       : 10.86540921849913
2 days, 23:43:41.516314 INFO: mobility_error : 0.1
2 days, 23:43:41.516371 INFO: num_candidates : 3
2 days, 23:43:41.516428 INFO: ms1_error      : 15.0
2 days, 23:43:41.516484 INFO: ms2_error      : 15.0
2 days, 23:43:41.516539 INFO: fwhm_rt        : 2.467947483062744
2 days, 23:43:41.516593 INFO: quant_window   : 3
2 days, 23:43:41.516647 INFO: ==============================================
2 days, 23:43:41.517647 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:41.517702 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:41.517744 INFO: FWHM in RT is 2.47 seconds, sigma is 0.41
2 days, 23:43:41.517774 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.95
2 days, 23:43:41.522423 INFO: Starting candidate selection
2 days, 23:43:42.104129 INFO: Starting candidate scoring
2 days, 23:43:42.216276 INFO: Finished candidate processing
2 days, 23:43:42.216424 INFO: Collecting candidate features
2 days, 23:43:42.232408 WARNING: intensity_correlation has 22 NaNs ( 0.69 % out of 3178)
2 days, 23:43:42.232727 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3178)
2 days, 23:43:42.239271 INFO: Collecting fragment features
2 days, 23:43:42.243375 INFO: Finished candidate scoring
2 days, 23:43:42.245369 INFO: performing precursor FDR with 47 features
2 days, 23:43:42.245433 INFO: Decoy channel: -1
2 days, 23:43:42.245492 INFO: competitive: True
2 days, 23:43:42.249210 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:42.251799 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:43:42.251952 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:43:42.252065 WARNING: FDR calculation for 1671 target and 1484 decoy PSMs
2 days, 23:43:42.252110 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:43:42.253574 INFO: Estimating optimal hyperparameters - samples: 2,524, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:42.253744 INFO: Using random state 908305 for train-test-split
2 days, 23:43:42.599205 INFO: Test AUC: 0.867
2 days, 23:43:42.599313 INFO: Train AUC: 0.876
2 days, 23:43:42.599343 INFO: AUC difference: 1.01%
2 days, 23:43:42.872944 INFO: Resetting torch num_threads to 80
2 days, 23:43:42.873616 PROGRESS: === Extracted 3178 precursors and 21681 fragments ===
2 days, 23:43:42.874083 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:42.874700 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:42.874798 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:42.874869 PROGRESS: Target precursors: 584 (97.33%)
2 days, 23:43:42.874929 PROGRESS: Decoy precursors: 16 (2.67%)
2 days, 23:43:42.874983 PROGRESS: 
2 days, 23:43:42.875036 PROGRESS: Precursor Summary:
2 days, 23:43:42.876182 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   571; 0.001 FDR:   444
2 days, 23:43:42.876278 PROGRESS: 
2 days, 23:43:42.876343 PROGRESS: Protein Summary:
2 days, 23:43:42.877712 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   417; 0.001 FDR:   326
2 days, 23:43:42.877809 PROGRESS: =========================================================================
2 days, 23:43:42.878006 INFO: Target number of precursors reached.
2 days, 23:43:42.884193 INFO: fragments_df: keeping 5000 of 21681 [sum(precursor_idx_mask)=13311 sum(mass_error_mask)=21681 stop_rank=5000
2 days, 23:43:42.887738 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:43.109407 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:43.298135 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:43.502366 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:44.304538 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:44.304991 INFO: Using score_cutoff 15.357510955810548 (fac=0.99, q=1)
2 days, 23:43:44.305391 INFO: Updating optimization_manager: fwhm_rt             : 2.467947483062744 -> 2.481955051422119
2 days, 23:43:44.305495 INFO: Updating optimization_manager: fwhm_mobility       : 0.0035973351914435625 -> 0.0036012560594826937
2 days, 23:43:44.305576 INFO: Updating optimization_manager: score_cutoff        : 14.205846770095826 -> 15.357510955810548
2 days, 23:43:44.305652 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:44.306839 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:44.308320 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:44.309179 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:44.311398 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:44.311521 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 23:43:44.313592 INFO: Updating optimization_manager: rt_error            : 10.86540921849913 -> 14.707461535628736
2 days, 23:43:44.313714 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 14.7075.
2 days, 23:43:44.313800 INFO: ==============================================
2 days, 23:43:44.313909 INFO: Starting optimization step 7.
2 days, 23:43:44.313996 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:44.314081 INFO: Using python extraction backend
2 days, 23:43:44.314212 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:44.314309 INFO: === Search parameters used ===
2 days, 23:43:44.314386 INFO: rt_error       : 14.707461535628736
2 days, 23:43:44.314457 INFO: mobility_error : 0.1
2 days, 23:43:44.314524 INFO: num_candidates : 3
2 days, 23:43:44.314590 INFO: ms1_error      : 15.0
2 days, 23:43:44.314660 INFO: ms2_error      : 15.0
2 days, 23:43:44.314724 INFO: fwhm_rt        : 2.481955051422119
2 days, 23:43:44.314788 INFO: quant_window   : 3
2 days, 23:43:44.314850 INFO: ==============================================
2 days, 23:43:44.316089 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:44.316146 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:44.316204 INFO: FWHM in RT is 2.48 seconds, sigma is 0.41
2 days, 23:43:44.316240 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.95
2 days, 23:43:44.338045 INFO: Starting candidate selection
2 days, 23:43:44.955313 INFO: Starting candidate scoring
2 days, 23:43:45.060302 INFO: Finished candidate processing
2 days, 23:43:45.060438 INFO: Collecting candidate features
2 days, 23:43:45.076665 WARNING: intensity_correlation has 22 NaNs ( 0.69 % out of 3188)
2 days, 23:43:45.077011 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3188)
2 days, 23:43:45.084795 INFO: Collecting fragment features
2 days, 23:43:45.090990 INFO: Finished candidate scoring
2 days, 23:43:45.094438 INFO: performing precursor FDR with 47 features
2 days, 23:43:45.094549 INFO: Decoy channel: -1
2 days, 23:43:45.094594 INFO: competitive: True
2 days, 23:43:45.100677 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:45.103557 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:43:45.103645 WARNING: dropped 20 decoy PSMs due to missing features
2 days, 23:43:45.103716 WARNING: FDR calculation for 1666 target and 1499 decoy PSMs
2 days, 23:43:45.103763 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:43:45.105721 INFO: Estimating optimal hyperparameters - samples: 2,532, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:45.105850 INFO: Using random state 908305 for train-test-split
2 days, 23:43:45.424663 INFO: Test AUC: 0.880
2 days, 23:43:45.424775 INFO: Train AUC: 0.875
2 days, 23:43:45.424819 INFO: AUC difference: 0.58%
2 days, 23:43:45.785003 INFO: Resetting torch num_threads to 80
2 days, 23:43:45.785949 PROGRESS: === Extracted 3188 precursors and 21756 fragments ===
2 days, 23:43:45.786553 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:45.787458 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:45.787602 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:45.787711 PROGRESS: Target precursors: 583 (97.17%)
2 days, 23:43:45.787800 PROGRESS: Decoy precursors: 17 (2.83%)
2 days, 23:43:45.787883 PROGRESS: 
2 days, 23:43:45.787963 PROGRESS: Precursor Summary:
2 days, 23:43:45.789715 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   557; 0.001 FDR:   467
2 days, 23:43:45.789841 PROGRESS: 
2 days, 23:43:45.789943 PROGRESS: Protein Summary:
2 days, 23:43:45.792043 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   409; 0.001 FDR:   341
2 days, 23:43:45.792161 PROGRESS: =========================================================================
2 days, 23:43:45.792352 INFO: Target number of precursors reached.
2 days, 23:43:45.798460 INFO: fragments_df: keeping 5000 of 21756 [sum(precursor_idx_mask)=12984 sum(mass_error_mask)=21756 stop_rank=5000
2 days, 23:43:45.802181 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:46.035590 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:46.225485 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:46.437633 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:47.308640 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:47.309127 INFO: Using score_cutoff 16.087249350357055 (fac=0.99, q=1)
2 days, 23:43:47.309508 INFO: Updating optimization_manager: fwhm_rt             : 2.481955051422119 -> 2.4826760292053223
2 days, 23:43:47.309615 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036012560594826937 -> 0.0036124472972005606
2 days, 23:43:47.309699 INFO: Updating optimization_manager: score_cutoff        : 15.357510955810548 -> 16.087249350357055
2 days, 23:43:47.309783 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:47.310944 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:47.312626 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:47.313734 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:47.316193 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:47.316341 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 23:43:47.319107 INFO: Updating optimization_manager: rt_error            : 14.707461535628736 -> 10.93670684362368
2 days, 23:43:47.319256 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 10.9367.
2 days, 23:43:47.319367 INFO: ==============================================
2 days, 23:43:47.319481 INFO: Starting optimization step 8.
2 days, 23:43:47.319579 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:47.319692 INFO: Using python extraction backend
2 days, 23:43:47.319843 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:47.319953 INFO: === Search parameters used ===
2 days, 23:43:47.320033 INFO: rt_error       : 10.93670684362368
2 days, 23:43:47.320112 INFO: mobility_error : 0.1
2 days, 23:43:47.320198 INFO: num_candidates : 3
2 days, 23:43:47.320282 INFO: ms1_error      : 15.0
2 days, 23:43:47.320364 INFO: ms2_error      : 15.0
2 days, 23:43:47.320448 INFO: fwhm_rt        : 2.4826760292053223
2 days, 23:43:47.320529 INFO: quant_window   : 3
2 days, 23:43:47.320612 INFO: ==============================================
2 days, 23:43:47.321854 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:47.321943 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:47.322009 INFO: FWHM in RT is 2.48 seconds, sigma is 0.41
2 days, 23:43:47.322054 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.96
2 days, 23:43:47.326661 INFO: Starting candidate selection
2 days, 23:43:47.915047 INFO: Starting candidate scoring
2 days, 23:43:48.040503 INFO: Finished candidate processing
2 days, 23:43:48.040618 INFO: Collecting candidate features
2 days, 23:43:48.053450 WARNING: intensity_correlation has 22 NaNs ( 0.69 % out of 3178)
2 days, 23:43:48.053705 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3178)
2 days, 23:43:48.058760 INFO: Collecting fragment features
2 days, 23:43:48.063520 INFO: Finished candidate scoring
2 days, 23:43:48.065706 INFO: performing precursor FDR with 47 features
2 days, 23:43:48.065763 INFO: Decoy channel: -1
2 days, 23:43:48.065794 INFO: competitive: True
2 days, 23:43:48.069637 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:48.071619 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:43:48.071684 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:43:48.071730 WARNING: FDR calculation for 1668 target and 1487 decoy PSMs
2 days, 23:43:48.071768 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:43:48.073016 INFO: Estimating optimal hyperparameters - samples: 2,524, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:48.073127 INFO: Using random state 908305 for train-test-split
2 days, 23:43:48.396448 INFO: Test AUC: 0.871
2 days, 23:43:48.396584 INFO: Train AUC: 0.875
2 days, 23:43:48.396626 INFO: AUC difference: 0.49%
2 days, 23:43:48.792773 INFO: Resetting torch num_threads to 80
2 days, 23:43:48.793716 PROGRESS: === Extracted 3178 precursors and 21684 fragments ===
2 days, 23:43:48.794355 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:48.795364 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:48.795547 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:48.795706 PROGRESS: Target precursors: 583 (97.17%)
2 days, 23:43:48.795862 PROGRESS: Decoy precursors: 17 (2.83%)
2 days, 23:43:48.796010 PROGRESS: 
2 days, 23:43:48.796155 PROGRESS: Precursor Summary:
2 days, 23:43:48.798138 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   570; 0.001 FDR:   473
2 days, 23:43:48.798330 PROGRESS: 
2 days, 23:43:48.798483 PROGRESS: Protein Summary:
2 days, 23:43:48.800847 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   417; 0.001 FDR:   346
2 days, 23:43:48.801033 PROGRESS: =========================================================================
2 days, 23:43:48.801324 INFO: Target number of precursors reached.
2 days, 23:43:48.810601 INFO: fragments_df: keeping 5000 of 21684 [sum(precursor_idx_mask)=13292 sum(mass_error_mask)=21684 stop_rank=5000
2 days, 23:43:48.815768 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:49.086241 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:49.286382 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:49.459741 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:50.237216 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:50.237697 INFO: Using score_cutoff 15.525092363262177 (fac=0.99, q=1)
2 days, 23:43:50.238098 INFO: Updating optimization_manager: fwhm_rt             : 2.4826760292053223 -> 2.4821925163269043
2 days, 23:43:50.238196 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036124472972005606 -> 0.003599300514906645
2 days, 23:43:50.238268 INFO: Updating optimization_manager: score_cutoff        : 16.087249350357055 -> 15.525092363262177
2 days, 23:43:50.238337 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:50.239494 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:50.240931 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:50.241781 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:50.243832 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:50.243944 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2 days, 23:43:50.245990 INFO: Updating optimization_manager: rt_error            : 10.93670684362368 -> 10.506297570338125
2 days, 23:43:50.246106 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 10.5063.
2 days, 23:43:50.246185 INFO: ==============================================
2 days, 23:43:50.246269 INFO: Starting optimization step 9.
2 days, 23:43:50.246343 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:50.246413 INFO: Using python extraction backend
2 days, 23:43:50.246525 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:50.246603 INFO: === Search parameters used ===
2 days, 23:43:50.246665 INFO: rt_error       : 10.506297570338125
2 days, 23:43:50.246721 INFO: mobility_error : 0.1
2 days, 23:43:50.246776 INFO: num_candidates : 3
2 days, 23:43:50.246830 INFO: ms1_error      : 15.0
2 days, 23:43:50.246884 INFO: ms2_error      : 15.0
2 days, 23:43:50.246937 INFO: fwhm_rt        : 2.4821925163269043
2 days, 23:43:50.246991 INFO: quant_window   : 3
2 days, 23:43:50.247044 INFO: ==============================================
2 days, 23:43:50.248163 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:50.248215 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:50.248257 INFO: FWHM in RT is 2.48 seconds, sigma is 0.41
2 days, 23:43:50.248291 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.95
2 days, 23:43:50.255730 INFO: Starting candidate selection
2 days, 23:43:50.794095 INFO: Starting candidate scoring
2 days, 23:43:50.907520 INFO: Finished candidate processing
2 days, 23:43:50.907651 INFO: Collecting candidate features
2 days, 23:43:50.924099 WARNING: intensity_correlation has 20 NaNs ( 0.63 % out of 3171)
2 days, 23:43:50.924466 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3171)
2 days, 23:43:50.934045 INFO: Collecting fragment features
2 days, 23:43:50.939932 INFO: Finished candidate scoring
2 days, 23:43:50.942931 INFO: performing precursor FDR with 47 features
2 days, 23:43:50.943021 INFO: Decoy channel: -1
2 days, 23:43:50.943060 INFO: competitive: True
2 days, 23:43:50.947672 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:50.949301 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:43:50.949360 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:43:50.949425 WARNING: FDR calculation for 1665 target and 1485 decoy PSMs
2 days, 23:43:50.949457 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:43:50.950545 INFO: Estimating optimal hyperparameters - samples: 2,520, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:50.950641 INFO: Using random state 908305 for train-test-split
2 days, 23:43:51.283309 INFO: Test AUC: 0.894
2 days, 23:43:51.283430 INFO: Train AUC: 0.871
2 days, 23:43:51.283474 INFO: AUC difference: 2.69%
2 days, 23:43:51.616926 INFO: Resetting torch num_threads to 80
2 days, 23:43:51.617593 PROGRESS: === Extracted 3171 precursors and 21626 fragments ===
2 days, 23:43:51.618081 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:43:51.618726 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:51.618831 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:51.618920 PROGRESS: Target precursors: 582 (97.00%)
2 days, 23:43:51.618997 PROGRESS: Decoy precursors: 18 (3.00%)
2 days, 23:43:51.619070 PROGRESS: 
2 days, 23:43:51.619139 PROGRESS: Precursor Summary:
2 days, 23:43:51.620307 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   571; 0.001 FDR:   464
2 days, 23:43:51.620413 PROGRESS: 
2 days, 23:43:51.620491 PROGRESS: Protein Summary:
2 days, 23:43:51.621919 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   418; 0.001 FDR:   339
2 days, 23:43:51.622037 PROGRESS: =========================================================================
2 days, 23:43:51.622246 INFO: Target number of precursors reached.
2 days, 23:43:51.628325 INFO: fragments_df: keeping 5000 of 21626 [sum(precursor_idx_mask)=13270 sum(mass_error_mask)=21626 stop_rank=5000
2 days, 23:43:51.632237 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:51.868486 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:52.153150 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:52.465690 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:53.400203 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:53.400798 INFO: Using score_cutoff 14.741674658775331 (fac=0.99, q=1)
2 days, 23:43:53.401220 INFO: Updating optimization_manager: fwhm_rt             : 2.4821925163269043 -> 2.4761223793029785
2 days, 23:43:53.401316 INFO: Updating optimization_manager: fwhm_mobility       : 0.003599300514906645 -> 0.003572432091459632
2 days, 23:43:53.401373 INFO: Updating optimization_manager: score_cutoff        : 15.525092363262177 -> 14.741674658775331
2 days, 23:43:53.401439 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:53.402827 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:53.404521 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:53.405548 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:53.407749 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:53.407898 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
2 days, 23:43:53.409093 INFO: Updating optimization_manager: rt_error            : 10.506297570338125 -> 10.506297570338125
2 days, 23:43:53.409269 INFO: Updating optimization_manager: classifier_version  : 3 -> 13
2 days, 23:43:53.409446 INFO: Updating optimization_manager: score_cutoff        : 14.741674658775331 -> 14.741674658775331
2 days, 23:43:53.409565 INFO: Updating optimization_manager: fwhm_rt             : 2.4761223793029785 -> 2.4761223793029785
2 days, 23:43:53.409661 INFO: Updating optimization_manager: fwhm_mobility       : 0.003572432091459632 -> 0.003572432091459632
2 days, 23:43:53.409762 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 10.5063 found after 10 searches.
2 days, 23:43:53.409827 INFO: ==============================================
2 days, 23:43:53.409924 PROGRESS: Optimization finished for rt_error.
2 days, 23:43:53.413812 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:53.414874 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:53.416411 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:53.417308 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:53.419556 INFO: Starting optimization step 0.
2 days, 23:43:53.419689 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:53.419799 INFO: Using python extraction backend
2 days, 23:43:53.419917 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:53.419989 INFO: === Search parameters used ===
2 days, 23:43:53.420042 INFO: rt_error       : 10.506297570338125
2 days, 23:43:53.420089 INFO: mobility_error : 0.1
2 days, 23:43:53.420135 INFO: num_candidates : 3
2 days, 23:43:53.420182 INFO: ms1_error      : 15.0
2 days, 23:43:53.420226 INFO: ms2_error      : 15.0
2 days, 23:43:53.420268 INFO: fwhm_rt        : 2.4761223793029785
2 days, 23:43:53.420311 INFO: quant_window   : 3
2 days, 23:43:53.420352 INFO: ==============================================
2 days, 23:43:53.421263 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:53.421313 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:53.421360 INFO: FWHM in RT is 2.48 seconds, sigma is 0.41
2 days, 23:43:53.421390 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.94
2 days, 23:43:53.434048 INFO: Starting candidate selection
2 days, 23:43:53.977338 INFO: Starting candidate scoring
2 days, 23:43:54.087485 INFO: Finished candidate processing
2 days, 23:43:54.087651 INFO: Collecting candidate features
2 days, 23:43:54.102376 WARNING: intensity_correlation has 20 NaNs ( 0.63 % out of 3168)
2 days, 23:43:54.102664 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3168)
2 days, 23:43:54.107711 INFO: Collecting fragment features
2 days, 23:43:54.112283 INFO: Finished candidate scoring
2 days, 23:43:54.114575 INFO: performing precursor FDR with 47 features
2 days, 23:43:54.114641 INFO: Decoy channel: -1
2 days, 23:43:54.114671 INFO: competitive: True
2 days, 23:43:54.118523 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:54.120395 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:43:54.120450 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:43:54.120496 WARNING: FDR calculation for 1667 target and 1480 decoy PSMs
2 days, 23:43:54.120525 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:43:54.121727 INFO: Estimating optimal hyperparameters - samples: 2,517, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:54.121818 INFO: Using random state 424419 for train-test-split
2 days, 23:43:54.426741 INFO: Test AUC: 0.880
2 days, 23:43:54.426878 INFO: Train AUC: 0.883
2 days, 23:43:54.426934 INFO: AUC difference: 0.29%
2 days, 23:43:54.746054 INFO: Resetting torch num_threads to 80
2 days, 23:43:54.746829 PROGRESS: === Extracted 3168 precursors and 21596 fragments ===
2 days, 23:43:54.747420 INFO: === FDR correction performed with classifier version 13 ===
2 days, 23:43:54.748371 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:54.748496 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:54.748596 PROGRESS: Target precursors: 586 (97.67%)
2 days, 23:43:54.748690 PROGRESS: Decoy precursors: 14 (2.33%)
2 days, 23:43:54.748777 PROGRESS: 
2 days, 23:43:54.748857 PROGRESS: Precursor Summary:
2 days, 23:43:54.750797 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   573; 0.001 FDR:   487
2 days, 23:43:54.750938 PROGRESS: 
2 days, 23:43:54.751029 PROGRESS: Protein Summary:
2 days, 23:43:54.753318 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   419; 0.001 FDR:   356
2 days, 23:43:54.753446 PROGRESS: =========================================================================
2 days, 23:43:54.753664 INFO: Target number of precursors reached.
2 days, 23:43:54.762907 INFO: fragments_df: keeping 5000 of 21596 [sum(precursor_idx_mask)=13307 sum(mass_error_mask)=21596 stop_rank=5000
2 days, 23:43:54.767664 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:54.973829 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:55.163394 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:55.342469 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:56.088360 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:56.088828 INFO: Using score_cutoff 14.750017379379273 (fac=0.99, q=1)
2 days, 23:43:56.089189 INFO: Updating optimization_manager: fwhm_rt             : 2.4761223793029785 -> 2.480337142944336
2 days, 23:43:56.089286 INFO: Updating optimization_manager: fwhm_mobility       : 0.003572432091459632 -> 0.003568139625713229
2 days, 23:43:56.089355 INFO: Updating optimization_manager: score_cutoff        : 14.741674658775331 -> 14.750017379379273
2 days, 23:43:56.089423 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:56.090576 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:56.091978 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:56.092795 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:56.095030 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:56.095185 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:43:56.097227 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06333720874122505
2 days, 23:43:56.097360 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0633.
2 days, 23:43:56.097459 INFO: ==============================================
2 days, 23:43:56.097567 INFO: Starting optimization step 1.
2 days, 23:43:56.097663 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:56.097759 INFO: Using python extraction backend
2 days, 23:43:56.097927 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:56.098047 INFO: === Search parameters used ===
2 days, 23:43:56.098138 INFO: rt_error       : 10.506297570338125
2 days, 23:43:56.098225 INFO: mobility_error : 0.06333720874122505
2 days, 23:43:56.098310 INFO: num_candidates : 3
2 days, 23:43:56.098399 INFO: ms1_error      : 15.0
2 days, 23:43:56.098480 INFO: ms2_error      : 15.0
2 days, 23:43:56.098559 INFO: fwhm_rt        : 2.480337142944336
2 days, 23:43:56.098637 INFO: quant_window   : 3
2 days, 23:43:56.098716 INFO: ==============================================
2 days, 23:43:56.099970 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:56.100038 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:56.100092 INFO: FWHM in RT is 2.48 seconds, sigma is 0.41
2 days, 23:43:56.100129 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.93
2 days, 23:43:56.114654 INFO: Starting candidate selection
2 days, 23:43:56.693765 INFO: Starting candidate scoring
2 days, 23:43:56.794332 INFO: Finished candidate processing
2 days, 23:43:56.794472 INFO: Collecting candidate features
2 days, 23:43:56.810843 WARNING: intensity_correlation has 21 NaNs ( 0.67 % out of 3150)
2 days, 23:43:56.811188 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3150)
2 days, 23:43:56.817911 INFO: Collecting fragment features
2 days, 23:43:56.822745 INFO: Finished candidate scoring
2 days, 23:43:56.825775 INFO: performing precursor FDR with 47 features
2 days, 23:43:56.825852 INFO: Decoy channel: -1
2 days, 23:43:56.825906 INFO: competitive: True
2 days, 23:43:56.830729 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:56.833133 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:43:56.833208 WARNING: dropped 16 decoy PSMs due to missing features
2 days, 23:43:56.833290 WARNING: FDR calculation for 1665 target and 1463 decoy PSMs
2 days, 23:43:56.833329 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:43:56.834829 INFO: Estimating optimal hyperparameters - samples: 2,502, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:56.834969 INFO: Using random state 424419 for train-test-split
2 days, 23:43:57.191014 INFO: Test AUC: 0.873
2 days, 23:43:57.191132 INFO: Train AUC: 0.889
2 days, 23:43:57.191178 INFO: AUC difference: 1.69%
2 days, 23:43:57.522852 INFO: Resetting torch num_threads to 80
2 days, 23:43:57.523626 PROGRESS: === Extracted 3150 precursors and 21384 fragments ===
2 days, 23:43:57.524197 INFO: === FDR correction performed with classifier version 13 ===
2 days, 23:43:57.525106 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:43:57.525229 PROGRESS: Total precursors accumulated: 600
2 days, 23:43:57.525331 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:43:57.525420 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:43:57.525499 PROGRESS: 
2 days, 23:43:57.525573 PROGRESS: Precursor Summary:
2 days, 23:43:57.527596 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   578; 0.001 FDR:   534
2 days, 23:43:57.527731 PROGRESS: 
2 days, 23:43:57.527829 PROGRESS: Protein Summary:
2 days, 23:43:57.530169 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   423; 0.001 FDR:   393
2 days, 23:43:57.530288 PROGRESS: =========================================================================
2 days, 23:43:57.530473 INFO: Target number of precursors reached.
2 days, 23:43:57.539607 INFO: fragments_df: keeping 5000 of 21384 [sum(precursor_idx_mask)=13323 sum(mass_error_mask)=21384 stop_rank=5000
2 days, 23:43:57.544623 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:57.765803 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:57.985830 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:58.244610 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:59.057145 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:43:59.057812 INFO: Using score_cutoff 14.189002128410339 (fac=0.99, q=1)
2 days, 23:43:59.058270 INFO: Updating optimization_manager: fwhm_rt             : 2.480337142944336 -> 2.470670700073242
2 days, 23:43:59.058384 INFO: Updating optimization_manager: fwhm_mobility       : 0.003568139625713229 -> 0.003517079632729292
2 days, 23:43:59.058469 INFO: Updating optimization_manager: score_cutoff        : 14.750017379379273 -> 14.189002128410339
2 days, 23:43:59.058556 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:43:59.059916 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:43:59.061321 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:43:59.062172 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:43:59.064141 INFO: === checking if optimization conditions were reached ===
2 days, 23:43:59.064266 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:43:59.066028 INFO: Updating optimization_manager: mobility_error      : 0.06333720874122505 -> 0.05487390286899641
2 days, 23:43:59.066162 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0549.
2 days, 23:43:59.066260 INFO: ==============================================
2 days, 23:43:59.066370 INFO: Starting optimization step 2.
2 days, 23:43:59.066466 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:43:59.066565 INFO: Using python extraction backend
2 days, 23:43:59.066707 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:43:59.066805 INFO: === Search parameters used ===
2 days, 23:43:59.066886 INFO: rt_error       : 10.506297570338125
2 days, 23:43:59.066960 INFO: mobility_error : 0.05487390286899641
2 days, 23:43:59.067043 INFO: num_candidates : 3
2 days, 23:43:59.067118 INFO: ms1_error      : 15.0
2 days, 23:43:59.067196 INFO: ms2_error      : 15.0
2 days, 23:43:59.067271 INFO: fwhm_rt        : 2.470670700073242
2 days, 23:43:59.067344 INFO: quant_window   : 3
2 days, 23:43:59.067414 INFO: ==============================================
2 days, 23:43:59.068375 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:43:59.068433 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:43:59.068488 INFO: FWHM in RT is 2.47 seconds, sigma is 0.41
2 days, 23:43:59.068530 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.91
2 days, 23:43:59.075191 INFO: Starting candidate selection
2 days, 23:43:59.675349 INFO: Starting candidate scoring
2 days, 23:43:59.774935 INFO: Finished candidate processing
2 days, 23:43:59.775085 INFO: Collecting candidate features
2 days, 23:43:59.792935 WARNING: intensity_correlation has 22 NaNs ( 0.70 % out of 3141)
2 days, 23:43:59.793295 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3141)
2 days, 23:43:59.801204 INFO: Collecting fragment features
2 days, 23:43:59.807156 INFO: Finished candidate scoring
2 days, 23:43:59.810982 INFO: performing precursor FDR with 47 features
2 days, 23:43:59.811071 INFO: Decoy channel: -1
2 days, 23:43:59.811121 INFO: competitive: True
2 days, 23:43:59.816132 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:43:59.818514 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:43:59.818596 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:43:59.818676 WARNING: FDR calculation for 1665 target and 1453 decoy PSMs
2 days, 23:43:59.818714 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:43:59.820212 INFO: Estimating optimal hyperparameters - samples: 2,494, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:43:59.820324 INFO: Using random state 424419 for train-test-split
2 days, 23:44:00.171580 INFO: Test AUC: 0.870
2 days, 23:44:00.171705 INFO: Train AUC: 0.891
2 days, 23:44:00.171751 INFO: AUC difference: 2.37%
2 days, 23:44:00.505899 INFO: Resetting torch num_threads to 80
2 days, 23:44:00.506560 PROGRESS: === Extracted 3141 precursors and 21279 fragments ===
2 days, 23:44:00.507015 INFO: === FDR correction performed with classifier version 13 ===
2 days, 23:44:00.507635 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:44:00.507743 PROGRESS: Total precursors accumulated: 600
2 days, 23:44:00.507825 PROGRESS: Target precursors: 586 (97.67%)
2 days, 23:44:00.507901 PROGRESS: Decoy precursors: 14 (2.33%)
2 days, 23:44:00.507982 PROGRESS: 
2 days, 23:44:00.508050 PROGRESS: Precursor Summary:
2 days, 23:44:00.509199 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   575; 0.001 FDR:   520
2 days, 23:44:00.509307 PROGRESS: 
2 days, 23:44:00.509384 PROGRESS: Protein Summary:
2 days, 23:44:00.510790 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   422; 0.001 FDR:   384
2 days, 23:44:00.510901 PROGRESS: =========================================================================
2 days, 23:44:00.511077 INFO: Target number of precursors reached.
2 days, 23:44:00.516889 INFO: fragments_df: keeping 5000 of 21279 [sum(precursor_idx_mask)=13241 sum(mass_error_mask)=21279 stop_rank=5000
2 days, 23:44:00.520404 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:00.734419 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:00.992412 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:01.239848 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:02.086226 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:44:02.086831 INFO: Using score_cutoff 14.08847781829834 (fac=0.99, q=1)
2 days, 23:44:02.087289 INFO: Updating optimization_manager: fwhm_rt             : 2.470670700073242 -> 2.466259717941284
2 days, 23:44:02.087411 INFO: Updating optimization_manager: fwhm_mobility       : 0.003517079632729292 -> 0.0035172889474779367
2 days, 23:44:02.087497 INFO: Updating optimization_manager: score_cutoff        : 14.189002128410339 -> 14.08847781829834
2 days, 23:44:02.087581 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:02.089111 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:02.090837 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:02.091931 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:02.094353 INFO: === checking if optimization conditions were reached ===
2 days, 23:44:02.094492 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:44:02.095502 INFO: Updating optimization_manager: mobility_error      : 0.05487390286899641 -> 0.06333720874122505
2 days, 23:44:02.095652 INFO: Updating optimization_manager: classifier_version  : 13 -> 15
2 days, 23:44:02.095773 INFO: Updating optimization_manager: score_cutoff        : 14.08847781829834 -> 14.189002128410339
2 days, 23:44:02.095886 INFO: Updating optimization_manager: fwhm_rt             : 2.466259717941284 -> 2.470670700073242
2 days, 23:44:02.096012 INFO: Updating optimization_manager: fwhm_mobility       : 0.0035172889474779367 -> 0.003517079632729292
2 days, 23:44:02.096126 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0633 found after 3 searches.
2 days, 23:44:02.096203 INFO: ==============================================
2 days, 23:44:02.096287 PROGRESS: Optimization finished for mobility_error.
2 days, 23:44:02.099425 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:02.100346 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:02.101700 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:02.102525 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:02.104410 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:44:02.104514 PROGRESS: ==============================================
2 days, 23:44:02.104596 PROGRESS: ms2_error      : 15.0000
2 days, 23:44:02.104670 PROGRESS: ms1_error      : 15.0000
2 days, 23:44:02.104744 PROGRESS: rt_error       : 10.5063
2 days, 23:44:02.104817 PROGRESS: mobility_error : 0.0633
2 days, 23:44:02.104881 PROGRESS: ==============================================
2 days, 23:44:02.105491 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:02.109159 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:02.125185 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:02.128920 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:02.163937 INFO: Using python extraction backend
2 days, 23:44:02.170728 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:44:02.171271 INFO: === Search parameters used ===
2 days, 23:44:02.171540 INFO: rt_error       : 10.506297570338125
2 days, 23:44:02.171762 INFO: mobility_error : 0.06333720874122505
2 days, 23:44:02.171965 INFO: num_candidates : 3
2 days, 23:44:02.172168 INFO: ms1_error      : 15.0
2 days, 23:44:02.172372 INFO: ms2_error      : 15.0
2 days, 23:44:02.172565 INFO: fwhm_rt        : 2.470670700073242
2 days, 23:44:02.172751 INFO: quant_window   : 3
2 days, 23:44:02.172935 INFO: ==============================================
2 days, 23:44:02.180714 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:44:02.180910 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:44:02.181011 INFO: FWHM in RT is 2.47 seconds, sigma is 0.41
2 days, 23:44:02.181089 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.91
2 days, 23:44:02.194010 INFO: Starting candidate selection
2 days, 23:44:04.091557 INFO: Removed 19592 precursors with score below cutoff 14.189002128410339
2 days, 23:44:04.422580 INFO: Starting candidate scoring
2 days, 23:44:05.322895 INFO: Finished candidate processing
2 days, 23:44:05.323163 INFO: Collecting candidate features
2 days, 23:44:05.449387 WARNING: intensity_correlation has 196 NaNs ( 0.34 % out of 57051)
2 days, 23:44:05.449847 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 57051)
2 days, 23:44:05.457976 INFO: Collecting fragment features
2 days, 23:44:05.497661 INFO: Finished candidate scoring
2 days, 23:44:05.530146 INFO: === Performing FDR correction with classifier version 15 ===
2 days, 23:44:05.530601 INFO: performing precursor FDR with 47 features
2 days, 23:44:05.530639 INFO: Decoy channel: -1
2 days, 23:44:05.530668 INFO: competitive: True
2 days, 23:44:05.549135 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:44:05.560029 WARNING: dropped 49 target PSMs due to missing features
2 days, 23:44:05.560168 WARNING: dropped 152 decoy PSMs due to missing features
2 days, 23:44:05.560226 WARNING: FDR calculation for 34806 target and 22044 decoy PSMs
2 days, 23:44:05.560256 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:44:05.575485 INFO: Estimating optimal hyperparameters - samples: 45,480, batch_size: 186, learning_rate: 2.13e-04
2 days, 23:44:05.575765 INFO: Using random state 547377 for train-test-split
2 days, 23:44:10.271660 INFO: Test AUC: 0.896
2 days, 23:44:10.271785 INFO: Train AUC: 0.900
2 days, 23:44:10.271829 INFO: AUC difference: 0.44%
2 days, 23:44:10.593913 INFO: Resetting torch num_threads to 80
2 days, 23:44:10.596876 INFO: Removing fragments below FDR threshold
2 days, 23:44:10.606195 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:44:10.606412 PROGRESS: Total precursors accumulated: 13,068
2 days, 23:44:10.606502 PROGRESS: Target precursors: 12,939 (99.01%)
2 days, 23:44:10.606582 PROGRESS: Decoy precursors: 129 (0.99%)
2 days, 23:44:10.606657 PROGRESS: 
2 days, 23:44:10.606730 PROGRESS: Precursor Summary:
2 days, 23:44:10.612248 PROGRESS: Channel   0:	 0.050 FDR: 12,939; 0.010 FDR: 12,939; 0.001 FDR: 11,481
2 days, 23:44:10.612426 PROGRESS: 
2 days, 23:44:10.612528 PROGRESS: Protein Summary:
2 days, 23:44:10.618508 PROGRESS: Channel   0:	 0.050 FDR: 1,681; 0.010 FDR: 1,681; 0.001 FDR: 1,631
2 days, 23:44:10.618675 PROGRESS: =========================================================================
2 days, 23:44:10.619768 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R1/psm.parquet
2 days, 23:44:10.693364 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R1/frag.parquet
2 days, 23:44:10.746344 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R1
2 days, 23:44:10.751401 PROGRESS: Loading raw file 2/12: A9_G_DIA_nLC_tTOF_R2 
2 days, 23:44:10.751531 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:44:10.751613 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R2/figures
2 days, 23:44:10.751819 INFO: Initializing TimingManager
2 days, 23:44:10.752361 INFO: Initializing RawFileManager
2 days, 23:44:10.752523 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:10.752594 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:10.752634 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:10.913116 INFO: Reading 22,623 frames with 354,406,482 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:14.638633 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d...
2 days, 23:44:14.639640 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:14.647067 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:14.647383 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:14.647885 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:14.649558 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:14.682273 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:14.682648 INFO: Indexing quadrupole dimension
2 days, 23:44:14.855433 INFO: Transposing detector events
2 days, 23:44:16.636178 INFO: Finished transposing data
2 days, 23:44:16.636361 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
2 days, 23:44:16.636720 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:44:16.636781 INFO: RT duration (sec)   : 2399.9
2 days, 23:44:16.636819 INFO: RT duration (min)   : 40.0
2 days, 23:44:16.636849 INFO: Cycle len (scans)   : 12
2 days, 23:44:16.636880 INFO: Cycle len (sec)     : 1.27
2 days, 23:44:16.636909 INFO: Number of cycles    : 1885
2 days, 23:44:16.636937 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:44:16.636974 INFO: Creating DIA data object took: 5.8844544887542725
2 days, 23:44:16.642427 INFO: Initializing CalibrationManager
2 days, 23:44:16.642615 INFO: Setting up calibration estimators ..
2 days, 23:44:16.642694 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:44:16.642768 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:44:16.642844 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:44:16.642910 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:44:16.642978 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:44:16.643046 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:44:16.643108 INFO: Done setting up calibration estimators.
2 days, 23:44:16.643212 INFO: Initializing OptimizationManager
2 days, 23:44:16.643314 INFO: initial parameter: ms1_error = 30
2 days, 23:44:16.643373 INFO: initial parameter: ms2_error = 30
2 days, 23:44:16.643429 INFO: initial parameter: rt_error = 1199.9447605
2 days, 23:44:16.643482 INFO: initial parameter: mobility_error = 0.1
2 days, 23:44:16.643534 INFO: initial parameter: num_candidates = 1
2 days, 23:44:16.643585 INFO: initial parameter: fwhm_rt = 5
2 days, 23:44:16.643638 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:44:16.643688 INFO: initial parameter: score_cutoff = 0
2 days, 23:44:16.643738 INFO: initial parameter: classifier_version = -1
2 days, 23:44:16.643814 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R2
2 days, 23:44:16.643978 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:44:16.644016 INFO: Initializing FDRManager
2 days, 23:44:16.644054 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:44:16.651019 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:44:16.655558 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:44:16.655841 INFO: Updating optimization_manager: rt_error            : 1199.9447605 -> 1199.9447605
2 days, 23:44:16.655952 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:44:16.656165 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:44:16.656260 PROGRESS: Starting initial search for precursors.
2 days, 23:44:16.656349 INFO: Starting optimization step 0.
2 days, 23:44:16.656422 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:44:16.656497 INFO: Using python extraction backend
2 days, 23:44:16.656611 PROGRESS: Extracting batch of 399 precursors
2 days, 23:44:16.656686 INFO: === Search parameters used ===
2 days, 23:44:16.656750 INFO: rt_error       : 1199.9447605
2 days, 23:44:16.656807 INFO: mobility_error : 0.1
2 days, 23:44:16.656860 INFO: num_candidates : 1
2 days, 23:44:16.656913 INFO: ms1_error      : 30
2 days, 23:44:16.656963 INFO: ms2_error      : 30
2 days, 23:44:16.657013 INFO: fwhm_rt        : 5
2 days, 23:44:16.657063 INFO: quant_window   : 3
2 days, 23:44:16.657111 INFO: ==============================================
2 days, 23:44:16.657775 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:44:16.657826 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:44:16.657858 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:44:16.657903 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:44:16.662950 INFO: Starting candidate selection
2 days, 23:44:20.435066 INFO: Starting candidate scoring
2 days, 23:44:20.485206 INFO: Finished candidate processing
2 days, 23:44:20.485325 INFO: Collecting candidate features
2 days, 23:44:20.503828 INFO: Collecting fragment features
2 days, 23:44:20.507698 INFO: Finished candidate scoring
2 days, 23:44:20.508924 INFO: performing precursor FDR with 47 features
2 days, 23:44:20.508991 INFO: Decoy channel: -1
2 days, 23:44:20.509036 INFO: competitive: True
2 days, 23:44:20.511058 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:44:20.513648 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:44:20.514838 INFO: Using random state 613602 for train-test-split
2 days, 23:44:20.544137 INFO: Test AUC: 0.705
2 days, 23:44:20.544290 INFO: Train AUC: 0.649
2 days, 23:44:20.544490 INFO: AUC difference: 8.53%
2 days, 23:44:20.544652 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:44:20.928415 INFO: Resetting torch num_threads to 80
2 days, 23:44:20.929193 PROGRESS: === Extracted 399 precursors and 3678 fragments ===
2 days, 23:44:20.930238 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:44:20.932859 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:44:20.933115 PROGRESS: Total precursors accumulated: 200
2 days, 23:44:20.933323 PROGRESS: Target precursors: 132 (66.00%)
2 days, 23:44:20.933531 PROGRESS: Decoy precursors: 68 (34.00%)
2 days, 23:44:20.933724 PROGRESS: 
2 days, 23:44:20.933956 PROGRESS: Precursor Summary:
2 days, 23:44:20.935759 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 23:44:20.935996 PROGRESS: 
2 days, 23:44:20.936214 PROGRESS: Protein Summary:
2 days, 23:44:20.938093 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 23:44:20.938232 PROGRESS: =========================================================================
2 days, 23:44:20.938422 INFO: Target number of precursors not reached yet.
2 days, 23:44:20.943761 INFO: Starting optimization step 1.
2 days, 23:44:20.943900 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:44:20.944009 INFO: Using python extraction backend
2 days, 23:44:20.944156 PROGRESS: Extracting batch of 798 precursors
2 days, 23:44:20.944263 INFO: === Search parameters used ===
2 days, 23:44:20.944345 INFO: rt_error       : 1199.9447605
2 days, 23:44:20.944420 INFO: mobility_error : 0.1
2 days, 23:44:20.944490 INFO: num_candidates : 1
2 days, 23:44:20.944559 INFO: ms1_error      : 30
2 days, 23:44:20.944629 INFO: ms2_error      : 30
2 days, 23:44:20.944697 INFO: fwhm_rt        : 5
2 days, 23:44:20.944777 INFO: quant_window   : 3
2 days, 23:44:20.944845 INFO: ==============================================
2 days, 23:44:20.945788 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:44:20.945854 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:44:20.945931 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:44:20.945982 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:44:20.963129 INFO: Starting candidate selection
2 days, 23:44:26.770402 INFO: Starting candidate scoring
2 days, 23:44:26.836404 INFO: Finished candidate processing
2 days, 23:44:26.836517 INFO: Collecting candidate features
2 days, 23:44:26.849780 INFO: Collecting fragment features
2 days, 23:44:26.852910 INFO: Finished candidate scoring
2 days, 23:44:26.855614 INFO: performing precursor FDR with 47 features
2 days, 23:44:26.855679 INFO: Decoy channel: -1
2 days, 23:44:26.855711 INFO: competitive: True
2 days, 23:44:26.859436 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:44:26.861598 INFO: Estimating optimal hyperparameters - samples: 957, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:44:26.861693 INFO: Using random state 78955 for train-test-split
2 days, 23:44:26.947259 INFO: Test AUC: 0.764
2 days, 23:44:26.947384 INFO: Train AUC: 0.772
2 days, 23:44:26.947424 INFO: AUC difference: 1.12%
2 days, 23:44:27.248243 INFO: Resetting torch num_threads to 80
2 days, 23:44:27.250160 PROGRESS: === Extracted 1197 precursors and 11339 fragments ===
2 days, 23:44:27.250760 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:44:27.251620 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:44:27.251757 PROGRESS: Total precursors accumulated: 600
2 days, 23:44:27.251869 PROGRESS: Target precursors: 454 (75.67%)
2 days, 23:44:27.251972 PROGRESS: Decoy precursors: 146 (24.33%)
2 days, 23:44:27.252051 PROGRESS: 
2 days, 23:44:27.252126 PROGRESS: Precursor Summary:
2 days, 23:44:27.253959 PROGRESS: Channel   0:	 0.050 FDR:   291; 0.010 FDR:   233; 0.001 FDR:   218
2 days, 23:44:27.254081 PROGRESS: 
2 days, 23:44:27.254161 PROGRESS: Protein Summary:
2 days, 23:44:27.256033 PROGRESS: Channel   0:	 0.050 FDR:   213; 0.010 FDR:   169; 0.001 FDR:   158
2 days, 23:44:27.256154 PROGRESS: =========================================================================
2 days, 23:44:27.256381 INFO: Target number of precursors reached.
2 days, 23:44:27.261048 INFO: fragments_df: keeping 1981 of 11339 [sum(precursor_idx_mask)=2414 sum(mass_error_mask)=11339 stop_rank=1981
2 days, 23:44:27.264873 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:27.419150 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:27.563432 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:27.721374 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:28.049650 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:44:28.050140 INFO: Using score_cutoff 32.69186139221192 (fac=0.99, q=1)
2 days, 23:44:28.050504 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.792027473449707
2 days, 23:44:28.050605 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007355421781539917
2 days, 23:44:28.050686 INFO: Updating optimization_manager: score_cutoff        : 0 -> 32.69186139221192
2 days, 23:44:28.050771 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:28.051913 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:28.053301 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:28.054151 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:28.056240 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2 days, 23:44:28.056361 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:44:28.056478 INFO: Starting optimization step 2.
2 days, 23:44:28.056564 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:44:28.056648 INFO: Using python extraction backend
2 days, 23:44:28.056771 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:44:28.056860 INFO: === Search parameters used ===
2 days, 23:44:28.056934 INFO: rt_error       : 1199.9447605
2 days, 23:44:28.057002 INFO: mobility_error : 0.1
2 days, 23:44:28.057072 INFO: num_candidates : 3
2 days, 23:44:28.057139 INFO: ms1_error      : 30
2 days, 23:44:28.057205 INFO: ms2_error      : 30
2 days, 23:44:28.057269 INFO: fwhm_rt        : 2.792027473449707
2 days, 23:44:28.057333 INFO: quant_window   : 3
2 days, 23:44:28.057396 INFO: ==============================================
2 days, 23:44:28.058318 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:44:28.058376 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:44:28.058432 INFO: FWHM in RT is 2.79 seconds, sigma is 0.47
2 days, 23:44:28.058466 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.99
2 days, 23:44:28.069998 INFO: Starting candidate selection
2 days, 23:44:36.980444 INFO: Starting candidate scoring
2 days, 23:44:37.115943 INFO: Finished candidate processing
2 days, 23:44:37.116083 INFO: Collecting candidate features
2 days, 23:44:37.140841 INFO: Collecting fragment features
2 days, 23:44:37.146950 INFO: Finished candidate scoring
2 days, 23:44:37.150595 INFO: performing precursor FDR with 47 features
2 days, 23:44:37.150762 INFO: Decoy channel: -1
2 days, 23:44:37.150850 INFO: competitive: True
2 days, 23:44:37.154797 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:44:37.157294 INFO: Estimating optimal hyperparameters - samples: 2,732, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:44:37.157416 INFO: Using random state 701735 for train-test-split
2 days, 23:44:37.410852 INFO: Test AUC: 0.676
2 days, 23:44:37.410963 INFO: Train AUC: 0.712
2 days, 23:44:37.411003 INFO: AUC difference: 4.96%
2 days, 23:44:37.751266 INFO: Resetting torch num_threads to 80
2 days, 23:44:37.751947 PROGRESS: === Extracted 3415 precursors and 31259 fragments ===
2 days, 23:44:37.752439 INFO: === FDR correction performed with classifier version 1 ===
2 days, 23:44:37.753170 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:44:37.753297 PROGRESS: Total precursors accumulated: 600
2 days, 23:44:37.753397 PROGRESS: Target precursors: 493 (82.17%)
2 days, 23:44:37.753487 PROGRESS: Decoy precursors: 107 (17.83%)
2 days, 23:44:37.753570 PROGRESS: 
2 days, 23:44:37.753650 PROGRESS: Precursor Summary:
2 days, 23:44:37.754857 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   301; 0.001 FDR:   264
2 days, 23:44:37.754980 PROGRESS: 
2 days, 23:44:37.755072 PROGRESS: Protein Summary:
2 days, 23:44:37.756485 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   218; 0.001 FDR:   190
2 days, 23:44:37.756611 PROGRESS: =========================================================================
2 days, 23:44:37.756831 INFO: Target number of precursors reached.
2 days, 23:44:37.763719 INFO: fragments_df: keeping 5000 of 31259 [sum(precursor_idx_mask)=8397 sum(mass_error_mask)=31259 stop_rank=5000
2 days, 23:44:37.767308 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:37.943351 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:38.102356 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:38.267863 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:39.095212 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:44:39.095762 INFO: Using score_cutoff 33.03245441436768 (fac=0.99, q=1)
2 days, 23:44:39.096164 INFO: Updating optimization_manager: fwhm_rt             : 2.792027473449707 -> 2.722515344619751
2 days, 23:44:39.096283 INFO: Updating optimization_manager: fwhm_mobility       : 0.007355421781539917 -> 0.006603988353163004
2 days, 23:44:39.096377 INFO: Updating optimization_manager: score_cutoff        : 32.69186139221192 -> 33.03245441436768
2 days, 23:44:39.096493 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:39.097767 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:39.099519 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:39.100609 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:39.103119 INFO: === checking if optimization conditions were reached ===
2 days, 23:44:39.105432 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.649764634570715
2 days, 23:44:39.105571 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2 days, 23:44:39.105673 PROGRESS: ❌ ms2_error      : 17.6498 > 15.0000 or insufficient steps taken.
2 days, 23:44:39.107271 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:44:39.107421 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
2 days, 23:44:39.107533 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:44:39.107640 INFO: ==============================================
2 days, 23:44:39.107765 INFO: Starting optimization step 3.
2 days, 23:44:39.107872 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:44:39.107973 INFO: Using python extraction backend
2 days, 23:44:39.108139 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:44:39.108254 INFO: === Search parameters used ===
2 days, 23:44:39.108353 INFO: rt_error       : 1199.9447605
2 days, 23:44:39.108450 INFO: mobility_error : 0.1
2 days, 23:44:39.108540 INFO: num_candidates : 3
2 days, 23:44:39.108633 INFO: ms1_error      : 15.0
2 days, 23:44:39.108721 INFO: ms2_error      : 17.649764634570715
2 days, 23:44:39.108812 INFO: fwhm_rt        : 2.722515344619751
2 days, 23:44:39.108885 INFO: quant_window   : 3
2 days, 23:44:39.108948 INFO: ==============================================
2 days, 23:44:39.110477 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:44:39.110553 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:44:39.110616 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
2 days, 23:44:39.110664 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.58
2 days, 23:44:39.117189 INFO: Starting candidate selection
2 days, 23:44:47.105606 INFO: Starting candidate scoring
2 days, 23:44:47.232963 INFO: Finished candidate processing
2 days, 23:44:47.233091 INFO: Collecting candidate features
2 days, 23:44:47.252591 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3424)
2 days, 23:44:47.260517 INFO: Collecting fragment features
2 days, 23:44:47.266439 INFO: Finished candidate scoring
2 days, 23:44:47.268589 INFO: performing precursor FDR with 47 features
2 days, 23:44:47.268653 INFO: Decoy channel: -1
2 days, 23:44:47.268689 INFO: competitive: True
2 days, 23:44:47.271996 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:44:47.273516 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:44:47.274643 INFO: Estimating optimal hyperparameters - samples: 2,738, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:44:47.274747 INFO: Using random state 183200 for train-test-split
2 days, 23:44:47.552860 INFO: Test AUC: 0.747
2 days, 23:44:47.552996 INFO: Train AUC: 0.755
2 days, 23:44:47.553046 INFO: AUC difference: 1.07%
2 days, 23:44:47.913498 INFO: Resetting torch num_threads to 80
2 days, 23:44:47.914296 PROGRESS: === Extracted 3424 precursors and 28441 fragments ===
2 days, 23:44:47.914898 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:44:47.915836 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:44:47.915968 PROGRESS: Total precursors accumulated: 600
2 days, 23:44:47.916083 PROGRESS: Target precursors: 528 (88.00%)
2 days, 23:44:47.916189 PROGRESS: Decoy precursors: 72 (12.00%)
2 days, 23:44:47.916281 PROGRESS: 
2 days, 23:44:47.916373 PROGRESS: Precursor Summary:
2 days, 23:44:47.918283 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   372; 0.001 FDR:   335
2 days, 23:44:47.918419 PROGRESS: 
2 days, 23:44:47.918523 PROGRESS: Protein Summary:
2 days, 23:44:47.920747 PROGRESS: Channel   0:	 0.050 FDR:   315; 0.010 FDR:   271; 0.001 FDR:   243
2 days, 23:44:47.920875 PROGRESS: =========================================================================
2 days, 23:44:47.921117 INFO: Target number of precursors reached.
2 days, 23:44:47.931067 INFO: fragments_df: keeping 5000 of 28441 [sum(precursor_idx_mask)=9870 sum(mass_error_mask)=28441 stop_rank=5000
2 days, 23:44:47.938209 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:48.171578 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:48.366726 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:48.532996 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:49.410757 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:44:49.411362 INFO: Using score_cutoff 27.84137322807312 (fac=0.99, q=1)
2 days, 23:44:49.411865 INFO: Updating optimization_manager: fwhm_rt             : 2.722515344619751 -> 2.667537212371826
2 days, 23:44:49.411984 INFO: Updating optimization_manager: fwhm_mobility       : 0.006603988353163004 -> 0.005441710818558931
2 days, 23:44:49.412085 INFO: Updating optimization_manager: score_cutoff        : 33.03245441436768 -> 27.84137322807312
2 days, 23:44:49.412197 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:49.413812 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:49.415656 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:49.416826 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:49.419356 INFO: === checking if optimization conditions were reached ===
2 days, 23:44:49.421751 INFO: Updating optimization_manager: ms2_error           : 17.649764634570715 -> 15.0
2 days, 23:44:49.421926 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:44:49.422046 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:44:49.423605 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:44:49.423757 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:44:49.423872 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:44:49.423973 INFO: ==============================================
2 days, 23:44:49.424090 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:44:49.429555 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:49.430819 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:49.432618 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:49.433788 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:44:49.436474 INFO: Starting optimization step 0.
2 days, 23:44:49.436612 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:44:49.436727 INFO: Using python extraction backend
2 days, 23:44:49.436932 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:44:49.437062 INFO: === Search parameters used ===
2 days, 23:44:49.437160 INFO: rt_error       : 1199.9447605
2 days, 23:44:49.437242 INFO: mobility_error : 0.1
2 days, 23:44:49.437333 INFO: num_candidates : 3
2 days, 23:44:49.437425 INFO: ms1_error      : 15.0
2 days, 23:44:49.437516 INFO: ms2_error      : 15.0
2 days, 23:44:49.437608 INFO: fwhm_rt        : 2.667537212371826
2 days, 23:44:49.437690 INFO: quant_window   : 3
2 days, 23:44:49.437763 INFO: ==============================================
2 days, 23:44:49.439344 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:44:49.439419 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:44:49.439484 INFO: FWHM in RT is 2.67 seconds, sigma is 0.44
2 days, 23:44:49.439528 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.95
2 days, 23:44:49.450123 INFO: Starting candidate selection
2 days, 23:44:57.719231 INFO: Starting candidate scoring
2 days, 23:44:57.832063 INFO: Finished candidate processing
2 days, 23:44:57.832205 INFO: Collecting candidate features
2 days, 23:44:57.846585 WARNING: intensity_correlation has 3 NaNs ( 0.09 % out of 3392)
2 days, 23:44:57.851708 INFO: Collecting fragment features
2 days, 23:44:57.856937 INFO: Finished candidate scoring
2 days, 23:44:57.859251 INFO: performing precursor FDR with 47 features
2 days, 23:44:57.859318 INFO: Decoy channel: -1
2 days, 23:44:57.859371 INFO: competitive: True
2 days, 23:44:57.863297 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:44:57.865231 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:44:57.865289 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:44:57.866585 INFO: Estimating optimal hyperparameters - samples: 2,711, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:44:57.866681 INFO: Using random state 685176 for train-test-split
2 days, 23:44:58.230066 INFO: Test AUC: 0.772
2 days, 23:44:58.230203 INFO: Train AUC: 0.774
2 days, 23:44:58.230259 INFO: AUC difference: 0.24%
2 days, 23:44:58.624275 INFO: Resetting torch num_threads to 80
2 days, 23:44:58.625134 PROGRESS: === Extracted 3392 precursors and 27448 fragments ===
2 days, 23:44:58.625777 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:44:58.626900 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:44:58.627044 PROGRESS: Total precursors accumulated: 600
2 days, 23:44:58.627161 PROGRESS: Target precursors: 529 (88.17%)
2 days, 23:44:58.627270 PROGRESS: Decoy precursors: 71 (11.83%)
2 days, 23:44:58.627363 PROGRESS: 
2 days, 23:44:58.627445 PROGRESS: Precursor Summary:
2 days, 23:44:58.629378 PROGRESS: Channel   0:	 0.050 FDR:   450; 0.010 FDR:   373; 0.001 FDR:   351
2 days, 23:44:58.629509 PROGRESS: 
2 days, 23:44:58.629615 PROGRESS: Protein Summary:
2 days, 23:44:58.631795 PROGRESS: Channel   0:	 0.050 FDR:   333; 0.010 FDR:   270; 0.001 FDR:   255
2 days, 23:44:58.631930 PROGRESS: =========================================================================
2 days, 23:44:58.632169 INFO: Target number of precursors reached.
2 days, 23:44:58.641882 INFO: fragments_df: keeping 5000 of 27448 [sum(precursor_idx_mask)=9708 sum(mass_error_mask)=27448 stop_rank=5000
2 days, 23:44:58.647776 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:44:58.818187 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:44:58.990593 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:44:59.176531 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:00.019696 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:00.020201 INFO: Using score_cutoff 26.678703268432617 (fac=0.99, q=1)
2 days, 23:45:00.020576 INFO: Updating optimization_manager: fwhm_rt             : 2.667537212371826 -> 2.611794948577881
2 days, 23:45:00.020680 INFO: Updating optimization_manager: fwhm_mobility       : 0.005441710818558931 -> 0.005095161031931639
2 days, 23:45:00.020765 INFO: Updating optimization_manager: score_cutoff        : 27.84137322807312 -> 26.678703268432617
2 days, 23:45:00.020854 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:00.022055 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:00.023473 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:00.024323 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:00.026412 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:00.026543 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:45:00.028314 INFO: Updating optimization_manager: rt_error            : 1199.9447605 -> 225.78640125928538
2 days, 23:45:00.028448 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 225.7864.
2 days, 23:45:00.028537 INFO: ==============================================
2 days, 23:45:00.028636 INFO: Starting optimization step 1.
2 days, 23:45:00.028723 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:00.028813 INFO: Using python extraction backend
2 days, 23:45:00.028957 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:00.029053 INFO: === Search parameters used ===
2 days, 23:45:00.029143 INFO: rt_error       : 225.78640125928538
2 days, 23:45:00.029217 INFO: mobility_error : 0.1
2 days, 23:45:00.029280 INFO: num_candidates : 3
2 days, 23:45:00.029342 INFO: ms1_error      : 15.0
2 days, 23:45:00.029402 INFO: ms2_error      : 15.0
2 days, 23:45:00.029462 INFO: fwhm_rt        : 2.611794948577881
2 days, 23:45:00.029521 INFO: quant_window   : 3
2 days, 23:45:00.029579 INFO: ==============================================
2 days, 23:45:00.030629 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:00.030684 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:00.030738 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
2 days, 23:45:00.030778 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.76
2 days, 23:45:00.035184 INFO: Starting candidate selection
2 days, 23:45:02.796414 INFO: Starting candidate scoring
2 days, 23:45:02.899702 INFO: Finished candidate processing
2 days, 23:45:02.899846 INFO: Collecting candidate features
2 days, 23:45:02.916225 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3342)
2 days, 23:45:02.923641 INFO: Collecting fragment features
2 days, 23:45:02.929050 INFO: Finished candidate scoring
2 days, 23:45:02.931099 INFO: performing precursor FDR with 47 features
2 days, 23:45:02.931173 INFO: Decoy channel: -1
2 days, 23:45:02.931205 INFO: competitive: True
2 days, 23:45:02.934556 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:02.936038 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 23:45:02.937162 INFO: Estimating optimal hyperparameters - samples: 2,670, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:02.937254 INFO: Using random state 685176 for train-test-split
2 days, 23:45:03.269416 INFO: Test AUC: 0.760
2 days, 23:45:03.269573 INFO: Train AUC: 0.789
2 days, 23:45:03.269624 INFO: AUC difference: 3.74%
2 days, 23:45:03.644010 INFO: Resetting torch num_threads to 80
2 days, 23:45:03.644820 PROGRESS: === Extracted 3342 precursors and 25890 fragments ===
2 days, 23:45:03.645413 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:03.646310 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:03.646437 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:03.646519 PROGRESS: Target precursors: 546 (91.00%)
2 days, 23:45:03.646603 PROGRESS: Decoy precursors: 54 (9.00%)
2 days, 23:45:03.646677 PROGRESS: 
2 days, 23:45:03.646751 PROGRESS: Precursor Summary:
2 days, 23:45:03.648513 PROGRESS: Channel   0:	 0.050 FDR:   510; 0.010 FDR:   447; 0.001 FDR:   377
2 days, 23:45:03.648633 PROGRESS: 
2 days, 23:45:03.648715 PROGRESS: Protein Summary:
2 days, 23:45:03.650753 PROGRESS: Channel   0:	 0.050 FDR:   375; 0.010 FDR:   331; 0.001 FDR:   275
2 days, 23:45:03.650884 PROGRESS: =========================================================================
2 days, 23:45:03.651113 INFO: Target number of precursors reached.
2 days, 23:45:03.660507 INFO: fragments_df: keeping 5000 of 25890 [sum(precursor_idx_mask)=11249 sum(mass_error_mask)=25890 stop_rank=5000
2 days, 23:45:03.665909 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:03.867877 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:04.073104 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:04.287127 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:05.091191 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:05.091655 INFO: Using score_cutoff 21.67774484024048 (fac=0.99, q=1)
2 days, 23:45:05.092010 INFO: Updating optimization_manager: fwhm_rt             : 2.611794948577881 -> 2.5627214908599854
2 days, 23:45:05.092099 INFO: Updating optimization_manager: fwhm_mobility       : 0.005095161031931639 -> 0.004615633748471737
2 days, 23:45:05.092159 INFO: Updating optimization_manager: score_cutoff        : 26.678703268432617 -> 21.67774484024048
2 days, 23:45:05.092218 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:05.093340 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:05.094768 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:05.095610 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:05.097621 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:05.097727 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:45:05.099513 INFO: Updating optimization_manager: rt_error            : 225.78640125928538 -> 52.49166456002923
2 days, 23:45:05.099624 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 52.4917.
2 days, 23:45:05.099704 INFO: ==============================================
2 days, 23:45:05.099778 INFO: Starting optimization step 2.
2 days, 23:45:05.099841 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:05.099902 INFO: Using python extraction backend
2 days, 23:45:05.100001 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:05.100067 INFO: === Search parameters used ===
2 days, 23:45:05.100118 INFO: rt_error       : 52.49166456002923
2 days, 23:45:05.100165 INFO: mobility_error : 0.1
2 days, 23:45:05.100209 INFO: num_candidates : 3
2 days, 23:45:05.100252 INFO: ms1_error      : 15.0
2 days, 23:45:05.100295 INFO: ms2_error      : 15.0
2 days, 23:45:05.100337 INFO: fwhm_rt        : 2.5627214908599854
2 days, 23:45:05.100379 INFO: quant_window   : 3
2 days, 23:45:05.100424 INFO: ==============================================
2 days, 23:45:05.101289 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:05.101337 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:05.101374 INFO: FWHM in RT is 2.56 seconds, sigma is 0.43
2 days, 23:45:05.101398 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.50
2 days, 23:45:05.106119 INFO: Starting candidate selection
2 days, 23:45:05.997661 INFO: Starting candidate scoring
2 days, 23:45:06.097953 INFO: Finished candidate processing
2 days, 23:45:06.098085 INFO: Collecting candidate features
2 days, 23:45:06.113638 WARNING: intensity_correlation has 16 NaNs ( 0.49 % out of 3243)
2 days, 23:45:06.119075 INFO: Collecting fragment features
2 days, 23:45:06.124502 INFO: Finished candidate scoring
2 days, 23:45:06.128106 INFO: performing precursor FDR with 47 features
2 days, 23:45:06.128212 INFO: Decoy channel: -1
2 days, 23:45:06.128258 INFO: competitive: True
2 days, 23:45:06.133168 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:06.135720 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:45:06.135800 WARNING: dropped 14 decoy PSMs due to missing features
2 days, 23:45:06.137267 INFO: Estimating optimal hyperparameters - samples: 2,581, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:06.137375 INFO: Using random state 685176 for train-test-split
2 days, 23:45:06.378910 INFO: Test AUC: 0.792
2 days, 23:45:06.379038 INFO: Train AUC: 0.845
2 days, 23:45:06.379081 INFO: AUC difference: 6.27%
2 days, 23:45:06.379112 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:45:06.648880 INFO: Resetting torch num_threads to 80
2 days, 23:45:06.649559 PROGRESS: === Extracted 3243 precursors and 23808 fragments ===
2 days, 23:45:06.650042 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:06.650704 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:06.650823 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:06.650907 PROGRESS: Target precursors: 575 (95.83%)
2 days, 23:45:06.650978 PROGRESS: Decoy precursors: 25 (4.17%)
2 days, 23:45:06.651045 PROGRESS: 
2 days, 23:45:06.651114 PROGRESS: Precursor Summary:
2 days, 23:45:06.652339 PROGRESS: Channel   0:	 0.050 FDR:   575; 0.010 FDR:   533; 0.001 FDR:   406
2 days, 23:45:06.652451 PROGRESS: 
2 days, 23:45:06.652537 PROGRESS: Protein Summary:
2 days, 23:45:06.653958 PROGRESS: Channel   0:	 0.050 FDR:   418; 0.010 FDR:   391; 0.001 FDR:   301
2 days, 23:45:06.654075 PROGRESS: =========================================================================
2 days, 23:45:06.654256 INFO: Target number of precursors reached.
2 days, 23:45:06.660861 INFO: fragments_df: keeping 5000 of 23808 [sum(precursor_idx_mask)=12846 sum(mass_error_mask)=23808 stop_rank=5000
2 days, 23:45:06.664464 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:06.882360 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:07.051694 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:07.247586 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:08.109452 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:08.110071 INFO: Using score_cutoff 18.224722924804688 (fac=0.99, q=1)
2 days, 23:45:08.110563 INFO: Updating optimization_manager: fwhm_rt             : 2.5627214908599854 -> 2.515881061553955
2 days, 23:45:08.110678 INFO: Updating optimization_manager: fwhm_mobility       : 0.004615633748471737 -> 0.004266819451004267
2 days, 23:45:08.110774 INFO: Updating optimization_manager: score_cutoff        : 21.67774484024048 -> 18.224722924804688
2 days, 23:45:08.110856 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:08.112289 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:08.114043 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:08.115138 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:08.117541 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:08.117665 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:45:08.119634 INFO: Updating optimization_manager: rt_error            : 52.49166456002923 -> 30.241147914604515
2 days, 23:45:08.119761 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 30.2411.
2 days, 23:45:08.119859 INFO: ==============================================
2 days, 23:45:08.119961 INFO: Starting optimization step 3.
2 days, 23:45:08.120055 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:08.120142 INFO: Using python extraction backend
2 days, 23:45:08.120270 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:08.120361 INFO: === Search parameters used ===
2 days, 23:45:08.120432 INFO: rt_error       : 30.241147914604515
2 days, 23:45:08.120501 INFO: mobility_error : 0.1
2 days, 23:45:08.120567 INFO: num_candidates : 3
2 days, 23:45:08.120637 INFO: ms1_error      : 15.0
2 days, 23:45:08.120708 INFO: ms2_error      : 15.0
2 days, 23:45:08.120774 INFO: fwhm_rt        : 2.515881061553955
2 days, 23:45:08.120821 INFO: quant_window   : 3
2 days, 23:45:08.120864 INFO: ==============================================
2 days, 23:45:08.121807 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:08.121856 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:08.121908 INFO: FWHM in RT is 2.52 seconds, sigma is 0.42
2 days, 23:45:08.121932 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.31
2 days, 23:45:08.126948 INFO: Starting candidate selection
2 days, 23:45:08.763986 INFO: Starting candidate scoring
2 days, 23:45:08.859836 INFO: Finished candidate processing
2 days, 23:45:08.859954 INFO: Collecting candidate features
2 days, 23:45:08.872522 WARNING: intensity_correlation has 21 NaNs ( 0.65 % out of 3210)
2 days, 23:45:08.877778 INFO: Collecting fragment features
2 days, 23:45:08.882538 INFO: Finished candidate scoring
2 days, 23:45:08.884847 INFO: performing precursor FDR with 47 features
2 days, 23:45:08.884915 INFO: Decoy channel: -1
2 days, 23:45:08.884970 INFO: competitive: True
2 days, 23:45:08.888958 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:08.891093 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:45:08.891175 WARNING: dropped 18 decoy PSMs due to missing features
2 days, 23:45:08.892431 INFO: Estimating optimal hyperparameters - samples: 2,551, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:08.892582 INFO: Using random state 685176 for train-test-split
2 days, 23:45:09.123345 INFO: Test AUC: 0.849
2 days, 23:45:09.123461 INFO: Train AUC: 0.867
2 days, 23:45:09.123504 INFO: AUC difference: 2.07%
2 days, 23:45:09.393264 INFO: Resetting torch num_threads to 80
2 days, 23:45:09.393883 PROGRESS: === Extracted 3210 precursors and 23120 fragments ===
2 days, 23:45:09.394346 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:09.394982 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:09.395086 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:09.395159 PROGRESS: Target precursors: 584 (97.33%)
2 days, 23:45:09.395229 PROGRESS: Decoy precursors: 16 (2.67%)
2 days, 23:45:09.395300 PROGRESS: 
2 days, 23:45:09.395363 PROGRESS: Precursor Summary:
2 days, 23:45:09.396545 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   549; 0.001 FDR:   430
2 days, 23:45:09.396648 PROGRESS: 
2 days, 23:45:09.396720 PROGRESS: Protein Summary:
2 days, 23:45:09.398079 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   406; 0.001 FDR:   318
2 days, 23:45:09.398185 PROGRESS: =========================================================================
2 days, 23:45:09.398342 INFO: Target number of precursors reached.
2 days, 23:45:09.407551 INFO: fragments_df: keeping 5000 of 23120 [sum(precursor_idx_mask)=13012 sum(mass_error_mask)=23120 stop_rank=5000
2 days, 23:45:09.413316 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:09.600713 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:09.777336 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:09.971777 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:10.751286 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:10.751791 INFO: Using score_cutoff 17.221573203277586 (fac=0.99, q=1)
2 days, 23:45:10.752218 INFO: Updating optimization_manager: fwhm_rt             : 2.515881061553955 -> 2.517890214920044
2 days, 23:45:10.752330 INFO: Updating optimization_manager: fwhm_mobility       : 0.004266819451004267 -> 0.0040718624368309975
2 days, 23:45:10.752418 INFO: Updating optimization_manager: score_cutoff        : 18.224722924804688 -> 17.221573203277586
2 days, 23:45:10.752501 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:10.753683 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:10.755207 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:10.756107 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:10.758312 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:10.758447 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:45:10.760481 INFO: Updating optimization_manager: rt_error            : 30.241147914604515 -> 15.796108964084963
2 days, 23:45:10.760615 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 15.7961.
2 days, 23:45:10.760725 INFO: ==============================================
2 days, 23:45:10.760843 INFO: Starting optimization step 4.
2 days, 23:45:10.760961 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:10.761055 INFO: Using python extraction backend
2 days, 23:45:10.761194 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:10.761292 INFO: === Search parameters used ===
2 days, 23:45:10.761377 INFO: rt_error       : 15.796108964084963
2 days, 23:45:10.761448 INFO: mobility_error : 0.1
2 days, 23:45:10.761518 INFO: num_candidates : 3
2 days, 23:45:10.761583 INFO: ms1_error      : 15.0
2 days, 23:45:10.761644 INFO: ms2_error      : 15.0
2 days, 23:45:10.761704 INFO: fwhm_rt        : 2.517890214920044
2 days, 23:45:10.761763 INFO: quant_window   : 3
2 days, 23:45:10.761822 INFO: ==============================================
2 days, 23:45:10.762804 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:10.762859 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:10.762909 INFO: FWHM in RT is 2.52 seconds, sigma is 0.42
2 days, 23:45:10.762949 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.21
2 days, 23:45:10.770040 INFO: Starting candidate selection
2 days, 23:45:11.369824 INFO: Starting candidate scoring
2 days, 23:45:11.477058 INFO: Finished candidate processing
2 days, 23:45:11.477183 INFO: Collecting candidate features
2 days, 23:45:11.493232 WARNING: intensity_correlation has 25 NaNs ( 0.78 % out of 3206)
2 days, 23:45:11.493711 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3206)
2 days, 23:45:11.499900 INFO: Collecting fragment features
2 days, 23:45:11.505612 INFO: Finished candidate scoring
2 days, 23:45:11.509055 INFO: performing precursor FDR with 47 features
2 days, 23:45:11.509149 INFO: Decoy channel: -1
2 days, 23:45:11.509186 INFO: competitive: True
2 days, 23:45:11.513981 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:11.516437 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:45:11.516515 WARNING: dropped 22 decoy PSMs due to missing features
2 days, 23:45:11.517987 INFO: Estimating optimal hyperparameters - samples: 2,544, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:11.518106 INFO: Using random state 685176 for train-test-split
2 days, 23:45:11.788936 INFO: Test AUC: 0.833
2 days, 23:45:11.789046 INFO: Train AUC: 0.880
2 days, 23:45:11.789086 INFO: AUC difference: 5.31%
2 days, 23:45:11.789118 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:45:12.078770 INFO: Resetting torch num_threads to 80
2 days, 23:45:12.079479 PROGRESS: === Extracted 3206 precursors and 22693 fragments ===
2 days, 23:45:12.079992 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:12.080627 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:12.080729 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:12.080811 PROGRESS: Target precursors: 589 (98.17%)
2 days, 23:45:12.080886 PROGRESS: Decoy precursors: 11 (1.83%)
2 days, 23:45:12.080958 PROGRESS: 
2 days, 23:45:12.081026 PROGRESS: Precursor Summary:
2 days, 23:45:12.082246 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   565; 0.001 FDR:   490
2 days, 23:45:12.082359 PROGRESS: 
2 days, 23:45:12.082439 PROGRESS: Protein Summary:
2 days, 23:45:12.083843 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   415; 0.001 FDR:   362
2 days, 23:45:12.083953 PROGRESS: =========================================================================
2 days, 23:45:12.084124 INFO: Target number of precursors reached.
2 days, 23:45:12.090344 INFO: fragments_df: keeping 5000 of 22693 [sum(precursor_idx_mask)=13357 sum(mass_error_mask)=22693 stop_rank=5000
2 days, 23:45:12.095160 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:12.281473 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:12.500288 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:12.780704 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:13.670039 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:13.670680 INFO: Using score_cutoff 16.555172126770017 (fac=0.99, q=1)
2 days, 23:45:13.671179 INFO: Updating optimization_manager: fwhm_rt             : 2.517890214920044 -> 2.514219284057617
2 days, 23:45:13.671292 INFO: Updating optimization_manager: fwhm_mobility       : 0.0040718624368309975 -> 0.00387505698017776
2 days, 23:45:13.671382 INFO: Updating optimization_manager: score_cutoff        : 17.221573203277586 -> 16.555172126770017
2 days, 23:45:13.671492 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:13.673137 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:13.675010 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:13.676193 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:13.678750 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:13.678909 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:45:13.681934 INFO: Updating optimization_manager: rt_error            : 15.796108964084963 -> 11.305310519299491
2 days, 23:45:13.682080 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 11.3053.
2 days, 23:45:13.682183 INFO: ==============================================
2 days, 23:45:13.682305 INFO: Starting optimization step 5.
2 days, 23:45:13.682408 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:13.682518 INFO: Using python extraction backend
2 days, 23:45:13.682689 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:13.682806 INFO: === Search parameters used ===
2 days, 23:45:13.682901 INFO: rt_error       : 11.305310519299491
2 days, 23:45:13.682981 INFO: mobility_error : 0.1
2 days, 23:45:13.683065 INFO: num_candidates : 3
2 days, 23:45:13.683145 INFO: ms1_error      : 15.0
2 days, 23:45:13.683221 INFO: ms2_error      : 15.0
2 days, 23:45:13.683298 INFO: fwhm_rt        : 2.514219284057617
2 days, 23:45:13.683379 INFO: quant_window   : 3
2 days, 23:45:13.683462 INFO: ==============================================
2 days, 23:45:13.685154 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:13.685225 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:13.685286 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:45:13.685324 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.10
2 days, 23:45:13.692936 INFO: Starting candidate selection
2 days, 23:45:14.364924 INFO: Starting candidate scoring
2 days, 23:45:14.472848 INFO: Finished candidate processing
2 days, 23:45:14.473018 INFO: Collecting candidate features
2 days, 23:45:14.489485 WARNING: intensity_correlation has 25 NaNs ( 0.79 % out of 3184)
2 days, 23:45:14.489847 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3184)
2 days, 23:45:14.497844 INFO: Collecting fragment features
2 days, 23:45:14.503754 INFO: Finished candidate scoring
2 days, 23:45:14.507208 INFO: performing precursor FDR with 47 features
2 days, 23:45:14.507301 INFO: Decoy channel: -1
2 days, 23:45:14.507341 INFO: competitive: True
2 days, 23:45:14.513575 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:14.515997 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:45:14.516079 WARNING: dropped 24 decoy PSMs due to missing features
2 days, 23:45:14.517365 INFO: Estimating optimal hyperparameters - samples: 2,526, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:14.517468 INFO: Using random state 685176 for train-test-split
2 days, 23:45:14.839589 INFO: Test AUC: 0.876
2 days, 23:45:14.839738 INFO: Train AUC: 0.870
2 days, 23:45:14.839795 INFO: AUC difference: 0.65%
2 days, 23:45:15.167227 INFO: Resetting torch num_threads to 80
2 days, 23:45:15.167840 PROGRESS: === Extracted 3184 precursors and 22530 fragments ===
2 days, 23:45:15.168315 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:15.168970 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:15.169081 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:15.169163 PROGRESS: Target precursors: 585 (97.50%)
2 days, 23:45:15.169233 PROGRESS: Decoy precursors: 15 (2.50%)
2 days, 23:45:15.169297 PROGRESS: 
2 days, 23:45:15.169358 PROGRESS: Precursor Summary:
2 days, 23:45:15.170547 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   561; 0.001 FDR:   476
2 days, 23:45:15.170670 PROGRESS: 
2 days, 23:45:15.170753 PROGRESS: Protein Summary:
2 days, 23:45:15.172133 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   412; 0.001 FDR:   353
2 days, 23:45:15.172234 PROGRESS: =========================================================================
2 days, 23:45:15.172416 INFO: Target number of precursors reached.
2 days, 23:45:15.178534 INFO: fragments_df: keeping 5000 of 22530 [sum(precursor_idx_mask)=13245 sum(mass_error_mask)=22530 stop_rank=5000
2 days, 23:45:15.182134 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:15.470923 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:15.659971 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:15.853053 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:16.648582 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:16.649192 INFO: Using score_cutoff 16.60166863632202 (fac=0.99, q=1)
2 days, 23:45:16.649624 INFO: Updating optimization_manager: fwhm_rt             : 2.514219284057617 -> 2.5149664878845215
2 days, 23:45:16.649734 INFO: Updating optimization_manager: fwhm_mobility       : 0.00387505698017776 -> 0.00387505698017776
2 days, 23:45:16.649835 INFO: Updating optimization_manager: score_cutoff        : 16.555172126770017 -> 16.60166863632202
2 days, 23:45:16.649969 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:16.651579 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:16.653390 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:16.654567 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:16.657131 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:16.657267 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 23:45:16.660120 INFO: Updating optimization_manager: rt_error            : 11.305310519299491 -> 10.592609022285153
2 days, 23:45:16.660273 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 10.5926.
2 days, 23:45:16.660406 INFO: ==============================================
2 days, 23:45:16.660527 INFO: Starting optimization step 6.
2 days, 23:45:16.660629 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:16.660720 INFO: Using python extraction backend
2 days, 23:45:16.660875 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:16.660998 INFO: === Search parameters used ===
2 days, 23:45:16.661082 INFO: rt_error       : 10.592609022285153
2 days, 23:45:16.661152 INFO: mobility_error : 0.1
2 days, 23:45:16.661219 INFO: num_candidates : 3
2 days, 23:45:16.661286 INFO: ms1_error      : 15.0
2 days, 23:45:16.661364 INFO: ms2_error      : 15.0
2 days, 23:45:16.661438 INFO: fwhm_rt        : 2.5149664878845215
2 days, 23:45:16.661519 INFO: quant_window   : 3
2 days, 23:45:16.661602 INFO: ==============================================
2 days, 23:45:16.663425 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:16.663499 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:16.663557 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:45:16.663599 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.10
2 days, 23:45:16.678041 INFO: Starting candidate selection
2 days, 23:45:17.207709 INFO: Starting candidate scoring
2 days, 23:45:17.310046 INFO: Finished candidate processing
2 days, 23:45:17.310160 INFO: Collecting candidate features
2 days, 23:45:17.323151 WARNING: intensity_correlation has 23 NaNs ( 0.73 % out of 3171)
2 days, 23:45:17.323382 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3171)
2 days, 23:45:17.329414 INFO: Collecting fragment features
2 days, 23:45:17.333748 INFO: Finished candidate scoring
2 days, 23:45:17.335701 INFO: performing precursor FDR with 47 features
2 days, 23:45:17.335757 INFO: Decoy channel: -1
2 days, 23:45:17.335786 INFO: competitive: True
2 days, 23:45:17.339435 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:17.341231 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:45:17.341285 WARNING: dropped 22 decoy PSMs due to missing features
2 days, 23:45:17.342471 INFO: Estimating optimal hyperparameters - samples: 2,517, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:17.342565 INFO: Using random state 685176 for train-test-split
2 days, 23:45:17.638871 INFO: Test AUC: 0.875
2 days, 23:45:17.638990 INFO: Train AUC: 0.869
2 days, 23:45:17.639029 INFO: AUC difference: 0.60%
2 days, 23:45:17.942163 INFO: Resetting torch num_threads to 80
2 days, 23:45:17.942807 PROGRESS: === Extracted 3171 precursors and 22430 fragments ===
2 days, 23:45:17.943302 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:17.944018 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:17.944119 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:17.944192 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:45:17.944258 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:45:17.944316 PROGRESS: 
2 days, 23:45:17.944372 PROGRESS: Precursor Summary:
2 days, 23:45:17.945762 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   562; 0.001 FDR:   463
2 days, 23:45:17.945873 PROGRESS: 
2 days, 23:45:17.945945 PROGRESS: Protein Summary:
2 days, 23:45:17.947594 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   412; 0.001 FDR:   345
2 days, 23:45:17.947696 PROGRESS: =========================================================================
2 days, 23:45:17.947882 INFO: Target number of precursors reached.
2 days, 23:45:17.955847 INFO: fragments_df: keeping 5000 of 22430 [sum(precursor_idx_mask)=13203 sum(mass_error_mask)=22430 stop_rank=5000
2 days, 23:45:17.959855 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:18.197084 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:18.393637 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:18.599507 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:19.433829 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:19.434322 INFO: Using score_cutoff 16.440827077674868 (fac=0.99, q=1)
2 days, 23:45:19.434740 INFO: Updating optimization_manager: fwhm_rt             : 2.5149664878845215 -> 2.51440691947937
2 days, 23:45:19.434848 INFO: Updating optimization_manager: fwhm_mobility       : 0.00387505698017776 -> 0.003848197404295206
2 days, 23:45:19.434918 INFO: Updating optimization_manager: score_cutoff        : 16.60166863632202 -> 16.440827077674868
2 days, 23:45:19.434987 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:19.436173 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:19.437654 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:19.438544 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:19.440561 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:19.440677 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 23:45:19.442793 INFO: Updating optimization_manager: rt_error            : 10.592609022285153 -> 11.221968352476408
2 days, 23:45:19.442916 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 11.2220.
2 days, 23:45:19.442997 INFO: ==============================================
2 days, 23:45:19.443086 INFO: Starting optimization step 7.
2 days, 23:45:19.443158 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:19.443230 INFO: Using python extraction backend
2 days, 23:45:19.443342 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:19.443421 INFO: === Search parameters used ===
2 days, 23:45:19.443481 INFO: rt_error       : 11.221968352476408
2 days, 23:45:19.443541 INFO: mobility_error : 0.1
2 days, 23:45:19.443601 INFO: num_candidates : 3
2 days, 23:45:19.443656 INFO: ms1_error      : 15.0
2 days, 23:45:19.443712 INFO: ms2_error      : 15.0
2 days, 23:45:19.443765 INFO: fwhm_rt        : 2.51440691947937
2 days, 23:45:19.443818 INFO: quant_window   : 3
2 days, 23:45:19.443869 INFO: ==============================================
2 days, 23:45:19.444754 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:19.444809 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:19.444851 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:45:19.444879 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.09
2 days, 23:45:19.454021 INFO: Starting candidate selection
2 days, 23:45:19.987338 INFO: Starting candidate scoring
2 days, 23:45:20.088403 INFO: Finished candidate processing
2 days, 23:45:20.088527 INFO: Collecting candidate features
2 days, 23:45:20.104834 WARNING: intensity_correlation has 28 NaNs ( 0.88 % out of 3182)
2 days, 23:45:20.105183 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3182)
2 days, 23:45:20.112942 INFO: Collecting fragment features
2 days, 23:45:20.118611 INFO: Finished candidate scoring
2 days, 23:45:20.121961 INFO: performing precursor FDR with 47 features
2 days, 23:45:20.122050 INFO: Decoy channel: -1
2 days, 23:45:20.122082 INFO: competitive: True
2 days, 23:45:20.125639 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:20.127292 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:45:20.127359 WARNING: dropped 26 decoy PSMs due to missing features
2 days, 23:45:20.128425 INFO: Estimating optimal hyperparameters - samples: 2,522, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:20.128524 INFO: Using random state 685176 for train-test-split
2 days, 23:45:20.358636 INFO: Test AUC: 0.875
2 days, 23:45:20.358775 INFO: Train AUC: 0.868
2 days, 23:45:20.358847 INFO: AUC difference: 0.79%
2 days, 23:45:20.669467 INFO: Resetting torch num_threads to 80
2 days, 23:45:20.670082 PROGRESS: === Extracted 3182 precursors and 22503 fragments ===
2 days, 23:45:20.670545 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:20.671181 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:20.671283 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:20.671361 PROGRESS: Target precursors: 588 (98.00%)
2 days, 23:45:20.671429 PROGRESS: Decoy precursors: 12 (2.00%)
2 days, 23:45:20.671499 PROGRESS: 
2 days, 23:45:20.671562 PROGRESS: Precursor Summary:
2 days, 23:45:20.672714 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   562; 0.001 FDR:   470
2 days, 23:45:20.672813 PROGRESS: 
2 days, 23:45:20.672879 PROGRESS: Protein Summary:
2 days, 23:45:20.674499 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   413; 0.001 FDR:   351
2 days, 23:45:20.674623 PROGRESS: =========================================================================
2 days, 23:45:20.674817 INFO: Target number of precursors reached.
2 days, 23:45:20.683970 INFO: fragments_df: keeping 5000 of 22503 [sum(precursor_idx_mask)=13223 sum(mass_error_mask)=22503 stop_rank=5000
2 days, 23:45:20.688926 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:20.864129 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:21.076923 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:21.323755 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:22.203229 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:22.203696 INFO: Using score_cutoff 16.353779443931582 (fac=0.99, q=1)
2 days, 23:45:22.204044 INFO: Updating optimization_manager: fwhm_rt             : 2.51440691947937 -> 2.51440691947937
2 days, 23:45:22.204137 INFO: Updating optimization_manager: fwhm_mobility       : 0.003848197404295206 -> 0.003866900224238634
2 days, 23:45:22.204207 INFO: Updating optimization_manager: score_cutoff        : 16.440827077674868 -> 16.353779443931582
2 days, 23:45:22.204275 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:22.205397 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:22.206801 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:22.207649 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:22.209660 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:22.209773 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 23:45:22.211797 INFO: Updating optimization_manager: rt_error            : 11.221968352476408 -> 10.555245695995211
2 days, 23:45:22.211929 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 10.5552.
2 days, 23:45:22.212026 INFO: ==============================================
2 days, 23:45:22.212124 INFO: Starting optimization step 8.
2 days, 23:45:22.212210 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:22.212304 INFO: Using python extraction backend
2 days, 23:45:22.212440 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:22.212530 INFO: === Search parameters used ===
2 days, 23:45:22.212610 INFO: rt_error       : 10.555245695995211
2 days, 23:45:22.212679 INFO: mobility_error : 0.1
2 days, 23:45:22.212742 INFO: num_candidates : 3
2 days, 23:45:22.212803 INFO: ms1_error      : 15.0
2 days, 23:45:22.212864 INFO: ms2_error      : 15.0
2 days, 23:45:22.212924 INFO: fwhm_rt        : 2.51440691947937
2 days, 23:45:22.212984 INFO: quant_window   : 3
2 days, 23:45:22.213042 INFO: ==============================================
2 days, 23:45:22.213906 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:22.213959 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:22.214007 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:45:22.214041 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.10
2 days, 23:45:22.219660 INFO: Starting candidate selection
2 days, 23:45:22.800134 INFO: Starting candidate scoring
2 days, 23:45:22.907988 INFO: Finished candidate processing
2 days, 23:45:22.908116 INFO: Collecting candidate features
2 days, 23:45:22.923945 WARNING: intensity_correlation has 23 NaNs ( 0.73 % out of 3170)
2 days, 23:45:22.924289 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3170)
2 days, 23:45:22.928806 INFO: Collecting fragment features
2 days, 23:45:22.933062 INFO: Finished candidate scoring
2 days, 23:45:22.935047 INFO: performing precursor FDR with 47 features
2 days, 23:45:22.935119 INFO: Decoy channel: -1
2 days, 23:45:22.935157 INFO: competitive: True
2 days, 23:45:22.938316 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:22.940125 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:45:22.940193 WARNING: dropped 22 decoy PSMs due to missing features
2 days, 23:45:22.941583 INFO: Estimating optimal hyperparameters - samples: 2,516, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:22.941694 INFO: Using random state 685176 for train-test-split
2 days, 23:45:23.305336 INFO: Test AUC: 0.879
2 days, 23:45:23.305462 INFO: Train AUC: 0.867
2 days, 23:45:23.305506 INFO: AUC difference: 1.44%
2 days, 23:45:23.654880 INFO: Resetting torch num_threads to 80
2 days, 23:45:23.655686 PROGRESS: === Extracted 3170 precursors and 22431 fragments ===
2 days, 23:45:23.656263 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:23.657130 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:23.657260 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:23.657373 PROGRESS: Target precursors: 586 (97.67%)
2 days, 23:45:23.657470 PROGRESS: Decoy precursors: 14 (2.33%)
2 days, 23:45:23.657565 PROGRESS: 
2 days, 23:45:23.657659 PROGRESS: Precursor Summary:
2 days, 23:45:23.660352 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   567; 0.001 FDR:   455
2 days, 23:45:23.660506 PROGRESS: 
2 days, 23:45:23.660603 PROGRESS: Protein Summary:
2 days, 23:45:23.662950 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   415; 0.001 FDR:   339
2 days, 23:45:23.663087 PROGRESS: =========================================================================
2 days, 23:45:23.663300 INFO: Target number of precursors reached.
2 days, 23:45:23.673041 INFO: fragments_df: keeping 5000 of 22431 [sum(precursor_idx_mask)=13300 sum(mass_error_mask)=22431 stop_rank=5000
2 days, 23:45:23.678630 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:23.876897 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:24.083621 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:24.335473 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:25.257596 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:25.258155 INFO: Using score_cutoff 16.168829332351685 (fac=0.99, q=1)
2 days, 23:45:25.258544 INFO: Updating optimization_manager: fwhm_rt             : 2.51440691947937 -> 2.5098390579223633
2 days, 23:45:25.258648 INFO: Updating optimization_manager: fwhm_mobility       : 0.003866900224238634 -> 0.0038544442504644394
2 days, 23:45:25.258737 INFO: Updating optimization_manager: score_cutoff        : 16.353779443931582 -> 16.168829332351685
2 days, 23:45:25.258831 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:25.260008 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:25.261547 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:25.262430 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:25.264589 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:25.264715 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2 days, 23:45:25.266733 INFO: Updating optimization_manager: rt_error            : 10.555245695995211 -> 11.184084754520212
2 days, 23:45:25.266870 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 11.1841.
2 days, 23:45:25.266968 INFO: ==============================================
2 days, 23:45:25.267070 INFO: Starting optimization step 9.
2 days, 23:45:25.267164 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:25.267251 INFO: Using python extraction backend
2 days, 23:45:25.267382 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:25.267472 INFO: === Search parameters used ===
2 days, 23:45:25.267545 INFO: rt_error       : 11.184084754520212
2 days, 23:45:25.267617 INFO: mobility_error : 0.1
2 days, 23:45:25.267685 INFO: num_candidates : 3
2 days, 23:45:25.267756 INFO: ms1_error      : 15.0
2 days, 23:45:25.267822 INFO: ms2_error      : 15.0
2 days, 23:45:25.267887 INFO: fwhm_rt        : 2.5098390579223633
2 days, 23:45:25.267953 INFO: quant_window   : 3
2 days, 23:45:25.268024 INFO: ==============================================
2 days, 23:45:25.268893 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:25.268950 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:25.269007 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:45:25.269048 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.09
2 days, 23:45:25.274147 INFO: Starting candidate selection
2 days, 23:45:25.818889 INFO: Starting candidate scoring
2 days, 23:45:25.929230 INFO: Finished candidate processing
2 days, 23:45:25.929359 INFO: Collecting candidate features
2 days, 23:45:25.946075 WARNING: intensity_correlation has 28 NaNs ( 0.88 % out of 3182)
2 days, 23:45:25.946594 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3182)
2 days, 23:45:25.954571 INFO: Collecting fragment features
2 days, 23:45:25.960968 INFO: Finished candidate scoring
2 days, 23:45:25.964416 INFO: performing precursor FDR with 47 features
2 days, 23:45:25.964559 INFO: Decoy channel: -1
2 days, 23:45:25.964597 INFO: competitive: True
2 days, 23:45:25.969417 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:25.971835 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:45:25.971958 WARNING: dropped 26 decoy PSMs due to missing features
2 days, 23:45:25.973403 INFO: Estimating optimal hyperparameters - samples: 2,522, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:25.973539 INFO: Using random state 685176 for train-test-split
2 days, 23:45:26.316109 INFO: Test AUC: 0.848
2 days, 23:45:26.316235 INFO: Train AUC: 0.875
2 days, 23:45:26.316274 INFO: AUC difference: 3.14%
2 days, 23:45:26.676129 INFO: Resetting torch num_threads to 80
2 days, 23:45:26.676724 PROGRESS: === Extracted 3182 precursors and 22536 fragments ===
2 days, 23:45:26.677189 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:26.677849 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:26.677974 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:26.678071 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:45:26.678149 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:45:26.678221 PROGRESS: 
2 days, 23:45:26.678290 PROGRESS: Precursor Summary:
2 days, 23:45:26.679749 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   561; 0.001 FDR:   451
2 days, 23:45:26.679867 PROGRESS: 
2 days, 23:45:26.679960 PROGRESS: Protein Summary:
2 days, 23:45:26.681984 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   412; 0.001 FDR:   336
2 days, 23:45:26.682115 PROGRESS: =========================================================================
2 days, 23:45:26.682312 INFO: Target number of precursors reached.
2 days, 23:45:26.691642 INFO: fragments_df: keeping 5000 of 22536 [sum(precursor_idx_mask)=13210 sum(mass_error_mask)=22536 stop_rank=5000
2 days, 23:45:26.696847 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:26.911434 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:27.119916 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:27.305002 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:28.251478 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:28.252056 INFO: Using score_cutoff 16.350351676940917 (fac=0.99, q=1)
2 days, 23:45:28.252515 INFO: Updating optimization_manager: fwhm_rt             : 2.5098390579223633 -> 2.514594554901123
2 days, 23:45:28.252648 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038544442504644394 -> 0.0038670883513987064
2 days, 23:45:28.252761 INFO: Updating optimization_manager: score_cutoff        : 16.168829332351685 -> 16.350351676940917
2 days, 23:45:28.252882 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:28.254399 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:28.256145 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:28.257254 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:28.259458 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:28.259574 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
2 days, 23:45:28.261524 INFO: Updating optimization_manager: rt_error            : 11.184084754520212 -> 10.5605466791576
2 days, 23:45:28.261672 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 10.5605.
2 days, 23:45:28.261758 INFO: ==============================================
2 days, 23:45:28.261876 INFO: Starting optimization step 10.
2 days, 23:45:28.261967 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:28.262053 INFO: Using python extraction backend
2 days, 23:45:28.262199 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:28.262304 INFO: === Search parameters used ===
2 days, 23:45:28.262387 INFO: rt_error       : 10.5605466791576
2 days, 23:45:28.262461 INFO: mobility_error : 0.1
2 days, 23:45:28.262534 INFO: num_candidates : 3
2 days, 23:45:28.262615 INFO: ms1_error      : 15.0
2 days, 23:45:28.262693 INFO: ms2_error      : 15.0
2 days, 23:45:28.262752 INFO: fwhm_rt        : 2.514594554901123
2 days, 23:45:28.262816 INFO: quant_window   : 3
2 days, 23:45:28.262880 INFO: ==============================================
2 days, 23:45:28.265025 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:28.265080 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:28.265134 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:45:28.265175 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.10
2 days, 23:45:28.271299 INFO: Starting candidate selection
2 days, 23:45:28.821917 INFO: Starting candidate scoring
2 days, 23:45:28.919952 INFO: Finished candidate processing
2 days, 23:45:28.920065 INFO: Collecting candidate features
2 days, 23:45:28.932768 WARNING: intensity_correlation has 23 NaNs ( 0.73 % out of 3170)
2 days, 23:45:28.933023 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3170)
2 days, 23:45:28.937976 INFO: Collecting fragment features
2 days, 23:45:28.942509 INFO: Finished candidate scoring
2 days, 23:45:28.944741 INFO: performing precursor FDR with 47 features
2 days, 23:45:28.944855 INFO: Decoy channel: -1
2 days, 23:45:28.944890 INFO: competitive: True
2 days, 23:45:28.948747 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:28.950680 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:45:28.950746 WARNING: dropped 22 decoy PSMs due to missing features
2 days, 23:45:28.951944 INFO: Estimating optimal hyperparameters - samples: 2,516, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:28.952039 INFO: Using random state 685176 for train-test-split
2 days, 23:45:29.189906 INFO: Test AUC: 0.869
2 days, 23:45:29.190028 INFO: Train AUC: 0.872
2 days, 23:45:29.190065 INFO: AUC difference: 0.35%
2 days, 23:45:29.491433 INFO: Resetting torch num_threads to 80
2 days, 23:45:29.492111 PROGRESS: === Extracted 3170 precursors and 22425 fragments ===
2 days, 23:45:29.492615 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:29.493334 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:29.493441 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:29.493512 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:45:29.493574 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:45:29.493634 PROGRESS: 
2 days, 23:45:29.493690 PROGRESS: Precursor Summary:
2 days, 23:45:29.495090 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   562; 0.001 FDR:   477
2 days, 23:45:29.495208 PROGRESS: 
2 days, 23:45:29.495278 PROGRESS: Protein Summary:
2 days, 23:45:29.496924 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   412; 0.001 FDR:   354
2 days, 23:45:29.497031 PROGRESS: =========================================================================
2 days, 23:45:29.497234 INFO: Target number of precursors reached.
2 days, 23:45:29.505409 INFO: fragments_df: keeping 5000 of 22425 [sum(precursor_idx_mask)=13202 sum(mass_error_mask)=22425 stop_rank=5000
2 days, 23:45:29.510024 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:29.714220 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:29.965754 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:30.192680 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:30.984077 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:30.984589 INFO: Using score_cutoff 16.322040711021426 (fac=0.99, q=1)
2 days, 23:45:30.984937 INFO: Updating optimization_manager: fwhm_rt             : 2.514594554901123 -> 2.5113070011138916
2 days, 23:45:30.985031 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038670883513987064 -> 0.0038655344396829605
2 days, 23:45:30.985101 INFO: Updating optimization_manager: score_cutoff        : 16.350351676940917 -> 16.322040711021426
2 days, 23:45:30.985173 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:30.986322 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:30.987711 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:30.988531 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:30.990534 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:30.990663 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
2 days, 23:45:30.992652 INFO: Updating optimization_manager: rt_error            : 10.5605466791576 -> 10.441351134680144
2 days, 23:45:30.992786 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 10.4414.
2 days, 23:45:30.992888 INFO: ==============================================
2 days, 23:45:30.992995 INFO: Starting optimization step 11.
2 days, 23:45:30.993089 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:30.993182 INFO: Using python extraction backend
2 days, 23:45:30.993327 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:30.993440 INFO: === Search parameters used ===
2 days, 23:45:30.993528 INFO: rt_error       : 10.441351134680144
2 days, 23:45:30.993604 INFO: mobility_error : 0.1
2 days, 23:45:30.993675 INFO: num_candidates : 3
2 days, 23:45:30.993742 INFO: ms1_error      : 15.0
2 days, 23:45:30.993808 INFO: ms2_error      : 15.0
2 days, 23:45:30.993881 INFO: fwhm_rt        : 2.5113070011138916
2 days, 23:45:30.993954 INFO: quant_window   : 3
2 days, 23:45:30.994020 INFO: ==============================================
2 days, 23:45:30.994961 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:30.995017 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:30.995069 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:45:30.995117 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.09
2 days, 23:45:31.026042 INFO: Starting candidate selection
2 days, 23:45:31.585374 INFO: Starting candidate scoring
2 days, 23:45:31.690485 INFO: Finished candidate processing
2 days, 23:45:31.690596 INFO: Collecting candidate features
2 days, 23:45:31.703731 WARNING: intensity_correlation has 23 NaNs ( 0.73 % out of 3170)
2 days, 23:45:31.703969 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3170)
2 days, 23:45:31.709283 INFO: Collecting fragment features
2 days, 23:45:31.714053 INFO: Finished candidate scoring
2 days, 23:45:31.716124 INFO: performing precursor FDR with 47 features
2 days, 23:45:31.716176 INFO: Decoy channel: -1
2 days, 23:45:31.716208 INFO: competitive: True
2 days, 23:45:31.719877 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:31.721701 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:45:31.721755 WARNING: dropped 22 decoy PSMs due to missing features
2 days, 23:45:31.722939 INFO: Estimating optimal hyperparameters - samples: 2,516, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:31.723037 INFO: Using random state 685176 for train-test-split
2 days, 23:45:32.026544 INFO: Test AUC: 0.855
2 days, 23:45:32.026645 INFO: Train AUC: 0.871
2 days, 23:45:32.026677 INFO: AUC difference: 1.91%
2 days, 23:45:32.284415 INFO: Resetting torch num_threads to 80
2 days, 23:45:32.285169 PROGRESS: === Extracted 3170 precursors and 22427 fragments ===
2 days, 23:45:32.285740 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:45:32.286618 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:32.286763 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:32.286855 PROGRESS: Target precursors: 585 (97.50%)
2 days, 23:45:32.286938 PROGRESS: Decoy precursors: 15 (2.50%)
2 days, 23:45:32.287018 PROGRESS: 
2 days, 23:45:32.287096 PROGRESS: Precursor Summary:
2 days, 23:45:32.288863 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   554; 0.001 FDR:   452
2 days, 23:45:32.288996 PROGRESS: 
2 days, 23:45:32.289092 PROGRESS: Protein Summary:
2 days, 23:45:32.291176 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   407; 0.001 FDR:   337
2 days, 23:45:32.291293 PROGRESS: =========================================================================
2 days, 23:45:32.291481 INFO: Target number of precursors reached.
2 days, 23:45:32.297746 INFO: fragments_df: keeping 5000 of 22427 [sum(precursor_idx_mask)=13077 sum(mass_error_mask)=22427 stop_rank=5000
2 days, 23:45:32.302546 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:32.527185 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:32.712384 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:32.966701 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:33.929615 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:33.930193 INFO: Using score_cutoff 16.65918236274719 (fac=0.99, q=1)
2 days, 23:45:33.930728 INFO: Updating optimization_manager: fwhm_rt             : 2.5113070011138916 -> 2.5147805213928223
2 days, 23:45:33.930855 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038655344396829605 -> 0.003866900224238634
2 days, 23:45:33.930941 INFO: Updating optimization_manager: score_cutoff        : 16.322040711021426 -> 16.65918236274719
2 days, 23:45:33.931027 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:33.932517 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:33.935273 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:33.936570 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:33.939185 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:33.939336 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
2 days, 23:45:33.940796 INFO: Updating optimization_manager: rt_error            : 10.441351134680144 -> 10.441351134680144
2 days, 23:45:33.941004 INFO: Updating optimization_manager: classifier_version  : 3 -> 15
2 days, 23:45:33.941171 INFO: Updating optimization_manager: score_cutoff        : 16.65918236274719 -> 16.65918236274719
2 days, 23:45:33.941334 INFO: Updating optimization_manager: fwhm_rt             : 2.5147805213928223 -> 2.5147805213928223
2 days, 23:45:33.941494 INFO: Updating optimization_manager: fwhm_mobility       : 0.003866900224238634 -> 0.003866900224238634
2 days, 23:45:33.941649 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 10.4414 found after 12 searches.
2 days, 23:45:33.941758 INFO: ==============================================
2 days, 23:45:33.941893 PROGRESS: Optimization finished for rt_error.
2 days, 23:45:33.946292 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:33.947515 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:33.949297 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:33.950472 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:33.953006 INFO: Starting optimization step 0.
2 days, 23:45:33.953138 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:33.953248 INFO: Using python extraction backend
2 days, 23:45:33.953418 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:33.953532 INFO: === Search parameters used ===
2 days, 23:45:33.953622 INFO: rt_error       : 10.441351134680144
2 days, 23:45:33.953724 INFO: mobility_error : 0.1
2 days, 23:45:33.953818 INFO: num_candidates : 3
2 days, 23:45:33.953928 INFO: ms1_error      : 15.0
2 days, 23:45:33.954031 INFO: ms2_error      : 15.0
2 days, 23:45:33.954114 INFO: fwhm_rt        : 2.5147805213928223
2 days, 23:45:33.954196 INFO: quant_window   : 3
2 days, 23:45:33.954278 INFO: ==============================================
2 days, 23:45:33.955446 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:33.955518 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:33.955584 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:45:33.955630 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.10
2 days, 23:45:33.966076 INFO: Starting candidate selection
2 days, 23:45:34.537418 INFO: Starting candidate scoring
2 days, 23:45:34.643210 INFO: Finished candidate processing
2 days, 23:45:34.643337 INFO: Collecting candidate features
2 days, 23:45:34.660049 WARNING: intensity_correlation has 22 NaNs ( 0.69 % out of 3168)
2 days, 23:45:34.660363 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3168)
2 days, 23:45:34.667989 INFO: Collecting fragment features
2 days, 23:45:34.673370 INFO: Finished candidate scoring
2 days, 23:45:34.676361 INFO: performing precursor FDR with 47 features
2 days, 23:45:34.676432 INFO: Decoy channel: -1
2 days, 23:45:34.676475 INFO: competitive: True
2 days, 23:45:34.680875 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:34.682779 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:45:34.682846 WARNING: dropped 21 decoy PSMs due to missing features
2 days, 23:45:34.683851 INFO: Estimating optimal hyperparameters - samples: 2,516, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:34.683932 INFO: Using random state 881116 for train-test-split
2 days, 23:45:34.931468 INFO: Test AUC: 0.864
2 days, 23:45:34.931600 INFO: Train AUC: 0.883
2 days, 23:45:34.931655 INFO: AUC difference: 2.11%
2 days, 23:45:35.256753 INFO: Resetting torch num_threads to 80
2 days, 23:45:35.257550 PROGRESS: === Extracted 3168 precursors and 22401 fragments ===
2 days, 23:45:35.258032 INFO: === FDR correction performed with classifier version 15 ===
2 days, 23:45:35.258701 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:35.258807 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:35.258895 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:45:35.258972 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:45:35.259042 PROGRESS: 
2 days, 23:45:35.259108 PROGRESS: Precursor Summary:
2 days, 23:45:35.260306 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   569; 0.001 FDR:   468
2 days, 23:45:35.260415 PROGRESS: 
2 days, 23:45:35.260497 PROGRESS: Protein Summary:
2 days, 23:45:35.261894 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   419; 0.001 FDR:   350
2 days, 23:45:35.262007 PROGRESS: =========================================================================
2 days, 23:45:35.262260 INFO: Target number of precursors reached.
2 days, 23:45:35.268250 INFO: fragments_df: keeping 5000 of 22401 [sum(precursor_idx_mask)=13305 sum(mass_error_mask)=22401 stop_rank=5000
2 days, 23:45:35.272264 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:35.448315 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:35.625741 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:35.878497 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:36.658070 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:36.658577 INFO: Using score_cutoff 15.426594370651245 (fac=0.99, q=1)
2 days, 23:45:36.658952 INFO: Updating optimization_manager: fwhm_rt             : 2.5147805213928223 -> 2.4952211380004883
2 days, 23:45:36.659060 INFO: Updating optimization_manager: fwhm_mobility       : 0.003866900224238634 -> 0.0037796173710376024
2 days, 23:45:36.659149 INFO: Updating optimization_manager: score_cutoff        : 16.65918236274719 -> 15.426594370651245
2 days, 23:45:36.659247 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:36.660400 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:36.661890 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:36.662760 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:36.664787 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:36.664919 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:45:36.666652 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06014269872777741
2 days, 23:45:36.666796 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0601.
2 days, 23:45:36.666897 INFO: ==============================================
2 days, 23:45:36.667002 INFO: Starting optimization step 1.
2 days, 23:45:36.667099 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:36.667202 INFO: Using python extraction backend
2 days, 23:45:36.667340 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:36.667435 INFO: === Search parameters used ===
2 days, 23:45:36.667514 INFO: rt_error       : 10.441351134680144
2 days, 23:45:36.667589 INFO: mobility_error : 0.06014269872777741
2 days, 23:45:36.667661 INFO: num_candidates : 3
2 days, 23:45:36.667733 INFO: ms1_error      : 15.0
2 days, 23:45:36.667799 INFO: ms2_error      : 15.0
2 days, 23:45:36.667865 INFO: fwhm_rt        : 2.4952211380004883
2 days, 23:45:36.667929 INFO: quant_window   : 3
2 days, 23:45:36.667998 INFO: ==============================================
2 days, 23:45:36.668922 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:36.668978 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:36.669039 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:45:36.669078 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.05
2 days, 23:45:36.674685 INFO: Starting candidate selection
2 days, 23:45:37.199919 INFO: Starting candidate scoring
2 days, 23:45:37.297749 INFO: Finished candidate processing
2 days, 23:45:37.297861 INFO: Collecting candidate features
2 days, 23:45:37.310186 WARNING: intensity_correlation has 20 NaNs ( 0.64 % out of 3144)
2 days, 23:45:37.310429 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3144)
2 days, 23:45:37.315412 INFO: Collecting fragment features
2 days, 23:45:37.319801 INFO: Finished candidate scoring
2 days, 23:45:37.321800 INFO: performing precursor FDR with 47 features
2 days, 23:45:37.321914 INFO: Decoy channel: -1
2 days, 23:45:37.321953 INFO: competitive: True
2 days, 23:45:37.325640 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:37.327580 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:45:37.327644 WARNING: dropped 20 decoy PSMs due to missing features
2 days, 23:45:37.327691 WARNING: FDR calculation for 1648 target and 1475 decoy PSMs
2 days, 23:45:37.327720 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:45:37.328907 INFO: Estimating optimal hyperparameters - samples: 2,498, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:37.329051 INFO: Using random state 881116 for train-test-split
2 days, 23:45:37.566967 INFO: Test AUC: 0.876
2 days, 23:45:37.567102 INFO: Train AUC: 0.882
2 days, 23:45:37.567138 INFO: AUC difference: 0.67%
2 days, 23:45:37.871674 INFO: Resetting torch num_threads to 80
2 days, 23:45:37.872327 PROGRESS: === Extracted 3144 precursors and 22113 fragments ===
2 days, 23:45:37.872820 INFO: === FDR correction performed with classifier version 15 ===
2 days, 23:45:37.873506 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:37.873605 PROGRESS: Total precursors accumulated: 600
2 days, 23:45:37.873676 PROGRESS: Target precursors: 585 (97.50%)
2 days, 23:45:37.873748 PROGRESS: Decoy precursors: 15 (2.50%)
2 days, 23:45:37.873813 PROGRESS: 
2 days, 23:45:37.873879 PROGRESS: Precursor Summary:
2 days, 23:45:37.875326 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   562; 0.001 FDR:   541
2 days, 23:45:37.875430 PROGRESS: 
2 days, 23:45:37.875498 PROGRESS: Protein Summary:
2 days, 23:45:37.877189 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   416; 0.001 FDR:   401
2 days, 23:45:37.877292 PROGRESS: =========================================================================
2 days, 23:45:37.877459 INFO: Target number of precursors reached.
2 days, 23:45:37.885554 INFO: fragments_df: keeping 5000 of 22113 [sum(precursor_idx_mask)=13205 sum(mass_error_mask)=22113 stop_rank=5000
2 days, 23:45:37.889558 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:38.143295 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:38.364848 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:38.565164 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:39.427124 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:39.427611 INFO: Using score_cutoff 16.58715363521576 (fac=0.99, q=1)
2 days, 23:45:39.428014 INFO: Updating optimization_manager: fwhm_rt             : 2.4952211380004883 -> 2.504268169403076
2 days, 23:45:39.428114 INFO: Updating optimization_manager: fwhm_mobility       : 0.0037796173710376024 -> 0.0038108243606984615
2 days, 23:45:39.428185 INFO: Updating optimization_manager: score_cutoff        : 15.426594370651245 -> 16.58715363521576
2 days, 23:45:39.428257 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:39.429435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:39.431062 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:39.432006 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:39.434115 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:39.434263 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:45:39.435988 INFO: Updating optimization_manager: mobility_error      : 0.06014269872777741 -> 0.04872698616609722
2 days, 23:45:39.436112 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0487.
2 days, 23:45:39.436206 INFO: ==============================================
2 days, 23:45:39.436297 INFO: Starting optimization step 2.
2 days, 23:45:39.436373 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:45:39.436450 INFO: Using python extraction backend
2 days, 23:45:39.436569 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:45:39.436647 INFO: === Search parameters used ===
2 days, 23:45:39.436711 INFO: rt_error       : 10.441351134680144
2 days, 23:45:39.436767 INFO: mobility_error : 0.04872698616609722
2 days, 23:45:39.436821 INFO: num_candidates : 3
2 days, 23:45:39.436872 INFO: ms1_error      : 15.0
2 days, 23:45:39.436923 INFO: ms2_error      : 15.0
2 days, 23:45:39.436975 INFO: fwhm_rt        : 2.504268169403076
2 days, 23:45:39.437026 INFO: quant_window   : 3
2 days, 23:45:39.437082 INFO: ==============================================
2 days, 23:45:39.438064 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:39.438121 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:39.438162 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:45:39.438193 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.07
2 days, 23:45:39.502056 INFO: Starting candidate selection
2 days, 23:45:39.991986 INFO: Starting candidate scoring
2 days, 23:45:40.087252 INFO: Finished candidate processing
2 days, 23:45:40.087389 INFO: Collecting candidate features
2 days, 23:45:40.104064 WARNING: intensity_correlation has 24 NaNs ( 0.77 % out of 3134)
2 days, 23:45:40.104419 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3134)
2 days, 23:45:40.112123 INFO: Collecting fragment features
2 days, 23:45:40.117857 INFO: Finished candidate scoring
2 days, 23:45:40.121097 INFO: performing precursor FDR with 47 features
2 days, 23:45:40.121180 INFO: Decoy channel: -1
2 days, 23:45:40.121221 INFO: competitive: True
2 days, 23:45:40.125476 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:40.127077 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:45:40.127141 WARNING: dropped 23 decoy PSMs due to missing features
2 days, 23:45:40.127204 WARNING: FDR calculation for 1642 target and 1467 decoy PSMs
2 days, 23:45:40.127247 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:45:40.128286 INFO: Estimating optimal hyperparameters - samples: 2,487, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:45:40.128388 INFO: Using random state 881116 for train-test-split
2 days, 23:45:40.433941 INFO: Test AUC: 0.880
2 days, 23:45:40.434086 INFO: Train AUC: 0.882
2 days, 23:45:40.434134 INFO: AUC difference: 0.12%
2 days, 23:45:40.778531 INFO: Resetting torch num_threads to 80
2 days, 23:45:40.779269 PROGRESS: === Extracted 3134 precursors and 21875 fragments ===
2 days, 23:45:40.779886 INFO: === FDR correction performed with classifier version 15 ===
2 days, 23:45:40.780851 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:40.780975 PROGRESS: Total precursors accumulated: 599
2 days, 23:45:40.781083 PROGRESS: Target precursors: 582 (97.16%)
2 days, 23:45:40.781176 PROGRESS: Decoy precursors: 17 (2.84%)
2 days, 23:45:40.781265 PROGRESS: 
2 days, 23:45:40.781355 PROGRESS: Precursor Summary:
2 days, 23:45:40.783299 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   555; 0.001 FDR:   517
2 days, 23:45:40.783436 PROGRESS: 
2 days, 23:45:40.783533 PROGRESS: Protein Summary:
2 days, 23:45:40.785862 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   411; 0.001 FDR:   385
2 days, 23:45:40.786018 PROGRESS: =========================================================================
2 days, 23:45:40.786226 INFO: Target number of precursors reached.
2 days, 23:45:40.795457 INFO: fragments_df: keeping 5000 of 21875 [sum(precursor_idx_mask)=12967 sum(mass_error_mask)=21875 stop_rank=5000
2 days, 23:45:40.800326 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:40.998667 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:41.205026 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:41.428300 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:42.349517 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:45:42.350118 INFO: Using score_cutoff 16.58841154747009 (fac=0.99, q=1)
2 days, 23:45:42.350610 INFO: Updating optimization_manager: fwhm_rt             : 2.504268169403076 -> 2.5098390579223633
2 days, 23:45:42.350735 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038108243606984615 -> 0.0038667123299092054
2 days, 23:45:42.350851 INFO: Updating optimization_manager: score_cutoff        : 16.58715363521576 -> 16.58841154747009
2 days, 23:45:42.350961 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:42.352462 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:42.354226 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:42.355418 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:42.357837 INFO: === checking if optimization conditions were reached ===
2 days, 23:45:42.357980 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:45:42.358993 INFO: Updating optimization_manager: mobility_error      : 0.04872698616609722 -> 0.1
2 days, 23:45:42.359166 INFO: Updating optimization_manager: classifier_version  : 15 -> 16
2 days, 23:45:42.359315 INFO: Updating optimization_manager: score_cutoff        : 16.58841154747009 -> 15.426594370651245
2 days, 23:45:42.359467 INFO: Updating optimization_manager: fwhm_rt             : 2.5098390579223633 -> 2.4952211380004883
2 days, 23:45:42.359601 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038667123299092054 -> 0.0037796173710376024
2 days, 23:45:42.359734 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
2 days, 23:45:42.359822 INFO: ==============================================
2 days, 23:45:42.359923 PROGRESS: Optimization finished for mobility_error.
2 days, 23:45:42.363608 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:42.364469 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:42.365925 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:42.366806 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:42.368849 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:45:42.368960 PROGRESS: ==============================================
2 days, 23:45:42.369061 PROGRESS: ms2_error      : 15.0000
2 days, 23:45:42.369178 PROGRESS: ms1_error      : 15.0000
2 days, 23:45:42.369268 PROGRESS: rt_error       : 10.4414
2 days, 23:45:42.369345 PROGRESS: mobility_error : 0.1000
2 days, 23:45:42.369416 PROGRESS: ==============================================
2 days, 23:45:42.370334 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:45:42.374297 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:45:42.391165 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:45:42.395073 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:45:42.441761 INFO: Using python extraction backend
2 days, 23:45:42.442290 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:45:42.442475 INFO: === Search parameters used ===
2 days, 23:45:42.442619 INFO: rt_error       : 10.441351134680144
2 days, 23:45:42.442741 INFO: mobility_error : 0.1
2 days, 23:45:42.442859 INFO: num_candidates : 3
2 days, 23:45:42.442965 INFO: ms1_error      : 15.0
2 days, 23:45:42.443089 INFO: ms2_error      : 15.0
2 days, 23:45:42.443212 INFO: fwhm_rt        : 2.4952211380004883
2 days, 23:45:42.443320 INFO: quant_window   : 3
2 days, 23:45:42.443453 INFO: ==============================================
2 days, 23:45:42.452492 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:42.452752 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:42.452935 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:45:42.453069 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.05
2 days, 23:45:42.478347 INFO: Starting candidate selection
2 days, 23:45:45.234133 INFO: Removed 20740 precursors with score below cutoff 15.426594370651245
2 days, 23:45:45.570359 INFO: Starting candidate scoring
2 days, 23:45:46.536563 INFO: Finished candidate processing
2 days, 23:45:46.536683 INFO: Collecting candidate features
2 days, 23:45:46.630681 WARNING: intensity_correlation has 128 NaNs ( 0.23 % out of 56295)
2 days, 23:45:46.630990 WARNING: height_correlation has 3 NaNs ( 0.01 % out of 56295)
2 days, 23:45:46.637199 INFO: Collecting fragment features
2 days, 23:45:46.681421 INFO: Finished candidate scoring
2 days, 23:45:46.714919 INFO: === Performing FDR correction with classifier version 16 ===
2 days, 23:45:46.715265 INFO: performing precursor FDR with 47 features
2 days, 23:45:46.715305 INFO: Decoy channel: -1
2 days, 23:45:46.715331 INFO: competitive: True
2 days, 23:45:46.730156 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:45:46.738735 WARNING: dropped 32 target PSMs due to missing features
2 days, 23:45:46.738868 WARNING: dropped 98 decoy PSMs due to missing features
2 days, 23:45:46.738928 WARNING: FDR calculation for 34332 target and 21833 decoy PSMs
2 days, 23:45:46.738981 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:45:46.748626 INFO: Estimating optimal hyperparameters - samples: 44,932, batch_size: 184, learning_rate: 2.12e-04
2 days, 23:45:46.748864 INFO: Using random state 33712 for train-test-split
2 days, 23:45:50.019652 INFO: Test AUC: 0.899
2 days, 23:45:50.019774 INFO: Train AUC: 0.906
2 days, 23:45:50.019809 INFO: AUC difference: 0.76%
2 days, 23:45:50.375070 INFO: Resetting torch num_threads to 80
2 days, 23:45:50.379710 INFO: Removing fragments below FDR threshold
2 days, 23:45:50.393807 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:45:50.394068 PROGRESS: Total precursors accumulated: 13,089
2 days, 23:45:50.394191 PROGRESS: Target precursors: 12,960 (99.01%)
2 days, 23:45:50.394297 PROGRESS: Decoy precursors: 129 (0.99%)
2 days, 23:45:50.394393 PROGRESS: 
2 days, 23:45:50.394486 PROGRESS: Precursor Summary:
2 days, 23:45:50.400212 PROGRESS: Channel   0:	 0.050 FDR: 12,960; 0.010 FDR: 12,960; 0.001 FDR: 12,044
2 days, 23:45:50.400384 PROGRESS: 
2 days, 23:45:50.400455 PROGRESS: Protein Summary:
2 days, 23:45:50.406452 PROGRESS: Channel   0:	 0.050 FDR: 1,680; 0.010 FDR: 1,680; 0.001 FDR: 1,660
2 days, 23:45:50.406606 PROGRESS: =========================================================================
2 days, 23:45:50.407736 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R2/psm.parquet
2 days, 23:45:50.482527 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R2/frag.parquet
2 days, 23:45:50.548534 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R2
2 days, 23:45:50.556423 PROGRESS: Loading raw file 3/12: A9_G_DIA_nLC_tTOF_R3 
2 days, 23:45:50.556533 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:45:50.556602 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R3/figures
2 days, 23:45:50.556778 INFO: Initializing TimingManager
2 days, 23:45:50.557175 INFO: Initializing RawFileManager
2 days, 23:45:50.557287 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:50.557340 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:50.557374 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:50.790083 INFO: Reading 22,623 frames with 375,308,789 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:54.568435 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d...
2 days, 23:45:54.569738 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:54.571876 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:54.572145 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:54.572741 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:54.575202 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:54.606616 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:54.607009 INFO: Indexing quadrupole dimension
2 days, 23:45:54.755862 INFO: Transposing detector events
2 days, 23:45:57.224436 INFO: Finished transposing data
2 days, 23:45:57.224596 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
2 days, 23:45:57.225066 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:45:57.225136 INFO: RT duration (sec)   : 2400.0
2 days, 23:45:57.225180 INFO: RT duration (min)   : 40.0
2 days, 23:45:57.225223 INFO: Cycle len (scans)   : 12
2 days, 23:45:57.225265 INFO: Cycle len (sec)     : 1.27
2 days, 23:45:57.225305 INFO: Number of cycles    : 1885
2 days, 23:45:57.225344 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:45:57.225406 INFO: Creating DIA data object took: 6.668118476867676
2 days, 23:45:57.235415 INFO: Initializing CalibrationManager
2 days, 23:45:57.235700 INFO: Setting up calibration estimators ..
2 days, 23:45:57.235780 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:45:57.235860 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:45:57.235945 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:45:57.236016 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:45:57.236087 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:45:57.236160 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:45:57.236226 INFO: Done setting up calibration estimators.
2 days, 23:45:57.236358 INFO: Initializing OptimizationManager
2 days, 23:45:57.236473 INFO: initial parameter: ms1_error = 30
2 days, 23:45:57.236540 INFO: initial parameter: ms2_error = 30
2 days, 23:45:57.236602 INFO: initial parameter: rt_error = 1199.9776575
2 days, 23:45:57.236661 INFO: initial parameter: mobility_error = 0.1
2 days, 23:45:57.236719 INFO: initial parameter: num_candidates = 1
2 days, 23:45:57.236777 INFO: initial parameter: fwhm_rt = 5
2 days, 23:45:57.236835 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:45:57.236896 INFO: initial parameter: score_cutoff = 0
2 days, 23:45:57.236945 INFO: initial parameter: classifier_version = -1
2 days, 23:45:57.237018 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R3
2 days, 23:45:57.237210 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:45:57.237243 INFO: Initializing FDRManager
2 days, 23:45:57.237274 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:45:57.244567 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:45:57.249654 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:45:57.250078 INFO: Updating optimization_manager: rt_error            : 1199.9776575 -> 1199.9776575
2 days, 23:45:57.250218 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:45:57.250478 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:45:57.250599 PROGRESS: Starting initial search for precursors.
2 days, 23:45:57.250723 INFO: Starting optimization step 0.
2 days, 23:45:57.250821 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:45:57.250932 INFO: Using python extraction backend
2 days, 23:45:57.251094 PROGRESS: Extracting batch of 399 precursors
2 days, 23:45:57.251204 INFO: === Search parameters used ===
2 days, 23:45:57.251291 INFO: rt_error       : 1199.9776575
2 days, 23:45:57.251373 INFO: mobility_error : 0.1
2 days, 23:45:57.251452 INFO: num_candidates : 1
2 days, 23:45:57.251533 INFO: ms1_error      : 30
2 days, 23:45:57.251620 INFO: ms2_error      : 30
2 days, 23:45:57.251696 INFO: fwhm_rt        : 5
2 days, 23:45:57.251781 INFO: quant_window   : 3
2 days, 23:45:57.251863 INFO: ==============================================
2 days, 23:45:57.252867 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:45:57.252931 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:45:57.252991 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:45:57.253035 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:45:57.282064 INFO: Starting candidate selection
2 days, 23:46:00.865358 INFO: Starting candidate scoring
2 days, 23:46:00.921056 INFO: Finished candidate processing
2 days, 23:46:00.921169 INFO: Collecting candidate features
2 days, 23:46:00.933843 INFO: Collecting fragment features
2 days, 23:46:00.936645 INFO: Finished candidate scoring
2 days, 23:46:00.937676 INFO: performing precursor FDR with 47 features
2 days, 23:46:00.937727 INFO: Decoy channel: -1
2 days, 23:46:00.937760 INFO: competitive: True
2 days, 23:46:00.939261 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:46:00.941250 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:46:00.942208 INFO: Using random state 735192 for train-test-split
2 days, 23:46:00.969652 INFO: Test AUC: 0.528
2 days, 23:46:00.969739 INFO: Train AUC: 0.561
2 days, 23:46:00.969771 INFO: AUC difference: 5.78%
2 days, 23:46:00.969794 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:46:01.264434 INFO: Resetting torch num_threads to 80
2 days, 23:46:01.264919 PROGRESS: === Extracted 399 precursors and 3680 fragments ===
2 days, 23:46:01.265357 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:46:01.265962 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:46:01.266061 PROGRESS: Total precursors accumulated: 200
2 days, 23:46:01.266124 PROGRESS: Target precursors: 107 (53.50%)
2 days, 23:46:01.266179 PROGRESS: Decoy precursors: 93 (46.50%)
2 days, 23:46:01.266229 PROGRESS: 
2 days, 23:46:01.266276 PROGRESS: Precursor Summary:
2 days, 23:46:01.267239 PROGRESS: Channel   0:	 0.050 FDR:    18; 0.010 FDR:    18; 0.001 FDR:    18
2 days, 23:46:01.267331 PROGRESS: 
2 days, 23:46:01.267390 PROGRESS: Protein Summary:
2 days, 23:46:01.268456 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
2 days, 23:46:01.268547 PROGRESS: =========================================================================
2 days, 23:46:01.268659 INFO: Target number of precursors not reached yet.
2 days, 23:46:01.271582 INFO: Starting optimization step 1.
2 days, 23:46:01.271702 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:46:01.271800 INFO: Using python extraction backend
2 days, 23:46:01.271937 PROGRESS: Extracting batch of 798 precursors
2 days, 23:46:01.272030 INFO: === Search parameters used ===
2 days, 23:46:01.272109 INFO: rt_error       : 1199.9776575
2 days, 23:46:01.272178 INFO: mobility_error : 0.1
2 days, 23:46:01.272245 INFO: num_candidates : 1
2 days, 23:46:01.272307 INFO: ms1_error      : 30
2 days, 23:46:01.272368 INFO: ms2_error      : 30
2 days, 23:46:01.272428 INFO: fwhm_rt        : 5
2 days, 23:46:01.272488 INFO: quant_window   : 3
2 days, 23:46:01.272547 INFO: ==============================================
2 days, 23:46:01.273233 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:46:01.273282 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:46:01.273321 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:46:01.273352 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:46:01.300102 INFO: Starting candidate selection
2 days, 23:46:06.221168 INFO: Starting candidate scoring
2 days, 23:46:06.283854 INFO: Finished candidate processing
2 days, 23:46:06.283970 INFO: Collecting candidate features
2 days, 23:46:06.295629 INFO: Collecting fragment features
2 days, 23:46:06.298329 INFO: Finished candidate scoring
2 days, 23:46:06.300580 INFO: performing precursor FDR with 47 features
2 days, 23:46:06.300656 INFO: Decoy channel: -1
2 days, 23:46:06.300693 INFO: competitive: True
2 days, 23:46:06.303943 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:46:06.306161 INFO: Estimating optimal hyperparameters - samples: 957, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:46:06.306292 INFO: Using random state 680827 for train-test-split
2 days, 23:46:06.392989 INFO: Test AUC: 0.810
2 days, 23:46:06.393092 INFO: Train AUC: 0.772
2 days, 23:46:06.393125 INFO: AUC difference: 4.88%
2 days, 23:46:06.678454 INFO: Resetting torch num_threads to 80
2 days, 23:46:06.679725 PROGRESS: === Extracted 1197 precursors and 11323 fragments ===
2 days, 23:46:06.680149 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:46:06.680784 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:46:06.680880 PROGRESS: Total precursors accumulated: 600
2 days, 23:46:06.680947 PROGRESS: Target precursors: 474 (79.00%)
2 days, 23:46:06.681010 PROGRESS: Decoy precursors: 126 (21.00%)
2 days, 23:46:06.681062 PROGRESS: 
2 days, 23:46:06.681111 PROGRESS: Precursor Summary:
2 days, 23:46:06.682242 PROGRESS: Channel   0:	 0.050 FDR:   257; 0.010 FDR:   180; 0.001 FDR:   176
2 days, 23:46:06.682341 PROGRESS: 
2 days, 23:46:06.682400 PROGRESS: Protein Summary:
2 days, 23:46:06.683607 PROGRESS: Channel   0:	 0.050 FDR:   195; 0.010 FDR:   135; 0.001 FDR:   132
2 days, 23:46:06.683719 PROGRESS: =========================================================================
2 days, 23:46:06.683926 INFO: Target number of precursors not reached yet.
2 days, 23:46:06.688171 INFO: Starting optimization step 2.
2 days, 23:46:06.688305 PROGRESS: === Extracting elution groups 600 to 1400 ===
2 days, 23:46:06.688413 INFO: Using python extraction backend
2 days, 23:46:06.688541 PROGRESS: Extracting batch of 1599 precursors
2 days, 23:46:06.688632 INFO: === Search parameters used ===
2 days, 23:46:06.688704 INFO: rt_error       : 1199.9776575
2 days, 23:46:06.688771 INFO: mobility_error : 0.1
2 days, 23:46:06.688839 INFO: num_candidates : 1
2 days, 23:46:06.688912 INFO: ms1_error      : 30
2 days, 23:46:06.688989 INFO: ms2_error      : 30
2 days, 23:46:06.689060 INFO: fwhm_rt        : 5
2 days, 23:46:06.689123 INFO: quant_window   : 3
2 days, 23:46:06.689188 INFO: ==============================================
2 days, 23:46:06.690150 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:46:06.690214 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:46:06.690252 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:46:06.690283 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:46:06.714920 INFO: Starting candidate selection
2 days, 23:46:16.301270 INFO: Starting candidate scoring
2 days, 23:46:16.395937 INFO: Finished candidate processing
2 days, 23:46:16.396085 INFO: Collecting candidate features
2 days, 23:46:16.409338 INFO: Collecting fragment features
2 days, 23:46:16.412503 INFO: Finished candidate scoring
2 days, 23:46:16.415644 INFO: performing precursor FDR with 47 features
2 days, 23:46:16.415708 INFO: Decoy channel: -1
2 days, 23:46:16.415738 INFO: competitive: True
2 days, 23:46:16.419332 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:46:16.421904 INFO: Estimating optimal hyperparameters - samples: 2,232, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:46:16.422003 INFO: Using random state 884296 for train-test-split
2 days, 23:46:16.692029 INFO: Test AUC: 0.782
2 days, 23:46:16.692166 INFO: Train AUC: 0.785
2 days, 23:46:16.692217 INFO: AUC difference: 0.43%
2 days, 23:46:17.088305 INFO: Resetting torch num_threads to 80
2 days, 23:46:17.090904 PROGRESS: === Extracted 2791 precursors and 26536 fragments ===
2 days, 23:46:17.091542 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:46:17.092600 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:46:17.092732 PROGRESS: Total precursors accumulated: 1,400
2 days, 23:46:17.092834 PROGRESS: Target precursors: 1,090 (77.86%)
2 days, 23:46:17.092927 PROGRESS: Decoy precursors: 310 (22.14%)
2 days, 23:46:17.093010 PROGRESS: 
2 days, 23:46:17.093092 PROGRESS: Precursor Summary:
2 days, 23:46:17.094920 PROGRESS: Channel   0:	 0.050 FDR:   685; 0.010 FDR:   624; 0.001 FDR:   624
2 days, 23:46:17.095052 PROGRESS: 
2 days, 23:46:17.095143 PROGRESS: Protein Summary:
2 days, 23:46:17.097252 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   353; 0.001 FDR:   353
2 days, 23:46:17.097370 PROGRESS: =========================================================================
2 days, 23:46:17.097586 INFO: Target number of precursors reached.
2 days, 23:46:17.103763 INFO: fragments_df: keeping 5000 of 26536 [sum(precursor_idx_mask)=6581 sum(mass_error_mask)=26536 stop_rank=5000
2 days, 23:46:17.108955 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:46:17.362816 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:46:17.630765 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:46:17.949620 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:46:18.861937 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:46:18.862403 INFO: Using score_cutoff 33.93545795288085 (fac=0.99, q=1)
2 days, 23:46:18.862751 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.904262065887451
2 days, 23:46:18.862835 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007012601476162672
2 days, 23:46:18.862909 INFO: Updating optimization_manager: score_cutoff        : 0 -> 33.93545795288085
2 days, 23:46:18.863002 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:46:18.864156 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:46:18.865579 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:46:18.866416 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:46:18.868552 INFO: Updating optimization_manager: classifier_version  : -1 -> 2
2 days, 23:46:18.868669 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:46:18.868789 INFO: Starting optimization step 3.
2 days, 23:46:18.868883 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:46:18.868978 INFO: Using python extraction backend
2 days, 23:46:18.869120 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:46:18.869213 INFO: === Search parameters used ===
2 days, 23:46:18.869283 INFO: rt_error       : 1199.9776575
2 days, 23:46:18.869348 INFO: mobility_error : 0.1
2 days, 23:46:18.869411 INFO: num_candidates : 3
2 days, 23:46:18.869473 INFO: ms1_error      : 30
2 days, 23:46:18.869534 INFO: ms2_error      : 30
2 days, 23:46:18.869605 INFO: fwhm_rt        : 2.904262065887451
2 days, 23:46:18.869671 INFO: quant_window   : 3
2 days, 23:46:18.869734 INFO: ==============================================
2 days, 23:46:18.870693 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:46:18.870750 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:46:18.870802 INFO: FWHM in RT is 2.90 seconds, sigma is 0.48
2 days, 23:46:18.870839 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.80
2 days, 23:46:18.875228 INFO: Starting candidate selection
2 days, 23:46:27.476727 INFO: Starting candidate scoring
2 days, 23:46:27.602516 INFO: Finished candidate processing
2 days, 23:46:27.602681 INFO: Collecting candidate features
2 days, 23:46:27.627868 INFO: Collecting fragment features
2 days, 23:46:27.634381 INFO: Finished candidate scoring
2 days, 23:46:27.638072 INFO: performing precursor FDR with 47 features
2 days, 23:46:27.638187 INFO: Decoy channel: -1
2 days, 23:46:27.638246 INFO: competitive: True
2 days, 23:46:27.643629 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:46:27.646144 INFO: Estimating optimal hyperparameters - samples: 2,732, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:46:27.646278 INFO: Using random state 788784 for train-test-split
2 days, 23:46:27.892835 INFO: Test AUC: 0.663
2 days, 23:46:27.892953 INFO: Train AUC: 0.697
2 days, 23:46:27.892998 INFO: AUC difference: 4.94%
2 days, 23:46:28.238278 INFO: Resetting torch num_threads to 80
2 days, 23:46:28.238858 PROGRESS: === Extracted 3416 precursors and 31188 fragments ===
2 days, 23:46:28.239334 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:46:28.239977 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:46:28.240083 PROGRESS: Total precursors accumulated: 600
2 days, 23:46:28.240158 PROGRESS: Target precursors: 510 (85.00%)
2 days, 23:46:28.240225 PROGRESS: Decoy precursors: 90 (15.00%)
2 days, 23:46:28.240288 PROGRESS: 
2 days, 23:46:28.240348 PROGRESS: Precursor Summary:
2 days, 23:46:28.241459 PROGRESS: Channel   0:	 0.050 FDR:   418; 0.010 FDR:   418; 0.001 FDR:   418
2 days, 23:46:28.241559 PROGRESS: 
2 days, 23:46:28.241630 PROGRESS: Protein Summary:
2 days, 23:46:28.242963 PROGRESS: Channel   0:	 0.050 FDR:   314; 0.010 FDR:   314; 0.001 FDR:   314
2 days, 23:46:28.243071 PROGRESS: =========================================================================
2 days, 23:46:28.243288 INFO: Target number of precursors reached.
2 days, 23:46:28.250270 INFO: fragments_df: keeping 5000 of 31188 [sum(precursor_idx_mask)=11584 sum(mass_error_mask)=31188 stop_rank=5000
2 days, 23:46:28.255633 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:46:28.448911 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:46:28.699606 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:46:28.868038 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:46:29.657408 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:46:29.658016 INFO: Using score_cutoff 29.934396616744994 (fac=0.99, q=1)
2 days, 23:46:29.658525 INFO: Updating optimization_manager: fwhm_rt             : 2.904262065887451 -> 2.8447277545928955
2 days, 23:46:29.658646 INFO: Updating optimization_manager: fwhm_mobility       : 0.007012601476162672 -> 0.0059021818451583385
2 days, 23:46:29.658750 INFO: Updating optimization_manager: score_cutoff        : 33.93545795288085 -> 29.934396616744994
2 days, 23:46:29.658856 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:46:29.660387 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:46:29.662179 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:46:29.663357 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:46:29.665812 INFO: === checking if optimization conditions were reached ===
2 days, 23:46:29.667985 INFO: Updating optimization_manager: ms2_error           : 30 -> 18.950648891326544
2 days, 23:46:29.668123 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:46:29.668224 PROGRESS: ❌ ms2_error      : 18.9506 > 15.0000 or insufficient steps taken.
2 days, 23:46:29.669647 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:46:29.669774 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:46:29.669888 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:46:29.669980 INFO: ==============================================
2 days, 23:46:29.670092 INFO: Starting optimization step 4.
2 days, 23:46:29.670174 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:46:29.670250 INFO: Using python extraction backend
2 days, 23:46:29.670379 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:46:29.670463 INFO: === Search parameters used ===
2 days, 23:46:29.670527 INFO: rt_error       : 1199.9776575
2 days, 23:46:29.670586 INFO: mobility_error : 0.1
2 days, 23:46:29.670645 INFO: num_candidates : 3
2 days, 23:46:29.670707 INFO: ms1_error      : 15.0
2 days, 23:46:29.670766 INFO: ms2_error      : 18.950648891326544
2 days, 23:46:29.670825 INFO: fwhm_rt        : 2.8447277545928955
2 days, 23:46:29.670884 INFO: quant_window   : 3
2 days, 23:46:29.670944 INFO: ==============================================
2 days, 23:46:29.671870 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:46:29.671926 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:46:29.671962 INFO: FWHM in RT is 2.84 seconds, sigma is 0.47
2 days, 23:46:29.671985 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.20
2 days, 23:46:29.682060 INFO: Starting candidate selection
2 days, 23:46:39.209325 INFO: Starting candidate scoring
2 days, 23:46:39.325441 INFO: Finished candidate processing
2 days, 23:46:39.325560 INFO: Collecting candidate features
2 days, 23:46:39.338179 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3385)
2 days, 23:46:39.343403 INFO: Collecting fragment features
2 days, 23:46:39.347941 INFO: Finished candidate scoring
2 days, 23:46:39.350052 INFO: performing precursor FDR with 47 features
2 days, 23:46:39.350106 INFO: Decoy channel: -1
2 days, 23:46:39.350138 INFO: competitive: True
2 days, 23:46:39.353980 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:46:39.355653 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 23:46:39.356910 INFO: Estimating optimal hyperparameters - samples: 2,707, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:46:39.357004 INFO: Using random state 439095 for train-test-split
2 days, 23:46:39.636570 INFO: Test AUC: 0.720
2 days, 23:46:39.636715 INFO: Train AUC: 0.750
2 days, 23:46:39.636773 INFO: AUC difference: 4.01%
2 days, 23:46:39.958875 INFO: Resetting torch num_threads to 80
2 days, 23:46:39.959603 PROGRESS: === Extracted 3385 precursors and 28273 fragments ===
2 days, 23:46:39.960199 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:46:39.961119 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:46:39.961254 PROGRESS: Total precursors accumulated: 600
2 days, 23:46:39.961364 PROGRESS: Target precursors: 528 (88.00%)
2 days, 23:46:39.961462 PROGRESS: Decoy precursors: 72 (12.00%)
2 days, 23:46:39.961554 PROGRESS: 
2 days, 23:46:39.961653 PROGRESS: Precursor Summary:
2 days, 23:46:39.963468 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   409; 0.001 FDR:     0
2 days, 23:46:39.963608 PROGRESS: 
2 days, 23:46:39.963692 PROGRESS: Protein Summary:
2 days, 23:46:39.965856 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   306; 0.001 FDR:     0
2 days, 23:46:39.966009 PROGRESS: =========================================================================
2 days, 23:46:39.966241 INFO: Target number of precursors reached.
2 days, 23:46:39.976227 INFO: fragments_df: keeping 5000 of 28273 [sum(precursor_idx_mask)=10691 sum(mass_error_mask)=28273 stop_rank=5000
2 days, 23:46:39.983392 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:46:40.187176 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:46:40.358298 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:46:40.543113 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:46:41.315643 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:46:41.316125 INFO: Using score_cutoff 27.619783044433596 (fac=0.99, q=1)
2 days, 23:46:41.316476 INFO: Updating optimization_manager: fwhm_rt             : 2.8447277545928955 -> 2.742652654647827
2 days, 23:46:41.316566 INFO: Updating optimization_manager: fwhm_mobility       : 0.0059021818451583385 -> 0.005250096321105957
2 days, 23:46:41.316637 INFO: Updating optimization_manager: score_cutoff        : 29.934396616744994 -> 27.619783044433596
2 days, 23:46:41.316718 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:46:41.317980 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:46:41.319438 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:46:41.320292 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:46:41.322381 INFO: === checking if optimization conditions were reached ===
2 days, 23:46:41.324073 INFO: Updating optimization_manager: ms2_error           : 18.950648891326544 -> 15.0
2 days, 23:46:41.324208 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2 days, 23:46:41.324310 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:46:41.325381 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:46:41.325495 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
2 days, 23:46:41.325589 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:46:41.325672 INFO: ==============================================
2 days, 23:46:41.325769 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:46:41.329425 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:46:41.330491 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:46:41.331891 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:46:41.332723 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:46:41.334730 INFO: Starting optimization step 0.
2 days, 23:46:41.334844 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:46:41.334930 INFO: Using python extraction backend
2 days, 23:46:41.335057 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:46:41.335141 INFO: === Search parameters used ===
2 days, 23:46:41.335210 INFO: rt_error       : 1199.9776575
2 days, 23:46:41.335279 INFO: mobility_error : 0.1
2 days, 23:46:41.335335 INFO: num_candidates : 3
2 days, 23:46:41.335390 INFO: ms1_error      : 15.0
2 days, 23:46:41.335444 INFO: ms2_error      : 15.0
2 days, 23:46:41.335497 INFO: fwhm_rt        : 2.742652654647827
2 days, 23:46:41.335551 INFO: quant_window   : 3
2 days, 23:46:41.335603 INFO: ==============================================
2 days, 23:46:41.336643 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:46:41.336727 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:46:41.336776 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
2 days, 23:46:41.336807 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.85
2 days, 23:46:41.342826 INFO: Starting candidate selection
2 days, 23:46:49.786408 INFO: Starting candidate scoring
2 days, 23:46:49.886875 INFO: Finished candidate processing
2 days, 23:46:49.886992 INFO: Collecting candidate features
2 days, 23:46:49.899571 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3412)
2 days, 23:46:49.904682 INFO: Collecting fragment features
2 days, 23:46:49.909487 INFO: Finished candidate scoring
2 days, 23:46:49.911729 INFO: performing precursor FDR with 47 features
2 days, 23:46:49.911792 INFO: Decoy channel: -1
2 days, 23:46:49.911825 INFO: competitive: True
2 days, 23:46:49.916598 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:46:49.918357 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 23:46:49.919698 INFO: Estimating optimal hyperparameters - samples: 2,728, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:46:49.919810 INFO: Using random state 281559 for train-test-split
2 days, 23:46:50.241577 INFO: Test AUC: 0.737
2 days, 23:46:50.241736 INFO: Train AUC: 0.771
2 days, 23:46:50.241790 INFO: AUC difference: 4.41%
2 days, 23:46:50.608205 INFO: Resetting torch num_threads to 80
2 days, 23:46:50.608950 PROGRESS: === Extracted 3412 precursors and 27451 fragments ===
2 days, 23:46:50.609559 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:46:50.610578 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:46:50.610719 PROGRESS: Total precursors accumulated: 600
2 days, 23:46:50.610830 PROGRESS: Target precursors: 542 (90.33%)
2 days, 23:46:50.610929 PROGRESS: Decoy precursors: 58 (9.67%)
2 days, 23:46:50.611026 PROGRESS: 
2 days, 23:46:50.611124 PROGRESS: Precursor Summary:
2 days, 23:46:50.612958 PROGRESS: Channel   0:	 0.050 FDR:   457; 0.010 FDR:   405; 0.001 FDR:   405
2 days, 23:46:50.613088 PROGRESS: 
2 days, 23:46:50.613173 PROGRESS: Protein Summary:
2 days, 23:46:50.615316 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   304; 0.001 FDR:   304
2 days, 23:46:50.615460 PROGRESS: =========================================================================
2 days, 23:46:50.615699 INFO: Target number of precursors reached.
2 days, 23:46:50.624210 INFO: fragments_df: keeping 5000 of 27451 [sum(precursor_idx_mask)=10479 sum(mass_error_mask)=27451 stop_rank=5000
2 days, 23:46:50.629199 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:46:50.903222 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:46:57.204092 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:46:57.383660 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:46:58.246099 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:46:58.246724 INFO: Using score_cutoff 27.755763402557374 (fac=0.99, q=1)
2 days, 23:46:58.247204 INFO: Updating optimization_manager: fwhm_rt             : 2.742652654647827 -> 2.629641532897949
2 days, 23:46:58.247326 INFO: Updating optimization_manager: fwhm_mobility       : 0.005250096321105957 -> 0.004870951641350985
2 days, 23:46:58.247422 INFO: Updating optimization_manager: score_cutoff        : 27.619783044433596 -> 27.755763402557374
2 days, 23:46:58.247525 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:46:58.249127 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:46:58.251098 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:46:58.252318 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:46:58.255274 INFO: === checking if optimization conditions were reached ===
2 days, 23:46:58.255431 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:46:58.257899 INFO: Updating optimization_manager: rt_error            : 1199.9776575 -> 702.1973637114064
2 days, 23:46:58.258050 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 702.1974.
2 days, 23:46:58.258187 INFO: ==============================================
2 days, 23:46:58.258337 INFO: Starting optimization step 1.
2 days, 23:46:58.258451 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:46:58.258556 INFO: Using python extraction backend
2 days, 23:46:58.258723 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:46:58.258844 INFO: === Search parameters used ===
2 days, 23:46:58.259045 INFO: rt_error       : 702.1973637114064
2 days, 23:46:58.259263 INFO: mobility_error : 0.1
2 days, 23:46:58.259403 INFO: num_candidates : 3
2 days, 23:46:58.259487 INFO: ms1_error      : 15.0
2 days, 23:46:58.259562 INFO: ms2_error      : 15.0
2 days, 23:46:58.259633 INFO: fwhm_rt        : 2.629641532897949
2 days, 23:46:58.259706 INFO: quant_window   : 3
2 days, 23:46:58.259785 INFO: ==============================================
2 days, 23:46:58.261179 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:46:58.261249 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:46:58.261307 INFO: FWHM in RT is 2.63 seconds, sigma is 0.44
2 days, 23:46:58.261348 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.64
2 days, 23:46:58.294061 INFO: Starting candidate selection
2 days, 23:47:03.737210 INFO: Starting candidate scoring
2 days, 23:47:03.839303 INFO: Finished candidate processing
2 days, 23:47:03.839421 INFO: Collecting candidate features
2 days, 23:47:03.853049 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3372)
2 days, 23:47:03.858402 INFO: Collecting fragment features
2 days, 23:47:03.864024 INFO: Finished candidate scoring
2 days, 23:47:03.869567 INFO: performing precursor FDR with 47 features
2 days, 23:47:03.869662 INFO: Decoy channel: -1
2 days, 23:47:03.869694 INFO: competitive: True
2 days, 23:47:03.874222 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:47:03.876233 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 23:47:03.877635 INFO: Estimating optimal hyperparameters - samples: 2,696, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:47:03.877752 INFO: Using random state 281559 for train-test-split
2 days, 23:47:04.262007 INFO: Test AUC: 0.758
2 days, 23:47:04.262142 INFO: Train AUC: 0.772
2 days, 23:47:04.262191 INFO: AUC difference: 1.81%
2 days, 23:47:04.593215 INFO: Resetting torch num_threads to 80
2 days, 23:47:04.594149 PROGRESS: === Extracted 3372 precursors and 27040 fragments ===
2 days, 23:47:04.594774 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:47:04.595813 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:47:04.595946 PROGRESS: Total precursors accumulated: 600
2 days, 23:47:04.596059 PROGRESS: Target precursors: 543 (90.50%)
2 days, 23:47:04.596159 PROGRESS: Decoy precursors: 57 (9.50%)
2 days, 23:47:04.596254 PROGRESS: 
2 days, 23:47:04.596351 PROGRESS: Precursor Summary:
2 days, 23:47:04.598339 PROGRESS: Channel   0:	 0.050 FDR:   461; 0.010 FDR:   423; 0.001 FDR:   423
2 days, 23:47:04.598492 PROGRESS: 
2 days, 23:47:04.598596 PROGRESS: Protein Summary:
2 days, 23:47:04.600940 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   313; 0.001 FDR:   313
2 days, 23:47:04.601062 PROGRESS: =========================================================================
2 days, 23:47:04.601263 INFO: Target number of precursors reached.
2 days, 23:47:04.611840 INFO: fragments_df: keeping 5000 of 27040 [sum(precursor_idx_mask)=10839 sum(mass_error_mask)=27040 stop_rank=5000
2 days, 23:47:04.619660 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:04.847955 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:05.028245 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:05.253723 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:06.041966 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:47:06.042445 INFO: Using score_cutoff 27.74262289581299 (fac=0.99, q=1)
2 days, 23:47:06.042797 INFO: Updating optimization_manager: fwhm_rt             : 2.629641532897949 -> 2.6420364379882812
2 days, 23:47:06.042881 INFO: Updating optimization_manager: fwhm_mobility       : 0.004870951641350985 -> 0.00470699043944478
2 days, 23:47:06.042938 INFO: Updating optimization_manager: score_cutoff        : 27.755763402557374 -> 27.74262289581299
2 days, 23:47:06.042995 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:06.044219 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:06.045674 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:06.046529 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:06.048601 INFO: === checking if optimization conditions were reached ===
2 days, 23:47:06.048716 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:47:06.050907 INFO: Updating optimization_manager: rt_error            : 702.1973637114064 -> 565.6971348060856
2 days, 23:47:06.051042 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 565.6971.
2 days, 23:47:06.051147 INFO: ==============================================
2 days, 23:47:06.051248 INFO: Starting optimization step 2.
2 days, 23:47:06.051336 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:47:06.051422 INFO: Using python extraction backend
2 days, 23:47:06.051570 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:47:06.051672 INFO: === Search parameters used ===
2 days, 23:47:06.051750 INFO: rt_error       : 565.6971348060856
2 days, 23:47:06.051819 INFO: mobility_error : 0.1
2 days, 23:47:06.051890 INFO: num_candidates : 3
2 days, 23:47:06.051956 INFO: ms1_error      : 15.0
2 days, 23:47:06.052023 INFO: ms2_error      : 15.0
2 days, 23:47:06.052090 INFO: fwhm_rt        : 2.6420364379882812
2 days, 23:47:06.052160 INFO: quant_window   : 3
2 days, 23:47:06.052240 INFO: ==============================================
2 days, 23:47:06.053806 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:47:06.053884 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:47:06.053943 INFO: FWHM in RT is 2.64 seconds, sigma is 0.44
2 days, 23:47:06.053980 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
2 days, 23:47:06.058787 INFO: Starting candidate selection
2 days, 23:47:09.690079 INFO: Starting candidate scoring
2 days, 23:47:09.798575 INFO: Finished candidate processing
2 days, 23:47:09.798694 INFO: Collecting candidate features
2 days, 23:47:09.812180 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3377)
2 days, 23:47:09.817383 INFO: Collecting fragment features
2 days, 23:47:09.823075 INFO: Finished candidate scoring
2 days, 23:47:09.827776 INFO: performing precursor FDR with 47 features
2 days, 23:47:09.827849 INFO: Decoy channel: -1
2 days, 23:47:09.827881 INFO: competitive: True
2 days, 23:47:09.832081 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:47:09.834108 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:47:09.834173 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 23:47:09.835625 INFO: Estimating optimal hyperparameters - samples: 2,700, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:47:09.835753 INFO: Using random state 281559 for train-test-split
2 days, 23:47:10.203801 INFO: Test AUC: 0.726
2 days, 23:47:10.203919 INFO: Train AUC: 0.788
2 days, 23:47:10.203962 INFO: AUC difference: 7.88%
2 days, 23:47:10.203996 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:47:10.544642 INFO: Resetting torch num_threads to 80
2 days, 23:47:10.545310 PROGRESS: === Extracted 3377 precursors and 26833 fragments ===
2 days, 23:47:10.545755 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:47:10.546453 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:47:10.546563 PROGRESS: Total precursors accumulated: 600
2 days, 23:47:10.546643 PROGRESS: Target precursors: 536 (89.33%)
2 days, 23:47:10.546714 PROGRESS: Decoy precursors: 64 (10.67%)
2 days, 23:47:10.546776 PROGRESS: 
2 days, 23:47:10.546837 PROGRESS: Precursor Summary:
2 days, 23:47:10.548043 PROGRESS: Channel   0:	 0.050 FDR:   458; 0.010 FDR:   439; 0.001 FDR:   439
2 days, 23:47:10.548161 PROGRESS: 
2 days, 23:47:10.548233 PROGRESS: Protein Summary:
2 days, 23:47:10.549586 PROGRESS: Channel   0:	 0.050 FDR:   335; 0.010 FDR:   320; 0.001 FDR:   320
2 days, 23:47:10.549703 PROGRESS: =========================================================================
2 days, 23:47:10.549877 INFO: Target number of precursors reached.
2 days, 23:47:10.556542 INFO: fragments_df: keeping 5000 of 26833 [sum(precursor_idx_mask)=11123 sum(mass_error_mask)=26833 stop_rank=5000
2 days, 23:47:10.561735 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:10.767584 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:10.931368 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:11.109917 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:11.906482 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:47:11.907029 INFO: Using score_cutoff 25.79576794052124 (fac=0.99, q=1)
2 days, 23:47:11.907393 INFO: Updating optimization_manager: fwhm_rt             : 2.6420364379882812 -> 2.6117441654205322
2 days, 23:47:11.907503 INFO: Updating optimization_manager: fwhm_mobility       : 0.00470699043944478 -> 0.004626111593097448
2 days, 23:47:11.907592 INFO: Updating optimization_manager: score_cutoff        : 27.74262289581299 -> 25.79576794052124
2 days, 23:47:11.907684 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:11.909135 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:11.910878 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:11.911928 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:11.914448 INFO: === checking if optimization conditions were reached ===
2 days, 23:47:11.914579 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:47:11.916919 INFO: Updating optimization_manager: rt_error            : 565.6971348060856 -> 509.80784513581307
2 days, 23:47:11.917054 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 509.8078.
2 days, 23:47:11.917129 INFO: ==============================================
2 days, 23:47:11.917206 INFO: Starting optimization step 3.
2 days, 23:47:11.917269 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:47:11.917332 INFO: Using python extraction backend
2 days, 23:47:11.917434 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:47:11.917502 INFO: === Search parameters used ===
2 days, 23:47:11.917555 INFO: rt_error       : 509.80784513581307
2 days, 23:47:11.917605 INFO: mobility_error : 0.1
2 days, 23:47:11.917651 INFO: num_candidates : 3
2 days, 23:47:11.917695 INFO: ms1_error      : 15.0
2 days, 23:47:11.917783 INFO: ms2_error      : 15.0
2 days, 23:47:11.917875 INFO: fwhm_rt        : 2.6117441654205322
2 days, 23:47:11.917948 INFO: quant_window   : 3
2 days, 23:47:11.918010 INFO: ==============================================
2 days, 23:47:11.919168 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:47:11.919220 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:47:11.919263 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
2 days, 23:47:11.919310 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.51
2 days, 23:47:11.946077 INFO: Starting candidate selection
2 days, 23:47:15.428075 INFO: Starting candidate scoring
2 days, 23:47:15.531533 INFO: Finished candidate processing
2 days, 23:47:15.531813 INFO: Collecting candidate features
2 days, 23:47:15.545526 WARNING: intensity_correlation has 3 NaNs ( 0.09 % out of 3369)
2 days, 23:47:15.550984 INFO: Collecting fragment features
2 days, 23:47:15.556283 INFO: Finished candidate scoring
2 days, 23:47:15.560909 INFO: performing precursor FDR with 47 features
2 days, 23:47:15.561007 INFO: Decoy channel: -1
2 days, 23:47:15.561037 INFO: competitive: True
2 days, 23:47:15.565307 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:47:15.567436 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:47:15.567501 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:47:15.568810 INFO: Estimating optimal hyperparameters - samples: 2,692, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:47:15.568940 INFO: Using random state 281559 for train-test-split
2 days, 23:47:15.903446 INFO: Test AUC: 0.729
2 days, 23:47:15.903562 INFO: Train AUC: 0.786
2 days, 23:47:15.903613 INFO: AUC difference: 7.27%
2 days, 23:47:15.903653 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:47:16.232757 INFO: Resetting torch num_threads to 80
2 days, 23:47:16.233701 PROGRESS: === Extracted 3369 precursors and 26748 fragments ===
2 days, 23:47:16.234344 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:47:16.235447 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:47:16.235608 PROGRESS: Total precursors accumulated: 600
2 days, 23:47:16.235708 PROGRESS: Target precursors: 542 (90.33%)
2 days, 23:47:16.235791 PROGRESS: Decoy precursors: 58 (9.67%)
2 days, 23:47:16.235872 PROGRESS: 
2 days, 23:47:16.235950 PROGRESS: Precursor Summary:
2 days, 23:47:16.237735 PROGRESS: Channel   0:	 0.050 FDR:   462; 0.010 FDR:   437; 0.001 FDR:     0
2 days, 23:47:16.237881 PROGRESS: 
2 days, 23:47:16.237973 PROGRESS: Protein Summary:
2 days, 23:47:16.239908 PROGRESS: Channel   0:	 0.050 FDR:   344; 0.010 FDR:   324; 0.001 FDR:     0
2 days, 23:47:16.240031 PROGRESS: =========================================================================
2 days, 23:47:16.240238 INFO: Target number of precursors reached.
2 days, 23:47:16.247209 INFO: fragments_df: keeping 5000 of 26748 [sum(precursor_idx_mask)=11100 sum(mass_error_mask)=26748 stop_rank=5000
2 days, 23:47:16.251202 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:16.442441 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:16.653419 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:16.861694 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:17.661233 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:47:17.661734 INFO: Using score_cutoff 25.317241177368164 (fac=0.99, q=1)
2 days, 23:47:17.662104 INFO: Updating optimization_manager: fwhm_rt             : 2.6117441654205322 -> 2.6192002296447754
2 days, 23:47:17.662194 INFO: Updating optimization_manager: fwhm_mobility       : 0.004626111593097448 -> 0.004501283634454012
2 days, 23:47:17.662254 INFO: Updating optimization_manager: score_cutoff        : 25.79576794052124 -> 25.317241177368164
2 days, 23:47:17.662310 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:17.663490 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:17.664950 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:17.665779 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:17.667865 INFO: === checking if optimization conditions were reached ===
2 days, 23:47:17.667980 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:47:17.669948 INFO: Updating optimization_manager: rt_error            : 509.80784513581307 -> 492.6865219160817
2 days, 23:47:17.670058 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 492.6865.
2 days, 23:47:17.670142 INFO: ==============================================
2 days, 23:47:17.670221 INFO: Starting optimization step 4.
2 days, 23:47:17.670284 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:47:17.670353 INFO: Using python extraction backend
2 days, 23:47:17.670455 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:47:17.670537 INFO: === Search parameters used ===
2 days, 23:47:17.670591 INFO: rt_error       : 492.6865219160817
2 days, 23:47:17.670637 INFO: mobility_error : 0.1
2 days, 23:47:17.670686 INFO: num_candidates : 3
2 days, 23:47:17.670730 INFO: ms1_error      : 15.0
2 days, 23:47:17.670777 INFO: ms2_error      : 15.0
2 days, 23:47:17.670824 INFO: fwhm_rt        : 2.6192002296447754
2 days, 23:47:17.670868 INFO: quant_window   : 3
2 days, 23:47:17.670911 INFO: ==============================================
2 days, 23:47:17.671831 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:47:17.671880 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:47:17.671917 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:47:17.671940 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.44
2 days, 23:47:17.687876 INFO: Starting candidate selection
2 days, 23:47:22.614606 INFO: Starting candidate scoring
2 days, 23:47:22.718251 INFO: Finished candidate processing
2 days, 23:47:22.718391 INFO: Collecting candidate features
2 days, 23:47:22.735740 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3370)
2 days, 23:47:22.743332 INFO: Collecting fragment features
2 days, 23:47:22.748711 INFO: Finished candidate scoring
2 days, 23:47:22.752524 INFO: performing precursor FDR with 47 features
2 days, 23:47:22.752612 INFO: Decoy channel: -1
2 days, 23:47:22.752654 INFO: competitive: True
2 days, 23:47:22.757087 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:47:22.758668 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 23:47:22.759835 INFO: Estimating optimal hyperparameters - samples: 2,695, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:47:22.759954 INFO: Using random state 281559 for train-test-split
2 days, 23:47:23.145159 INFO: Test AUC: 0.769
2 days, 23:47:23.145281 INFO: Train AUC: 0.780
2 days, 23:47:23.145321 INFO: AUC difference: 1.41%
2 days, 23:47:23.435739 INFO: Resetting torch num_threads to 80
2 days, 23:47:23.436423 PROGRESS: === Extracted 3370 precursors and 26775 fragments ===
2 days, 23:47:23.436872 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:47:23.437569 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:47:23.437678 PROGRESS: Total precursors accumulated: 600
2 days, 23:47:23.437757 PROGRESS: Target precursors: 534 (89.00%)
2 days, 23:47:23.437827 PROGRESS: Decoy precursors: 66 (11.00%)
2 days, 23:47:23.437910 PROGRESS: 
2 days, 23:47:23.437978 PROGRESS: Precursor Summary:
2 days, 23:47:23.439223 PROGRESS: Channel   0:	 0.050 FDR:   466; 0.010 FDR:   429; 0.001 FDR:   429
2 days, 23:47:23.439335 PROGRESS: 
2 days, 23:47:23.439410 PROGRESS: Protein Summary:
2 days, 23:47:23.440769 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   314; 0.001 FDR:   314
2 days, 23:47:23.440876 PROGRESS: =========================================================================
2 days, 23:47:23.441032 INFO: Target number of precursors reached.
2 days, 23:47:23.447702 INFO: fragments_df: keeping 5000 of 26775 [sum(precursor_idx_mask)=10929 sum(mass_error_mask)=26775 stop_rank=5000
2 days, 23:47:23.451385 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:23.641741 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:23.816121 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:24.016443 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:24.901907 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:47:24.902372 INFO: Using score_cutoff 26.29578795776367 (fac=0.99, q=1)
2 days, 23:47:24.902734 INFO: Updating optimization_manager: fwhm_rt             : 2.6192002296447754 -> 2.64786958694458
2 days, 23:47:24.902823 INFO: Updating optimization_manager: fwhm_mobility       : 0.004501283634454012 -> 0.0045676035806536674
2 days, 23:47:24.902887 INFO: Updating optimization_manager: score_cutoff        : 25.317241177368164 -> 26.29578795776367
2 days, 23:47:24.902951 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:24.904180 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:24.905672 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:24.906542 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:24.908583 INFO: === checking if optimization conditions were reached ===
2 days, 23:47:24.908713 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:47:24.909763 INFO: Updating optimization_manager: rt_error            : 492.6865219160817 -> 492.6865219160817
2 days, 23:47:24.909904 INFO: Updating optimization_manager: classifier_version  : 4 -> 9
2 days, 23:47:24.910037 INFO: Updating optimization_manager: score_cutoff        : 26.29578795776367 -> 26.29578795776367
2 days, 23:47:24.910176 INFO: Updating optimization_manager: fwhm_rt             : 2.64786958694458 -> 2.64786958694458
2 days, 23:47:24.910309 INFO: Updating optimization_manager: fwhm_mobility       : 0.0045676035806536674 -> 0.0045676035806536674
2 days, 23:47:24.910440 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 492.6865 found after 5 searches.
2 days, 23:47:24.910536 INFO: ==============================================
2 days, 23:47:24.910636 PROGRESS: Optimization finished for rt_error.
2 days, 23:47:24.914454 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:24.915697 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:24.917515 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:24.918715 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:24.921373 INFO: Starting optimization step 0.
2 days, 23:47:24.921525 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:47:24.921638 INFO: Using python extraction backend
2 days, 23:47:24.921808 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:47:24.921939 INFO: === Search parameters used ===
2 days, 23:47:24.922040 INFO: rt_error       : 492.6865219160817
2 days, 23:47:24.922137 INFO: mobility_error : 0.1
2 days, 23:47:24.922229 INFO: num_candidates : 3
2 days, 23:47:24.922318 INFO: ms1_error      : 15.0
2 days, 23:47:24.922410 INFO: ms2_error      : 15.0
2 days, 23:47:24.922495 INFO: fwhm_rt        : 2.64786958694458
2 days, 23:47:24.922579 INFO: quant_window   : 3
2 days, 23:47:24.922646 INFO: ==============================================
2 days, 23:47:24.923906 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:47:24.923975 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:47:24.924036 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
2 days, 23:47:24.924081 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.48
2 days, 23:47:24.934085 INFO: Starting candidate selection
2 days, 23:47:29.138815 INFO: Starting candidate scoring
2 days, 23:47:29.252614 INFO: Finished candidate processing
2 days, 23:47:29.252746 INFO: Collecting candidate features
2 days, 23:47:29.269648 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3379)
2 days, 23:47:29.277997 INFO: Collecting fragment features
2 days, 23:47:29.284415 INFO: Finished candidate scoring
2 days, 23:47:29.289440 INFO: performing precursor FDR with 47 features
2 days, 23:47:29.289558 INFO: Decoy channel: -1
2 days, 23:47:29.289603 INFO: competitive: True
2 days, 23:47:29.294657 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:47:29.297188 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:47:29.297272 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:47:29.298790 INFO: Estimating optimal hyperparameters - samples: 2,700, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:47:29.298922 INFO: Using random state 170179 for train-test-split
2 days, 23:47:29.668486 INFO: Test AUC: 0.769
2 days, 23:47:29.668603 INFO: Train AUC: 0.798
2 days, 23:47:29.668648 INFO: AUC difference: 3.67%
2 days, 23:47:29.924945 INFO: Resetting torch num_threads to 80
2 days, 23:47:29.925638 PROGRESS: === Extracted 3379 precursors and 26828 fragments ===
2 days, 23:47:29.926094 INFO: === FDR correction performed with classifier version 9 ===
2 days, 23:47:29.926805 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:47:29.926906 PROGRESS: Total precursors accumulated: 600
2 days, 23:47:29.926975 PROGRESS: Target precursors: 531 (88.50%)
2 days, 23:47:29.927034 PROGRESS: Decoy precursors: 69 (11.50%)
2 days, 23:47:29.927090 PROGRESS: 
2 days, 23:47:29.927141 PROGRESS: Precursor Summary:
2 days, 23:47:29.928233 PROGRESS: Channel   0:	 0.050 FDR:   374; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 23:47:29.928343 PROGRESS: 
2 days, 23:47:29.928408 PROGRESS: Protein Summary:
2 days, 23:47:29.929610 PROGRESS: Channel   0:	 0.050 FDR:   278; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 23:47:29.929710 PROGRESS: =========================================================================
2 days, 23:47:29.929858 INFO: Target number of precursors not reached yet.
2 days, 23:47:29.933762 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:29.934933 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:29.936590 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:29.937483 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:29.939979 INFO: === skipping optimization until target number of precursors are found ===
2 days, 23:47:29.940112 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
2 days, 23:47:29.940241 INFO: Starting optimization step 1.
2 days, 23:47:29.940335 PROGRESS: === Extracting elution groups 600 to 1400 ===
2 days, 23:47:29.940427 INFO: Using python extraction backend
2 days, 23:47:29.940571 PROGRESS: Extracting batch of 1599 precursors
2 days, 23:47:29.940675 INFO: === Search parameters used ===
2 days, 23:47:29.940757 INFO: rt_error       : 492.6865219160817
2 days, 23:47:29.940832 INFO: mobility_error : 0.1
2 days, 23:47:29.940905 INFO: num_candidates : 3
2 days, 23:47:29.940974 INFO: ms1_error      : 15.0
2 days, 23:47:29.941042 INFO: ms2_error      : 15.0
2 days, 23:47:29.941115 INFO: fwhm_rt        : 2.64786958694458
2 days, 23:47:29.941191 INFO: quant_window   : 3
2 days, 23:47:29.941263 INFO: ==============================================
2 days, 23:47:29.942328 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:47:29.942386 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:47:29.942445 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
2 days, 23:47:29.942486 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.48
2 days, 23:47:29.958185 INFO: Starting candidate selection
2 days, 23:47:34.337422 INFO: Starting candidate scoring
2 days, 23:47:34.484857 INFO: Finished candidate processing
2 days, 23:47:34.484993 INFO: Collecting candidate features
2 days, 23:47:34.502750 WARNING: intensity_correlation has 2 NaNs ( 0.04 % out of 4511)
2 days, 23:47:34.507100 INFO: Collecting fragment features
2 days, 23:47:34.512785 INFO: Finished candidate scoring
2 days, 23:47:34.519451 INFO: performing precursor FDR with 47 features
2 days, 23:47:34.519586 INFO: Decoy channel: -1
2 days, 23:47:34.519625 INFO: competitive: True
2 days, 23:47:34.529621 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:47:34.533622 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:47:34.533736 WARNING: dropped 3 decoy PSMs due to missing features
2 days, 23:47:34.536229 INFO: Estimating optimal hyperparameters - samples: 6,307, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:47:34.536381 INFO: Using random state 170179 for train-test-split
2 days, 23:47:35.189842 INFO: Test AUC: 0.769
2 days, 23:47:35.190031 INFO: Train AUC: 0.789
2 days, 23:47:35.190089 INFO: AUC difference: 2.45%
2 days, 23:47:35.526407 INFO: Resetting torch num_threads to 80
2 days, 23:47:35.529519 PROGRESS: === Extracted 7890 precursors and 63423 fragments ===
2 days, 23:47:35.530196 INFO: === FDR correction performed with classifier version 9 ===
2 days, 23:47:35.531338 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:47:35.531471 PROGRESS: Total precursors accumulated: 1,400
2 days, 23:47:35.531552 PROGRESS: Target precursors: 1,256 (89.71%)
2 days, 23:47:35.531619 PROGRESS: Decoy precursors: 144 (10.29%)
2 days, 23:47:35.531681 PROGRESS: 
2 days, 23:47:35.531742 PROGRESS: Precursor Summary:
2 days, 23:47:35.533434 PROGRESS: Channel   0:	 0.050 FDR: 1,069; 0.010 FDR:   857; 0.001 FDR:   569
2 days, 23:47:35.533541 PROGRESS: 
2 days, 23:47:35.533605 PROGRESS: Protein Summary:
2 days, 23:47:35.535152 PROGRESS: Channel   0:	 0.050 FDR:   599; 0.010 FDR:   477; 0.001 FDR:   317
2 days, 23:47:35.535254 PROGRESS: =========================================================================
2 days, 23:47:35.535410 INFO: Target number of precursors reached.
2 days, 23:47:35.549127 INFO: fragments_df: keeping 5000 of 63423 [sum(precursor_idx_mask)=22593 sum(mass_error_mask)=63423 stop_rank=5000
2 days, 23:47:35.555106 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:35.776307 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:36.038567 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:36.292465 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:37.117783 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:47:37.118280 INFO: Using score_cutoff 27.27175520324707 (fac=0.99, q=1)
2 days, 23:47:37.118658 INFO: Updating optimization_manager: fwhm_rt             : 2.64786958694458 -> 2.689127206802368
2 days, 23:47:37.118769 INFO: Updating optimization_manager: fwhm_mobility       : 0.0045676035806536674 -> 0.005087571684271097
2 days, 23:47:37.118841 INFO: Updating optimization_manager: score_cutoff        : 26.29578795776367 -> 27.27175520324707
2 days, 23:47:37.118912 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:37.120116 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:37.121591 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:37.122454 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:37.124516 INFO: === checking if optimization conditions were reached ===
2 days, 23:47:37.124637 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:47:37.126330 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06467671953591932
2 days, 23:47:37.126453 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0647.
2 days, 23:47:37.126535 INFO: ==============================================
2 days, 23:47:37.126618 INFO: Starting optimization step 2.
2 days, 23:47:37.126698 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:47:37.126771 INFO: Using python extraction backend
2 days, 23:47:37.126885 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:47:37.126965 INFO: === Search parameters used ===
2 days, 23:47:37.127026 INFO: rt_error       : 492.6865219160817
2 days, 23:47:37.127080 INFO: mobility_error : 0.06467671953591932
2 days, 23:47:37.127132 INFO: num_candidates : 3
2 days, 23:47:37.127194 INFO: ms1_error      : 15.0
2 days, 23:47:37.127249 INFO: ms2_error      : 15.0
2 days, 23:47:37.127301 INFO: fwhm_rt        : 2.689127206802368
2 days, 23:47:37.127351 INFO: quant_window   : 3
2 days, 23:47:37.127401 INFO: ==============================================
2 days, 23:47:37.128343 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:47:37.128396 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:47:37.128435 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
2 days, 23:47:37.128462 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.76
2 days, 23:47:37.143941 INFO: Starting candidate selection
2 days, 23:47:39.992938 INFO: Starting candidate scoring
2 days, 23:47:40.102220 INFO: Finished candidate processing
2 days, 23:47:40.102350 INFO: Collecting candidate features
2 days, 23:47:40.119468 WARNING: intensity_correlation has 3 NaNs ( 0.09 % out of 3378)
2 days, 23:47:40.127925 INFO: Collecting fragment features
2 days, 23:47:40.134521 INFO: Finished candidate scoring
2 days, 23:47:40.138963 INFO: performing precursor FDR with 47 features
2 days, 23:47:40.139074 INFO: Decoy channel: -1
2 days, 23:47:40.139112 INFO: competitive: True
2 days, 23:47:40.144121 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:47:40.146711 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:47:40.146806 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:47:40.148368 INFO: Estimating optimal hyperparameters - samples: 2,700, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:47:40.148499 INFO: Using random state 170179 for train-test-split
2 days, 23:47:40.428521 INFO: Test AUC: 0.771
2 days, 23:47:40.428698 INFO: Train AUC: 0.785
2 days, 23:47:40.428761 INFO: AUC difference: 1.75%
2 days, 23:47:40.749089 INFO: Resetting torch num_threads to 80
2 days, 23:47:40.749766 PROGRESS: === Extracted 3378 precursors and 26716 fragments ===
2 days, 23:47:40.750247 INFO: === FDR correction performed with classifier version 9 ===
2 days, 23:47:40.750953 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:47:40.751071 PROGRESS: Total precursors accumulated: 600
2 days, 23:47:40.751142 PROGRESS: Target precursors: 546 (91.00%)
2 days, 23:47:40.751200 PROGRESS: Decoy precursors: 54 (9.00%)
2 days, 23:47:40.751263 PROGRESS: 
2 days, 23:47:40.751314 PROGRESS: Precursor Summary:
2 days, 23:47:40.752579 PROGRESS: Channel   0:	 0.050 FDR:   483; 0.010 FDR:   443; 0.001 FDR:   443
2 days, 23:47:40.752687 PROGRESS: 
2 days, 23:47:40.752756 PROGRESS: Protein Summary:
2 days, 23:47:40.754696 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   325; 0.001 FDR:   325
2 days, 23:47:40.754831 PROGRESS: =========================================================================
2 days, 23:47:40.755091 INFO: Target number of precursors reached.
2 days, 23:47:40.765338 INFO: fragments_df: keeping 5000 of 26716 [sum(precursor_idx_mask)=11302 sum(mass_error_mask)=26716 stop_rank=5000
2 days, 23:47:40.770705 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:40.959445 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:41.148304 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:41.330703 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:42.258498 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:47:42.259147 INFO: Using score_cutoff 24.737672395706177 (fac=0.99, q=1)
2 days, 23:47:42.259624 INFO: Updating optimization_manager: fwhm_rt             : 2.689127206802368 -> 2.623745918273926
2 days, 23:47:42.259744 INFO: Updating optimization_manager: fwhm_mobility       : 0.005087571684271097 -> 0.0045676035806536674
2 days, 23:47:42.259848 INFO: Updating optimization_manager: score_cutoff        : 27.27175520324707 -> 24.737672395706177
2 days, 23:47:42.259943 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:42.261527 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:42.263430 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:42.264611 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:42.267253 INFO: === checking if optimization conditions were reached ===
2 days, 23:47:42.267408 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:47:42.269603 INFO: Updating optimization_manager: mobility_error      : 0.06467671953591932 -> 0.04954208602499969
2 days, 23:47:42.269738 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0495.
2 days, 23:47:42.269837 INFO: ==============================================
2 days, 23:47:42.269959 INFO: Starting optimization step 3.
2 days, 23:47:42.270062 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:47:42.270162 INFO: Using python extraction backend
2 days, 23:47:42.270311 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:47:42.270415 INFO: === Search parameters used ===
2 days, 23:47:42.270497 INFO: rt_error       : 492.6865219160817
2 days, 23:47:42.270575 INFO: mobility_error : 0.04954208602499969
2 days, 23:47:42.270650 INFO: num_candidates : 3
2 days, 23:47:42.270723 INFO: ms1_error      : 15.0
2 days, 23:47:42.270797 INFO: ms2_error      : 15.0
2 days, 23:47:42.270869 INFO: fwhm_rt        : 2.623745918273926
2 days, 23:47:42.270941 INFO: quant_window   : 3
2 days, 23:47:42.271012 INFO: ==============================================
2 days, 23:47:42.272285 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:47:42.272349 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:47:42.272402 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:47:42.272439 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.48
2 days, 23:47:42.278546 INFO: Starting candidate selection
2 days, 23:47:44.560395 INFO: Starting candidate scoring
2 days, 23:47:44.670071 INFO: Finished candidate processing
2 days, 23:47:44.670206 INFO: Collecting candidate features
2 days, 23:47:44.687407 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3342)
2 days, 23:47:44.695719 INFO: Collecting fragment features
2 days, 23:47:44.702235 INFO: Finished candidate scoring
2 days, 23:47:44.706920 INFO: performing precursor FDR with 47 features
2 days, 23:47:44.707031 INFO: Decoy channel: -1
2 days, 23:47:44.707068 INFO: competitive: True
2 days, 23:47:44.711711 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:47:44.713351 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:47:44.714635 INFO: Estimating optimal hyperparameters - samples: 2,672, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:47:44.714777 INFO: Using random state 170179 for train-test-split
2 days, 23:47:45.060028 INFO: Test AUC: 0.782
2 days, 23:47:45.060162 INFO: Train AUC: 0.789
2 days, 23:47:45.060223 INFO: AUC difference: 0.82%
2 days, 23:47:45.400554 INFO: Resetting torch num_threads to 80
2 days, 23:47:45.401432 PROGRESS: === Extracted 3342 precursors and 26207 fragments ===
2 days, 23:47:45.402254 INFO: === FDR correction performed with classifier version 9 ===
2 days, 23:47:45.403437 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:47:45.403689 PROGRESS: Total precursors accumulated: 600
2 days, 23:47:45.403918 PROGRESS: Target precursors: 541 (90.17%)
2 days, 23:47:45.404133 PROGRESS: Decoy precursors: 59 (9.83%)
2 days, 23:47:45.404335 PROGRESS: 
2 days, 23:47:45.404548 PROGRESS: Precursor Summary:
2 days, 23:47:45.406581 PROGRESS: Channel   0:	 0.050 FDR:   461; 0.010 FDR:   447; 0.001 FDR:     0
2 days, 23:47:45.406735 PROGRESS: 
2 days, 23:47:45.406853 PROGRESS: Protein Summary:
2 days, 23:47:45.408993 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   328; 0.001 FDR:     0
2 days, 23:47:45.409128 PROGRESS: =========================================================================
2 days, 23:47:45.409350 INFO: Target number of precursors reached.
2 days, 23:47:45.419652 INFO: fragments_df: keeping 5000 of 26207 [sum(precursor_idx_mask)=11349 sum(mass_error_mask)=26207 stop_rank=5000
2 days, 23:47:45.424861 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:45.655411 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:45.833015 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:46.046360 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:46.891469 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:47:46.892091 INFO: Using score_cutoff 25.16318987503052 (fac=0.99, q=1)
2 days, 23:47:46.892538 INFO: Updating optimization_manager: fwhm_rt             : 2.623745918273926 -> 2.620474338531494
2 days, 23:47:46.892655 INFO: Updating optimization_manager: fwhm_mobility       : 0.0045676035806536674 -> 0.004394236020743847
2 days, 23:47:46.892745 INFO: Updating optimization_manager: score_cutoff        : 24.737672395706177 -> 25.16318987503052
2 days, 23:47:46.892837 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:46.894390 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:46.896255 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:46.897454 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:46.900098 INFO: === checking if optimization conditions were reached ===
2 days, 23:47:46.900267 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:47:46.902765 INFO: Updating optimization_manager: mobility_error      : 0.04954208602499969 -> 0.045529348690402184
2 days, 23:47:46.902909 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0455.
2 days, 23:47:46.903021 INFO: ==============================================
2 days, 23:47:46.903137 INFO: Starting optimization step 4.
2 days, 23:47:46.903242 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:47:46.903344 INFO: Using python extraction backend
2 days, 23:47:46.903513 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:47:46.903631 INFO: === Search parameters used ===
2 days, 23:47:46.903732 INFO: rt_error       : 492.6865219160817
2 days, 23:47:46.903821 INFO: mobility_error : 0.045529348690402184
2 days, 23:47:46.903905 INFO: num_candidates : 3
2 days, 23:47:46.903993 INFO: ms1_error      : 15.0
2 days, 23:47:46.904084 INFO: ms2_error      : 15.0
2 days, 23:47:46.904170 INFO: fwhm_rt        : 2.620474338531494
2 days, 23:47:46.904256 INFO: quant_window   : 3
2 days, 23:47:46.904335 INFO: ==============================================
2 days, 23:47:46.905657 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:47:46.905723 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:47:46.905779 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:47:46.905816 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.38
2 days, 23:47:46.918010 INFO: Starting candidate selection
2 days, 23:47:48.751303 INFO: Starting candidate scoring
2 days, 23:47:48.873131 INFO: Finished candidate processing
2 days, 23:47:48.873247 INFO: Collecting candidate features
2 days, 23:47:48.886348 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3336)
2 days, 23:47:48.891653 INFO: Collecting fragment features
2 days, 23:47:48.896653 INFO: Finished candidate scoring
2 days, 23:47:48.900050 INFO: performing precursor FDR with 47 features
2 days, 23:47:48.900123 INFO: Decoy channel: -1
2 days, 23:47:48.900153 INFO: competitive: True
2 days, 23:47:48.905079 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:47:48.906842 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:47:48.908130 INFO: Estimating optimal hyperparameters - samples: 2,668, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:47:48.908228 INFO: Using random state 170179 for train-test-split
2 days, 23:47:49.164118 INFO: Test AUC: 0.796
2 days, 23:47:49.164251 INFO: Train AUC: 0.794
2 days, 23:47:49.164294 INFO: AUC difference: 0.30%
2 days, 23:47:49.541825 INFO: Resetting torch num_threads to 80
2 days, 23:47:49.542544 PROGRESS: === Extracted 3336 precursors and 26064 fragments ===
2 days, 23:47:49.543007 INFO: === FDR correction performed with classifier version 9 ===
2 days, 23:47:49.543664 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:47:49.543766 PROGRESS: Total precursors accumulated: 600
2 days, 23:47:49.543834 PROGRESS: Target precursors: 543 (90.50%)
2 days, 23:47:49.543888 PROGRESS: Decoy precursors: 57 (9.50%)
2 days, 23:47:49.543937 PROGRESS: 
2 days, 23:47:49.543983 PROGRESS: Precursor Summary:
2 days, 23:47:49.545141 PROGRESS: Channel   0:	 0.050 FDR:   485; 0.010 FDR:   449; 0.001 FDR:   449
2 days, 23:47:49.545243 PROGRESS: 
2 days, 23:47:49.545306 PROGRESS: Protein Summary:
2 days, 23:47:49.546708 PROGRESS: Channel   0:	 0.050 FDR:   358; 0.010 FDR:   332; 0.001 FDR:   332
2 days, 23:47:49.546816 PROGRESS: =========================================================================
2 days, 23:47:49.546978 INFO: Target number of precursors reached.
2 days, 23:47:49.553440 INFO: fragments_df: keeping 5000 of 26064 [sum(precursor_idx_mask)=11407 sum(mass_error_mask)=26064 stop_rank=5000
2 days, 23:47:49.556945 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:49.751898 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:49.929877 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:50.119595 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:50.950922 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:47:50.951511 INFO: Using score_cutoff 24.912767807006833 (fac=0.99, q=1)
2 days, 23:47:50.952014 INFO: Updating optimization_manager: fwhm_rt             : 2.620474338531494 -> 2.6070423126220703
2 days, 23:47:50.952143 INFO: Updating optimization_manager: fwhm_mobility       : 0.004394236020743847 -> 0.004386979155242443
2 days, 23:47:50.952242 INFO: Updating optimization_manager: score_cutoff        : 25.16318987503052 -> 24.912767807006833
2 days, 23:47:50.952337 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:50.953916 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:50.955848 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:50.957037 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:50.959665 INFO: === checking if optimization conditions were reached ===
2 days, 23:47:50.959809 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:47:50.960902 INFO: Updating optimization_manager: mobility_error      : 0.045529348690402184 -> 0.045529348690402184
2 days, 23:47:50.961088 INFO: Updating optimization_manager: classifier_version  : 9 -> 14
2 days, 23:47:50.961255 INFO: Updating optimization_manager: score_cutoff        : 24.912767807006833 -> 24.912767807006833
2 days, 23:47:50.961419 INFO: Updating optimization_manager: fwhm_rt             : 2.6070423126220703 -> 2.6070423126220703
2 days, 23:47:50.961575 INFO: Updating optimization_manager: fwhm_mobility       : 0.004386979155242443 -> 0.004386979155242443
2 days, 23:47:50.961732 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0455 found after 4 searches.
2 days, 23:47:50.961837 INFO: ==============================================
2 days, 23:47:50.961965 PROGRESS: Optimization finished for mobility_error.
2 days, 23:47:50.966634 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:50.967999 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:50.969855 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:50.971111 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:50.973694 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:47:50.973832 PROGRESS: ==============================================
2 days, 23:47:50.973959 PROGRESS: ms2_error      : 15.0000
2 days, 23:47:50.974061 PROGRESS: ms1_error      : 15.0000
2 days, 23:47:50.974161 PROGRESS: rt_error       : 492.6865
2 days, 23:47:50.974261 PROGRESS: mobility_error : 0.0455
2 days, 23:47:50.974355 PROGRESS: ==============================================
2 days, 23:47:50.975226 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:47:50.979906 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:47:50.998558 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:47:51.002591 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:47:51.052745 INFO: Using python extraction backend
2 days, 23:47:51.058351 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:47:51.058840 INFO: === Search parameters used ===
2 days, 23:47:51.058940 INFO: rt_error       : 492.6865219160817
2 days, 23:47:51.059026 INFO: mobility_error : 0.045529348690402184
2 days, 23:47:51.059104 INFO: num_candidates : 3
2 days, 23:47:51.059182 INFO: ms1_error      : 15.0
2 days, 23:47:51.059253 INFO: ms2_error      : 15.0
2 days, 23:47:51.059335 INFO: fwhm_rt        : 2.6070423126220703
2 days, 23:47:51.059409 INFO: quant_window   : 3
2 days, 23:47:51.059478 INFO: ==============================================
2 days, 23:47:51.065678 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:47:51.065933 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:47:51.066129 INFO: FWHM in RT is 2.61 seconds, sigma is 0.43
2 days, 23:47:51.066226 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.38
2 days, 23:47:51.087075 INFO: Starting candidate selection
2 days, 23:48:21.504055 INFO: Removed 16116 precursors with score below cutoff 24.912767807006833
2 days, 23:48:21.998986 INFO: Starting candidate scoring
2 days, 23:48:23.073940 INFO: Finished candidate processing
2 days, 23:48:23.074065 INFO: Collecting candidate features
2 days, 23:48:23.172621 WARNING: intensity_correlation has 13 NaNs ( 0.02 % out of 61842)
2 days, 23:48:23.181082 INFO: Collecting fragment features
2 days, 23:48:23.230415 INFO: Finished candidate scoring
2 days, 23:48:23.279526 INFO: === Performing FDR correction with classifier version 14 ===
2 days, 23:48:23.280544 INFO: performing precursor FDR with 47 features
2 days, 23:48:23.280602 INFO: Decoy channel: -1
2 days, 23:48:23.280646 INFO: competitive: True
2 days, 23:48:23.302603 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:48:23.312640 WARNING: dropped 5 target PSMs due to missing features
2 days, 23:48:23.312764 WARNING: dropped 8 decoy PSMs due to missing features
2 days, 23:48:23.312829 WARNING: FDR calculation for 34538 target and 27291 decoy PSMs
2 days, 23:48:23.312862 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:48:23.323616 INFO: Estimating optimal hyperparameters - samples: 49,463, batch_size: 202, learning_rate: 2.22e-04
2 days, 23:48:23.323920 INFO: Using random state 738003 for train-test-split
2 days, 23:48:27.230831 INFO: Test AUC: 0.774
2 days, 23:48:27.230966 INFO: Train AUC: 0.782
2 days, 23:48:27.231007 INFO: AUC difference: 1.07%
2 days, 23:48:27.596251 INFO: Resetting torch num_threads to 80
2 days, 23:48:27.599281 INFO: Removing fragments below FDR threshold
2 days, 23:48:27.610265 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:48:27.610485 PROGRESS: Total precursors accumulated: 9,747
2 days, 23:48:27.610576 PROGRESS: Target precursors: 9,651 (99.02%)
2 days, 23:48:27.610647 PROGRESS: Decoy precursors: 96 (0.98%)
2 days, 23:48:27.610716 PROGRESS: 
2 days, 23:48:27.610769 PROGRESS: Precursor Summary:
2 days, 23:48:27.616045 PROGRESS: Channel   0:	 0.050 FDR: 9,651; 0.010 FDR: 9,651; 0.001 FDR: 7,649
2 days, 23:48:27.616288 PROGRESS: 
2 days, 23:48:27.616394 PROGRESS: Protein Summary:
2 days, 23:48:27.624425 PROGRESS: Channel   0:	 0.050 FDR: 1,516; 0.010 FDR: 1,516; 0.001 FDR: 1,355
2 days, 23:48:27.624652 PROGRESS: =========================================================================
2 days, 23:48:27.625568 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R3/psm.parquet
2 days, 23:48:27.687383 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R3/frag.parquet
2 days, 23:48:27.741495 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R3
2 days, 23:48:27.747289 PROGRESS: Loading raw file 4/12: A9_G_DIA_nLC_tTOF_R4 
2 days, 23:48:27.747437 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:48:27.747521 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R4/figures
2 days, 23:48:27.747732 INFO: Initializing TimingManager
2 days, 23:48:27.748406 INFO: Initializing RawFileManager
2 days, 23:48:27.748564 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:27.748633 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:27.748680 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:27.970484 INFO: Reading 22,622 frames with 404,833,767 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:31.933036 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d...
2 days, 23:48:31.934050 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:31.936004 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:31.936230 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:31.936646 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:31.938277 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:31.967011 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:31.971857 INFO: Indexing quadrupole dimension
2 days, 23:48:32.117496 INFO: Transposing detector events
2 days, 23:48:34.402885 INFO: Finished transposing data
2 days, 23:48:34.403017 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
2 days, 23:48:34.403366 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:48:34.403417 INFO: RT duration (sec)   : 2399.9
2 days, 23:48:34.403446 INFO: RT duration (min)   : 40.0
2 days, 23:48:34.403472 INFO: Cycle len (scans)   : 12
2 days, 23:48:34.403498 INFO: Cycle len (sec)     : 1.27
2 days, 23:48:34.403522 INFO: Number of cycles    : 1885
2 days, 23:48:34.403547 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:48:34.403580 INFO: Creating DIA data object took: 6.655022144317627
2 days, 23:48:34.410250 INFO: Initializing CalibrationManager
2 days, 23:48:34.410459 INFO: Setting up calibration estimators ..
2 days, 23:48:34.410530 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:48:34.410605 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:48:34.410682 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:48:34.410751 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:48:34.410818 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:48:34.410886 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:48:34.410946 INFO: Done setting up calibration estimators.
2 days, 23:48:34.411052 INFO: Initializing OptimizationManager
2 days, 23:48:34.411186 INFO: initial parameter: ms1_error = 30
2 days, 23:48:34.411245 INFO: initial parameter: ms2_error = 30
2 days, 23:48:34.411301 INFO: initial parameter: rt_error = 1199.9717345
2 days, 23:48:34.411355 INFO: initial parameter: mobility_error = 0.1
2 days, 23:48:34.411408 INFO: initial parameter: num_candidates = 1
2 days, 23:48:34.411460 INFO: initial parameter: fwhm_rt = 5
2 days, 23:48:34.411513 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:48:34.411565 INFO: initial parameter: score_cutoff = 0
2 days, 23:48:34.411617 INFO: initial parameter: classifier_version = -1
2 days, 23:48:34.411698 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R4
2 days, 23:48:34.411878 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:48:34.411914 INFO: Initializing FDRManager
2 days, 23:48:34.411953 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:48:34.419926 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:48:34.424813 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:48:34.425146 INFO: Updating optimization_manager: rt_error            : 1199.9717345 -> 1199.9717345
2 days, 23:48:34.425254 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:48:34.425461 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:48:34.425553 PROGRESS: Starting initial search for precursors.
2 days, 23:48:34.425643 INFO: Starting optimization step 0.
2 days, 23:48:34.425712 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:48:34.425787 INFO: Using python extraction backend
2 days, 23:48:34.425924 PROGRESS: Extracting batch of 399 precursors
2 days, 23:48:34.426017 INFO: === Search parameters used ===
2 days, 23:48:34.426080 INFO: rt_error       : 1199.9717345
2 days, 23:48:34.426136 INFO: mobility_error : 0.1
2 days, 23:48:34.426190 INFO: num_candidates : 1
2 days, 23:48:34.426244 INFO: ms1_error      : 30
2 days, 23:48:34.426296 INFO: ms2_error      : 30
2 days, 23:48:34.426348 INFO: fwhm_rt        : 5
2 days, 23:48:34.426398 INFO: quant_window   : 3
2 days, 23:48:34.426450 INFO: ==============================================
2 days, 23:48:34.427193 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:48:34.427246 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:48:34.427279 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:48:34.427308 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:48:34.462183 INFO: Starting candidate selection
2 days, 23:48:37.978627 INFO: Starting candidate scoring
2 days, 23:48:38.026001 INFO: Finished candidate processing
2 days, 23:48:38.026147 INFO: Collecting candidate features
2 days, 23:48:38.044832 INFO: Collecting fragment features
2 days, 23:48:38.048785 INFO: Finished candidate scoring
2 days, 23:48:38.050068 INFO: performing precursor FDR with 47 features
2 days, 23:48:38.050131 INFO: Decoy channel: -1
2 days, 23:48:38.050164 INFO: competitive: True
2 days, 23:48:38.051691 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:48:38.053572 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:48:38.054661 INFO: Using random state 788858 for train-test-split
2 days, 23:48:38.094125 INFO: Test AUC: 0.691
2 days, 23:48:38.094265 INFO: Train AUC: 0.729
2 days, 23:48:38.094314 INFO: AUC difference: 5.26%
2 days, 23:48:38.094351 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:48:38.422053 INFO: Resetting torch num_threads to 80
2 days, 23:48:38.422593 PROGRESS: === Extracted 399 precursors and 3752 fragments ===
2 days, 23:48:38.423111 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:48:38.423826 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:48:38.423929 PROGRESS: Total precursors accumulated: 200
2 days, 23:48:38.424003 PROGRESS: Target precursors: 146 (73.00%)
2 days, 23:48:38.424067 PROGRESS: Decoy precursors: 54 (27.00%)
2 days, 23:48:38.424126 PROGRESS: 
2 days, 23:48:38.424183 PROGRESS: Precursor Summary:
2 days, 23:48:38.425154 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
2 days, 23:48:38.425252 PROGRESS: 
2 days, 23:48:38.425318 PROGRESS: Protein Summary:
2 days, 23:48:38.426418 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2 days, 23:48:38.426522 PROGRESS: =========================================================================
2 days, 23:48:38.426645 INFO: Target number of precursors not reached yet.
2 days, 23:48:38.429453 INFO: Starting optimization step 1.
2 days, 23:48:38.429574 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:48:38.429671 INFO: Using python extraction backend
2 days, 23:48:38.429792 PROGRESS: Extracting batch of 798 precursors
2 days, 23:48:38.429888 INFO: === Search parameters used ===
2 days, 23:48:38.429963 INFO: rt_error       : 1199.9717345
2 days, 23:48:38.430021 INFO: mobility_error : 0.1
2 days, 23:48:38.430076 INFO: num_candidates : 1
2 days, 23:48:38.430129 INFO: ms1_error      : 30
2 days, 23:48:38.430180 INFO: ms2_error      : 30
2 days, 23:48:38.430233 INFO: fwhm_rt        : 5
2 days, 23:48:38.430284 INFO: quant_window   : 3
2 days, 23:48:38.430335 INFO: ==============================================
2 days, 23:48:38.431048 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:48:38.431100 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:48:38.431133 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:48:38.431167 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:48:38.441968 INFO: Starting candidate selection
2 days, 23:48:43.164259 INFO: Starting candidate scoring
2 days, 23:48:43.239250 INFO: Finished candidate processing
2 days, 23:48:43.239389 INFO: Collecting candidate features
2 days, 23:48:43.258227 INFO: Collecting fragment features
2 days, 23:48:43.262555 INFO: Finished candidate scoring
2 days, 23:48:43.265898 INFO: performing precursor FDR with 47 features
2 days, 23:48:43.265969 INFO: Decoy channel: -1
2 days, 23:48:43.266010 INFO: competitive: True
2 days, 23:48:43.270486 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:48:43.273000 INFO: Estimating optimal hyperparameters - samples: 957, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:48:43.273169 INFO: Using random state 283985 for train-test-split
2 days, 23:48:43.386633 INFO: Test AUC: 0.770
2 days, 23:48:43.386738 INFO: Train AUC: 0.799
2 days, 23:48:43.386770 INFO: AUC difference: 3.61%
2 days, 23:48:43.774308 INFO: Resetting torch num_threads to 80
2 days, 23:48:43.776294 PROGRESS: === Extracted 1197 precursors and 11557 fragments ===
2 days, 23:48:43.776882 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:48:43.777797 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:48:43.777947 PROGRESS: Total precursors accumulated: 600
2 days, 23:48:43.778050 PROGRESS: Target precursors: 476 (79.33%)
2 days, 23:48:43.778141 PROGRESS: Decoy precursors: 124 (20.67%)
2 days, 23:48:43.778227 PROGRESS: 
2 days, 23:48:43.778323 PROGRESS: Precursor Summary:
2 days, 23:48:43.780911 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   248; 0.001 FDR:   155
2 days, 23:48:43.781040 PROGRESS: 
2 days, 23:48:43.781137 PROGRESS: Protein Summary:
2 days, 23:48:43.783307 PROGRESS: Channel   0:	 0.050 FDR:   244; 0.010 FDR:   181; 0.001 FDR:   116
2 days, 23:48:43.783442 PROGRESS: =========================================================================
2 days, 23:48:43.783664 INFO: Target number of precursors reached.
2 days, 23:48:43.789044 INFO: fragments_df: keeping 2111 of 11557 [sum(precursor_idx_mask)=2593 sum(mass_error_mask)=11557 stop_rank=2111
2 days, 23:48:43.794085 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:48:43.947159 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:48:44.135797 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:48:44.349162 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:48:44.796469 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:48:44.796934 INFO: Using score_cutoff 35.98789796562195 (fac=0.99, q=1)
2 days, 23:48:44.797288 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.9196152687072754
2 days, 23:48:44.797385 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007082799449563026
2 days, 23:48:44.797457 INFO: Updating optimization_manager: score_cutoff        : 0 -> 35.98789796562195
2 days, 23:48:44.797529 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:48:44.798987 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:48:44.800875 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:48:44.802089 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:48:44.804814 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2 days, 23:48:44.804971 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:48:44.805105 INFO: Starting optimization step 2.
2 days, 23:48:44.805221 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:48:44.805333 INFO: Using python extraction backend
2 days, 23:48:44.805505 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:48:44.805628 INFO: === Search parameters used ===
2 days, 23:48:44.805731 INFO: rt_error       : 1199.9717345
2 days, 23:48:44.805842 INFO: mobility_error : 0.1
2 days, 23:48:44.805957 INFO: num_candidates : 3
2 days, 23:48:44.806049 INFO: ms1_error      : 30
2 days, 23:48:44.806138 INFO: ms2_error      : 30
2 days, 23:48:44.806227 INFO: fwhm_rt        : 2.9196152687072754
2 days, 23:48:44.806317 INFO: quant_window   : 3
2 days, 23:48:44.806401 INFO: ==============================================
2 days, 23:48:44.807835 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:48:44.807902 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:48:44.807953 INFO: FWHM in RT is 2.92 seconds, sigma is 0.49
2 days, 23:48:44.807986 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.84
2 days, 23:48:44.818378 INFO: Starting candidate selection
2 days, 23:48:52.000812 INFO: Starting candidate scoring
2 days, 23:48:52.153522 INFO: Finished candidate processing
2 days, 23:48:52.153642 INFO: Collecting candidate features
2 days, 23:48:52.171952 INFO: Collecting fragment features
2 days, 23:48:52.177286 INFO: Finished candidate scoring
2 days, 23:48:52.180420 INFO: performing precursor FDR with 47 features
2 days, 23:48:52.180504 INFO: Decoy channel: -1
2 days, 23:48:52.180536 INFO: competitive: True
2 days, 23:48:52.184534 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:48:52.187409 INFO: Estimating optimal hyperparameters - samples: 2,747, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:48:52.187527 INFO: Using random state 687767 for train-test-split
2 days, 23:48:52.524400 INFO: Test AUC: 0.707
2 days, 23:48:52.524529 INFO: Train AUC: 0.697
2 days, 23:48:52.524568 INFO: AUC difference: 1.42%
2 days, 23:48:52.866592 INFO: Resetting torch num_threads to 80
2 days, 23:48:52.867395 PROGRESS: === Extracted 3434 precursors and 31916 fragments ===
2 days, 23:48:52.868011 INFO: === FDR correction performed with classifier version 1 ===
2 days, 23:48:52.868987 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:48:52.869131 PROGRESS: Total precursors accumulated: 600
2 days, 23:48:52.869239 PROGRESS: Target precursors: 505 (84.17%)
2 days, 23:48:52.869343 PROGRESS: Decoy precursors: 95 (15.83%)
2 days, 23:48:52.869439 PROGRESS: 
2 days, 23:48:52.869530 PROGRESS: Precursor Summary:
2 days, 23:48:52.871474 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   323; 0.001 FDR:   317
2 days, 23:48:52.871607 PROGRESS: 
2 days, 23:48:52.871697 PROGRESS: Protein Summary:
2 days, 23:48:52.873891 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   238; 0.001 FDR:   234
2 days, 23:48:52.874032 PROGRESS: =========================================================================
2 days, 23:48:52.874258 INFO: Target number of precursors reached.
2 days, 23:48:52.885099 INFO: fragments_df: keeping 5000 of 31916 [sum(precursor_idx_mask)=9097 sum(mass_error_mask)=31916 stop_rank=5000
2 days, 23:48:52.890369 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:48:53.162604 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:48:53.385955 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:48:53.607011 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:48:54.527048 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:48:54.527516 INFO: Using score_cutoff 29.9417713886261 (fac=0.99, q=1)
2 days, 23:48:54.527871 INFO: Updating optimization_manager: fwhm_rt             : 2.9196152687072754 -> 2.8325729370117188
2 days, 23:48:54.527980 INFO: Updating optimization_manager: fwhm_mobility       : 0.007082799449563026 -> 0.006428279913961887
2 days, 23:48:54.528053 INFO: Updating optimization_manager: score_cutoff        : 35.98789796562195 -> 29.9417713886261
2 days, 23:48:54.528122 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:48:54.529403 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:48:54.531279 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:48:54.532417 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:48:54.535075 INFO: === checking if optimization conditions were reached ===
2 days, 23:48:54.537543 INFO: Updating optimization_manager: ms2_error           : 30 -> 18.05419622210978
2 days, 23:48:54.537684 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2 days, 23:48:54.537793 PROGRESS: ❌ ms2_error      : 18.0542 > 15.0000 or insufficient steps taken.
2 days, 23:48:54.539348 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:48:54.539482 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
2 days, 23:48:54.539585 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:48:54.539670 INFO: ==============================================
2 days, 23:48:54.539759 INFO: Starting optimization step 3.
2 days, 23:48:54.539843 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:48:54.539927 INFO: Using python extraction backend
2 days, 23:48:54.540090 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:48:54.540213 INFO: === Search parameters used ===
2 days, 23:48:54.540312 INFO: rt_error       : 1199.9717345
2 days, 23:48:54.540407 INFO: mobility_error : 0.1
2 days, 23:48:54.540504 INFO: num_candidates : 3
2 days, 23:48:54.540599 INFO: ms1_error      : 15.0
2 days, 23:48:54.540690 INFO: ms2_error      : 18.05419622210978
2 days, 23:48:54.540770 INFO: fwhm_rt        : 2.8325729370117188
2 days, 23:48:54.540851 INFO: quant_window   : 3
2 days, 23:48:54.540938 INFO: ==============================================
2 days, 23:48:54.542336 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:48:54.542408 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:48:54.542464 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
2 days, 23:48:54.542506 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.48
2 days, 23:48:54.567477 INFO: Starting candidate selection
2 days, 23:49:00.659534 INFO: Starting candidate scoring
2 days, 23:49:00.778554 INFO: Finished candidate processing
2 days, 23:49:00.778779 INFO: Collecting candidate features
2 days, 23:49:00.794061 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3411)
2 days, 23:49:00.803242 INFO: Collecting fragment features
2 days, 23:49:00.809824 INFO: Finished candidate scoring
2 days, 23:49:00.813804 INFO: performing precursor FDR with 47 features
2 days, 23:49:00.814044 INFO: Decoy channel: -1
2 days, 23:49:00.814177 INFO: competitive: True
2 days, 23:49:00.819531 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:00.821967 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 23:49:00.823647 INFO: Estimating optimal hyperparameters - samples: 2,728, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:00.823832 INFO: Using random state 154013 for train-test-split
2 days, 23:49:01.160958 INFO: Test AUC: 0.747
2 days, 23:49:01.161100 INFO: Train AUC: 0.747
2 days, 23:49:01.161150 INFO: AUC difference: 0.03%
2 days, 23:49:01.542639 INFO: Resetting torch num_threads to 80
2 days, 23:49:01.543459 PROGRESS: === Extracted 3411 precursors and 29102 fragments ===
2 days, 23:49:01.544070 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:49:01.545060 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:01.545188 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:01.545286 PROGRESS: Target precursors: 525 (87.50%)
2 days, 23:49:01.545372 PROGRESS: Decoy precursors: 75 (12.50%)
2 days, 23:49:01.545452 PROGRESS: 
2 days, 23:49:01.545537 PROGRESS: Precursor Summary:
2 days, 23:49:01.547485 PROGRESS: Channel   0:	 0.050 FDR:   452; 0.010 FDR:   402; 0.001 FDR:   355
2 days, 23:49:01.547640 PROGRESS: 
2 days, 23:49:01.547751 PROGRESS: Protein Summary:
2 days, 23:49:01.549958 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:   295; 0.001 FDR:   263
2 days, 23:49:01.550099 PROGRESS: =========================================================================
2 days, 23:49:01.550338 INFO: Target number of precursors reached.
2 days, 23:49:01.560767 INFO: fragments_df: keeping 5000 of 29102 [sum(precursor_idx_mask)=10729 sum(mass_error_mask)=29102 stop_rank=5000
2 days, 23:49:01.565741 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:01.740552 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:01.908815 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:02.135998 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:03.096030 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:03.096517 INFO: Using score_cutoff 24.338500792121888 (fac=0.99, q=1)
2 days, 23:49:03.096935 INFO: Updating optimization_manager: fwhm_rt             : 2.8325729370117188 -> 2.6889164447784424
2 days, 23:49:03.097052 INFO: Updating optimization_manager: fwhm_mobility       : 0.006428279913961887 -> 0.0053056515753269196
2 days, 23:49:03.097135 INFO: Updating optimization_manager: score_cutoff        : 29.9417713886261 -> 24.338500792121888
2 days, 23:49:03.097216 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:03.098433 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:03.100014 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:03.100934 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:03.103325 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:03.105138 INFO: Updating optimization_manager: ms2_error           : 18.05419622210978 -> 15.0
2 days, 23:49:03.105263 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:49:03.105359 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:49:03.106478 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:49:03.106601 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:49:03.106690 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:49:03.106771 INFO: ==============================================
2 days, 23:49:03.106865 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:49:03.110502 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:03.111418 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:03.112872 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:03.113704 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:03.115762 INFO: Starting optimization step 0.
2 days, 23:49:03.115895 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:03.116024 INFO: Using python extraction backend
2 days, 23:49:03.116155 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:03.116237 INFO: === Search parameters used ===
2 days, 23:49:03.116299 INFO: rt_error       : 1199.9717345
2 days, 23:49:03.116358 INFO: mobility_error : 0.1
2 days, 23:49:03.116411 INFO: num_candidates : 3
2 days, 23:49:03.116470 INFO: ms1_error      : 15.0
2 days, 23:49:03.116527 INFO: ms2_error      : 15.0
2 days, 23:49:03.116578 INFO: fwhm_rt        : 2.6889164447784424
2 days, 23:49:03.116630 INFO: quant_window   : 3
2 days, 23:49:03.116690 INFO: ==============================================
2 days, 23:49:03.117611 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:03.117666 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:03.117707 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
2 days, 23:49:03.117733 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.88
2 days, 23:49:03.122865 INFO: Starting candidate selection
2 days, 23:49:12.200118 INFO: Starting candidate scoring
2 days, 23:49:12.309266 INFO: Finished candidate processing
2 days, 23:49:12.309393 INFO: Collecting candidate features
2 days, 23:49:12.325619 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3375)
2 days, 23:49:12.333882 INFO: Collecting fragment features
2 days, 23:49:12.340274 INFO: Finished candidate scoring
2 days, 23:49:12.343616 INFO: performing precursor FDR with 47 features
2 days, 23:49:12.343695 INFO: Decoy channel: -1
2 days, 23:49:12.343735 INFO: competitive: True
2 days, 23:49:12.348468 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:12.350658 WARNING: dropped 1 decoy PSMs due to missing features
2 days, 23:49:12.352117 INFO: Estimating optimal hyperparameters - samples: 2,699, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:12.352222 INFO: Using random state 607432 for train-test-split
2 days, 23:49:12.633016 INFO: Test AUC: 0.741
2 days, 23:49:12.633128 INFO: Train AUC: 0.763
2 days, 23:49:12.633169 INFO: AUC difference: 2.90%
2 days, 23:49:12.925767 INFO: Resetting torch num_threads to 80
2 days, 23:49:12.926352 PROGRESS: === Extracted 3375 precursors and 27732 fragments ===
2 days, 23:49:12.926790 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:12.927400 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:12.927495 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:12.927572 PROGRESS: Target precursors: 528 (88.00%)
2 days, 23:49:12.927639 PROGRESS: Decoy precursors: 72 (12.00%)
2 days, 23:49:12.927699 PROGRESS: 
2 days, 23:49:12.927757 PROGRESS: Precursor Summary:
2 days, 23:49:12.928895 PROGRESS: Channel   0:	 0.050 FDR:   457; 0.010 FDR:   391; 0.001 FDR:   375
2 days, 23:49:12.929002 PROGRESS: 
2 days, 23:49:12.929073 PROGRESS: Protein Summary:
2 days, 23:49:12.930397 PROGRESS: Channel   0:	 0.050 FDR:   334; 0.010 FDR:   290; 0.001 FDR:   280
2 days, 23:49:12.930501 PROGRESS: =========================================================================
2 days, 23:49:12.930659 INFO: Target number of precursors reached.
2 days, 23:49:12.937237 INFO: fragments_df: keeping 5000 of 27732 [sum(precursor_idx_mask)=10170 sum(mass_error_mask)=27732 stop_rank=5000
2 days, 23:49:12.940723 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:13.122605 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:13.271210 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:13.454407 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:14.291413 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:14.291931 INFO: Using score_cutoff 24.75371367073059 (fac=0.99, q=1)
2 days, 23:49:14.292341 INFO: Updating optimization_manager: fwhm_rt             : 2.6889164447784424 -> 2.7156810760498047
2 days, 23:49:14.292453 INFO: Updating optimization_manager: fwhm_mobility       : 0.0053056515753269196 -> 0.005197020713239908
2 days, 23:49:14.292536 INFO: Updating optimization_manager: score_cutoff        : 24.338500792121888 -> 24.75371367073059
2 days, 23:49:14.292626 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:14.293812 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:14.295433 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:14.296357 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:14.298643 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:14.298797 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:49:14.300574 INFO: Updating optimization_manager: rt_error            : 1199.9717345 -> 267.9677613908207
2 days, 23:49:14.300702 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 267.9678.
2 days, 23:49:14.300792 INFO: ==============================================
2 days, 23:49:14.300892 INFO: Starting optimization step 1.
2 days, 23:49:14.300979 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:14.301061 INFO: Using python extraction backend
2 days, 23:49:14.301183 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:14.301273 INFO: === Search parameters used ===
2 days, 23:49:14.301341 INFO: rt_error       : 267.9677613908207
2 days, 23:49:14.301394 INFO: mobility_error : 0.1
2 days, 23:49:14.301440 INFO: num_candidates : 3
2 days, 23:49:14.301483 INFO: ms1_error      : 15.0
2 days, 23:49:14.301528 INFO: ms2_error      : 15.0
2 days, 23:49:14.301570 INFO: fwhm_rt        : 2.7156810760498047
2 days, 23:49:14.301612 INFO: quant_window   : 3
2 days, 23:49:14.301654 INFO: ==============================================
2 days, 23:49:14.302652 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:14.302708 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:14.302766 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
2 days, 23:49:14.302804 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.82
2 days, 23:49:14.314275 INFO: Starting candidate selection
2 days, 23:49:17.756989 INFO: Starting candidate scoring
2 days, 23:49:17.870987 INFO: Finished candidate processing
2 days, 23:49:17.871126 INFO: Collecting candidate features
2 days, 23:49:17.887661 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3316)
2 days, 23:49:17.892941 INFO: Collecting fragment features
2 days, 23:49:17.897223 INFO: Finished candidate scoring
2 days, 23:49:17.899533 INFO: performing precursor FDR with 47 features
2 days, 23:49:17.899602 INFO: Decoy channel: -1
2 days, 23:49:17.899641 INFO: competitive: True
2 days, 23:49:17.902896 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:17.904376 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 23:49:17.905485 INFO: Estimating optimal hyperparameters - samples: 2,649, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:17.905588 INFO: Using random state 607432 for train-test-split
2 days, 23:49:18.201476 INFO: Test AUC: 0.772
2 days, 23:49:18.201619 INFO: Train AUC: 0.787
2 days, 23:49:18.201674 INFO: AUC difference: 1.96%
2 days, 23:49:18.502264 INFO: Resetting torch num_threads to 80
2 days, 23:49:18.503053 PROGRESS: === Extracted 3316 precursors and 26536 fragments ===
2 days, 23:49:18.503675 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:18.504595 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:18.504724 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:18.504837 PROGRESS: Target precursors: 548 (91.33%)
2 days, 23:49:18.504933 PROGRESS: Decoy precursors: 52 (8.67%)
2 days, 23:49:18.505024 PROGRESS: 
2 days, 23:49:18.505114 PROGRESS: Precursor Summary:
2 days, 23:49:18.507096 PROGRESS: Channel   0:	 0.050 FDR:   504; 0.010 FDR:   460; 0.001 FDR:   417
2 days, 23:49:18.507233 PROGRESS: 
2 days, 23:49:18.507332 PROGRESS: Protein Summary:
2 days, 23:49:18.509537 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   338; 0.001 FDR:   309
2 days, 23:49:18.509666 PROGRESS: =========================================================================
2 days, 23:49:18.509922 INFO: Target number of precursors reached.
2 days, 23:49:18.519959 INFO: fragments_df: keeping 5000 of 26536 [sum(precursor_idx_mask)=11670 sum(mass_error_mask)=26536 stop_rank=5000
2 days, 23:49:18.524915 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:18.699132 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:18.861441 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:19.043060 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:19.874496 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:19.874943 INFO: Using score_cutoff 23.177194318199156 (fac=0.99, q=1)
2 days, 23:49:19.875294 INFO: Updating optimization_manager: fwhm_rt             : 2.7156810760498047 -> 2.65139102935791
2 days, 23:49:19.875392 INFO: Updating optimization_manager: fwhm_mobility       : 0.005197020713239908 -> 0.00466372724622488
2 days, 23:49:19.875471 INFO: Updating optimization_manager: score_cutoff        : 24.75371367073059 -> 23.177194318199156
2 days, 23:49:19.875554 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:19.876675 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:19.878177 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:19.879012 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:19.881087 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:19.881211 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:49:19.883082 INFO: Updating optimization_manager: rt_error            : 267.9677613908207 -> 54.902813600209065
2 days, 23:49:19.883197 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 54.9028.
2 days, 23:49:19.883282 INFO: ==============================================
2 days, 23:49:19.883366 INFO: Starting optimization step 2.
2 days, 23:49:19.883438 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:19.883505 INFO: Using python extraction backend
2 days, 23:49:19.883613 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:19.883690 INFO: === Search parameters used ===
2 days, 23:49:19.883758 INFO: rt_error       : 54.902813600209065
2 days, 23:49:19.883816 INFO: mobility_error : 0.1
2 days, 23:49:19.883869 INFO: num_candidates : 3
2 days, 23:49:19.883924 INFO: ms1_error      : 15.0
2 days, 23:49:19.883978 INFO: ms2_error      : 15.0
2 days, 23:49:19.884031 INFO: fwhm_rt        : 2.65139102935791
2 days, 23:49:19.884083 INFO: quant_window   : 3
2 days, 23:49:19.884134 INFO: ==============================================
2 days, 23:49:19.885011 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:19.885066 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:19.885106 INFO: FWHM in RT is 2.65 seconds, sigma is 0.44
2 days, 23:49:19.885135 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
2 days, 23:49:19.898039 INFO: Starting candidate selection
2 days, 23:49:20.763416 INFO: Starting candidate scoring
2 days, 23:49:20.880995 INFO: Finished candidate processing
2 days, 23:49:20.881117 INFO: Collecting candidate features
2 days, 23:49:20.893861 WARNING: intensity_correlation has 11 NaNs ( 0.33 % out of 3285)
2 days, 23:49:20.899236 INFO: Collecting fragment features
2 days, 23:49:20.904257 INFO: Finished candidate scoring
2 days, 23:49:20.906748 INFO: performing precursor FDR with 47 features
2 days, 23:49:20.906813 INFO: Decoy channel: -1
2 days, 23:49:20.906844 INFO: competitive: True
2 days, 23:49:20.910844 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:20.912811 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:49:20.912873 WARNING: dropped 8 decoy PSMs due to missing features
2 days, 23:49:20.914116 INFO: Estimating optimal hyperparameters - samples: 2,619, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:20.914215 INFO: Using random state 607432 for train-test-split
2 days, 23:49:21.249113 INFO: Test AUC: 0.808
2 days, 23:49:21.249253 INFO: Train AUC: 0.846
2 days, 23:49:21.249291 INFO: AUC difference: 4.42%
2 days, 23:49:21.554049 INFO: Resetting torch num_threads to 80
2 days, 23:49:21.554696 PROGRESS: === Extracted 3285 precursors and 24663 fragments ===
2 days, 23:49:21.555191 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:21.555963 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:21.556066 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:21.556135 PROGRESS: Target precursors: 573 (95.50%)
2 days, 23:49:21.556196 PROGRESS: Decoy precursors: 27 (4.50%)
2 days, 23:49:21.556253 PROGRESS: 
2 days, 23:49:21.556315 PROGRESS: Precursor Summary:
2 days, 23:49:21.557708 PROGRESS: Channel   0:	 0.050 FDR:   573; 0.010 FDR:   531; 0.001 FDR:   460
2 days, 23:49:21.557808 PROGRESS: 
2 days, 23:49:21.557888 PROGRESS: Protein Summary:
2 days, 23:49:21.559625 PROGRESS: Channel   0:	 0.050 FDR:   419; 0.010 FDR:   390; 0.001 FDR:   343
2 days, 23:49:21.559733 PROGRESS: =========================================================================
2 days, 23:49:21.559916 INFO: Target number of precursors reached.
2 days, 23:49:21.568712 INFO: fragments_df: keeping 5000 of 24663 [sum(precursor_idx_mask)=13124 sum(mass_error_mask)=24663 stop_rank=5000
2 days, 23:49:21.573201 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:21.743773 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:21.963240 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:22.162229 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:23.105693 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:23.106194 INFO: Using score_cutoff 18.668434690475465 (fac=0.99, q=1)
2 days, 23:49:23.106579 INFO: Updating optimization_manager: fwhm_rt             : 2.65139102935791 -> 2.623599052429199
2 days, 23:49:23.106682 INFO: Updating optimization_manager: fwhm_mobility       : 0.00466372724622488 -> 0.004256363492459059
2 days, 23:49:23.106761 INFO: Updating optimization_manager: score_cutoff        : 23.177194318199156 -> 18.668434690475465
2 days, 23:49:23.106841 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:23.108049 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:23.109631 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:23.110544 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:23.112739 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:23.112880 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:49:23.114987 INFO: Updating optimization_manager: rt_error            : 54.902813600209065 -> 34.8229885118132
2 days, 23:49:23.115115 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 34.8230.
2 days, 23:49:23.115195 INFO: ==============================================
2 days, 23:49:23.115281 INFO: Starting optimization step 3.
2 days, 23:49:23.115359 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:23.115437 INFO: Using python extraction backend
2 days, 23:49:23.115552 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:23.115632 INFO: === Search parameters used ===
2 days, 23:49:23.115697 INFO: rt_error       : 34.8229885118132
2 days, 23:49:23.115754 INFO: mobility_error : 0.1
2 days, 23:49:23.115808 INFO: num_candidates : 3
2 days, 23:49:23.115863 INFO: ms1_error      : 15.0
2 days, 23:49:23.115916 INFO: ms2_error      : 15.0
2 days, 23:49:23.115967 INFO: fwhm_rt        : 2.623599052429199
2 days, 23:49:23.116019 INFO: quant_window   : 3
2 days, 23:49:23.116069 INFO: ==============================================
2 days, 23:49:23.117027 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:23.117083 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:23.117124 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:49:23.117155 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.31
2 days, 23:49:23.130025 INFO: Starting candidate selection
2 days, 23:49:24.015217 INFO: Starting candidate scoring
2 days, 23:49:24.126655 INFO: Finished candidate processing
2 days, 23:49:24.126768 INFO: Collecting candidate features
2 days, 23:49:24.139295 WARNING: intensity_correlation has 13 NaNs ( 0.40 % out of 3259)
2 days, 23:49:24.144451 INFO: Collecting fragment features
2 days, 23:49:24.149027 INFO: Finished candidate scoring
2 days, 23:49:24.151432 INFO: performing precursor FDR with 47 features
2 days, 23:49:24.151492 INFO: Decoy channel: -1
2 days, 23:49:24.151523 INFO: competitive: True
2 days, 23:49:24.155329 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:24.157246 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:49:24.157315 WARNING: dropped 11 decoy PSMs due to missing features
2 days, 23:49:24.158527 INFO: Estimating optimal hyperparameters - samples: 2,596, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:24.158627 INFO: Using random state 607432 for train-test-split
2 days, 23:49:24.474866 INFO: Test AUC: 0.886
2 days, 23:49:24.474990 INFO: Train AUC: 0.853
2 days, 23:49:24.475025 INFO: AUC difference: 3.96%
2 days, 23:49:24.779904 INFO: Resetting torch num_threads to 80
2 days, 23:49:24.780614 PROGRESS: === Extracted 3259 precursors and 24286 fragments ===
2 days, 23:49:24.781121 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:24.781837 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:24.781955 PROGRESS: Total precursors accumulated: 599
2 days, 23:49:24.782028 PROGRESS: Target precursors: 578 (96.49%)
2 days, 23:49:24.782096 PROGRESS: Decoy precursors: 21 (3.51%)
2 days, 23:49:24.782157 PROGRESS: 
2 days, 23:49:24.782214 PROGRESS: Precursor Summary:
2 days, 23:49:24.783620 PROGRESS: Channel   0:	 0.050 FDR:   578; 0.010 FDR:   537; 0.001 FDR:   466
2 days, 23:49:24.783725 PROGRESS: 
2 days, 23:49:24.783794 PROGRESS: Protein Summary:
2 days, 23:49:24.785436 PROGRESS: Channel   0:	 0.050 FDR:   423; 0.010 FDR:   397; 0.001 FDR:   350
2 days, 23:49:24.785541 PROGRESS: =========================================================================
2 days, 23:49:24.785716 INFO: Target number of precursors reached.
2 days, 23:49:24.794345 INFO: fragments_df: keeping 5000 of 24286 [sum(precursor_idx_mask)=13283 sum(mass_error_mask)=24286 stop_rank=5000
2 days, 23:49:24.798590 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:25.004557 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:25.240458 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:25.444423 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:26.247207 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:26.247717 INFO: Using score_cutoff 17.08449908065796 (fac=0.99, q=1)
2 days, 23:49:26.248112 INFO: Updating optimization_manager: fwhm_rt             : 2.623599052429199 -> 2.6021080017089844
2 days, 23:49:26.248220 INFO: Updating optimization_manager: fwhm_mobility       : 0.004256363492459059 -> 0.004161025397479534
2 days, 23:49:26.248307 INFO: Updating optimization_manager: score_cutoff        : 18.668434690475465 -> 17.08449908065796
2 days, 23:49:26.248392 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:26.249565 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:26.251032 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:26.251870 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:26.254083 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:26.254221 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:49:26.256217 INFO: Updating optimization_manager: rt_error            : 34.8229885118132 -> 19.297696011186506
2 days, 23:49:26.256340 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 19.2977.
2 days, 23:49:26.256436 INFO: ==============================================
2 days, 23:49:26.256524 INFO: Starting optimization step 4.
2 days, 23:49:26.256612 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:26.256704 INFO: Using python extraction backend
2 days, 23:49:26.256848 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:26.256943 INFO: === Search parameters used ===
2 days, 23:49:26.257024 INFO: rt_error       : 19.297696011186506
2 days, 23:49:26.257095 INFO: mobility_error : 0.1
2 days, 23:49:26.257175 INFO: num_candidates : 3
2 days, 23:49:26.257248 INFO: ms1_error      : 15.0
2 days, 23:49:26.257312 INFO: ms2_error      : 15.0
2 days, 23:49:26.257383 INFO: fwhm_rt        : 2.6021080017089844
2 days, 23:49:26.257445 INFO: quant_window   : 3
2 days, 23:49:26.257505 INFO: ==============================================
2 days, 23:49:26.258429 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:26.258483 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:26.258533 INFO: FWHM in RT is 2.60 seconds, sigma is 0.43
2 days, 23:49:26.258570 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.26
2 days, 23:49:26.270116 INFO: Starting candidate selection
2 days, 23:49:26.814701 INFO: Starting candidate scoring
2 days, 23:49:26.923088 INFO: Finished candidate processing
2 days, 23:49:26.923220 INFO: Collecting candidate features
2 days, 23:49:26.938829 WARNING: intensity_correlation has 17 NaNs ( 0.53 % out of 3237)
2 days, 23:49:26.944777 INFO: Collecting fragment features
2 days, 23:49:26.949243 INFO: Finished candidate scoring
2 days, 23:49:26.951586 INFO: performing precursor FDR with 47 features
2 days, 23:49:26.951669 INFO: Decoy channel: -1
2 days, 23:49:26.951708 INFO: competitive: True
2 days, 23:49:26.955040 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:26.956798 WARNING: dropped 7 target PSMs due to missing features
2 days, 23:49:26.956905 WARNING: dropped 10 decoy PSMs due to missing features
2 days, 23:49:26.958032 INFO: Estimating optimal hyperparameters - samples: 2,576, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:26.958136 INFO: Using random state 607432 for train-test-split
2 days, 23:49:27.299596 INFO: Test AUC: 0.889
2 days, 23:49:27.299736 INFO: Train AUC: 0.870
2 days, 23:49:27.299802 INFO: AUC difference: 2.15%
2 days, 23:49:27.613662 INFO: Resetting torch num_threads to 80
2 days, 23:49:27.614336 PROGRESS: === Extracted 3237 precursors and 23497 fragments ===
2 days, 23:49:27.614852 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:27.615613 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:27.615733 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:27.615823 PROGRESS: Target precursors: 590 (98.33%)
2 days, 23:49:27.615901 PROGRESS: Decoy precursors: 10 (1.67%)
2 days, 23:49:27.615974 PROGRESS: 
2 days, 23:49:27.616038 PROGRESS: Precursor Summary:
2 days, 23:49:27.617389 PROGRESS: Channel   0:	 0.050 FDR:   590; 0.010 FDR:   577; 0.001 FDR:   522
2 days, 23:49:27.617508 PROGRESS: 
2 days, 23:49:27.617591 PROGRESS: Protein Summary:
2 days, 23:49:27.619091 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   422; 0.001 FDR:   390
2 days, 23:49:27.619209 PROGRESS: =========================================================================
2 days, 23:49:27.619392 INFO: Target number of precursors reached.
2 days, 23:49:27.626170 INFO: fragments_df: keeping 5000 of 23497 [sum(precursor_idx_mask)=13970 sum(mass_error_mask)=23497 stop_rank=5000
2 days, 23:49:27.630158 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:27.846013 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:28.088917 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:28.290945 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:29.084997 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:29.085569 INFO: Using score_cutoff 14.963298850250245 (fac=0.99, q=1)
2 days, 23:49:29.086031 INFO: Updating optimization_manager: fwhm_rt             : 2.6021080017089844 -> 2.578964948654175
2 days, 23:49:29.086149 INFO: Updating optimization_manager: fwhm_mobility       : 0.004161025397479534 -> 0.003981673624366522
2 days, 23:49:29.086239 INFO: Updating optimization_manager: score_cutoff        : 17.08449908065796 -> 14.963298850250245
2 days, 23:49:29.086324 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:29.087768 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:29.089525 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:29.090539 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:29.092669 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:29.092781 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:49:29.094773 INFO: Updating optimization_manager: rt_error            : 19.297696011186506 -> 12.721276466370153
2 days, 23:49:29.094891 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 12.7213.
2 days, 23:49:29.094962 INFO: ==============================================
2 days, 23:49:29.095044 INFO: Starting optimization step 5.
2 days, 23:49:29.095110 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:29.095173 INFO: Using python extraction backend
2 days, 23:49:29.095274 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:29.095342 INFO: === Search parameters used ===
2 days, 23:49:29.095393 INFO: rt_error       : 12.721276466370153
2 days, 23:49:29.095440 INFO: mobility_error : 0.1
2 days, 23:49:29.095486 INFO: num_candidates : 3
2 days, 23:49:29.095531 INFO: ms1_error      : 15.0
2 days, 23:49:29.095575 INFO: ms2_error      : 15.0
2 days, 23:49:29.095618 INFO: fwhm_rt        : 2.578964948654175
2 days, 23:49:29.095663 INFO: quant_window   : 3
2 days, 23:49:29.095707 INFO: ==============================================
2 days, 23:49:29.096554 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:29.096603 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:29.096639 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:29.096662 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.16
2 days, 23:49:29.103079 INFO: Starting candidate selection
2 days, 23:49:29.664904 INFO: Starting candidate scoring
2 days, 23:49:29.776122 INFO: Finished candidate processing
2 days, 23:49:29.776247 INFO: Collecting candidate features
2 days, 23:49:29.788074 WARNING: intensity_correlation has 20 NaNs ( 0.62 % out of 3220)
2 days, 23:49:29.792269 INFO: Collecting fragment features
2 days, 23:49:29.796491 INFO: Finished candidate scoring
2 days, 23:49:29.798631 INFO: performing precursor FDR with 47 features
2 days, 23:49:29.798714 INFO: Decoy channel: -1
2 days, 23:49:29.798750 INFO: competitive: True
2 days, 23:49:29.802775 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:29.804565 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:49:29.804635 WARNING: dropped 18 decoy PSMs due to missing features
2 days, 23:49:29.805700 INFO: Estimating optimal hyperparameters - samples: 2,560, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:29.805809 INFO: Using random state 607432 for train-test-split
2 days, 23:49:30.100871 INFO: Test AUC: 0.859
2 days, 23:49:30.101002 INFO: Train AUC: 0.880
2 days, 23:49:30.101047 INFO: AUC difference: 2.32%
2 days, 23:49:30.412483 INFO: Resetting torch num_threads to 80
2 days, 23:49:30.413186 PROGRESS: === Extracted 3220 precursors and 23485 fragments ===
2 days, 23:49:30.413686 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:30.414374 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:30.414496 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:30.414594 PROGRESS: Target precursors: 586 (97.67%)
2 days, 23:49:30.414675 PROGRESS: Decoy precursors: 14 (2.33%)
2 days, 23:49:30.414751 PROGRESS: 
2 days, 23:49:30.414822 PROGRESS: Precursor Summary:
2 days, 23:49:30.416028 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   566; 0.001 FDR:   502
2 days, 23:49:30.416148 PROGRESS: 
2 days, 23:49:30.416238 PROGRESS: Protein Summary:
2 days, 23:49:30.417734 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   417; 0.001 FDR:   373
2 days, 23:49:30.417848 PROGRESS: =========================================================================
2 days, 23:49:30.418050 INFO: Target number of precursors reached.
2 days, 23:49:30.424810 INFO: fragments_df: keeping 5000 of 23485 [sum(precursor_idx_mask)=13688 sum(mass_error_mask)=23485 stop_rank=5000
2 days, 23:49:30.428393 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:30.627228 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:30.814456 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:31.064758 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:31.925999 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:31.926520 INFO: Using score_cutoff 15.215285363674163 (fac=0.99, q=1)
2 days, 23:49:31.926910 INFO: Updating optimization_manager: fwhm_rt             : 2.578964948654175 -> 2.582272529602051
2 days, 23:49:31.927025 INFO: Updating optimization_manager: fwhm_mobility       : 0.003981673624366522 -> 0.003974167630076408
2 days, 23:49:31.927110 INFO: Updating optimization_manager: score_cutoff        : 14.963298850250245 -> 15.215285363674163
2 days, 23:49:31.927186 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:31.928337 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:31.929811 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:31.930689 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:31.932787 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:31.932909 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 23:49:31.934945 INFO: Updating optimization_manager: rt_error            : 12.721276466370153 -> 10.63892938666839
2 days, 23:49:31.935066 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 10.6389.
2 days, 23:49:31.935148 INFO: ==============================================
2 days, 23:49:31.935232 INFO: Starting optimization step 6.
2 days, 23:49:31.935311 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:31.935381 INFO: Using python extraction backend
2 days, 23:49:31.935494 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:31.935571 INFO: === Search parameters used ===
2 days, 23:49:31.935629 INFO: rt_error       : 10.63892938666839
2 days, 23:49:31.935683 INFO: mobility_error : 0.1
2 days, 23:49:31.935735 INFO: num_candidates : 3
2 days, 23:49:31.935785 INFO: ms1_error      : 15.0
2 days, 23:49:31.935834 INFO: ms2_error      : 15.0
2 days, 23:49:31.935884 INFO: fwhm_rt        : 2.582272529602051
2 days, 23:49:31.935933 INFO: quant_window   : 3
2 days, 23:49:31.935982 INFO: ==============================================
2 days, 23:49:31.936855 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:31.936910 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:31.936961 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:31.936997 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.15
2 days, 23:49:31.943890 INFO: Starting candidate selection
2 days, 23:49:32.490055 INFO: Starting candidate scoring
2 days, 23:49:32.597534 INFO: Finished candidate processing
2 days, 23:49:32.597667 INFO: Collecting candidate features
2 days, 23:49:32.613940 WARNING: intensity_correlation has 20 NaNs ( 0.62 % out of 3214)
2 days, 23:49:32.622431 INFO: Collecting fragment features
2 days, 23:49:32.628538 INFO: Finished candidate scoring
2 days, 23:49:32.631934 INFO: performing precursor FDR with 47 features
2 days, 23:49:32.632032 INFO: Decoy channel: -1
2 days, 23:49:32.632070 INFO: competitive: True
2 days, 23:49:32.636874 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:32.639278 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:49:32.639360 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:49:32.640787 INFO: Estimating optimal hyperparameters - samples: 2,555, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:32.640892 INFO: Using random state 607432 for train-test-split
2 days, 23:49:32.854773 INFO: Test AUC: 0.859
2 days, 23:49:32.854888 INFO: Train AUC: 0.880
2 days, 23:49:32.854922 INFO: AUC difference: 2.40%
2 days, 23:49:33.140940 INFO: Resetting torch num_threads to 80
2 days, 23:49:33.141547 PROGRESS: === Extracted 3214 precursors and 23360 fragments ===
2 days, 23:49:33.142152 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:33.143009 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:33.143123 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:33.143205 PROGRESS: Target precursors: 589 (98.17%)
2 days, 23:49:33.143273 PROGRESS: Decoy precursors: 11 (1.83%)
2 days, 23:49:33.143334 PROGRESS: 
2 days, 23:49:33.143392 PROGRESS: Precursor Summary:
2 days, 23:49:33.144960 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   581; 0.001 FDR:   498
2 days, 23:49:33.145076 PROGRESS: 
2 days, 23:49:33.145165 PROGRESS: Protein Summary:
2 days, 23:49:33.146946 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   428; 0.001 FDR:   371
2 days, 23:49:33.147091 PROGRESS: =========================================================================
2 days, 23:49:33.147295 INFO: Target number of precursors reached.
2 days, 23:49:33.155176 INFO: fragments_df: keeping 5000 of 23360 [sum(precursor_idx_mask)=14003 sum(mass_error_mask)=23360 stop_rank=5000
2 days, 23:49:33.159384 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:33.369842 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:33.580320 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:33.797532 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:34.579488 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:34.579937 INFO: Using score_cutoff 14.784597513198854 (fac=0.99, q=1)
2 days, 23:49:34.580272 INFO: Updating optimization_manager: fwhm_rt             : 2.582272529602051 -> 2.5727720260620117
2 days, 23:49:34.580369 INFO: Updating optimization_manager: fwhm_mobility       : 0.003974167630076408 -> 0.003988002426922321
2 days, 23:49:34.580437 INFO: Updating optimization_manager: score_cutoff        : 15.215285363674163 -> 14.784597513198854
2 days, 23:49:34.580496 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:34.581594 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:34.582967 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:34.583782 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:34.585772 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:34.585899 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 23:49:34.587830 INFO: Updating optimization_manager: rt_error            : 10.63892938666839 -> 13.733547736206768
2 days, 23:49:34.587945 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 13.7335.
2 days, 23:49:34.588028 INFO: ==============================================
2 days, 23:49:34.588109 INFO: Starting optimization step 7.
2 days, 23:49:34.588173 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:34.588233 INFO: Using python extraction backend
2 days, 23:49:34.588332 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:34.588413 INFO: === Search parameters used ===
2 days, 23:49:34.588467 INFO: rt_error       : 13.733547736206768
2 days, 23:49:34.588514 INFO: mobility_error : 0.1
2 days, 23:49:34.588561 INFO: num_candidates : 3
2 days, 23:49:34.588609 INFO: ms1_error      : 15.0
2 days, 23:49:34.588661 INFO: ms2_error      : 15.0
2 days, 23:49:34.588708 INFO: fwhm_rt        : 2.5727720260620117
2 days, 23:49:34.588753 INFO: quant_window   : 3
2 days, 23:49:34.588796 INFO: ==============================================
2 days, 23:49:34.589619 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:34.589675 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:34.589711 INFO: FWHM in RT is 2.57 seconds, sigma is 0.43
2 days, 23:49:34.589734 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.16
2 days, 23:49:34.602016 INFO: Starting candidate selection
2 days, 23:49:35.223505 INFO: Starting candidate scoring
2 days, 23:49:35.330806 INFO: Finished candidate processing
2 days, 23:49:35.330937 INFO: Collecting candidate features
2 days, 23:49:35.343593 WARNING: intensity_correlation has 18 NaNs ( 0.56 % out of 3223)
2 days, 23:49:35.348862 INFO: Collecting fragment features
2 days, 23:49:35.353371 INFO: Finished candidate scoring
2 days, 23:49:35.355625 INFO: performing precursor FDR with 47 features
2 days, 23:49:35.355697 INFO: Decoy channel: -1
2 days, 23:49:35.355799 INFO: competitive: True
2 days, 23:49:35.359575 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:35.361431 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:49:35.361510 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:49:35.362735 INFO: Estimating optimal hyperparameters - samples: 2,564, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:35.362849 INFO: Using random state 607432 for train-test-split
2 days, 23:49:35.611844 INFO: Test AUC: 0.854
2 days, 23:49:35.611969 INFO: Train AUC: 0.884
2 days, 23:49:35.612007 INFO: AUC difference: 3.36%
2 days, 23:49:35.916489 INFO: Resetting torch num_threads to 80
2 days, 23:49:35.917174 PROGRESS: === Extracted 3223 precursors and 23486 fragments ===
2 days, 23:49:35.917661 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:35.918386 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:35.918494 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:35.918570 PROGRESS: Target precursors: 591 (98.50%)
2 days, 23:49:35.918643 PROGRESS: Decoy precursors: 9 (1.50%)
2 days, 23:49:35.918705 PROGRESS: 
2 days, 23:49:35.918763 PROGRESS: Precursor Summary:
2 days, 23:49:35.920157 PROGRESS: Channel   0:	 0.050 FDR:   591; 0.010 FDR:   579; 0.001 FDR:   490
2 days, 23:49:35.920264 PROGRESS: 
2 days, 23:49:35.920335 PROGRESS: Protein Summary:
2 days, 23:49:35.922035 PROGRESS: Channel   0:	 0.050 FDR:   435; 0.010 FDR:   426; 0.001 FDR:   362
2 days, 23:49:35.922146 PROGRESS: =========================================================================
2 days, 23:49:35.922319 INFO: Target number of precursors reached.
2 days, 23:49:35.930697 INFO: fragments_df: keeping 5000 of 23486 [sum(precursor_idx_mask)=13965 sum(mass_error_mask)=23486 stop_rank=5000
2 days, 23:49:35.934813 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:36.127630 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:36.332852 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:36.531100 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:37.299107 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:37.299604 INFO: Using score_cutoff 14.888751088142396 (fac=0.99, q=1)
2 days, 23:49:37.300023 INFO: Updating optimization_manager: fwhm_rt             : 2.5727720260620117 -> 2.579401731491089
2 days, 23:49:37.300135 INFO: Updating optimization_manager: fwhm_mobility       : 0.003988002426922321 -> 0.003960333298891783
2 days, 23:49:37.300224 INFO: Updating optimization_manager: score_cutoff        : 14.784597513198854 -> 14.888751088142396
2 days, 23:49:37.300312 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:37.301496 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:37.303036 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:37.303951 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:37.306067 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:37.306197 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 23:49:37.308256 INFO: Updating optimization_manager: rt_error            : 13.733547736206768 -> 10.550586382215347
2 days, 23:49:37.308384 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 10.5506.
2 days, 23:49:37.308479 INFO: ==============================================
2 days, 23:49:37.308577 INFO: Starting optimization step 8.
2 days, 23:49:37.308692 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:37.308792 INFO: Using python extraction backend
2 days, 23:49:37.308938 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:37.309033 INFO: === Search parameters used ===
2 days, 23:49:37.309110 INFO: rt_error       : 10.550586382215347
2 days, 23:49:37.309179 INFO: mobility_error : 0.1
2 days, 23:49:37.309242 INFO: num_candidates : 3
2 days, 23:49:37.309306 INFO: ms1_error      : 15.0
2 days, 23:49:37.309368 INFO: ms2_error      : 15.0
2 days, 23:49:37.309428 INFO: fwhm_rt        : 2.579401731491089
2 days, 23:49:37.309488 INFO: quant_window   : 3
2 days, 23:49:37.309549 INFO: ==============================================
2 days, 23:49:37.310553 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:37.310614 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:37.310663 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:37.310697 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.15
2 days, 23:49:37.322016 INFO: Starting candidate selection
2 days, 23:49:37.942421 INFO: Starting candidate scoring
2 days, 23:49:38.056157 INFO: Finished candidate processing
2 days, 23:49:38.056272 INFO: Collecting candidate features
2 days, 23:49:38.068455 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3217)
2 days, 23:49:38.073610 INFO: Collecting fragment features
2 days, 23:49:38.078189 INFO: Finished candidate scoring
2 days, 23:49:38.080537 INFO: performing precursor FDR with 47 features
2 days, 23:49:38.080601 INFO: Decoy channel: -1
2 days, 23:49:38.080632 INFO: competitive: True
2 days, 23:49:38.084513 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:38.086505 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:49:38.086570 WARNING: dropped 16 decoy PSMs due to missing features
2 days, 23:49:38.087790 INFO: Estimating optimal hyperparameters - samples: 2,558, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:38.087880 INFO: Using random state 607432 for train-test-split
2 days, 23:49:38.320788 INFO: Test AUC: 0.874
2 days, 23:49:38.320914 INFO: Train AUC: 0.874
2 days, 23:49:38.320951 INFO: AUC difference: 0.03%
2 days, 23:49:38.625920 INFO: Resetting torch num_threads to 80
2 days, 23:49:38.626549 PROGRESS: === Extracted 3217 precursors and 23374 fragments ===
2 days, 23:49:38.627043 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:38.627783 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:38.627889 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:38.627961 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:49:38.628024 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:49:38.628083 PROGRESS: 
2 days, 23:49:38.628140 PROGRESS: Precursor Summary:
2 days, 23:49:38.629521 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   579; 0.001 FDR:   501
2 days, 23:49:38.629629 PROGRESS: 
2 days, 23:49:38.629696 PROGRESS: Protein Summary:
2 days, 23:49:38.631365 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   427; 0.001 FDR:   374
2 days, 23:49:38.631475 PROGRESS: =========================================================================
2 days, 23:49:38.631650 INFO: Target number of precursors reached.
2 days, 23:49:38.640093 INFO: fragments_df: keeping 5000 of 23374 [sum(precursor_idx_mask)=13956 sum(mass_error_mask)=23374 stop_rank=5000
2 days, 23:49:38.644261 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:38.837399 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:39.013929 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:39.239285 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:39.976224 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:39.976782 INFO: Using score_cutoff 14.912539484024048 (fac=0.99, q=1)
2 days, 23:49:39.977201 INFO: Updating optimization_manager: fwhm_rt             : 2.579401731491089 -> 2.576359510421753
2 days, 23:49:39.977313 INFO: Updating optimization_manager: fwhm_mobility       : 0.003960333298891783 -> 0.003992828540503979
2 days, 23:49:39.977401 INFO: Updating optimization_manager: score_cutoff        : 14.888751088142396 -> 14.912539484024048
2 days, 23:49:39.977502 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:39.978699 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:39.980157 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:39.981029 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:39.983159 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:39.983300 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2 days, 23:49:39.985336 INFO: Updating optimization_manager: rt_error            : 10.550586382215347 -> 13.74375131781159
2 days, 23:49:39.985461 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 13.7438.
2 days, 23:49:39.985556 INFO: ==============================================
2 days, 23:49:39.985659 INFO: Starting optimization step 9.
2 days, 23:49:39.985751 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:39.985841 INFO: Using python extraction backend
2 days, 23:49:39.986000 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:39.986095 INFO: === Search parameters used ===
2 days, 23:49:39.986174 INFO: rt_error       : 13.74375131781159
2 days, 23:49:39.986244 INFO: mobility_error : 0.1
2 days, 23:49:39.986309 INFO: num_candidates : 3
2 days, 23:49:39.986371 INFO: ms1_error      : 15.0
2 days, 23:49:39.986432 INFO: ms2_error      : 15.0
2 days, 23:49:39.986492 INFO: fwhm_rt        : 2.576359510421753
2 days, 23:49:39.986551 INFO: quant_window   : 3
2 days, 23:49:39.986609 INFO: ==============================================
2 days, 23:49:39.987525 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:39.987578 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:39.987626 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:39.987661 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.16
2 days, 23:49:40.006057 INFO: Starting candidate selection
2 days, 23:49:40.617070 INFO: Starting candidate scoring
2 days, 23:49:40.736490 INFO: Finished candidate processing
2 days, 23:49:40.736637 INFO: Collecting candidate features
2 days, 23:49:40.753039 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3221)
2 days, 23:49:40.760968 INFO: Collecting fragment features
2 days, 23:49:40.766520 INFO: Finished candidate scoring
2 days, 23:49:40.768851 INFO: performing precursor FDR with 47 features
2 days, 23:49:40.768911 INFO: Decoy channel: -1
2 days, 23:49:40.768939 INFO: competitive: True
2 days, 23:49:40.772086 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:40.773640 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:49:40.773694 WARNING: dropped 16 decoy PSMs due to missing features
2 days, 23:49:40.774730 INFO: Estimating optimal hyperparameters - samples: 2,561, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:40.774818 INFO: Using random state 607432 for train-test-split
2 days, 23:49:41.056898 INFO: Test AUC: 0.871
2 days, 23:49:41.057082 INFO: Train AUC: 0.879
2 days, 23:49:41.057151 INFO: AUC difference: 0.92%
2 days, 23:49:41.349696 INFO: Resetting torch num_threads to 80
2 days, 23:49:41.350312 PROGRESS: === Extracted 3221 precursors and 23463 fragments ===
2 days, 23:49:41.350767 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:41.351408 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:41.351520 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:41.351621 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:49:41.351707 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:49:41.351782 PROGRESS: 
2 days, 23:49:41.351853 PROGRESS: Precursor Summary:
2 days, 23:49:41.353046 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   580; 0.001 FDR:   499
2 days, 23:49:41.353158 PROGRESS: 
2 days, 23:49:41.353244 PROGRESS: Protein Summary:
2 days, 23:49:41.354657 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   427; 0.001 FDR:   371
2 days, 23:49:41.354777 PROGRESS: =========================================================================
2 days, 23:49:41.354963 INFO: Target number of precursors reached.
2 days, 23:49:41.361277 INFO: fragments_df: keeping 5000 of 23463 [sum(precursor_idx_mask)=13977 sum(mass_error_mask)=23463 stop_rank=5000
2 days, 23:49:41.365060 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:41.562577 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:41.751813 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:41.936848 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:42.822552 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:42.823126 INFO: Using score_cutoff 14.720838477230071 (fac=0.99, q=1)
2 days, 23:49:42.823604 INFO: Updating optimization_manager: fwhm_rt             : 2.576359510421753 -> 2.5762457847595215
2 days, 23:49:42.823723 INFO: Updating optimization_manager: fwhm_mobility       : 0.003992828540503979 -> 0.003910426050424576
2 days, 23:49:42.823819 INFO: Updating optimization_manager: score_cutoff        : 14.912539484024048 -> 14.720838477230071
2 days, 23:49:42.823922 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:42.825388 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:42.827153 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:42.828250 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:42.830709 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:42.830850 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
2 days, 23:49:42.833340 INFO: Updating optimization_manager: rt_error            : 13.74375131781159 -> 10.331868638436966
2 days, 23:49:42.833464 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 10.3319.
2 days, 23:49:42.833548 INFO: ==============================================
2 days, 23:49:42.833635 INFO: Starting optimization step 10.
2 days, 23:49:42.833715 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:42.833781 INFO: Using python extraction backend
2 days, 23:49:42.833899 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:42.833993 INFO: === Search parameters used ===
2 days, 23:49:42.834054 INFO: rt_error       : 10.331868638436966
2 days, 23:49:42.834100 INFO: mobility_error : 0.1
2 days, 23:49:42.834144 INFO: num_candidates : 3
2 days, 23:49:42.834187 INFO: ms1_error      : 15.0
2 days, 23:49:42.834229 INFO: ms2_error      : 15.0
2 days, 23:49:42.834270 INFO: fwhm_rt        : 2.5762457847595215
2 days, 23:49:42.834321 INFO: quant_window   : 3
2 days, 23:49:42.834370 INFO: ==============================================
2 days, 23:49:42.835446 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:42.835503 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:42.835546 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:42.835577 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.12
2 days, 23:49:42.840033 INFO: Starting candidate selection
2 days, 23:49:43.462697 INFO: Starting candidate scoring
2 days, 23:49:43.575545 INFO: Finished candidate processing
2 days, 23:49:43.575659 INFO: Collecting candidate features
2 days, 23:49:43.587971 WARNING: intensity_correlation has 17 NaNs ( 0.53 % out of 3214)
2 days, 23:49:43.593104 INFO: Collecting fragment features
2 days, 23:49:43.597663 INFO: Finished candidate scoring
2 days, 23:49:43.599912 INFO: performing precursor FDR with 47 features
2 days, 23:49:43.599977 INFO: Decoy channel: -1
2 days, 23:49:43.600008 INFO: competitive: True
2 days, 23:49:43.604503 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:43.606424 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:49:43.606484 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:49:43.606528 WARNING: FDR calculation for 1680 target and 1517 decoy PSMs
2 days, 23:49:43.606555 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:49:43.607738 INFO: Estimating optimal hyperparameters - samples: 2,557, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:43.607827 INFO: Using random state 607432 for train-test-split
2 days, 23:49:43.849352 INFO: Test AUC: 0.875
2 days, 23:49:43.849493 INFO: Train AUC: 0.875
2 days, 23:49:43.849546 INFO: AUC difference: 0.05%
2 days, 23:49:44.210333 INFO: Resetting torch num_threads to 80
2 days, 23:49:44.211079 PROGRESS: === Extracted 3214 precursors and 23351 fragments ===
2 days, 23:49:44.211655 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:44.212547 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:44.212674 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:44.212773 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:49:44.212863 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:49:44.212951 PROGRESS: 
2 days, 23:49:44.213043 PROGRESS: Precursor Summary:
2 days, 23:49:44.215039 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   581; 0.001 FDR:   494
2 days, 23:49:44.215174 PROGRESS: 
2 days, 23:49:44.215276 PROGRESS: Protein Summary:
2 days, 23:49:44.217584 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   428; 0.001 FDR:   368
2 days, 23:49:44.217713 PROGRESS: =========================================================================
2 days, 23:49:44.217937 INFO: Target number of precursors reached.
2 days, 23:49:44.227802 INFO: fragments_df: keeping 5000 of 23351 [sum(precursor_idx_mask)=14020 sum(mass_error_mask)=23351 stop_rank=5000
2 days, 23:49:44.233365 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:44.423136 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:44.641695 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:44.877889 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:45.823298 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:45.823759 INFO: Using score_cutoff 14.76951170539856 (fac=0.99, q=1)
2 days, 23:49:45.824122 INFO: Updating optimization_manager: fwhm_rt             : 2.5762457847595215 -> 2.5761351585388184
2 days, 23:49:45.824220 INFO: Updating optimization_manager: fwhm_mobility       : 0.003910426050424576 -> 0.003919762093573809
2 days, 23:49:45.824301 INFO: Updating optimization_manager: score_cutoff        : 14.720838477230071 -> 14.76951170539856
2 days, 23:49:45.824379 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:45.825500 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:45.826902 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:45.827728 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:45.829715 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:45.829822 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
2 days, 23:49:45.831803 INFO: Updating optimization_manager: rt_error            : 10.331868638436966 -> 13.742434599615853
2 days, 23:49:45.831920 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 13.7424.
2 days, 23:49:45.831999 INFO: ==============================================
2 days, 23:49:45.832081 INFO: Starting optimization step 11.
2 days, 23:49:45.832155 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:45.832224 INFO: Using python extraction backend
2 days, 23:49:45.832335 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:45.832418 INFO: === Search parameters used ===
2 days, 23:49:45.832478 INFO: rt_error       : 13.742434599615853
2 days, 23:49:45.832533 INFO: mobility_error : 0.1
2 days, 23:49:45.832586 INFO: num_candidates : 3
2 days, 23:49:45.832637 INFO: ms1_error      : 15.0
2 days, 23:49:45.832688 INFO: ms2_error      : 15.0
2 days, 23:49:45.832738 INFO: fwhm_rt        : 2.5761351585388184
2 days, 23:49:45.832789 INFO: quant_window   : 3
2 days, 23:49:45.832840 INFO: ==============================================
2 days, 23:49:45.833702 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:45.833753 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:45.833793 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:45.833822 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.12
2 days, 23:49:45.870094 INFO: Starting candidate selection
2 days, 23:49:46.505354 INFO: Starting candidate scoring
2 days, 23:49:46.638603 INFO: Finished candidate processing
2 days, 23:49:46.638720 INFO: Collecting candidate features
2 days, 23:49:46.650879 WARNING: intensity_correlation has 18 NaNs ( 0.56 % out of 3224)
2 days, 23:49:46.655984 INFO: Collecting fragment features
2 days, 23:49:46.660514 INFO: Finished candidate scoring
2 days, 23:49:46.662673 INFO: performing precursor FDR with 47 features
2 days, 23:49:46.662740 INFO: Decoy channel: -1
2 days, 23:49:46.662774 INFO: competitive: True
2 days, 23:49:46.666750 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:46.668632 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:49:46.668690 WARNING: dropped 16 decoy PSMs due to missing features
2 days, 23:49:46.669906 INFO: Estimating optimal hyperparameters - samples: 2,564, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:46.670000 INFO: Using random state 607432 for train-test-split
2 days, 23:49:46.915143 INFO: Test AUC: 0.854
2 days, 23:49:46.915265 INFO: Train AUC: 0.879
2 days, 23:49:46.915304 INFO: AUC difference: 2.75%
2 days, 23:49:47.221325 INFO: Resetting torch num_threads to 80
2 days, 23:49:47.221969 PROGRESS: === Extracted 3224 precursors and 23487 fragments ===
2 days, 23:49:47.222458 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:47.223179 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:47.223277 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:47.223347 PROGRESS: Target precursors: 588 (98.00%)
2 days, 23:49:47.223408 PROGRESS: Decoy precursors: 12 (2.00%)
2 days, 23:49:47.223464 PROGRESS: 
2 days, 23:49:47.223519 PROGRESS: Precursor Summary:
2 days, 23:49:47.224891 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   553; 0.001 FDR:   494
2 days, 23:49:47.224994 PROGRESS: 
2 days, 23:49:47.225061 PROGRESS: Protein Summary:
2 days, 23:49:47.226743 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   408; 0.001 FDR:   367
2 days, 23:49:47.226855 PROGRESS: =========================================================================
2 days, 23:49:47.227036 INFO: Target number of precursors reached.
2 days, 23:49:47.235599 INFO: fragments_df: keeping 5000 of 23487 [sum(precursor_idx_mask)=13518 sum(mass_error_mask)=23487 stop_rank=5000
2 days, 23:49:47.239904 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:47.519537 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:47.727102 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:47.920920 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:48.772488 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:48.772938 INFO: Using score_cutoff 16.223465931701657 (fac=0.99, q=1)
2 days, 23:49:48.773273 INFO: Updating optimization_manager: fwhm_rt             : 2.5761351585388184 -> 2.582416296005249
2 days, 23:49:48.773363 INFO: Updating optimization_manager: fwhm_mobility       : 0.003919762093573809 -> 0.004028328228741884
2 days, 23:49:48.773433 INFO: Updating optimization_manager: score_cutoff        : 14.76951170539856 -> 16.223465931701657
2 days, 23:49:48.773503 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:48.774617 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:48.775988 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:48.776793 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:48.778744 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:48.778864 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
2 days, 23:49:48.780811 INFO: Updating optimization_manager: rt_error            : 13.742434599615853 -> 10.655185285027938
2 days, 23:49:48.780942 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 10.6552.
2 days, 23:49:48.781042 INFO: ==============================================
2 days, 23:49:48.781143 INFO: Starting optimization step 12.
2 days, 23:49:48.781251 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:48.781340 INFO: Using python extraction backend
2 days, 23:49:48.781481 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:48.781575 INFO: === Search parameters used ===
2 days, 23:49:48.781655 INFO: rt_error       : 10.655185285027938
2 days, 23:49:48.781725 INFO: mobility_error : 0.1
2 days, 23:49:48.781790 INFO: num_candidates : 3
2 days, 23:49:48.781853 INFO: ms1_error      : 15.0
2 days, 23:49:48.781934 INFO: ms2_error      : 15.0
2 days, 23:49:48.781998 INFO: fwhm_rt        : 2.582416296005249
2 days, 23:49:48.782058 INFO: quant_window   : 3
2 days, 23:49:48.782119 INFO: ==============================================
2 days, 23:49:48.782992 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:48.783045 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:48.783095 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:48.783134 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.18
2 days, 23:49:48.794085 INFO: Starting candidate selection
2 days, 23:49:49.296405 INFO: Starting candidate scoring
2 days, 23:49:49.404541 INFO: Finished candidate processing
2 days, 23:49:49.404676 INFO: Collecting candidate features
2 days, 23:49:49.420619 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3221)
2 days, 23:49:49.429329 INFO: Collecting fragment features
2 days, 23:49:49.434953 INFO: Finished candidate scoring
2 days, 23:49:49.438179 INFO: performing precursor FDR with 47 features
2 days, 23:49:49.438255 INFO: Decoy channel: -1
2 days, 23:49:49.438302 INFO: competitive: True
2 days, 23:49:49.442930 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:49.445125 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:49:49.445188 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:49:49.446591 INFO: Estimating optimal hyperparameters - samples: 2,561, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:49.446701 INFO: Using random state 607432 for train-test-split
2 days, 23:49:49.796450 INFO: Test AUC: 0.874
2 days, 23:49:49.796581 INFO: Train AUC: 0.875
2 days, 23:49:49.796628 INFO: AUC difference: 0.10%
2 days, 23:49:50.166801 INFO: Resetting torch num_threads to 80
2 days, 23:49:50.167537 PROGRESS: === Extracted 3221 precursors and 23409 fragments ===
2 days, 23:49:50.168127 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:50.169061 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:50.169185 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:50.169295 PROGRESS: Target precursors: 589 (98.17%)
2 days, 23:49:50.169395 PROGRESS: Decoy precursors: 11 (1.83%)
2 days, 23:49:50.169493 PROGRESS: 
2 days, 23:49:50.169579 PROGRESS: Precursor Summary:
2 days, 23:49:50.171520 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   582; 0.001 FDR:   485
2 days, 23:49:50.171659 PROGRESS: 
2 days, 23:49:50.171763 PROGRESS: Protein Summary:
2 days, 23:49:50.174111 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   429; 0.001 FDR:   359
2 days, 23:49:50.174245 PROGRESS: =========================================================================
2 days, 23:49:50.174446 INFO: Target number of precursors reached.
2 days, 23:49:50.184196 INFO: fragments_df: keeping 5000 of 23409 [sum(precursor_idx_mask)=14026 sum(mass_error_mask)=23409 stop_rank=5000
2 days, 23:49:50.188931 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:50.427117 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:50.647492 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:50.886779 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:51.695066 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:51.695720 INFO: Using score_cutoff 15.255448740005495 (fac=0.99, q=1)
2 days, 23:49:51.696297 INFO: Updating optimization_manager: fwhm_rt             : 2.582416296005249 -> 2.5762457847595215
2 days, 23:49:51.696453 INFO: Updating optimization_manager: fwhm_mobility       : 0.004028328228741884 -> 0.004004988353699446
2 days, 23:49:51.696566 INFO: Updating optimization_manager: score_cutoff        : 16.223465931701657 -> 15.255448740005495
2 days, 23:49:51.696676 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:51.698278 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:51.700242 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:51.701468 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:51.704083 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:51.704230 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 2 ===
2 days, 23:49:51.707069 INFO: Updating optimization_manager: rt_error            : 10.655185285027938 -> 13.701207209032065
2 days, 23:49:51.707225 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 13.7012.
2 days, 23:49:51.707340 INFO: ==============================================
2 days, 23:49:51.707455 INFO: Starting optimization step 13.
2 days, 23:49:51.707565 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:51.707765 INFO: Using python extraction backend
2 days, 23:49:51.707999 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:51.708129 INFO: === Search parameters used ===
2 days, 23:49:51.708250 INFO: rt_error       : 13.701207209032065
2 days, 23:49:51.708363 INFO: mobility_error : 0.1
2 days, 23:49:51.708460 INFO: num_candidates : 3
2 days, 23:49:51.708549 INFO: ms1_error      : 15.0
2 days, 23:49:51.708639 INFO: ms2_error      : 15.0
2 days, 23:49:51.708740 INFO: fwhm_rt        : 2.5762457847595215
2 days, 23:49:51.708838 INFO: quant_window   : 3
2 days, 23:49:51.708945 INFO: ==============================================
2 days, 23:49:51.710375 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:51.710469 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:51.710550 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:51.710623 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.17
2 days, 23:49:51.722056 INFO: Starting candidate selection
2 days, 23:49:52.245830 INFO: Starting candidate scoring
2 days, 23:49:52.355397 INFO: Finished candidate processing
2 days, 23:49:52.355517 INFO: Collecting candidate features
2 days, 23:49:52.368935 WARNING: intensity_correlation has 17 NaNs ( 0.53 % out of 3224)
2 days, 23:49:52.374166 INFO: Collecting fragment features
2 days, 23:49:52.378814 INFO: Finished candidate scoring
2 days, 23:49:52.381270 INFO: performing precursor FDR with 47 features
2 days, 23:49:52.381339 INFO: Decoy channel: -1
2 days, 23:49:52.381371 INFO: competitive: True
2 days, 23:49:52.385206 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:52.387086 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:49:52.387149 WARNING: dropped 14 decoy PSMs due to missing features
2 days, 23:49:52.388376 INFO: Estimating optimal hyperparameters - samples: 2,565, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:52.388469 INFO: Using random state 607432 for train-test-split
2 days, 23:49:52.679029 INFO: Test AUC: 0.880
2 days, 23:49:52.679156 INFO: Train AUC: 0.876
2 days, 23:49:52.679196 INFO: AUC difference: 0.36%
2 days, 23:49:52.980978 INFO: Resetting torch num_threads to 80
2 days, 23:49:52.981731 PROGRESS: === Extracted 3224 precursors and 23494 fragments ===
2 days, 23:49:52.982284 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:52.982975 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:52.983074 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:52.983142 PROGRESS: Target precursors: 588 (98.00%)
2 days, 23:49:52.983202 PROGRESS: Decoy precursors: 12 (2.00%)
2 days, 23:49:52.983258 PROGRESS: 
2 days, 23:49:52.983314 PROGRESS: Precursor Summary:
2 days, 23:49:52.984668 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   581; 0.001 FDR:   493
2 days, 23:49:52.984775 PROGRESS: 
2 days, 23:49:52.984840 PROGRESS: Protein Summary:
2 days, 23:49:52.986482 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   428; 0.001 FDR:   366
2 days, 23:49:52.986588 PROGRESS: =========================================================================
2 days, 23:49:52.986747 INFO: Target number of precursors reached.
2 days, 23:49:52.995139 INFO: fragments_df: keeping 5000 of 23494 [sum(precursor_idx_mask)=14010 sum(mass_error_mask)=23494 stop_rank=5000
2 days, 23:49:52.999892 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:53.199296 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:53.472911 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:53.697988 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:54.662415 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:54.663002 INFO: Using score_cutoff 14.725998481750487 (fac=0.99, q=1)
2 days, 23:49:54.663523 INFO: Updating optimization_manager: fwhm_rt             : 2.5762457847595215 -> 2.5821285247802734
2 days, 23:49:54.663656 INFO: Updating optimization_manager: fwhm_mobility       : 0.004004988353699446 -> 0.003960333298891783
2 days, 23:49:54.663758 INFO: Updating optimization_manager: score_cutoff        : 15.255448740005495 -> 14.725998481750487
2 days, 23:49:54.663852 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:54.665419 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:54.667222 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:54.668363 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:54.670810 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:54.670950 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 2 ===
2 days, 23:49:54.673254 INFO: Updating optimization_manager: rt_error            : 13.701207209032065 -> 11.07099358792425
2 days, 23:49:54.673364 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 11.0710.
2 days, 23:49:54.673445 INFO: ==============================================
2 days, 23:49:54.673519 INFO: Starting optimization step 14.
2 days, 23:49:54.673584 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:54.673645 INFO: Using python extraction backend
2 days, 23:49:54.673746 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:54.673815 INFO: === Search parameters used ===
2 days, 23:49:54.673881 INFO: rt_error       : 11.07099358792425
2 days, 23:49:54.673961 INFO: mobility_error : 0.1
2 days, 23:49:54.674019 INFO: num_candidates : 3
2 days, 23:49:54.674067 INFO: ms1_error      : 15.0
2 days, 23:49:54.674116 INFO: ms2_error      : 15.0
2 days, 23:49:54.674162 INFO: fwhm_rt        : 2.5821285247802734
2 days, 23:49:54.674208 INFO: quant_window   : 3
2 days, 23:49:54.674254 INFO: ==============================================
2 days, 23:49:54.675089 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:54.675140 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:54.675178 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:54.675205 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.15
2 days, 23:49:54.694023 INFO: Starting candidate selection
2 days, 23:49:55.354031 INFO: Starting candidate scoring
2 days, 23:49:55.471772 INFO: Finished candidate processing
2 days, 23:49:55.471902 INFO: Collecting candidate features
2 days, 23:49:55.487581 WARNING: intensity_correlation has 18 NaNs ( 0.56 % out of 3224)
2 days, 23:49:55.492367 INFO: Collecting fragment features
2 days, 23:49:55.496252 INFO: Finished candidate scoring
2 days, 23:49:55.498160 INFO: performing precursor FDR with 47 features
2 days, 23:49:55.498228 INFO: Decoy channel: -1
2 days, 23:49:55.498254 INFO: competitive: True
2 days, 23:49:55.501355 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:55.502947 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:49:55.503005 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:49:55.503981 INFO: Estimating optimal hyperparameters - samples: 2,564, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:55.504066 INFO: Using random state 607432 for train-test-split
2 days, 23:49:55.828529 INFO: Test AUC: 0.876
2 days, 23:49:55.828654 INFO: Train AUC: 0.873
2 days, 23:49:55.828695 INFO: AUC difference: 0.35%
2 days, 23:49:56.170183 INFO: Resetting torch num_threads to 80
2 days, 23:49:56.170747 PROGRESS: === Extracted 3224 precursors and 23455 fragments ===
2 days, 23:49:56.171187 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:56.171796 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:56.171894 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:56.171961 PROGRESS: Target precursors: 589 (98.17%)
2 days, 23:49:56.172019 PROGRESS: Decoy precursors: 11 (1.83%)
2 days, 23:49:56.172074 PROGRESS: 
2 days, 23:49:56.172127 PROGRESS: Precursor Summary:
2 days, 23:49:56.173267 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   578; 0.001 FDR:   482
2 days, 23:49:56.173365 PROGRESS: 
2 days, 23:49:56.173432 PROGRESS: Protein Summary:
2 days, 23:49:56.174795 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   425; 0.001 FDR:   360
2 days, 23:49:56.174895 PROGRESS: =========================================================================
2 days, 23:49:56.175057 INFO: Target number of precursors reached.
2 days, 23:49:56.181720 INFO: fragments_df: keeping 5000 of 23455 [sum(precursor_idx_mask)=13965 sum(mass_error_mask)=23455 stop_rank=5000
2 days, 23:49:56.185163 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:56.356112 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:56.568789 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:56.756483 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:57.542126 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:49:57.542625 INFO: Using score_cutoff 14.912117615032196 (fac=0.99, q=1)
2 days, 23:49:57.542978 INFO: Updating optimization_manager: fwhm_rt             : 2.5821285247802734 -> 2.58294677734375
2 days, 23:49:57.543077 INFO: Updating optimization_manager: fwhm_mobility       : 0.003960333298891783 -> 0.003994564525783062
2 days, 23:49:57.543159 INFO: Updating optimization_manager: score_cutoff        : 14.725998481750487 -> 14.912117615032196
2 days, 23:49:57.543247 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:57.544374 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:57.545755 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:57.546598 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:49:57.548617 INFO: === checking if optimization conditions were reached ===
2 days, 23:49:57.548740 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 2 ===
2 days, 23:49:57.550822 INFO: Updating optimization_manager: rt_error            : 11.07099358792425 -> 10.962176232343097
2 days, 23:49:57.550956 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 10.9622.
2 days, 23:49:57.551054 INFO: ==============================================
2 days, 23:49:57.551153 INFO: Starting optimization step 15.
2 days, 23:49:57.551240 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:49:57.551322 INFO: Using python extraction backend
2 days, 23:49:57.551445 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:49:57.551535 INFO: === Search parameters used ===
2 days, 23:49:57.551608 INFO: rt_error       : 10.962176232343097
2 days, 23:49:57.551677 INFO: mobility_error : 0.1
2 days, 23:49:57.551744 INFO: num_candidates : 3
2 days, 23:49:57.551809 INFO: ms1_error      : 15.0
2 days, 23:49:57.551874 INFO: ms2_error      : 15.0
2 days, 23:49:57.551938 INFO: fwhm_rt        : 2.58294677734375
2 days, 23:49:57.552001 INFO: quant_window   : 3
2 days, 23:49:57.552064 INFO: ==============================================
2 days, 23:49:57.552900 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:49:57.552958 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:49:57.553022 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:49:57.553066 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.16
2 days, 23:49:57.594184 INFO: Starting candidate selection
2 days, 23:49:58.175759 INFO: Starting candidate scoring
2 days, 23:49:58.290782 INFO: Finished candidate processing
2 days, 23:49:58.290917 INFO: Collecting candidate features
2 days, 23:49:58.301615 WARNING: intensity_correlation has 18 NaNs ( 0.56 % out of 3214)
2 days, 23:49:58.305630 INFO: Collecting fragment features
2 days, 23:49:58.309372 INFO: Finished candidate scoring
2 days, 23:49:58.311383 INFO: performing precursor FDR with 47 features
2 days, 23:49:58.311442 INFO: Decoy channel: -1
2 days, 23:49:58.311467 INFO: competitive: True
2 days, 23:49:58.315263 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:49:58.316841 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:49:58.316894 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:49:58.317904 INFO: Estimating optimal hyperparameters - samples: 2,556, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:49:58.317994 INFO: Using random state 607432 for train-test-split
2 days, 23:49:58.621808 INFO: Test AUC: 0.877
2 days, 23:49:58.621933 INFO: Train AUC: 0.875
2 days, 23:49:58.621975 INFO: AUC difference: 0.28%
2 days, 23:49:58.891882 INFO: Resetting torch num_threads to 80
2 days, 23:49:58.892448 PROGRESS: === Extracted 3214 precursors and 23391 fragments ===
2 days, 23:49:58.892874 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:49:58.893509 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:49:58.893612 PROGRESS: Total precursors accumulated: 600
2 days, 23:49:58.893682 PROGRESS: Target precursors: 589 (98.17%)
2 days, 23:49:58.893743 PROGRESS: Decoy precursors: 11 (1.83%)
2 days, 23:49:58.893799 PROGRESS: 
2 days, 23:49:58.893854 PROGRESS: Precursor Summary:
2 days, 23:49:58.895045 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   580; 0.001 FDR:   492
2 days, 23:49:58.895144 PROGRESS: 
2 days, 23:49:58.895214 PROGRESS: Protein Summary:
2 days, 23:49:58.896550 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   427; 0.001 FDR:   367
2 days, 23:49:58.896649 PROGRESS: =========================================================================
2 days, 23:49:58.896820 INFO: Target number of precursors reached.
2 days, 23:49:58.903233 INFO: fragments_df: keeping 5000 of 23391 [sum(precursor_idx_mask)=14003 sum(mass_error_mask)=23391 stop_rank=5000
2 days, 23:49:58.906671 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:49:59.090662 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:49:59.282638 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:49:59.493459 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:00.346566 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:50:00.347023 INFO: Using score_cutoff 14.917027441978455 (fac=0.99, q=1)
2 days, 23:50:00.347369 INFO: Updating optimization_manager: fwhm_rt             : 2.58294677734375 -> 2.576247215270996
2 days, 23:50:00.347464 INFO: Updating optimization_manager: fwhm_mobility       : 0.003994564525783062 -> 0.004004988353699446
2 days, 23:50:00.347537 INFO: Updating optimization_manager: score_cutoff        : 14.912117615032196 -> 14.917027441978455
2 days, 23:50:00.347611 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:00.348736 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:00.350163 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:00.351000 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:00.353003 INFO: === checking if optimization conditions were reached ===
2 days, 23:50:00.353116 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 2 ===
2 days, 23:50:00.354193 INFO: Updating optimization_manager: rt_error            : 10.962176232343097 -> 10.331868638436966
2 days, 23:50:00.354342 INFO: Updating optimization_manager: classifier_version  : 3 -> 14
2 days, 23:50:00.354456 INFO: Updating optimization_manager: score_cutoff        : 14.917027441978455 -> 14.76951170539856
2 days, 23:50:00.354560 INFO: Updating optimization_manager: fwhm_rt             : 2.576247215270996 -> 2.5761351585388184
2 days, 23:50:00.354661 INFO: Updating optimization_manager: fwhm_mobility       : 0.004004988353699446 -> 0.003919762093573809
2 days, 23:50:00.354763 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 10.3319 found after 16 searches.
2 days, 23:50:00.354836 INFO: ==============================================
2 days, 23:50:00.354914 PROGRESS: Optimization finished for rt_error.
2 days, 23:50:00.358040 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:00.358919 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:00.360284 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:00.361095 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:00.363151 INFO: Starting optimization step 0.
2 days, 23:50:00.363264 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:50:00.363351 INFO: Using python extraction backend
2 days, 23:50:00.363487 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:50:00.363578 INFO: === Search parameters used ===
2 days, 23:50:00.363648 INFO: rt_error       : 10.331868638436966
2 days, 23:50:00.363713 INFO: mobility_error : 0.1
2 days, 23:50:00.363778 INFO: num_candidates : 3
2 days, 23:50:00.363848 INFO: ms1_error      : 15.0
2 days, 23:50:00.363917 INFO: ms2_error      : 15.0
2 days, 23:50:00.363986 INFO: fwhm_rt        : 2.5761351585388184
2 days, 23:50:00.364057 INFO: quant_window   : 3
2 days, 23:50:00.364129 INFO: ==============================================
2 days, 23:50:00.365325 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:50:00.365388 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:50:00.365442 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:50:00.365494 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.12
2 days, 23:50:00.370974 INFO: Starting candidate selection
2 days, 23:50:01.080930 INFO: Starting candidate scoring
2 days, 23:50:01.184604 INFO: Finished candidate processing
2 days, 23:50:01.184721 INFO: Collecting candidate features
2 days, 23:50:01.199127 WARNING: intensity_correlation has 16 NaNs ( 0.50 % out of 3211)
2 days, 23:50:01.204336 INFO: Collecting fragment features
2 days, 23:50:01.208997 INFO: Finished candidate scoring
2 days, 23:50:01.211263 INFO: performing precursor FDR with 47 features
2 days, 23:50:01.211333 INFO: Decoy channel: -1
2 days, 23:50:01.211364 INFO: competitive: True
2 days, 23:50:01.215292 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:50:01.217243 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:50:01.217306 WARNING: dropped 14 decoy PSMs due to missing features
2 days, 23:50:01.217352 WARNING: FDR calculation for 1680 target and 1515 decoy PSMs
2 days, 23:50:01.217382 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:50:01.218670 INFO: Estimating optimal hyperparameters - samples: 2,556, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:50:01.218776 INFO: Using random state 775332 for train-test-split
2 days, 23:50:01.473812 INFO: Test AUC: 0.886
2 days, 23:50:01.473961 INFO: Train AUC: 0.883
2 days, 23:50:01.474023 INFO: AUC difference: 0.35%
2 days, 23:50:01.777363 INFO: Resetting torch num_threads to 80
2 days, 23:50:01.777968 PROGRESS: === Extracted 3211 precursors and 23311 fragments ===
2 days, 23:50:01.778447 INFO: === FDR correction performed with classifier version 14 ===
2 days, 23:50:01.779090 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:50:01.779206 PROGRESS: Total precursors accumulated: 600
2 days, 23:50:01.779303 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:50:01.779398 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:50:01.779487 PROGRESS: 
2 days, 23:50:01.779570 PROGRESS: Precursor Summary:
2 days, 23:50:01.780750 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   578; 0.001 FDR:   532
2 days, 23:50:01.780865 PROGRESS: 
2 days, 23:50:01.780956 PROGRESS: Protein Summary:
2 days, 23:50:01.782389 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   424; 0.001 FDR:   395
2 days, 23:50:01.782520 PROGRESS: =========================================================================
2 days, 23:50:01.782702 INFO: Target number of precursors reached.
2 days, 23:50:01.789041 INFO: fragments_df: keeping 5000 of 23311 [sum(precursor_idx_mask)=13988 sum(mass_error_mask)=23311 stop_rank=5000
2 days, 23:50:01.792462 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:01.967314 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:02.191466 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:02.505882 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:03.272887 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:50:03.273500 INFO: Using score_cutoff 14.68322674598694 (fac=0.99, q=1)
2 days, 23:50:03.273997 INFO: Updating optimization_manager: fwhm_rt             : 2.5761351585388184 -> 2.562075138092041
2 days, 23:50:03.274120 INFO: Updating optimization_manager: fwhm_mobility       : 0.003919762093573809 -> 0.0038901311345398426
2 days, 23:50:03.274223 INFO: Updating optimization_manager: score_cutoff        : 14.76951170539856 -> 14.68322674598694
2 days, 23:50:03.274322 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:03.275861 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:03.277601 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:03.278739 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:03.281277 INFO: === checking if optimization conditions were reached ===
2 days, 23:50:03.281412 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:50:03.283600 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06321102613374999
2 days, 23:50:03.283748 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0632.
2 days, 23:50:03.283852 INFO: ==============================================
2 days, 23:50:03.283968 INFO: Starting optimization step 1.
2 days, 23:50:03.284075 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:50:03.284256 INFO: Using python extraction backend
2 days, 23:50:03.284419 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:50:03.284528 INFO: === Search parameters used ===
2 days, 23:50:03.284610 INFO: rt_error       : 10.331868638436966
2 days, 23:50:03.284685 INFO: mobility_error : 0.06321102613374999
2 days, 23:50:03.284757 INFO: num_candidates : 3
2 days, 23:50:03.284828 INFO: ms1_error      : 15.0
2 days, 23:50:03.284899 INFO: ms2_error      : 15.0
2 days, 23:50:03.284969 INFO: fwhm_rt        : 2.562075138092041
2 days, 23:50:03.285043 INFO: quant_window   : 3
2 days, 23:50:03.285130 INFO: ==============================================
2 days, 23:50:03.286419 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:50:03.286491 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:50:03.286557 INFO: FWHM in RT is 2.56 seconds, sigma is 0.43
2 days, 23:50:03.286605 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.11
2 days, 23:50:03.314026 INFO: Starting candidate selection
2 days, 23:50:03.873366 INFO: Starting candidate scoring
2 days, 23:50:03.972333 INFO: Finished candidate processing
2 days, 23:50:03.972456 INFO: Collecting candidate features
2 days, 23:50:03.986232 WARNING: intensity_correlation has 18 NaNs ( 0.56 % out of 3199)
2 days, 23:50:03.991452 INFO: Collecting fragment features
2 days, 23:50:03.996197 INFO: Finished candidate scoring
2 days, 23:50:03.998702 INFO: performing precursor FDR with 47 features
2 days, 23:50:03.998786 INFO: Decoy channel: -1
2 days, 23:50:03.998821 INFO: competitive: True
2 days, 23:50:04.002808 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:50:04.004770 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:50:04.004890 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:50:04.004941 WARNING: FDR calculation for 1677 target and 1504 decoy PSMs
2 days, 23:50:04.004969 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:50:04.006177 INFO: Estimating optimal hyperparameters - samples: 2,544, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:50:04.006278 INFO: Using random state 775332 for train-test-split
2 days, 23:50:04.282059 INFO: Test AUC: 0.871
2 days, 23:50:04.282171 INFO: Train AUC: 0.888
2 days, 23:50:04.282212 INFO: AUC difference: 1.91%
2 days, 23:50:04.622993 INFO: Resetting torch num_threads to 80
2 days, 23:50:04.623731 PROGRESS: === Extracted 3199 precursors and 23127 fragments ===
2 days, 23:50:04.624328 INFO: === FDR correction performed with classifier version 14 ===
2 days, 23:50:04.625251 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:50:04.625371 PROGRESS: Total precursors accumulated: 600
2 days, 23:50:04.625465 PROGRESS: Target precursors: 591 (98.50%)
2 days, 23:50:04.625558 PROGRESS: Decoy precursors: 9 (1.50%)
2 days, 23:50:04.625634 PROGRESS: 
2 days, 23:50:04.625707 PROGRESS: Precursor Summary:
2 days, 23:50:04.627675 PROGRESS: Channel   0:	 0.050 FDR:   591; 0.010 FDR:   581; 0.001 FDR:   503
2 days, 23:50:04.627803 PROGRESS: 
2 days, 23:50:04.627903 PROGRESS: Protein Summary:
2 days, 23:50:04.630189 PROGRESS: Channel   0:	 0.050 FDR:   435; 0.010 FDR:   428; 0.001 FDR:   375
2 days, 23:50:04.630315 PROGRESS: =========================================================================
2 days, 23:50:04.630521 INFO: Target number of precursors reached.
2 days, 23:50:04.640175 INFO: fragments_df: keeping 5000 of 23127 [sum(precursor_idx_mask)=14023 sum(mass_error_mask)=23127 stop_rank=5000
2 days, 23:50:04.644759 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:04.845270 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:05.017405 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:05.206280 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:06.208493 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:50:06.209086 INFO: Using score_cutoff 14.904716171264647 (fac=0.99, q=1)
2 days, 23:50:06.209532 INFO: Updating optimization_manager: fwhm_rt             : 2.562075138092041 -> 2.568242311477661
2 days, 23:50:06.209650 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038901311345398426 -> 0.003988002426922321
2 days, 23:50:06.209739 INFO: Updating optimization_manager: score_cutoff        : 14.68322674598694 -> 14.904716171264647
2 days, 23:50:06.209844 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:06.211413 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:06.213134 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:06.214255 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:06.216703 INFO: === checking if optimization conditions were reached ===
2 days, 23:50:06.216850 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:50:06.218869 INFO: Updating optimization_manager: mobility_error      : 0.06321102613374999 -> 0.05084000073125574
2 days, 23:50:06.218984 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0508.
2 days, 23:50:06.219070 INFO: ==============================================
2 days, 23:50:06.219172 INFO: Starting optimization step 2.
2 days, 23:50:06.219264 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:50:06.219352 INFO: Using python extraction backend
2 days, 23:50:06.219460 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:50:06.219531 INFO: === Search parameters used ===
2 days, 23:50:06.219584 INFO: rt_error       : 10.331868638436966
2 days, 23:50:06.219633 INFO: mobility_error : 0.05084000073125574
2 days, 23:50:06.219680 INFO: num_candidates : 3
2 days, 23:50:06.219725 INFO: ms1_error      : 15.0
2 days, 23:50:06.219770 INFO: ms2_error      : 15.0
2 days, 23:50:06.219814 INFO: fwhm_rt        : 2.568242311477661
2 days, 23:50:06.219861 INFO: quant_window   : 3
2 days, 23:50:06.219915 INFO: ==============================================
2 days, 23:50:06.220873 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:50:06.220927 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:50:06.220966 INFO: FWHM in RT is 2.57 seconds, sigma is 0.43
2 days, 23:50:06.220994 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.16
2 days, 23:50:06.226953 INFO: Starting candidate selection
2 days, 23:50:06.733758 INFO: Starting candidate scoring
2 days, 23:50:06.847740 INFO: Finished candidate processing
2 days, 23:50:06.847865 INFO: Collecting candidate features
2 days, 23:50:06.864598 WARNING: intensity_correlation has 23 NaNs ( 0.72 % out of 3185)
2 days, 23:50:06.872793 INFO: Collecting fragment features
2 days, 23:50:06.879020 INFO: Finished candidate scoring
2 days, 23:50:06.882196 INFO: performing precursor FDR with 47 features
2 days, 23:50:06.882278 INFO: Decoy channel: -1
2 days, 23:50:06.882320 INFO: competitive: True
2 days, 23:50:06.886967 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:50:06.889343 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:50:06.889404 WARNING: dropped 19 decoy PSMs due to missing features
2 days, 23:50:06.889452 WARNING: FDR calculation for 1676 target and 1486 decoy PSMs
2 days, 23:50:06.889483 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:50:06.890901 INFO: Estimating optimal hyperparameters - samples: 2,529, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:50:06.891013 INFO: Using random state 775332 for train-test-split
2 days, 23:50:07.218311 INFO: Test AUC: 0.857
2 days, 23:50:07.218455 INFO: Train AUC: 0.893
2 days, 23:50:07.218514 INFO: AUC difference: 4.04%
2 days, 23:50:07.571892 INFO: Resetting torch num_threads to 80
2 days, 23:50:07.572439 PROGRESS: === Extracted 3185 precursors and 22924 fragments ===
2 days, 23:50:07.572902 INFO: === FDR correction performed with classifier version 14 ===
2 days, 23:50:07.573538 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:50:07.573645 PROGRESS: Total precursors accumulated: 600
2 days, 23:50:07.573732 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:50:07.573809 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:50:07.573894 PROGRESS: 
2 days, 23:50:07.573966 PROGRESS: Precursor Summary:
2 days, 23:50:07.575164 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   577; 0.001 FDR:   529
2 days, 23:50:07.575271 PROGRESS: 
2 days, 23:50:07.575352 PROGRESS: Protein Summary:
2 days, 23:50:07.576757 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   425; 0.001 FDR:   394
2 days, 23:50:07.576867 PROGRESS: =========================================================================
2 days, 23:50:07.577042 INFO: Target number of precursors reached.
2 days, 23:50:07.583275 INFO: fragments_df: keeping 5000 of 22924 [sum(precursor_idx_mask)=13906 sum(mass_error_mask)=22924 stop_rank=5000
2 days, 23:50:07.586668 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:07.816302 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:07.988332 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:08.248080 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:09.113354 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:50:09.113844 INFO: Using score_cutoff 14.695571042633057 (fac=0.99, q=1)
2 days, 23:50:09.114275 INFO: Updating optimization_manager: fwhm_rt             : 2.568242311477661 -> 2.5288357734680176
2 days, 23:50:09.114377 INFO: Updating optimization_manager: fwhm_mobility       : 0.003988002426922321 -> 0.0038374189753085375
2 days, 23:50:09.114459 INFO: Updating optimization_manager: score_cutoff        : 14.904716171264647 -> 14.695571042633057
2 days, 23:50:09.114530 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:09.115681 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:09.117086 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:09.117928 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:09.119935 INFO: === checking if optimization conditions were reached ===
2 days, 23:50:09.120064 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:50:09.120902 INFO: Updating optimization_manager: mobility_error      : 0.05084000073125574 -> 0.06321102613374999
2 days, 23:50:09.121060 INFO: Updating optimization_manager: classifier_version  : 14 -> 21
2 days, 23:50:09.121192 INFO: Updating optimization_manager: score_cutoff        : 14.695571042633057 -> 14.904716171264647
2 days, 23:50:09.121341 INFO: Updating optimization_manager: fwhm_rt             : 2.5288357734680176 -> 2.568242311477661
2 days, 23:50:09.121510 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038374189753085375 -> 0.003988002426922321
2 days, 23:50:09.121678 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0632 found after 3 searches.
2 days, 23:50:09.121776 INFO: ==============================================
2 days, 23:50:09.121896 PROGRESS: Optimization finished for mobility_error.
2 days, 23:50:09.125705 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:09.126821 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:09.128427 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:09.129360 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:09.131628 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:50:09.131752 PROGRESS: ==============================================
2 days, 23:50:09.131840 PROGRESS: ms2_error      : 15.0000
2 days, 23:50:09.131917 PROGRESS: ms1_error      : 15.0000
2 days, 23:50:09.132014 PROGRESS: rt_error       : 10.3319
2 days, 23:50:09.132116 PROGRESS: mobility_error : 0.0632
2 days, 23:50:09.132191 PROGRESS: ==============================================
2 days, 23:50:09.132771 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:09.136668 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:09.153657 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:09.157730 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:09.203084 INFO: Using python extraction backend
2 days, 23:50:09.213059 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:50:09.213481 INFO: === Search parameters used ===
2 days, 23:50:09.213575 INFO: rt_error       : 10.331868638436966
2 days, 23:50:09.213671 INFO: mobility_error : 0.06321102613374999
2 days, 23:50:09.213753 INFO: num_candidates : 3
2 days, 23:50:09.213829 INFO: ms1_error      : 15.0
2 days, 23:50:09.214022 INFO: ms2_error      : 15.0
2 days, 23:50:09.214106 INFO: fwhm_rt        : 2.568242311477661
2 days, 23:50:09.214182 INFO: quant_window   : 3
2 days, 23:50:09.214256 INFO: ==============================================
2 days, 23:50:09.222062 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:50:09.222188 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:50:09.222250 INFO: FWHM in RT is 2.57 seconds, sigma is 0.43
2 days, 23:50:09.222285 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.16
2 days, 23:50:09.274073 INFO: Starting candidate selection
2 days, 23:50:11.332654 INFO: Removed 18791 precursors with score below cutoff 14.904716171264647
2 days, 23:50:11.739834 INFO: Starting candidate scoring
2 days, 23:50:12.752961 INFO: Finished candidate processing
2 days, 23:50:12.753100 INFO: Collecting candidate features
2 days, 23:50:12.887164 WARNING: intensity_correlation has 158 NaNs ( 0.27 % out of 58151)
2 days, 23:50:12.887592 WARNING: height_correlation has 3 NaNs ( 0.01 % out of 58151)
2 days, 23:50:12.898225 INFO: Collecting fragment features
2 days, 23:50:12.929455 INFO: Finished candidate scoring
2 days, 23:50:12.957171 INFO: === Performing FDR correction with classifier version 21 ===
2 days, 23:50:12.957606 INFO: performing precursor FDR with 47 features
2 days, 23:50:12.957667 INFO: Decoy channel: -1
2 days, 23:50:12.957717 INFO: competitive: True
2 days, 23:50:12.980232 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:50:12.992423 WARNING: dropped 39 target PSMs due to missing features
2 days, 23:50:12.992567 WARNING: dropped 121 decoy PSMs due to missing features
2 days, 23:50:12.992627 WARNING: FDR calculation for 34966 target and 23025 decoy PSMs
2 days, 23:50:12.992682 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:50:13.005180 INFO: Estimating optimal hyperparameters - samples: 46,392, batch_size: 190, learning_rate: 2.15e-04
2 days, 23:50:13.005431 INFO: Using random state 465033 for train-test-split
2 days, 23:50:17.932431 INFO: Test AUC: 0.896
2 days, 23:50:17.932585 INFO: Train AUC: 0.903
2 days, 23:50:17.932659 INFO: AUC difference: 0.72%
2 days, 23:50:18.345170 INFO: Resetting torch num_threads to 80
2 days, 23:50:18.348244 INFO: Removing fragments below FDR threshold
2 days, 23:50:18.357914 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:50:18.358145 PROGRESS: Total precursors accumulated: 13,280
2 days, 23:50:18.358248 PROGRESS: Target precursors: 13,149 (99.01%)
2 days, 23:50:18.358338 PROGRESS: Decoy precursors: 131 (0.99%)
2 days, 23:50:18.358419 PROGRESS: 
2 days, 23:50:18.358495 PROGRESS: Precursor Summary:
2 days, 23:50:18.363284 PROGRESS: Channel   0:	 0.050 FDR: 13,149; 0.010 FDR: 13,149; 0.001 FDR: 11,775
2 days, 23:50:18.363481 PROGRESS: 
2 days, 23:50:18.363572 PROGRESS: Protein Summary:
2 days, 23:50:18.369628 PROGRESS: Channel   0:	 0.050 FDR: 1,683; 0.010 FDR: 1,683; 0.001 FDR: 1,660
2 days, 23:50:18.369803 PROGRESS: =========================================================================
2 days, 23:50:18.370888 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R4/psm.parquet
2 days, 23:50:18.429185 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R4/frag.parquet
2 days, 23:50:18.490342 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R4
2 days, 23:50:18.496639 PROGRESS: Loading raw file 5/12: A9_G_DIA_nLC_tTOF_R5 
2 days, 23:50:18.496781 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:50:18.496865 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R5/figures
2 days, 23:50:18.497053 INFO: Initializing TimingManager
2 days, 23:50:18.497549 INFO: Initializing RawFileManager
2 days, 23:50:18.497705 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:18.497764 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:18.497804 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:18.747545 INFO: Reading 22,622 frames with 405,356,946 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:22.562171 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d...
2 days, 23:50:22.563133 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:22.565030 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:22.565266 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:22.565700 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:22.567300 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:22.599664 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:22.600021 INFO: Indexing quadrupole dimension
2 days, 23:50:22.732669 INFO: Transposing detector events
2 days, 23:50:24.738602 INFO: Finished transposing data
2 days, 23:50:24.738801 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
2 days, 23:50:24.739277 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:50:24.739410 INFO: RT duration (sec)   : 2399.9
2 days, 23:50:24.739665 INFO: RT duration (min)   : 40.0
2 days, 23:50:24.739754 INFO: Cycle len (scans)   : 12
2 days, 23:50:24.739789 INFO: Cycle len (sec)     : 1.27
2 days, 23:50:24.739820 INFO: Number of cycles    : 1885
2 days, 23:50:24.739851 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:50:24.739900 INFO: Creating DIA data object took: 6.242192506790161
2 days, 23:50:24.746139 INFO: Initializing CalibrationManager
2 days, 23:50:24.746421 INFO: Setting up calibration estimators ..
2 days, 23:50:24.746492 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:50:24.746569 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:50:24.746648 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:50:24.746719 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:50:24.746809 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:50:24.746885 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:50:24.746950 INFO: Done setting up calibration estimators.
2 days, 23:50:24.747088 INFO: Initializing OptimizationManager
2 days, 23:50:24.747196 INFO: initial parameter: ms1_error = 30
2 days, 23:50:24.747257 INFO: initial parameter: ms2_error = 30
2 days, 23:50:24.747318 INFO: initial parameter: rt_error = 1199.943863
2 days, 23:50:24.747376 INFO: initial parameter: mobility_error = 0.1
2 days, 23:50:24.747432 INFO: initial parameter: num_candidates = 1
2 days, 23:50:24.747486 INFO: initial parameter: fwhm_rt = 5
2 days, 23:50:24.747541 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:50:24.747596 INFO: initial parameter: score_cutoff = 0
2 days, 23:50:24.747649 INFO: initial parameter: classifier_version = -1
2 days, 23:50:24.747734 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R5
2 days, 23:50:24.747941 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:50:24.747988 INFO: Initializing FDRManager
2 days, 23:50:24.748025 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:50:24.756095 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:50:24.761599 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:50:24.762018 INFO: Updating optimization_manager: rt_error            : 1199.943863 -> 1199.943863
2 days, 23:50:24.762141 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:50:24.762352 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:50:24.762446 PROGRESS: Starting initial search for precursors.
2 days, 23:50:24.762536 INFO: Starting optimization step 0.
2 days, 23:50:24.762617 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:50:24.762693 INFO: Using python extraction backend
2 days, 23:50:24.762814 PROGRESS: Extracting batch of 399 precursors
2 days, 23:50:24.762891 INFO: === Search parameters used ===
2 days, 23:50:24.762952 INFO: rt_error       : 1199.943863
2 days, 23:50:24.763010 INFO: mobility_error : 0.1
2 days, 23:50:24.763065 INFO: num_candidates : 1
2 days, 23:50:24.763119 INFO: ms1_error      : 30
2 days, 23:50:24.763172 INFO: ms2_error      : 30
2 days, 23:50:24.763225 INFO: fwhm_rt        : 5
2 days, 23:50:24.763278 INFO: quant_window   : 3
2 days, 23:50:24.763330 INFO: ==============================================
2 days, 23:50:24.764094 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:50:24.764148 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:50:24.764190 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:50:24.764221 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:50:24.781991 INFO: Starting candidate selection
2 days, 23:50:28.252355 INFO: Starting candidate scoring
2 days, 23:50:28.310409 INFO: Finished candidate processing
2 days, 23:50:28.310568 INFO: Collecting candidate features
2 days, 23:50:28.328155 INFO: Collecting fragment features
2 days, 23:50:28.331723 INFO: Finished candidate scoring
2 days, 23:50:28.333033 INFO: performing precursor FDR with 47 features
2 days, 23:50:28.333097 INFO: Decoy channel: -1
2 days, 23:50:28.333136 INFO: competitive: True
2 days, 23:50:28.334923 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:50:28.337035 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:50:28.337815 INFO: Using random state 220829 for train-test-split
2 days, 23:50:28.362043 INFO: Test AUC: 0.528
2 days, 23:50:28.362143 INFO: Train AUC: 0.663
2 days, 23:50:28.362184 INFO: AUC difference: 20.35%
2 days, 23:50:28.362214 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:50:28.708467 INFO: Resetting torch num_threads to 80
2 days, 23:50:28.709125 PROGRESS: === Extracted 399 precursors and 3758 fragments ===
2 days, 23:50:28.709745 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:50:28.710658 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:50:28.710795 PROGRESS: Total precursors accumulated: 200
2 days, 23:50:28.710898 PROGRESS: Target precursors: 128 (64.00%)
2 days, 23:50:28.711000 PROGRESS: Decoy precursors: 72 (36.00%)
2 days, 23:50:28.711099 PROGRESS: 
2 days, 23:50:28.711190 PROGRESS: Precursor Summary:
2 days, 23:50:28.712762 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
2 days, 23:50:28.712885 PROGRESS: 
2 days, 23:50:28.712978 PROGRESS: Protein Summary:
2 days, 23:50:28.714833 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
2 days, 23:50:28.714965 PROGRESS: =========================================================================
2 days, 23:50:28.715172 INFO: Target number of precursors not reached yet.
2 days, 23:50:28.719023 INFO: Starting optimization step 1.
2 days, 23:50:28.719172 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:50:28.719283 INFO: Using python extraction backend
2 days, 23:50:28.719437 PROGRESS: Extracting batch of 798 precursors
2 days, 23:50:28.719540 INFO: === Search parameters used ===
2 days, 23:50:28.719626 INFO: rt_error       : 1199.943863
2 days, 23:50:28.719702 INFO: mobility_error : 0.1
2 days, 23:50:28.719779 INFO: num_candidates : 1
2 days, 23:50:28.719851 INFO: ms1_error      : 30
2 days, 23:50:28.719925 INFO: ms2_error      : 30
2 days, 23:50:28.719995 INFO: fwhm_rt        : 5
2 days, 23:50:28.720066 INFO: quant_window   : 3
2 days, 23:50:28.720174 INFO: ==============================================
2 days, 23:50:28.721140 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:50:28.721205 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:50:28.721248 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:50:28.721280 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:50:28.747736 INFO: Starting candidate selection
2 days, 23:50:33.781153 INFO: Starting candidate scoring
2 days, 23:50:33.847053 INFO: Finished candidate processing
2 days, 23:50:33.847192 INFO: Collecting candidate features
2 days, 23:50:33.865917 INFO: Collecting fragment features
2 days, 23:50:33.869853 INFO: Finished candidate scoring
2 days, 23:50:33.872971 INFO: performing precursor FDR with 47 features
2 days, 23:50:33.873050 INFO: Decoy channel: -1
2 days, 23:50:33.873094 INFO: competitive: True
2 days, 23:50:33.877167 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:50:33.879889 INFO: Estimating optimal hyperparameters - samples: 957, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:50:33.880022 INFO: Using random state 198081 for train-test-split
2 days, 23:50:34.004683 INFO: Test AUC: 0.764
2 days, 23:50:34.004794 INFO: Train AUC: 0.782
2 days, 23:50:34.004826 INFO: AUC difference: 2.33%
2 days, 23:50:34.379520 INFO: Resetting torch num_threads to 80
2 days, 23:50:34.381361 PROGRESS: === Extracted 1197 precursors and 11416 fragments ===
2 days, 23:50:34.381960 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:50:34.382884 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:50:34.383019 PROGRESS: Total precursors accumulated: 600
2 days, 23:50:34.383130 PROGRESS: Target precursors: 469 (78.17%)
2 days, 23:50:34.383243 PROGRESS: Decoy precursors: 131 (21.83%)
2 days, 23:50:34.383338 PROGRESS: 
2 days, 23:50:34.383425 PROGRESS: Precursor Summary:
2 days, 23:50:34.385180 PROGRESS: Channel   0:	 0.050 FDR:   293; 0.010 FDR:   242; 0.001 FDR:   179
2 days, 23:50:34.385309 PROGRESS: 
2 days, 23:50:34.385404 PROGRESS: Protein Summary:
2 days, 23:50:34.387452 PROGRESS: Channel   0:	 0.050 FDR:   219; 0.010 FDR:   179; 0.001 FDR:   131
2 days, 23:50:34.387578 PROGRESS: =========================================================================
2 days, 23:50:34.387788 INFO: Target number of precursors reached.
2 days, 23:50:34.392931 INFO: fragments_df: keeping 2000 of 11416 [sum(precursor_idx_mask)=2492 sum(mass_error_mask)=11416 stop_rank=2000
2 days, 23:50:34.397614 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:34.570519 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:34.714634 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:34.870737 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:35.213960 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:50:35.214506 INFO: Using score_cutoff 35.36992242279053 (fac=0.99, q=1)
2 days, 23:50:35.214966 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.9616668224334717
2 days, 23:50:35.215075 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.00759007828310132
2 days, 23:50:35.215162 INFO: Updating optimization_manager: score_cutoff        : 0 -> 35.36992242279053
2 days, 23:50:35.215266 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:35.216538 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:35.218204 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:35.219310 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:35.221773 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2 days, 23:50:35.221907 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:50:35.222012 INFO: Starting optimization step 2.
2 days, 23:50:35.222090 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:50:35.222167 INFO: Using python extraction backend
2 days, 23:50:35.222294 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:50:35.222378 INFO: === Search parameters used ===
2 days, 23:50:35.222462 INFO: rt_error       : 1199.943863
2 days, 23:50:35.222522 INFO: mobility_error : 0.1
2 days, 23:50:35.222579 INFO: num_candidates : 3
2 days, 23:50:35.222638 INFO: ms1_error      : 30
2 days, 23:50:35.222692 INFO: ms2_error      : 30
2 days, 23:50:35.222746 INFO: fwhm_rt        : 2.9616668224334717
2 days, 23:50:35.222800 INFO: quant_window   : 3
2 days, 23:50:35.222854 INFO: ==============================================
2 days, 23:50:35.224059 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:50:35.224119 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:50:35.224178 INFO: FWHM in RT is 2.96 seconds, sigma is 0.49
2 days, 23:50:35.224210 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.11
2 days, 23:50:35.237991 INFO: Starting candidate selection
2 days, 23:50:43.941260 INFO: Starting candidate scoring
2 days, 23:50:44.105582 INFO: Finished candidate processing
2 days, 23:50:44.105701 INFO: Collecting candidate features
2 days, 23:50:44.123018 INFO: Collecting fragment features
2 days, 23:50:44.127806 INFO: Finished candidate scoring
2 days, 23:50:44.129985 INFO: performing precursor FDR with 47 features
2 days, 23:50:44.130056 INFO: Decoy channel: -1
2 days, 23:50:44.130087 INFO: competitive: True
2 days, 23:50:44.134537 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:50:44.137245 INFO: Estimating optimal hyperparameters - samples: 2,742, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:50:44.137352 INFO: Using random state 888588 for train-test-split
2 days, 23:50:44.394475 INFO: Test AUC: 0.681
2 days, 23:50:44.394597 INFO: Train AUC: 0.697
2 days, 23:50:44.394636 INFO: AUC difference: 2.31%
2 days, 23:50:44.703360 INFO: Resetting torch num_threads to 80
2 days, 23:50:44.704018 PROGRESS: === Extracted 3428 precursors and 31786 fragments ===
2 days, 23:50:44.704524 INFO: === FDR correction performed with classifier version 1 ===
2 days, 23:50:44.705327 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:50:44.705445 PROGRESS: Total precursors accumulated: 600
2 days, 23:50:44.705520 PROGRESS: Target precursors: 481 (80.17%)
2 days, 23:50:44.705586 PROGRESS: Decoy precursors: 119 (19.83%)
2 days, 23:50:44.705646 PROGRESS: 
2 days, 23:50:44.705703 PROGRESS: Precursor Summary:
2 days, 23:50:44.707018 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   281; 0.001 FDR:   199
2 days, 23:50:44.707129 PROGRESS: 
2 days, 23:50:44.707200 PROGRESS: Protein Summary:
2 days, 23:50:44.708673 PROGRESS: Channel   0:	 0.050 FDR:   260; 0.010 FDR:   208; 0.001 FDR:   143
2 days, 23:50:44.708779 PROGRESS: =========================================================================
2 days, 23:50:44.708964 INFO: Target number of precursors reached.
2 days, 23:50:44.717736 INFO: fragments_df: keeping 4861 of 31786 [sum(precursor_idx_mask)=7946 sum(mass_error_mask)=31786 stop_rank=4861
2 days, 23:50:44.721951 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:44.875774 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:45.027634 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:45.213935 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:46.004249 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:50:46.004693 INFO: Using score_cutoff 33.62487732696533 (fac=0.99, q=1)
2 days, 23:50:46.005043 INFO: Updating optimization_manager: fwhm_rt             : 2.9616668224334717 -> 2.966561794281006
2 days, 23:50:46.005143 INFO: Updating optimization_manager: fwhm_mobility       : 0.00759007828310132 -> 0.0072181071154773235
2 days, 23:50:46.005210 INFO: Updating optimization_manager: score_cutoff        : 35.36992242279053 -> 33.62487732696533
2 days, 23:50:46.005275 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:46.006435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:46.007933 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:46.008783 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:46.010813 INFO: === checking if optimization conditions were reached ===
2 days, 23:50:46.012432 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.59822064881461
2 days, 23:50:46.012545 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2 days, 23:50:46.012620 PROGRESS: ❌ ms2_error      : 17.5982 > 15.0000 or insufficient steps taken.
2 days, 23:50:46.013639 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:50:46.013745 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
2 days, 23:50:46.013820 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:50:46.013902 INFO: ==============================================
2 days, 23:50:46.013989 INFO: Starting optimization step 3.
2 days, 23:50:46.014058 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:50:46.014124 INFO: Using python extraction backend
2 days, 23:50:46.014229 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:50:46.014299 INFO: === Search parameters used ===
2 days, 23:50:46.014354 INFO: rt_error       : 1199.943863
2 days, 23:50:46.014410 INFO: mobility_error : 0.1
2 days, 23:50:46.014460 INFO: num_candidates : 3
2 days, 23:50:46.014507 INFO: ms1_error      : 15.0
2 days, 23:50:46.014553 INFO: ms2_error      : 17.59822064881461
2 days, 23:50:46.014601 INFO: fwhm_rt        : 2.966561794281006
2 days, 23:50:46.014646 INFO: quant_window   : 3
2 days, 23:50:46.014691 INFO: ==============================================
2 days, 23:50:46.015577 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:50:46.015629 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:50:46.015667 INFO: FWHM in RT is 2.97 seconds, sigma is 0.49
2 days, 23:50:46.015693 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.91
2 days, 23:50:46.018553 INFO: Starting candidate selection
2 days, 23:50:53.714105 INFO: Starting candidate scoring
2 days, 23:50:53.849818 INFO: Finished candidate processing
2 days, 23:50:53.849947 INFO: Collecting candidate features
2 days, 23:50:53.862482 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3431)
2 days, 23:50:53.867654 INFO: Collecting fragment features
2 days, 23:50:53.872410 INFO: Finished candidate scoring
2 days, 23:50:53.874561 INFO: performing precursor FDR with 47 features
2 days, 23:50:53.874624 INFO: Decoy channel: -1
2 days, 23:50:53.874657 INFO: competitive: True
2 days, 23:50:53.878413 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:50:53.880076 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:50:53.881325 INFO: Estimating optimal hyperparameters - samples: 2,743, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:50:53.881431 INFO: Using random state 216188 for train-test-split
2 days, 23:50:54.233978 INFO: Test AUC: 0.718
2 days, 23:50:54.234117 INFO: Train AUC: 0.734
2 days, 23:50:54.234170 INFO: AUC difference: 2.12%
2 days, 23:50:54.538714 INFO: Resetting torch num_threads to 80
2 days, 23:50:54.539357 PROGRESS: === Extracted 3431 precursors and 28843 fragments ===
2 days, 23:50:54.539849 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:50:54.540601 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:50:54.540709 PROGRESS: Total precursors accumulated: 600
2 days, 23:50:54.540785 PROGRESS: Target precursors: 527 (87.83%)
2 days, 23:50:54.540849 PROGRESS: Decoy precursors: 73 (12.17%)
2 days, 23:50:54.540909 PROGRESS: 
2 days, 23:50:54.540966 PROGRESS: Precursor Summary:
2 days, 23:50:54.542326 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   385; 0.001 FDR:   307
2 days, 23:50:54.542436 PROGRESS: 
2 days, 23:50:54.542507 PROGRESS: Protein Summary:
2 days, 23:50:54.544069 PROGRESS: Channel   0:	 0.050 FDR:   319; 0.010 FDR:   282; 0.001 FDR:   231
2 days, 23:50:54.544174 PROGRESS: =========================================================================
2 days, 23:50:54.544340 INFO: Target number of precursors reached.
2 days, 23:50:54.552960 INFO: fragments_df: keeping 5000 of 28843 [sum(precursor_idx_mask)=10269 sum(mass_error_mask)=28843 stop_rank=5000
2 days, 23:50:54.556928 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:54.727479 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:54.888747 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:55.078218 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:56.061158 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:50:56.061732 INFO: Using score_cutoff 27.73890178527832 (fac=0.99, q=1)
2 days, 23:50:56.062153 INFO: Updating optimization_manager: fwhm_rt             : 2.966561794281006 -> 2.7785532474517822
2 days, 23:50:56.062255 INFO: Updating optimization_manager: fwhm_mobility       : 0.0072181071154773235 -> 0.0056611658073961735
2 days, 23:50:56.062318 INFO: Updating optimization_manager: score_cutoff        : 33.62487732696533 -> 27.73890178527832
2 days, 23:50:56.062380 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:56.063507 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:56.064918 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:56.065723 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:56.067747 INFO: === checking if optimization conditions were reached ===
2 days, 23:50:56.069492 INFO: Updating optimization_manager: ms2_error           : 17.59822064881461 -> 15.0
2 days, 23:50:56.069600 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:50:56.069669 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:50:56.070717 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:50:56.070822 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:50:56.070887 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:50:56.070945 INFO: ==============================================
2 days, 23:50:56.071012 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:50:56.074309 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:50:56.075205 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:50:56.076619 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:50:56.077472 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:50:56.079583 INFO: Starting optimization step 0.
2 days, 23:50:56.079701 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:50:56.079806 INFO: Using python extraction backend
2 days, 23:50:56.079940 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:50:56.080050 INFO: === Search parameters used ===
2 days, 23:50:56.080132 INFO: rt_error       : 1199.943863
2 days, 23:50:56.080201 INFO: mobility_error : 0.1
2 days, 23:50:56.080271 INFO: num_candidates : 3
2 days, 23:50:56.080338 INFO: ms1_error      : 15.0
2 days, 23:50:56.080401 INFO: ms2_error      : 15.0
2 days, 23:50:56.080465 INFO: fwhm_rt        : 2.7785532474517822
2 days, 23:50:56.080529 INFO: quant_window   : 3
2 days, 23:50:56.080592 INFO: ==============================================
2 days, 23:50:56.081444 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:50:56.081500 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:50:56.081558 INFO: FWHM in RT is 2.78 seconds, sigma is 0.46
2 days, 23:50:56.081599 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.07
2 days, 23:50:56.094466 INFO: Starting candidate selection
2 days, 23:51:03.627604 INFO: Starting candidate scoring
2 days, 23:51:03.742866 INFO: Finished candidate processing
2 days, 23:51:03.743059 INFO: Collecting candidate features
2 days, 23:51:03.760913 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3394)
2 days, 23:51:03.766776 INFO: Collecting fragment features
2 days, 23:51:03.773188 INFO: Finished candidate scoring
2 days, 23:51:03.776836 INFO: performing precursor FDR with 47 features
2 days, 23:51:03.776936 INFO: Decoy channel: -1
2 days, 23:51:03.776978 INFO: competitive: True
2 days, 23:51:03.782076 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:03.784275 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:51:03.785860 INFO: Estimating optimal hyperparameters - samples: 2,713, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:03.786005 INFO: Using random state 882121 for train-test-split
2 days, 23:51:04.103387 INFO: Test AUC: 0.715
2 days, 23:51:04.103515 INFO: Train AUC: 0.758
2 days, 23:51:04.103558 INFO: AUC difference: 5.66%
2 days, 23:51:04.103610 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:51:04.411800 INFO: Resetting torch num_threads to 80
2 days, 23:51:04.412358 PROGRESS: === Extracted 3394 precursors and 27808 fragments ===
2 days, 23:51:04.412808 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:04.413444 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:04.413543 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:04.413612 PROGRESS: Target precursors: 526 (87.67%)
2 days, 23:51:04.413672 PROGRESS: Decoy precursors: 74 (12.33%)
2 days, 23:51:04.413726 PROGRESS: 
2 days, 23:51:04.413777 PROGRESS: Precursor Summary:
2 days, 23:51:04.414883 PROGRESS: Channel   0:	 0.050 FDR:   439; 0.010 FDR:   377; 0.001 FDR:   307
2 days, 23:51:04.414987 PROGRESS: 
2 days, 23:51:04.415053 PROGRESS: Protein Summary:
2 days, 23:51:04.416398 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   276; 0.001 FDR:   228
2 days, 23:51:04.416511 PROGRESS: =========================================================================
2 days, 23:51:04.416659 INFO: Target number of precursors reached.
2 days, 23:51:04.422893 INFO: fragments_df: keeping 5000 of 27808 [sum(precursor_idx_mask)=9935 sum(mass_error_mask)=27808 stop_rank=5000
2 days, 23:51:04.426265 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:04.634389 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:04.828554 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:04.997764 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:05.794593 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:05.795118 INFO: Using score_cutoff 27.14506893539429 (fac=0.99, q=1)
2 days, 23:51:05.795495 INFO: Updating optimization_manager: fwhm_rt             : 2.7785532474517822 -> 2.701176166534424
2 days, 23:51:05.795595 INFO: Updating optimization_manager: fwhm_mobility       : 0.0056611658073961735 -> 0.005429493263363838
2 days, 23:51:05.795671 INFO: Updating optimization_manager: score_cutoff        : 27.73890178527832 -> 27.14506893539429
2 days, 23:51:05.795751 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:05.796929 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:05.798378 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:05.799242 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:05.801399 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:05.801523 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:51:05.803571 INFO: Updating optimization_manager: rt_error            : 1199.943863 -> 174.44251539550984
2 days, 23:51:05.803704 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 174.4425.
2 days, 23:51:05.803799 INFO: ==============================================
2 days, 23:51:05.803900 INFO: Starting optimization step 1.
2 days, 23:51:05.803986 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:05.804070 INFO: Using python extraction backend
2 days, 23:51:05.804207 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:05.804302 INFO: === Search parameters used ===
2 days, 23:51:05.804392 INFO: rt_error       : 174.44251539550984
2 days, 23:51:05.804463 INFO: mobility_error : 0.1
2 days, 23:51:05.804529 INFO: num_candidates : 3
2 days, 23:51:05.804597 INFO: ms1_error      : 15.0
2 days, 23:51:05.804662 INFO: ms2_error      : 15.0
2 days, 23:51:05.804727 INFO: fwhm_rt        : 2.701176166534424
2 days, 23:51:05.804790 INFO: quant_window   : 3
2 days, 23:51:05.804851 INFO: ==============================================
2 days, 23:51:05.806058 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:05.806133 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:05.806202 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
2 days, 23:51:05.806239 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.94
2 days, 23:51:05.811348 INFO: Starting candidate selection
2 days, 23:51:07.915867 INFO: Starting candidate scoring
2 days, 23:51:08.025779 INFO: Finished candidate processing
2 days, 23:51:08.025946 INFO: Collecting candidate features
2 days, 23:51:08.039680 WARNING: intensity_correlation has 6 NaNs ( 0.18 % out of 3339)
2 days, 23:51:08.039941 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3339)
2 days, 23:51:08.045052 INFO: Collecting fragment features
2 days, 23:51:08.049752 INFO: Finished candidate scoring
2 days, 23:51:08.052621 INFO: performing precursor FDR with 47 features
2 days, 23:51:08.052681 INFO: Decoy channel: -1
2 days, 23:51:08.052715 INFO: competitive: True
2 days, 23:51:08.056804 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:08.058820 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:51:08.058885 WARNING: dropped 5 decoy PSMs due to missing features
2 days, 23:51:08.060276 INFO: Estimating optimal hyperparameters - samples: 2,666, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:08.060377 INFO: Using random state 882121 for train-test-split
2 days, 23:51:08.449773 INFO: Test AUC: 0.795
2 days, 23:51:08.449921 INFO: Train AUC: 0.785
2 days, 23:51:08.449958 INFO: AUC difference: 1.33%
2 days, 23:51:08.742316 INFO: Resetting torch num_threads to 80
2 days, 23:51:08.742900 PROGRESS: === Extracted 3339 precursors and 26254 fragments ===
2 days, 23:51:08.743367 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:08.743992 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:08.744088 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:08.744153 PROGRESS: Target precursors: 552 (92.00%)
2 days, 23:51:08.744210 PROGRESS: Decoy precursors: 48 (8.00%)
2 days, 23:51:08.744261 PROGRESS: 
2 days, 23:51:08.744311 PROGRESS: Precursor Summary:
2 days, 23:51:08.745460 PROGRESS: Channel   0:	 0.050 FDR:   508; 0.010 FDR:   441; 0.001 FDR:   432
2 days, 23:51:08.745556 PROGRESS: 
2 days, 23:51:08.745617 PROGRESS: Protein Summary:
2 days, 23:51:08.746950 PROGRESS: Channel   0:	 0.050 FDR:   372; 0.010 FDR:   324; 0.001 FDR:   319
2 days, 23:51:08.747051 PROGRESS: =========================================================================
2 days, 23:51:08.747197 INFO: Target number of precursors reached.
2 days, 23:51:08.753413 INFO: fragments_df: keeping 5000 of 26254 [sum(precursor_idx_mask)=11336 sum(mass_error_mask)=26254 stop_rank=5000
2 days, 23:51:08.756849 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:09.000022 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:09.176342 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:09.406749 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:10.242032 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:10.242652 INFO: Using score_cutoff 22.582813774108885 (fac=0.99, q=1)
2 days, 23:51:10.243148 INFO: Updating optimization_manager: fwhm_rt             : 2.701176166534424 -> 2.6410305500030518
2 days, 23:51:10.243273 INFO: Updating optimization_manager: fwhm_mobility       : 0.005429493263363838 -> 0.00490337610244751
2 days, 23:51:10.243377 INFO: Updating optimization_manager: score_cutoff        : 27.14506893539429 -> 22.582813774108885
2 days, 23:51:10.243479 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:10.245046 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:10.247014 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:10.248227 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:10.250770 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:10.250907 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:51:10.253574 INFO: Updating optimization_manager: rt_error            : 174.44251539550984 -> 76.30840483481106
2 days, 23:51:10.253713 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 76.3084.
2 days, 23:51:10.253814 INFO: ==============================================
2 days, 23:51:10.253932 INFO: Starting optimization step 2.
2 days, 23:51:10.254036 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:10.254141 INFO: Using python extraction backend
2 days, 23:51:10.254304 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:10.254426 INFO: === Search parameters used ===
2 days, 23:51:10.254537 INFO: rt_error       : 76.30840483481106
2 days, 23:51:10.254632 INFO: mobility_error : 0.1
2 days, 23:51:10.254722 INFO: num_candidates : 3
2 days, 23:51:10.254815 INFO: ms1_error      : 15.0
2 days, 23:51:10.254902 INFO: ms2_error      : 15.0
2 days, 23:51:10.254987 INFO: fwhm_rt        : 2.6410305500030518
2 days, 23:51:10.255071 INFO: quant_window   : 3
2 days, 23:51:10.255153 INFO: ==============================================
2 days, 23:51:10.256437 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:10.256502 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:10.256556 INFO: FWHM in RT is 2.64 seconds, sigma is 0.44
2 days, 23:51:10.256595 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.66
2 days, 23:51:10.262758 INFO: Starting candidate selection
2 days, 23:51:11.251790 INFO: Starting candidate scoring
2 days, 23:51:11.355967 INFO: Finished candidate processing
2 days, 23:51:11.356136 INFO: Collecting candidate features
2 days, 23:51:11.369642 WARNING: intensity_correlation has 5 NaNs ( 0.15 % out of 3266)
2 days, 23:51:11.374940 INFO: Collecting fragment features
2 days, 23:51:11.379575 INFO: Finished candidate scoring
2 days, 23:51:11.382322 INFO: performing precursor FDR with 47 features
2 days, 23:51:11.382382 INFO: Decoy channel: -1
2 days, 23:51:11.382415 INFO: competitive: True
2 days, 23:51:11.390229 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:11.392277 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:51:11.392344 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 23:51:11.393905 INFO: Estimating optimal hyperparameters - samples: 2,608, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:11.394044 INFO: Using random state 882121 for train-test-split
2 days, 23:51:11.619450 INFO: Test AUC: 0.810
2 days, 23:51:11.619590 INFO: Train AUC: 0.814
2 days, 23:51:11.619649 INFO: AUC difference: 0.50%
2 days, 23:51:11.932690 INFO: Resetting torch num_threads to 80
2 days, 23:51:11.933464 PROGRESS: === Extracted 3266 precursors and 24818 fragments ===
2 days, 23:51:11.934107 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:11.935079 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:11.935217 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:11.935304 PROGRESS: Target precursors: 564 (94.00%)
2 days, 23:51:11.935377 PROGRESS: Decoy precursors: 36 (6.00%)
2 days, 23:51:11.935439 PROGRESS: 
2 days, 23:51:11.935505 PROGRESS: Precursor Summary:
2 days, 23:51:11.936935 PROGRESS: Channel   0:	 0.050 FDR:   555; 0.010 FDR:   480; 0.001 FDR:   432
2 days, 23:51:11.937036 PROGRESS: 
2 days, 23:51:11.937106 PROGRESS: Protein Summary:
2 days, 23:51:11.939067 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   352; 0.001 FDR:   318
2 days, 23:51:11.939198 PROGRESS: =========================================================================
2 days, 23:51:11.939396 INFO: Target number of precursors reached.
2 days, 23:51:11.948862 INFO: fragments_df: keeping 5000 of 24818 [sum(precursor_idx_mask)=12051 sum(mass_error_mask)=24818 stop_rank=5000
2 days, 23:51:11.953924 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:12.168499 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:12.347000 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:12.512037 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:13.413950 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:13.414434 INFO: Using score_cutoff 20.549809173202515 (fac=0.99, q=1)
2 days, 23:51:13.414825 INFO: Updating optimization_manager: fwhm_rt             : 2.6410305500030518 -> 2.6260523796081543
2 days, 23:51:13.414932 INFO: Updating optimization_manager: fwhm_mobility       : 0.00490337610244751 -> 0.004679095931351185
2 days, 23:51:13.415016 INFO: Updating optimization_manager: score_cutoff        : 22.582813774108885 -> 20.549809173202515
2 days, 23:51:13.415096 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:13.416272 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:13.417817 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:13.418778 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:13.420824 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:13.420943 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:51:13.422977 INFO: Updating optimization_manager: rt_error            : 76.30840483481106 -> 17.328560457817307
2 days, 23:51:13.423108 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 17.3286.
2 days, 23:51:13.423203 INFO: ==============================================
2 days, 23:51:13.423305 INFO: Starting optimization step 3.
2 days, 23:51:13.423393 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:13.423481 INFO: Using python extraction backend
2 days, 23:51:13.423615 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:13.423706 INFO: === Search parameters used ===
2 days, 23:51:13.423782 INFO: rt_error       : 17.328560457817307
2 days, 23:51:13.423851 INFO: mobility_error : 0.1
2 days, 23:51:13.423913 INFO: num_candidates : 3
2 days, 23:51:13.423973 INFO: ms1_error      : 15.0
2 days, 23:51:13.424032 INFO: ms2_error      : 15.0
2 days, 23:51:13.424091 INFO: fwhm_rt        : 2.6260523796081543
2 days, 23:51:13.424149 INFO: quant_window   : 3
2 days, 23:51:13.424207 INFO: ==============================================
2 days, 23:51:13.425152 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:13.425203 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:13.425251 INFO: FWHM in RT is 2.63 seconds, sigma is 0.44
2 days, 23:51:13.425286 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.54
2 days, 23:51:13.446087 INFO: Starting candidate selection
2 days, 23:51:14.093523 INFO: Starting candidate scoring
2 days, 23:51:14.203623 INFO: Finished candidate processing
2 days, 23:51:14.203764 INFO: Collecting candidate features
2 days, 23:51:14.218563 WARNING: intensity_correlation has 22 NaNs ( 0.68 % out of 3214)
2 days, 23:51:14.222769 INFO: Collecting fragment features
2 days, 23:51:14.226788 INFO: Finished candidate scoring
2 days, 23:51:14.228559 INFO: performing precursor FDR with 47 features
2 days, 23:51:14.228622 INFO: Decoy channel: -1
2 days, 23:51:14.228655 INFO: competitive: True
2 days, 23:51:14.231711 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:14.233391 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:51:14.233454 WARNING: dropped 18 decoy PSMs due to missing features
2 days, 23:51:14.233566 WARNING: FDR calculation for 1684 target and 1508 decoy PSMs
2 days, 23:51:14.233612 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:14.234873 INFO: Estimating optimal hyperparameters - samples: 2,553, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:14.234992 INFO: Using random state 882121 for train-test-split
2 days, 23:51:14.585698 INFO: Test AUC: 0.893
2 days, 23:51:14.585811 INFO: Train AUC: 0.866
2 days, 23:51:14.585853 INFO: AUC difference: 3.18%
2 days, 23:51:14.901425 INFO: Resetting torch num_threads to 80
2 days, 23:51:14.901987 PROGRESS: === Extracted 3214 precursors and 23132 fragments ===
2 days, 23:51:14.902464 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:14.903093 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:14.903199 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:14.903287 PROGRESS: Target precursors: 584 (97.33%)
2 days, 23:51:14.903372 PROGRESS: Decoy precursors: 16 (2.67%)
2 days, 23:51:14.903444 PROGRESS: 
2 days, 23:51:14.903511 PROGRESS: Precursor Summary:
2 days, 23:51:14.904673 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   524; 0.001 FDR:   483
2 days, 23:51:14.904781 PROGRESS: 
2 days, 23:51:14.904869 PROGRESS: Protein Summary:
2 days, 23:51:14.906288 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   388; 0.001 FDR:   356
2 days, 23:51:14.906417 PROGRESS: =========================================================================
2 days, 23:51:14.906592 INFO: Target number of precursors reached.
2 days, 23:51:14.915212 INFO: fragments_df: keeping 5000 of 23132 [sum(precursor_idx_mask)=12853 sum(mass_error_mask)=23132 stop_rank=5000
2 days, 23:51:14.920109 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:15.119229 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:15.299517 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:15.496662 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:16.317698 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:16.318224 INFO: Using score_cutoff 18.479400013160706 (fac=0.99, q=1)
2 days, 23:51:16.318680 INFO: Updating optimization_manager: fwhm_rt             : 2.6260523796081543 -> 2.6176185607910156
2 days, 23:51:16.318799 INFO: Updating optimization_manager: fwhm_mobility       : 0.004679095931351185 -> 0.004402093589305878
2 days, 23:51:16.318873 INFO: Updating optimization_manager: score_cutoff        : 20.549809173202515 -> 18.479400013160706
2 days, 23:51:16.318939 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:16.320123 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:16.321610 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:16.322593 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:16.324655 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:16.324777 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:51:16.326827 INFO: Updating optimization_manager: rt_error            : 17.328560457817307 -> 10.042689100491929
2 days, 23:51:16.326957 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 10.0427.
2 days, 23:51:16.327059 INFO: ==============================================
2 days, 23:51:16.327177 INFO: Starting optimization step 4.
2 days, 23:51:16.327264 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:16.327356 INFO: Using python extraction backend
2 days, 23:51:16.327495 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:16.327587 INFO: === Search parameters used ===
2 days, 23:51:16.327658 INFO: rt_error       : 10.042689100491929
2 days, 23:51:16.327710 INFO: mobility_error : 0.1
2 days, 23:51:16.327768 INFO: num_candidates : 3
2 days, 23:51:16.327816 INFO: ms1_error      : 15.0
2 days, 23:51:16.327863 INFO: ms2_error      : 15.0
2 days, 23:51:16.327909 INFO: fwhm_rt        : 2.6176185607910156
2 days, 23:51:16.327954 INFO: quant_window   : 3
2 days, 23:51:16.327997 INFO: ==============================================
2 days, 23:51:16.328829 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:16.328884 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:16.328921 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:51:16.328952 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.39
2 days, 23:51:16.336616 INFO: Starting candidate selection
2 days, 23:51:16.895341 INFO: Starting candidate scoring
2 days, 23:51:17.023296 INFO: Finished candidate processing
2 days, 23:51:17.023427 INFO: Collecting candidate features
2 days, 23:51:17.039029 WARNING: intensity_correlation has 19 NaNs ( 0.60 % out of 3178)
2 days, 23:51:17.047161 INFO: Collecting fragment features
2 days, 23:51:17.052995 INFO: Finished candidate scoring
2 days, 23:51:17.056308 INFO: performing precursor FDR with 47 features
2 days, 23:51:17.056412 INFO: Decoy channel: -1
2 days, 23:51:17.056456 INFO: competitive: True
2 days, 23:51:17.061144 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:17.063644 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:51:17.063719 WARNING: dropped 16 decoy PSMs due to missing features
2 days, 23:51:17.063779 WARNING: FDR calculation for 1663 target and 1496 decoy PSMs
2 days, 23:51:17.063816 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:17.065260 INFO: Estimating optimal hyperparameters - samples: 2,527, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:17.065428 INFO: Using random state 882121 for train-test-split
2 days, 23:51:17.306545 INFO: Test AUC: 0.850
2 days, 23:51:17.306653 INFO: Train AUC: 0.875
2 days, 23:51:17.306686 INFO: AUC difference: 2.77%
2 days, 23:51:17.634091 INFO: Resetting torch num_threads to 80
2 days, 23:51:17.634807 PROGRESS: === Extracted 3178 precursors and 22967 fragments ===
2 days, 23:51:17.635406 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:17.636285 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:17.636412 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:17.636514 PROGRESS: Target precursors: 584 (97.33%)
2 days, 23:51:17.636612 PROGRESS: Decoy precursors: 16 (2.67%)
2 days, 23:51:17.636699 PROGRESS: 
2 days, 23:51:17.636770 PROGRESS: Precursor Summary:
2 days, 23:51:17.638771 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   531; 0.001 FDR:   467
2 days, 23:51:17.638898 PROGRESS: 
2 days, 23:51:17.638991 PROGRESS: Protein Summary:
2 days, 23:51:17.641124 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   393; 0.001 FDR:   344
2 days, 23:51:17.641255 PROGRESS: =========================================================================
2 days, 23:51:17.641462 INFO: Target number of precursors reached.
2 days, 23:51:17.650437 INFO: fragments_df: keeping 5000 of 22967 [sum(precursor_idx_mask)=12959 sum(mass_error_mask)=22967 stop_rank=5000
2 days, 23:51:17.653943 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:17.858995 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:18.080382 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:18.278635 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:19.132812 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:19.133319 INFO: Using score_cutoff 17.791112600326535 (fac=0.99, q=1)
2 days, 23:51:19.133667 INFO: Updating optimization_manager: fwhm_rt             : 2.6176185607910156 -> 2.617828845977783
2 days, 23:51:19.133761 INFO: Updating optimization_manager: fwhm_mobility       : 0.004402093589305878 -> 0.004391415975987911
2 days, 23:51:19.133827 INFO: Updating optimization_manager: score_cutoff        : 18.479400013160706 -> 17.791112600326535
2 days, 23:51:19.133914 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:19.135037 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:19.136416 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:19.137220 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:19.139158 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:19.139266 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:51:19.141160 INFO: Updating optimization_manager: rt_error            : 10.042689100491929 -> 9.33048018737581
2 days, 23:51:19.141285 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 9.3305.
2 days, 23:51:19.141381 INFO: ==============================================
2 days, 23:51:19.141488 INFO: Starting optimization step 5.
2 days, 23:51:19.141578 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:19.141664 INFO: Using python extraction backend
2 days, 23:51:19.141797 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:19.141901 INFO: === Search parameters used ===
2 days, 23:51:19.141985 INFO: rt_error       : 9.33048018737581
2 days, 23:51:19.142057 INFO: mobility_error : 0.1
2 days, 23:51:19.142120 INFO: num_candidates : 3
2 days, 23:51:19.142182 INFO: ms1_error      : 15.0
2 days, 23:51:19.142242 INFO: ms2_error      : 15.0
2 days, 23:51:19.142305 INFO: fwhm_rt        : 2.617828845977783
2 days, 23:51:19.142366 INFO: quant_window   : 3
2 days, 23:51:19.142427 INFO: ==============================================
2 days, 23:51:19.143292 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:19.143344 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:19.143393 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:51:19.143427 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.38
2 days, 23:51:19.154219 INFO: Starting candidate selection
2 days, 23:51:19.804437 INFO: Starting candidate scoring
2 days, 23:51:19.920515 INFO: Finished candidate processing
2 days, 23:51:19.920654 INFO: Collecting candidate features
2 days, 23:51:19.936914 WARNING: intensity_correlation has 17 NaNs ( 0.53 % out of 3178)
2 days, 23:51:19.944867 INFO: Collecting fragment features
2 days, 23:51:19.950505 INFO: Finished candidate scoring
2 days, 23:51:19.953727 INFO: performing precursor FDR with 47 features
2 days, 23:51:19.953809 INFO: Decoy channel: -1
2 days, 23:51:19.953849 INFO: competitive: True
2 days, 23:51:19.958420 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:19.960662 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:51:19.960738 WARNING: dropped 14 decoy PSMs due to missing features
2 days, 23:51:19.960795 WARNING: FDR calculation for 1666 target and 1495 decoy PSMs
2 days, 23:51:19.960833 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:19.962242 INFO: Estimating optimal hyperparameters - samples: 2,528, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:19.962357 INFO: Using random state 882121 for train-test-split
2 days, 23:51:20.287630 INFO: Test AUC: 0.877
2 days, 23:51:20.287749 INFO: Train AUC: 0.865
2 days, 23:51:20.287799 INFO: AUC difference: 1.31%
2 days, 23:51:20.580427 INFO: Resetting torch num_threads to 80
2 days, 23:51:20.581141 PROGRESS: === Extracted 3178 precursors and 22924 fragments ===
2 days, 23:51:20.581748 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:20.582698 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:20.582837 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:20.582941 PROGRESS: Target precursors: 582 (97.00%)
2 days, 23:51:20.583042 PROGRESS: Decoy precursors: 18 (3.00%)
2 days, 23:51:20.583142 PROGRESS: 
2 days, 23:51:20.583235 PROGRESS: Precursor Summary:
2 days, 23:51:20.585089 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   526; 0.001 FDR:   472
2 days, 23:51:20.585238 PROGRESS: 
2 days, 23:51:20.585344 PROGRESS: Protein Summary:
2 days, 23:51:20.587639 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   390; 0.001 FDR:   348
2 days, 23:51:20.587793 PROGRESS: =========================================================================
2 days, 23:51:20.588004 INFO: Target number of precursors reached.
2 days, 23:51:20.597374 INFO: fragments_df: keeping 5000 of 22924 [sum(precursor_idx_mask)=12838 sum(mass_error_mask)=22924 stop_rank=5000
2 days, 23:51:20.602231 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:20.828429 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:21.018662 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:21.199576 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:22.028685 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:22.029158 INFO: Using score_cutoff 17.817541937828064 (fac=0.99, q=1)
2 days, 23:51:22.029543 INFO: Updating optimization_manager: fwhm_rt             : 2.617828845977783 -> 2.6208267211914062
2 days, 23:51:22.029641 INFO: Updating optimization_manager: fwhm_mobility       : 0.004391415975987911 -> 0.00442224508151412
2 days, 23:51:22.029709 INFO: Updating optimization_manager: score_cutoff        : 17.791112600326535 -> 17.817541937828064
2 days, 23:51:22.029775 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:22.030956 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:22.032485 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:22.033409 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:22.035535 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:22.035665 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 23:51:22.037778 INFO: Updating optimization_manager: rt_error            : 9.33048018737581 -> 8.442772343930146
2 days, 23:51:22.037915 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 8.4428.
2 days, 23:51:22.038000 INFO: ==============================================
2 days, 23:51:22.038080 INFO: Starting optimization step 6.
2 days, 23:51:22.038148 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:22.038217 INFO: Using python extraction backend
2 days, 23:51:22.038324 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:22.038400 INFO: === Search parameters used ===
2 days, 23:51:22.038457 INFO: rt_error       : 8.442772343930146
2 days, 23:51:22.038509 INFO: mobility_error : 0.1
2 days, 23:51:22.038559 INFO: num_candidates : 3
2 days, 23:51:22.038609 INFO: ms1_error      : 15.0
2 days, 23:51:22.038659 INFO: ms2_error      : 15.0
2 days, 23:51:22.038709 INFO: fwhm_rt        : 2.6208267211914062
2 days, 23:51:22.038759 INFO: quant_window   : 3
2 days, 23:51:22.038811 INFO: ==============================================
2 days, 23:51:22.039718 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:22.039775 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:22.039825 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:51:22.039860 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.40
2 days, 23:51:22.050062 INFO: Starting candidate selection
2 days, 23:51:22.636550 INFO: Starting candidate scoring
2 days, 23:51:22.746063 INFO: Finished candidate processing
2 days, 23:51:22.746198 INFO: Collecting candidate features
2 days, 23:51:22.758852 WARNING: intensity_correlation has 21 NaNs ( 0.66 % out of 3183)
2 days, 23:51:22.763198 INFO: Collecting fragment features
2 days, 23:51:22.767429 INFO: Finished candidate scoring
2 days, 23:51:22.769382 INFO: performing precursor FDR with 47 features
2 days, 23:51:22.769449 INFO: Decoy channel: -1
2 days, 23:51:22.769481 INFO: competitive: True
2 days, 23:51:22.772619 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:22.774589 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:51:22.774656 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:51:22.774716 WARNING: FDR calculation for 1667 target and 1495 decoy PSMs
2 days, 23:51:22.774749 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:22.775734 INFO: Estimating optimal hyperparameters - samples: 2,529, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:22.775825 INFO: Using random state 882121 for train-test-split
2 days, 23:51:23.082797 INFO: Test AUC: 0.849
2 days, 23:51:23.082935 INFO: Train AUC: 0.871
2 days, 23:51:23.082994 INFO: AUC difference: 2.50%
2 days, 23:51:23.392366 INFO: Resetting torch num_threads to 80
2 days, 23:51:23.393083 PROGRESS: === Extracted 3183 precursors and 22920 fragments ===
2 days, 23:51:23.393669 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:23.394614 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:23.394748 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:23.394846 PROGRESS: Target precursors: 581 (96.83%)
2 days, 23:51:23.394943 PROGRESS: Decoy precursors: 19 (3.17%)
2 days, 23:51:23.395032 PROGRESS: 
2 days, 23:51:23.395113 PROGRESS: Precursor Summary:
2 days, 23:51:23.396971 PROGRESS: Channel   0:	 0.050 FDR:   581; 0.010 FDR:   530; 0.001 FDR:   476
2 days, 23:51:23.397093 PROGRESS: 
2 days, 23:51:23.397176 PROGRESS: Protein Summary:
2 days, 23:51:23.399428 PROGRESS: Channel   0:	 0.050 FDR:   425; 0.010 FDR:   393; 0.001 FDR:   350
2 days, 23:51:23.399562 PROGRESS: =========================================================================
2 days, 23:51:23.399769 INFO: Target number of precursors reached.
2 days, 23:51:23.409261 INFO: fragments_df: keeping 5000 of 22920 [sum(precursor_idx_mask)=12918 sum(mass_error_mask)=22920 stop_rank=5000
2 days, 23:51:23.414130 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:23.688468 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:23.902443 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:24.098982 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:24.960428 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:24.961021 INFO: Using score_cutoff 17.789322421073916 (fac=0.99, q=1)
2 days, 23:51:24.961498 INFO: Updating optimization_manager: fwhm_rt             : 2.6208267211914062 -> 2.6150577068328857
2 days, 23:51:24.961630 INFO: Updating optimization_manager: fwhm_mobility       : 0.00442224508151412 -> 0.004402093589305878
2 days, 23:51:24.961734 INFO: Updating optimization_manager: score_cutoff        : 17.817541937828064 -> 17.789322421073916
2 days, 23:51:24.961833 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:24.963392 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:24.965232 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:24.966425 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:24.968886 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:24.969027 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 23:51:24.971870 INFO: Updating optimization_manager: rt_error            : 8.442772343930146 -> 9.023219467092629
2 days, 23:51:24.972016 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 9.0232.
2 days, 23:51:24.972124 INFO: ==============================================
2 days, 23:51:24.972245 INFO: Starting optimization step 7.
2 days, 23:51:24.972358 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:24.972463 INFO: Using python extraction backend
2 days, 23:51:24.972617 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:24.972739 INFO: === Search parameters used ===
2 days, 23:51:24.972838 INFO: rt_error       : 9.023219467092629
2 days, 23:51:24.972932 INFO: mobility_error : 0.1
2 days, 23:51:24.973017 INFO: num_candidates : 3
2 days, 23:51:24.973124 INFO: ms1_error      : 15.0
2 days, 23:51:24.973309 INFO: ms2_error      : 15.0
2 days, 23:51:24.973404 INFO: fwhm_rt        : 2.6150577068328857
2 days, 23:51:24.973480 INFO: quant_window   : 3
2 days, 23:51:24.973549 INFO: ==============================================
2 days, 23:51:24.975039 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:24.975108 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:24.975163 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:51:24.975207 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.39
2 days, 23:51:24.980307 INFO: Starting candidate selection
2 days, 23:51:25.623407 INFO: Starting candidate scoring
2 days, 23:51:25.722229 INFO: Finished candidate processing
2 days, 23:51:25.722352 INFO: Collecting candidate features
2 days, 23:51:25.734378 WARNING: intensity_correlation has 18 NaNs ( 0.57 % out of 3181)
2 days, 23:51:25.739540 INFO: Collecting fragment features
2 days, 23:51:25.744037 INFO: Finished candidate scoring
2 days, 23:51:25.746061 INFO: performing precursor FDR with 47 features
2 days, 23:51:25.746123 INFO: Decoy channel: -1
2 days, 23:51:25.746153 INFO: competitive: True
2 days, 23:51:25.750685 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:25.752556 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:51:25.752619 WARNING: dropped 14 decoy PSMs due to missing features
2 days, 23:51:25.752667 WARNING: FDR calculation for 1664 target and 1499 decoy PSMs
2 days, 23:51:25.752693 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:25.753805 INFO: Estimating optimal hyperparameters - samples: 2,530, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:25.753981 INFO: Using random state 882121 for train-test-split
2 days, 23:51:26.053718 INFO: Test AUC: 0.872
2 days, 23:51:26.053837 INFO: Train AUC: 0.869
2 days, 23:51:26.053886 INFO: AUC difference: 0.27%
2 days, 23:51:26.352888 INFO: Resetting torch num_threads to 80
2 days, 23:51:26.353643 PROGRESS: === Extracted 3181 precursors and 22931 fragments ===
2 days, 23:51:26.354201 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:26.354915 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:26.355016 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:26.355087 PROGRESS: Target precursors: 582 (97.00%)
2 days, 23:51:26.355147 PROGRESS: Decoy precursors: 18 (3.00%)
2 days, 23:51:26.355203 PROGRESS: 
2 days, 23:51:26.355258 PROGRESS: Precursor Summary:
2 days, 23:51:26.356605 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   529; 0.001 FDR:   476
2 days, 23:51:26.356705 PROGRESS: 
2 days, 23:51:26.356769 PROGRESS: Protein Summary:
2 days, 23:51:26.358404 PROGRESS: Channel   0:	 0.050 FDR:   426; 0.010 FDR:   392; 0.001 FDR:   351
2 days, 23:51:26.358511 PROGRESS: =========================================================================
2 days, 23:51:26.358674 INFO: Target number of precursors reached.
2 days, 23:51:26.366864 INFO: fragments_df: keeping 5000 of 22931 [sum(precursor_idx_mask)=12860 sum(mass_error_mask)=22931 stop_rank=5000
2 days, 23:51:26.371016 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:26.594891 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:26.822291 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:26.987250 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:27.731188 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:27.731666 INFO: Using score_cutoff 17.315493138885497 (fac=0.99, q=1)
2 days, 23:51:27.732049 INFO: Updating optimization_manager: fwhm_rt             : 2.6150577068328857 -> 2.6257481575012207
2 days, 23:51:27.732155 INFO: Updating optimization_manager: fwhm_mobility       : 0.004402093589305878 -> 0.00440239068120718
2 days, 23:51:27.732248 INFO: Updating optimization_manager: score_cutoff        : 17.789322421073916 -> 17.315493138885497
2 days, 23:51:27.732334 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:27.733477 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:27.734902 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:27.735734 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:27.737740 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:27.737854 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 23:51:27.739856 INFO: Updating optimization_manager: rt_error            : 9.023219467092629 -> 8.441113974046594
2 days, 23:51:27.739979 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 8.4411.
2 days, 23:51:27.740069 INFO: ==============================================
2 days, 23:51:27.740148 INFO: Starting optimization step 8.
2 days, 23:51:27.740224 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:27.740300 INFO: Using python extraction backend
2 days, 23:51:27.740408 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:27.740483 INFO: === Search parameters used ===
2 days, 23:51:27.740549 INFO: rt_error       : 8.441113974046594
2 days, 23:51:27.740605 INFO: mobility_error : 0.1
2 days, 23:51:27.740658 INFO: num_candidates : 3
2 days, 23:51:27.740707 INFO: ms1_error      : 15.0
2 days, 23:51:27.740753 INFO: ms2_error      : 15.0
2 days, 23:51:27.740799 INFO: fwhm_rt        : 2.6257481575012207
2 days, 23:51:27.740845 INFO: quant_window   : 3
2 days, 23:51:27.740890 INFO: ==============================================
2 days, 23:51:27.741913 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:27.741968 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:27.742018 INFO: FWHM in RT is 2.63 seconds, sigma is 0.44
2 days, 23:51:27.742045 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.39
2 days, 23:51:27.747153 INFO: Starting candidate selection
2 days, 23:51:28.299352 INFO: Starting candidate scoring
2 days, 23:51:28.399523 INFO: Finished candidate processing
2 days, 23:51:28.399636 INFO: Collecting candidate features
2 days, 23:51:28.411854 WARNING: intensity_correlation has 19 NaNs ( 0.60 % out of 3181)
2 days, 23:51:28.417859 INFO: Collecting fragment features
2 days, 23:51:28.422403 INFO: Finished candidate scoring
2 days, 23:51:28.424485 INFO: performing precursor FDR with 47 features
2 days, 23:51:28.424544 INFO: Decoy channel: -1
2 days, 23:51:28.424594 INFO: competitive: True
2 days, 23:51:28.428425 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:28.430365 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:51:28.430447 WARNING: dropped 16 decoy PSMs due to missing features
2 days, 23:51:28.430506 WARNING: FDR calculation for 1665 target and 1497 decoy PSMs
2 days, 23:51:28.430549 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:28.431796 INFO: Estimating optimal hyperparameters - samples: 2,529, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:28.431905 INFO: Using random state 882121 for train-test-split
2 days, 23:51:28.665455 INFO: Test AUC: 0.840
2 days, 23:51:28.665590 INFO: Train AUC: 0.876
2 days, 23:51:28.665633 INFO: AUC difference: 4.05%
2 days, 23:51:28.996708 INFO: Resetting torch num_threads to 80
2 days, 23:51:28.997340 PROGRESS: === Extracted 3181 precursors and 22924 fragments ===
2 days, 23:51:28.997806 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:28.998444 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:28.998555 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:28.998647 PROGRESS: Target precursors: 581 (96.83%)
2 days, 23:51:28.998737 PROGRESS: Decoy precursors: 19 (3.17%)
2 days, 23:51:28.998824 PROGRESS: 
2 days, 23:51:28.998891 PROGRESS: Precursor Summary:
2 days, 23:51:29.000027 PROGRESS: Channel   0:	 0.050 FDR:   581; 0.010 FDR:   527; 0.001 FDR:   468
2 days, 23:51:29.000137 PROGRESS: 
2 days, 23:51:29.000230 PROGRESS: Protein Summary:
2 days, 23:51:29.001619 PROGRESS: Channel   0:	 0.050 FDR:   425; 0.010 FDR:   391; 0.001 FDR:   346
2 days, 23:51:29.001731 PROGRESS: =========================================================================
2 days, 23:51:29.001919 INFO: Target number of precursors reached.
2 days, 23:51:29.007976 INFO: fragments_df: keeping 5000 of 22924 [sum(precursor_idx_mask)=12857 sum(mass_error_mask)=22924 stop_rank=5000
2 days, 23:51:29.011625 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:29.223346 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:29.413645 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:29.621438 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:30.510353 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:30.510809 INFO: Using score_cutoff 17.828684403991698 (fac=0.99, q=1)
2 days, 23:51:30.511168 INFO: Updating optimization_manager: fwhm_rt             : 2.6257481575012207 -> 2.6257481575012207
2 days, 23:51:30.511276 INFO: Updating optimization_manager: fwhm_mobility       : 0.00440239068120718 -> 0.004407831002026796
2 days, 23:51:30.511350 INFO: Updating optimization_manager: score_cutoff        : 17.315493138885497 -> 17.828684403991698
2 days, 23:51:30.511425 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:30.512705 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:30.514529 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:30.515681 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:30.518212 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:30.518361 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2 days, 23:51:30.521132 INFO: Updating optimization_manager: rt_error            : 8.441113974046594 -> 8.383182551553148
2 days, 23:51:30.521282 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 8.3832.
2 days, 23:51:30.521395 INFO: ==============================================
2 days, 23:51:30.521521 INFO: Starting optimization step 9.
2 days, 23:51:30.521628 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:30.521739 INFO: Using python extraction backend
2 days, 23:51:30.521945 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:30.522094 INFO: === Search parameters used ===
2 days, 23:51:30.522184 INFO: rt_error       : 8.383182551553148
2 days, 23:51:30.522260 INFO: mobility_error : 0.1
2 days, 23:51:30.522326 INFO: num_candidates : 3
2 days, 23:51:30.522394 INFO: ms1_error      : 15.0
2 days, 23:51:30.522468 INFO: ms2_error      : 15.0
2 days, 23:51:30.522536 INFO: fwhm_rt        : 2.6257481575012207
2 days, 23:51:30.522617 INFO: quant_window   : 3
2 days, 23:51:30.522710 INFO: ==============================================
2 days, 23:51:30.523995 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:30.524065 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:30.524124 INFO: FWHM in RT is 2.63 seconds, sigma is 0.44
2 days, 23:51:30.524169 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.39
2 days, 23:51:30.562325 INFO: Starting candidate selection
2 days, 23:51:31.157135 INFO: Starting candidate scoring
2 days, 23:51:31.262847 INFO: Finished candidate processing
2 days, 23:51:31.262970 INFO: Collecting candidate features
2 days, 23:51:31.275308 WARNING: intensity_correlation has 19 NaNs ( 0.60 % out of 3186)
2 days, 23:51:31.280463 INFO: Collecting fragment features
2 days, 23:51:31.285159 INFO: Finished candidate scoring
2 days, 23:51:31.287391 INFO: performing precursor FDR with 47 features
2 days, 23:51:31.287451 INFO: Decoy channel: -1
2 days, 23:51:31.287482 INFO: competitive: True
2 days, 23:51:31.291199 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:31.293057 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:51:31.293113 WARNING: dropped 16 decoy PSMs due to missing features
2 days, 23:51:31.293158 WARNING: FDR calculation for 1667 target and 1500 decoy PSMs
2 days, 23:51:31.293194 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:31.294366 INFO: Estimating optimal hyperparameters - samples: 2,533, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:31.294465 INFO: Using random state 882121 for train-test-split
2 days, 23:51:31.538378 INFO: Test AUC: 0.849
2 days, 23:51:31.538498 INFO: Train AUC: 0.872
2 days, 23:51:31.538543 INFO: AUC difference: 2.66%
2 days, 23:51:38.075157 INFO: Resetting torch num_threads to 80
2 days, 23:51:38.076027 PROGRESS: === Extracted 3186 precursors and 22942 fragments ===
2 days, 23:51:38.076630 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:51:38.077664 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:38.077797 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:38.077915 PROGRESS: Target precursors: 581 (96.83%)
2 days, 23:51:38.078008 PROGRESS: Decoy precursors: 19 (3.17%)
2 days, 23:51:38.078085 PROGRESS: 
2 days, 23:51:38.078161 PROGRESS: Precursor Summary:
2 days, 23:51:38.080109 PROGRESS: Channel   0:	 0.050 FDR:   581; 0.010 FDR:   529; 0.001 FDR:   472
2 days, 23:51:38.080252 PROGRESS: 
2 days, 23:51:38.080343 PROGRESS: Protein Summary:
2 days, 23:51:38.082306 PROGRESS: Channel   0:	 0.050 FDR:   425; 0.010 FDR:   392; 0.001 FDR:   346
2 days, 23:51:38.082410 PROGRESS: =========================================================================
2 days, 23:51:38.082558 INFO: Target number of precursors reached.
2 days, 23:51:38.089132 INFO: fragments_df: keeping 5000 of 22942 [sum(precursor_idx_mask)=12854 sum(mass_error_mask)=22942 stop_rank=5000
2 days, 23:51:38.093164 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:38.338891 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:38.602741 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:38.812402 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:39.652963 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:39.653440 INFO: Using score_cutoff 17.60950369720459 (fac=0.99, q=1)
2 days, 23:51:39.653814 INFO: Updating optimization_manager: fwhm_rt             : 2.6257481575012207 -> 2.6194872856140137
2 days, 23:51:39.653920 INFO: Updating optimization_manager: fwhm_mobility       : 0.004407831002026796 -> 0.0043974146246910095
2 days, 23:51:39.653986 INFO: Updating optimization_manager: score_cutoff        : 17.828684403991698 -> 17.60950369720459
2 days, 23:51:39.654053 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:39.655308 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:39.656904 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:39.657826 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:39.660086 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:39.660204 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
2 days, 23:51:39.661243 INFO: Updating optimization_manager: rt_error            : 8.383182551553148 -> 8.383182551553148
2 days, 23:51:39.661382 INFO: Updating optimization_manager: classifier_version  : 3 -> 13
2 days, 23:51:39.661491 INFO: Updating optimization_manager: score_cutoff        : 17.60950369720459 -> 17.60950369720459
2 days, 23:51:39.661591 INFO: Updating optimization_manager: fwhm_rt             : 2.6194872856140137 -> 2.6194872856140137
2 days, 23:51:39.661702 INFO: Updating optimization_manager: fwhm_mobility       : 0.0043974146246910095 -> 0.0043974146246910095
2 days, 23:51:39.661804 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 8.3832 found after 10 searches.
2 days, 23:51:39.661882 INFO: ==============================================
2 days, 23:51:39.661962 PROGRESS: Optimization finished for rt_error.
2 days, 23:51:39.665261 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:39.666188 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:39.667610 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:39.668434 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:39.670539 INFO: Starting optimization step 0.
2 days, 23:51:39.670651 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:39.670724 INFO: Using python extraction backend
2 days, 23:51:39.670830 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:39.670900 INFO: === Search parameters used ===
2 days, 23:51:39.670954 INFO: rt_error       : 8.383182551553148
2 days, 23:51:39.671000 INFO: mobility_error : 0.1
2 days, 23:51:39.671045 INFO: num_candidates : 3
2 days, 23:51:39.671090 INFO: ms1_error      : 15.0
2 days, 23:51:39.671137 INFO: ms2_error      : 15.0
2 days, 23:51:39.671181 INFO: fwhm_rt        : 2.6194872856140137
2 days, 23:51:39.671225 INFO: quant_window   : 3
2 days, 23:51:39.671268 INFO: ==============================================
2 days, 23:51:39.672166 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:39.672214 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:39.672250 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:51:39.672273 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.38
2 days, 23:51:39.682225 INFO: Starting candidate selection
2 days, 23:51:40.401220 INFO: Starting candidate scoring
2 days, 23:51:40.499953 INFO: Finished candidate processing
2 days, 23:51:40.500092 INFO: Collecting candidate features
2 days, 23:51:40.517119 WARNING: intensity_correlation has 20 NaNs ( 0.63 % out of 3184)
2 days, 23:51:40.525473 INFO: Collecting fragment features
2 days, 23:51:40.532342 INFO: Finished candidate scoring
2 days, 23:51:40.539637 INFO: performing precursor FDR with 47 features
2 days, 23:51:40.539843 INFO: Decoy channel: -1
2 days, 23:51:40.539925 INFO: competitive: True
2 days, 23:51:40.544326 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:40.546204 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:51:40.546265 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:51:40.546320 WARNING: FDR calculation for 1666 target and 1498 decoy PSMs
2 days, 23:51:40.546359 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:40.547451 INFO: Estimating optimal hyperparameters - samples: 2,531, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:40.547586 INFO: Using random state 519348 for train-test-split
2 days, 23:51:40.861926 INFO: Test AUC: 0.862
2 days, 23:51:40.862037 INFO: Train AUC: 0.885
2 days, 23:51:40.862078 INFO: AUC difference: 2.64%
2 days, 23:51:41.242401 INFO: Resetting torch num_threads to 80
2 days, 23:51:41.243298 PROGRESS: === Extracted 3184 precursors and 22923 fragments ===
2 days, 23:51:41.243912 INFO: === FDR correction performed with classifier version 13 ===
2 days, 23:51:41.244921 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:41.245049 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:41.245134 PROGRESS: Target precursors: 584 (97.33%)
2 days, 23:51:41.245215 PROGRESS: Decoy precursors: 16 (2.67%)
2 days, 23:51:41.245293 PROGRESS: 
2 days, 23:51:41.245369 PROGRESS: Precursor Summary:
2 days, 23:51:41.247454 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   536; 0.001 FDR:   477
2 days, 23:51:41.247615 PROGRESS: 
2 days, 23:51:41.247701 PROGRESS: Protein Summary:
2 days, 23:51:41.249835 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   398; 0.001 FDR:   351
2 days, 23:51:41.249978 PROGRESS: =========================================================================
2 days, 23:51:41.250188 INFO: Target number of precursors reached.
2 days, 23:51:41.259467 INFO: fragments_df: keeping 5000 of 22923 [sum(precursor_idx_mask)=12981 sum(mass_error_mask)=22923 stop_rank=5000
2 days, 23:51:41.264956 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:41.488654 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:41.694561 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:41.896064 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:42.777638 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:42.778187 INFO: Using score_cutoff 16.981063616752625 (fac=0.99, q=1)
2 days, 23:51:42.778570 INFO: Updating optimization_manager: fwhm_rt             : 2.6194872856140137 -> 2.580504894256592
2 days, 23:51:42.778669 INFO: Updating optimization_manager: fwhm_mobility       : 0.0043974146246910095 -> 0.0042639528401196
2 days, 23:51:42.778752 INFO: Updating optimization_manager: score_cutoff        : 17.60950369720459 -> 16.981063616752625
2 days, 23:51:42.778830 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:42.780103 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:42.781633 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:42.782537 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:42.784712 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:42.784840 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:51:42.786471 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.05727150972088045
2 days, 23:51:42.786608 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0573.
2 days, 23:51:42.786693 INFO: ==============================================
2 days, 23:51:42.786784 INFO: Starting optimization step 1.
2 days, 23:51:42.786860 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:42.786970 INFO: Using python extraction backend
2 days, 23:51:42.787104 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:42.787193 INFO: === Search parameters used ===
2 days, 23:51:42.787259 INFO: rt_error       : 8.383182551553148
2 days, 23:51:42.787318 INFO: mobility_error : 0.05727150972088045
2 days, 23:51:42.787373 INFO: num_candidates : 3
2 days, 23:51:42.787428 INFO: ms1_error      : 15.0
2 days, 23:51:42.787481 INFO: ms2_error      : 15.0
2 days, 23:51:42.787534 INFO: fwhm_rt        : 2.580504894256592
2 days, 23:51:42.787587 INFO: quant_window   : 3
2 days, 23:51:42.787637 INFO: ==============================================
2 days, 23:51:42.788622 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:42.788676 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:42.788717 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:51:42.788747 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.31
2 days, 23:51:42.810035 INFO: Starting candidate selection
2 days, 23:51:43.370389 INFO: Starting candidate scoring
2 days, 23:51:43.484450 INFO: Finished candidate processing
2 days, 23:51:43.484563 INFO: Collecting candidate features
2 days, 23:51:43.498550 WARNING: intensity_correlation has 20 NaNs ( 0.63 % out of 3167)
2 days, 23:51:43.503914 INFO: Collecting fragment features
2 days, 23:51:43.508985 INFO: Finished candidate scoring
2 days, 23:51:43.513954 INFO: performing precursor FDR with 47 features
2 days, 23:51:43.514039 INFO: Decoy channel: -1
2 days, 23:51:43.514070 INFO: competitive: True
2 days, 23:51:43.518285 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:43.520406 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:51:43.520472 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:51:43.520518 WARNING: FDR calculation for 1658 target and 1489 decoy PSMs
2 days, 23:51:43.520548 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:43.522030 INFO: Estimating optimal hyperparameters - samples: 2,517, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:43.522169 INFO: Using random state 519348 for train-test-split
2 days, 23:51:43.832921 INFO: Test AUC: 0.899
2 days, 23:51:43.833048 INFO: Train AUC: 0.888
2 days, 23:51:43.833106 INFO: AUC difference: 1.21%
2 days, 23:51:44.149184 INFO: Resetting torch num_threads to 80
2 days, 23:51:44.149994 PROGRESS: === Extracted 3167 precursors and 22595 fragments ===
2 days, 23:51:44.150503 INFO: === FDR correction performed with classifier version 13 ===
2 days, 23:51:44.151373 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:44.151479 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:44.151551 PROGRESS: Target precursors: 586 (97.67%)
2 days, 23:51:44.151614 PROGRESS: Decoy precursors: 14 (2.33%)
2 days, 23:51:44.151673 PROGRESS: 
2 days, 23:51:44.151732 PROGRESS: Precursor Summary:
2 days, 23:51:44.153243 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   563; 0.001 FDR:   477
2 days, 23:51:44.153358 PROGRESS: 
2 days, 23:51:44.153426 PROGRESS: Protein Summary:
2 days, 23:51:44.155150 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   415; 0.001 FDR:   354
2 days, 23:51:44.155261 PROGRESS: =========================================================================
2 days, 23:51:44.155436 INFO: Target number of precursors reached.
2 days, 23:51:44.164053 INFO: fragments_df: keeping 5000 of 22595 [sum(precursor_idx_mask)=13419 sum(mass_error_mask)=22595 stop_rank=5000
2 days, 23:51:44.168612 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:44.377404 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:44.564808 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:44.760380 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:45.596581 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:45.597082 INFO: Using score_cutoff 16.08178521080017 (fac=0.99, q=1)
2 days, 23:51:45.597461 INFO: Updating optimization_manager: fwhm_rt             : 2.580504894256592 -> 2.5619699954986572
2 days, 23:51:45.597572 INFO: Updating optimization_manager: fwhm_mobility       : 0.0042639528401196 -> 0.004177332390099764
2 days, 23:51:45.597659 INFO: Updating optimization_manager: score_cutoff        : 16.981063616752625 -> 16.08178521080017
2 days, 23:51:45.597741 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:45.598999 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:45.600507 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:45.601376 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:45.603494 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:45.603631 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:51:45.605305 INFO: Updating optimization_manager: mobility_error      : 0.05727150972088045 -> 0.05094681948312699
2 days, 23:51:45.605431 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0509.
2 days, 23:51:45.605528 INFO: ==============================================
2 days, 23:51:45.605631 INFO: Starting optimization step 2.
2 days, 23:51:45.605723 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:51:45.605811 INFO: Using python extraction backend
2 days, 23:51:45.605979 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:51:45.606077 INFO: === Search parameters used ===
2 days, 23:51:45.606155 INFO: rt_error       : 8.383182551553148
2 days, 23:51:45.606224 INFO: mobility_error : 0.05094681948312699
2 days, 23:51:45.606286 INFO: num_candidates : 3
2 days, 23:51:45.606354 INFO: ms1_error      : 15.0
2 days, 23:51:45.606418 INFO: ms2_error      : 15.0
2 days, 23:51:45.606477 INFO: fwhm_rt        : 2.5619699954986572
2 days, 23:51:45.606537 INFO: quant_window   : 3
2 days, 23:51:45.606595 INFO: ==============================================
2 days, 23:51:45.607599 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:45.607649 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:45.607697 INFO: FWHM in RT is 2.56 seconds, sigma is 0.43
2 days, 23:51:45.607733 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.26
2 days, 23:51:45.619600 INFO: Starting candidate selection
2 days, 23:51:46.258840 INFO: Starting candidate scoring
2 days, 23:51:46.371949 INFO: Finished candidate processing
2 days, 23:51:46.372092 INFO: Collecting candidate features
2 days, 23:51:46.388458 WARNING: intensity_correlation has 19 NaNs ( 0.60 % out of 3155)
2 days, 23:51:46.393677 INFO: Collecting fragment features
2 days, 23:51:46.398056 INFO: Finished candidate scoring
2 days, 23:51:46.402063 INFO: performing precursor FDR with 47 features
2 days, 23:51:46.402139 INFO: Decoy channel: -1
2 days, 23:51:46.402166 INFO: competitive: True
2 days, 23:51:46.406374 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:46.408146 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:51:46.408204 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:51:46.408244 WARNING: FDR calculation for 1651 target and 1485 decoy PSMs
2 days, 23:51:46.408268 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:46.409317 INFO: Estimating optimal hyperparameters - samples: 2,508, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:51:46.409432 INFO: Using random state 519348 for train-test-split
2 days, 23:51:46.778873 INFO: Test AUC: 0.871
2 days, 23:51:46.778989 INFO: Train AUC: 0.893
2 days, 23:51:46.779032 INFO: AUC difference: 2.46%
2 days, 23:51:47.107972 INFO: Resetting torch num_threads to 80
2 days, 23:51:47.108702 PROGRESS: === Extracted 3155 precursors and 22423 fragments ===
2 days, 23:51:47.109169 INFO: === FDR correction performed with classifier version 13 ===
2 days, 23:51:47.110032 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:47.110159 PROGRESS: Total precursors accumulated: 600
2 days, 23:51:47.110249 PROGRESS: Target precursors: 586 (97.67%)
2 days, 23:51:47.110331 PROGRESS: Decoy precursors: 14 (2.33%)
2 days, 23:51:47.110404 PROGRESS: 
2 days, 23:51:47.110470 PROGRESS: Precursor Summary:
2 days, 23:51:47.111838 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   559; 0.001 FDR:   468
2 days, 23:51:47.111966 PROGRESS: 
2 days, 23:51:47.112050 PROGRESS: Protein Summary:
2 days, 23:51:47.113600 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   411; 0.001 FDR:   348
2 days, 23:51:47.113717 PROGRESS: =========================================================================
2 days, 23:51:47.113908 INFO: Target number of precursors reached.
2 days, 23:51:47.120658 INFO: fragments_df: keeping 5000 of 22423 [sum(precursor_idx_mask)=13352 sum(mass_error_mask)=22423 stop_rank=5000
2 days, 23:51:47.125094 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:47.332037 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:47.570223 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:47.752452 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:48.665685 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:51:48.666171 INFO: Using score_cutoff 16.270664275360108 (fac=0.99, q=1)
2 days, 23:51:48.666528 INFO: Updating optimization_manager: fwhm_rt             : 2.5619699954986572 -> 2.5739586353302
2 days, 23:51:48.666621 INFO: Updating optimization_manager: fwhm_mobility       : 0.004177332390099764 -> 0.004185917787253857
2 days, 23:51:48.666690 INFO: Updating optimization_manager: score_cutoff        : 16.08178521080017 -> 16.270664275360108
2 days, 23:51:48.666757 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:48.667943 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:48.669404 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:48.670251 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:48.672329 INFO: === checking if optimization conditions were reached ===
2 days, 23:51:48.672446 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:51:48.673215 INFO: Updating optimization_manager: mobility_error      : 0.05094681948312699 -> 0.05727150972088045
2 days, 23:51:48.673356 INFO: Updating optimization_manager: classifier_version  : 13 -> 15
2 days, 23:51:48.673473 INFO: Updating optimization_manager: score_cutoff        : 16.270664275360108 -> 16.08178521080017
2 days, 23:51:48.673584 INFO: Updating optimization_manager: fwhm_rt             : 2.5739586353302 -> 2.5619699954986572
2 days, 23:51:48.673700 INFO: Updating optimization_manager: fwhm_mobility       : 0.004185917787253857 -> 0.004177332390099764
2 days, 23:51:48.673809 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0573 found after 3 searches.
2 days, 23:51:48.673897 INFO: ==============================================
2 days, 23:51:48.673983 PROGRESS: Optimization finished for mobility_error.
2 days, 23:51:48.677181 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:48.678073 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:48.679459 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:48.680285 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:48.682328 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:51:48.682443 PROGRESS: ==============================================
2 days, 23:51:48.682523 PROGRESS: ms2_error      : 15.0000
2 days, 23:51:48.682588 PROGRESS: ms1_error      : 15.0000
2 days, 23:51:48.682649 PROGRESS: rt_error       : 8.3832
2 days, 23:51:48.682705 PROGRESS: mobility_error : 0.0573
2 days, 23:51:48.682760 PROGRESS: ==============================================
2 days, 23:51:48.683303 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:51:48.687209 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:51:48.703995 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:51:48.708844 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:51:48.746978 INFO: Using python extraction backend
2 days, 23:51:48.747421 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:51:48.747539 INFO: === Search parameters used ===
2 days, 23:51:48.747629 INFO: rt_error       : 8.383182551553148
2 days, 23:51:48.747713 INFO: mobility_error : 0.05727150972088045
2 days, 23:51:48.747794 INFO: num_candidates : 3
2 days, 23:51:48.747873 INFO: ms1_error      : 15.0
2 days, 23:51:48.747950 INFO: ms2_error      : 15.0
2 days, 23:51:48.748026 INFO: fwhm_rt        : 2.5619699954986572
2 days, 23:51:48.748103 INFO: quant_window   : 3
2 days, 23:51:48.748179 INFO: ==============================================
2 days, 23:51:48.754773 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:51:48.754886 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:51:48.754947 INFO: FWHM in RT is 2.56 seconds, sigma is 0.43
2 days, 23:51:48.754982 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.26
2 days, 23:51:48.810078 INFO: Starting candidate selection
2 days, 23:51:50.750693 INFO: Removed 23478 precursors with score below cutoff 16.08178521080017
2 days, 23:51:51.086767 INFO: Starting candidate scoring
2 days, 23:51:52.083886 INFO: Finished candidate processing
2 days, 23:51:52.084102 INFO: Collecting candidate features
2 days, 23:51:52.167829 WARNING: intensity_correlation has 86 NaNs ( 0.16 % out of 53660)
2 days, 23:51:52.168116 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 53660)
2 days, 23:51:52.175184 INFO: Collecting fragment features
2 days, 23:51:52.206272 INFO: Finished candidate scoring
2 days, 23:51:52.250423 INFO: === Performing FDR correction with classifier version 15 ===
2 days, 23:51:52.252726 INFO: performing precursor FDR with 47 features
2 days, 23:51:52.252798 INFO: Decoy channel: -1
2 days, 23:51:52.252838 INFO: competitive: True
2 days, 23:51:52.275561 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:51:52.287575 WARNING: dropped 21 target PSMs due to missing features
2 days, 23:51:52.287724 WARNING: dropped 65 decoy PSMs due to missing features
2 days, 23:51:52.287790 WARNING: FDR calculation for 33354 target and 20220 decoy PSMs
2 days, 23:51:52.287835 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:51:52.296947 INFO: Estimating optimal hyperparameters - samples: 42,859, batch_size: 175, learning_rate: 2.07e-04
2 days, 23:51:52.297187 INFO: Using random state 717097 for train-test-split
2 days, 23:51:57.348989 INFO: Test AUC: 0.909
2 days, 23:51:57.349205 INFO: Train AUC: 0.908
2 days, 23:51:57.349247 INFO: AUC difference: 0.01%
2 days, 23:51:57.750749 INFO: Resetting torch num_threads to 80
2 days, 23:51:57.754163 INFO: Removing fragments below FDR threshold
2 days, 23:51:57.763246 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:51:57.763499 PROGRESS: Total precursors accumulated: 13,022
2 days, 23:51:57.763599 PROGRESS: Target precursors: 12,894 (99.02%)
2 days, 23:51:57.763684 PROGRESS: Decoy precursors: 128 (0.98%)
2 days, 23:51:57.763762 PROGRESS: 
2 days, 23:51:57.763834 PROGRESS: Precursor Summary:
2 days, 23:51:57.768615 PROGRESS: Channel   0:	 0.050 FDR: 12,894; 0.010 FDR: 12,894; 0.001 FDR: 11,923
2 days, 23:51:57.768773 PROGRESS: 
2 days, 23:51:57.768878 PROGRESS: Protein Summary:
2 days, 23:51:57.774961 PROGRESS: Channel   0:	 0.050 FDR: 1,681; 0.010 FDR: 1,681; 0.001 FDR: 1,662
2 days, 23:51:57.775110 PROGRESS: =========================================================================
2 days, 23:51:57.775724 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R5/psm.parquet
2 days, 23:51:57.839829 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R5/frag.parquet
2 days, 23:51:57.912091 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R5
2 days, 23:51:57.916951 PROGRESS: Loading raw file 6/12: A9_G_DIA_nLC_tTOF_R6 
2 days, 23:51:57.917103 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:51:57.917199 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R6/figures
2 days, 23:51:57.917417 INFO: Initializing TimingManager
2 days, 23:51:57.918401 INFO: Initializing RawFileManager
2 days, 23:51:57.918556 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:51:57.918626 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:51:57.918676 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:51:58.169375 INFO: Reading 22,622 frames with 397,467,912 detector events for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:52:02.073951 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d...
2 days, 23:52:02.075129 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:52:02.077291 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:52:02.077574 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:52:02.078176 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:52:02.080024 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:52:02.110353 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:52:02.110700 INFO: Indexing quadrupole dimension
2 days, 23:52:02.238721 INFO: Transposing detector events
2 days, 23:52:04.104798 INFO: Finished transposing data
2 days, 23:52:04.105129 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
2 days, 23:52:04.105892 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:52:04.105967 INFO: RT duration (sec)   : 2399.9
2 days, 23:52:04.106008 INFO: RT duration (min)   : 40.0
2 days, 23:52:04.106046 INFO: Cycle len (scans)   : 12
2 days, 23:52:04.106081 INFO: Cycle len (sec)     : 1.27
2 days, 23:52:04.106115 INFO: Number of cycles    : 1885
2 days, 23:52:04.106150 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:52:04.106196 INFO: Creating DIA data object took: 6.187642574310303
2 days, 23:52:04.113457 INFO: Initializing CalibrationManager
2 days, 23:52:04.113788 INFO: Setting up calibration estimators ..
2 days, 23:52:04.113895 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:52:04.113995 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:52:04.114091 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:52:04.114188 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:52:04.114272 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:52:04.114348 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:52:04.114414 INFO: Done setting up calibration estimators.
2 days, 23:52:04.114541 INFO: Initializing OptimizationManager
2 days, 23:52:04.114652 INFO: initial parameter: ms1_error = 30
2 days, 23:52:04.114712 INFO: initial parameter: ms2_error = 30
2 days, 23:52:04.114770 INFO: initial parameter: rt_error = 1199.968138
2 days, 23:52:04.114829 INFO: initial parameter: mobility_error = 0.1
2 days, 23:52:04.114885 INFO: initial parameter: num_candidates = 1
2 days, 23:52:04.114944 INFO: initial parameter: fwhm_rt = 5
2 days, 23:52:04.115037 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:52:04.115114 INFO: initial parameter: score_cutoff = 0
2 days, 23:52:04.115184 INFO: initial parameter: classifier_version = -1
2 days, 23:52:04.115291 PROGRESS: Initializing workflow A9_G_DIA_nLC_tTOF_R6
2 days, 23:52:04.115540 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:52:04.115590 INFO: Initializing FDRManager
2 days, 23:52:04.115628 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:52:04.122723 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:52:04.129581 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:52:04.130118 INFO: Updating optimization_manager: rt_error            : 1199.968138 -> 1199.968138
2 days, 23:52:04.130271 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:52:04.130556 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:52:04.130685 PROGRESS: Starting initial search for precursors.
2 days, 23:52:04.130816 INFO: Starting optimization step 0.
2 days, 23:52:04.130954 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:52:04.131087 INFO: Using python extraction backend
2 days, 23:52:04.131281 PROGRESS: Extracting batch of 399 precursors
2 days, 23:52:04.131419 INFO: === Search parameters used ===
2 days, 23:52:04.131542 INFO: rt_error       : 1199.968138
2 days, 23:52:04.131660 INFO: mobility_error : 0.1
2 days, 23:52:04.131780 INFO: num_candidates : 1
2 days, 23:52:04.131892 INFO: ms1_error      : 30
2 days, 23:52:04.132004 INFO: ms2_error      : 30
2 days, 23:52:04.132115 INFO: fwhm_rt        : 5
2 days, 23:52:04.132218 INFO: quant_window   : 3
2 days, 23:52:04.132322 INFO: ==============================================
2 days, 23:52:04.133410 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:04.133500 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:04.133660 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:52:04.133722 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:52:04.142052 INFO: Starting candidate selection
2 days, 23:52:07.770603 INFO: Starting candidate scoring
2 days, 23:52:07.827759 INFO: Finished candidate processing
2 days, 23:52:07.827896 INFO: Collecting candidate features
2 days, 23:52:07.846234 INFO: Collecting fragment features
2 days, 23:52:07.850393 INFO: Finished candidate scoring
2 days, 23:52:07.851755 INFO: performing precursor FDR with 47 features
2 days, 23:52:07.851823 INFO: Decoy channel: -1
2 days, 23:52:07.851856 INFO: competitive: True
2 days, 23:52:07.853583 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:07.855490 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:07.856319 INFO: Using random state 283838 for train-test-split
2 days, 23:52:07.882279 INFO: Test AUC: 0.598
2 days, 23:52:07.882400 INFO: Train AUC: 0.638
2 days, 23:52:07.882454 INFO: AUC difference: 6.25%
2 days, 23:52:07.882495 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:52:08.171863 INFO: Resetting torch num_threads to 80
2 days, 23:52:08.172458 PROGRESS: === Extracted 399 precursors and 3754 fragments ===
2 days, 23:52:08.172917 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:52:08.173593 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:08.173709 PROGRESS: Total precursors accumulated: 200
2 days, 23:52:08.173798 PROGRESS: Target precursors: 129 (64.50%)
2 days, 23:52:08.173892 PROGRESS: Decoy precursors: 71 (35.50%)
2 days, 23:52:08.173972 PROGRESS: 
2 days, 23:52:08.174060 PROGRESS: Precursor Summary:
2 days, 23:52:08.175103 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 23:52:08.175213 PROGRESS: 
2 days, 23:52:08.175296 PROGRESS: Protein Summary:
2 days, 23:52:08.176416 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 23:52:08.176524 PROGRESS: =========================================================================
2 days, 23:52:08.176660 INFO: Target number of precursors not reached yet.
2 days, 23:52:08.180643 INFO: Starting optimization step 1.
2 days, 23:52:08.180788 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:52:08.180886 INFO: Using python extraction backend
2 days, 23:52:08.181015 PROGRESS: Extracting batch of 798 precursors
2 days, 23:52:08.181108 INFO: === Search parameters used ===
2 days, 23:52:08.181185 INFO: rt_error       : 1199.968138
2 days, 23:52:08.181256 INFO: mobility_error : 0.1
2 days, 23:52:08.181325 INFO: num_candidates : 1
2 days, 23:52:08.181406 INFO: ms1_error      : 30
2 days, 23:52:08.181472 INFO: ms2_error      : 30
2 days, 23:52:08.181538 INFO: fwhm_rt        : 5
2 days, 23:52:08.181604 INFO: quant_window   : 3
2 days, 23:52:08.181669 INFO: ==============================================
2 days, 23:52:08.182474 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:08.182532 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:08.182579 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:52:08.182612 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:52:08.194170 INFO: Starting candidate selection
2 days, 23:52:14.608189 INFO: Starting candidate scoring
2 days, 23:52:14.684054 INFO: Finished candidate processing
2 days, 23:52:14.684167 INFO: Collecting candidate features
2 days, 23:52:14.697837 INFO: Collecting fragment features
2 days, 23:52:14.701260 INFO: Finished candidate scoring
2 days, 23:52:14.704401 INFO: performing precursor FDR with 47 features
2 days, 23:52:14.704461 INFO: Decoy channel: -1
2 days, 23:52:14.704494 INFO: competitive: True
2 days, 23:52:14.708654 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:14.711026 INFO: Estimating optimal hyperparameters - samples: 956, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:14.711136 INFO: Using random state 864429 for train-test-split
2 days, 23:52:14.800847 INFO: Test AUC: 0.785
2 days, 23:52:14.800962 INFO: Train AUC: 0.766
2 days, 23:52:14.801000 INFO: AUC difference: 2.43%
2 days, 23:52:15.090446 INFO: Resetting torch num_threads to 80
2 days, 23:52:15.091869 PROGRESS: === Extracted 1196 precursors and 11484 fragments ===
2 days, 23:52:15.092300 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:52:15.092965 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:15.093069 PROGRESS: Total precursors accumulated: 600
2 days, 23:52:15.093134 PROGRESS: Target precursors: 467 (77.83%)
2 days, 23:52:15.093200 PROGRESS: Decoy precursors: 133 (22.17%)
2 days, 23:52:15.093254 PROGRESS: 
2 days, 23:52:15.093307 PROGRESS: Precursor Summary:
2 days, 23:52:15.094506 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   225; 0.001 FDR:   198
2 days, 23:52:15.094615 PROGRESS: 
2 days, 23:52:15.094678 PROGRESS: Protein Summary:
2 days, 23:52:15.095958 PROGRESS: Channel   0:	 0.050 FDR:   236; 0.010 FDR:   168; 0.001 FDR:   152
2 days, 23:52:15.096061 PROGRESS: =========================================================================
2 days, 23:52:15.096229 INFO: Target number of precursors reached.
2 days, 23:52:15.099687 INFO: fragments_df: keeping 1886 of 11484 [sum(precursor_idx_mask)=2369 sum(mass_error_mask)=11484 stop_rank=1886
2 days, 23:52:15.104311 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:15.289272 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:15.439779 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:15.610567 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:15.965520 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:52:15.966179 INFO: Using score_cutoff 37.05797227478027 (fac=0.99, q=1)
2 days, 23:52:15.966961 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.9287703037261963
2 days, 23:52:15.967158 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007392760831862688
2 days, 23:52:15.967412 INFO: Updating optimization_manager: score_cutoff        : 0 -> 37.05797227478027
2 days, 23:52:15.967675 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:15.969501 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:15.971685 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:15.973119 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:15.976186 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2 days, 23:52:15.976651 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:52:15.977182 INFO: Starting optimization step 2.
2 days, 23:52:15.977418 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:52:15.977737 INFO: Using python extraction backend
2 days, 23:52:15.978117 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:52:15.978549 INFO: === Search parameters used ===
2 days, 23:52:15.978796 INFO: rt_error       : 1199.968138
2 days, 23:52:15.979106 INFO: mobility_error : 0.1
2 days, 23:52:15.979416 INFO: num_candidates : 3
2 days, 23:52:15.979692 INFO: ms1_error      : 30
2 days, 23:52:15.979923 INFO: ms2_error      : 30
2 days, 23:52:15.980270 INFO: fwhm_rt        : 2.9287703037261963
2 days, 23:52:15.980536 INFO: quant_window   : 3
2 days, 23:52:15.980875 INFO: ==============================================
2 days, 23:52:15.982624 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:15.982724 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:15.982814 INFO: FWHM in RT is 2.93 seconds, sigma is 0.49
2 days, 23:52:15.982872 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 4.01
2 days, 23:52:15.994066 INFO: Starting candidate selection
2 days, 23:52:23.057595 INFO: Starting candidate scoring
2 days, 23:52:23.217338 INFO: Finished candidate processing
2 days, 23:52:23.217464 INFO: Collecting candidate features
2 days, 23:52:23.237045 INFO: Collecting fragment features
2 days, 23:52:23.242238 INFO: Finished candidate scoring
2 days, 23:52:23.246440 INFO: performing precursor FDR with 47 features
2 days, 23:52:23.246504 INFO: Decoy channel: -1
2 days, 23:52:23.246538 INFO: competitive: True
2 days, 23:52:23.250681 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:23.253453 INFO: Estimating optimal hyperparameters - samples: 2,730, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:23.253559 INFO: Using random state 447549 for train-test-split
2 days, 23:52:23.611337 INFO: Test AUC: 0.673
2 days, 23:52:23.611459 INFO: Train AUC: 0.721
2 days, 23:52:23.611496 INFO: AUC difference: 6.64%
2 days, 23:52:23.611529 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:52:23.926315 INFO: Resetting torch num_threads to 80
2 days, 23:52:23.927037 PROGRESS: === Extracted 3413 precursors and 31594 fragments ===
2 days, 23:52:23.927515 INFO: === FDR correction performed with classifier version 1 ===
2 days, 23:52:23.928298 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:23.928408 PROGRESS: Total precursors accumulated: 600
2 days, 23:52:23.928487 PROGRESS: Target precursors: 498 (83.00%)
2 days, 23:52:23.928554 PROGRESS: Decoy precursors: 102 (17.00%)
2 days, 23:52:23.928616 PROGRESS: 
2 days, 23:52:23.928676 PROGRESS: Precursor Summary:
2 days, 23:52:23.930128 PROGRESS: Channel   0:	 0.050 FDR:   372; 0.010 FDR:   247; 0.001 FDR:   188
2 days, 23:52:23.930245 PROGRESS: 
2 days, 23:52:23.930316 PROGRESS: Protein Summary:
2 days, 23:52:23.931840 PROGRESS: Channel   0:	 0.050 FDR:   278; 0.010 FDR:   183; 0.001 FDR:   138
2 days, 23:52:23.931944 PROGRESS: =========================================================================
2 days, 23:52:23.932130 INFO: Target number of precursors reached.
2 days, 23:52:23.940676 INFO: fragments_df: keeping 4382 of 31594 [sum(precursor_idx_mask)=6894 sum(mass_error_mask)=31594 stop_rank=4382
2 days, 23:52:23.944884 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:24.184212 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:24.422572 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:24.622159 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:25.425482 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:52:25.425973 INFO: Using score_cutoff 34.87568377532959 (fac=0.99, q=1)
2 days, 23:52:25.426298 INFO: Updating optimization_manager: fwhm_rt             : 2.9287703037261963 -> 2.997274398803711
2 days, 23:52:25.426396 INFO: Updating optimization_manager: fwhm_mobility       : 0.007392760831862688 -> 0.0074698058888316154
2 days, 23:52:25.426457 INFO: Updating optimization_manager: score_cutoff        : 37.05797227478027 -> 34.87568377532959
2 days, 23:52:25.426516 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:25.427731 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:25.429216 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:25.430093 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:25.432236 INFO: === checking if optimization conditions were reached ===
2 days, 23:52:25.433955 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.11580382566057
2 days, 23:52:25.434089 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2 days, 23:52:25.434191 PROGRESS: ❌ ms2_error      : 17.1158 > 15.0000 or insufficient steps taken.
2 days, 23:52:25.435342 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:52:25.435454 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
2 days, 23:52:25.435539 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:52:25.435619 INFO: ==============================================
2 days, 23:52:25.435709 INFO: Starting optimization step 3.
2 days, 23:52:25.435791 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:52:25.435873 INFO: Using python extraction backend
2 days, 23:52:25.435996 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:52:25.436084 INFO: === Search parameters used ===
2 days, 23:52:25.436160 INFO: rt_error       : 1199.968138
2 days, 23:52:25.436239 INFO: mobility_error : 0.1
2 days, 23:52:25.436308 INFO: num_candidates : 3
2 days, 23:52:25.436374 INFO: ms1_error      : 15.0
2 days, 23:52:25.436440 INFO: ms2_error      : 17.11580382566057
2 days, 23:52:25.436510 INFO: fwhm_rt        : 2.997274398803711
2 days, 23:52:25.436577 INFO: quant_window   : 3
2 days, 23:52:25.436641 INFO: ==============================================
2 days, 23:52:25.437625 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:25.437682 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:25.437736 INFO: FWHM in RT is 3.00 seconds, sigma is 0.50
2 days, 23:52:25.437773 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 4.05
2 days, 23:52:25.442692 INFO: Starting candidate selection
2 days, 23:52:32.169894 INFO: Starting candidate scoring
2 days, 23:52:32.299937 INFO: Finished candidate processing
2 days, 23:52:32.300092 INFO: Collecting candidate features
2 days, 23:52:32.314877 INFO: Collecting fragment features
2 days, 23:52:32.319271 INFO: Finished candidate scoring
2 days, 23:52:32.323070 INFO: performing precursor FDR with 47 features
2 days, 23:52:32.323159 INFO: Decoy channel: -1
2 days, 23:52:32.323199 INFO: competitive: True
2 days, 23:52:32.326845 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:32.329418 INFO: Estimating optimal hyperparameters - samples: 2,738, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:32.329557 INFO: Using random state 667434 for train-test-split
2 days, 23:52:32.602670 INFO: Test AUC: 0.743
2 days, 23:52:32.602798 INFO: Train AUC: 0.749
2 days, 23:52:32.602847 INFO: AUC difference: 0.80%
2 days, 23:52:32.973837 INFO: Resetting torch num_threads to 80
2 days, 23:52:32.974716 PROGRESS: === Extracted 3423 precursors and 28916 fragments ===
2 days, 23:52:32.975344 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:52:32.976393 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:32.976530 PROGRESS: Total precursors accumulated: 600
2 days, 23:52:32.976622 PROGRESS: Target precursors: 539 (89.83%)
2 days, 23:52:32.976700 PROGRESS: Decoy precursors: 61 (10.17%)
2 days, 23:52:32.976785 PROGRESS: 
2 days, 23:52:32.976893 PROGRESS: Precursor Summary:
2 days, 23:52:32.979021 PROGRESS: Channel   0:	 0.050 FDR:   469; 0.010 FDR:   361; 0.001 FDR:   228
2 days, 23:52:32.979186 PROGRESS: 
2 days, 23:52:32.979291 PROGRESS: Protein Summary:
2 days, 23:52:32.981542 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:   266; 0.001 FDR:   169
2 days, 23:52:32.981670 PROGRESS: =========================================================================
2 days, 23:52:32.981903 INFO: Target number of precursors reached.
2 days, 23:52:32.992287 INFO: fragments_df: keeping 5000 of 28916 [sum(precursor_idx_mask)=9597 sum(mass_error_mask)=28916 stop_rank=5000
2 days, 23:52:32.997510 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:33.165802 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:33.333185 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:33.502063 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:34.310746 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:52:34.311201 INFO: Using score_cutoff 27.80155951309204 (fac=0.99, q=1)
2 days, 23:52:34.311551 INFO: Updating optimization_manager: fwhm_rt             : 2.997274398803711 -> 2.774725914001465
2 days, 23:52:34.311646 INFO: Updating optimization_manager: fwhm_mobility       : 0.0074698058888316154 -> 0.005903994664549828
2 days, 23:52:34.311730 INFO: Updating optimization_manager: score_cutoff        : 34.87568377532959 -> 27.80155951309204
2 days, 23:52:34.311801 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:34.312995 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:34.314502 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:34.315368 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:34.317449 INFO: === checking if optimization conditions were reached ===
2 days, 23:52:34.319191 INFO: Updating optimization_manager: ms2_error           : 17.11580382566057 -> 15.0
2 days, 23:52:34.319315 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:52:34.319401 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:52:34.320451 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:52:34.320565 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:52:34.320647 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:52:34.320720 INFO: ==============================================
2 days, 23:52:34.320800 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:52:34.324016 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:34.324921 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:34.326381 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:34.327239 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:34.329296 INFO: Starting optimization step 0.
2 days, 23:52:34.329421 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:52:34.329528 INFO: Using python extraction backend
2 days, 23:52:34.329682 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:52:34.329796 INFO: === Search parameters used ===
2 days, 23:52:34.329926 INFO: rt_error       : 1199.968138
2 days, 23:52:34.330014 INFO: mobility_error : 0.1
2 days, 23:52:34.330098 INFO: num_candidates : 3
2 days, 23:52:34.330180 INFO: ms1_error      : 15.0
2 days, 23:52:34.330256 INFO: ms2_error      : 15.0
2 days, 23:52:34.330332 INFO: fwhm_rt        : 2.774725914001465
2 days, 23:52:34.330408 INFO: quant_window   : 3
2 days, 23:52:34.330468 INFO: ==============================================
2 days, 23:52:34.331415 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:34.331470 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:34.331515 INFO: FWHM in RT is 2.77 seconds, sigma is 0.46
2 days, 23:52:34.331561 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.20
2 days, 23:52:34.346202 INFO: Starting candidate selection
2 days, 23:52:41.019711 INFO: Starting candidate scoring
2 days, 23:52:41.126717 INFO: Finished candidate processing
2 days, 23:52:41.126857 INFO: Collecting candidate features
2 days, 23:52:41.142327 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3409)
2 days, 23:52:41.142566 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3409)
2 days, 23:52:41.146708 INFO: Collecting fragment features
2 days, 23:52:41.151076 INFO: Finished candidate scoring
2 days, 23:52:41.154399 INFO: performing precursor FDR with 47 features
2 days, 23:52:41.154474 INFO: Decoy channel: -1
2 days, 23:52:41.154504 INFO: competitive: True
2 days, 23:52:41.157915 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:41.159497 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:52:41.160588 INFO: Estimating optimal hyperparameters - samples: 2,726, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:41.160684 INFO: Using random state 39100 for train-test-split
2 days, 23:52:41.519120 INFO: Test AUC: 0.727
2 days, 23:52:41.519260 INFO: Train AUC: 0.785
2 days, 23:52:41.519306 INFO: AUC difference: 7.32%
2 days, 23:52:41.519522 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:52:41.870919 INFO: Resetting torch num_threads to 80
2 days, 23:52:41.871596 PROGRESS: === Extracted 3409 precursors and 27969 fragments ===
2 days, 23:52:41.872121 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:52:41.872864 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:41.872980 PROGRESS: Total precursors accumulated: 600
2 days, 23:52:41.873056 PROGRESS: Target precursors: 532 (88.67%)
2 days, 23:52:41.873122 PROGRESS: Decoy precursors: 68 (11.33%)
2 days, 23:52:41.873182 PROGRESS: 
2 days, 23:52:41.873238 PROGRESS: Precursor Summary:
2 days, 23:52:41.874545 PROGRESS: Channel   0:	 0.050 FDR:   462; 0.010 FDR:   376; 0.001 FDR:   240
2 days, 23:52:41.874673 PROGRESS: 
2 days, 23:52:41.874748 PROGRESS: Protein Summary:
2 days, 23:52:41.876368 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   278; 0.001 FDR:   177
2 days, 23:52:41.876487 PROGRESS: =========================================================================
2 days, 23:52:41.876706 INFO: Target number of precursors reached.
2 days, 23:52:41.883628 INFO: fragments_df: keeping 5000 of 27969 [sum(precursor_idx_mask)=9782 sum(mass_error_mask)=27969 stop_rank=5000
2 days, 23:52:41.887432 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:42.051259 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:42.220410 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:42.410671 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:43.179720 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:52:43.180238 INFO: Using score_cutoff 26.617844953536988 (fac=0.99, q=1)
2 days, 23:52:43.180637 INFO: Updating optimization_manager: fwhm_rt             : 2.774725914001465 -> 2.7393646240234375
2 days, 23:52:43.180755 INFO: Updating optimization_manager: fwhm_mobility       : 0.005903994664549828 -> 0.005632984451949596
2 days, 23:52:43.180845 INFO: Updating optimization_manager: score_cutoff        : 27.80155951309204 -> 26.617844953536988
2 days, 23:52:43.180933 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:43.182261 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:43.183816 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:43.184761 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:43.187143 INFO: === checking if optimization conditions were reached ===
2 days, 23:52:43.187312 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:52:43.189400 INFO: Updating optimization_manager: rt_error            : 1199.968138 -> 259.7937047686113
2 days, 23:52:43.189537 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 259.7937.
2 days, 23:52:43.189640 INFO: ==============================================
2 days, 23:52:43.189744 INFO: Starting optimization step 1.
2 days, 23:52:43.189831 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:52:43.189940 INFO: Using python extraction backend
2 days, 23:52:43.190087 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:52:43.190191 INFO: === Search parameters used ===
2 days, 23:52:43.190283 INFO: rt_error       : 259.7937047686113
2 days, 23:52:43.190356 INFO: mobility_error : 0.1
2 days, 23:52:43.190421 INFO: num_candidates : 3
2 days, 23:52:43.190484 INFO: ms1_error      : 15.0
2 days, 23:52:43.190548 INFO: ms2_error      : 15.0
2 days, 23:52:43.190609 INFO: fwhm_rt        : 2.7393646240234375
2 days, 23:52:43.190669 INFO: quant_window   : 3
2 days, 23:52:43.190727 INFO: ==============================================
2 days, 23:52:43.191793 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:43.191852 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:43.191906 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
2 days, 23:52:43.191940 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.05
2 days, 23:52:43.194587 INFO: Starting candidate selection
2 days, 23:52:45.198807 INFO: Starting candidate scoring
2 days, 23:52:45.313112 INFO: Finished candidate processing
2 days, 23:52:45.313251 INFO: Collecting candidate features
2 days, 23:52:45.330400 WARNING: intensity_correlation has 5 NaNs ( 0.15 % out of 3358)
2 days, 23:52:45.338546 INFO: Collecting fragment features
2 days, 23:52:45.344386 INFO: Finished candidate scoring
2 days, 23:52:45.347995 INFO: performing precursor FDR with 47 features
2 days, 23:52:45.348088 INFO: Decoy channel: -1
2 days, 23:52:45.348128 INFO: competitive: True
2 days, 23:52:45.352972 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:45.355567 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:52:45.355641 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 23:52:45.357219 INFO: Estimating optimal hyperparameters - samples: 2,682, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:45.357345 INFO: Using random state 39100 for train-test-split
2 days, 23:52:45.723359 INFO: Test AUC: 0.776
2 days, 23:52:45.723466 INFO: Train AUC: 0.798
2 days, 23:52:45.723502 INFO: AUC difference: 2.70%
2 days, 23:52:46.055513 INFO: Resetting torch num_threads to 80
2 days, 23:52:46.056345 PROGRESS: === Extracted 3358 precursors and 26528 fragments ===
2 days, 23:52:46.056958 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:52:46.057941 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:46.058078 PROGRESS: Total precursors accumulated: 600
2 days, 23:52:46.058188 PROGRESS: Target precursors: 552 (92.00%)
2 days, 23:52:46.058296 PROGRESS: Decoy precursors: 48 (8.00%)
2 days, 23:52:46.058392 PROGRESS: 
2 days, 23:52:46.058479 PROGRESS: Precursor Summary:
2 days, 23:52:46.060435 PROGRESS: Channel   0:	 0.050 FDR:   502; 0.010 FDR:   446; 0.001 FDR:   389
2 days, 23:52:46.060576 PROGRESS: 
2 days, 23:52:46.060681 PROGRESS: Protein Summary:
2 days, 23:52:46.062937 PROGRESS: Channel   0:	 0.050 FDR:   369; 0.010 FDR:   325; 0.001 FDR:   289
2 days, 23:52:46.063078 PROGRESS: =========================================================================
2 days, 23:52:46.063292 INFO: Target number of precursors reached.
2 days, 23:52:46.073344 INFO: fragments_df: keeping 5000 of 26528 [sum(precursor_idx_mask)=11265 sum(mass_error_mask)=26528 stop_rank=5000
2 days, 23:52:46.078346 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:46.242830 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:46.475337 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:46.726267 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:47.696031 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:52:47.696546 INFO: Using score_cutoff 23.171281883239747 (fac=0.99, q=1)
2 days, 23:52:47.696907 INFO: Updating optimization_manager: fwhm_rt             : 2.7393646240234375 -> 2.6553356647491455
2 days, 23:52:47.696998 INFO: Updating optimization_manager: fwhm_mobility       : 0.005632984451949596 -> 0.005064424127340317
2 days, 23:52:47.697070 INFO: Updating optimization_manager: score_cutoff        : 26.617844953536988 -> 23.171281883239747
2 days, 23:52:47.697136 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:47.698448 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:47.700064 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:47.700994 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:47.703261 INFO: === checking if optimization conditions were reached ===
2 days, 23:52:47.703389 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:52:47.705455 INFO: Updating optimization_manager: rt_error            : 259.7937047686113 -> 88.45023973499407
2 days, 23:52:47.705570 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 88.4502.
2 days, 23:52:47.705659 INFO: ==============================================
2 days, 23:52:47.705741 INFO: Starting optimization step 2.
2 days, 23:52:47.705819 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:52:47.705904 INFO: Using python extraction backend
2 days, 23:52:47.706027 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:52:47.706102 INFO: === Search parameters used ===
2 days, 23:52:47.706159 INFO: rt_error       : 88.45023973499407
2 days, 23:52:47.706213 INFO: mobility_error : 0.1
2 days, 23:52:47.706266 INFO: num_candidates : 3
2 days, 23:52:47.706318 INFO: ms1_error      : 15.0
2 days, 23:52:47.706372 INFO: ms2_error      : 15.0
2 days, 23:52:47.706423 INFO: fwhm_rt        : 2.6553356647491455
2 days, 23:52:47.706473 INFO: quant_window   : 3
2 days, 23:52:47.706523 INFO: ==============================================
2 days, 23:52:47.707617 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:47.707673 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:47.707716 INFO: FWHM in RT is 2.66 seconds, sigma is 0.44
2 days, 23:52:47.707742 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.74
2 days, 23:52:47.718388 INFO: Starting candidate selection
2 days, 23:52:48.824429 INFO: Starting candidate scoring
2 days, 23:52:48.941947 INFO: Finished candidate processing
2 days, 23:52:48.942128 INFO: Collecting candidate features
2 days, 23:52:48.955266 WARNING: intensity_correlation has 8 NaNs ( 0.24 % out of 3300)
2 days, 23:52:48.961318 INFO: Collecting fragment features
2 days, 23:52:48.968035 INFO: Finished candidate scoring
2 days, 23:52:48.972561 INFO: performing precursor FDR with 47 features
2 days, 23:52:48.972683 INFO: Decoy channel: -1
2 days, 23:52:48.972725 INFO: competitive: True
2 days, 23:52:48.978050 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:48.980715 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:52:48.980795 WARNING: dropped 6 decoy PSMs due to missing features
2 days, 23:52:48.982404 INFO: Estimating optimal hyperparameters - samples: 2,633, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:48.982562 INFO: Using random state 39100 for train-test-split
2 days, 23:52:49.351923 INFO: Test AUC: 0.801
2 days, 23:52:49.352045 INFO: Train AUC: 0.826
2 days, 23:52:49.352079 INFO: AUC difference: 3.12%
2 days, 23:52:49.704206 INFO: Resetting torch num_threads to 80
2 days, 23:52:49.704871 PROGRESS: === Extracted 3300 precursors and 25072 fragments ===
2 days, 23:52:49.705326 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:52:49.706044 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:49.706145 PROGRESS: Total precursors accumulated: 600
2 days, 23:52:49.706213 PROGRESS: Target precursors: 577 (96.17%)
2 days, 23:52:49.706273 PROGRESS: Decoy precursors: 23 (3.83%)
2 days, 23:52:49.706326 PROGRESS: 
2 days, 23:52:49.706385 PROGRESS: Precursor Summary:
2 days, 23:52:49.707580 PROGRESS: Channel   0:	 0.050 FDR:   577; 0.010 FDR:   492; 0.001 FDR:   296
2 days, 23:52:49.707683 PROGRESS: 
2 days, 23:52:49.707748 PROGRESS: Protein Summary:
2 days, 23:52:49.709102 PROGRESS: Channel   0:	 0.050 FDR:   420; 0.010 FDR:   361; 0.001 FDR:   223
2 days, 23:52:49.709197 PROGRESS: =========================================================================
2 days, 23:52:49.709353 INFO: Target number of precursors reached.
2 days, 23:52:49.715968 INFO: fragments_df: keeping 5000 of 25072 [sum(precursor_idx_mask)=12171 sum(mass_error_mask)=25072 stop_rank=5000
2 days, 23:52:49.719639 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:49.903503 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:50.121089 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:50.319893 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:51.157708 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:52:51.158225 INFO: Using score_cutoff 22.33654549598694 (fac=0.99, q=1)
2 days, 23:52:51.158626 INFO: Updating optimization_manager: fwhm_rt             : 2.6553356647491455 -> 2.6337218284606934
2 days, 23:52:51.158738 INFO: Updating optimization_manager: fwhm_mobility       : 0.005064424127340317 -> 0.004699167795479298
2 days, 23:52:51.158821 INFO: Updating optimization_manager: score_cutoff        : 23.171281883239747 -> 22.33654549598694
2 days, 23:52:51.158905 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:51.160157 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:51.161889 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:51.162847 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:51.165130 INFO: === checking if optimization conditions were reached ===
2 days, 23:52:51.165273 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:52:51.167344 INFO: Updating optimization_manager: rt_error            : 88.45023973499407 -> 41.86341639134312
2 days, 23:52:51.167481 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 41.8634.
2 days, 23:52:51.167578 INFO: ==============================================
2 days, 23:52:51.167682 INFO: Starting optimization step 3.
2 days, 23:52:51.167784 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:52:51.167857 INFO: Using python extraction backend
2 days, 23:52:51.167969 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:52:51.168045 INFO: === Search parameters used ===
2 days, 23:52:51.168103 INFO: rt_error       : 41.86341639134312
2 days, 23:52:51.168157 INFO: mobility_error : 0.1
2 days, 23:52:51.168212 INFO: num_candidates : 3
2 days, 23:52:51.168269 INFO: ms1_error      : 15.0
2 days, 23:52:51.168322 INFO: ms2_error      : 15.0
2 days, 23:52:51.168375 INFO: fwhm_rt        : 2.6337218284606934
2 days, 23:52:51.168426 INFO: quant_window   : 3
2 days, 23:52:51.168476 INFO: ==============================================
2 days, 23:52:51.169495 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:51.169552 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:51.169593 INFO: FWHM in RT is 2.63 seconds, sigma is 0.44
2 days, 23:52:51.169621 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
2 days, 23:52:51.188208 INFO: Starting candidate selection
2 days, 23:52:51.977722 INFO: Starting candidate scoring
2 days, 23:52:52.090480 INFO: Finished candidate processing
2 days, 23:52:52.090622 INFO: Collecting candidate features
2 days, 23:52:52.105563 WARNING: intensity_correlation has 9 NaNs ( 0.28 % out of 3259)
2 days, 23:52:52.113848 INFO: Collecting fragment features
2 days, 23:52:52.120366 INFO: Finished candidate scoring
2 days, 23:52:52.124622 INFO: performing precursor FDR with 47 features
2 days, 23:52:52.124729 INFO: Decoy channel: -1
2 days, 23:52:52.124772 INFO: competitive: True
2 days, 23:52:52.130240 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:52.132834 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:52:52.132909 WARNING: dropped 7 decoy PSMs due to missing features
2 days, 23:52:52.134492 INFO: Estimating optimal hyperparameters - samples: 2,600, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:52.134626 INFO: Using random state 39100 for train-test-split
2 days, 23:52:52.501356 INFO: Test AUC: 0.832
2 days, 23:52:52.501489 INFO: Train AUC: 0.844
2 days, 23:52:52.501532 INFO: AUC difference: 1.50%
2 days, 23:52:52.823949 INFO: Resetting torch num_threads to 80
2 days, 23:52:52.824663 PROGRESS: === Extracted 3259 precursors and 24086 fragments ===
2 days, 23:52:52.825131 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:52:52.825830 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:52.825961 PROGRESS: Total precursors accumulated: 600
2 days, 23:52:52.826049 PROGRESS: Target precursors: 578 (96.33%)
2 days, 23:52:52.826127 PROGRESS: Decoy precursors: 22 (3.67%)
2 days, 23:52:52.826203 PROGRESS: 
2 days, 23:52:52.826278 PROGRESS: Precursor Summary:
2 days, 23:52:52.827498 PROGRESS: Channel   0:	 0.050 FDR:   578; 0.010 FDR:   515; 0.001 FDR:   291
2 days, 23:52:52.827610 PROGRESS: 
2 days, 23:52:52.827698 PROGRESS: Protein Summary:
2 days, 23:52:52.829089 PROGRESS: Channel   0:	 0.050 FDR:   423; 0.010 FDR:   380; 0.001 FDR:   219
2 days, 23:52:52.829200 PROGRESS: =========================================================================
2 days, 23:52:52.829391 INFO: Target number of precursors reached.
2 days, 23:52:52.836080 INFO: fragments_df: keeping 5000 of 24086 [sum(precursor_idx_mask)=12515 sum(mass_error_mask)=24086 stop_rank=5000
2 days, 23:52:52.839767 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:53.016074 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:53.249349 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:53.436284 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:54.315492 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:52:54.315979 INFO: Using score_cutoff 19.263497147369385 (fac=0.99, q=1)
2 days, 23:52:54.316361 INFO: Updating optimization_manager: fwhm_rt             : 2.6337218284606934 -> 2.620856523513794
2 days, 23:52:54.316461 INFO: Updating optimization_manager: fwhm_mobility       : 0.004699167795479298 -> 0.0044417311437428
2 days, 23:52:54.316545 INFO: Updating optimization_manager: score_cutoff        : 22.33654549598694 -> 19.263497147369385
2 days, 23:52:54.316627 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:54.317835 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:54.319401 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:54.320267 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:54.322444 INFO: === checking if optimization conditions were reached ===
2 days, 23:52:54.322584 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:52:54.324649 INFO: Updating optimization_manager: rt_error            : 41.86341639134312 -> 9.815837872651363
2 days, 23:52:54.324777 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 9.8158.
2 days, 23:52:54.324915 INFO: ==============================================
2 days, 23:52:54.325021 INFO: Starting optimization step 4.
2 days, 23:52:54.325112 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:52:54.325197 INFO: Using python extraction backend
2 days, 23:52:54.325339 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:52:54.325434 INFO: === Search parameters used ===
2 days, 23:52:54.325513 INFO: rt_error       : 9.815837872651363
2 days, 23:52:54.325581 INFO: mobility_error : 0.1
2 days, 23:52:54.325653 INFO: num_candidates : 3
2 days, 23:52:54.325721 INFO: ms1_error      : 15.0
2 days, 23:52:54.325783 INFO: ms2_error      : 15.0
2 days, 23:52:54.325845 INFO: fwhm_rt        : 2.620856523513794
2 days, 23:52:54.325923 INFO: quant_window   : 3
2 days, 23:52:54.325987 INFO: ==============================================
2 days, 23:52:54.326963 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:54.327015 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:54.327065 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:52:54.327100 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.41
2 days, 23:52:54.332838 INFO: Starting candidate selection
2 days, 23:52:54.990297 INFO: Starting candidate scoring
2 days, 23:52:55.100770 INFO: Finished candidate processing
2 days, 23:52:55.100910 INFO: Collecting candidate features
2 days, 23:52:55.111848 WARNING: intensity_correlation has 11 NaNs ( 0.34 % out of 3205)
2 days, 23:52:55.112166 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3205)
2 days, 23:52:55.120049 INFO: Collecting fragment features
2 days, 23:52:55.126238 INFO: Finished candidate scoring
2 days, 23:52:55.130485 INFO: performing precursor FDR with 47 features
2 days, 23:52:55.130589 INFO: Decoy channel: -1
2 days, 23:52:55.130625 INFO: competitive: True
2 days, 23:52:55.135912 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:55.138555 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:52:55.138645 WARNING: dropped 11 decoy PSMs due to missing features
2 days, 23:52:55.140284 INFO: Estimating optimal hyperparameters - samples: 2,553, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:55.140442 INFO: Using random state 39100 for train-test-split
2 days, 23:52:55.424536 INFO: Test AUC: 0.835
2 days, 23:52:55.424659 INFO: Train AUC: 0.869
2 days, 23:52:55.424702 INFO: AUC difference: 3.90%
2 days, 23:52:55.771862 INFO: Resetting torch num_threads to 80
2 days, 23:52:55.772524 PROGRESS: === Extracted 3205 precursors and 22944 fragments ===
2 days, 23:52:55.772994 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:52:55.773724 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:55.773839 PROGRESS: Total precursors accumulated: 600
2 days, 23:52:55.773945 PROGRESS: Target precursors: 586 (97.67%)
2 days, 23:52:55.774024 PROGRESS: Decoy precursors: 14 (2.33%)
2 days, 23:52:55.774098 PROGRESS: 
2 days, 23:52:55.774168 PROGRESS: Precursor Summary:
2 days, 23:52:55.775413 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   565; 0.001 FDR:   379
2 days, 23:52:55.775530 PROGRESS: 
2 days, 23:52:55.775618 PROGRESS: Protein Summary:
2 days, 23:52:55.777061 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   416; 0.001 FDR:   285
2 days, 23:52:55.777174 PROGRESS: =========================================================================
2 days, 23:52:55.777361 INFO: Target number of precursors reached.
2 days, 23:52:55.783657 INFO: fragments_df: keeping 5000 of 22944 [sum(precursor_idx_mask)=13316 sum(mass_error_mask)=22944 stop_rank=5000
2 days, 23:52:55.787221 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:55.977116 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:56.170936 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:56.370361 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:57.162154 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:52:57.162648 INFO: Using score_cutoff 15.333013116073607 (fac=0.99, q=1)
2 days, 23:52:57.163045 INFO: Updating optimization_manager: fwhm_rt             : 2.620856523513794 -> 2.547071933746338
2 days, 23:52:57.163148 INFO: Updating optimization_manager: fwhm_mobility       : 0.0044417311437428 -> 0.004125097766518593
2 days, 23:52:57.163229 INFO: Updating optimization_manager: score_cutoff        : 19.263497147369385 -> 15.333013116073607
2 days, 23:52:57.163311 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:57.164500 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:57.166096 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:57.167015 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:52:57.169326 INFO: === checking if optimization conditions were reached ===
2 days, 23:52:57.169459 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:52:57.171549 INFO: Updating optimization_manager: rt_error            : 9.815837872651363 -> 10.690421807987128
2 days, 23:52:57.171680 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 10.6904.
2 days, 23:52:57.171777 INFO: ==============================================
2 days, 23:52:57.171888 INFO: Starting optimization step 5.
2 days, 23:52:57.171979 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:52:57.172063 INFO: Using python extraction backend
2 days, 23:52:57.172202 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:52:57.172293 INFO: === Search parameters used ===
2 days, 23:52:57.172369 INFO: rt_error       : 10.690421807987128
2 days, 23:52:57.172439 INFO: mobility_error : 0.1
2 days, 23:52:57.172502 INFO: num_candidates : 3
2 days, 23:52:57.172563 INFO: ms1_error      : 15.0
2 days, 23:52:57.172624 INFO: ms2_error      : 15.0
2 days, 23:52:57.172684 INFO: fwhm_rt        : 2.547071933746338
2 days, 23:52:57.172745 INFO: quant_window   : 3
2 days, 23:52:57.172803 INFO: ==============================================
2 days, 23:52:57.173829 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:52:57.173900 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:52:57.173952 INFO: FWHM in RT is 2.55 seconds, sigma is 0.42
2 days, 23:52:57.173995 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.24
2 days, 23:52:57.188126 INFO: Starting candidate selection
2 days, 23:52:57.840868 INFO: Starting candidate scoring
2 days, 23:52:57.943144 INFO: Finished candidate processing
2 days, 23:52:57.943279 INFO: Collecting candidate features
2 days, 23:52:57.955733 WARNING: intensity_correlation has 14 NaNs ( 0.44 % out of 3216)
2 days, 23:52:57.955969 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3216)
2 days, 23:52:57.959927 INFO: Collecting fragment features
2 days, 23:52:57.963888 INFO: Finished candidate scoring
2 days, 23:52:57.966569 INFO: performing precursor FDR with 47 features
2 days, 23:52:57.966625 INFO: Decoy channel: -1
2 days, 23:52:57.966652 INFO: competitive: True
2 days, 23:52:57.969853 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:52:57.971523 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:52:57.971583 WARNING: dropped 13 decoy PSMs due to missing features
2 days, 23:52:57.972646 INFO: Estimating optimal hyperparameters - samples: 2,560, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:52:57.972746 INFO: Using random state 39100 for train-test-split
2 days, 23:52:58.270508 INFO: Test AUC: 0.865
2 days, 23:52:58.270619 INFO: Train AUC: 0.870
2 days, 23:52:58.270652 INFO: AUC difference: 0.58%
2 days, 23:52:58.571192 INFO: Resetting torch num_threads to 80
2 days, 23:52:58.571747 PROGRESS: === Extracted 3216 precursors and 23011 fragments ===
2 days, 23:52:58.572177 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:52:58.572840 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:52:58.572936 PROGRESS: Total precursors accumulated: 600
2 days, 23:52:58.573003 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:52:58.573059 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:52:58.573111 PROGRESS: 
2 days, 23:52:58.573161 PROGRESS: Precursor Summary:
2 days, 23:52:58.574355 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   569; 0.001 FDR:   308
2 days, 23:52:58.574470 PROGRESS: 
2 days, 23:52:58.574535 PROGRESS: Protein Summary:
2 days, 23:52:58.575910 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   419; 0.001 FDR:   231
2 days, 23:52:58.576005 PROGRESS: =========================================================================
2 days, 23:52:58.576153 INFO: Target number of precursors reached.
2 days, 23:52:58.582537 INFO: fragments_df: keeping 5000 of 23011 [sum(precursor_idx_mask)=13399 sum(mass_error_mask)=23011 stop_rank=5000
2 days, 23:52:58.586156 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:52:58.791309 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:52:59.004423 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:52:59.233798 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:00.233406 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:53:00.233902 INFO: Using score_cutoff 14.616909767532348 (fac=0.99, q=1)
2 days, 23:53:00.234252 INFO: Updating optimization_manager: fwhm_rt             : 2.547071933746338 -> 2.5376131534576416
2 days, 23:53:00.234344 INFO: Updating optimization_manager: fwhm_mobility       : 0.004125097766518593 -> 0.004099969286471605
2 days, 23:53:00.234411 INFO: Updating optimization_manager: score_cutoff        : 15.333013116073607 -> 14.616909767532348
2 days, 23:53:00.234479 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:00.235607 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:00.237095 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:00.238002 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:00.240110 INFO: === checking if optimization conditions were reached ===
2 days, 23:53:00.240234 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 23:53:00.242249 INFO: Updating optimization_manager: rt_error            : 10.690421807987128 -> 8.797602730090658
2 days, 23:53:00.242370 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 8.7976.
2 days, 23:53:00.242452 INFO: ==============================================
2 days, 23:53:00.242539 INFO: Starting optimization step 6.
2 days, 23:53:00.242617 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:53:00.242693 INFO: Using python extraction backend
2 days, 23:53:00.242808 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:53:00.242889 INFO: === Search parameters used ===
2 days, 23:53:00.242957 INFO: rt_error       : 8.797602730090658
2 days, 23:53:00.243016 INFO: mobility_error : 0.1
2 days, 23:53:00.243072 INFO: num_candidates : 3
2 days, 23:53:00.243127 INFO: ms1_error      : 15.0
2 days, 23:53:00.243181 INFO: ms2_error      : 15.0
2 days, 23:53:00.243235 INFO: fwhm_rt        : 2.5376131534576416
2 days, 23:53:00.243289 INFO: quant_window   : 3
2 days, 23:53:00.243341 INFO: ==============================================
2 days, 23:53:00.244239 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:00.244294 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:00.244336 INFO: FWHM in RT is 2.54 seconds, sigma is 0.42
2 days, 23:53:00.244366 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.22
2 days, 23:53:00.254071 INFO: Starting candidate selection
2 days, 23:53:00.828667 INFO: Starting candidate scoring
2 days, 23:53:00.940969 INFO: Finished candidate processing
2 days, 23:53:00.941109 INFO: Collecting candidate features
2 days, 23:53:00.957181 WARNING: intensity_correlation has 11 NaNs ( 0.34 % out of 3208)
2 days, 23:53:00.957634 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3208)
2 days, 23:53:00.965828 INFO: Collecting fragment features
2 days, 23:53:00.972319 INFO: Finished candidate scoring
2 days, 23:53:00.976188 INFO: performing precursor FDR with 47 features
2 days, 23:53:00.976294 INFO: Decoy channel: -1
2 days, 23:53:00.976338 INFO: competitive: True
2 days, 23:53:00.981539 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:00.984167 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:53:00.984249 WARNING: dropped 9 decoy PSMs due to missing features
2 days, 23:53:00.985715 INFO: Estimating optimal hyperparameters - samples: 2,556, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:53:00.985839 INFO: Using random state 39100 for train-test-split
2 days, 23:53:01.225589 INFO: Test AUC: 0.853
2 days, 23:53:01.225720 INFO: Train AUC: 0.867
2 days, 23:53:01.225765 INFO: AUC difference: 1.66%
2 days, 23:53:01.542080 INFO: Resetting torch num_threads to 80
2 days, 23:53:01.542772 PROGRESS: === Extracted 3208 precursors and 22966 fragments ===
2 days, 23:53:01.543253 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:53:01.543967 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:01.544086 PROGRESS: Total precursors accumulated: 600
2 days, 23:53:01.544178 PROGRESS: Target precursors: 585 (97.50%)
2 days, 23:53:01.544260 PROGRESS: Decoy precursors: 15 (2.50%)
2 days, 23:53:01.544332 PROGRESS: 
2 days, 23:53:01.544397 PROGRESS: Precursor Summary:
2 days, 23:53:01.545596 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   568; 0.001 FDR:   343
2 days, 23:53:01.545716 PROGRESS: 
2 days, 23:53:01.545799 PROGRESS: Protein Summary:
2 days, 23:53:01.547305 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   420; 0.001 FDR:   259
2 days, 23:53:01.547418 PROGRESS: =========================================================================
2 days, 23:53:01.547614 INFO: Target number of precursors reached.
2 days, 23:53:01.554116 INFO: fragments_df: keeping 5000 of 22966 [sum(precursor_idx_mask)=13357 sum(mass_error_mask)=22966 stop_rank=5000
2 days, 23:53:01.557917 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:01.738811 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:01.925897 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:02.175797 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:03.177514 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:53:03.178018 INFO: Using score_cutoff 14.61492380247116 (fac=0.99, q=1)
2 days, 23:53:03.178411 INFO: Updating optimization_manager: fwhm_rt             : 2.5376131534576416 -> 2.536367416381836
2 days, 23:53:03.178511 INFO: Updating optimization_manager: fwhm_mobility       : 0.004099969286471605 -> 0.0041012875735759735
2 days, 23:53:03.178604 INFO: Updating optimization_manager: score_cutoff        : 14.616909767532348 -> 14.61492380247116
2 days, 23:53:03.178693 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:03.179853 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:03.181403 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:03.182328 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:03.184449 INFO: === checking if optimization conditions were reached ===
2 days, 23:53:03.184577 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 23:53:03.186615 INFO: Updating optimization_manager: rt_error            : 8.797602730090658 -> 9.507888671801783
2 days, 23:53:03.186744 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 9.5079.
2 days, 23:53:03.186853 INFO: ==============================================
2 days, 23:53:03.186952 INFO: Starting optimization step 7.
2 days, 23:53:03.187037 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:53:03.187119 INFO: Using python extraction backend
2 days, 23:53:03.187256 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:53:03.187349 INFO: === Search parameters used ===
2 days, 23:53:03.187425 INFO: rt_error       : 9.507888671801783
2 days, 23:53:03.187492 INFO: mobility_error : 0.1
2 days, 23:53:03.187555 INFO: num_candidates : 3
2 days, 23:53:03.187615 INFO: ms1_error      : 15.0
2 days, 23:53:03.187681 INFO: ms2_error      : 15.0
2 days, 23:53:03.187742 INFO: fwhm_rt        : 2.536367416381836
2 days, 23:53:03.187802 INFO: quant_window   : 3
2 days, 23:53:03.187861 INFO: ==============================================
2 days, 23:53:03.188819 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:03.188869 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:03.188921 INFO: FWHM in RT is 2.54 seconds, sigma is 0.42
2 days, 23:53:03.188957 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.22
2 days, 23:53:03.195924 INFO: Starting candidate selection
2 days, 23:53:03.775760 INFO: Starting candidate scoring
2 days, 23:53:03.897278 INFO: Finished candidate processing
2 days, 23:53:03.897394 INFO: Collecting candidate features
2 days, 23:53:03.910375 WARNING: intensity_correlation has 10 NaNs ( 0.31 % out of 3216)
2 days, 23:53:03.910635 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3216)
2 days, 23:53:03.915671 INFO: Collecting fragment features
2 days, 23:53:03.920528 INFO: Finished candidate scoring
2 days, 23:53:03.923280 INFO: performing precursor FDR with 47 features
2 days, 23:53:03.923352 INFO: Decoy channel: -1
2 days, 23:53:03.923386 INFO: competitive: True
2 days, 23:53:03.927458 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:03.929492 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:53:03.929550 WARNING: dropped 9 decoy PSMs due to missing features
2 days, 23:53:03.930780 INFO: Estimating optimal hyperparameters - samples: 2,564, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:53:03.930882 INFO: Using random state 39100 for train-test-split
2 days, 23:53:04.183154 INFO: Test AUC: 0.862
2 days, 23:53:04.183280 INFO: Train AUC: 0.865
2 days, 23:53:04.183316 INFO: AUC difference: 0.36%
2 days, 23:53:04.498703 INFO: Resetting torch num_threads to 80
2 days, 23:53:04.499420 PROGRESS: === Extracted 3216 precursors and 23024 fragments ===
2 days, 23:53:04.499913 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:53:04.500639 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:04.500740 PROGRESS: Total precursors accumulated: 600
2 days, 23:53:04.500812 PROGRESS: Target precursors: 585 (97.50%)
2 days, 23:53:04.500875 PROGRESS: Decoy precursors: 15 (2.50%)
2 days, 23:53:04.500938 PROGRESS: 
2 days, 23:53:04.500994 PROGRESS: Precursor Summary:
2 days, 23:53:04.502386 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   568; 0.001 FDR:   352
2 days, 23:53:04.502501 PROGRESS: 
2 days, 23:53:04.502569 PROGRESS: Protein Summary:
2 days, 23:53:04.504210 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   419; 0.001 FDR:   267
2 days, 23:53:04.504312 PROGRESS: =========================================================================
2 days, 23:53:04.504492 INFO: Target number of precursors reached.
2 days, 23:53:04.513072 INFO: fragments_df: keeping 5000 of 23024 [sum(precursor_idx_mask)=13403 sum(mass_error_mask)=23024 stop_rank=5000
2 days, 23:53:04.517350 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:04.719439 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:04.906060 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:05.104690 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:05.986917 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:53:05.987430 INFO: Using score_cutoff 14.614738222789764 (fac=0.99, q=1)
2 days, 23:53:05.987813 INFO: Updating optimization_manager: fwhm_rt             : 2.536367416381836 -> 2.536367416381836
2 days, 23:53:05.987919 INFO: Updating optimization_manager: fwhm_mobility       : 0.0041012875735759735 -> 0.0041012875735759735
2 days, 23:53:05.987994 INFO: Updating optimization_manager: score_cutoff        : 14.61492380247116 -> 14.614738222789764
2 days, 23:53:05.988069 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:05.989217 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:05.990737 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:05.991590 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:05.993683 INFO: === checking if optimization conditions were reached ===
2 days, 23:53:05.993801 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 23:53:05.995781 INFO: Updating optimization_manager: rt_error            : 9.507888671801783 -> 9.620374394488126
2 days, 23:53:05.995902 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 9.6204.
2 days, 23:53:05.995981 INFO: ==============================================
2 days, 23:53:05.996066 INFO: Starting optimization step 8.
2 days, 23:53:05.996142 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:53:05.996225 INFO: Using python extraction backend
2 days, 23:53:05.996341 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:53:05.996417 INFO: === Search parameters used ===
2 days, 23:53:05.996478 INFO: rt_error       : 9.620374394488126
2 days, 23:53:05.996533 INFO: mobility_error : 0.1
2 days, 23:53:05.996588 INFO: num_candidates : 3
2 days, 23:53:05.996640 INFO: ms1_error      : 15.0
2 days, 23:53:05.996692 INFO: ms2_error      : 15.0
2 days, 23:53:05.996743 INFO: fwhm_rt        : 2.536367416381836
2 days, 23:53:05.996794 INFO: quant_window   : 3
2 days, 23:53:05.996845 INFO: ==============================================
2 days, 23:53:05.997768 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:05.997822 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:05.997876 INFO: FWHM in RT is 2.54 seconds, sigma is 0.42
2 days, 23:53:05.997915 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.22
2 days, 23:53:06.003096 INFO: Starting candidate selection
2 days, 23:53:06.552914 INFO: Starting candidate scoring
2 days, 23:53:06.666551 INFO: Finished candidate processing
2 days, 23:53:06.666682 INFO: Collecting candidate features
2 days, 23:53:06.682978 WARNING: intensity_correlation has 12 NaNs ( 0.37 % out of 3219)
2 days, 23:53:06.683293 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3219)
2 days, 23:53:06.690313 INFO: Collecting fragment features
2 days, 23:53:06.694974 INFO: Finished candidate scoring
2 days, 23:53:06.697356 INFO: performing precursor FDR with 47 features
2 days, 23:53:06.697422 INFO: Decoy channel: -1
2 days, 23:53:06.697480 INFO: competitive: True
2 days, 23:53:06.701601 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:06.703385 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:53:06.703452 WARNING: dropped 11 decoy PSMs due to missing features
2 days, 23:53:06.704694 INFO: Estimating optimal hyperparameters - samples: 2,564, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:53:06.704870 INFO: Using random state 39100 for train-test-split
2 days, 23:53:06.950399 INFO: Test AUC: 0.847
2 days, 23:53:06.950536 INFO: Train AUC: 0.869
2 days, 23:53:06.950584 INFO: AUC difference: 2.53%
2 days, 23:53:07.344857 INFO: Resetting torch num_threads to 80
2 days, 23:53:07.345653 PROGRESS: === Extracted 3219 precursors and 23052 fragments ===
2 days, 23:53:07.346274 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:53:07.347247 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:07.347373 PROGRESS: Total precursors accumulated: 600
2 days, 23:53:07.347481 PROGRESS: Target precursors: 585 (97.50%)
2 days, 23:53:07.347578 PROGRESS: Decoy precursors: 15 (2.50%)
2 days, 23:53:07.347666 PROGRESS: 
2 days, 23:53:07.347754 PROGRESS: Precursor Summary:
2 days, 23:53:07.349671 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   555; 0.001 FDR:   333
2 days, 23:53:07.349809 PROGRESS: 
2 days, 23:53:07.349932 PROGRESS: Protein Summary:
2 days, 23:53:07.352185 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   411; 0.001 FDR:   252
2 days, 23:53:07.352315 PROGRESS: =========================================================================
2 days, 23:53:07.352532 INFO: Target number of precursors reached.
2 days, 23:53:07.362138 INFO: fragments_df: keeping 5000 of 23052 [sum(precursor_idx_mask)=13174 sum(mass_error_mask)=23052 stop_rank=5000
2 days, 23:53:07.366894 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:07.570133 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:07.759903 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:08.030007 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:08.788635 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:53:08.789101 INFO: Using score_cutoff 15.66812041568756 (fac=0.99, q=1)
2 days, 23:53:08.789447 INFO: Updating optimization_manager: fwhm_rt             : 2.536367416381836 -> 2.5384411811828613
2 days, 23:53:08.789537 INFO: Updating optimization_manager: fwhm_mobility       : 0.0041012875735759735 -> 0.004125097766518593
2 days, 23:53:08.789609 INFO: Updating optimization_manager: score_cutoff        : 14.614738222789764 -> 15.66812041568756
2 days, 23:53:08.789677 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:08.790790 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:08.792256 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:08.793087 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:08.795172 INFO: === checking if optimization conditions were reached ===
2 days, 23:53:08.795293 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2 days, 23:53:08.796360 INFO: Updating optimization_manager: rt_error            : 9.620374394488126 -> 8.797602730090658
2 days, 23:53:08.796504 INFO: Updating optimization_manager: classifier_version  : 3 -> 10
2 days, 23:53:08.796623 INFO: Updating optimization_manager: score_cutoff        : 15.66812041568756 -> 14.61492380247116
2 days, 23:53:08.796738 INFO: Updating optimization_manager: fwhm_rt             : 2.5384411811828613 -> 2.536367416381836
2 days, 23:53:08.796850 INFO: Updating optimization_manager: fwhm_mobility       : 0.004125097766518593 -> 0.0041012875735759735
2 days, 23:53:08.796961 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 8.7976 found after 9 searches.
2 days, 23:53:08.797039 INFO: ==============================================
2 days, 23:53:08.797116 PROGRESS: Optimization finished for rt_error.
2 days, 23:53:08.800115 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:08.801007 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:08.802425 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:08.803246 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:08.805253 INFO: Starting optimization step 0.
2 days, 23:53:08.805366 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:53:08.805453 INFO: Using python extraction backend
2 days, 23:53:08.805572 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:53:08.805654 INFO: === Search parameters used ===
2 days, 23:53:08.805710 INFO: rt_error       : 8.797602730090658
2 days, 23:53:08.805773 INFO: mobility_error : 0.1
2 days, 23:53:08.805831 INFO: num_candidates : 3
2 days, 23:53:08.805901 INFO: ms1_error      : 15.0
2 days, 23:53:08.805955 INFO: ms2_error      : 15.0
2 days, 23:53:08.806003 INFO: fwhm_rt        : 2.536367416381836
2 days, 23:53:08.806049 INFO: quant_window   : 3
2 days, 23:53:08.806098 INFO: ==============================================
2 days, 23:53:08.806889 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:08.806939 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:08.806975 INFO: FWHM in RT is 2.54 seconds, sigma is 0.42
2 days, 23:53:08.806998 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.22
2 days, 23:53:08.819869 INFO: Starting candidate selection
2 days, 23:53:09.491662 INFO: Starting candidate scoring
2 days, 23:53:09.609168 INFO: Finished candidate processing
2 days, 23:53:09.609301 INFO: Collecting candidate features
2 days, 23:53:09.623607 WARNING: intensity_correlation has 10 NaNs ( 0.31 % out of 3208)
2 days, 23:53:09.623825 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3208)
2 days, 23:53:09.628720 INFO: Collecting fragment features
2 days, 23:53:09.632757 INFO: Finished candidate scoring
2 days, 23:53:09.634839 INFO: performing precursor FDR with 47 features
2 days, 23:53:09.634892 INFO: Decoy channel: -1
2 days, 23:53:09.634919 INFO: competitive: True
2 days, 23:53:09.638078 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:09.639676 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:53:09.639730 WARNING: dropped 8 decoy PSMs due to missing features
2 days, 23:53:09.640749 INFO: Estimating optimal hyperparameters - samples: 2,557, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:53:09.640833 INFO: Using random state 508069 for train-test-split
2 days, 23:53:09.947724 INFO: Test AUC: 0.847
2 days, 23:53:09.947880 INFO: Train AUC: 0.883
2 days, 23:53:09.947935 INFO: AUC difference: 4.08%
2 days, 23:53:10.315982 INFO: Resetting torch num_threads to 80
2 days, 23:53:10.316563 PROGRESS: === Extracted 3208 precursors and 22970 fragments ===
2 days, 23:53:10.317000 INFO: === FDR correction performed with classifier version 10 ===
2 days, 23:53:10.317642 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:10.317744 PROGRESS: Total precursors accumulated: 600
2 days, 23:53:10.317833 PROGRESS: Target precursors: 585 (97.50%)
2 days, 23:53:10.317922 PROGRESS: Decoy precursors: 15 (2.50%)
2 days, 23:53:10.317996 PROGRESS: 
2 days, 23:53:10.318058 PROGRESS: Precursor Summary:
2 days, 23:53:10.319273 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   570; 0.001 FDR:   380
2 days, 23:53:10.319380 PROGRESS: 
2 days, 23:53:10.319462 PROGRESS: Protein Summary:
2 days, 23:53:10.320827 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   421; 0.001 FDR:   290
2 days, 23:53:10.320933 PROGRESS: =========================================================================
2 days, 23:53:10.321102 INFO: Target number of precursors reached.
2 days, 23:53:10.327433 INFO: fragments_df: keeping 5000 of 22970 [sum(precursor_idx_mask)=13384 sum(mass_error_mask)=22970 stop_rank=5000
2 days, 23:53:10.330947 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:10.521609 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:10.737172 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:11.002702 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:11.750482 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:53:11.750985 INFO: Using score_cutoff 14.615694775772095 (fac=0.99, q=1)
2 days, 23:53:11.751343 INFO: Updating optimization_manager: fwhm_rt             : 2.536367416381836 -> 2.5311601161956787
2 days, 23:53:11.751438 INFO: Updating optimization_manager: fwhm_mobility       : 0.0041012875735759735 -> 0.004080125130712986
2 days, 23:53:11.751523 INFO: Updating optimization_manager: score_cutoff        : 14.61492380247116 -> 14.615694775772095
2 days, 23:53:11.751605 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:11.752759 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:11.754373 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:11.755449 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:11.757990 INFO: === checking if optimization conditions were reached ===
2 days, 23:53:11.758145 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:53:11.760296 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06341358175440351
2 days, 23:53:11.760423 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0634.
2 days, 23:53:11.760530 INFO: ==============================================
2 days, 23:53:11.760662 INFO: Starting optimization step 1.
2 days, 23:53:11.760769 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:53:11.760868 INFO: Using python extraction backend
2 days, 23:53:11.761032 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:53:11.761150 INFO: === Search parameters used ===
2 days, 23:53:11.761245 INFO: rt_error       : 8.797602730090658
2 days, 23:53:11.761325 INFO: mobility_error : 0.06341358175440351
2 days, 23:53:11.761402 INFO: num_candidates : 3
2 days, 23:53:11.761513 INFO: ms1_error      : 15.0
2 days, 23:53:11.761600 INFO: ms2_error      : 15.0
2 days, 23:53:11.761684 INFO: fwhm_rt        : 2.5311601161956787
2 days, 23:53:11.761770 INFO: quant_window   : 3
2 days, 23:53:11.761854 INFO: ==============================================
2 days, 23:53:11.763202 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:11.763274 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:11.763419 INFO: FWHM in RT is 2.53 seconds, sigma is 0.42
2 days, 23:53:11.763468 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.21
2 days, 23:53:11.778051 INFO: Starting candidate selection
2 days, 23:53:12.319329 INFO: Starting candidate scoring
2 days, 23:53:12.422170 INFO: Finished candidate processing
2 days, 23:53:12.422306 INFO: Collecting candidate features
2 days, 23:53:12.438855 WARNING: intensity_correlation has 15 NaNs ( 0.47 % out of 3201)
2 days, 23:53:12.439198 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3201)
2 days, 23:53:12.447104 INFO: Collecting fragment features
2 days, 23:53:12.452705 INFO: Finished candidate scoring
2 days, 23:53:12.456024 INFO: performing precursor FDR with 47 features
2 days, 23:53:12.456108 INFO: Decoy channel: -1
2 days, 23:53:12.456146 INFO: competitive: True
2 days, 23:53:12.461135 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:12.463482 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:53:12.463552 WARNING: dropped 13 decoy PSMs due to missing features
2 days, 23:53:12.465034 INFO: Estimating optimal hyperparameters - samples: 2,548, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:53:12.465153 INFO: Using random state 508069 for train-test-split
2 days, 23:53:12.779385 INFO: Test AUC: 0.851
2 days, 23:53:12.779529 INFO: Train AUC: 0.882
2 days, 23:53:12.779582 INFO: AUC difference: 3.54%
2 days, 23:53:13.126409 INFO: Resetting torch num_threads to 80
2 days, 23:53:13.127170 PROGRESS: === Extracted 3201 precursors and 22750 fragments ===
2 days, 23:53:13.127733 INFO: === FDR correction performed with classifier version 10 ===
2 days, 23:53:13.128559 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:13.128670 PROGRESS: Total precursors accumulated: 600
2 days, 23:53:13.128747 PROGRESS: Target precursors: 586 (97.67%)
2 days, 23:53:13.128816 PROGRESS: Decoy precursors: 14 (2.33%)
2 days, 23:53:13.128881 PROGRESS: 
2 days, 23:53:13.128942 PROGRESS: Precursor Summary:
2 days, 23:53:13.130232 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   565; 0.001 FDR:   403
2 days, 23:53:13.130357 PROGRESS: 
2 days, 23:53:13.130443 PROGRESS: Protein Summary:
2 days, 23:53:13.131858 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   417; 0.001 FDR:   301
2 days, 23:53:13.131971 PROGRESS: =========================================================================
2 days, 23:53:13.132156 INFO: Target number of precursors reached.
2 days, 23:53:13.138287 INFO: fragments_df: keeping 5000 of 22750 [sum(precursor_idx_mask)=13283 sum(mass_error_mask)=22750 stop_rank=5000
2 days, 23:53:13.141713 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:13.363881 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:13.548141 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:13.771142 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:14.639300 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:53:14.639846 INFO: Using score_cutoff 14.612559823608397 (fac=0.99, q=1)
2 days, 23:53:14.640290 INFO: Updating optimization_manager: fwhm_rt             : 2.5311601161956787 -> 2.537075996398926
2 days, 23:53:14.640412 INFO: Updating optimization_manager: fwhm_mobility       : 0.004080125130712986 -> 0.004097938537597656
2 days, 23:53:14.640502 INFO: Updating optimization_manager: score_cutoff        : 14.615694775772095 -> 14.612559823608397
2 days, 23:53:14.640599 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:14.641813 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:14.643443 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:14.644365 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:14.646735 INFO: === checking if optimization conditions were reached ===
2 days, 23:53:14.646880 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:53:14.648601 INFO: Updating optimization_manager: mobility_error      : 0.06341358175440351 -> 0.049419450983915696
2 days, 23:53:14.648720 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0494.
2 days, 23:53:14.648800 INFO: ==============================================
2 days, 23:53:14.648884 INFO: Starting optimization step 2.
2 days, 23:53:14.648957 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:53:14.649030 INFO: Using python extraction backend
2 days, 23:53:14.649145 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:53:14.649227 INFO: === Search parameters used ===
2 days, 23:53:14.649295 INFO: rt_error       : 8.797602730090658
2 days, 23:53:14.649350 INFO: mobility_error : 0.049419450983915696
2 days, 23:53:14.649403 INFO: num_candidates : 3
2 days, 23:53:14.649456 INFO: ms1_error      : 15.0
2 days, 23:53:14.649510 INFO: ms2_error      : 15.0
2 days, 23:53:14.649562 INFO: fwhm_rt        : 2.537075996398926
2 days, 23:53:14.649613 INFO: quant_window   : 3
2 days, 23:53:14.649665 INFO: ==============================================
2 days, 23:53:14.650692 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:14.650753 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:14.650795 INFO: FWHM in RT is 2.54 seconds, sigma is 0.42
2 days, 23:53:14.650823 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.22
2 days, 23:53:14.663198 INFO: Starting candidate selection
2 days, 23:53:15.201084 INFO: Starting candidate scoring
2 days, 23:53:15.311567 INFO: Finished candidate processing
2 days, 23:53:15.311705 INFO: Collecting candidate features
2 days, 23:53:15.327868 WARNING: intensity_correlation has 17 NaNs ( 0.54 % out of 3159)
2 days, 23:53:15.328163 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3159)
2 days, 23:53:15.335329 INFO: Collecting fragment features
2 days, 23:53:15.339759 INFO: Finished candidate scoring
2 days, 23:53:15.341849 INFO: performing precursor FDR with 47 features
2 days, 23:53:15.341930 INFO: Decoy channel: -1
2 days, 23:53:15.341959 INFO: competitive: True
2 days, 23:53:15.346170 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:15.347764 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:53:15.347813 WARNING: dropped 14 decoy PSMs due to missing features
2 days, 23:53:15.347852 WARNING: FDR calculation for 1658 target and 1484 decoy PSMs
2 days, 23:53:15.347875 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:53:15.348958 INFO: Estimating optimal hyperparameters - samples: 2,513, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:53:15.349045 INFO: Using random state 508069 for train-test-split
2 days, 23:53:15.677877 INFO: Test AUC: 0.885
2 days, 23:53:15.678011 INFO: Train AUC: 0.877
2 days, 23:53:15.678067 INFO: AUC difference: 0.91%
2 days, 23:53:15.945121 INFO: Resetting torch num_threads to 80
2 days, 23:53:15.945634 PROGRESS: === Extracted 3159 precursors and 22418 fragments ===
2 days, 23:53:15.946066 INFO: === FDR correction performed with classifier version 10 ===
2 days, 23:53:15.946676 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:15.946766 PROGRESS: Total precursors accumulated: 599
2 days, 23:53:15.946829 PROGRESS: Target precursors: 585 (97.66%)
2 days, 23:53:15.946883 PROGRESS: Decoy precursors: 14 (2.34%)
2 days, 23:53:15.946933 PROGRESS: 
2 days, 23:53:15.946981 PROGRESS: Precursor Summary:
2 days, 23:53:15.948086 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   570; 0.001 FDR:   352
2 days, 23:53:15.948183 PROGRESS: 
2 days, 23:53:15.948243 PROGRESS: Protein Summary:
2 days, 23:53:15.949586 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   422; 0.001 FDR:   265
2 days, 23:53:15.949690 PROGRESS: =========================================================================
2 days, 23:53:15.949847 INFO: Target number of precursors reached.
2 days, 23:53:15.956074 INFO: fragments_df: keeping 5000 of 22418 [sum(precursor_idx_mask)=13299 sum(mass_error_mask)=22418 stop_rank=5000
2 days, 23:53:15.959497 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:16.167220 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:16.393130 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:16.606116 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:17.412519 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:53:17.413129 INFO: Using score_cutoff 14.513644474983215 (fac=0.99, q=1)
2 days, 23:53:17.413608 INFO: Updating optimization_manager: fwhm_rt             : 2.537075996398926 -> 2.5341663360595703
2 days, 23:53:17.413744 INFO: Updating optimization_manager: fwhm_mobility       : 0.004097938537597656 -> 0.0040692538022994995
2 days, 23:53:17.413846 INFO: Updating optimization_manager: score_cutoff        : 14.612559823608397 -> 14.513644474983215
2 days, 23:53:17.413969 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:17.415558 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:17.417460 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:17.418648 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:17.421231 INFO: === checking if optimization conditions were reached ===
2 days, 23:53:17.421377 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:53:17.422527 INFO: Updating optimization_manager: mobility_error      : 0.049419450983915696 -> 0.049419450983915696
2 days, 23:53:17.422702 INFO: Updating optimization_manager: classifier_version  : 10 -> 15
2 days, 23:53:17.422857 INFO: Updating optimization_manager: score_cutoff        : 14.513644474983215 -> 14.513644474983215
2 days, 23:53:17.423031 INFO: Updating optimization_manager: fwhm_rt             : 2.5341663360595703 -> 2.5341663360595703
2 days, 23:53:17.423214 INFO: Updating optimization_manager: fwhm_mobility       : 0.0040692538022994995 -> 0.0040692538022994995
2 days, 23:53:17.423377 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0494 found after 3 searches.
2 days, 23:53:17.423485 INFO: ==============================================
2 days, 23:53:17.423606 PROGRESS: Optimization finished for mobility_error.
2 days, 23:53:17.428073 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:17.429309 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:17.431105 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:17.432266 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:17.434846 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:53:17.434993 PROGRESS: ==============================================
2 days, 23:53:17.435102 PROGRESS: ms2_error      : 15.0000
2 days, 23:53:17.435202 PROGRESS: ms1_error      : 15.0000
2 days, 23:53:17.435300 PROGRESS: rt_error       : 8.7976
2 days, 23:53:17.435395 PROGRESS: mobility_error : 0.0494
2 days, 23:53:17.435487 PROGRESS: ==============================================
2 days, 23:53:17.436317 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:17.440770 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:17.458836 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:17.463598 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:17.506361 INFO: Using python extraction backend
2 days, 23:53:17.506710 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:53:17.506819 INFO: === Search parameters used ===
2 days, 23:53:17.506892 INFO: rt_error       : 8.797602730090658
2 days, 23:53:17.506958 INFO: mobility_error : 0.049419450983915696
2 days, 23:53:17.507021 INFO: num_candidates : 3
2 days, 23:53:17.507083 INFO: ms1_error      : 15.0
2 days, 23:53:17.507143 INFO: ms2_error      : 15.0
2 days, 23:53:17.507215 INFO: fwhm_rt        : 2.5341663360595703
2 days, 23:53:17.507277 INFO: quant_window   : 3
2 days, 23:53:17.507335 INFO: ==============================================
2 days, 23:53:17.513539 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:17.513644 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:17.513695 INFO: FWHM in RT is 2.53 seconds, sigma is 0.42
2 days, 23:53:17.513726 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.21
2 days, 23:53:17.538435 INFO: Starting candidate selection
2 days, 23:53:19.131377 INFO: Removed 19281 precursors with score below cutoff 14.513644474983215
2 days, 23:53:19.489133 INFO: Starting candidate scoring
2 days, 23:53:20.470479 INFO: Finished candidate processing
2 days, 23:53:20.470624 INFO: Collecting candidate features
2 days, 23:53:20.576772 WARNING: intensity_correlation has 162 NaNs ( 0.28 % out of 57373)
2 days, 23:53:20.577074 WARNING: height_correlation has 4 NaNs ( 0.01 % out of 57373)
2 days, 23:53:20.583406 INFO: Collecting fragment features
2 days, 23:53:20.615192 INFO: Finished candidate scoring
2 days, 23:53:20.647446 INFO: === Performing FDR correction with classifier version 15 ===
2 days, 23:53:20.647865 INFO: performing precursor FDR with 47 features
2 days, 23:53:20.647908 INFO: Decoy channel: -1
2 days, 23:53:20.647944 INFO: competitive: True
2 days, 23:53:20.664848 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:20.674279 WARNING: dropped 34 target PSMs due to missing features
2 days, 23:53:20.674408 WARNING: dropped 131 decoy PSMs due to missing features
2 days, 23:53:20.674474 WARNING: FDR calculation for 34563 target and 22645 decoy PSMs
2 days, 23:53:20.674511 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:53:20.684123 INFO: Estimating optimal hyperparameters - samples: 45,766, batch_size: 187, learning_rate: 2.14e-04
2 days, 23:53:20.684402 INFO: Using random state 538701 for train-test-split
2 days, 23:53:25.280440 INFO: Test AUC: 0.898
2 days, 23:53:25.280594 INFO: Train AUC: 0.903
2 days, 23:53:25.280644 INFO: AUC difference: 0.62%
2 days, 23:53:25.673117 INFO: Resetting torch num_threads to 80
2 days, 23:53:25.677145 INFO: Removing fragments below FDR threshold
2 days, 23:53:25.690302 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:25.690559 PROGRESS: Total precursors accumulated: 13,044
2 days, 23:53:25.690674 PROGRESS: Target precursors: 12,915 (99.01%)
2 days, 23:53:25.690773 PROGRESS: Decoy precursors: 129 (0.99%)
2 days, 23:53:25.690861 PROGRESS: 
2 days, 23:53:25.690961 PROGRESS: Precursor Summary:
2 days, 23:53:25.698266 PROGRESS: Channel   0:	 0.050 FDR: 12,915; 0.010 FDR: 12,915; 0.001 FDR: 11,906
2 days, 23:53:25.698477 PROGRESS: 
2 days, 23:53:25.698581 PROGRESS: Protein Summary:
2 days, 23:53:25.708044 PROGRESS: Channel   0:	 0.050 FDR: 1,682; 0.010 FDR: 1,682; 0.001 FDR: 1,667
2 days, 23:53:25.708239 PROGRESS: =========================================================================
2 days, 23:53:25.709654 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R6/psm.parquet
2 days, 23:53:25.779585 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R6/frag.parquet
2 days, 23:53:25.827965 INFO: Finished workflow for A9_G_DIA_nLC_tTOF_R6
2 days, 23:53:25.831998 PROGRESS: Loading raw file 7/12: B9_G_DIA_nLC_tTOF_R1 
2 days, 23:53:25.832104 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:53:25.832170 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R1/figures
2 days, 23:53:25.832345 INFO: Initializing TimingManager
2 days, 23:53:25.832780 INFO: Initializing RawFileManager
2 days, 23:53:25.832902 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:25.832962 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:25.833005 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:26.072565 INFO: Reading 22,622 frames with 343,415,986 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:29.977759 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d...
2 days, 23:53:29.978994 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:29.981176 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:29.981440 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:29.982009 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:29.983733 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:30.009903 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:30.014189 INFO: Indexing quadrupole dimension
2 days, 23:53:30.150401 INFO: Transposing detector events
2 days, 23:53:31.821349 INFO: Finished transposing data
2 days, 23:53:31.821509 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
2 days, 23:53:31.821915 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:53:31.821981 INFO: RT duration (sec)   : 2399.9
2 days, 23:53:31.822025 INFO: RT duration (min)   : 40.0
2 days, 23:53:31.822062 INFO: Cycle len (scans)   : 12
2 days, 23:53:31.822097 INFO: Cycle len (sec)     : 1.27
2 days, 23:53:31.822132 INFO: Number of cycles    : 1885
2 days, 23:53:31.822169 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:53:31.822214 INFO: Creating DIA data object took: 5.989312171936035
2 days, 23:53:31.829598 INFO: Initializing CalibrationManager
2 days, 23:53:31.829857 INFO: Setting up calibration estimators ..
2 days, 23:53:31.829978 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:53:31.830062 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:53:31.830143 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:53:31.830213 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:53:31.830283 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:53:31.830356 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:53:31.830422 INFO: Done setting up calibration estimators.
2 days, 23:53:31.830536 INFO: Initializing OptimizationManager
2 days, 23:53:31.830646 INFO: initial parameter: ms1_error = 30
2 days, 23:53:31.830706 INFO: initial parameter: ms2_error = 30
2 days, 23:53:31.830765 INFO: initial parameter: rt_error = 1199.951526
2 days, 23:53:31.830822 INFO: initial parameter: mobility_error = 0.1
2 days, 23:53:31.830876 INFO: initial parameter: num_candidates = 1
2 days, 23:53:31.830930 INFO: initial parameter: fwhm_rt = 5
2 days, 23:53:31.830986 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:53:31.831043 INFO: initial parameter: score_cutoff = 0
2 days, 23:53:31.831097 INFO: initial parameter: classifier_version = -1
2 days, 23:53:31.831185 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R1
2 days, 23:53:31.831375 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:53:31.831414 INFO: Initializing FDRManager
2 days, 23:53:31.831455 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:53:31.839332 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:53:31.844546 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:53:31.844990 INFO: Updating optimization_manager: rt_error            : 1199.951526 -> 1199.951526
2 days, 23:53:31.845126 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:53:31.845369 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:53:31.845478 PROGRESS: Starting initial search for precursors.
2 days, 23:53:31.845585 INFO: Starting optimization step 0.
2 days, 23:53:31.845672 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:53:31.845753 INFO: Using python extraction backend
2 days, 23:53:31.845883 PROGRESS: Extracting batch of 399 precursors
2 days, 23:53:31.845969 INFO: === Search parameters used ===
2 days, 23:53:31.846035 INFO: rt_error       : 1199.951526
2 days, 23:53:31.846097 INFO: mobility_error : 0.1
2 days, 23:53:31.846164 INFO: num_candidates : 1
2 days, 23:53:31.846231 INFO: ms1_error      : 30
2 days, 23:53:31.846292 INFO: ms2_error      : 30
2 days, 23:53:31.846353 INFO: fwhm_rt        : 5
2 days, 23:53:31.846414 INFO: quant_window   : 3
2 days, 23:53:31.846474 INFO: ==============================================
2 days, 23:53:31.847320 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:31.847372 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:31.847413 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:53:31.847448 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:53:31.865026 INFO: Starting candidate selection
2 days, 23:53:35.432499 INFO: Starting candidate scoring
2 days, 23:53:35.476975 INFO: Finished candidate processing
2 days, 23:53:35.477113 INFO: Collecting candidate features
2 days, 23:53:35.495877 INFO: Collecting fragment features
2 days, 23:53:35.500003 INFO: Finished candidate scoring
2 days, 23:53:35.501368 INFO: performing precursor FDR with 47 features
2 days, 23:53:35.501445 INFO: Decoy channel: -1
2 days, 23:53:35.501487 INFO: competitive: True
2 days, 23:53:35.503499 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:35.506194 INFO: Estimating optimal hyperparameters - samples: 318, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:53:35.507380 INFO: Using random state 7451 for train-test-split
2 days, 23:53:35.532683 INFO: Test AUC: 0.520
2 days, 23:53:35.532892 INFO: Train AUC: 0.513
2 days, 23:53:35.532951 INFO: AUC difference: 1.28%
2 days, 23:53:35.902852 INFO: Resetting torch num_threads to 80
2 days, 23:53:35.903394 PROGRESS: === Extracted 398 precursors and 3624 fragments ===
2 days, 23:53:35.903852 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:53:35.904459 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:35.904571 PROGRESS: Total precursors accumulated: 200
2 days, 23:53:35.904664 PROGRESS: Target precursors: 107 (53.50%)
2 days, 23:53:35.904745 PROGRESS: Decoy precursors: 93 (46.50%)
2 days, 23:53:35.904818 PROGRESS: 
2 days, 23:53:35.904886 PROGRESS: Precursor Summary:
2 days, 23:53:35.905857 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 23:53:35.905984 PROGRESS: 
2 days, 23:53:35.906070 PROGRESS: Protein Summary:
2 days, 23:53:35.907144 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 23:53:35.907251 PROGRESS: =========================================================================
2 days, 23:53:35.907403 INFO: Target number of precursors not reached yet.
2 days, 23:53:35.910540 INFO: Starting optimization step 1.
2 days, 23:53:35.910664 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:53:35.910768 INFO: Using python extraction backend
2 days, 23:53:35.910909 PROGRESS: Extracting batch of 798 precursors
2 days, 23:53:35.911002 INFO: === Search parameters used ===
2 days, 23:53:35.911082 INFO: rt_error       : 1199.951526
2 days, 23:53:35.911152 INFO: mobility_error : 0.1
2 days, 23:53:35.911216 INFO: num_candidates : 1
2 days, 23:53:35.911280 INFO: ms1_error      : 30
2 days, 23:53:35.911342 INFO: ms2_error      : 30
2 days, 23:53:35.911402 INFO: fwhm_rt        : 5
2 days, 23:53:35.911464 INFO: quant_window   : 3
2 days, 23:53:35.911528 INFO: ==============================================
2 days, 23:53:35.912214 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:35.912267 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:35.912308 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:53:35.912343 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:53:35.918844 INFO: Starting candidate selection
2 days, 23:53:42.069918 INFO: Starting candidate scoring
2 days, 23:53:42.140685 INFO: Finished candidate processing
2 days, 23:53:42.140824 INFO: Collecting candidate features
2 days, 23:53:42.159885 INFO: Collecting fragment features
2 days, 23:53:42.164579 INFO: Finished candidate scoring
2 days, 23:53:42.168171 INFO: performing precursor FDR with 47 features
2 days, 23:53:42.168278 INFO: Decoy channel: -1
2 days, 23:53:42.168355 INFO: competitive: True
2 days, 23:53:42.173509 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:42.176551 INFO: Estimating optimal hyperparameters - samples: 956, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:53:42.176762 INFO: Using random state 143593 for train-test-split
2 days, 23:53:42.270198 INFO: Test AUC: 0.753
2 days, 23:53:42.270316 INFO: Train AUC: 0.742
2 days, 23:53:42.270363 INFO: AUC difference: 1.39%
2 days, 23:53:42.607373 INFO: Resetting torch num_threads to 80
2 days, 23:53:42.609199 PROGRESS: === Extracted 1196 precursors and 11176 fragments ===
2 days, 23:53:42.609773 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:53:42.610648 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:42.610775 PROGRESS: Total precursors accumulated: 600
2 days, 23:53:42.610867 PROGRESS: Target precursors: 443 (73.83%)
2 days, 23:53:42.610959 PROGRESS: Decoy precursors: 157 (26.17%)
2 days, 23:53:42.611037 PROGRESS: 
2 days, 23:53:42.611112 PROGRESS: Precursor Summary:
2 days, 23:53:42.612716 PROGRESS: Channel   0:	 0.050 FDR:   182; 0.010 FDR:    91; 0.001 FDR:    91
2 days, 23:53:42.612837 PROGRESS: 
2 days, 23:53:42.612921 PROGRESS: Protein Summary:
2 days, 23:53:42.614524 PROGRESS: Channel   0:	 0.050 FDR:   133; 0.010 FDR:    63; 0.001 FDR:    63
2 days, 23:53:42.614645 PROGRESS: =========================================================================
2 days, 23:53:42.614824 INFO: Target number of precursors not reached yet.
2 days, 23:53:42.618607 INFO: Starting optimization step 2.
2 days, 23:53:42.618726 PROGRESS: === Extracting elution groups 600 to 1400 ===
2 days, 23:53:42.618807 INFO: Using python extraction backend
2 days, 23:53:42.618914 PROGRESS: Extracting batch of 1599 precursors
2 days, 23:53:42.618989 INFO: === Search parameters used ===
2 days, 23:53:42.619041 INFO: rt_error       : 1199.951526
2 days, 23:53:42.619088 INFO: mobility_error : 0.1
2 days, 23:53:42.619134 INFO: num_candidates : 1
2 days, 23:53:42.619178 INFO: ms1_error      : 30
2 days, 23:53:42.619221 INFO: ms2_error      : 30
2 days, 23:53:42.619263 INFO: fwhm_rt        : 5
2 days, 23:53:42.619306 INFO: quant_window   : 3
2 days, 23:53:42.619348 INFO: ==============================================
2 days, 23:53:42.620219 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:42.620269 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:42.620301 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:53:42.620322 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:53:42.638424 INFO: Starting candidate selection
2 days, 23:53:52.704122 INFO: Starting candidate scoring
2 days, 23:53:52.781947 INFO: Finished candidate processing
2 days, 23:53:52.782088 INFO: Collecting candidate features
2 days, 23:53:52.804685 INFO: Collecting fragment features
2 days, 23:53:52.809597 INFO: Finished candidate scoring
2 days, 23:53:52.814296 INFO: performing precursor FDR with 47 features
2 days, 23:53:52.814404 INFO: Decoy channel: -1
2 days, 23:53:52.814445 INFO: competitive: True
2 days, 23:53:52.819141 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:53:52.822475 INFO: Estimating optimal hyperparameters - samples: 2,235, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:53:52.822599 INFO: Using random state 573824 for train-test-split
2 days, 23:53:53.035225 INFO: Test AUC: 0.783
2 days, 23:53:53.035333 INFO: Train AUC: 0.780
2 days, 23:53:53.035369 INFO: AUC difference: 0.36%
2 days, 23:53:53.412778 INFO: Resetting torch num_threads to 80
2 days, 23:53:53.415214 PROGRESS: === Extracted 2794 precursors and 26437 fragments ===
2 days, 23:53:53.415843 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:53:53.416865 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:53:53.417003 PROGRESS: Total precursors accumulated: 1,400
2 days, 23:53:53.417097 PROGRESS: Target precursors: 1,092 (78.00%)
2 days, 23:53:53.417186 PROGRESS: Decoy precursors: 308 (22.00%)
2 days, 23:53:53.417272 PROGRESS: 
2 days, 23:53:53.417351 PROGRESS: Precursor Summary:
2 days, 23:53:53.419250 PROGRESS: Channel   0:	 0.050 FDR:   701; 0.010 FDR:   597; 0.001 FDR:   502
2 days, 23:53:53.419390 PROGRESS: 
2 days, 23:53:53.419478 PROGRESS: Protein Summary:
2 days, 23:53:53.421319 PROGRESS: Channel   0:	 0.050 FDR:   399; 0.010 FDR:   337; 0.001 FDR:   285
2 days, 23:53:53.421448 PROGRESS: =========================================================================
2 days, 23:53:53.421633 INFO: Target number of precursors reached.
2 days, 23:53:53.427556 INFO: fragments_df: keeping 4988 of 26437 [sum(precursor_idx_mask)=6240 sum(mass_error_mask)=26437 stop_rank=4988
2 days, 23:53:53.431650 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:53.621898 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:53.821075 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:54.027520 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:54.899693 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:53:54.900148 INFO: Using score_cutoff 33.7325111251831 (fac=0.99, q=1)
2 days, 23:53:54.900545 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.818964719772339
2 days, 23:53:54.900649 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007067431230098009
2 days, 23:53:54.900725 INFO: Updating optimization_manager: score_cutoff        : 0 -> 33.7325111251831
2 days, 23:53:54.900801 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:53:54.902017 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:53:54.903566 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:53:54.904552 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:53:54.906925 INFO: Updating optimization_manager: classifier_version  : -1 -> 2
2 days, 23:53:54.907034 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:53:54.907121 INFO: Starting optimization step 3.
2 days, 23:53:54.907187 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:53:54.907251 INFO: Using python extraction backend
2 days, 23:53:54.907352 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:53:54.907421 INFO: === Search parameters used ===
2 days, 23:53:54.907493 INFO: rt_error       : 1199.951526
2 days, 23:53:54.907578 INFO: mobility_error : 0.1
2 days, 23:53:54.907640 INFO: num_candidates : 3
2 days, 23:53:54.907699 INFO: ms1_error      : 30
2 days, 23:53:54.907757 INFO: ms2_error      : 30
2 days, 23:53:54.907823 INFO: fwhm_rt        : 2.818964719772339
2 days, 23:53:54.907882 INFO: quant_window   : 3
2 days, 23:53:54.907942 INFO: ==============================================
2 days, 23:53:54.909073 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:53:54.909136 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:53:54.909195 INFO: FWHM in RT is 2.82 seconds, sigma is 0.47
2 days, 23:53:54.909240 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.83
2 days, 23:53:54.941220 INFO: Starting candidate selection
2 days, 23:54:04.116086 INFO: Starting candidate scoring
2 days, 23:54:04.264751 INFO: Finished candidate processing
2 days, 23:54:04.264881 INFO: Collecting candidate features
2 days, 23:54:04.288250 INFO: Collecting fragment features
2 days, 23:54:04.294786 INFO: Finished candidate scoring
2 days, 23:54:04.298009 INFO: performing precursor FDR with 47 features
2 days, 23:54:04.298099 INFO: Decoy channel: -1
2 days, 23:54:04.298149 INFO: competitive: True
2 days, 23:54:04.303114 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:04.306425 INFO: Estimating optimal hyperparameters - samples: 2,742, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:04.306551 INFO: Using random state 372269 for train-test-split
2 days, 23:54:04.566020 INFO: Test AUC: 0.680
2 days, 23:54:04.566134 INFO: Train AUC: 0.707
2 days, 23:54:04.566177 INFO: AUC difference: 3.88%
2 days, 23:54:04.843896 INFO: Resetting torch num_threads to 80
2 days, 23:54:04.844670 PROGRESS: === Extracted 3428 precursors and 31004 fragments ===
2 days, 23:54:04.845289 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:54:04.846245 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:04.846392 PROGRESS: Total precursors accumulated: 600
2 days, 23:54:04.846504 PROGRESS: Target precursors: 494 (82.33%)
2 days, 23:54:04.846608 PROGRESS: Decoy precursors: 106 (17.67%)
2 days, 23:54:04.846703 PROGRESS: 
2 days, 23:54:04.846794 PROGRESS: Precursor Summary:
2 days, 23:54:04.848647 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   317; 0.001 FDR:   251
2 days, 23:54:04.848781 PROGRESS: 
2 days, 23:54:04.848882 PROGRESS: Protein Summary:
2 days, 23:54:04.850900 PROGRESS: Channel   0:	 0.050 FDR:   264; 0.010 FDR:   238; 0.001 FDR:   183
2 days, 23:54:04.851035 PROGRESS: =========================================================================
2 days, 23:54:04.851316 INFO: Target number of precursors reached.
2 days, 23:54:04.861598 INFO: fragments_df: keeping 5000 of 31004 [sum(precursor_idx_mask)=8506 sum(mass_error_mask)=31004 stop_rank=5000
2 days, 23:54:04.868859 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:05.038059 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:05.196861 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:05.387189 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:06.197507 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:06.197997 INFO: Using score_cutoff 31.222523426055908 (fac=0.99, q=1)
2 days, 23:54:06.198348 INFO: Updating optimization_manager: fwhm_rt             : 2.818964719772339 -> 2.7709884643554688
2 days, 23:54:06.198449 INFO: Updating optimization_manager: fwhm_mobility       : 0.007067431230098009 -> 0.006354751996695995
2 days, 23:54:06.198527 INFO: Updating optimization_manager: score_cutoff        : 33.7325111251831 -> 31.222523426055908
2 days, 23:54:06.198613 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:06.199721 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:06.201126 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:06.201969 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:06.204076 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:06.205770 INFO: Updating optimization_manager: ms2_error           : 30 -> 18.36241347679274
2 days, 23:54:06.205905 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:54:06.206002 PROGRESS: ❌ ms2_error      : 18.3624 > 15.0000 or insufficient steps taken.
2 days, 23:54:06.207159 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:54:06.207277 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:54:06.207369 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:54:06.207455 INFO: ==============================================
2 days, 23:54:06.207559 INFO: Starting optimization step 4.
2 days, 23:54:06.207648 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:06.207733 INFO: Using python extraction backend
2 days, 23:54:06.207865 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:06.207960 INFO: === Search parameters used ===
2 days, 23:54:06.208034 INFO: rt_error       : 1199.951526
2 days, 23:54:06.208103 INFO: mobility_error : 0.1
2 days, 23:54:06.208169 INFO: num_candidates : 3
2 days, 23:54:06.208232 INFO: ms1_error      : 15.0
2 days, 23:54:06.208296 INFO: ms2_error      : 18.36241347679274
2 days, 23:54:06.208363 INFO: fwhm_rt        : 2.7709884643554688
2 days, 23:54:06.208430 INFO: quant_window   : 3
2 days, 23:54:06.208493 INFO: ==============================================
2 days, 23:54:06.209349 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:06.209402 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:06.209455 INFO: FWHM in RT is 2.77 seconds, sigma is 0.46
2 days, 23:54:06.209491 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.45
2 days, 23:54:06.215341 INFO: Starting candidate selection
2 days, 23:54:15.048114 INFO: Starting candidate scoring
2 days, 23:54:15.145224 INFO: Finished candidate processing
2 days, 23:54:15.145339 INFO: Collecting candidate features
2 days, 23:54:15.163260 INFO: Collecting fragment features
2 days, 23:54:15.168308 INFO: Finished candidate scoring
2 days, 23:54:15.170812 INFO: performing precursor FDR with 47 features
2 days, 23:54:15.170962 INFO: Decoy channel: -1
2 days, 23:54:15.171042 INFO: competitive: True
2 days, 23:54:15.175085 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:15.177960 INFO: Estimating optimal hyperparameters - samples: 2,726, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:15.178147 INFO: Using random state 141155 for train-test-split
2 days, 23:54:15.507127 INFO: Test AUC: 0.746
2 days, 23:54:15.507257 INFO: Train AUC: 0.736
2 days, 23:54:15.507295 INFO: AUC difference: 1.42%
2 days, 23:54:15.843755 INFO: Resetting torch num_threads to 80
2 days, 23:54:15.844309 PROGRESS: === Extracted 3408 precursors and 28004 fragments ===
2 days, 23:54:15.844744 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:54:15.845367 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:15.845460 PROGRESS: Total precursors accumulated: 600
2 days, 23:54:15.845526 PROGRESS: Target precursors: 518 (86.33%)
2 days, 23:54:15.845587 PROGRESS: Decoy precursors: 82 (13.67%)
2 days, 23:54:15.845643 PROGRESS: 
2 days, 23:54:15.845693 PROGRESS: Precursor Summary:
2 days, 23:54:15.846828 PROGRESS: Channel   0:	 0.050 FDR:   421; 0.010 FDR:   379; 0.001 FDR:   304
2 days, 23:54:15.846936 PROGRESS: 
2 days, 23:54:15.847001 PROGRESS: Protein Summary:
2 days, 23:54:15.848290 PROGRESS: Channel   0:	 0.050 FDR:   314; 0.010 FDR:   284; 0.001 FDR:   226
2 days, 23:54:15.848387 PROGRESS: =========================================================================
2 days, 23:54:15.848533 INFO: Target number of precursors reached.
2 days, 23:54:15.854638 INFO: fragments_df: keeping 5000 of 28004 [sum(precursor_idx_mask)=9736 sum(mass_error_mask)=28004 stop_rank=5000
2 days, 23:54:15.857916 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:16.015974 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:16.224002 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:16.474189 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:17.234893 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:17.235367 INFO: Using score_cutoff 27.455223679733276 (fac=0.99, q=1)
2 days, 23:54:17.235726 INFO: Updating optimization_manager: fwhm_rt             : 2.7709884643554688 -> 2.610288381576538
2 days, 23:54:17.235814 INFO: Updating optimization_manager: fwhm_mobility       : 0.006354751996695995 -> 0.0054498715326189995
2 days, 23:54:17.235874 INFO: Updating optimization_manager: score_cutoff        : 31.222523426055908 -> 27.455223679733276
2 days, 23:54:17.235938 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:17.237085 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:17.238599 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:17.239640 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:17.241877 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:17.243667 INFO: Updating optimization_manager: ms2_error           : 18.36241347679274 -> 15.0
2 days, 23:54:17.243802 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2 days, 23:54:17.243897 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:54:17.245029 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:54:17.245158 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
2 days, 23:54:17.245269 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:54:17.245383 INFO: ==============================================
2 days, 23:54:17.245487 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:54:17.249110 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:17.250172 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:17.251616 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:17.252617 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:17.254848 INFO: Starting optimization step 0.
2 days, 23:54:17.254966 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:17.255047 INFO: Using python extraction backend
2 days, 23:54:17.255162 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:17.255244 INFO: === Search parameters used ===
2 days, 23:54:17.255306 INFO: rt_error       : 1199.951526
2 days, 23:54:17.255359 INFO: mobility_error : 0.1
2 days, 23:54:17.255422 INFO: num_candidates : 3
2 days, 23:54:17.255476 INFO: ms1_error      : 15.0
2 days, 23:54:17.255526 INFO: ms2_error      : 15.0
2 days, 23:54:17.255577 INFO: fwhm_rt        : 2.610288381576538
2 days, 23:54:17.255630 INFO: quant_window   : 3
2 days, 23:54:17.255691 INFO: ==============================================
2 days, 23:54:17.256733 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:17.256788 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:17.256842 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
2 days, 23:54:17.256875 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.96
2 days, 23:54:17.262631 INFO: Starting candidate selection
2 days, 23:54:25.723027 INFO: Starting candidate scoring
2 days, 23:54:25.832911 INFO: Finished candidate processing
2 days, 23:54:25.833048 INFO: Collecting candidate features
2 days, 23:54:25.849343 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3403)
2 days, 23:54:25.856829 INFO: Collecting fragment features
2 days, 23:54:25.861335 INFO: Finished candidate scoring
2 days, 23:54:25.863895 INFO: performing precursor FDR with 47 features
2 days, 23:54:25.863972 INFO: Decoy channel: -1
2 days, 23:54:25.864009 INFO: competitive: True
2 days, 23:54:25.868538 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:25.870751 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 23:54:25.872323 INFO: Estimating optimal hyperparameters - samples: 2,719, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:25.872442 INFO: Using random state 685108 for train-test-split
2 days, 23:54:26.221201 INFO: Test AUC: 0.746
2 days, 23:54:26.221323 INFO: Train AUC: 0.768
2 days, 23:54:26.221366 INFO: AUC difference: 2.91%
2 days, 23:54:26.542175 INFO: Resetting torch num_threads to 80
2 days, 23:54:26.542809 PROGRESS: === Extracted 3403 precursors and 26935 fragments ===
2 days, 23:54:26.543295 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:54:26.543972 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:26.544093 PROGRESS: Total precursors accumulated: 600
2 days, 23:54:26.544190 PROGRESS: Target precursors: 527 (87.83%)
2 days, 23:54:26.544276 PROGRESS: Decoy precursors: 73 (12.17%)
2 days, 23:54:26.544353 PROGRESS: 
2 days, 23:54:26.544422 PROGRESS: Precursor Summary:
2 days, 23:54:26.545567 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   385; 0.001 FDR:   332
2 days, 23:54:26.545688 PROGRESS: 
2 days, 23:54:26.545779 PROGRESS: Protein Summary:
2 days, 23:54:26.547159 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   288; 0.001 FDR:   243
2 days, 23:54:26.547279 PROGRESS: =========================================================================
2 days, 23:54:26.547470 INFO: Target number of precursors reached.
2 days, 23:54:26.556711 INFO: fragments_df: keeping 5000 of 26935 [sum(precursor_idx_mask)=9664 sum(mass_error_mask)=26935 stop_rank=5000
2 days, 23:54:26.561822 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:26.768804 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:26.952361 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:27.105979 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:27.915818 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:27.916284 INFO: Using score_cutoff 25.49375502319336 (fac=0.99, q=1)
2 days, 23:54:27.916670 INFO: Updating optimization_manager: fwhm_rt             : 2.610288381576538 -> 2.6080312728881836
2 days, 23:54:27.916774 INFO: Updating optimization_manager: fwhm_mobility       : 0.0054498715326189995 -> 0.005118570290505886
2 days, 23:54:27.916860 INFO: Updating optimization_manager: score_cutoff        : 27.455223679733276 -> 25.49375502319336
2 days, 23:54:27.916942 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:27.918105 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:27.919506 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:27.920344 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:27.922380 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:27.922506 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:54:27.924165 INFO: Updating optimization_manager: rt_error            : 1199.951526 -> 482.3605618195141
2 days, 23:54:27.924285 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 482.3606.
2 days, 23:54:27.924383 INFO: ==============================================
2 days, 23:54:27.924494 INFO: Starting optimization step 1.
2 days, 23:54:27.924587 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:27.924675 INFO: Using python extraction backend
2 days, 23:54:27.924812 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:27.924905 INFO: === Search parameters used ===
2 days, 23:54:27.924983 INFO: rt_error       : 482.3605618195141
2 days, 23:54:27.925053 INFO: mobility_error : 0.1
2 days, 23:54:27.925117 INFO: num_candidates : 3
2 days, 23:54:27.925178 INFO: ms1_error      : 15.0
2 days, 23:54:27.925238 INFO: ms2_error      : 15.0
2 days, 23:54:27.925298 INFO: fwhm_rt        : 2.6080312728881836
2 days, 23:54:27.925358 INFO: quant_window   : 3
2 days, 23:54:27.925417 INFO: ==============================================
2 days, 23:54:27.926295 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:27.926348 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:27.926396 INFO: FWHM in RT is 2.61 seconds, sigma is 0.43
2 days, 23:54:27.926432 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.78
2 days, 23:54:27.938024 INFO: Starting candidate selection
2 days, 23:54:32.819247 INFO: Starting candidate scoring
2 days, 23:54:32.924640 INFO: Finished candidate processing
2 days, 23:54:32.924787 INFO: Collecting candidate features
2 days, 23:54:32.937959 WARNING: intensity_correlation has 5 NaNs ( 0.15 % out of 3390)
2 days, 23:54:32.942181 INFO: Collecting fragment features
2 days, 23:54:32.946381 INFO: Finished candidate scoring
2 days, 23:54:32.948760 INFO: performing precursor FDR with 47 features
2 days, 23:54:32.948833 INFO: Decoy channel: -1
2 days, 23:54:32.948867 INFO: competitive: True
2 days, 23:54:32.952142 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:32.953651 WARNING: dropped 5 decoy PSMs due to missing features
2 days, 23:54:32.955135 INFO: Estimating optimal hyperparameters - samples: 2,708, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:32.955239 INFO: Using random state 685108 for train-test-split
2 days, 23:54:33.293770 INFO: Test AUC: 0.738
2 days, 23:54:33.293908 INFO: Train AUC: 0.778
2 days, 23:54:33.293951 INFO: AUC difference: 5.22%
2 days, 23:54:33.293983 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:54:33.598541 INFO: Resetting torch num_threads to 80
2 days, 23:54:33.599224 PROGRESS: === Extracted 3390 precursors and 26489 fragments ===
2 days, 23:54:33.599735 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:54:33.600485 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:33.600590 PROGRESS: Total precursors accumulated: 600
2 days, 23:54:33.600666 PROGRESS: Target precursors: 535 (89.17%)
2 days, 23:54:33.600733 PROGRESS: Decoy precursors: 65 (10.83%)
2 days, 23:54:33.600794 PROGRESS: 
2 days, 23:54:33.600855 PROGRESS: Precursor Summary:
2 days, 23:54:33.602247 PROGRESS: Channel   0:	 0.050 FDR:   463; 0.010 FDR:   421; 0.001 FDR:   325
2 days, 23:54:33.602375 PROGRESS: 
2 days, 23:54:33.602447 PROGRESS: Protein Summary:
2 days, 23:54:33.603997 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   312; 0.001 FDR:   245
2 days, 23:54:33.604100 PROGRESS: =========================================================================
2 days, 23:54:33.604269 INFO: Target number of precursors reached.
2 days, 23:54:33.612550 INFO: fragments_df: keeping 5000 of 26489 [sum(precursor_idx_mask)=10430 sum(mass_error_mask)=26489 stop_rank=5000
2 days, 23:54:33.616624 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:33.826716 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:34.022571 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:34.212994 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:35.168208 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:35.168812 INFO: Using score_cutoff 23.03105743789673 (fac=0.99, q=1)
2 days, 23:54:35.169292 INFO: Updating optimization_manager: fwhm_rt             : 2.6080312728881836 -> 2.5760090351104736
2 days, 23:54:35.169411 INFO: Updating optimization_manager: fwhm_mobility       : 0.005118570290505886 -> 0.004707526881247759
2 days, 23:54:35.169508 INFO: Updating optimization_manager: score_cutoff        : 25.49375502319336 -> 23.03105743789673
2 days, 23:54:35.169615 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:35.171208 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:35.172988 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:35.174162 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:35.176784 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:35.176934 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:54:35.179493 INFO: Updating optimization_manager: rt_error            : 482.3605618195141 -> 147.43272120995434
2 days, 23:54:35.179639 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 147.4327.
2 days, 23:54:35.179774 INFO: ==============================================
2 days, 23:54:35.179915 INFO: Starting optimization step 2.
2 days, 23:54:35.180044 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:35.180160 INFO: Using python extraction backend
2 days, 23:54:35.180331 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:35.180472 INFO: === Search parameters used ===
2 days, 23:54:35.180592 INFO: rt_error       : 147.43272120995434
2 days, 23:54:35.180708 INFO: mobility_error : 0.1
2 days, 23:54:35.180822 INFO: num_candidates : 3
2 days, 23:54:35.180936 INFO: ms1_error      : 15.0
2 days, 23:54:35.181108 INFO: ms2_error      : 15.0
2 days, 23:54:35.181251 INFO: fwhm_rt        : 2.5760090351104736
2 days, 23:54:35.181368 INFO: quant_window   : 3
2 days, 23:54:35.181488 INFO: ==============================================
2 days, 23:54:35.182762 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:35.182854 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:35.182928 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:54:35.182989 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
2 days, 23:54:35.194016 INFO: Starting candidate selection
2 days, 23:54:36.998421 INFO: Starting candidate scoring
2 days, 23:54:37.104569 INFO: Finished candidate processing
2 days, 23:54:37.104686 INFO: Collecting candidate features
2 days, 23:54:37.118203 WARNING: intensity_correlation has 5 NaNs ( 0.15 % out of 3322)
2 days, 23:54:37.123422 INFO: Collecting fragment features
2 days, 23:54:37.128080 INFO: Finished candidate scoring
2 days, 23:54:37.130431 INFO: performing precursor FDR with 47 features
2 days, 23:54:37.130496 INFO: Decoy channel: -1
2 days, 23:54:37.130529 INFO: competitive: True
2 days, 23:54:37.134366 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:37.136280 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:54:37.136337 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 23:54:37.137553 INFO: Estimating optimal hyperparameters - samples: 2,653, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:37.137651 INFO: Using random state 685108 for train-test-split
2 days, 23:54:37.383460 INFO: Test AUC: 0.794
2 days, 23:54:37.383596 INFO: Train AUC: 0.811
2 days, 23:54:37.383633 INFO: AUC difference: 2.17%
2 days, 23:54:37.682274 INFO: Resetting torch num_threads to 80
2 days, 23:54:37.682843 PROGRESS: === Extracted 3322 precursors and 24794 fragments ===
2 days, 23:54:37.683275 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:54:37.683895 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:37.683994 PROGRESS: Total precursors accumulated: 600
2 days, 23:54:37.684070 PROGRESS: Target precursors: 564 (94.00%)
2 days, 23:54:37.684136 PROGRESS: Decoy precursors: 36 (6.00%)
2 days, 23:54:37.684197 PROGRESS: 
2 days, 23:54:37.684257 PROGRESS: Precursor Summary:
2 days, 23:54:37.685417 PROGRESS: Channel   0:	 0.050 FDR:   554; 0.010 FDR:   485; 0.001 FDR:   456
2 days, 23:54:37.685514 PROGRESS: 
2 days, 23:54:37.685583 PROGRESS: Protein Summary:
2 days, 23:54:37.686919 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   355; 0.001 FDR:   337
2 days, 23:54:37.687032 PROGRESS: =========================================================================
2 days, 23:54:37.687223 INFO: Target number of precursors reached.
2 days, 23:54:37.696426 INFO: fragments_df: keeping 5000 of 24794 [sum(precursor_idx_mask)=11721 sum(mass_error_mask)=24794 stop_rank=5000
2 days, 23:54:37.701367 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:37.890871 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:38.092945 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:38.292356 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:39.153349 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:39.153827 INFO: Using score_cutoff 20.068439234161378 (fac=0.99, q=1)
2 days, 23:54:39.154215 INFO: Updating optimization_manager: fwhm_rt             : 2.5760090351104736 -> 2.558229446411133
2 days, 23:54:39.154323 INFO: Updating optimization_manager: fwhm_mobility       : 0.004707526881247759 -> 0.00415644608438015
2 days, 23:54:39.154392 INFO: Updating optimization_manager: score_cutoff        : 23.03105743789673 -> 20.068439234161378
2 days, 23:54:39.154465 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:39.155636 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:39.157109 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:39.157987 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:39.160027 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:39.160138 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:54:39.162116 INFO: Updating optimization_manager: rt_error            : 147.43272120995434 -> 29.140839722733915
2 days, 23:54:39.162251 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 29.1408.
2 days, 23:54:39.162329 INFO: ==============================================
2 days, 23:54:39.162408 INFO: Starting optimization step 3.
2 days, 23:54:39.162478 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:39.162546 INFO: Using python extraction backend
2 days, 23:54:39.162649 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:39.162724 INFO: === Search parameters used ===
2 days, 23:54:39.162782 INFO: rt_error       : 29.140839722733915
2 days, 23:54:39.162838 INFO: mobility_error : 0.1
2 days, 23:54:39.162891 INFO: num_candidates : 3
2 days, 23:54:39.162943 INFO: ms1_error      : 15.0
2 days, 23:54:39.163002 INFO: ms2_error      : 15.0
2 days, 23:54:39.163055 INFO: fwhm_rt        : 2.558229446411133
2 days, 23:54:39.163107 INFO: quant_window   : 3
2 days, 23:54:39.163158 INFO: ==============================================
2 days, 23:54:39.164052 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:39.164110 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:39.164148 INFO: FWHM in RT is 2.56 seconds, sigma is 0.43
2 days, 23:54:39.164176 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.25
2 days, 23:54:39.178005 INFO: Starting candidate selection
2 days, 23:54:39.888514 INFO: Starting candidate scoring
2 days, 23:54:39.996036 INFO: Finished candidate processing
2 days, 23:54:39.996166 INFO: Collecting candidate features
2 days, 23:54:40.012262 WARNING: intensity_correlation has 25 NaNs ( 0.78 % out of 3222)
2 days, 23:54:40.020532 INFO: Collecting fragment features
2 days, 23:54:40.026395 INFO: Finished candidate scoring
2 days, 23:54:40.029696 INFO: performing precursor FDR with 47 features
2 days, 23:54:40.029780 INFO: Decoy channel: -1
2 days, 23:54:40.029814 INFO: competitive: True
2 days, 23:54:40.034520 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:40.036834 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:54:40.036906 WARNING: dropped 23 decoy PSMs due to missing features
2 days, 23:54:40.038309 INFO: Estimating optimal hyperparameters - samples: 2,557, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:40.038423 INFO: Using random state 685108 for train-test-split
2 days, 23:54:40.371507 INFO: Test AUC: 0.870
2 days, 23:54:40.371631 INFO: Train AUC: 0.868
2 days, 23:54:40.371693 INFO: AUC difference: 0.25%
2 days, 23:54:40.691009 INFO: Resetting torch num_threads to 80
2 days, 23:54:40.691540 PROGRESS: === Extracted 3222 precursors and 22629 fragments ===
2 days, 23:54:40.691996 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:54:40.692627 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:40.692729 PROGRESS: Total precursors accumulated: 599
2 days, 23:54:40.692808 PROGRESS: Target precursors: 585 (97.66%)
2 days, 23:54:40.692875 PROGRESS: Decoy precursors: 14 (2.34%)
2 days, 23:54:40.692933 PROGRESS: 
2 days, 23:54:40.692993 PROGRESS: Precursor Summary:
2 days, 23:54:40.694176 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   567; 0.001 FDR:   507
2 days, 23:54:40.694277 PROGRESS: 
2 days, 23:54:40.694351 PROGRESS: Protein Summary:
2 days, 23:54:40.695724 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   421; 0.001 FDR:   379
2 days, 23:54:40.695824 PROGRESS: =========================================================================
2 days, 23:54:40.695966 INFO: Target number of precursors reached.
2 days, 23:54:40.702052 INFO: fragments_df: keeping 5000 of 22629 [sum(precursor_idx_mask)=13216 sum(mass_error_mask)=22629 stop_rank=5000
2 days, 23:54:40.705440 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:40.876892 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:41.074745 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:41.279433 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:42.181921 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:42.182387 INFO: Using score_cutoff 17.387786659240724 (fac=0.99, q=1)
2 days, 23:54:42.182732 INFO: Updating optimization_manager: fwhm_rt             : 2.558229446411133 -> 2.514662504196167
2 days, 23:54:42.182816 INFO: Updating optimization_manager: fwhm_mobility       : 0.00415644608438015 -> 0.003722842549905181
2 days, 23:54:42.182881 INFO: Updating optimization_manager: score_cutoff        : 20.068439234161378 -> 17.387786659240724
2 days, 23:54:42.182950 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:42.184079 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:42.185460 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:42.186291 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:42.188337 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:42.188445 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:54:42.190529 INFO: Updating optimization_manager: rt_error            : 29.140839722733915 -> 17.149567890563993
2 days, 23:54:42.190658 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 17.1496.
2 days, 23:54:42.190744 INFO: ==============================================
2 days, 23:54:42.190826 INFO: Starting optimization step 4.
2 days, 23:54:42.190898 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:42.190977 INFO: Using python extraction backend
2 days, 23:54:42.191088 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:42.191162 INFO: === Search parameters used ===
2 days, 23:54:42.191219 INFO: rt_error       : 17.149567890563993
2 days, 23:54:42.191271 INFO: mobility_error : 0.1
2 days, 23:54:42.191322 INFO: num_candidates : 3
2 days, 23:54:42.191372 INFO: ms1_error      : 15.0
2 days, 23:54:42.191422 INFO: ms2_error      : 15.0
2 days, 23:54:42.191470 INFO: fwhm_rt        : 2.514662504196167
2 days, 23:54:42.191519 INFO: quant_window   : 3
2 days, 23:54:42.191567 INFO: ==============================================
2 days, 23:54:42.192430 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:42.192481 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:42.192520 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:54:42.192548 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.02
2 days, 23:54:42.199571 INFO: Starting candidate selection
2 days, 23:54:42.838372 INFO: Starting candidate scoring
2 days, 23:54:42.936834 INFO: Finished candidate processing
2 days, 23:54:42.936968 INFO: Collecting candidate features
2 days, 23:54:42.952893 WARNING: intensity_correlation has 29 NaNs ( 0.91 % out of 3183)
2 days, 23:54:42.953366 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3183)
2 days, 23:54:42.960606 INFO: Collecting fragment features
2 days, 23:54:42.965724 INFO: Finished candidate scoring
2 days, 23:54:42.967630 INFO: performing precursor FDR with 47 features
2 days, 23:54:42.967691 INFO: Decoy channel: -1
2 days, 23:54:42.967726 INFO: competitive: True
2 days, 23:54:42.970821 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:42.972454 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:54:42.972509 WARNING: dropped 28 decoy PSMs due to missing features
2 days, 23:54:42.973624 INFO: Estimating optimal hyperparameters - samples: 2,522, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:42.973726 INFO: Using random state 685108 for train-test-split
2 days, 23:54:43.168886 INFO: Test AUC: 0.853
2 days, 23:54:43.168995 INFO: Train AUC: 0.886
2 days, 23:54:43.169037 INFO: AUC difference: 3.69%
2 days, 23:54:43.455713 INFO: Resetting torch num_threads to 80
2 days, 23:54:43.456268 PROGRESS: === Extracted 3183 precursors and 22075 fragments ===
2 days, 23:54:43.456703 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:54:43.457316 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:43.457416 PROGRESS: Total precursors accumulated: 599
2 days, 23:54:43.457488 PROGRESS: Target precursors: 589 (98.33%)
2 days, 23:54:43.457553 PROGRESS: Decoy precursors: 10 (1.67%)
2 days, 23:54:43.457615 PROGRESS: 
2 days, 23:54:43.457674 PROGRESS: Precursor Summary:
2 days, 23:54:43.458828 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   585; 0.001 FDR:   473
2 days, 23:54:43.458931 PROGRESS: 
2 days, 23:54:43.458997 PROGRESS: Protein Summary:
2 days, 23:54:43.460361 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   431; 0.001 FDR:   356
2 days, 23:54:43.460456 PROGRESS: =========================================================================
2 days, 23:54:43.460609 INFO: Target number of precursors reached.
2 days, 23:54:43.466583 INFO: fragments_df: keeping 5000 of 22075 [sum(precursor_idx_mask)=13481 sum(mass_error_mask)=22075 stop_rank=5000
2 days, 23:54:43.469995 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:43.649065 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:43.881936 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:44.096907 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:44.931709 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:44.932209 INFO: Using score_cutoff 15.67670736579895 (fac=0.99, q=1)
2 days, 23:54:44.932565 INFO: Updating optimization_manager: fwhm_rt             : 2.514662504196167 -> 2.502976417541504
2 days, 23:54:44.932661 INFO: Updating optimization_manager: fwhm_mobility       : 0.003722842549905181 -> 0.003685507457703352
2 days, 23:54:44.932737 INFO: Updating optimization_manager: score_cutoff        : 17.387786659240724 -> 15.67670736579895
2 days, 23:54:44.932811 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:44.933970 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:44.935376 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:44.936196 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:44.938188 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:44.938319 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:54:44.940349 INFO: Updating optimization_manager: rt_error            : 17.149567890563993 -> 12.466822566581351
2 days, 23:54:44.940469 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 12.4668.
2 days, 23:54:44.940552 INFO: ==============================================
2 days, 23:54:44.940639 INFO: Starting optimization step 5.
2 days, 23:54:44.940717 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:44.940793 INFO: Using python extraction backend
2 days, 23:54:44.940910 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:44.940991 INFO: === Search parameters used ===
2 days, 23:54:44.941059 INFO: rt_error       : 12.466822566581351
2 days, 23:54:44.941120 INFO: mobility_error : 0.1
2 days, 23:54:44.941177 INFO: num_candidates : 3
2 days, 23:54:44.941233 INFO: ms1_error      : 15.0
2 days, 23:54:44.941289 INFO: ms2_error      : 15.0
2 days, 23:54:44.941344 INFO: fwhm_rt        : 2.502976417541504
2 days, 23:54:44.941399 INFO: quant_window   : 3
2 days, 23:54:44.941453 INFO: ==============================================
2 days, 23:54:44.942338 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:44.942396 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:44.942438 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:54:44.942470 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.00
2 days, 23:54:44.946986 INFO: Starting candidate selection
2 days, 23:54:45.524714 INFO: Starting candidate scoring
2 days, 23:54:45.640388 INFO: Finished candidate processing
2 days, 23:54:45.640489 INFO: Collecting candidate features
2 days, 23:54:45.650621 WARNING: intensity_correlation has 19 NaNs ( 0.60 % out of 3164)
2 days, 23:54:45.650844 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3164)
2 days, 23:54:45.654735 INFO: Collecting fragment features
2 days, 23:54:45.658457 INFO: Finished candidate scoring
2 days, 23:54:45.660281 INFO: performing precursor FDR with 47 features
2 days, 23:54:45.660343 INFO: Decoy channel: -1
2 days, 23:54:45.660375 INFO: competitive: True
2 days, 23:54:45.663530 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:45.665095 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:54:45.665157 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:54:45.665207 WARNING: FDR calculation for 1652 target and 1491 decoy PSMs
2 days, 23:54:45.665238 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:54:45.666269 INFO: Estimating optimal hyperparameters - samples: 2,514, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:45.666368 INFO: Using random state 685108 for train-test-split
2 days, 23:54:45.940878 INFO: Test AUC: 0.857
2 days, 23:54:45.941001 INFO: Train AUC: 0.885
2 days, 23:54:45.941045 INFO: AUC difference: 3.17%
2 days, 23:54:46.299891 INFO: Resetting torch num_threads to 80
2 days, 23:54:46.300458 PROGRESS: === Extracted 3164 precursors and 21935 fragments ===
2 days, 23:54:46.300902 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:54:46.301517 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:46.301618 PROGRESS: Total precursors accumulated: 599
2 days, 23:54:46.301700 PROGRESS: Target precursors: 589 (98.33%)
2 days, 23:54:46.301770 PROGRESS: Decoy precursors: 10 (1.67%)
2 days, 23:54:46.301830 PROGRESS: 
2 days, 23:54:46.301902 PROGRESS: Precursor Summary:
2 days, 23:54:46.303067 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   575; 0.001 FDR:   529
2 days, 23:54:46.303167 PROGRESS: 
2 days, 23:54:46.303240 PROGRESS: Protein Summary:
2 days, 23:54:46.304600 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   425; 0.001 FDR:   393
2 days, 23:54:46.304703 PROGRESS: =========================================================================
2 days, 23:54:46.304854 INFO: Target number of precursors reached.
2 days, 23:54:46.310784 INFO: fragments_df: keeping 5000 of 21935 [sum(precursor_idx_mask)=13283 sum(mass_error_mask)=21935 stop_rank=5000
2 days, 23:54:46.314130 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:46.572576 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:46.782703 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:47.052450 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:47.928930 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:47.929526 INFO: Using score_cutoff 16.61511357078552 (fac=0.99, q=1)
2 days, 23:54:47.930002 INFO: Updating optimization_manager: fwhm_rt             : 2.502976417541504 -> 2.501936912536621
2 days, 23:54:47.930117 INFO: Updating optimization_manager: fwhm_mobility       : 0.003685507457703352 -> 0.003708347212523222
2 days, 23:54:47.930210 INFO: Updating optimization_manager: score_cutoff        : 15.67670736579895 -> 16.61511357078552
2 days, 23:54:47.930300 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:47.931809 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:47.933603 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:47.934786 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:47.937410 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:47.937532 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 23:54:47.940320 INFO: Updating optimization_manager: rt_error            : 12.466822566581351 -> 9.328807091210116
2 days, 23:54:47.940455 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 9.3288.
2 days, 23:54:47.940542 INFO: ==============================================
2 days, 23:54:47.940632 INFO: Starting optimization step 6.
2 days, 23:54:47.940719 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:47.940806 INFO: Using python extraction backend
2 days, 23:54:47.940948 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:47.941047 INFO: === Search parameters used ===
2 days, 23:54:47.941128 INFO: rt_error       : 9.328807091210116
2 days, 23:54:47.941200 INFO: mobility_error : 0.1
2 days, 23:54:47.941271 INFO: num_candidates : 3
2 days, 23:54:47.941342 INFO: ms1_error      : 15.0
2 days, 23:54:47.941413 INFO: ms2_error      : 15.0
2 days, 23:54:47.941478 INFO: fwhm_rt        : 2.501936912536621
2 days, 23:54:47.941552 INFO: quant_window   : 3
2 days, 23:54:47.941636 INFO: ==============================================
2 days, 23:54:47.942841 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:47.942908 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:47.942958 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:54:47.942991 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.01
2 days, 23:54:47.946957 INFO: Starting candidate selection
2 days, 23:54:48.594868 INFO: Starting candidate scoring
2 days, 23:54:48.702484 INFO: Finished candidate processing
2 days, 23:54:48.702638 INFO: Collecting candidate features
2 days, 23:54:48.714038 WARNING: intensity_correlation has 21 NaNs ( 0.67 % out of 3156)
2 days, 23:54:48.714313 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3156)
2 days, 23:54:48.718696 INFO: Collecting fragment features
2 days, 23:54:48.722778 INFO: Finished candidate scoring
2 days, 23:54:48.725007 INFO: performing precursor FDR with 47 features
2 days, 23:54:48.725087 INFO: Decoy channel: -1
2 days, 23:54:48.725122 INFO: competitive: True
2 days, 23:54:48.728440 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:48.730070 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:54:48.730134 WARNING: dropped 19 decoy PSMs due to missing features
2 days, 23:54:48.730182 WARNING: FDR calculation for 1649 target and 1484 decoy PSMs
2 days, 23:54:48.730213 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:54:48.731228 INFO: Estimating optimal hyperparameters - samples: 2,506, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:48.731324 INFO: Using random state 685108 for train-test-split
2 days, 23:54:48.982979 INFO: Test AUC: 0.843
2 days, 23:54:48.983124 INFO: Train AUC: 0.881
2 days, 23:54:48.983207 INFO: AUC difference: 4.29%
2 days, 23:54:49.304407 INFO: Resetting torch num_threads to 80
2 days, 23:54:49.305152 PROGRESS: === Extracted 3156 precursors and 21883 fragments ===
2 days, 23:54:49.305763 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:54:49.306709 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:49.306841 PROGRESS: Total precursors accumulated: 599
2 days, 23:54:49.306952 PROGRESS: Target precursors: 588 (98.16%)
2 days, 23:54:49.307054 PROGRESS: Decoy precursors: 11 (1.84%)
2 days, 23:54:49.307153 PROGRESS: 
2 days, 23:54:49.307233 PROGRESS: Precursor Summary:
2 days, 23:54:49.309049 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   578; 0.001 FDR:   537
2 days, 23:54:49.309179 PROGRESS: 
2 days, 23:54:49.309274 PROGRESS: Protein Summary:
2 days, 23:54:49.311578 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   428; 0.001 FDR:   397
2 days, 23:54:49.311720 PROGRESS: =========================================================================
2 days, 23:54:49.311931 INFO: Target number of precursors reached.
2 days, 23:54:49.321328 INFO: fragments_df: keeping 5000 of 21883 [sum(precursor_idx_mask)=13276 sum(mass_error_mask)=21883 stop_rank=5000
2 days, 23:54:49.327008 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:49.502953 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:49.708805 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:49.895566 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:50.686671 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:50.687155 INFO: Using score_cutoff 15.627256177711487 (fac=0.99, q=1)
2 days, 23:54:50.687499 INFO: Updating optimization_manager: fwhm_rt             : 2.501936912536621 -> 2.5131006240844727
2 days, 23:54:50.687590 INFO: Updating optimization_manager: fwhm_mobility       : 0.003708347212523222 -> 0.0036612646654248238
2 days, 23:54:50.687656 INFO: Updating optimization_manager: score_cutoff        : 16.61511357078552 -> 15.627256177711487
2 days, 23:54:50.687722 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:50.688863 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:50.690270 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:50.691099 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:50.693120 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:50.693232 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 23:54:50.695214 INFO: Updating optimization_manager: rt_error            : 9.328807091210116 -> 9.254616087575595
2 days, 23:54:50.695336 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 9.2546.
2 days, 23:54:50.695418 INFO: ==============================================
2 days, 23:54:50.695505 INFO: Starting optimization step 7.
2 days, 23:54:50.695581 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:50.695655 INFO: Using python extraction backend
2 days, 23:54:50.695771 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:50.695860 INFO: === Search parameters used ===
2 days, 23:54:50.695926 INFO: rt_error       : 9.254616087575595
2 days, 23:54:50.695987 INFO: mobility_error : 0.1
2 days, 23:54:50.696046 INFO: num_candidates : 3
2 days, 23:54:50.696100 INFO: ms1_error      : 15.0
2 days, 23:54:50.696152 INFO: ms2_error      : 15.0
2 days, 23:54:50.696204 INFO: fwhm_rt        : 2.5131006240844727
2 days, 23:54:50.696257 INFO: quant_window   : 3
2 days, 23:54:50.696308 INFO: ==============================================
2 days, 23:54:50.697181 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:50.697237 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:50.697278 INFO: FWHM in RT is 2.51 seconds, sigma is 0.42
2 days, 23:54:50.697307 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.99
2 days, 23:54:50.709975 INFO: Starting candidate selection
2 days, 23:54:51.273769 INFO: Starting candidate scoring
2 days, 23:54:51.369563 INFO: Finished candidate processing
2 days, 23:54:51.369696 INFO: Collecting candidate features
2 days, 23:54:51.382441 WARNING: intensity_correlation has 19 NaNs ( 0.60 % out of 3151)
2 days, 23:54:51.382724 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3151)
2 days, 23:54:51.386664 INFO: Collecting fragment features
2 days, 23:54:51.391052 INFO: Finished candidate scoring
2 days, 23:54:51.393399 INFO: performing precursor FDR with 47 features
2 days, 23:54:51.393542 INFO: Decoy channel: -1
2 days, 23:54:51.393585 INFO: competitive: True
2 days, 23:54:51.398438 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:51.401020 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:54:51.401152 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:54:51.401265 WARNING: FDR calculation for 1648 target and 1482 decoy PSMs
2 days, 23:54:51.401361 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:54:51.402894 INFO: Estimating optimal hyperparameters - samples: 2,504, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:51.403079 INFO: Using random state 685108 for train-test-split
2 days, 23:54:51.670663 INFO: Test AUC: 0.881
2 days, 23:54:51.670920 INFO: Train AUC: 0.876
2 days, 23:54:51.671038 INFO: AUC difference: 0.58%
2 days, 23:54:51.995246 INFO: Resetting torch num_threads to 80
2 days, 23:54:51.995810 PROGRESS: === Extracted 3151 precursors and 21863 fragments ===
2 days, 23:54:51.996269 INFO: === FDR correction performed with classifier version 4 ===
2 days, 23:54:51.996909 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:51.997020 PROGRESS: Total precursors accumulated: 599
2 days, 23:54:51.997108 PROGRESS: Target precursors: 586 (97.83%)
2 days, 23:54:51.997183 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:54:51.997250 PROGRESS: 
2 days, 23:54:51.997313 PROGRESS: Precursor Summary:
2 days, 23:54:51.998502 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   573; 0.001 FDR:   520
2 days, 23:54:51.998618 PROGRESS: 
2 days, 23:54:51.998699 PROGRESS: Protein Summary:
2 days, 23:54:52.000091 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   425; 0.001 FDR:   386
2 days, 23:54:52.000210 PROGRESS: =========================================================================
2 days, 23:54:52.000396 INFO: Target number of precursors reached.
2 days, 23:54:52.006472 INFO: fragments_df: keeping 5000 of 21863 [sum(precursor_idx_mask)=13203 sum(mass_error_mask)=21863 stop_rank=5000
2 days, 23:54:52.009993 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:52.209211 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:52.464000 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:52.744474 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:53.603981 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:53.604436 INFO: Using score_cutoff 16.37733913192749 (fac=0.99, q=1)
2 days, 23:54:53.604781 INFO: Updating optimization_manager: fwhm_rt             : 2.5131006240844727 -> 2.502976417541504
2 days, 23:54:53.604866 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036612646654248238 -> 0.0036467222962528467
2 days, 23:54:53.604924 INFO: Updating optimization_manager: score_cutoff        : 15.627256177711487 -> 16.37733913192749
2 days, 23:54:53.604980 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:53.606109 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:53.607597 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:53.608423 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:53.610478 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:53.610584 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 23:54:53.611597 INFO: Updating optimization_manager: rt_error            : 9.254616087575595 -> 9.254616087575595
2 days, 23:54:53.611747 INFO: Updating optimization_manager: classifier_version  : 4 -> 12
2 days, 23:54:53.611863 INFO: Updating optimization_manager: score_cutoff        : 16.37733913192749 -> 16.37733913192749
2 days, 23:54:53.611971 INFO: Updating optimization_manager: fwhm_rt             : 2.502976417541504 -> 2.502976417541504
2 days, 23:54:53.612078 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036467222962528467 -> 0.0036467222962528467
2 days, 23:54:53.612185 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 9.2546 found after 8 searches.
2 days, 23:54:53.612260 INFO: ==============================================
2 days, 23:54:53.612331 PROGRESS: Optimization finished for rt_error.
2 days, 23:54:53.615594 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:53.616460 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:53.617821 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:53.618736 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:53.621121 INFO: Starting optimization step 0.
2 days, 23:54:53.621241 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:53.621341 INFO: Using python extraction backend
2 days, 23:54:53.621500 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:53.621603 INFO: === Search parameters used ===
2 days, 23:54:53.621679 INFO: rt_error       : 9.254616087575595
2 days, 23:54:53.621751 INFO: mobility_error : 0.1
2 days, 23:54:53.621824 INFO: num_candidates : 3
2 days, 23:54:53.621940 INFO: ms1_error      : 15.0
2 days, 23:54:53.622023 INFO: ms2_error      : 15.0
2 days, 23:54:53.622096 INFO: fwhm_rt        : 2.502976417541504
2 days, 23:54:53.622175 INFO: quant_window   : 3
2 days, 23:54:53.622247 INFO: ==============================================
2 days, 23:54:53.623330 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:53.623398 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:53.623453 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:54:53.623489 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.98
2 days, 23:54:53.634053 INFO: Starting candidate selection
2 days, 23:54:54.217496 INFO: Starting candidate scoring
2 days, 23:54:54.321901 INFO: Finished candidate processing
2 days, 23:54:54.322023 INFO: Collecting candidate features
2 days, 23:54:54.334882 WARNING: intensity_correlation has 19 NaNs ( 0.60 % out of 3150)
2 days, 23:54:54.335142 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3150)
2 days, 23:54:54.340125 INFO: Collecting fragment features
2 days, 23:54:54.345150 INFO: Finished candidate scoring
2 days, 23:54:54.347280 INFO: performing precursor FDR with 47 features
2 days, 23:54:54.347342 INFO: Decoy channel: -1
2 days, 23:54:54.347376 INFO: competitive: True
2 days, 23:54:54.352208 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:54.354147 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:54:54.354213 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:54:54.354260 WARNING: FDR calculation for 1646 target and 1483 decoy PSMs
2 days, 23:54:54.354291 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:54:54.355497 INFO: Estimating optimal hyperparameters - samples: 2,503, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:54.355589 INFO: Using random state 708379 for train-test-split
2 days, 23:54:54.655464 INFO: Test AUC: 0.877
2 days, 23:54:54.655597 INFO: Train AUC: 0.890
2 days, 23:54:54.655637 INFO: AUC difference: 1.55%
2 days, 23:54:54.985010 INFO: Resetting torch num_threads to 80
2 days, 23:54:54.985724 PROGRESS: === Extracted 3150 precursors and 21849 fragments ===
2 days, 23:54:54.986312 INFO: === FDR correction performed with classifier version 12 ===
2 days, 23:54:54.987189 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:54.987314 PROGRESS: Total precursors accumulated: 599
2 days, 23:54:54.987411 PROGRESS: Target precursors: 590 (98.50%)
2 days, 23:54:54.987499 PROGRESS: Decoy precursors: 9 (1.50%)
2 days, 23:54:54.987579 PROGRESS: 
2 days, 23:54:54.987656 PROGRESS: Precursor Summary:
2 days, 23:54:54.989412 PROGRESS: Channel   0:	 0.050 FDR:   590; 0.010 FDR:   580; 0.001 FDR:   552
2 days, 23:54:54.989543 PROGRESS: 
2 days, 23:54:54.989635 PROGRESS: Protein Summary:
2 days, 23:54:54.991679 PROGRESS: Channel   0:	 0.050 FDR:   436; 0.010 FDR:   429; 0.001 FDR:   408
2 days, 23:54:54.991801 PROGRESS: =========================================================================
2 days, 23:54:54.991981 INFO: Target number of precursors reached.
2 days, 23:54:55.000557 INFO: fragments_df: keeping 5000 of 21849 [sum(precursor_idx_mask)=13280 sum(mass_error_mask)=21849 stop_rank=5000
2 days, 23:54:55.005491 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:55.224334 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:55.426429 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:55.612785 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:56.531832 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:56.532272 INFO: Using score_cutoff 15.817557764911651 (fac=0.99, q=1)
2 days, 23:54:56.532611 INFO: Updating optimization_manager: fwhm_rt             : 2.502976417541504 -> 2.4984474182128906
2 days, 23:54:56.532698 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036467222962528467 -> 0.0036229523830115795
2 days, 23:54:56.532755 INFO: Updating optimization_manager: score_cutoff        : 16.37733913192749 -> 15.817557764911651
2 days, 23:54:56.532823 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:56.533951 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:56.535376 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:56.536190 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:56.538225 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:56.538339 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:54:56.539850 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06192525754708888
2 days, 23:54:56.539957 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0619.
2 days, 23:54:56.540028 INFO: ==============================================
2 days, 23:54:56.540099 INFO: Starting optimization step 1.
2 days, 23:54:56.540169 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:56.540233 INFO: Using python extraction backend
2 days, 23:54:56.540331 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:56.540401 INFO: === Search parameters used ===
2 days, 23:54:56.540455 INFO: rt_error       : 9.254616087575595
2 days, 23:54:56.540513 INFO: mobility_error : 0.06192525754708888
2 days, 23:54:56.540562 INFO: num_candidates : 3
2 days, 23:54:56.540611 INFO: ms1_error      : 15.0
2 days, 23:54:56.540657 INFO: ms2_error      : 15.0
2 days, 23:54:56.540704 INFO: fwhm_rt        : 2.4984474182128906
2 days, 23:54:56.540750 INFO: quant_window   : 3
2 days, 23:54:56.540797 INFO: ==============================================
2 days, 23:54:56.541673 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:56.541724 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:56.541760 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:54:56.541785 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.96
2 days, 23:54:56.568874 INFO: Starting candidate selection
2 days, 23:54:57.150355 INFO: Starting candidate scoring
2 days, 23:54:57.256148 INFO: Finished candidate processing
2 days, 23:54:57.256264 INFO: Collecting candidate features
2 days, 23:54:57.268615 WARNING: intensity_correlation has 17 NaNs ( 0.54 % out of 3143)
2 days, 23:54:57.268872 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3143)
2 days, 23:54:57.273772 INFO: Collecting fragment features
2 days, 23:54:57.278297 INFO: Finished candidate scoring
2 days, 23:54:57.280352 INFO: performing precursor FDR with 47 features
2 days, 23:54:57.280405 INFO: Decoy channel: -1
2 days, 23:54:57.280437 INFO: competitive: True
2 days, 23:54:57.284878 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:57.286753 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:54:57.286817 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:54:57.286865 WARNING: FDR calculation for 1645 target and 1479 decoy PSMs
2 days, 23:54:57.286906 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:54:57.288061 INFO: Estimating optimal hyperparameters - samples: 2,499, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:57.288153 INFO: Using random state 708379 for train-test-split
2 days, 23:54:57.520909 INFO: Test AUC: 0.862
2 days, 23:54:57.521024 INFO: Train AUC: 0.897
2 days, 23:54:57.521061 INFO: AUC difference: 3.95%
2 days, 23:54:57.817343 INFO: Resetting torch num_threads to 80
2 days, 23:54:57.818058 PROGRESS: === Extracted 3143 precursors and 21626 fragments ===
2 days, 23:54:57.818554 INFO: === FDR correction performed with classifier version 12 ===
2 days, 23:54:57.819301 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:54:57.819407 PROGRESS: Total precursors accumulated: 599
2 days, 23:54:57.819476 PROGRESS: Target precursors: 592 (98.83%)
2 days, 23:54:57.819536 PROGRESS: Decoy precursors: 7 (1.17%)
2 days, 23:54:57.819592 PROGRESS: 
2 days, 23:54:57.819647 PROGRESS: Precursor Summary:
2 days, 23:54:57.821027 PROGRESS: Channel   0:	 0.050 FDR:   592; 0.010 FDR:   582; 0.001 FDR:   555
2 days, 23:54:57.821131 PROGRESS: 
2 days, 23:54:57.821202 PROGRESS: Protein Summary:
2 days, 23:54:57.822857 PROGRESS: Channel   0:	 0.050 FDR:   437; 0.010 FDR:   431; 0.001 FDR:   411
2 days, 23:54:57.822964 PROGRESS: =========================================================================
2 days, 23:54:57.823150 INFO: Target number of precursors reached.
2 days, 23:54:57.831192 INFO: fragments_df: keeping 5000 of 21626 [sum(precursor_idx_mask)=13261 sum(mass_error_mask)=21626 stop_rank=5000
2 days, 23:54:57.835368 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:58.016837 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:58.193253 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:58.427322 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:59.279549 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:54:59.280023 INFO: Using score_cutoff 15.763631884002685 (fac=0.99, q=1)
2 days, 23:54:59.280379 INFO: Updating optimization_manager: fwhm_rt             : 2.4984474182128906 -> 2.4865052700042725
2 days, 23:54:59.280477 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036229523830115795 -> 0.0036229523830115795
2 days, 23:54:59.280549 INFO: Updating optimization_manager: score_cutoff        : 15.817557764911651 -> 15.763631884002685
2 days, 23:54:59.280618 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:54:59.281733 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:54:59.283125 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:54:59.283945 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:54:59.285908 INFO: === checking if optimization conditions were reached ===
2 days, 23:54:59.286030 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:54:59.287629 INFO: Updating optimization_manager: mobility_error      : 0.06192525754708888 -> 0.04837263608169295
2 days, 23:54:59.287741 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0484.
2 days, 23:54:59.287825 INFO: ==============================================
2 days, 23:54:59.287908 INFO: Starting optimization step 2.
2 days, 23:54:59.287984 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:54:59.288060 INFO: Using python extraction backend
2 days, 23:54:59.288180 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:54:59.288260 INFO: === Search parameters used ===
2 days, 23:54:59.288323 INFO: rt_error       : 9.254616087575595
2 days, 23:54:59.288379 INFO: mobility_error : 0.04837263608169295
2 days, 23:54:59.288431 INFO: num_candidates : 3
2 days, 23:54:59.288484 INFO: ms1_error      : 15.0
2 days, 23:54:59.288544 INFO: ms2_error      : 15.0
2 days, 23:54:59.288598 INFO: fwhm_rt        : 2.4865052700042725
2 days, 23:54:59.288651 INFO: quant_window   : 3
2 days, 23:54:59.288703 INFO: ==============================================
2 days, 23:54:59.289555 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:54:59.289608 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:54:59.289646 INFO: FWHM in RT is 2.49 seconds, sigma is 0.41
2 days, 23:54:59.289681 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.96
2 days, 23:54:59.302029 INFO: Starting candidate selection
2 days, 23:54:59.785817 INFO: Starting candidate scoring
2 days, 23:54:59.886110 INFO: Finished candidate processing
2 days, 23:54:59.886236 INFO: Collecting candidate features
2 days, 23:54:59.902703 WARNING: intensity_correlation has 19 NaNs ( 0.61 % out of 3123)
2 days, 23:54:59.903050 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3123)
2 days, 23:54:59.910783 INFO: Collecting fragment features
2 days, 23:54:59.916594 INFO: Finished candidate scoring
2 days, 23:54:59.919812 INFO: performing precursor FDR with 47 features
2 days, 23:54:59.919905 INFO: Decoy channel: -1
2 days, 23:54:59.919941 INFO: competitive: True
2 days, 23:54:59.925536 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:54:59.927622 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:54:59.927692 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:54:59.927740 WARNING: FDR calculation for 1643 target and 1459 decoy PSMs
2 days, 23:54:59.927768 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:54:59.928745 INFO: Estimating optimal hyperparameters - samples: 2,481, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:54:59.928841 INFO: Using random state 708379 for train-test-split
2 days, 23:55:00.185987 INFO: Test AUC: 0.881
2 days, 23:55:00.186102 INFO: Train AUC: 0.889
2 days, 23:55:00.186139 INFO: AUC difference: 0.98%
2 days, 23:55:00.520984 INFO: Resetting torch num_threads to 80
2 days, 23:55:00.521722 PROGRESS: === Extracted 3123 precursors and 21348 fragments ===
2 days, 23:55:00.522304 INFO: === FDR correction performed with classifier version 12 ===
2 days, 23:55:00.523190 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:55:00.523328 PROGRESS: Total precursors accumulated: 599
2 days, 23:55:00.523436 PROGRESS: Target precursors: 589 (98.33%)
2 days, 23:55:00.523538 PROGRESS: Decoy precursors: 10 (1.67%)
2 days, 23:55:00.523634 PROGRESS: 
2 days, 23:55:00.523726 PROGRESS: Precursor Summary:
2 days, 23:55:00.525644 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   584; 0.001 FDR:   550
2 days, 23:55:00.525940 PROGRESS: 
2 days, 23:55:00.526059 PROGRESS: Protein Summary:
2 days, 23:55:00.528384 PROGRESS: Channel   0:	 0.050 FDR:   435; 0.010 FDR:   432; 0.001 FDR:   407
2 days, 23:55:00.528528 PROGRESS: =========================================================================
2 days, 23:55:00.528738 INFO: Target number of precursors reached.
2 days, 23:55:00.537999 INFO: fragments_df: keeping 5000 of 21348 [sum(precursor_idx_mask)=13221 sum(mass_error_mask)=21348 stop_rank=5000
2 days, 23:55:00.542919 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:00.724331 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:00.921788 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:01.126111 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:01.953599 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:55:01.954075 INFO: Using score_cutoff 13.881660215377808 (fac=0.99, q=1)
2 days, 23:55:01.954416 INFO: Updating optimization_manager: fwhm_rt             : 2.4865052700042725 -> 2.4941625595092773
2 days, 23:55:01.954509 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036229523830115795 -> 0.0035907006822526455
2 days, 23:55:01.954594 INFO: Updating optimization_manager: score_cutoff        : 15.763631884002685 -> 13.881660215377808
2 days, 23:55:01.954668 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:01.955769 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:01.957142 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:01.957971 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:01.959968 INFO: === checking if optimization conditions were reached ===
2 days, 23:55:01.960077 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:55:01.960823 INFO: Updating optimization_manager: mobility_error      : 0.04837263608169295 -> 0.04837263608169295
2 days, 23:55:01.960973 INFO: Updating optimization_manager: classifier_version  : 12 -> 15
2 days, 23:55:01.961091 INFO: Updating optimization_manager: score_cutoff        : 13.881660215377808 -> 13.881660215377808
2 days, 23:55:01.961200 INFO: Updating optimization_manager: fwhm_rt             : 2.4941625595092773 -> 2.4941625595092773
2 days, 23:55:01.961307 INFO: Updating optimization_manager: fwhm_mobility       : 0.0035907006822526455 -> 0.0035907006822526455
2 days, 23:55:01.961412 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0484 found after 3 searches.
2 days, 23:55:01.961488 INFO: ==============================================
2 days, 23:55:01.961568 PROGRESS: Optimization finished for mobility_error.
2 days, 23:55:01.964536 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:01.965390 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:01.966764 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:01.967586 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:01.969505 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:55:01.969613 PROGRESS: ==============================================
2 days, 23:55:01.969700 PROGRESS: ms2_error      : 15.0000
2 days, 23:55:01.969781 PROGRESS: ms1_error      : 15.0000
2 days, 23:55:01.969853 PROGRESS: rt_error       : 9.2546
2 days, 23:55:01.969948 PROGRESS: mobility_error : 0.0484
2 days, 23:55:01.970014 PROGRESS: ==============================================
2 days, 23:55:01.970654 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:01.974433 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:01.990565 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:01.994407 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:02.033158 INFO: Using python extraction backend
2 days, 23:55:02.033489 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:55:02.033623 INFO: === Search parameters used ===
2 days, 23:55:02.033722 INFO: rt_error       : 9.254616087575595
2 days, 23:55:02.033808 INFO: mobility_error : 0.04837263608169295
2 days, 23:55:02.033911 INFO: num_candidates : 3
2 days, 23:55:02.033994 INFO: ms1_error      : 15.0
2 days, 23:55:02.034076 INFO: ms2_error      : 15.0
2 days, 23:55:02.034157 INFO: fwhm_rt        : 2.4941625595092773
2 days, 23:55:02.034258 INFO: quant_window   : 3
2 days, 23:55:02.034355 INFO: ==============================================
2 days, 23:55:02.041417 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:55:02.041549 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:55:02.041611 INFO: FWHM in RT is 2.49 seconds, sigma is 0.42
2 days, 23:55:02.041648 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.95
2 days, 23:55:02.070025 INFO: Starting candidate selection
2 days, 23:55:03.673162 INFO: Removed 19720 precursors with score below cutoff 13.881660215377808
2 days, 23:55:03.982990 INFO: Starting candidate scoring
2 days, 23:55:04.853854 INFO: Finished candidate processing
2 days, 23:55:04.854004 INFO: Collecting candidate features
2 days, 23:55:04.962451 WARNING: intensity_correlation has 180 NaNs ( 0.32 % out of 56661)
2 days, 23:55:04.962873 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 56661)
2 days, 23:55:04.969442 INFO: Collecting fragment features
2 days, 23:55:05.009939 INFO: Finished candidate scoring
2 days, 23:55:05.048399 INFO: === Performing FDR correction with classifier version 15 ===
2 days, 23:55:05.048817 INFO: performing precursor FDR with 47 features
2 days, 23:55:05.048872 INFO: Decoy channel: -1
2 days, 23:55:05.048912 INFO: competitive: True
2 days, 23:55:05.069556 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:55:05.081688 WARNING: dropped 42 target PSMs due to missing features
2 days, 23:55:05.081845 WARNING: dropped 139 decoy PSMs due to missing features
2 days, 23:55:05.081928 WARNING: FDR calculation for 34765 target and 21715 decoy PSMs
2 days, 23:55:05.081967 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:55:05.094055 INFO: Estimating optimal hyperparameters - samples: 45,184, batch_size: 185, learning_rate: 2.13e-04
2 days, 23:55:05.094350 INFO: Using random state 454787 for train-test-split
2 days, 23:55:09.850786 INFO: Test AUC: 0.900
2 days, 23:55:09.850905 INFO: Train AUC: 0.909
2 days, 23:55:09.850945 INFO: AUC difference: 0.95%
2 days, 23:55:10.173935 INFO: Resetting torch num_threads to 80
2 days, 23:55:10.178247 INFO: Removing fragments below FDR threshold
2 days, 23:55:10.195630 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:55:10.195894 PROGRESS: Total precursors accumulated: 13,383
2 days, 23:55:10.196010 PROGRESS: Target precursors: 13,251 (99.01%)
2 days, 23:55:10.196131 PROGRESS: Decoy precursors: 132 (0.99%)
2 days, 23:55:10.196221 PROGRESS: 
2 days, 23:55:10.196303 PROGRESS: Precursor Summary:
2 days, 23:55:10.204767 PROGRESS: Channel   0:	 0.050 FDR: 13,251; 0.010 FDR: 13,251; 0.001 FDR: 12,570
2 days, 23:55:10.205083 PROGRESS: 
2 days, 23:55:10.205340 PROGRESS: Protein Summary:
2 days, 23:55:10.214420 PROGRESS: Channel   0:	 0.050 FDR: 1,683; 0.010 FDR: 1,683; 0.001 FDR: 1,681
2 days, 23:55:10.214670 PROGRESS: =========================================================================
2 days, 23:55:10.215783 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R1/psm.parquet
2 days, 23:55:10.281009 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R1/frag.parquet
2 days, 23:55:10.345284 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R1
2 days, 23:55:10.349350 PROGRESS: Loading raw file 8/12: B9_G_DIA_nLC_tTOF_R2 
2 days, 23:55:10.349460 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:55:10.349522 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R2/figures
2 days, 23:55:10.349696 INFO: Initializing TimingManager
2 days, 23:55:10.350140 INFO: Initializing RawFileManager
2 days, 23:55:10.350271 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:10.350321 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:10.350354 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:10.553072 INFO: Reading 22,624 frames with 313,858,254 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:14.355083 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d...
2 days, 23:55:14.356012 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:14.357848 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:14.358099 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:14.358524 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:14.360039 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:14.379700 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:14.379909 INFO: Indexing quadrupole dimension
2 days, 23:55:14.507290 INFO: Transposing detector events
2 days, 23:55:16.427989 INFO: Finished transposing data
2 days, 23:55:16.428227 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
2 days, 23:55:16.428684 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:55:16.428755 INFO: RT duration (sec)   : 2399.9
2 days, 23:55:16.428797 INFO: RT duration (min)   : 40.0
2 days, 23:55:16.428840 INFO: Cycle len (scans)   : 12
2 days, 23:55:16.428875 INFO: Cycle len (sec)     : 1.27
2 days, 23:55:16.428910 INFO: Number of cycles    : 1885
2 days, 23:55:16.428946 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:55:16.428993 INFO: Creating DIA data object took: 6.078720331192017
2 days, 23:55:16.436563 INFO: Initializing CalibrationManager
2 days, 23:55:16.436821 INFO: Setting up calibration estimators ..
2 days, 23:55:16.436930 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:55:16.437037 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:55:16.437159 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:55:16.437291 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:55:16.437417 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:55:16.437526 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:55:16.437627 INFO: Done setting up calibration estimators.
2 days, 23:55:16.437774 INFO: Initializing OptimizationManager
2 days, 23:55:16.437948 INFO: initial parameter: ms1_error = 30
2 days, 23:55:16.438041 INFO: initial parameter: ms2_error = 30
2 days, 23:55:16.438136 INFO: initial parameter: rt_error = 1199.9678125
2 days, 23:55:16.438223 INFO: initial parameter: mobility_error = 0.1
2 days, 23:55:16.438316 INFO: initial parameter: num_candidates = 1
2 days, 23:55:16.438404 INFO: initial parameter: fwhm_rt = 5
2 days, 23:55:16.438494 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:55:16.438583 INFO: initial parameter: score_cutoff = 0
2 days, 23:55:16.438664 INFO: initial parameter: classifier_version = -1
2 days, 23:55:16.438780 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R2
2 days, 23:55:16.438997 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:55:16.439046 INFO: Initializing FDRManager
2 days, 23:55:16.439092 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:55:16.448662 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:55:16.454243 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:55:16.454647 INFO: Updating optimization_manager: rt_error            : 1199.9678125 -> 1199.9678125
2 days, 23:55:16.454787 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:55:16.455054 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:55:16.455184 PROGRESS: Starting initial search for precursors.
2 days, 23:55:16.455297 INFO: Starting optimization step 0.
2 days, 23:55:16.455386 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:55:16.455503 INFO: Using python extraction backend
2 days, 23:55:16.455662 PROGRESS: Extracting batch of 399 precursors
2 days, 23:55:16.455758 INFO: === Search parameters used ===
2 days, 23:55:16.455832 INFO: rt_error       : 1199.9678125
2 days, 23:55:16.455907 INFO: mobility_error : 0.1
2 days, 23:55:16.455979 INFO: num_candidates : 1
2 days, 23:55:16.456045 INFO: ms1_error      : 30
2 days, 23:55:16.456110 INFO: ms2_error      : 30
2 days, 23:55:16.456177 INFO: fwhm_rt        : 5
2 days, 23:55:16.456242 INFO: quant_window   : 3
2 days, 23:55:16.456307 INFO: ==============================================
2 days, 23:55:16.457189 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:55:16.457251 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:55:16.457292 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:55:16.457326 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:55:16.482246 INFO: Starting candidate selection
2 days, 23:55:19.950087 INFO: Starting candidate scoring
2 days, 23:55:20.002130 INFO: Finished candidate processing
2 days, 23:55:20.002270 INFO: Collecting candidate features
2 days, 23:55:20.020263 INFO: Collecting fragment features
2 days, 23:55:20.024354 INFO: Finished candidate scoring
2 days, 23:55:20.025682 INFO: performing precursor FDR with 47 features
2 days, 23:55:20.025756 INFO: Decoy channel: -1
2 days, 23:55:20.025801 INFO: competitive: True
2 days, 23:55:20.027820 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:55:20.030465 INFO: Estimating optimal hyperparameters - samples: 318, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:55:20.031640 INFO: Using random state 864599 for train-test-split
2 days, 23:55:20.064900 INFO: Test AUC: 0.579
2 days, 23:55:20.065022 INFO: Train AUC: 0.673
2 days, 23:55:20.065064 INFO: AUC difference: 13.99%
2 days, 23:55:20.065095 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:55:20.399357 INFO: Resetting torch num_threads to 80
2 days, 23:55:20.399998 PROGRESS: === Extracted 398 precursors and 3673 fragments ===
2 days, 23:55:20.400600 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:55:20.401488 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:55:20.401619 PROGRESS: Total precursors accumulated: 200
2 days, 23:55:20.401733 PROGRESS: Target precursors: 140 (70.00%)
2 days, 23:55:20.401837 PROGRESS: Decoy precursors: 60 (30.00%)
2 days, 23:55:20.401952 PROGRESS: 
2 days, 23:55:20.402040 PROGRESS: Precursor Summary:
2 days, 23:55:20.403702 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 23:55:20.403834 PROGRESS: 
2 days, 23:55:20.403926 PROGRESS: Protein Summary:
2 days, 23:55:20.405717 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2 days, 23:55:20.405853 PROGRESS: =========================================================================
2 days, 23:55:20.406056 INFO: Target number of precursors not reached yet.
2 days, 23:55:20.410190 INFO: Starting optimization step 1.
2 days, 23:55:20.410346 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:55:20.410491 INFO: Using python extraction backend
2 days, 23:55:20.410664 PROGRESS: Extracting batch of 798 precursors
2 days, 23:55:20.410781 INFO: === Search parameters used ===
2 days, 23:55:20.410899 INFO: rt_error       : 1199.9678125
2 days, 23:55:20.411014 INFO: mobility_error : 0.1
2 days, 23:55:20.411131 INFO: num_candidates : 1
2 days, 23:55:20.411232 INFO: ms1_error      : 30
2 days, 23:55:20.411333 INFO: ms2_error      : 30
2 days, 23:55:20.411438 INFO: fwhm_rt        : 5
2 days, 23:55:20.411550 INFO: quant_window   : 3
2 days, 23:55:20.411652 INFO: ==============================================
2 days, 23:55:20.412702 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:55:20.412769 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:55:20.412832 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:55:20.412881 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:55:20.425039 INFO: Starting candidate selection
2 days, 23:55:26.397975 INFO: Starting candidate scoring
2 days, 23:55:26.472726 INFO: Finished candidate processing
2 days, 23:55:26.472836 INFO: Collecting candidate features
2 days, 23:55:26.486785 INFO: Collecting fragment features
2 days, 23:55:26.489813 INFO: Finished candidate scoring
2 days, 23:55:26.492286 INFO: performing precursor FDR with 47 features
2 days, 23:55:26.492344 INFO: Decoy channel: -1
2 days, 23:55:26.492376 INFO: competitive: True
2 days, 23:55:26.496105 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:55:26.498245 INFO: Estimating optimal hyperparameters - samples: 956, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:55:26.498342 INFO: Using random state 295563 for train-test-split
2 days, 23:55:26.611626 INFO: Test AUC: 0.779
2 days, 23:55:26.611746 INFO: Train AUC: 0.765
2 days, 23:55:26.611784 INFO: AUC difference: 1.94%
2 days, 23:55:26.884085 INFO: Resetting torch num_threads to 80
2 days, 23:55:26.885347 PROGRESS: === Extracted 1196 precursors and 11230 fragments ===
2 days, 23:55:26.885774 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:55:26.886513 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:55:26.886640 PROGRESS: Total precursors accumulated: 600
2 days, 23:55:26.886734 PROGRESS: Target precursors: 506 (84.33%)
2 days, 23:55:26.886824 PROGRESS: Decoy precursors: 94 (15.67%)
2 days, 23:55:26.886903 PROGRESS: 
2 days, 23:55:26.886974 PROGRESS: Precursor Summary:
2 days, 23:55:26.888095 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   254; 0.001 FDR:   202
2 days, 23:55:26.888206 PROGRESS: 
2 days, 23:55:26.888296 PROGRESS: Protein Summary:
2 days, 23:55:26.889550 PROGRESS: Channel   0:	 0.050 FDR:   221; 0.010 FDR:   188; 0.001 FDR:   151
2 days, 23:55:26.889680 PROGRESS: =========================================================================
2 days, 23:55:26.889884 INFO: Target number of precursors reached.
2 days, 23:55:26.893189 INFO: fragments_df: keeping 2159 of 11230 [sum(precursor_idx_mask)=2626 sum(mass_error_mask)=11230 stop_rank=2159
2 days, 23:55:26.896542 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:27.061421 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:27.235080 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:27.381081 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:27.843414 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:55:27.843902 INFO: Using score_cutoff 30.578036367988588 (fac=0.99, q=1)
2 days, 23:55:27.844301 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.7953975200653076
2 days, 23:55:27.844409 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007220354396849871
2 days, 23:55:27.844498 INFO: Updating optimization_manager: score_cutoff        : 0 -> 30.578036367988588
2 days, 23:55:27.844588 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:27.845771 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:27.847206 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:27.848043 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:27.850318 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2 days, 23:55:27.850450 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:55:27.850564 INFO: Starting optimization step 2.
2 days, 23:55:27.850656 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:55:27.850764 INFO: Using python extraction backend
2 days, 23:55:27.850896 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:55:27.850992 INFO: === Search parameters used ===
2 days, 23:55:27.851073 INFO: rt_error       : 1199.9678125
2 days, 23:55:27.851152 INFO: mobility_error : 0.1
2 days, 23:55:27.851234 INFO: num_candidates : 3
2 days, 23:55:27.851307 INFO: ms1_error      : 30
2 days, 23:55:27.851375 INFO: ms2_error      : 30
2 days, 23:55:27.851444 INFO: fwhm_rt        : 2.7953975200653076
2 days, 23:55:27.851513 INFO: quant_window   : 3
2 days, 23:55:27.851580 INFO: ==============================================
2 days, 23:55:27.852509 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:55:27.852570 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:55:27.852625 INFO: FWHM in RT is 2.80 seconds, sigma is 0.47
2 days, 23:55:27.852681 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.91
2 days, 23:55:27.866250 INFO: Starting candidate selection
2 days, 23:55:36.768884 INFO: Starting candidate scoring
2 days, 23:55:36.909843 INFO: Finished candidate processing
2 days, 23:55:36.909998 INFO: Collecting candidate features
2 days, 23:55:36.934301 INFO: Collecting fragment features
2 days, 23:55:36.940480 INFO: Finished candidate scoring
2 days, 23:55:36.943621 INFO: performing precursor FDR with 47 features
2 days, 23:55:36.943708 INFO: Decoy channel: -1
2 days, 23:55:36.943747 INFO: competitive: True
2 days, 23:55:36.948091 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:55:36.950362 INFO: Estimating optimal hyperparameters - samples: 2,764, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:55:36.950459 INFO: Using random state 986661 for train-test-split
2 days, 23:55:37.234613 INFO: Test AUC: 0.719
2 days, 23:55:37.234742 INFO: Train AUC: 0.703
2 days, 23:55:37.234797 INFO: AUC difference: 2.28%
2 days, 23:55:37.533159 INFO: Resetting torch num_threads to 80
2 days, 23:55:37.533849 PROGRESS: === Extracted 3455 precursors and 31286 fragments ===
2 days, 23:55:37.534316 INFO: === FDR correction performed with classifier version 1 ===
2 days, 23:55:37.534961 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:55:37.535078 PROGRESS: Total precursors accumulated: 600
2 days, 23:55:37.535168 PROGRESS: Target precursors: 507 (84.50%)
2 days, 23:55:37.535249 PROGRESS: Decoy precursors: 93 (15.50%)
2 days, 23:55:37.535324 PROGRESS: 
2 days, 23:55:37.535393 PROGRESS: Precursor Summary:
2 days, 23:55:37.536491 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   317; 0.001 FDR:   288
2 days, 23:55:37.536601 PROGRESS: 
2 days, 23:55:37.536685 PROGRESS: Protein Summary:
2 days, 23:55:37.537958 PROGRESS: Channel   0:	 0.050 FDR:   275; 0.010 FDR:   240; 0.001 FDR:   218
2 days, 23:55:37.538072 PROGRESS: =========================================================================
2 days, 23:55:37.538260 INFO: Target number of precursors reached.
2 days, 23:55:37.544874 INFO: fragments_df: keeping 5000 of 31286 [sum(precursor_idx_mask)=8859 sum(mass_error_mask)=31286 stop_rank=5000
2 days, 23:55:37.548948 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:37.730929 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:37.895367 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:38.047895 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:38.867449 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:55:38.867889 INFO: Using score_cutoff 30.69335916595459 (fac=0.99, q=1)
2 days, 23:55:38.868217 INFO: Updating optimization_manager: fwhm_rt             : 2.7953975200653076 -> 2.730236530303955
2 days, 23:55:38.868310 INFO: Updating optimization_manager: fwhm_mobility       : 0.007220354396849871 -> 0.00623706541955471
2 days, 23:55:38.868378 INFO: Updating optimization_manager: score_cutoff        : 30.578036367988588 -> 30.69335916595459
2 days, 23:55:38.868448 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:38.869584 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:38.870976 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:38.871790 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:38.873758 INFO: === checking if optimization conditions were reached ===
2 days, 23:55:38.875408 INFO: Updating optimization_manager: ms2_error           : 30 -> 18.423889970096084
2 days, 23:55:38.875517 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2 days, 23:55:38.875587 PROGRESS: ❌ ms2_error      : 18.4239 > 15.0000 or insufficient steps taken.
2 days, 23:55:38.876607 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:55:38.876706 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
2 days, 23:55:38.876772 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:55:38.876830 INFO: ==============================================
2 days, 23:55:38.876899 INFO: Starting optimization step 3.
2 days, 23:55:38.876960 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:55:38.877020 INFO: Using python extraction backend
2 days, 23:55:38.877119 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:55:38.877185 INFO: === Search parameters used ===
2 days, 23:55:38.877238 INFO: rt_error       : 1199.9678125
2 days, 23:55:38.877295 INFO: mobility_error : 0.1
2 days, 23:55:38.877345 INFO: num_candidates : 3
2 days, 23:55:38.877391 INFO: ms1_error      : 15.0
2 days, 23:55:38.877436 INFO: ms2_error      : 18.423889970096084
2 days, 23:55:38.877481 INFO: fwhm_rt        : 2.730236530303955
2 days, 23:55:38.877543 INFO: quant_window   : 3
2 days, 23:55:38.877595 INFO: ==============================================
2 days, 23:55:38.878451 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:55:38.878505 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:55:38.878542 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
2 days, 23:55:38.878565 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.38
2 days, 23:55:38.882696 INFO: Starting candidate selection
2 days, 23:55:46.925901 INFO: Starting candidate scoring
2 days, 23:55:47.034906 INFO: Finished candidate processing
2 days, 23:55:47.035011 INFO: Collecting candidate features
2 days, 23:55:47.045002 WARNING: intensity_correlation has 3 NaNs ( 0.09 % out of 3413)
2 days, 23:55:47.045279 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3413)
2 days, 23:55:47.049339 INFO: Collecting fragment features
2 days, 23:55:47.053517 INFO: Finished candidate scoring
2 days, 23:55:47.055534 INFO: performing precursor FDR with 47 features
2 days, 23:55:47.055598 INFO: Decoy channel: -1
2 days, 23:55:47.055635 INFO: competitive: True
2 days, 23:55:47.058903 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:55:47.060598 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:55:47.060666 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:55:47.061816 INFO: Estimating optimal hyperparameters - samples: 2,727, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:55:47.061939 INFO: Using random state 615334 for train-test-split
2 days, 23:55:47.298612 INFO: Test AUC: 0.727
2 days, 23:55:47.298730 INFO: Train AUC: 0.749
2 days, 23:55:47.298776 INFO: AUC difference: 2.89%
2 days, 23:55:47.567107 INFO: Resetting torch num_threads to 80
2 days, 23:55:47.567647 PROGRESS: === Extracted 3413 precursors and 28039 fragments ===
2 days, 23:55:47.568074 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:55:47.568677 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:55:47.568774 PROGRESS: Total precursors accumulated: 600
2 days, 23:55:47.568841 PROGRESS: Target precursors: 526 (87.67%)
2 days, 23:55:47.568897 PROGRESS: Decoy precursors: 74 (12.33%)
2 days, 23:55:47.568950 PROGRESS: 
2 days, 23:55:47.569010 PROGRESS: Precursor Summary:
2 days, 23:55:47.570102 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   361; 0.001 FDR:   335
2 days, 23:55:47.570201 PROGRESS: 
2 days, 23:55:47.570265 PROGRESS: Protein Summary:
2 days, 23:55:47.571522 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   271; 0.001 FDR:   251
2 days, 23:55:47.571619 PROGRESS: =========================================================================
2 days, 23:55:47.571778 INFO: Target number of precursors reached.
2 days, 23:55:47.577843 INFO: fragments_df: keeping 5000 of 28039 [sum(precursor_idx_mask)=9457 sum(mass_error_mask)=28039 stop_rank=5000
2 days, 23:55:47.582679 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:47.758600 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:47.986837 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:48.168840 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:48.939918 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:55:48.940409 INFO: Using score_cutoff 28.292165874481203 (fac=0.99, q=1)
2 days, 23:55:48.940778 INFO: Updating optimization_manager: fwhm_rt             : 2.730236530303955 -> 2.6049692630767822
2 days, 23:55:48.940881 INFO: Updating optimization_manager: fwhm_mobility       : 0.00623706541955471 -> 0.005398433189839125
2 days, 23:55:48.940963 INFO: Updating optimization_manager: score_cutoff        : 30.69335916595459 -> 28.292165874481203
2 days, 23:55:48.941046 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:48.942224 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:48.943659 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:48.944516 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:48.946575 INFO: === checking if optimization conditions were reached ===
2 days, 23:55:48.948359 INFO: Updating optimization_manager: ms2_error           : 18.423889970096084 -> 15.0
2 days, 23:55:48.948483 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:55:48.948575 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:55:48.949695 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:55:48.949810 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:55:48.949911 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:55:48.949998 INFO: ==============================================
2 days, 23:55:48.950090 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:55:48.953392 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:48.954336 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:48.955721 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:48.956551 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:48.958608 INFO: Starting optimization step 0.
2 days, 23:55:48.958734 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:55:48.958864 INFO: Using python extraction backend
2 days, 23:55:48.959025 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:55:48.959133 INFO: === Search parameters used ===
2 days, 23:55:48.959212 INFO: rt_error       : 1199.9678125
2 days, 23:55:48.959283 INFO: mobility_error : 0.1
2 days, 23:55:48.959352 INFO: num_candidates : 3
2 days, 23:55:48.959419 INFO: ms1_error      : 15.0
2 days, 23:55:48.959486 INFO: ms2_error      : 15.0
2 days, 23:55:48.959550 INFO: fwhm_rt        : 2.6049692630767822
2 days, 23:55:48.959615 INFO: quant_window   : 3
2 days, 23:55:48.959690 INFO: ==============================================
2 days, 23:55:48.960629 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:55:48.960686 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:55:48.960741 INFO: FWHM in RT is 2.60 seconds, sigma is 0.43
2 days, 23:55:48.960783 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.93
2 days, 23:55:48.967594 INFO: Starting candidate selection
2 days, 23:55:57.157202 INFO: Starting candidate scoring
2 days, 23:55:57.261391 INFO: Finished candidate processing
2 days, 23:55:57.261522 INFO: Collecting candidate features
2 days, 23:55:57.274803 WARNING: intensity_correlation has 3 NaNs ( 0.09 % out of 3404)
2 days, 23:55:57.278910 INFO: Collecting fragment features
2 days, 23:55:57.283166 INFO: Finished candidate scoring
2 days, 23:55:57.285152 INFO: performing precursor FDR with 47 features
2 days, 23:55:57.285293 INFO: Decoy channel: -1
2 days, 23:55:57.285352 INFO: competitive: True
2 days, 23:55:57.288734 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:55:57.290498 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:55:57.290564 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:55:57.291691 INFO: Estimating optimal hyperparameters - samples: 2,720, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:55:57.291796 INFO: Using random state 91840 for train-test-split
2 days, 23:55:57.655376 INFO: Test AUC: 0.745
2 days, 23:55:57.655531 INFO: Train AUC: 0.771
2 days, 23:55:57.655594 INFO: AUC difference: 3.34%
2 days, 23:55:57.981698 INFO: Resetting torch num_threads to 80
2 days, 23:55:57.982298 PROGRESS: === Extracted 3404 precursors and 26899 fragments ===
2 days, 23:55:57.982785 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:55:57.983431 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:55:57.983542 PROGRESS: Total precursors accumulated: 600
2 days, 23:55:57.983632 PROGRESS: Target precursors: 532 (88.67%)
2 days, 23:55:57.983722 PROGRESS: Decoy precursors: 68 (11.33%)
2 days, 23:55:57.983800 PROGRESS: 
2 days, 23:55:57.983874 PROGRESS: Precursor Summary:
2 days, 23:55:57.985006 PROGRESS: Channel   0:	 0.050 FDR:   455; 0.010 FDR:   361; 0.001 FDR:   344
2 days, 23:55:57.985116 PROGRESS: 
2 days, 23:55:57.985205 PROGRESS: Protein Summary:
2 days, 23:55:57.986537 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   268; 0.001 FDR:   255
2 days, 23:55:57.986652 PROGRESS: =========================================================================
2 days, 23:55:57.986846 INFO: Target number of precursors reached.
2 days, 23:55:57.993008 INFO: fragments_df: keeping 5000 of 26899 [sum(precursor_idx_mask)=9314 sum(mass_error_mask)=26899 stop_rank=5000
2 days, 23:55:57.997062 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:58.191917 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:58.382247 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:58.559786 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:59.418395 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:55:59.418983 INFO: Using score_cutoff 28.92842547225952 (fac=0.99, q=1)
2 days, 23:55:59.419456 INFO: Updating optimization_manager: fwhm_rt             : 2.6049692630767822 -> 2.602555274963379
2 days, 23:55:59.419583 INFO: Updating optimization_manager: fwhm_mobility       : 0.005398433189839125 -> 0.005112890154123306
2 days, 23:55:59.419679 INFO: Updating optimization_manager: score_cutoff        : 28.292165874481203 -> 28.92842547225952
2 days, 23:55:59.419780 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:55:59.421321 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:55:59.423138 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:55:59.424283 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:55:59.426805 INFO: === checking if optimization conditions were reached ===
2 days, 23:55:59.426950 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:55:59.429327 INFO: Updating optimization_manager: rt_error            : 1199.9678125 -> 214.55630546695974
2 days, 23:55:59.429474 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 214.5563.
2 days, 23:55:59.429572 INFO: ==============================================
2 days, 23:55:59.429694 INFO: Starting optimization step 1.
2 days, 23:55:59.429799 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:55:59.429918 INFO: Using python extraction backend
2 days, 23:55:59.430082 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:55:59.430205 INFO: === Search parameters used ===
2 days, 23:55:59.430308 INFO: rt_error       : 214.55630546695974
2 days, 23:55:59.430392 INFO: mobility_error : 0.1
2 days, 23:55:59.430467 INFO: num_candidates : 3
2 days, 23:55:59.430537 INFO: ms1_error      : 15.0
2 days, 23:55:59.430606 INFO: ms2_error      : 15.0
2 days, 23:55:59.430675 INFO: fwhm_rt        : 2.602555274963379
2 days, 23:55:59.430745 INFO: quant_window   : 3
2 days, 23:55:59.430813 INFO: ==============================================
2 days, 23:55:59.432007 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:55:59.432073 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:55:59.432131 INFO: FWHM in RT is 2.60 seconds, sigma is 0.43
2 days, 23:55:59.432174 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.77
2 days, 23:55:59.442087 INFO: Starting candidate selection
2 days, 23:56:01.881656 INFO: Starting candidate scoring
2 days, 23:56:01.994382 INFO: Finished candidate processing
2 days, 23:56:01.994516 INFO: Collecting candidate features
2 days, 23:56:02.011500 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3384)
2 days, 23:56:02.019589 INFO: Collecting fragment features
2 days, 23:56:02.025382 INFO: Finished candidate scoring
2 days, 23:56:02.028885 INFO: performing precursor FDR with 47 features
2 days, 23:56:02.028970 INFO: Decoy channel: -1
2 days, 23:56:02.029017 INFO: competitive: True
2 days, 23:56:02.033680 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:02.035980 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:56:02.036052 WARNING: dropped 3 decoy PSMs due to missing features
2 days, 23:56:02.037508 INFO: Estimating optimal hyperparameters - samples: 2,704, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:02.037616 INFO: Using random state 91840 for train-test-split
2 days, 23:56:02.366406 INFO: Test AUC: 0.801
2 days, 23:56:02.366546 INFO: Train AUC: 0.809
2 days, 23:56:02.366599 INFO: AUC difference: 1.02%
2 days, 23:56:02.677196 INFO: Resetting torch num_threads to 80
2 days, 23:56:02.677728 PROGRESS: === Extracted 3384 precursors and 25687 fragments ===
2 days, 23:56:02.678170 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:56:02.678795 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:02.678886 PROGRESS: Total precursors accumulated: 600
2 days, 23:56:02.678951 PROGRESS: Target precursors: 557 (92.83%)
2 days, 23:56:02.679004 PROGRESS: Decoy precursors: 43 (7.17%)
2 days, 23:56:02.679054 PROGRESS: 
2 days, 23:56:02.679102 PROGRESS: Precursor Summary:
2 days, 23:56:02.680197 PROGRESS: Channel   0:	 0.050 FDR:   526; 0.010 FDR:   429; 0.001 FDR:   315
2 days, 23:56:02.680290 PROGRESS: 
2 days, 23:56:02.680349 PROGRESS: Protein Summary:
2 days, 23:56:02.681632 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   322; 0.001 FDR:   243
2 days, 23:56:02.681798 PROGRESS: =========================================================================
2 days, 23:56:02.681955 INFO: Target number of precursors reached.
2 days, 23:56:02.687926 INFO: fragments_df: keeping 5000 of 25687 [sum(precursor_idx_mask)=10624 sum(mass_error_mask)=25687 stop_rank=5000
2 days, 23:56:02.691276 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:02.934128 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:03.144087 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:03.403500 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:04.322869 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:04.323338 INFO: Using score_cutoff 21.571219006347658 (fac=0.99, q=1)
2 days, 23:56:04.323685 INFO: Updating optimization_manager: fwhm_rt             : 2.602555274963379 -> 2.526331663131714
2 days, 23:56:04.323788 INFO: Updating optimization_manager: fwhm_mobility       : 0.005112890154123306 -> 0.004501124378293753
2 days, 23:56:04.323871 INFO: Updating optimization_manager: score_cutoff        : 28.92842547225952 -> 21.571219006347658
2 days, 23:56:04.323952 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:04.325089 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:04.326494 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:04.327319 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:04.329330 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:04.329445 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:56:04.331209 INFO: Updating optimization_manager: rt_error            : 214.55630546695974 -> 37.91014843472425
2 days, 23:56:04.331325 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 37.9101.
2 days, 23:56:04.331417 INFO: ==============================================
2 days, 23:56:04.331505 INFO: Starting optimization step 2.
2 days, 23:56:04.331581 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:56:04.331649 INFO: Using python extraction backend
2 days, 23:56:04.331761 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:56:04.331836 INFO: === Search parameters used ===
2 days, 23:56:04.331901 INFO: rt_error       : 37.91014843472425
2 days, 23:56:04.331956 INFO: mobility_error : 0.1
2 days, 23:56:04.332006 INFO: num_candidates : 3
2 days, 23:56:04.332057 INFO: ms1_error      : 15.0
2 days, 23:56:04.332109 INFO: ms2_error      : 15.0
2 days, 23:56:04.332160 INFO: fwhm_rt        : 2.526331663131714
2 days, 23:56:04.332212 INFO: quant_window   : 3
2 days, 23:56:04.332262 INFO: ==============================================
2 days, 23:56:04.333082 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:04.333136 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:04.333177 INFO: FWHM in RT is 2.53 seconds, sigma is 0.42
2 days, 23:56:04.333206 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.44
2 days, 23:56:04.346023 INFO: Starting candidate selection
2 days, 23:56:05.057468 INFO: Starting candidate scoring
2 days, 23:56:05.171858 INFO: Finished candidate processing
2 days, 23:56:05.171967 INFO: Collecting candidate features
2 days, 23:56:05.181598 WARNING: intensity_correlation has 13 NaNs ( 0.40 % out of 3248)
2 days, 23:56:05.181847 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3248)
2 days, 23:56:05.185812 INFO: Collecting fragment features
2 days, 23:56:05.190995 INFO: Finished candidate scoring
2 days, 23:56:05.194256 INFO: performing precursor FDR with 47 features
2 days, 23:56:05.194354 INFO: Decoy channel: -1
2 days, 23:56:05.194399 INFO: competitive: True
2 days, 23:56:05.199188 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:05.201701 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:56:05.201788 WARNING: dropped 11 decoy PSMs due to missing features
2 days, 23:56:05.203307 INFO: Estimating optimal hyperparameters - samples: 2,588, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:05.203436 INFO: Using random state 91840 for train-test-split
2 days, 23:56:05.533694 INFO: Test AUC: 0.847
2 days, 23:56:05.533816 INFO: Train AUC: 0.868
2 days, 23:56:05.533847 INFO: AUC difference: 2.37%
2 days, 23:56:05.840918 INFO: Resetting torch num_threads to 80
2 days, 23:56:05.841638 PROGRESS: === Extracted 3248 precursors and 23107 fragments ===
2 days, 23:56:05.842229 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:56:05.843091 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:05.843206 PROGRESS: Total precursors accumulated: 600
2 days, 23:56:05.843290 PROGRESS: Target precursors: 583 (97.17%)
2 days, 23:56:05.843365 PROGRESS: Decoy precursors: 17 (2.83%)
2 days, 23:56:05.843436 PROGRESS: 
2 days, 23:56:05.843511 PROGRESS: Precursor Summary:
2 days, 23:56:05.845142 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   552; 0.001 FDR:   352
2 days, 23:56:05.845255 PROGRESS: 
2 days, 23:56:05.845334 PROGRESS: Protein Summary:
2 days, 23:56:05.847201 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   408; 0.001 FDR:   270
2 days, 23:56:05.847317 PROGRESS: =========================================================================
2 days, 23:56:05.847489 INFO: Target number of precursors reached.
2 days, 23:56:05.856440 INFO: fragments_df: keeping 5000 of 23107 [sum(precursor_idx_mask)=12978 sum(mass_error_mask)=23107 stop_rank=5000
2 days, 23:56:05.861425 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:06.048693 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:06.260463 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:06.442439 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:07.182442 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:07.182910 INFO: Using score_cutoff 16.596926403236388 (fac=0.99, q=1)
2 days, 23:56:07.183256 INFO: Updating optimization_manager: fwhm_rt             : 2.526331663131714 -> 2.497955799102783
2 days, 23:56:07.183345 INFO: Updating optimization_manager: fwhm_mobility       : 0.004501124378293753 -> 0.0037675509229302406
2 days, 23:56:07.183413 INFO: Updating optimization_manager: score_cutoff        : 21.571219006347658 -> 16.596926403236388
2 days, 23:56:07.183479 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:07.184599 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:07.186009 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:07.186825 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:07.188938 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:07.189050 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:56:07.191027 INFO: Updating optimization_manager: rt_error            : 37.91014843472425 -> 20.63598999750065
2 days, 23:56:07.191152 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 20.6360.
2 days, 23:56:07.191238 INFO: ==============================================
2 days, 23:56:07.191320 INFO: Starting optimization step 3.
2 days, 23:56:07.191397 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:56:07.191465 INFO: Using python extraction backend
2 days, 23:56:07.191571 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:56:07.191647 INFO: === Search parameters used ===
2 days, 23:56:07.191703 INFO: rt_error       : 20.63598999750065
2 days, 23:56:07.191755 INFO: mobility_error : 0.1
2 days, 23:56:07.191804 INFO: num_candidates : 3
2 days, 23:56:07.191854 INFO: ms1_error      : 15.0
2 days, 23:56:07.191904 INFO: ms2_error      : 15.0
2 days, 23:56:07.191952 INFO: fwhm_rt        : 2.497955799102783
2 days, 23:56:07.192003 INFO: quant_window   : 3
2 days, 23:56:07.192051 INFO: ==============================================
2 days, 23:56:07.192894 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:07.192946 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:07.192985 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:56:07.193012 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.04
2 days, 23:56:07.199061 INFO: Starting candidate selection
2 days, 23:56:07.858717 INFO: Starting candidate scoring
2 days, 23:56:07.962191 INFO: Finished candidate processing
2 days, 23:56:07.962311 INFO: Collecting candidate features
2 days, 23:56:07.971973 WARNING: intensity_correlation has 25 NaNs ( 0.78 % out of 3206)
2 days, 23:56:07.976025 INFO: Collecting fragment features
2 days, 23:56:07.979633 INFO: Finished candidate scoring
2 days, 23:56:07.981359 INFO: performing precursor FDR with 47 features
2 days, 23:56:07.981431 INFO: Decoy channel: -1
2 days, 23:56:07.981473 INFO: competitive: True
2 days, 23:56:07.984454 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:07.986089 WARNING: dropped 5 target PSMs due to missing features
2 days, 23:56:07.986159 WARNING: dropped 20 decoy PSMs due to missing features
2 days, 23:56:07.987218 INFO: Estimating optimal hyperparameters - samples: 2,544, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:07.987315 INFO: Using random state 91840 for train-test-split
2 days, 23:56:08.297473 INFO: Test AUC: 0.861
2 days, 23:56:08.297583 INFO: Train AUC: 0.889
2 days, 23:56:08.297627 INFO: AUC difference: 3.19%
2 days, 23:56:08.584672 INFO: Resetting torch num_threads to 80
2 days, 23:56:08.585241 PROGRESS: === Extracted 3206 precursors and 22383 fragments ===
2 days, 23:56:08.585694 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:56:08.586335 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:08.586451 PROGRESS: Total precursors accumulated: 600
2 days, 23:56:08.586545 PROGRESS: Target precursors: 584 (97.33%)
2 days, 23:56:08.586627 PROGRESS: Decoy precursors: 16 (2.67%)
2 days, 23:56:08.586702 PROGRESS: 
2 days, 23:56:08.586770 PROGRESS: Precursor Summary:
2 days, 23:56:08.587961 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   558; 0.001 FDR:   395
2 days, 23:56:08.588069 PROGRESS: 
2 days, 23:56:08.588155 PROGRESS: Protein Summary:
2 days, 23:56:08.589535 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   410; 0.001 FDR:   300
2 days, 23:56:08.589648 PROGRESS: =========================================================================
2 days, 23:56:08.589825 INFO: Target number of precursors reached.
2 days, 23:56:08.595981 INFO: fragments_df: keeping 5000 of 22383 [sum(precursor_idx_mask)=13205 sum(mass_error_mask)=22383 stop_rank=5000
2 days, 23:56:08.599319 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:08.785855 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:09.050640 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:09.248090 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:10.060092 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:10.060584 INFO: Using score_cutoff 16.33197830657959 (fac=0.99, q=1)
2 days, 23:56:10.060971 INFO: Updating optimization_manager: fwhm_rt             : 2.497955799102783 -> 2.5028018951416016
2 days, 23:56:10.061070 INFO: Updating optimization_manager: fwhm_mobility       : 0.0037675509229302406 -> 0.0036961473524570465
2 days, 23:56:10.061146 INFO: Updating optimization_manager: score_cutoff        : 16.596926403236388 -> 16.33197830657959
2 days, 23:56:10.061218 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:10.062378 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:10.063846 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:10.064744 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:10.066865 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:10.066997 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:56:10.069218 INFO: Updating optimization_manager: rt_error            : 20.63598999750065 -> 14.505196517743046
2 days, 23:56:10.069352 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 14.5052.
2 days, 23:56:10.069464 INFO: ==============================================
2 days, 23:56:10.069568 INFO: Starting optimization step 4.
2 days, 23:56:10.069658 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:56:10.069746 INFO: Using python extraction backend
2 days, 23:56:10.069898 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:56:10.070004 INFO: === Search parameters used ===
2 days, 23:56:10.070079 INFO: rt_error       : 14.505196517743046
2 days, 23:56:10.070147 INFO: mobility_error : 0.1
2 days, 23:56:10.070220 INFO: num_candidates : 3
2 days, 23:56:10.070288 INFO: ms1_error      : 15.0
2 days, 23:56:10.070352 INFO: ms2_error      : 15.0
2 days, 23:56:10.070416 INFO: fwhm_rt        : 2.5028018951416016
2 days, 23:56:10.070480 INFO: quant_window   : 3
2 days, 23:56:10.070543 INFO: ==============================================
2 days, 23:56:10.071802 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:10.071866 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:10.071920 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:56:10.071972 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.00
2 days, 23:56:10.086369 INFO: Starting candidate selection
2 days, 23:56:10.678499 INFO: Starting candidate scoring
2 days, 23:56:10.793555 INFO: Finished candidate processing
2 days, 23:56:10.793671 INFO: Collecting candidate features
2 days, 23:56:10.805673 WARNING: intensity_correlation has 29 NaNs ( 0.91 % out of 3189)
2 days, 23:56:10.805931 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3189)
2 days, 23:56:10.811747 INFO: Collecting fragment features
2 days, 23:56:10.816270 INFO: Finished candidate scoring
2 days, 23:56:10.818280 INFO: performing precursor FDR with 47 features
2 days, 23:56:10.818335 INFO: Decoy channel: -1
2 days, 23:56:10.818366 INFO: competitive: True
2 days, 23:56:10.822083 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:10.823947 WARNING: dropped 7 target PSMs due to missing features
2 days, 23:56:10.824003 WARNING: dropped 22 decoy PSMs due to missing features
2 days, 23:56:10.824049 WARNING: FDR calculation for 1661 target and 1499 decoy PSMs
2 days, 23:56:10.824078 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:56:10.825210 INFO: Estimating optimal hyperparameters - samples: 2,528, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:10.825303 INFO: Using random state 91840 for train-test-split
2 days, 23:56:11.125439 INFO: Test AUC: 0.862
2 days, 23:56:11.125578 INFO: Train AUC: 0.887
2 days, 23:56:11.125616 INFO: AUC difference: 2.76%
2 days, 23:56:11.428266 INFO: Resetting torch num_threads to 80
2 days, 23:56:11.428909 PROGRESS: === Extracted 3189 precursors and 22120 fragments ===
2 days, 23:56:11.429395 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:56:11.430131 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:11.430239 PROGRESS: Total precursors accumulated: 600
2 days, 23:56:11.430309 PROGRESS: Target precursors: 589 (98.17%)
2 days, 23:56:11.430370 PROGRESS: Decoy precursors: 11 (1.83%)
2 days, 23:56:11.430427 PROGRESS: 
2 days, 23:56:11.430482 PROGRESS: Precursor Summary:
2 days, 23:56:11.431860 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   573; 0.001 FDR:   390
2 days, 23:56:11.431960 PROGRESS: 
2 days, 23:56:11.432025 PROGRESS: Protein Summary:
2 days, 23:56:11.433671 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   418; 0.001 FDR:   294
2 days, 23:56:11.433773 PROGRESS: =========================================================================
2 days, 23:56:11.433954 INFO: Target number of precursors reached.
2 days, 23:56:11.442160 INFO: fragments_df: keeping 5000 of 22120 [sum(precursor_idx_mask)=13430 sum(mass_error_mask)=22120 stop_rank=5000
2 days, 23:56:11.446260 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:11.736611 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:11.942307 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:12.142129 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:12.910339 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:12.910845 INFO: Using score_cutoff 15.129804988861084 (fac=0.99, q=1)
2 days, 23:56:12.911209 INFO: Updating optimization_manager: fwhm_rt             : 2.5028018951416016 -> 2.4832265377044678
2 days, 23:56:12.911308 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036961473524570465 -> 0.0036105462349951267
2 days, 23:56:12.911388 INFO: Updating optimization_manager: score_cutoff        : 16.33197830657959 -> 15.129804988861084
2 days, 23:56:12.911470 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:12.912615 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:12.914061 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:12.914897 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:12.916914 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:12.917035 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:56:12.919040 INFO: Updating optimization_manager: rt_error            : 14.505196517743046 -> 13.05983685710164
2 days, 23:56:12.919168 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 13.0598.
2 days, 23:56:12.919269 INFO: ==============================================
2 days, 23:56:12.919383 INFO: Starting optimization step 5.
2 days, 23:56:12.919480 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:56:12.919571 INFO: Using python extraction backend
2 days, 23:56:12.919707 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:56:12.919799 INFO: === Search parameters used ===
2 days, 23:56:12.919876 INFO: rt_error       : 13.05983685710164
2 days, 23:56:12.919943 INFO: mobility_error : 0.1
2 days, 23:56:12.920005 INFO: num_candidates : 3
2 days, 23:56:12.920066 INFO: ms1_error      : 15.0
2 days, 23:56:12.920127 INFO: ms2_error      : 15.0
2 days, 23:56:12.920186 INFO: fwhm_rt        : 2.4832265377044678
2 days, 23:56:12.920245 INFO: quant_window   : 3
2 days, 23:56:12.920305 INFO: ==============================================
2 days, 23:56:12.921196 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:12.921247 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:12.921296 INFO: FWHM in RT is 2.48 seconds, sigma is 0.41
2 days, 23:56:12.921350 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.96
2 days, 23:56:12.930065 INFO: Starting candidate selection
2 days, 23:56:13.486164 INFO: Starting candidate scoring
2 days, 23:56:13.586688 INFO: Finished candidate processing
2 days, 23:56:13.586854 INFO: Collecting candidate features
2 days, 23:56:13.597792 WARNING: intensity_correlation has 31 NaNs ( 0.97 % out of 3184)
2 days, 23:56:13.598128 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3184)
2 days, 23:56:13.602067 INFO: Collecting fragment features
2 days, 23:56:13.607078 INFO: Finished candidate scoring
2 days, 23:56:13.610039 INFO: performing precursor FDR with 47 features
2 days, 23:56:13.610110 INFO: Decoy channel: -1
2 days, 23:56:13.610153 INFO: competitive: True
2 days, 23:56:13.614703 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:13.617070 WARNING: dropped 8 target PSMs due to missing features
2 days, 23:56:13.617142 WARNING: dropped 23 decoy PSMs due to missing features
2 days, 23:56:13.617209 WARNING: FDR calculation for 1665 target and 1488 decoy PSMs
2 days, 23:56:13.617259 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:56:13.618674 INFO: Estimating optimal hyperparameters - samples: 2,522, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:13.618810 INFO: Using random state 91840 for train-test-split
2 days, 23:56:13.873660 INFO: Test AUC: 0.889
2 days, 23:56:13.873791 INFO: Train AUC: 0.881
2 days, 23:56:13.873847 INFO: AUC difference: 0.90%
2 days, 23:56:14.240890 INFO: Resetting torch num_threads to 80
2 days, 23:56:14.241568 PROGRESS: === Extracted 3184 precursors and 22087 fragments ===
2 days, 23:56:14.242177 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:56:14.243073 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:14.243212 PROGRESS: Total precursors accumulated: 600
2 days, 23:56:14.243324 PROGRESS: Target precursors: 586 (97.67%)
2 days, 23:56:14.243428 PROGRESS: Decoy precursors: 14 (2.33%)
2 days, 23:56:14.243527 PROGRESS: 
2 days, 23:56:14.243620 PROGRESS: Precursor Summary:
2 days, 23:56:14.245510 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   563; 0.001 FDR:   328
2 days, 23:56:14.245664 PROGRESS: 
2 days, 23:56:14.245779 PROGRESS: Protein Summary:
2 days, 23:56:14.247998 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   411; 0.001 FDR:   255
2 days, 23:56:14.248134 PROGRESS: =========================================================================
2 days, 23:56:14.248339 INFO: Target number of precursors reached.
2 days, 23:56:14.257658 INFO: fragments_df: keeping 5000 of 22087 [sum(precursor_idx_mask)=13291 sum(mass_error_mask)=22087 stop_rank=5000
2 days, 23:56:14.263396 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:14.496288 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:14.701674 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:14.897566 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:15.637142 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:15.637670 INFO: Using score_cutoff 15.033959767913819 (fac=0.99, q=1)
2 days, 23:56:15.638064 INFO: Updating optimization_manager: fwhm_rt             : 2.4832265377044678 -> 2.48889422416687
2 days, 23:56:15.638179 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036105462349951267 -> 0.0036562837194651365
2 days, 23:56:15.638267 INFO: Updating optimization_manager: score_cutoff        : 15.129804988861084 -> 15.033959767913819
2 days, 23:56:15.638364 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:15.639539 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:15.640962 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:15.641799 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:15.643912 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:15.644049 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 23:56:15.646091 INFO: Updating optimization_manager: rt_error            : 13.05983685710164 -> 11.770216650009584
2 days, 23:56:15.646230 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 11.7702.
2 days, 23:56:15.646334 INFO: ==============================================
2 days, 23:56:15.646446 INFO: Starting optimization step 6.
2 days, 23:56:15.646539 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:56:15.646622 INFO: Using python extraction backend
2 days, 23:56:15.646752 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:56:15.646860 INFO: === Search parameters used ===
2 days, 23:56:15.646943 INFO: rt_error       : 11.770216650009584
2 days, 23:56:15.647015 INFO: mobility_error : 0.1
2 days, 23:56:15.647078 INFO: num_candidates : 3
2 days, 23:56:15.647139 INFO: ms1_error      : 15.0
2 days, 23:56:15.647199 INFO: ms2_error      : 15.0
2 days, 23:56:15.647260 INFO: fwhm_rt        : 2.48889422416687
2 days, 23:56:15.647321 INFO: quant_window   : 3
2 days, 23:56:15.647382 INFO: ==============================================
2 days, 23:56:15.648262 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:15.648322 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:15.648372 INFO: FWHM in RT is 2.49 seconds, sigma is 0.42
2 days, 23:56:15.648405 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.98
2 days, 23:56:15.658302 INFO: Starting candidate selection
2 days, 23:56:16.314546 INFO: Starting candidate scoring
2 days, 23:56:16.414605 INFO: Finished candidate processing
2 days, 23:56:16.414737 INFO: Collecting candidate features
2 days, 23:56:16.427107 WARNING: intensity_correlation has 27 NaNs ( 0.85 % out of 3176)
2 days, 23:56:16.427353 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3176)
2 days, 23:56:16.432333 INFO: Collecting fragment features
2 days, 23:56:16.436675 INFO: Finished candidate scoring
2 days, 23:56:16.439039 INFO: performing precursor FDR with 47 features
2 days, 23:56:16.439163 INFO: Decoy channel: -1
2 days, 23:56:16.439238 INFO: competitive: True
2 days, 23:56:16.443054 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:16.445034 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:56:16.445152 WARNING: dropped 21 decoy PSMs due to missing features
2 days, 23:56:16.445251 WARNING: FDR calculation for 1659 target and 1490 decoy PSMs
2 days, 23:56:16.445328 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:56:16.446597 INFO: Estimating optimal hyperparameters - samples: 2,519, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:16.446747 INFO: Using random state 91840 for train-test-split
2 days, 23:56:16.670062 INFO: Test AUC: 0.880
2 days, 23:56:16.670173 INFO: Train AUC: 0.886
2 days, 23:56:16.670212 INFO: AUC difference: 0.64%
2 days, 23:56:16.956596 INFO: Resetting torch num_threads to 80
2 days, 23:56:16.957293 PROGRESS: === Extracted 3176 precursors and 21982 fragments ===
2 days, 23:56:16.957879 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:56:16.958804 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:16.958933 PROGRESS: Total precursors accumulated: 600
2 days, 23:56:16.959035 PROGRESS: Target precursors: 585 (97.50%)
2 days, 23:56:16.959135 PROGRESS: Decoy precursors: 15 (2.50%)
2 days, 23:56:16.959229 PROGRESS: 
2 days, 23:56:16.959320 PROGRESS: Precursor Summary:
2 days, 23:56:16.961218 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   548; 0.001 FDR:   361
2 days, 23:56:16.961335 PROGRESS: 
2 days, 23:56:16.961417 PROGRESS: Protein Summary:
2 days, 23:56:16.963617 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   403; 0.001 FDR:   279
2 days, 23:56:16.963756 PROGRESS: =========================================================================
2 days, 23:56:16.963962 INFO: Target number of precursors reached.
2 days, 23:56:16.973211 INFO: fragments_df: keeping 5000 of 21982 [sum(precursor_idx_mask)=13010 sum(mass_error_mask)=21982 stop_rank=5000
2 days, 23:56:16.977959 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:17.230465 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:17.431576 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:17.625699 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:18.393477 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:18.393968 INFO: Using score_cutoff 16.145349933815 (fac=0.99, q=1)
2 days, 23:56:18.394325 INFO: Updating optimization_manager: fwhm_rt             : 2.48889422416687 -> 2.4899234771728516
2 days, 23:56:18.394426 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036562837194651365 -> 0.003706618444994092
2 days, 23:56:18.394503 INFO: Updating optimization_manager: score_cutoff        : 15.033959767913819 -> 16.145349933815
2 days, 23:56:18.394571 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:18.395688 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:18.397079 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:18.397909 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:18.399929 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:18.400048 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 23:56:18.401997 INFO: Updating optimization_manager: rt_error            : 11.770216650009584 -> 11.205700932495555
2 days, 23:56:18.402114 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 11.2057.
2 days, 23:56:18.402193 INFO: ==============================================
2 days, 23:56:18.402271 INFO: Starting optimization step 7.
2 days, 23:56:18.402341 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:56:18.402408 INFO: Using python extraction backend
2 days, 23:56:18.402514 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:56:18.402588 INFO: === Search parameters used ===
2 days, 23:56:18.402646 INFO: rt_error       : 11.205700932495555
2 days, 23:56:18.402699 INFO: mobility_error : 0.1
2 days, 23:56:18.402753 INFO: num_candidates : 3
2 days, 23:56:18.402806 INFO: ms1_error      : 15.0
2 days, 23:56:18.402870 INFO: ms2_error      : 15.0
2 days, 23:56:18.402925 INFO: fwhm_rt        : 2.4899234771728516
2 days, 23:56:18.402976 INFO: quant_window   : 3
2 days, 23:56:18.403027 INFO: ==============================================
2 days, 23:56:18.403867 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:18.403919 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:18.403958 INFO: FWHM in RT is 2.49 seconds, sigma is 0.42
2 days, 23:56:18.403986 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.01
2 days, 23:56:18.430082 INFO: Starting candidate selection
2 days, 23:56:18.989250 INFO: Starting candidate scoring
2 days, 23:56:19.097515 INFO: Finished candidate processing
2 days, 23:56:19.097632 INFO: Collecting candidate features
2 days, 23:56:19.107481 WARNING: intensity_correlation has 24 NaNs ( 0.76 % out of 3175)
2 days, 23:56:19.107749 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3175)
2 days, 23:56:19.113303 INFO: Collecting fragment features
2 days, 23:56:19.119186 INFO: Finished candidate scoring
2 days, 23:56:19.122161 INFO: performing precursor FDR with 47 features
2 days, 23:56:19.122249 INFO: Decoy channel: -1
2 days, 23:56:19.122290 INFO: competitive: True
2 days, 23:56:19.127120 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:19.129613 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:56:19.129691 WARNING: dropped 18 decoy PSMs due to missing features
2 days, 23:56:19.129760 WARNING: FDR calculation for 1656 target and 1495 decoy PSMs
2 days, 23:56:19.129804 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:56:19.131306 INFO: Estimating optimal hyperparameters - samples: 2,520, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:19.131437 INFO: Using random state 91840 for train-test-split
2 days, 23:56:19.447011 INFO: Test AUC: 0.871
2 days, 23:56:19.447132 INFO: Train AUC: 0.887
2 days, 23:56:19.447171 INFO: AUC difference: 1.87%
2 days, 23:56:19.783872 INFO: Resetting torch num_threads to 80
2 days, 23:56:19.784437 PROGRESS: === Extracted 3175 precursors and 21979 fragments ===
2 days, 23:56:19.784893 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:56:19.785654 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:19.785771 PROGRESS: Total precursors accumulated: 600
2 days, 23:56:19.785853 PROGRESS: Target precursors: 583 (97.17%)
2 days, 23:56:19.785982 PROGRESS: Decoy precursors: 17 (2.83%)
2 days, 23:56:19.786056 PROGRESS: 
2 days, 23:56:19.786122 PROGRESS: Precursor Summary:
2 days, 23:56:19.787807 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   542; 0.001 FDR:   392
2 days, 23:56:19.787942 PROGRESS: 
2 days, 23:56:19.788027 PROGRESS: Protein Summary:
2 days, 23:56:19.790137 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   396; 0.001 FDR:   294
2 days, 23:56:19.790277 PROGRESS: =========================================================================
2 days, 23:56:19.790485 INFO: Target number of precursors reached.
2 days, 23:56:19.799733 INFO: fragments_df: keeping 5000 of 21979 [sum(precursor_idx_mask)=12857 sum(mass_error_mask)=21979 stop_rank=5000
2 days, 23:56:19.804936 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:20.019810 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:20.302781 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:20.482958 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:21.409846 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:21.410332 INFO: Using score_cutoff 16.008923036384584 (fac=0.99, q=1)
2 days, 23:56:21.410666 INFO: Updating optimization_manager: fwhm_rt             : 2.4899234771728516 -> 2.48889422416687
2 days, 23:56:21.410749 INFO: Updating optimization_manager: fwhm_mobility       : 0.003706618444994092 -> 0.0037099006585776806
2 days, 23:56:21.410806 INFO: Updating optimization_manager: score_cutoff        : 16.145349933815 -> 16.008923036384584
2 days, 23:56:21.410862 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:21.411946 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:21.413310 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:21.414119 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:21.416078 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:21.416178 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 23:56:21.417183 INFO: Updating optimization_manager: rt_error            : 11.205700932495555 -> 11.205700932495555
2 days, 23:56:21.417314 INFO: Updating optimization_manager: classifier_version  : 3 -> 11
2 days, 23:56:21.417419 INFO: Updating optimization_manager: score_cutoff        : 16.008923036384584 -> 16.008923036384584
2 days, 23:56:21.417516 INFO: Updating optimization_manager: fwhm_rt             : 2.48889422416687 -> 2.48889422416687
2 days, 23:56:21.417613 INFO: Updating optimization_manager: fwhm_mobility       : 0.0037099006585776806 -> 0.0037099006585776806
2 days, 23:56:21.417718 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 11.2057 found after 8 searches.
2 days, 23:56:21.417789 INFO: ==============================================
2 days, 23:56:21.417859 PROGRESS: Optimization finished for rt_error.
2 days, 23:56:21.420779 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:21.421620 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:21.422983 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:21.423806 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:21.425778 INFO: Starting optimization step 0.
2 days, 23:56:21.425897 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:56:21.425991 INFO: Using python extraction backend
2 days, 23:56:21.426117 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:56:21.426195 INFO: === Search parameters used ===
2 days, 23:56:21.426267 INFO: rt_error       : 11.205700932495555
2 days, 23:56:21.426324 INFO: mobility_error : 0.1
2 days, 23:56:21.426383 INFO: num_candidates : 3
2 days, 23:56:21.426440 INFO: ms1_error      : 15.0
2 days, 23:56:21.426497 INFO: ms2_error      : 15.0
2 days, 23:56:21.426552 INFO: fwhm_rt        : 2.48889422416687
2 days, 23:56:21.426605 INFO: quant_window   : 3
2 days, 23:56:21.426656 INFO: ==============================================
2 days, 23:56:21.427388 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:21.427445 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:21.427487 INFO: FWHM in RT is 2.49 seconds, sigma is 0.42
2 days, 23:56:21.427517 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.01
2 days, 23:56:21.442014 INFO: Starting candidate selection
2 days, 23:56:21.989929 INFO: Starting candidate scoring
2 days, 23:56:22.106102 INFO: Finished candidate processing
2 days, 23:56:22.106228 INFO: Collecting candidate features
2 days, 23:56:22.121977 WARNING: intensity_correlation has 24 NaNs ( 0.76 % out of 3177)
2 days, 23:56:22.122266 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3177)
2 days, 23:56:22.129235 INFO: Collecting fragment features
2 days, 23:56:22.133337 INFO: Finished candidate scoring
2 days, 23:56:22.135108 INFO: performing precursor FDR with 47 features
2 days, 23:56:22.135164 INFO: Decoy channel: -1
2 days, 23:56:22.135190 INFO: competitive: True
2 days, 23:56:22.138236 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:22.139808 WARNING: dropped 5 target PSMs due to missing features
2 days, 23:56:22.139867 WARNING: dropped 19 decoy PSMs due to missing features
2 days, 23:56:22.139917 WARNING: FDR calculation for 1659 target and 1494 decoy PSMs
2 days, 23:56:22.139950 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:56:22.140966 INFO: Estimating optimal hyperparameters - samples: 2,522, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:22.141062 INFO: Using random state 103805 for train-test-split
2 days, 23:56:22.369030 INFO: Test AUC: 0.859
2 days, 23:56:22.369137 INFO: Train AUC: 0.894
2 days, 23:56:22.369172 INFO: AUC difference: 3.84%
2 days, 23:56:22.659466 INFO: Resetting torch num_threads to 80
2 days, 23:56:22.659992 PROGRESS: === Extracted 3177 precursors and 21961 fragments ===
2 days, 23:56:22.660435 INFO: === FDR correction performed with classifier version 11 ===
2 days, 23:56:22.661064 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:22.661160 PROGRESS: Total precursors accumulated: 600
2 days, 23:56:22.661229 PROGRESS: Target precursors: 580 (96.67%)
2 days, 23:56:22.661288 PROGRESS: Decoy precursors: 20 (3.33%)
2 days, 23:56:22.661344 PROGRESS: 
2 days, 23:56:22.661397 PROGRESS: Precursor Summary:
2 days, 23:56:22.662567 PROGRESS: Channel   0:	 0.050 FDR:   580; 0.010 FDR:   538; 0.001 FDR:   432
2 days, 23:56:22.662672 PROGRESS: 
2 days, 23:56:22.662738 PROGRESS: Protein Summary:
2 days, 23:56:22.664097 PROGRESS: Channel   0:	 0.050 FDR:   422; 0.010 FDR:   396; 0.001 FDR:   327
2 days, 23:56:22.664194 PROGRESS: =========================================================================
2 days, 23:56:22.664328 INFO: Target number of precursors reached.
2 days, 23:56:22.670497 INFO: fragments_df: keeping 5000 of 21961 [sum(precursor_idx_mask)=12824 sum(mass_error_mask)=21961 stop_rank=5000
2 days, 23:56:22.673861 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:22.853429 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:23.047309 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:23.332742 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:24.153784 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:24.154266 INFO: Using score_cutoff 16.605275883865357 (fac=0.99, q=1)
2 days, 23:56:24.154629 INFO: Updating optimization_manager: fwhm_rt             : 2.48889422416687 -> 2.500680685043335
2 days, 23:56:24.154721 INFO: Updating optimization_manager: fwhm_mobility       : 0.0037099006585776806 -> 0.0037042428739368916
2 days, 23:56:24.154797 INFO: Updating optimization_manager: score_cutoff        : 16.008923036384584 -> 16.605275883865357
2 days, 23:56:24.154873 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:24.156023 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:24.157418 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:24.158269 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:24.160341 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:24.160456 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:56:24.162055 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0630102879611771
2 days, 23:56:24.162170 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0630.
2 days, 23:56:24.162246 INFO: ==============================================
2 days, 23:56:24.162325 INFO: Starting optimization step 1.
2 days, 23:56:24.162395 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:56:24.162465 INFO: Using python extraction backend
2 days, 23:56:24.162573 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:56:24.162647 INFO: === Search parameters used ===
2 days, 23:56:24.162708 INFO: rt_error       : 11.205700932495555
2 days, 23:56:24.162763 INFO: mobility_error : 0.0630102879611771
2 days, 23:56:24.162822 INFO: num_candidates : 3
2 days, 23:56:24.162879 INFO: ms1_error      : 15.0
2 days, 23:56:24.162935 INFO: ms2_error      : 15.0
2 days, 23:56:24.162991 INFO: fwhm_rt        : 2.500680685043335
2 days, 23:56:24.163045 INFO: quant_window   : 3
2 days, 23:56:24.163095 INFO: ==============================================
2 days, 23:56:24.163924 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:24.163980 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:24.164021 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:56:24.164047 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.01
2 days, 23:56:24.174016 INFO: Starting candidate selection
2 days, 23:56:24.781530 INFO: Starting candidate scoring
2 days, 23:56:24.887931 INFO: Finished candidate processing
2 days, 23:56:24.888064 INFO: Collecting candidate features
2 days, 23:56:24.900515 WARNING: intensity_correlation has 26 NaNs ( 0.82 % out of 3166)
2 days, 23:56:24.900796 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3166)
2 days, 23:56:24.906336 INFO: Collecting fragment features
2 days, 23:56:24.912293 INFO: Finished candidate scoring
2 days, 23:56:24.915714 INFO: performing precursor FDR with 47 features
2 days, 23:56:24.915814 INFO: Decoy channel: -1
2 days, 23:56:24.915862 INFO: competitive: True
2 days, 23:56:24.920722 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:24.923248 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:56:24.923337 WARNING: dropped 20 decoy PSMs due to missing features
2 days, 23:56:24.923399 WARNING: FDR calculation for 1659 target and 1481 decoy PSMs
2 days, 23:56:24.923444 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:56:24.924940 INFO: Estimating optimal hyperparameters - samples: 2,512, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:24.925055 INFO: Using random state 103805 for train-test-split
2 days, 23:56:25.210118 INFO: Test AUC: 0.882
2 days, 23:56:25.210243 INFO: Train AUC: 0.891
2 days, 23:56:25.210288 INFO: AUC difference: 1.01%
2 days, 23:56:25.537219 INFO: Resetting torch num_threads to 80
2 days, 23:56:25.538002 PROGRESS: === Extracted 3166 precursors and 21681 fragments ===
2 days, 23:56:25.538625 INFO: === FDR correction performed with classifier version 11 ===
2 days, 23:56:25.539593 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:25.539718 PROGRESS: Total precursors accumulated: 600
2 days, 23:56:25.539811 PROGRESS: Target precursors: 584 (97.33%)
2 days, 23:56:25.539891 PROGRESS: Decoy precursors: 16 (2.67%)
2 days, 23:56:25.539960 PROGRESS: 
2 days, 23:56:25.540032 PROGRESS: Precursor Summary:
2 days, 23:56:25.541976 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   535; 0.001 FDR:   418
2 days, 23:56:25.542133 PROGRESS: 
2 days, 23:56:25.542232 PROGRESS: Protein Summary:
2 days, 23:56:25.544492 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   396; 0.001 FDR:   318
2 days, 23:56:25.544618 PROGRESS: =========================================================================
2 days, 23:56:25.544826 INFO: Target number of precursors reached.
2 days, 23:56:25.554089 INFO: fragments_df: keeping 5000 of 21681 [sum(precursor_idx_mask)=12728 sum(mass_error_mask)=21681 stop_rank=5000
2 days, 23:56:25.559272 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:25.758425 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:26.047869 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:26.241558 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:34.653342 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:34.653985 INFO: Using score_cutoff 15.442616611862181 (fac=0.99, q=1)
2 days, 23:56:34.654472 INFO: Updating optimization_manager: fwhm_rt             : 2.500680685043335 -> 2.481233835220337
2 days, 23:56:34.654602 INFO: Updating optimization_manager: fwhm_mobility       : 0.0037042428739368916 -> 0.0036562837194651365
2 days, 23:56:34.654713 INFO: Updating optimization_manager: score_cutoff        : 16.605275883865357 -> 15.442616611862181
2 days, 23:56:34.654828 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:34.656572 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:34.658534 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:34.659786 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:34.662488 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:34.662661 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:56:34.665226 INFO: Updating optimization_manager: mobility_error      : 0.0630102879611771 -> 0.05121402786684313
2 days, 23:56:34.665387 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0512.
2 days, 23:56:34.665607 INFO: ==============================================
2 days, 23:56:34.665751 INFO: Starting optimization step 2.
2 days, 23:56:34.665860 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:56:34.665984 INFO: Using python extraction backend
2 days, 23:56:34.666151 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:56:34.666260 INFO: === Search parameters used ===
2 days, 23:56:34.666342 INFO: rt_error       : 11.205700932495555
2 days, 23:56:34.666417 INFO: mobility_error : 0.05121402786684313
2 days, 23:56:34.666486 INFO: num_candidates : 3
2 days, 23:56:34.666554 INFO: ms1_error      : 15.0
2 days, 23:56:34.666626 INFO: ms2_error      : 15.0
2 days, 23:56:34.666701 INFO: fwhm_rt        : 2.481233835220337
2 days, 23:56:34.666791 INFO: quant_window   : 3
2 days, 23:56:34.666884 INFO: ==============================================
2 days, 23:56:34.668298 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:34.668428 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:34.668539 INFO: FWHM in RT is 2.48 seconds, sigma is 0.41
2 days, 23:56:34.668638 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.98
2 days, 23:56:34.686221 INFO: Starting candidate selection
2 days, 23:56:35.211544 INFO: Starting candidate scoring
2 days, 23:56:35.320800 INFO: Finished candidate processing
2 days, 23:56:35.320938 INFO: Collecting candidate features
2 days, 23:56:35.335352 WARNING: intensity_correlation has 26 NaNs ( 0.83 % out of 3148)
2 days, 23:56:35.335587 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3148)
2 days, 23:56:35.340362 INFO: Collecting fragment features
2 days, 23:56:35.346522 INFO: Finished candidate scoring
2 days, 23:56:35.354341 INFO: performing precursor FDR with 47 features
2 days, 23:56:35.354477 INFO: Decoy channel: -1
2 days, 23:56:35.354517 INFO: competitive: True
2 days, 23:56:35.359908 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:35.362611 WARNING: dropped 7 target PSMs due to missing features
2 days, 23:56:35.362695 WARNING: dropped 19 decoy PSMs due to missing features
2 days, 23:56:35.362762 WARNING: FDR calculation for 1658 target and 1464 decoy PSMs
2 days, 23:56:35.362804 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:56:35.364343 INFO: Estimating optimal hyperparameters - samples: 2,497, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:35.364470 INFO: Using random state 103805 for train-test-split
2 days, 23:56:35.748719 INFO: Test AUC: 0.890
2 days, 23:56:35.748832 INFO: Train AUC: 0.889
2 days, 23:56:35.748865 INFO: AUC difference: 0.12%
2 days, 23:56:36.089659 INFO: Resetting torch num_threads to 80
2 days, 23:56:36.090387 PROGRESS: === Extracted 3148 precursors and 21459 fragments ===
2 days, 23:56:36.090844 INFO: === FDR correction performed with classifier version 11 ===
2 days, 23:56:36.091566 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:36.091664 PROGRESS: Total precursors accumulated: 599
2 days, 23:56:36.091727 PROGRESS: Target precursors: 583 (97.33%)
2 days, 23:56:36.091780 PROGRESS: Decoy precursors: 16 (2.67%)
2 days, 23:56:36.091827 PROGRESS: 
2 days, 23:56:36.091872 PROGRESS: Precursor Summary:
2 days, 23:56:36.093086 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   532; 0.001 FDR:   456
2 days, 23:56:36.093202 PROGRESS: 
2 days, 23:56:36.093262 PROGRESS: Protein Summary:
2 days, 23:56:36.094802 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   394; 0.001 FDR:   345
2 days, 23:56:36.094904 PROGRESS: =========================================================================
2 days, 23:56:36.095052 INFO: Target number of precursors reached.
2 days, 23:56:36.103408 INFO: fragments_df: keeping 5000 of 21459 [sum(precursor_idx_mask)=12676 sum(mass_error_mask)=21459 stop_rank=5000
2 days, 23:56:36.108805 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:36.281006 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:36.468481 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:36.641111 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:37.380433 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:56:37.380930 INFO: Using score_cutoff 15.954130125617983 (fac=0.99, q=1)
2 days, 23:56:37.381285 INFO: Updating optimization_manager: fwhm_rt             : 2.481233835220337 -> 2.48889422416687
2 days, 23:56:37.381386 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036562837194651365 -> 0.0036363571416586637
2 days, 23:56:37.381466 INFO: Updating optimization_manager: score_cutoff        : 15.442616611862181 -> 15.954130125617983
2 days, 23:56:37.381547 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:37.382770 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:37.384232 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:37.385106 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:37.387362 INFO: === checking if optimization conditions were reached ===
2 days, 23:56:37.387495 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:56:37.388274 INFO: Updating optimization_manager: mobility_error      : 0.05121402786684313 -> 0.1
2 days, 23:56:37.388421 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
2 days, 23:56:37.388549 INFO: Updating optimization_manager: score_cutoff        : 15.954130125617983 -> 16.605275883865357
2 days, 23:56:37.388669 INFO: Updating optimization_manager: fwhm_rt             : 2.48889422416687 -> 2.500680685043335
2 days, 23:56:37.388803 INFO: Updating optimization_manager: fwhm_mobility       : 0.0036363571416586637 -> 0.0037042428739368916
2 days, 23:56:37.388925 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
2 days, 23:56:37.389011 INFO: ==============================================
2 days, 23:56:37.389103 PROGRESS: Optimization finished for mobility_error.
2 days, 23:56:37.392281 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:37.393217 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:37.394774 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:37.395658 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:37.397699 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:56:37.397823 PROGRESS: ==============================================
2 days, 23:56:37.397954 PROGRESS: ms2_error      : 15.0000
2 days, 23:56:37.398059 PROGRESS: ms1_error      : 15.0000
2 days, 23:56:37.398151 PROGRESS: rt_error       : 11.2057
2 days, 23:56:37.398230 PROGRESS: mobility_error : 0.1000
2 days, 23:56:37.398298 PROGRESS: ==============================================
2 days, 23:56:37.398866 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:56:37.402640 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:56:37.418584 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:56:37.422773 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:56:37.472471 INFO: Using python extraction backend
2 days, 23:56:37.472893 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:56:37.473009 INFO: === Search parameters used ===
2 days, 23:56:37.473091 INFO: rt_error       : 11.205700932495555
2 days, 23:56:37.473160 INFO: mobility_error : 0.1
2 days, 23:56:37.473225 INFO: num_candidates : 3
2 days, 23:56:37.473290 INFO: ms1_error      : 15.0
2 days, 23:56:37.473353 INFO: ms2_error      : 15.0
2 days, 23:56:37.473416 INFO: fwhm_rt        : 2.500680685043335
2 days, 23:56:37.473479 INFO: quant_window   : 3
2 days, 23:56:37.473541 INFO: ==============================================
2 days, 23:56:37.480255 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:37.480364 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:37.480420 INFO: FWHM in RT is 2.50 seconds, sigma is 0.42
2 days, 23:56:37.480457 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.01
2 days, 23:56:37.506026 INFO: Starting candidate selection
2 days, 23:56:40.548578 INFO: Removed 27322 precursors with score below cutoff 16.605275883865357
2 days, 23:56:40.966743 INFO: Starting candidate scoring
2 days, 23:56:41.811473 INFO: Finished candidate processing
2 days, 23:56:41.811585 INFO: Collecting candidate features
2 days, 23:56:41.891018 WARNING: intensity_correlation has 94 NaNs ( 0.19 % out of 50004)
2 days, 23:56:41.891352 WARNING: height_correlation has 4 NaNs ( 0.01 % out of 50004)
2 days, 23:56:41.897285 INFO: Collecting fragment features
2 days, 23:56:41.924325 INFO: Finished candidate scoring
2 days, 23:56:41.959275 INFO: === Performing FDR correction with classifier version 12 ===
2 days, 23:56:41.963177 INFO: performing precursor FDR with 47 features
2 days, 23:56:41.963241 INFO: Decoy channel: -1
2 days, 23:56:41.963271 INFO: competitive: True
2 days, 23:56:41.978560 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:41.986848 WARNING: dropped 17 target PSMs due to missing features
2 days, 23:56:41.986975 WARNING: dropped 79 decoy PSMs due to missing features
2 days, 23:56:41.987021 WARNING: FDR calculation for 32211 target and 17697 decoy PSMs
2 days, 23:56:41.987046 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:56:41.994737 INFO: Estimating optimal hyperparameters - samples: 39,926, batch_size: 163, learning_rate: 1.99e-04
2 days, 23:56:41.995006 INFO: Using random state 28367 for train-test-split
2 days, 23:56:46.740859 INFO: Test AUC: 0.913
2 days, 23:56:46.740984 INFO: Train AUC: 0.918
2 days, 23:56:46.741019 INFO: AUC difference: 0.49%
2 days, 23:56:47.064718 INFO: Resetting torch num_threads to 80
2 days, 23:56:47.069021 INFO: Removing fragments below FDR threshold
2 days, 23:56:47.082210 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:47.082505 PROGRESS: Total precursors accumulated: 12,803
2 days, 23:56:47.082618 PROGRESS: Target precursors: 12,677 (99.02%)
2 days, 23:56:47.082719 PROGRESS: Decoy precursors: 126 (0.98%)
2 days, 23:56:47.082814 PROGRESS: 
2 days, 23:56:47.082902 PROGRESS: Precursor Summary:
2 days, 23:56:47.090292 PROGRESS: Channel   0:	 0.050 FDR: 12,677; 0.010 FDR: 12,677; 0.001 FDR: 12,076
2 days, 23:56:47.090595 PROGRESS: 
2 days, 23:56:47.090705 PROGRESS: Protein Summary:
2 days, 23:56:47.099138 PROGRESS: Channel   0:	 0.050 FDR: 1,676; 0.010 FDR: 1,676; 0.001 FDR: 1,670
2 days, 23:56:47.099384 PROGRESS: =========================================================================
2 days, 23:56:47.100423 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R2/psm.parquet
2 days, 23:56:47.168157 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R2/frag.parquet
2 days, 23:56:47.229564 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R2
2 days, 23:56:47.233714 PROGRESS: Loading raw file 9/12: B9_G_DIA_nLC_tTOF_R3 
2 days, 23:56:47.233838 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:56:47.233940 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R3/figures
2 days, 23:56:47.234148 INFO: Initializing TimingManager
2 days, 23:56:47.235005 INFO: Initializing RawFileManager
2 days, 23:56:47.235167 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:47.235237 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:47.235284 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:47.455533 INFO: Reading 22,622 frames with 373,160,144 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:51.314617 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d...
2 days, 23:56:51.315736 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:51.317766 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:51.318031 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:51.318573 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:51.320255 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:51.350116 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:51.350450 INFO: Indexing quadrupole dimension
2 days, 23:56:51.488575 INFO: Transposing detector events
2 days, 23:56:53.440631 INFO: Finished transposing data
2 days, 23:56:53.440829 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
2 days, 23:56:53.441566 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:56:53.441723 INFO: RT duration (sec)   : 2399.9
2 days, 23:56:53.441765 INFO: RT duration (min)   : 40.0
2 days, 23:56:53.441803 INFO: Cycle len (scans)   : 12
2 days, 23:56:53.441844 INFO: Cycle len (sec)     : 1.27
2 days, 23:56:53.441897 INFO: Number of cycles    : 1885
2 days, 23:56:53.441975 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:56:53.442035 INFO: Creating DIA data object took: 6.206865549087524
2 days, 23:56:53.447517 INFO: Initializing CalibrationManager
2 days, 23:56:53.447776 INFO: Setting up calibration estimators ..
2 days, 23:56:53.447883 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:56:53.447976 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:56:53.448072 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:56:53.448158 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:56:53.448244 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:56:53.448330 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:56:53.448409 INFO: Done setting up calibration estimators.
2 days, 23:56:53.448531 INFO: Initializing OptimizationManager
2 days, 23:56:53.448653 INFO: initial parameter: ms1_error = 30
2 days, 23:56:53.448721 INFO: initial parameter: ms2_error = 30
2 days, 23:56:53.448786 INFO: initial parameter: rt_error = 1199.951535
2 days, 23:56:53.448847 INFO: initial parameter: mobility_error = 0.1
2 days, 23:56:53.448907 INFO: initial parameter: num_candidates = 1
2 days, 23:56:53.448967 INFO: initial parameter: fwhm_rt = 5
2 days, 23:56:53.449028 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:56:53.449087 INFO: initial parameter: score_cutoff = 0
2 days, 23:56:53.449146 INFO: initial parameter: classifier_version = -1
2 days, 23:56:53.449239 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R3
2 days, 23:56:53.449437 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:56:53.449476 INFO: Initializing FDRManager
2 days, 23:56:53.449516 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:56:53.455982 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:56:53.460310 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:56:53.460702 INFO: Updating optimization_manager: rt_error            : 1199.951535 -> 1199.951535
2 days, 23:56:53.460834 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:56:53.461095 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:56:53.461210 PROGRESS: Starting initial search for precursors.
2 days, 23:56:53.461348 INFO: Starting optimization step 0.
2 days, 23:56:53.461433 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:56:53.461524 INFO: Using python extraction backend
2 days, 23:56:53.461671 PROGRESS: Extracting batch of 399 precursors
2 days, 23:56:53.461763 INFO: === Search parameters used ===
2 days, 23:56:53.461833 INFO: rt_error       : 1199.951535
2 days, 23:56:53.462021 INFO: mobility_error : 0.1
2 days, 23:56:53.462101 INFO: num_candidates : 1
2 days, 23:56:53.462173 INFO: ms1_error      : 30
2 days, 23:56:53.462238 INFO: ms2_error      : 30
2 days, 23:56:53.462301 INFO: fwhm_rt        : 5
2 days, 23:56:53.462365 INFO: quant_window   : 3
2 days, 23:56:53.462430 INFO: ==============================================
2 days, 23:56:53.463416 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:53.463479 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:53.463522 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:56:53.463556 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:56:53.473982 INFO: Starting candidate selection
2 days, 23:56:56.941006 INFO: Starting candidate scoring
2 days, 23:56:56.995517 INFO: Finished candidate processing
2 days, 23:56:56.995637 INFO: Collecting candidate features
2 days, 23:56:57.013200 INFO: Collecting fragment features
2 days, 23:56:57.017458 INFO: Finished candidate scoring
2 days, 23:56:57.019301 INFO: performing precursor FDR with 47 features
2 days, 23:56:57.019398 INFO: Decoy channel: -1
2 days, 23:56:57.019439 INFO: competitive: True
2 days, 23:56:57.021550 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:56:57.024460 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:56:57.025755 INFO: Using random state 197127 for train-test-split
2 days, 23:56:57.058357 INFO: Test AUC: 0.537
2 days, 23:56:57.058481 INFO: Train AUC: 0.524
2 days, 23:56:57.058525 INFO: AUC difference: 2.51%
2 days, 23:56:57.373689 INFO: Resetting torch num_threads to 80
2 days, 23:56:57.374315 PROGRESS: === Extracted 399 precursors and 3698 fragments ===
2 days, 23:56:57.374798 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:56:57.375481 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:56:57.375599 PROGRESS: Total precursors accumulated: 200
2 days, 23:56:57.375690 PROGRESS: Target precursors: 102 (51.00%)
2 days, 23:56:57.375771 PROGRESS: Decoy precursors: 98 (49.00%)
2 days, 23:56:57.375846 PROGRESS: 
2 days, 23:56:57.375920 PROGRESS: Precursor Summary:
2 days, 23:56:57.376920 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
2 days, 23:56:57.377029 PROGRESS: 
2 days, 23:56:57.377117 PROGRESS: Protein Summary:
2 days, 23:56:57.378292 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
2 days, 23:56:57.378409 PROGRESS: =========================================================================
2 days, 23:56:57.378562 INFO: Target number of precursors not reached yet.
2 days, 23:56:57.381647 INFO: Starting optimization step 1.
2 days, 23:56:57.381906 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:56:57.382046 INFO: Using python extraction backend
2 days, 23:56:57.382218 PROGRESS: Extracting batch of 798 precursors
2 days, 23:56:57.382320 INFO: === Search parameters used ===
2 days, 23:56:57.382401 INFO: rt_error       : 1199.951535
2 days, 23:56:57.382472 INFO: mobility_error : 0.1
2 days, 23:56:57.382538 INFO: num_candidates : 1
2 days, 23:56:57.382601 INFO: ms1_error      : 30
2 days, 23:56:57.382662 INFO: ms2_error      : 30
2 days, 23:56:57.382726 INFO: fwhm_rt        : 5
2 days, 23:56:57.382793 INFO: quant_window   : 3
2 days, 23:56:57.382852 INFO: ==============================================
2 days, 23:56:57.383651 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:56:57.383705 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:56:57.383745 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:56:57.383777 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:56:57.394020 INFO: Starting candidate selection
2 days, 23:57:04.023744 INFO: Starting candidate scoring
2 days, 23:57:04.107689 INFO: Finished candidate processing
2 days, 23:57:04.107827 INFO: Collecting candidate features
2 days, 23:57:04.127627 INFO: Collecting fragment features
2 days, 23:57:04.132367 INFO: Finished candidate scoring
2 days, 23:57:04.137369 INFO: performing precursor FDR with 47 features
2 days, 23:57:04.137469 INFO: Decoy channel: -1
2 days, 23:57:04.137520 INFO: competitive: True
2 days, 23:57:04.142916 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:04.145828 INFO: Estimating optimal hyperparameters - samples: 957, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:04.145987 INFO: Using random state 876709 for train-test-split
2 days, 23:57:04.237594 INFO: Test AUC: 0.765
2 days, 23:57:04.237729 INFO: Train AUC: 0.802
2 days, 23:57:04.237780 INFO: AUC difference: 4.65%
2 days, 23:57:04.639784 INFO: Resetting torch num_threads to 80
2 days, 23:57:04.641311 PROGRESS: === Extracted 1197 precursors and 11406 fragments ===
2 days, 23:57:04.641757 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:57:04.642508 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:04.642634 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:04.642707 PROGRESS: Target precursors: 479 (79.83%)
2 days, 23:57:04.642780 PROGRESS: Decoy precursors: 121 (20.17%)
2 days, 23:57:04.642842 PROGRESS: 
2 days, 23:57:04.642898 PROGRESS: Precursor Summary:
2 days, 23:57:04.644146 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   237; 0.001 FDR:   215
2 days, 23:57:04.644252 PROGRESS: 
2 days, 23:57:04.644316 PROGRESS: Protein Summary:
2 days, 23:57:04.645608 PROGRESS: Channel   0:	 0.050 FDR:   223; 0.010 FDR:   177; 0.001 FDR:   160
2 days, 23:57:04.645708 PROGRESS: =========================================================================
2 days, 23:57:04.645893 INFO: Target number of precursors reached.
2 days, 23:57:04.649391 INFO: fragments_df: keeping 2003 of 11406 [sum(precursor_idx_mask)=2430 sum(mass_error_mask)=11406 stop_rank=2003
2 days, 23:57:04.653862 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:04.887503 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:05.053213 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:05.252537 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:05.613187 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:57:05.613790 INFO: Using score_cutoff 34.827123381042476 (fac=0.99, q=1)
2 days, 23:57:05.614280 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.7940351963043213
2 days, 23:57:05.614394 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007241667713969946
2 days, 23:57:05.614478 INFO: Updating optimization_manager: score_cutoff        : 0 -> 34.827123381042476
2 days, 23:57:05.614565 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:05.616229 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:05.618222 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:05.619558 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:05.622327 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2 days, 23:57:05.622687 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:57:05.622890 INFO: Starting optimization step 2.
2 days, 23:57:05.623089 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:05.623207 INFO: Using python extraction backend
2 days, 23:57:05.623376 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:05.623503 INFO: === Search parameters used ===
2 days, 23:57:05.623597 INFO: rt_error       : 1199.951535
2 days, 23:57:05.623688 INFO: mobility_error : 0.1
2 days, 23:57:05.623779 INFO: num_candidates : 3
2 days, 23:57:05.623862 INFO: ms1_error      : 30
2 days, 23:57:05.623929 INFO: ms2_error      : 30
2 days, 23:57:05.623989 INFO: fwhm_rt        : 2.7940351963043213
2 days, 23:57:05.624050 INFO: quant_window   : 3
2 days, 23:57:05.624114 INFO: ==============================================
2 days, 23:57:05.625596 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:05.625671 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:05.625739 INFO: FWHM in RT is 2.79 seconds, sigma is 0.47
2 days, 23:57:05.625791 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.92
2 days, 23:57:05.630930 INFO: Starting candidate selection
2 days, 23:57:13.968664 INFO: Starting candidate scoring
2 days, 23:57:14.131477 INFO: Finished candidate processing
2 days, 23:57:14.131629 INFO: Collecting candidate features
2 days, 23:57:14.157550 INFO: Collecting fragment features
2 days, 23:57:14.164931 INFO: Finished candidate scoring
2 days, 23:57:14.170839 INFO: performing precursor FDR with 47 features
2 days, 23:57:14.170961 INFO: Decoy channel: -1
2 days, 23:57:14.171003 INFO: competitive: True
2 days, 23:57:14.176374 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:14.179994 INFO: Estimating optimal hyperparameters - samples: 2,759, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:14.180158 INFO: Using random state 82735 for train-test-split
2 days, 23:57:14.460034 INFO: Test AUC: 0.708
2 days, 23:57:14.460147 INFO: Train AUC: 0.712
2 days, 23:57:14.460178 INFO: AUC difference: 0.55%
2 days, 23:57:14.791199 INFO: Resetting torch num_threads to 80
2 days, 23:57:14.792030 PROGRESS: === Extracted 3449 precursors and 31687 fragments ===
2 days, 23:57:14.792637 INFO: === FDR correction performed with classifier version 1 ===
2 days, 23:57:14.793700 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:14.793850 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:14.793983 PROGRESS: Target precursors: 504 (84.00%)
2 days, 23:57:14.794092 PROGRESS: Decoy precursors: 96 (16.00%)
2 days, 23:57:14.794184 PROGRESS: 
2 days, 23:57:14.794277 PROGRESS: Precursor Summary:
2 days, 23:57:14.796438 PROGRESS: Channel   0:	 0.050 FDR:   363; 0.010 FDR:   318; 0.001 FDR:   231
2 days, 23:57:14.796613 PROGRESS: 
2 days, 23:57:14.796695 PROGRESS: Protein Summary:
2 days, 23:57:14.798990 PROGRESS: Channel   0:	 0.050 FDR:   280; 0.010 FDR:   242; 0.001 FDR:   172
2 days, 23:57:14.799132 PROGRESS: =========================================================================
2 days, 23:57:14.799368 INFO: Target number of precursors reached.
2 days, 23:57:14.810200 INFO: fragments_df: keeping 5000 of 31687 [sum(precursor_idx_mask)=8892 sum(mass_error_mask)=31687 stop_rank=5000
2 days, 23:57:14.816075 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:14.989149 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:15.166103 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:15.354062 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:16.263097 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:16.263690 INFO: Using score_cutoff 32.415404277420045 (fac=0.99, q=1)
2 days, 23:57:16.264163 INFO: Updating optimization_manager: fwhm_rt             : 2.7940351963043213 -> 2.755247116088867
2 days, 23:57:16.264294 INFO: Updating optimization_manager: fwhm_mobility       : 0.007241667713969946 -> 0.006744707003235817
2 days, 23:57:16.264383 INFO: Updating optimization_manager: score_cutoff        : 34.827123381042476 -> 32.415404277420045
2 days, 23:57:16.264468 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:16.266109 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:16.267993 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:16.269121 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:16.271872 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:16.274336 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.495425682381534
2 days, 23:57:16.274490 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2 days, 23:57:16.274608 PROGRESS: ❌ ms2_error      : 17.4954 > 15.0000 or insufficient steps taken.
2 days, 23:57:16.276134 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:57:16.276265 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
2 days, 23:57:16.276367 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:57:16.276464 INFO: ==============================================
2 days, 23:57:16.276575 INFO: Starting optimization step 3.
2 days, 23:57:16.276679 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:16.276785 INFO: Using python extraction backend
2 days, 23:57:16.276965 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:16.277089 INFO: === Search parameters used ===
2 days, 23:57:16.277189 INFO: rt_error       : 1199.951535
2 days, 23:57:16.277291 INFO: mobility_error : 0.1
2 days, 23:57:16.277385 INFO: num_candidates : 3
2 days, 23:57:16.277472 INFO: ms1_error      : 15.0
2 days, 23:57:16.277563 INFO: ms2_error      : 17.495425682381534
2 days, 23:57:16.277656 INFO: fwhm_rt        : 2.755247116088867
2 days, 23:57:16.277743 INFO: quant_window   : 3
2 days, 23:57:16.277824 INFO: ==============================================
2 days, 23:57:16.279194 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:16.279268 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:16.279335 INFO: FWHM in RT is 2.76 seconds, sigma is 0.46
2 days, 23:57:16.279384 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.66
2 days, 23:57:16.283271 INFO: Starting candidate selection
2 days, 23:57:23.041378 INFO: Starting candidate scoring
2 days, 23:57:23.150654 INFO: Finished candidate processing
2 days, 23:57:23.150792 INFO: Collecting candidate features
2 days, 23:57:23.175764 INFO: Collecting fragment features
2 days, 23:57:23.181688 INFO: Finished candidate scoring
2 days, 23:57:23.186051 INFO: performing precursor FDR with 47 features
2 days, 23:57:23.186141 INFO: Decoy channel: -1
2 days, 23:57:23.186178 INFO: competitive: True
2 days, 23:57:23.189681 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:23.192100 INFO: Estimating optimal hyperparameters - samples: 2,735, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:23.192216 INFO: Using random state 754727 for train-test-split
2 days, 23:57:23.464353 INFO: Test AUC: 0.749
2 days, 23:57:23.464467 INFO: Train AUC: 0.755
2 days, 23:57:23.464508 INFO: AUC difference: 0.81%
2 days, 23:57:23.816878 INFO: Resetting torch num_threads to 80
2 days, 23:57:23.818119 PROGRESS: === Extracted 3419 precursors and 28521 fragments ===
2 days, 23:57:23.818780 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:57:23.819872 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:23.820024 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:23.820132 PROGRESS: Target precursors: 520 (86.67%)
2 days, 23:57:23.820230 PROGRESS: Decoy precursors: 80 (13.33%)
2 days, 23:57:23.820314 PROGRESS: 
2 days, 23:57:23.820406 PROGRESS: Precursor Summary:
2 days, 23:57:23.822518 PROGRESS: Channel   0:	 0.050 FDR:   451; 0.010 FDR:   376; 0.001 FDR:   344
2 days, 23:57:23.822674 PROGRESS: 
2 days, 23:57:23.822779 PROGRESS: Protein Summary:
2 days, 23:57:23.824992 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   287; 0.001 FDR:   263
2 days, 23:57:23.825133 PROGRESS: =========================================================================
2 days, 23:57:23.825360 INFO: Target number of precursors reached.
2 days, 23:57:23.835600 INFO: fragments_df: keeping 5000 of 28521 [sum(precursor_idx_mask)=9967 sum(mass_error_mask)=28521 stop_rank=5000
2 days, 23:57:23.840438 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:24.029558 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:24.187454 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:24.356905 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:25.179038 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:25.179576 INFO: Using score_cutoff 27.99591004371643 (fac=0.99, q=1)
2 days, 23:57:25.179973 INFO: Updating optimization_manager: fwhm_rt             : 2.755247116088867 -> 2.7371115684509277
2 days, 23:57:25.180088 INFO: Updating optimization_manager: fwhm_mobility       : 0.006744707003235817 -> 0.0055116089060902596
2 days, 23:57:25.180174 INFO: Updating optimization_manager: score_cutoff        : 32.415404277420045 -> 27.99591004371643
2 days, 23:57:25.180259 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:25.181572 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:25.183148 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:25.184067 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:25.186312 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:25.188198 INFO: Updating optimization_manager: ms2_error           : 17.495425682381534 -> 15.0
2 days, 23:57:25.188320 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:57:25.188408 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:57:25.189522 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:57:25.189626 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:57:25.189701 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:57:25.189767 INFO: ==============================================
2 days, 23:57:25.189846 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:57:25.193306 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:25.194286 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:25.195744 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:25.196607 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:25.198704 INFO: Starting optimization step 0.
2 days, 23:57:25.198831 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:25.198933 INFO: Using python extraction backend
2 days, 23:57:25.199065 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:25.199148 INFO: === Search parameters used ===
2 days, 23:57:25.199208 INFO: rt_error       : 1199.951535
2 days, 23:57:25.199264 INFO: mobility_error : 0.1
2 days, 23:57:25.199317 INFO: num_candidates : 3
2 days, 23:57:25.199369 INFO: ms1_error      : 15.0
2 days, 23:57:25.199419 INFO: ms2_error      : 15.0
2 days, 23:57:25.199470 INFO: fwhm_rt        : 2.7371115684509277
2 days, 23:57:25.199520 INFO: quant_window   : 3
2 days, 23:57:25.199581 INFO: ==============================================
2 days, 23:57:25.200595 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:25.200651 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:25.200696 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
2 days, 23:57:25.200724 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.99
2 days, 23:57:25.214041 INFO: Starting candidate selection
2 days, 23:57:33.039723 INFO: Starting candidate scoring
2 days, 23:57:33.140484 INFO: Finished candidate processing
2 days, 23:57:33.140631 INFO: Collecting candidate features
2 days, 23:57:33.155924 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3406)
2 days, 23:57:33.163918 INFO: Collecting fragment features
2 days, 23:57:33.170767 INFO: Finished candidate scoring
2 days, 23:57:33.176678 INFO: performing precursor FDR with 47 features
2 days, 23:57:33.176819 INFO: Decoy channel: -1
2 days, 23:57:33.176867 INFO: competitive: True
2 days, 23:57:33.182601 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:33.185017 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:57:33.186741 INFO: Estimating optimal hyperparameters - samples: 2,723, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:33.186883 INFO: Using random state 352725 for train-test-split
2 days, 23:57:33.452505 INFO: Test AUC: 0.782
2 days, 23:57:33.452652 INFO: Train AUC: 0.780
2 days, 23:57:33.452709 INFO: AUC difference: 0.25%
2 days, 23:57:33.815238 INFO: Resetting torch num_threads to 80
2 days, 23:57:33.815840 PROGRESS: === Extracted 3406 precursors and 27618 fragments ===
2 days, 23:57:33.816298 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:57:33.816975 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:33.817078 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:33.817157 PROGRESS: Target precursors: 535 (89.17%)
2 days, 23:57:33.817218 PROGRESS: Decoy precursors: 65 (10.83%)
2 days, 23:57:33.817273 PROGRESS: 
2 days, 23:57:33.817325 PROGRESS: Precursor Summary:
2 days, 23:57:33.818561 PROGRESS: Channel   0:	 0.050 FDR:   456; 0.010 FDR:   404; 0.001 FDR:   352
2 days, 23:57:33.818683 PROGRESS: 
2 days, 23:57:33.818748 PROGRESS: Protein Summary:
2 days, 23:57:33.820084 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   309; 0.001 FDR:   270
2 days, 23:57:33.820193 PROGRESS: =========================================================================
2 days, 23:57:33.820343 INFO: Target number of precursors reached.
2 days, 23:57:33.826945 INFO: fragments_df: keeping 5000 of 27618 [sum(precursor_idx_mask)=10533 sum(mass_error_mask)=27618 stop_rank=5000
2 days, 23:57:33.830523 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:34.011525 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:34.189427 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:34.355190 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:35.312643 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:35.313111 INFO: Using score_cutoff 27.85482809486389 (fac=0.99, q=1)
2 days, 23:57:35.313476 INFO: Updating optimization_manager: fwhm_rt             : 2.7371115684509277 -> 2.697502613067627
2 days, 23:57:35.313566 INFO: Updating optimization_manager: fwhm_mobility       : 0.0055116089060902596 -> 0.00516916811466217
2 days, 23:57:35.313628 INFO: Updating optimization_manager: score_cutoff        : 27.99591004371643 -> 27.85482809486389
2 days, 23:57:35.313689 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:35.314886 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:35.316398 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:35.317355 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:35.319488 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:35.319613 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:57:35.321327 INFO: Updating optimization_manager: rt_error            : 1199.951535 -> 263.72493057461156
2 days, 23:57:35.321450 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 263.7249.
2 days, 23:57:35.321541 INFO: ==============================================
2 days, 23:57:35.321638 INFO: Starting optimization step 1.
2 days, 23:57:35.321723 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:35.321807 INFO: Using python extraction backend
2 days, 23:57:35.321953 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:35.322051 INFO: === Search parameters used ===
2 days, 23:57:35.322145 INFO: rt_error       : 263.72493057461156
2 days, 23:57:35.322218 INFO: mobility_error : 0.1
2 days, 23:57:35.322286 INFO: num_candidates : 3
2 days, 23:57:35.322354 INFO: ms1_error      : 15.0
2 days, 23:57:35.322422 INFO: ms2_error      : 15.0
2 days, 23:57:35.322487 INFO: fwhm_rt        : 2.697502613067627
2 days, 23:57:35.322552 INFO: quant_window   : 3
2 days, 23:57:35.322617 INFO: ==============================================
2 days, 23:57:35.323592 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:35.323648 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:35.323701 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
2 days, 23:57:35.323737 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.80
2 days, 23:57:35.338083 INFO: Starting candidate selection
2 days, 23:57:38.714361 INFO: Starting candidate scoring
2 days, 23:57:38.817382 INFO: Finished candidate processing
2 days, 23:57:38.817527 INFO: Collecting candidate features
2 days, 23:57:38.833460 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3343)
2 days, 23:57:38.833879 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3343)
2 days, 23:57:38.841876 INFO: Collecting fragment features
2 days, 23:57:38.849032 INFO: Finished candidate scoring
2 days, 23:57:38.854350 INFO: performing precursor FDR with 47 features
2 days, 23:57:38.854469 INFO: Decoy channel: -1
2 days, 23:57:38.854517 INFO: competitive: True
2 days, 23:57:38.860115 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:38.862857 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:57:38.862943 WARNING: dropped 3 decoy PSMs due to missing features
2 days, 23:57:38.864560 INFO: Estimating optimal hyperparameters - samples: 2,671, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:38.864690 INFO: Using random state 352725 for train-test-split
2 days, 23:57:39.206348 INFO: Test AUC: 0.812
2 days, 23:57:39.206502 INFO: Train AUC: 0.794
2 days, 23:57:39.206565 INFO: AUC difference: 2.25%
2 days, 23:57:39.504809 INFO: Resetting torch num_threads to 80
2 days, 23:57:39.505452 PROGRESS: === Extracted 3343 precursors and 26136 fragments ===
2 days, 23:57:39.505904 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:57:39.506589 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:39.506684 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:39.506749 PROGRESS: Target precursors: 562 (93.67%)
2 days, 23:57:39.506806 PROGRESS: Decoy precursors: 38 (6.33%)
2 days, 23:57:39.506859 PROGRESS: 
2 days, 23:57:39.506911 PROGRESS: Precursor Summary:
2 days, 23:57:39.508140 PROGRESS: Channel   0:	 0.050 FDR:   542; 0.010 FDR:   473; 0.001 FDR:   409
2 days, 23:57:39.508262 PROGRESS: 
2 days, 23:57:39.508350 PROGRESS: Protein Summary:
2 days, 23:57:39.509775 PROGRESS: Channel   0:	 0.050 FDR:   402; 0.010 FDR:   352; 0.001 FDR:   308
2 days, 23:57:39.509926 PROGRESS: =========================================================================
2 days, 23:57:39.510117 INFO: Target number of precursors reached.
2 days, 23:57:39.516776 INFO: fragments_df: keeping 5000 of 26136 [sum(precursor_idx_mask)=11888 sum(mass_error_mask)=26136 stop_rank=5000
2 days, 23:57:39.520336 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:39.712481 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:39.900974 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:40.132967 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:40.953694 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:40.954238 INFO: Using score_cutoff 24.397019666290284 (fac=0.99, q=1)
2 days, 23:57:40.954618 INFO: Updating optimization_manager: fwhm_rt             : 2.697502613067627 -> 2.6144700050354004
2 days, 23:57:40.954727 INFO: Updating optimization_manager: fwhm_mobility       : 0.00516916811466217 -> 0.004517747089266777
2 days, 23:57:40.954820 INFO: Updating optimization_manager: score_cutoff        : 27.85482809486389 -> 24.397019666290284
2 days, 23:57:40.954907 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:40.956174 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:40.957696 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:40.958609 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:40.960713 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:40.960840 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:57:40.962872 INFO: Updating optimization_manager: rt_error            : 263.72493057461156 -> 133.02360165901186
2 days, 23:57:40.962992 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 133.0236.
2 days, 23:57:40.963083 INFO: ==============================================
2 days, 23:57:40.963170 INFO: Starting optimization step 2.
2 days, 23:57:40.963254 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:40.963327 INFO: Using python extraction backend
2 days, 23:57:40.963445 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:40.963525 INFO: === Search parameters used ===
2 days, 23:57:40.963585 INFO: rt_error       : 133.02360165901186
2 days, 23:57:40.963640 INFO: mobility_error : 0.1
2 days, 23:57:40.963692 INFO: num_candidates : 3
2 days, 23:57:40.963746 INFO: ms1_error      : 15.0
2 days, 23:57:40.963797 INFO: ms2_error      : 15.0
2 days, 23:57:40.963846 INFO: fwhm_rt        : 2.6144700050354004
2 days, 23:57:40.963897 INFO: quant_window   : 3
2 days, 23:57:40.963951 INFO: ==============================================
2 days, 23:57:40.964964 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:40.965020 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:40.965060 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
2 days, 23:57:40.965092 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.45
2 days, 23:57:40.970989 INFO: Starting candidate selection
2 days, 23:57:42.435553 INFO: Starting candidate scoring
2 days, 23:57:42.547522 INFO: Finished candidate processing
2 days, 23:57:42.547651 INFO: Collecting candidate features
2 days, 23:57:42.561115 WARNING: intensity_correlation has 5 NaNs ( 0.15 % out of 3309)
2 days, 23:57:42.566527 INFO: Collecting fragment features
2 days, 23:57:42.571452 INFO: Finished candidate scoring
2 days, 23:57:42.575738 INFO: performing precursor FDR with 47 features
2 days, 23:57:42.575809 INFO: Decoy channel: -1
2 days, 23:57:42.575840 INFO: competitive: True
2 days, 23:57:42.580875 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:42.582979 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:57:42.583047 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 23:57:42.584426 INFO: Estimating optimal hyperparameters - samples: 2,643, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:42.584544 INFO: Using random state 352725 for train-test-split
2 days, 23:57:42.917365 INFO: Test AUC: 0.831
2 days, 23:57:42.917476 INFO: Train AUC: 0.816
2 days, 23:57:42.917511 INFO: AUC difference: 1.77%
2 days, 23:57:43.212730 INFO: Resetting torch num_threads to 80
2 days, 23:57:43.213372 PROGRESS: === Extracted 3309 precursors and 25123 fragments ===
2 days, 23:57:43.213798 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:57:43.214478 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:43.214576 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:43.214643 PROGRESS: Target precursors: 569 (94.83%)
2 days, 23:57:43.214699 PROGRESS: Decoy precursors: 31 (5.17%)
2 days, 23:57:43.214750 PROGRESS: 
2 days, 23:57:43.214807 PROGRESS: Precursor Summary:
2 days, 23:57:43.216011 PROGRESS: Channel   0:	 0.050 FDR:   568; 0.010 FDR:   521; 0.001 FDR:   434
2 days, 23:57:43.216105 PROGRESS: 
2 days, 23:57:43.216187 PROGRESS: Protein Summary:
2 days, 23:57:43.217561 PROGRESS: Channel   0:	 0.050 FDR:   417; 0.010 FDR:   382; 0.001 FDR:   327
2 days, 23:57:43.217664 PROGRESS: =========================================================================
2 days, 23:57:43.217810 INFO: Target number of precursors reached.
2 days, 23:57:43.224477 INFO: fragments_df: keeping 5000 of 25123 [sum(precursor_idx_mask)=12759 sum(mass_error_mask)=25123 stop_rank=5000
2 days, 23:57:43.227980 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:43.439554 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:43.637228 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:43.847603 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:44.690459 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:44.690939 INFO: Using score_cutoff 21.06804058456421 (fac=0.99, q=1)
2 days, 23:57:44.691289 INFO: Updating optimization_manager: fwhm_rt             : 2.6144700050354004 -> 2.593263626098633
2 days, 23:57:44.691392 INFO: Updating optimization_manager: fwhm_mobility       : 0.004517747089266777 -> 0.004365007858723402
2 days, 23:57:44.691461 INFO: Updating optimization_manager: score_cutoff        : 24.397019666290284 -> 21.06804058456421
2 days, 23:57:44.691529 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:44.692773 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:44.694293 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:44.695340 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:44.697823 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:44.697978 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:57:44.700797 INFO: Updating optimization_manager: rt_error            : 133.02360165901186 -> 53.21460745280913
2 days, 23:57:44.700948 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 53.2146.
2 days, 23:57:44.701059 INFO: ==============================================
2 days, 23:57:44.701187 INFO: Starting optimization step 3.
2 days, 23:57:44.701284 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:44.701373 INFO: Using python extraction backend
2 days, 23:57:44.701538 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:44.701662 INFO: === Search parameters used ===
2 days, 23:57:44.701756 INFO: rt_error       : 53.21460745280913
2 days, 23:57:44.701838 INFO: mobility_error : 0.1
2 days, 23:57:44.701942 INFO: num_candidates : 3
2 days, 23:57:44.702034 INFO: ms1_error      : 15.0
2 days, 23:57:44.702107 INFO: ms2_error      : 15.0
2 days, 23:57:44.702187 INFO: fwhm_rt        : 2.593263626098633
2 days, 23:57:44.702276 INFO: quant_window   : 3
2 days, 23:57:44.702355 INFO: ==============================================
2 days, 23:57:44.703713 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:44.703784 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:44.703843 INFO: FWHM in RT is 2.59 seconds, sigma is 0.43
2 days, 23:57:44.703889 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.37
2 days, 23:57:44.706474 INFO: Starting candidate selection
2 days, 23:57:45.634326 INFO: Starting candidate scoring
2 days, 23:57:45.747154 INFO: Finished candidate processing
2 days, 23:57:45.747299 INFO: Collecting candidate features
2 days, 23:57:45.764405 WARNING: intensity_correlation has 8 NaNs ( 0.24 % out of 3269)
2 days, 23:57:45.773715 INFO: Collecting fragment features
2 days, 23:57:45.780091 INFO: Finished candidate scoring
2 days, 23:57:45.783908 INFO: performing precursor FDR with 47 features
2 days, 23:57:45.784005 INFO: Decoy channel: -1
2 days, 23:57:45.784038 INFO: competitive: True
2 days, 23:57:45.788036 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:45.789929 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:57:45.790002 WARNING: dropped 7 decoy PSMs due to missing features
2 days, 23:57:45.791150 INFO: Estimating optimal hyperparameters - samples: 2,608, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:45.791260 INFO: Using random state 352725 for train-test-split
2 days, 23:57:46.092538 INFO: Test AUC: 0.849
2 days, 23:57:46.092688 INFO: Train AUC: 0.857
2 days, 23:57:46.092745 INFO: AUC difference: 0.95%
2 days, 23:57:46.455934 INFO: Resetting torch num_threads to 80
2 days, 23:57:46.456714 PROGRESS: === Extracted 3269 precursors and 24174 fragments ===
2 days, 23:57:46.457263 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:57:46.458193 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:46.458312 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:46.458400 PROGRESS: Target precursors: 583 (97.17%)
2 days, 23:57:46.458480 PROGRESS: Decoy precursors: 17 (2.83%)
2 days, 23:57:46.458550 PROGRESS: 
2 days, 23:57:46.458625 PROGRESS: Precursor Summary:
2 days, 23:57:46.460343 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   558; 0.001 FDR:   428
2 days, 23:57:46.460495 PROGRESS: 
2 days, 23:57:46.460569 PROGRESS: Protein Summary:
2 days, 23:57:46.462458 PROGRESS: Channel   0:	 0.050 FDR:   426; 0.010 FDR:   412; 0.001 FDR:   326
2 days, 23:57:46.462584 PROGRESS: =========================================================================
2 days, 23:57:46.462775 INFO: Target number of precursors reached.
2 days, 23:57:46.473021 INFO: fragments_df: keeping 5000 of 24174 [sum(precursor_idx_mask)=13384 sum(mass_error_mask)=24174 stop_rank=5000
2 days, 23:57:46.477795 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:46.692486 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:46.946303 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:47.180470 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:48.080233 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:48.080752 INFO: Using score_cutoff 18.13896398220062 (fac=0.99, q=1)
2 days, 23:57:48.081145 INFO: Updating optimization_manager: fwhm_rt             : 2.593263626098633 -> 2.5480268001556396
2 days, 23:57:48.081249 INFO: Updating optimization_manager: fwhm_mobility       : 0.004365007858723402 -> 0.004126410000026226
2 days, 23:57:48.081331 INFO: Updating optimization_manager: score_cutoff        : 21.06804058456421 -> 18.13896398220062
2 days, 23:57:48.081411 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:48.082687 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:48.084324 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:48.085257 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:48.087354 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:48.087481 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:57:48.089552 INFO: Updating optimization_manager: rt_error            : 53.21460745280913 -> 35.6485898370445
2 days, 23:57:48.089679 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 35.6486.
2 days, 23:57:48.089776 INFO: ==============================================
2 days, 23:57:48.089893 INFO: Starting optimization step 4.
2 days, 23:57:48.089996 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:48.090091 INFO: Using python extraction backend
2 days, 23:57:48.090229 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:48.090321 INFO: === Search parameters used ===
2 days, 23:57:48.090396 INFO: rt_error       : 35.6485898370445
2 days, 23:57:48.090464 INFO: mobility_error : 0.1
2 days, 23:57:48.090536 INFO: num_candidates : 3
2 days, 23:57:48.090601 INFO: ms1_error      : 15.0
2 days, 23:57:48.090663 INFO: ms2_error      : 15.0
2 days, 23:57:48.090724 INFO: fwhm_rt        : 2.5480268001556396
2 days, 23:57:48.090790 INFO: quant_window   : 3
2 days, 23:57:48.090851 INFO: ==============================================
2 days, 23:57:48.091820 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:48.091874 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:48.091923 INFO: FWHM in RT is 2.55 seconds, sigma is 0.42
2 days, 23:57:48.091958 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.24
2 days, 23:57:48.106018 INFO: Starting candidate selection
2 days, 23:57:48.929605 INFO: Starting candidate scoring
2 days, 23:57:49.039273 INFO: Finished candidate processing
2 days, 23:57:49.039410 INFO: Collecting candidate features
2 days, 23:57:49.056445 WARNING: intensity_correlation has 15 NaNs ( 0.46 % out of 3249)
2 days, 23:57:49.064780 INFO: Collecting fragment features
2 days, 23:57:49.071152 INFO: Finished candidate scoring
2 days, 23:57:49.075764 INFO: performing precursor FDR with 47 features
2 days, 23:57:49.075902 INFO: Decoy channel: -1
2 days, 23:57:49.075936 INFO: competitive: True
2 days, 23:57:49.081107 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:49.083607 WARNING: dropped 3 target PSMs due to missing features
2 days, 23:57:49.083689 WARNING: dropped 12 decoy PSMs due to missing features
2 days, 23:57:49.085239 INFO: Estimating optimal hyperparameters - samples: 2,587, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:49.085374 INFO: Using random state 352725 for train-test-split
2 days, 23:57:49.423776 INFO: Test AUC: 0.893
2 days, 23:57:49.423958 INFO: Train AUC: 0.862
2 days, 23:57:49.424040 INFO: AUC difference: 3.64%
2 days, 23:57:49.782957 INFO: Resetting torch num_threads to 80
2 days, 23:57:49.783675 PROGRESS: === Extracted 3249 precursors and 23676 fragments ===
2 days, 23:57:49.784152 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:57:49.784865 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:49.784980 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:49.785076 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:57:49.785161 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:57:49.785238 PROGRESS: 
2 days, 23:57:49.785308 PROGRESS: Precursor Summary:
2 days, 23:57:49.786559 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   558; 0.001 FDR:   432
2 days, 23:57:49.786716 PROGRESS: 
2 days, 23:57:49.786804 PROGRESS: Protein Summary:
2 days, 23:57:49.788234 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   411; 0.001 FDR:   327
2 days, 23:57:49.788353 PROGRESS: =========================================================================
2 days, 23:57:49.788546 INFO: Target number of precursors reached.
2 days, 23:57:49.795147 INFO: fragments_df: keeping 5000 of 23676 [sum(precursor_idx_mask)=13332 sum(mass_error_mask)=23676 stop_rank=5000
2 days, 23:57:49.799722 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:50.057496 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:50.272955 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:50.521998 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:51.332461 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:51.332906 INFO: Using score_cutoff 16.691301941871643 (fac=0.99, q=1)
2 days, 23:57:51.333239 INFO: Updating optimization_manager: fwhm_rt             : 2.5480268001556396 -> 2.5528855323791504
2 days, 23:57:51.333326 INFO: Updating optimization_manager: fwhm_mobility       : 0.004126410000026226 -> 0.004070320166647434
2 days, 23:57:51.333385 INFO: Updating optimization_manager: score_cutoff        : 18.13896398220062 -> 16.691301941871643
2 days, 23:57:51.333444 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:51.334631 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:51.336058 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:51.336932 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:51.339195 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:51.339322 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:57:51.341347 INFO: Updating optimization_manager: rt_error            : 35.6485898370445 -> 12.673274989763373
2 days, 23:57:51.341479 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 12.6733.
2 days, 23:57:51.341582 INFO: ==============================================
2 days, 23:57:51.341695 INFO: Starting optimization step 5.
2 days, 23:57:51.341787 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:51.341888 INFO: Using python extraction backend
2 days, 23:57:51.342035 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:51.342127 INFO: === Search parameters used ===
2 days, 23:57:51.342210 INFO: rt_error       : 12.673274989763373
2 days, 23:57:51.342265 INFO: mobility_error : 0.1
2 days, 23:57:51.342312 INFO: num_candidates : 3
2 days, 23:57:51.342357 INFO: ms1_error      : 15.0
2 days, 23:57:51.342401 INFO: ms2_error      : 15.0
2 days, 23:57:51.342444 INFO: fwhm_rt        : 2.5528855323791504
2 days, 23:57:51.342490 INFO: quant_window   : 3
2 days, 23:57:51.342535 INFO: ==============================================
2 days, 23:57:51.343458 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:51.343509 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:51.343557 INFO: FWHM in RT is 2.55 seconds, sigma is 0.43
2 days, 23:57:51.343593 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.21
2 days, 23:57:51.354167 INFO: Starting candidate selection
2 days, 23:57:51.922503 INFO: Starting candidate scoring
2 days, 23:57:52.020212 INFO: Finished candidate processing
2 days, 23:57:52.020337 INFO: Collecting candidate features
2 days, 23:57:52.034346 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3203)
2 days, 23:57:52.040752 INFO: Collecting fragment features
2 days, 23:57:52.045746 INFO: Finished candidate scoring
2 days, 23:57:52.049682 INFO: performing precursor FDR with 47 features
2 days, 23:57:52.049823 INFO: Decoy channel: -1
2 days, 23:57:52.049899 INFO: competitive: True
2 days, 23:57:52.054352 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:52.056418 WARNING: dropped 5 target PSMs due to missing features
2 days, 23:57:52.056475 WARNING: dropped 14 decoy PSMs due to missing features
2 days, 23:57:52.057770 INFO: Estimating optimal hyperparameters - samples: 2,547, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:52.057896 INFO: Using random state 352725 for train-test-split
2 days, 23:57:52.384350 INFO: Test AUC: 0.879
2 days, 23:57:52.384470 INFO: Train AUC: 0.896
2 days, 23:57:52.384515 INFO: AUC difference: 1.85%
2 days, 23:57:52.716971 INFO: Resetting torch num_threads to 80
2 days, 23:57:52.717742 PROGRESS: === Extracted 3203 precursors and 22861 fragments ===
2 days, 23:57:52.718323 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:57:52.719264 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:52.719384 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:52.719476 PROGRESS: Target precursors: 592 (98.67%)
2 days, 23:57:52.719554 PROGRESS: Decoy precursors: 8 (1.33%)
2 days, 23:57:52.719630 PROGRESS: 
2 days, 23:57:52.719706 PROGRESS: Precursor Summary:
2 days, 23:57:52.721533 PROGRESS: Channel   0:	 0.050 FDR:   592; 0.010 FDR:   589; 0.001 FDR:   581
2 days, 23:57:52.721677 PROGRESS: 
2 days, 23:57:52.721765 PROGRESS: Protein Summary:
2 days, 23:57:52.723681 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   431; 0.001 FDR:   426
2 days, 23:57:52.723800 PROGRESS: =========================================================================
2 days, 23:57:52.723985 INFO: Target number of precursors reached.
2 days, 23:57:52.730766 INFO: fragments_df: keeping 5000 of 22861 [sum(precursor_idx_mask)=13939 sum(mass_error_mask)=22861 stop_rank=5000
2 days, 23:57:52.734632 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:52.942465 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:53.146122 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:53.381362 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:54.167945 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:54.168398 INFO: Using score_cutoff 15.54000693283081 (fac=0.99, q=1)
2 days, 23:57:54.168726 INFO: Updating optimization_manager: fwhm_rt             : 2.5528855323791504 -> 2.5410706996917725
2 days, 23:57:54.168807 INFO: Updating optimization_manager: fwhm_mobility       : 0.004070320166647434 -> 0.0038000016938894987
2 days, 23:57:54.168876 INFO: Updating optimization_manager: score_cutoff        : 16.691301941871643 -> 15.54000693283081
2 days, 23:57:54.168950 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:54.170126 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:54.171580 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:54.172411 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:54.174463 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:54.174575 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 23:57:54.176569 INFO: Updating optimization_manager: rt_error            : 12.673274989763373 -> 11.082544397548192
2 days, 23:57:54.176683 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 11.0825.
2 days, 23:57:54.176758 INFO: ==============================================
2 days, 23:57:54.176836 INFO: Starting optimization step 6.
2 days, 23:57:54.176904 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:54.176971 INFO: Using python extraction backend
2 days, 23:57:54.177077 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:54.177150 INFO: === Search parameters used ===
2 days, 23:57:54.177206 INFO: rt_error       : 11.082544397548192
2 days, 23:57:54.177258 INFO: mobility_error : 0.1
2 days, 23:57:54.177309 INFO: num_candidates : 3
2 days, 23:57:54.177360 INFO: ms1_error      : 15.0
2 days, 23:57:54.177411 INFO: ms2_error      : 15.0
2 days, 23:57:54.177465 INFO: fwhm_rt        : 2.5410706996917725
2 days, 23:57:54.177518 INFO: quant_window   : 3
2 days, 23:57:54.177569 INFO: ==============================================
2 days, 23:57:54.178466 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:54.178523 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:54.178563 INFO: FWHM in RT is 2.54 seconds, sigma is 0.42
2 days, 23:57:54.178591 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.06
2 days, 23:57:54.182734 INFO: Starting candidate selection
2 days, 23:57:54.731262 INFO: Starting candidate scoring
2 days, 23:57:54.842469 INFO: Finished candidate processing
2 days, 23:57:54.842611 INFO: Collecting candidate features
2 days, 23:57:54.859098 WARNING: intensity_correlation has 20 NaNs ( 0.63 % out of 3189)
2 days, 23:57:54.865148 INFO: Collecting fragment features
2 days, 23:57:54.869275 INFO: Finished candidate scoring
2 days, 23:57:54.872143 INFO: performing precursor FDR with 47 features
2 days, 23:57:54.872201 INFO: Decoy channel: -1
2 days, 23:57:54.872228 INFO: competitive: True
2 days, 23:57:54.875448 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:54.877062 WARNING: dropped 5 target PSMs due to missing features
2 days, 23:57:54.877124 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:57:54.878179 INFO: Estimating optimal hyperparameters - samples: 2,535, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:54.878293 INFO: Using random state 352725 for train-test-split
2 days, 23:57:55.244850 INFO: Test AUC: 0.884
2 days, 23:57:55.244983 INFO: Train AUC: 0.898
2 days, 23:57:55.245025 INFO: AUC difference: 1.62%
2 days, 23:57:55.628639 INFO: Resetting torch num_threads to 80
2 days, 23:57:55.629423 PROGRESS: === Extracted 3189 precursors and 22704 fragments ===
2 days, 23:57:55.630061 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:57:55.631111 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:55.631259 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:55.631370 PROGRESS: Target precursors: 593 (98.83%)
2 days, 23:57:55.631477 PROGRESS: Decoy precursors: 7 (1.17%)
2 days, 23:57:55.631570 PROGRESS: 
2 days, 23:57:55.631659 PROGRESS: Precursor Summary:
2 days, 23:57:55.633548 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   591; 0.001 FDR:   582
2 days, 23:57:55.633690 PROGRESS: 
2 days, 23:57:55.633796 PROGRESS: Protein Summary:
2 days, 23:57:55.636223 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   432; 0.001 FDR:   426
2 days, 23:57:55.636361 PROGRESS: =========================================================================
2 days, 23:57:55.636586 INFO: Target number of precursors reached.
2 days, 23:57:55.646670 INFO: fragments_df: keeping 5000 of 22704 [sum(precursor_idx_mask)=13842 sum(mass_error_mask)=22704 stop_rank=5000
2 days, 23:57:55.652177 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:55.865230 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:56.037108 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:56.343646 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:57.195079 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:57.195565 INFO: Using score_cutoff 15.774090416908264 (fac=0.99, q=1)
2 days, 23:57:57.195943 INFO: Updating optimization_manager: fwhm_rt             : 2.5410706996917725 -> 2.5233376026153564
2 days, 23:57:57.196052 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038000016938894987 -> 0.0038000016938894987
2 days, 23:57:57.196139 INFO: Updating optimization_manager: score_cutoff        : 15.54000693283081 -> 15.774090416908264
2 days, 23:57:57.196220 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:57.197422 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:57.198946 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:57.199809 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:57.201935 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:57.202061 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 23:57:57.204139 INFO: Updating optimization_manager: rt_error            : 11.082544397548192 -> 11.514376746903963
2 days, 23:57:57.204263 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 11.5144.
2 days, 23:57:57.204357 INFO: ==============================================
2 days, 23:57:57.204454 INFO: Starting optimization step 7.
2 days, 23:57:57.204541 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:57.204628 INFO: Using python extraction backend
2 days, 23:57:57.204763 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:57.204849 INFO: === Search parameters used ===
2 days, 23:57:57.204922 INFO: rt_error       : 11.514376746903963
2 days, 23:57:57.204989 INFO: mobility_error : 0.1
2 days, 23:57:57.205053 INFO: num_candidates : 3
2 days, 23:57:57.205113 INFO: ms1_error      : 15.0
2 days, 23:57:57.205185 INFO: ms2_error      : 15.0
2 days, 23:57:57.205256 INFO: fwhm_rt        : 2.5233376026153564
2 days, 23:57:57.205318 INFO: quant_window   : 3
2 days, 23:57:57.205379 INFO: ==============================================
2 days, 23:57:57.206368 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:57.206424 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:57.206475 INFO: FWHM in RT is 2.52 seconds, sigma is 0.42
2 days, 23:57:57.206510 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.06
2 days, 23:57:57.218029 INFO: Starting candidate selection
2 days, 23:57:57.739532 INFO: Starting candidate scoring
2 days, 23:57:57.848790 INFO: Finished candidate processing
2 days, 23:57:57.848926 INFO: Collecting candidate features
2 days, 23:57:57.862217 WARNING: intensity_correlation has 20 NaNs ( 0.63 % out of 3193)
2 days, 23:57:57.867505 INFO: Collecting fragment features
2 days, 23:57:57.872138 INFO: Finished candidate scoring
2 days, 23:57:57.875497 INFO: performing precursor FDR with 47 features
2 days, 23:57:57.875556 INFO: Decoy channel: -1
2 days, 23:57:57.875587 INFO: competitive: True
2 days, 23:57:57.880048 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:57:57.882163 WARNING: dropped 6 target PSMs due to missing features
2 days, 23:57:57.882245 WARNING: dropped 14 decoy PSMs due to missing features
2 days, 23:57:57.883506 INFO: Estimating optimal hyperparameters - samples: 2,538, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:57:57.883611 INFO: Using random state 352725 for train-test-split
2 days, 23:57:58.127582 INFO: Test AUC: 0.880
2 days, 23:57:58.127701 INFO: Train AUC: 0.900
2 days, 23:57:58.127739 INFO: AUC difference: 2.22%
2 days, 23:57:58.417352 INFO: Resetting torch num_threads to 80
2 days, 23:57:58.418006 PROGRESS: === Extracted 3193 precursors and 22761 fragments ===
2 days, 23:57:58.418469 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:57:58.419171 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:57:58.419279 PROGRESS: Total precursors accumulated: 600
2 days, 23:57:58.419366 PROGRESS: Target precursors: 594 (99.00%)
2 days, 23:57:58.419443 PROGRESS: Decoy precursors: 6 (1.00%)
2 days, 23:57:58.419511 PROGRESS: 
2 days, 23:57:58.419578 PROGRESS: Precursor Summary:
2 days, 23:57:58.420793 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:   590; 0.001 FDR:   582
2 days, 23:57:58.420909 PROGRESS: 
2 days, 23:57:58.420992 PROGRESS: Protein Summary:
2 days, 23:57:58.422437 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   429; 0.001 FDR:   426
2 days, 23:57:58.422567 PROGRESS: =========================================================================
2 days, 23:57:58.422748 INFO: Target number of precursors reached.
2 days, 23:57:58.429170 INFO: fragments_df: keeping 5000 of 22761 [sum(precursor_idx_mask)=13845 sum(mass_error_mask)=22761 stop_rank=5000
2 days, 23:57:58.433205 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:58.617778 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:58.792063 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:59.062148 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:59.882024 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:57:59.882463 INFO: Using score_cutoff 15.97080562505722 (fac=0.99, q=1)
2 days, 23:57:59.882791 INFO: Updating optimization_manager: fwhm_rt             : 2.5233376026153564 -> 2.523381233215332
2 days, 23:57:59.882875 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038000016938894987 -> 0.0038258011918514967
2 days, 23:57:59.882932 INFO: Updating optimization_manager: score_cutoff        : 15.774090416908264 -> 15.97080562505722
2 days, 23:57:59.882987 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:59.884115 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:59.885552 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:59.886388 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:59.888414 INFO: === checking if optimization conditions were reached ===
2 days, 23:57:59.888519 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 23:57:59.889522 INFO: Updating optimization_manager: rt_error            : 11.514376746903963 -> 11.082544397548192
2 days, 23:57:59.889654 INFO: Updating optimization_manager: classifier_version  : 3 -> 10
2 days, 23:57:59.889761 INFO: Updating optimization_manager: score_cutoff        : 15.97080562505722 -> 15.774090416908264
2 days, 23:57:59.889860 INFO: Updating optimization_manager: fwhm_rt             : 2.523381233215332 -> 2.5233376026153564
2 days, 23:57:59.889973 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038258011918514967 -> 0.0038000016938894987
2 days, 23:57:59.890079 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 11.0825 found after 8 searches.
2 days, 23:57:59.890145 INFO: ==============================================
2 days, 23:57:59.890215 PROGRESS: Optimization finished for rt_error.
2 days, 23:57:59.893228 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:57:59.894090 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:57:59.895488 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:57:59.896305 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:57:59.898296 INFO: Starting optimization step 0.
2 days, 23:57:59.898401 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:57:59.898473 INFO: Using python extraction backend
2 days, 23:57:59.898576 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:57:59.898648 INFO: === Search parameters used ===
2 days, 23:57:59.898703 INFO: rt_error       : 11.082544397548192
2 days, 23:57:59.898750 INFO: mobility_error : 0.1
2 days, 23:57:59.898796 INFO: num_candidates : 3
2 days, 23:57:59.898842 INFO: ms1_error      : 15.0
2 days, 23:57:59.898886 INFO: ms2_error      : 15.0
2 days, 23:57:59.898930 INFO: fwhm_rt        : 2.5233376026153564
2 days, 23:57:59.898973 INFO: quant_window   : 3
2 days, 23:57:59.899015 INFO: ==============================================
2 days, 23:57:59.899784 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:57:59.899834 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:57:59.899869 INFO: FWHM in RT is 2.52 seconds, sigma is 0.42
2 days, 23:57:59.899894 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.06
2 days, 23:57:59.906736 INFO: Starting candidate selection
2 days, 23:58:00.464003 INFO: Starting candidate scoring
2 days, 23:58:00.564854 INFO: Finished candidate processing
2 days, 23:58:00.564991 INFO: Collecting candidate features
2 days, 23:58:00.581541 WARNING: intensity_correlation has 20 NaNs ( 0.63 % out of 3195)
2 days, 23:58:00.590088 INFO: Collecting fragment features
2 days, 23:58:00.596494 INFO: Finished candidate scoring
2 days, 23:58:00.600588 INFO: performing precursor FDR with 47 features
2 days, 23:58:00.600703 INFO: Decoy channel: -1
2 days, 23:58:00.600750 INFO: competitive: True
2 days, 23:58:00.605711 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:58:00.608203 WARNING: dropped 5 target PSMs due to missing features
2 days, 23:58:00.608284 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:58:00.609609 INFO: Estimating optimal hyperparameters - samples: 2,540, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:58:00.609720 INFO: Using random state 407485 for train-test-split
2 days, 23:58:00.917685 INFO: Test AUC: 0.909
2 days, 23:58:00.917835 INFO: Train AUC: 0.903
2 days, 23:58:00.917905 INFO: AUC difference: 0.68%
2 days, 23:58:01.205778 INFO: Resetting torch num_threads to 80
2 days, 23:58:01.206450 PROGRESS: === Extracted 3195 precursors and 22753 fragments ===
2 days, 23:58:01.206933 INFO: === FDR correction performed with classifier version 10 ===
2 days, 23:58:01.207668 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:58:01.207783 PROGRESS: Total precursors accumulated: 600
2 days, 23:58:01.207877 PROGRESS: Target precursors: 594 (99.00%)
2 days, 23:58:01.207958 PROGRESS: Decoy precursors: 6 (1.00%)
2 days, 23:58:01.208034 PROGRESS: 
2 days, 23:58:01.208108 PROGRESS: Precursor Summary:
2 days, 23:58:01.209373 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:   594; 0.001 FDR:   581
2 days, 23:58:01.209496 PROGRESS: 
2 days, 23:58:01.209580 PROGRESS: Protein Summary:
2 days, 23:58:01.211034 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   434; 0.001 FDR:   425
2 days, 23:58:01.211154 PROGRESS: =========================================================================
2 days, 23:58:01.211356 INFO: Target number of precursors reached.
2 days, 23:58:01.218223 INFO: fragments_df: keeping 5000 of 22753 [sum(precursor_idx_mask)=13936 sum(mass_error_mask)=22753 stop_rank=5000
2 days, 23:58:01.222143 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:01.412751 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:01.625092 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:01.840683 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:02.694802 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:58:02.695424 INFO: Using score_cutoff 15.772263586235045 (fac=0.99, q=1)
2 days, 23:58:02.695899 INFO: Updating optimization_manager: fwhm_rt             : 2.5233376026153564 -> 2.520866870880127
2 days, 23:58:02.696012 INFO: Updating optimization_manager: fwhm_mobility       : 0.0038000016938894987 -> 0.003747867653146386
2 days, 23:58:02.696110 INFO: Updating optimization_manager: score_cutoff        : 15.774090416908264 -> 15.772263586235045
2 days, 23:58:02.696214 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:02.697746 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:02.699626 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:02.700770 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:02.703334 INFO: === checking if optimization conditions were reached ===
2 days, 23:58:02.703479 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:58:02.705678 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0702361700361007
2 days, 23:58:02.705818 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0702.
2 days, 23:58:02.705940 INFO: ==============================================
2 days, 23:58:02.706080 INFO: Starting optimization step 1.
2 days, 23:58:02.706184 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:58:02.706289 INFO: Using python extraction backend
2 days, 23:58:02.706452 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:58:02.706566 INFO: === Search parameters used ===
2 days, 23:58:02.706662 INFO: rt_error       : 11.082544397548192
2 days, 23:58:02.706756 INFO: mobility_error : 0.0702361700361007
2 days, 23:58:02.706854 INFO: num_candidates : 3
2 days, 23:58:02.706935 INFO: ms1_error      : 15.0
2 days, 23:58:02.707007 INFO: ms2_error      : 15.0
2 days, 23:58:02.707075 INFO: fwhm_rt        : 2.520866870880127
2 days, 23:58:02.707144 INFO: quant_window   : 3
2 days, 23:58:02.707218 INFO: ==============================================
2 days, 23:58:02.708503 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:58:02.708570 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:58:02.708628 INFO: FWHM in RT is 2.52 seconds, sigma is 0.42
2 days, 23:58:02.708672 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.03
2 days, 23:58:02.718105 INFO: Starting candidate selection
2 days, 23:58:03.268303 INFO: Starting candidate scoring
2 days, 23:58:03.374072 INFO: Finished candidate processing
2 days, 23:58:03.374210 INFO: Collecting candidate features
2 days, 23:58:03.390930 WARNING: intensity_correlation has 20 NaNs ( 0.63 % out of 3185)
2 days, 23:58:03.399351 INFO: Collecting fragment features
2 days, 23:58:03.405508 INFO: Finished candidate scoring
2 days, 23:58:03.409683 INFO: performing precursor FDR with 47 features
2 days, 23:58:03.409827 INFO: Decoy channel: -1
2 days, 23:58:03.410009 INFO: competitive: True
2 days, 23:58:03.413830 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:58:03.415900 WARNING: dropped 5 target PSMs due to missing features
2 days, 23:58:03.415977 WARNING: dropped 15 decoy PSMs due to missing features
2 days, 23:58:03.417440 INFO: Estimating optimal hyperparameters - samples: 2,532, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:58:03.417618 INFO: Using random state 407485 for train-test-split
2 days, 23:58:03.698752 INFO: Test AUC: 0.883
2 days, 23:58:03.698866 INFO: Train AUC: 0.911
2 days, 23:58:03.698898 INFO: AUC difference: 3.06%
2 days, 23:58:04.033023 INFO: Resetting torch num_threads to 80
2 days, 23:58:04.033593 PROGRESS: === Extracted 3185 precursors and 22592 fragments ===
2 days, 23:58:04.034055 INFO: === FDR correction performed with classifier version 10 ===
2 days, 23:58:04.034724 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:58:04.034814 PROGRESS: Total precursors accumulated: 600
2 days, 23:58:04.034878 PROGRESS: Target precursors: 593 (98.83%)
2 days, 23:58:04.034934 PROGRESS: Decoy precursors: 7 (1.17%)
2 days, 23:58:04.034985 PROGRESS: 
2 days, 23:58:04.035033 PROGRESS: Precursor Summary:
2 days, 23:58:04.036204 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   592; 0.001 FDR:   584
2 days, 23:58:04.036303 PROGRESS: 
2 days, 23:58:04.036363 PROGRESS: Protein Summary:
2 days, 23:58:04.037740 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   433; 0.001 FDR:   427
2 days, 23:58:04.037843 PROGRESS: =========================================================================
2 days, 23:58:04.038018 INFO: Target number of precursors reached.
2 days, 23:58:04.044314 INFO: fragments_df: keeping 5000 of 22592 [sum(precursor_idx_mask)=13880 sum(mass_error_mask)=22592 stop_rank=5000
2 days, 23:58:04.047850 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:04.236078 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:04.502009 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:04.783287 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:05.589835 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:58:05.590306 INFO: Using score_cutoff 15.374363981437684 (fac=0.99, q=1)
2 days, 23:58:05.590643 INFO: Updating optimization_manager: fwhm_rt             : 2.520866870880127 -> 2.519517183303833
2 days, 23:58:05.590729 INFO: Updating optimization_manager: fwhm_mobility       : 0.003747867653146386 -> 0.0037546702660620213
2 days, 23:58:05.590790 INFO: Updating optimization_manager: score_cutoff        : 15.772263586235045 -> 15.374363981437684
2 days, 23:58:05.590851 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:05.591967 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:05.593373 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:05.594185 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:05.596204 INFO: === checking if optimization conditions were reached ===
2 days, 23:58:05.596317 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:58:05.597891 INFO: Updating optimization_manager: mobility_error      : 0.0702361700361007 -> 0.058221964741950065
2 days, 23:58:05.598008 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0582.
2 days, 23:58:05.598082 INFO: ==============================================
2 days, 23:58:05.598164 INFO: Starting optimization step 2.
2 days, 23:58:05.598228 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:58:05.598288 INFO: Using python extraction backend
2 days, 23:58:05.598388 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:58:05.598459 INFO: === Search parameters used ===
2 days, 23:58:05.598510 INFO: rt_error       : 11.082544397548192
2 days, 23:58:05.598557 INFO: mobility_error : 0.058221964741950065
2 days, 23:58:05.598604 INFO: num_candidates : 3
2 days, 23:58:05.598650 INFO: ms1_error      : 15.0
2 days, 23:58:05.598694 INFO: ms2_error      : 15.0
2 days, 23:58:05.598737 INFO: fwhm_rt        : 2.519517183303833
2 days, 23:58:05.598781 INFO: quant_window   : 3
2 days, 23:58:05.598826 INFO: ==============================================
2 days, 23:58:05.599679 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:58:05.599736 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:58:05.599775 INFO: FWHM in RT is 2.52 seconds, sigma is 0.42
2 days, 23:58:05.599800 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.03
2 days, 23:58:05.609997 INFO: Starting candidate selection
2 days, 23:58:06.214988 INFO: Starting candidate scoring
2 days, 23:58:06.318790 INFO: Finished candidate processing
2 days, 23:58:06.318926 INFO: Collecting candidate features
2 days, 23:58:06.335732 WARNING: intensity_correlation has 18 NaNs ( 0.57 % out of 3161)
2 days, 23:58:06.344121 INFO: Collecting fragment features
2 days, 23:58:06.350072 INFO: Finished candidate scoring
2 days, 23:58:06.353658 INFO: performing precursor FDR with 47 features
2 days, 23:58:06.353747 INFO: Decoy channel: -1
2 days, 23:58:06.353785 INFO: competitive: True
2 days, 23:58:06.358083 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:58:06.359832 WARNING: dropped 5 target PSMs due to missing features
2 days, 23:58:06.359888 WARNING: dropped 13 decoy PSMs due to missing features
2 days, 23:58:06.360914 INFO: Estimating optimal hyperparameters - samples: 2,514, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:58:06.361010 INFO: Using random state 407485 for train-test-split
2 days, 23:58:06.653612 INFO: Test AUC: 0.904
2 days, 23:58:06.653751 INFO: Train AUC: 0.902
2 days, 23:58:06.653805 INFO: AUC difference: 0.22%
2 days, 23:58:07.007338 INFO: Resetting torch num_threads to 80
2 days, 23:58:07.008139 PROGRESS: === Extracted 3161 precursors and 22383 fragments ===
2 days, 23:58:07.008713 INFO: === FDR correction performed with classifier version 10 ===
2 days, 23:58:07.009586 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:58:07.009693 PROGRESS: Total precursors accumulated: 600
2 days, 23:58:07.009771 PROGRESS: Target precursors: 595 (99.17%)
2 days, 23:58:07.009839 PROGRESS: Decoy precursors: 5 (0.83%)
2 days, 23:58:07.009935 PROGRESS: 
2 days, 23:58:07.010003 PROGRESS: Precursor Summary:
2 days, 23:58:07.011231 PROGRESS: Channel   0:	 0.050 FDR:   595; 0.010 FDR:   595; 0.001 FDR:   579
2 days, 23:58:07.011358 PROGRESS: 
2 days, 23:58:07.011447 PROGRESS: Protein Summary:
2 days, 23:58:07.013026 PROGRESS: Channel   0:	 0.050 FDR:   436; 0.010 FDR:   436; 0.001 FDR:   424
2 days, 23:58:07.013146 PROGRESS: =========================================================================
2 days, 23:58:07.013346 INFO: Target number of precursors reached.
2 days, 23:58:07.020851 INFO: fragments_df: keeping 5000 of 22383 [sum(precursor_idx_mask)=13880 sum(mass_error_mask)=22383 stop_rank=5000
2 days, 23:58:07.026250 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:07.230528 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:07.396674 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:07.578707 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:08.513639 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:58:08.514236 INFO: Using score_cutoff 14.899973145103454 (fac=0.99, q=1)
2 days, 23:58:08.514686 INFO: Updating optimization_manager: fwhm_rt             : 2.519517183303833 -> 2.5204238891601562
2 days, 23:58:08.514795 INFO: Updating optimization_manager: fwhm_mobility       : 0.0037546702660620213 -> 0.0037256507202982903
2 days, 23:58:08.514882 INFO: Updating optimization_manager: score_cutoff        : 15.374363981437684 -> 14.899973145103454
2 days, 23:58:08.514967 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:08.516439 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:08.518225 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:08.519232 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:08.521361 INFO: === checking if optimization conditions were reached ===
2 days, 23:58:08.521476 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:58:08.522269 INFO: Updating optimization_manager: mobility_error      : 0.058221964741950065 -> 0.058221964741950065
2 days, 23:58:08.522412 INFO: Updating optimization_manager: classifier_version  : 10 -> 14
2 days, 23:58:08.522538 INFO: Updating optimization_manager: score_cutoff        : 14.899973145103454 -> 14.899973145103454
2 days, 23:58:08.522641 INFO: Updating optimization_manager: fwhm_rt             : 2.5204238891601562 -> 2.5204238891601562
2 days, 23:58:08.522746 INFO: Updating optimization_manager: fwhm_mobility       : 0.0037256507202982903 -> 0.0037256507202982903
2 days, 23:58:08.522848 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0582 found after 3 searches.
2 days, 23:58:08.522923 INFO: ==============================================
2 days, 23:58:08.523003 PROGRESS: Optimization finished for mobility_error.
2 days, 23:58:08.526163 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:08.527062 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:08.528485 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:08.529329 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:08.531357 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:58:08.531484 PROGRESS: ==============================================
2 days, 23:58:08.531584 PROGRESS: ms2_error      : 15.0000
2 days, 23:58:08.531681 PROGRESS: ms1_error      : 15.0000
2 days, 23:58:08.531766 PROGRESS: rt_error       : 11.0825
2 days, 23:58:08.531832 PROGRESS: mobility_error : 0.0582
2 days, 23:58:08.531889 PROGRESS: ==============================================
2 days, 23:58:08.532568 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:08.536308 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:08.552435 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:08.556210 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:08.601119 INFO: Using python extraction backend
2 days, 23:58:08.614179 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:58:08.614298 INFO: === Search parameters used ===
2 days, 23:58:08.614368 INFO: rt_error       : 11.082544397548192
2 days, 23:58:08.614431 INFO: mobility_error : 0.058221964741950065
2 days, 23:58:08.614492 INFO: num_candidates : 3
2 days, 23:58:08.614552 INFO: ms1_error      : 15.0
2 days, 23:58:08.614609 INFO: ms2_error      : 15.0
2 days, 23:58:08.614666 INFO: fwhm_rt        : 2.5204238891601562
2 days, 23:58:08.614722 INFO: quant_window   : 3
2 days, 23:58:08.614777 INFO: ==============================================
2 days, 23:58:08.622214 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:58:08.622317 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:58:08.622366 INFO: FWHM in RT is 2.52 seconds, sigma is 0.42
2 days, 23:58:08.622402 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.02
2 days, 23:58:08.649511 INFO: Starting candidate selection
2 days, 23:58:10.594969 INFO: Removed 19598 precursors with score below cutoff 14.899973145103454
2 days, 23:58:10.944206 INFO: Starting candidate scoring
2 days, 23:58:11.919759 INFO: Finished candidate processing
2 days, 23:58:11.919881 INFO: Collecting candidate features
2 days, 23:58:12.036001 WARNING: intensity_correlation has 134 NaNs ( 0.23 % out of 57191)
2 days, 23:58:12.036360 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 57191)
2 days, 23:58:12.044411 INFO: Collecting fragment features
2 days, 23:58:12.087298 INFO: Finished candidate scoring
2 days, 23:58:12.120534 INFO: === Performing FDR correction with classifier version 14 ===
2 days, 23:58:12.121192 INFO: performing precursor FDR with 47 features
2 days, 23:58:12.121234 INFO: Decoy channel: -1
2 days, 23:58:12.121259 INFO: competitive: True
2 days, 23:58:12.137049 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:58:12.146333 WARNING: dropped 30 target PSMs due to missing features
2 days, 23:58:12.146458 WARNING: dropped 105 decoy PSMs due to missing features
2 days, 23:58:12.146504 WARNING: FDR calculation for 34903 target and 22153 decoy PSMs
2 days, 23:58:12.146548 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:58:12.155332 INFO: Estimating optimal hyperparameters - samples: 45,644, batch_size: 186, learning_rate: 2.13e-04
2 days, 23:58:12.155573 INFO: Using random state 471506 for train-test-split
2 days, 23:58:16.902535 INFO: Test AUC: 0.912
2 days, 23:58:16.902745 INFO: Train AUC: 0.916
2 days, 23:58:16.902798 INFO: AUC difference: 0.45%
2 days, 23:58:17.230562 INFO: Resetting torch num_threads to 80
2 days, 23:58:17.232898 INFO: Removing fragments below FDR threshold
2 days, 23:58:17.242623 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:58:17.242854 PROGRESS: Total precursors accumulated: 13,634
2 days, 23:58:17.242932 PROGRESS: Target precursors: 13,514 (99.12%)
2 days, 23:58:17.242999 PROGRESS: Decoy precursors: 120 (0.88%)
2 days, 23:58:17.243060 PROGRESS: 
2 days, 23:58:17.243118 PROGRESS: Precursor Summary:
2 days, 23:58:17.247825 PROGRESS: Channel   0:	 0.050 FDR: 13,514; 0.010 FDR: 13,514; 0.001 FDR: 12,877
2 days, 23:58:17.247985 PROGRESS: 
2 days, 23:58:17.248060 PROGRESS: Protein Summary:
2 days, 23:58:17.254288 PROGRESS: Channel   0:	 0.050 FDR: 1,682; 0.010 FDR: 1,682; 0.001 FDR: 1,682
2 days, 23:58:17.254460 PROGRESS: =========================================================================
2 days, 23:58:17.255573 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R3/psm.parquet
2 days, 23:58:17.330249 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R3/frag.parquet
2 days, 23:58:17.401754 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R3
2 days, 23:58:17.408540 PROGRESS: Loading raw file 10/12: B9_G_DIA_nLC_tTOF_R4 
2 days, 23:58:17.408722 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:58:17.408828 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R4/figures
2 days, 23:58:17.409098 INFO: Initializing TimingManager
2 days, 23:58:17.409882 INFO: Initializing RawFileManager
2 days, 23:58:17.410062 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:17.410145 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:17.410202 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:17.618829 INFO: Reading 22,623 frames with 398,008,957 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:21.508673 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d...
2 days, 23:58:21.509658 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:21.517497 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:21.517786 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:21.518299 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:21.520252 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:21.550167 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:21.550532 INFO: Indexing quadrupole dimension
2 days, 23:58:21.698025 INFO: Transposing detector events
2 days, 23:58:23.931101 INFO: Finished transposing data
2 days, 23:58:23.931233 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
2 days, 23:58:23.931558 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:58:23.931604 INFO: RT duration (sec)   : 2399.9
2 days, 23:58:23.931635 INFO: RT duration (min)   : 40.0
2 days, 23:58:23.931666 INFO: Cycle len (scans)   : 12
2 days, 23:58:23.931692 INFO: Cycle len (sec)     : 1.27
2 days, 23:58:23.931720 INFO: Number of cycles    : 1885
2 days, 23:58:23.931776 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:58:23.931815 INFO: Creating DIA data object took: 6.521756172180176
2 days, 23:58:23.939307 INFO: Initializing CalibrationManager
2 days, 23:58:23.939576 INFO: Setting up calibration estimators ..
2 days, 23:58:23.939669 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:58:23.939758 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:58:23.939847 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:58:23.939924 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:58:23.940004 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:58:23.940087 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:58:23.940160 INFO: Done setting up calibration estimators.
2 days, 23:58:23.940282 INFO: Initializing OptimizationManager
2 days, 23:58:23.940388 INFO: initial parameter: ms1_error = 30
2 days, 23:58:23.940445 INFO: initial parameter: ms2_error = 30
2 days, 23:58:23.940509 INFO: initial parameter: rt_error = 1199.9630585
2 days, 23:58:23.940568 INFO: initial parameter: mobility_error = 0.1
2 days, 23:58:23.940619 INFO: initial parameter: num_candidates = 1
2 days, 23:58:23.940670 INFO: initial parameter: fwhm_rt = 5
2 days, 23:58:23.940720 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:58:23.940771 INFO: initial parameter: score_cutoff = 0
2 days, 23:58:23.940820 INFO: initial parameter: classifier_version = -1
2 days, 23:58:23.940899 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R4
2 days, 23:58:23.941103 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:58:23.941138 INFO: Initializing FDRManager
2 days, 23:58:23.941172 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:58:23.949925 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:58:23.955781 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:58:23.956179 INFO: Updating optimization_manager: rt_error            : 1199.9630585 -> 1199.9630585
2 days, 23:58:23.956290 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:58:23.956494 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:58:23.956588 PROGRESS: Starting initial search for precursors.
2 days, 23:58:23.956679 INFO: Starting optimization step 0.
2 days, 23:58:23.956750 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:58:23.956825 INFO: Using python extraction backend
2 days, 23:58:23.956942 PROGRESS: Extracting batch of 399 precursors
2 days, 23:58:23.957012 INFO: === Search parameters used ===
2 days, 23:58:23.957092 INFO: rt_error       : 1199.9630585
2 days, 23:58:23.957174 INFO: mobility_error : 0.1
2 days, 23:58:23.957229 INFO: num_candidates : 1
2 days, 23:58:23.957282 INFO: ms1_error      : 30
2 days, 23:58:23.957333 INFO: ms2_error      : 30
2 days, 23:58:23.957384 INFO: fwhm_rt        : 5
2 days, 23:58:23.957435 INFO: quant_window   : 3
2 days, 23:58:23.957484 INFO: ==============================================
2 days, 23:58:23.958297 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:58:23.958361 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:58:23.958395 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:58:23.958424 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:58:23.974252 INFO: Starting candidate selection
2 days, 23:58:27.489551 INFO: Starting candidate scoring
2 days, 23:58:27.541750 INFO: Finished candidate processing
2 days, 23:58:27.541919 INFO: Collecting candidate features
2 days, 23:58:27.560605 INFO: Collecting fragment features
2 days, 23:58:27.564841 INFO: Finished candidate scoring
2 days, 23:58:27.566272 INFO: performing precursor FDR with 47 features
2 days, 23:58:27.566344 INFO: Decoy channel: -1
2 days, 23:58:27.566388 INFO: competitive: True
2 days, 23:58:27.568570 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:58:27.571345 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:58:27.572425 INFO: Using random state 421850 for train-test-split
2 days, 23:58:27.600062 INFO: Test AUC: 0.583
2 days, 23:58:27.600178 INFO: Train AUC: 0.632
2 days, 23:58:27.600259 INFO: AUC difference: 7.83%
2 days, 23:58:27.600319 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:58:27.924844 INFO: Resetting torch num_threads to 80
2 days, 23:58:27.925398 PROGRESS: === Extracted 399 precursors and 3761 fragments ===
2 days, 23:58:27.925861 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:58:27.926537 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:58:27.926655 PROGRESS: Total precursors accumulated: 200
2 days, 23:58:27.926749 PROGRESS: Target precursors: 127 (63.50%)
2 days, 23:58:27.926834 PROGRESS: Decoy precursors: 73 (36.50%)
2 days, 23:58:27.926908 PROGRESS: 
2 days, 23:58:27.926977 PROGRESS: Precursor Summary:
2 days, 23:58:27.927964 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 23:58:27.928075 PROGRESS: 
2 days, 23:58:27.928162 PROGRESS: Protein Summary:
2 days, 23:58:27.929250 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
2 days, 23:58:27.929360 PROGRESS: =========================================================================
2 days, 23:58:27.929518 INFO: Target number of precursors not reached yet.
2 days, 23:58:27.933627 INFO: Starting optimization step 1.
2 days, 23:58:27.933761 PROGRESS: === Extracting elution groups 200 to 600 ===
2 days, 23:58:27.933900 INFO: Using python extraction backend
2 days, 23:58:27.934049 PROGRESS: Extracting batch of 798 precursors
2 days, 23:58:27.934148 INFO: === Search parameters used ===
2 days, 23:58:27.934230 INFO: rt_error       : 1199.9630585
2 days, 23:58:27.934301 INFO: mobility_error : 0.1
2 days, 23:58:27.934367 INFO: num_candidates : 1
2 days, 23:58:27.934432 INFO: ms1_error      : 30
2 days, 23:58:27.934495 INFO: ms2_error      : 30
2 days, 23:58:27.934558 INFO: fwhm_rt        : 5
2 days, 23:58:27.934619 INFO: quant_window   : 3
2 days, 23:58:27.934680 INFO: ==============================================
2 days, 23:58:27.935435 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:58:27.935489 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:58:27.935531 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:58:27.935566 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:58:27.938605 INFO: Starting candidate selection
2 days, 23:58:33.696544 INFO: Starting candidate scoring
2 days, 23:58:33.772089 INFO: Finished candidate processing
2 days, 23:58:33.772225 INFO: Collecting candidate features
2 days, 23:58:33.791256 INFO: Collecting fragment features
2 days, 23:58:33.795914 INFO: Finished candidate scoring
2 days, 23:58:33.799383 INFO: performing precursor FDR with 47 features
2 days, 23:58:33.799470 INFO: Decoy channel: -1
2 days, 23:58:33.799522 INFO: competitive: True
2 days, 23:58:33.804486 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:58:33.807359 INFO: Estimating optimal hyperparameters - samples: 957, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:58:33.807482 INFO: Using random state 431652 for train-test-split
2 days, 23:58:33.919564 INFO: Test AUC: 0.774
2 days, 23:58:33.919697 INFO: Train AUC: 0.787
2 days, 23:58:33.919741 INFO: AUC difference: 1.69%
2 days, 23:58:34.306063 INFO: Resetting torch num_threads to 80
2 days, 23:58:34.307614 PROGRESS: === Extracted 1197 precursors and 11467 fragments ===
2 days, 23:58:34.308110 INFO: === FDR correction performed with classifier version -1 ===
2 days, 23:58:34.308867 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:58:34.309003 PROGRESS: Total precursors accumulated: 600
2 days, 23:58:34.309139 PROGRESS: Target precursors: 481 (80.17%)
2 days, 23:58:34.309221 PROGRESS: Decoy precursors: 119 (19.83%)
2 days, 23:58:34.309283 PROGRESS: 
2 days, 23:58:34.309340 PROGRESS: Precursor Summary:
2 days, 23:58:34.310746 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   239; 0.001 FDR:   238
2 days, 23:58:34.310886 PROGRESS: 
2 days, 23:58:34.310989 PROGRESS: Protein Summary:
2 days, 23:58:34.312469 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   180; 0.001 FDR:   179
2 days, 23:58:34.312577 PROGRESS: =========================================================================
2 days, 23:58:34.312771 INFO: Target number of precursors reached.
2 days, 23:58:34.317385 INFO: fragments_df: keeping 2030 of 11467 [sum(precursor_idx_mask)=2481 sum(mass_error_mask)=11467 stop_rank=2030
2 days, 23:58:34.321308 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:34.491496 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:34.667821 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:34.872596 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:35.296132 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2 days, 23:58:35.296691 INFO: Using score_cutoff 32.89774040908814 (fac=0.99, q=1)
2 days, 23:58:35.297092 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.9704060554504395
2 days, 23:58:35.297192 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007594570983201265
2 days, 23:58:35.297264 INFO: Updating optimization_manager: score_cutoff        : 0 -> 32.89774040908814
2 days, 23:58:35.297333 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:35.298562 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:35.300125 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:35.301014 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:35.303181 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2 days, 23:58:35.303317 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2 days, 23:58:35.303418 INFO: Starting optimization step 2.
2 days, 23:58:35.303502 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:58:35.303575 INFO: Using python extraction backend
2 days, 23:58:35.303693 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:58:35.303769 INFO: === Search parameters used ===
2 days, 23:58:35.303833 INFO: rt_error       : 1199.9630585
2 days, 23:58:35.303899 INFO: mobility_error : 0.1
2 days, 23:58:35.303967 INFO: num_candidates : 3
2 days, 23:58:35.304044 INFO: ms1_error      : 30
2 days, 23:58:35.304122 INFO: ms2_error      : 30
2 days, 23:58:35.304192 INFO: fwhm_rt        : 2.9704060554504395
2 days, 23:58:35.304266 INFO: quant_window   : 3
2 days, 23:58:35.304342 INFO: ==============================================
2 days, 23:58:35.305343 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:58:35.305399 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:58:35.305455 INFO: FWHM in RT is 2.97 seconds, sigma is 0.50
2 days, 23:58:35.305500 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.12
2 days, 23:58:35.326106 INFO: Starting candidate selection
2 days, 23:58:44.304797 INFO: Starting candidate scoring
2 days, 23:58:44.446243 INFO: Finished candidate processing
2 days, 23:58:44.446392 INFO: Collecting candidate features
2 days, 23:58:44.463618 INFO: Collecting fragment features
2 days, 23:58:44.468471 INFO: Finished candidate scoring
2 days, 23:58:44.471372 INFO: performing precursor FDR with 47 features
2 days, 23:58:44.471482 INFO: Decoy channel: -1
2 days, 23:58:44.471521 INFO: competitive: True
2 days, 23:58:44.475207 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:58:44.477765 INFO: Estimating optimal hyperparameters - samples: 2,764, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:58:44.477973 INFO: Using random state 16490 for train-test-split
2 days, 23:58:44.835107 INFO: Test AUC: 0.705
2 days, 23:58:44.835223 INFO: Train AUC: 0.715
2 days, 23:58:44.835267 INFO: AUC difference: 1.50%
2 days, 23:58:45.130929 INFO: Resetting torch num_threads to 80
2 days, 23:58:45.131566 PROGRESS: === Extracted 3456 precursors and 31949 fragments ===
2 days, 23:58:45.132046 INFO: === FDR correction performed with classifier version 1 ===
2 days, 23:58:45.132715 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:58:45.132829 PROGRESS: Total precursors accumulated: 600
2 days, 23:58:45.132919 PROGRESS: Target precursors: 513 (85.50%)
2 days, 23:58:45.133002 PROGRESS: Decoy precursors: 87 (14.50%)
2 days, 23:58:45.133079 PROGRESS: 
2 days, 23:58:45.133156 PROGRESS: Precursor Summary:
2 days, 23:58:45.134400 PROGRESS: Channel   0:	 0.050 FDR:   370; 0.010 FDR:   321; 0.001 FDR:   321
2 days, 23:58:45.134519 PROGRESS: 
2 days, 23:58:45.134605 PROGRESS: Protein Summary:
2 days, 23:58:45.135905 PROGRESS: Channel   0:	 0.050 FDR:   278; 0.010 FDR:   243; 0.001 FDR:   243
2 days, 23:58:45.136019 PROGRESS: =========================================================================
2 days, 23:58:45.136229 INFO: Target number of precursors reached.
2 days, 23:58:45.143171 INFO: fragments_df: keeping 5000 of 31949 [sum(precursor_idx_mask)=9106 sum(mass_error_mask)=31949 stop_rank=5000
2 days, 23:58:45.148060 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:45.353559 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:45.536991 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:45.745071 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:46.605016 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:58:46.605484 INFO: Using score_cutoff 31.031119926452636 (fac=0.99, q=1)
2 days, 23:58:46.605829 INFO: Updating optimization_manager: fwhm_rt             : 2.9704060554504395 -> 2.9532103538513184
2 days, 23:58:46.605933 INFO: Updating optimization_manager: fwhm_mobility       : 0.007594570983201265 -> 0.0064889490604400635
2 days, 23:58:46.605998 INFO: Updating optimization_manager: score_cutoff        : 32.89774040908814 -> 31.031119926452636
2 days, 23:58:46.606061 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:46.607227 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:46.608705 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:46.609526 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:46.611662 INFO: === checking if optimization conditions were reached ===
2 days, 23:58:46.613399 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.54385640651396
2 days, 23:58:46.613508 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2 days, 23:58:46.613579 PROGRESS: ❌ ms2_error      : 17.5439 > 15.0000 or insufficient steps taken.
2 days, 23:58:46.614617 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2 days, 23:58:46.614721 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
2 days, 23:58:46.614804 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2 days, 23:58:46.614862 INFO: ==============================================
2 days, 23:58:46.614930 INFO: Starting optimization step 3.
2 days, 23:58:46.614991 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:58:46.615049 INFO: Using python extraction backend
2 days, 23:58:46.615155 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:58:46.615222 INFO: === Search parameters used ===
2 days, 23:58:46.615271 INFO: rt_error       : 1199.9630585
2 days, 23:58:46.615324 INFO: mobility_error : 0.1
2 days, 23:58:46.615372 INFO: num_candidates : 3
2 days, 23:58:46.615416 INFO: ms1_error      : 15.0
2 days, 23:58:46.615459 INFO: ms2_error      : 17.54385640651396
2 days, 23:58:46.615503 INFO: fwhm_rt        : 2.9532103538513184
2 days, 23:58:46.615548 INFO: quant_window   : 3
2 days, 23:58:46.615591 INFO: ==============================================
2 days, 23:58:46.616513 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:58:46.616563 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:58:46.616599 INFO: FWHM in RT is 2.95 seconds, sigma is 0.49
2 days, 23:58:46.616623 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.52
2 days, 23:58:46.630017 INFO: Starting candidate selection
2 days, 23:58:55.547163 INFO: Starting candidate scoring
2 days, 23:58:55.668548 INFO: Finished candidate processing
2 days, 23:58:55.668664 INFO: Collecting candidate features
2 days, 23:58:55.687143 INFO: Collecting fragment features
2 days, 23:58:55.692033 INFO: Finished candidate scoring
2 days, 23:58:55.694690 INFO: performing precursor FDR with 47 features
2 days, 23:58:55.694751 INFO: Decoy channel: -1
2 days, 23:58:55.694783 INFO: competitive: True
2 days, 23:58:55.699679 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:58:55.702423 INFO: Estimating optimal hyperparameters - samples: 2,735, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:58:55.702535 INFO: Using random state 119511 for train-test-split
2 days, 23:58:56.044750 INFO: Test AUC: 0.720
2 days, 23:58:56.044870 INFO: Train AUC: 0.757
2 days, 23:58:56.044905 INFO: AUC difference: 4.87%
2 days, 23:58:56.375379 INFO: Resetting torch num_threads to 80
2 days, 23:58:56.375966 PROGRESS: === Extracted 3419 precursors and 28783 fragments ===
2 days, 23:58:56.376401 INFO: === FDR correction performed with classifier version 2 ===
2 days, 23:58:56.377027 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:58:56.377125 PROGRESS: Total precursors accumulated: 600
2 days, 23:58:56.377192 PROGRESS: Target precursors: 525 (87.50%)
2 days, 23:58:56.377250 PROGRESS: Decoy precursors: 75 (12.50%)
2 days, 23:58:56.377304 PROGRESS: 
2 days, 23:58:56.377354 PROGRESS: Precursor Summary:
2 days, 23:58:56.378514 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   397; 0.001 FDR:   397
2 days, 23:58:56.378614 PROGRESS: 
2 days, 23:58:56.378680 PROGRESS: Protein Summary:
2 days, 23:58:56.380005 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   302; 0.001 FDR:   302
2 days, 23:58:56.380105 PROGRESS: =========================================================================
2 days, 23:58:56.380257 INFO: Target number of precursors reached.
2 days, 23:58:56.386795 INFO: fragments_df: keeping 5000 of 28783 [sum(precursor_idx_mask)=10555 sum(mass_error_mask)=28783 stop_rank=5000
2 days, 23:58:56.390877 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:56.577954 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:56.736887 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:56.907813 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:57.733233 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:58:57.733711 INFO: Using score_cutoff 27.634094508361816 (fac=0.99, q=1)
2 days, 23:58:57.734098 INFO: Updating optimization_manager: fwhm_rt             : 2.9532103538513184 -> 2.794025182723999
2 days, 23:58:57.734201 INFO: Updating optimization_manager: fwhm_mobility       : 0.0064889490604400635 -> 0.005531940143555403
2 days, 23:58:57.734270 INFO: Updating optimization_manager: score_cutoff        : 31.031119926452636 -> 27.634094508361816
2 days, 23:58:57.734338 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:57.735490 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:57.736953 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:57.737772 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:57.739856 INFO: === checking if optimization conditions were reached ===
2 days, 23:58:57.741633 INFO: Updating optimization_manager: ms2_error           : 17.54385640651396 -> 15.0
2 days, 23:58:57.741752 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2 days, 23:58:57.741832 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2 days, 23:58:57.742912 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2 days, 23:58:57.743021 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
2 days, 23:58:57.743096 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2 days, 23:58:57.743169 INFO: ==============================================
2 days, 23:58:57.743251 PROGRESS: Optimization finished for ms2_error, ms1_error.
2 days, 23:58:57.746382 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:58:57.747264 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:58:57.748656 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:58:57.749467 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:58:57.751483 INFO: Starting optimization step 0.
2 days, 23:58:57.751599 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:58:57.751687 INFO: Using python extraction backend
2 days, 23:58:57.751810 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:58:57.751891 INFO: === Search parameters used ===
2 days, 23:58:57.751956 INFO: rt_error       : 1199.9630585
2 days, 23:58:57.752017 INFO: mobility_error : 0.1
2 days, 23:58:57.752073 INFO: num_candidates : 3
2 days, 23:58:57.752126 INFO: ms1_error      : 15.0
2 days, 23:58:57.752178 INFO: ms2_error      : 15.0
2 days, 23:58:57.752229 INFO: fwhm_rt        : 2.794025182723999
2 days, 23:58:57.752281 INFO: quant_window   : 3
2 days, 23:58:57.752342 INFO: ==============================================
2 days, 23:58:57.753164 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:58:57.753220 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:58:57.753262 INFO: FWHM in RT is 2.79 seconds, sigma is 0.47
2 days, 23:58:57.753289 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.00
2 days, 23:58:57.766336 INFO: Starting candidate selection
2 days, 23:59:06.604646 INFO: Starting candidate scoring
2 days, 23:59:06.716980 INFO: Finished candidate processing
2 days, 23:59:06.717119 INFO: Collecting candidate features
2 days, 23:59:06.734476 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3392)
2 days, 23:59:06.742149 INFO: Collecting fragment features
2 days, 23:59:06.747736 INFO: Finished candidate scoring
2 days, 23:59:06.750957 INFO: performing precursor FDR with 47 features
2 days, 23:59:06.751052 INFO: Decoy channel: -1
2 days, 23:59:06.751095 INFO: competitive: True
2 days, 23:59:06.757118 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:06.759441 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:59:06.761013 INFO: Estimating optimal hyperparameters - samples: 2,712, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:06.761139 INFO: Using random state 324173 for train-test-split
2 days, 23:59:07.069087 INFO: Test AUC: 0.749
2 days, 23:59:07.069203 INFO: Train AUC: 0.780
2 days, 23:59:07.069245 INFO: AUC difference: 4.05%
2 days, 23:59:07.358350 INFO: Resetting torch num_threads to 80
2 days, 23:59:07.358942 PROGRESS: === Extracted 3392 precursors and 27909 fragments ===
2 days, 23:59:07.359405 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:59:07.360065 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:07.360174 PROGRESS: Total precursors accumulated: 600
2 days, 23:59:07.360263 PROGRESS: Target precursors: 526 (87.67%)
2 days, 23:59:07.360344 PROGRESS: Decoy precursors: 74 (12.33%)
2 days, 23:59:07.360414 PROGRESS: 
2 days, 23:59:07.360481 PROGRESS: Precursor Summary:
2 days, 23:59:07.361636 PROGRESS: Channel   0:	 0.050 FDR:   447; 0.010 FDR:   408; 0.001 FDR:   408
2 days, 23:59:07.361746 PROGRESS: 
2 days, 23:59:07.361829 PROGRESS: Protein Summary:
2 days, 23:59:07.363189 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   308; 0.001 FDR:   308
2 days, 23:59:07.363307 PROGRESS: =========================================================================
2 days, 23:59:07.363495 INFO: Target number of precursors reached.
2 days, 23:59:07.370026 INFO: fragments_df: keeping 5000 of 27909 [sum(precursor_idx_mask)=10796 sum(mass_error_mask)=27909 stop_rank=5000
2 days, 23:59:07.373505 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:07.589823 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:07.786602 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:08.046188 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:08.938625 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:08.939071 INFO: Using score_cutoff 27.020430029869082 (fac=0.99, q=1)
2 days, 23:59:08.939393 INFO: Updating optimization_manager: fwhm_rt             : 2.794025182723999 -> 2.737734794616699
2 days, 23:59:08.939478 INFO: Updating optimization_manager: fwhm_mobility       : 0.005531940143555403 -> 0.005150061100721359
2 days, 23:59:08.939537 INFO: Updating optimization_manager: score_cutoff        : 27.634094508361816 -> 27.020430029869082
2 days, 23:59:08.939600 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:08.940680 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:08.942107 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:08.942905 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:08.944876 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:08.944981 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:59:08.946619 INFO: Updating optimization_manager: rt_error            : 1199.9630585 -> 343.3352155509295
2 days, 23:59:08.946730 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 343.3352.
2 days, 23:59:08.946800 INFO: ==============================================
2 days, 23:59:08.946873 INFO: Starting optimization step 1.
2 days, 23:59:08.946939 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:08.947001 INFO: Using python extraction backend
2 days, 23:59:08.947101 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:08.947169 INFO: === Search parameters used ===
2 days, 23:59:08.947229 INFO: rt_error       : 343.3352155509295
2 days, 23:59:08.947282 INFO: mobility_error : 0.1
2 days, 23:59:08.947329 INFO: num_candidates : 3
2 days, 23:59:08.947376 INFO: ms1_error      : 15.0
2 days, 23:59:08.947422 INFO: ms2_error      : 15.0
2 days, 23:59:08.947468 INFO: fwhm_rt        : 2.737734794616699
2 days, 23:59:08.947515 INFO: quant_window   : 3
2 days, 23:59:08.947562 INFO: ==============================================
2 days, 23:59:08.948390 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:08.948440 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:08.948477 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
2 days, 23:59:08.948504 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.79
2 days, 23:59:08.954570 INFO: Starting candidate selection
2 days, 23:59:12.804836 INFO: Starting candidate scoring
2 days, 23:59:12.904705 INFO: Finished candidate processing
2 days, 23:59:12.904849 INFO: Collecting candidate features
2 days, 23:59:12.922980 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3358)
2 days, 23:59:12.933292 INFO: Collecting fragment features
2 days, 23:59:12.939883 INFO: Finished candidate scoring
2 days, 23:59:12.943630 INFO: performing precursor FDR with 47 features
2 days, 23:59:12.943757 INFO: Decoy channel: -1
2 days, 23:59:12.943797 INFO: competitive: True
2 days, 23:59:12.947956 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:12.949755 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:59:12.949818 WARNING: dropped 2 decoy PSMs due to missing features
2 days, 23:59:12.950948 INFO: Estimating optimal hyperparameters - samples: 2,683, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:12.951056 INFO: Using random state 324173 for train-test-split
2 days, 23:59:13.282723 INFO: Test AUC: 0.747
2 days, 23:59:13.282846 INFO: Train AUC: 0.796
2 days, 23:59:13.282891 INFO: AUC difference: 6.14%
2 days, 23:59:13.282922 WARNING: AUC difference > 5%. This may indicate overfitting.
2 days, 23:59:13.624285 INFO: Resetting torch num_threads to 80
2 days, 23:59:13.625134 PROGRESS: === Extracted 3358 precursors and 27002 fragments ===
2 days, 23:59:13.625733 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:59:13.626611 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:13.626726 PROGRESS: Total precursors accumulated: 600
2 days, 23:59:13.626804 PROGRESS: Target precursors: 548 (91.33%)
2 days, 23:59:13.626874 PROGRESS: Decoy precursors: 52 (8.67%)
2 days, 23:59:13.626941 PROGRESS: 
2 days, 23:59:13.627003 PROGRESS: Precursor Summary:
2 days, 23:59:13.628308 PROGRESS: Channel   0:	 0.050 FDR:   502; 0.010 FDR:   452; 0.001 FDR:   448
2 days, 23:59:13.628403 PROGRESS: 
2 days, 23:59:13.628463 PROGRESS: Protein Summary:
2 days, 23:59:13.629798 PROGRESS: Channel   0:	 0.050 FDR:   374; 0.010 FDR:   343; 0.001 FDR:   340
2 days, 23:59:13.629920 PROGRESS: =========================================================================
2 days, 23:59:13.630111 INFO: Target number of precursors reached.
2 days, 23:59:13.637124 INFO: fragments_df: keeping 5000 of 27002 [sum(precursor_idx_mask)=11753 sum(mass_error_mask)=27002 stop_rank=5000
2 days, 23:59:13.640765 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:13.928739 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:14.162266 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:14.352669 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:15.139873 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:15.140325 INFO: Using score_cutoff 25.01571430206299 (fac=0.99, q=1)
2 days, 23:59:15.140687 INFO: Updating optimization_manager: fwhm_rt             : 2.737734794616699 -> 2.6936583518981934
2 days, 23:59:15.140788 INFO: Updating optimization_manager: fwhm_mobility       : 0.005150061100721359 -> 0.004753990098834038
2 days, 23:59:15.140858 INFO: Updating optimization_manager: score_cutoff        : 27.020430029869082 -> 25.01571430206299
2 days, 23:59:15.140929 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:15.142059 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:15.143564 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:15.144409 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:15.146485 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:15.146604 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:59:15.148433 INFO: Updating optimization_manager: rt_error            : 343.3352155509295 -> 166.80496892020633
2 days, 23:59:15.148561 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 166.8050.
2 days, 23:59:15.148648 INFO: ==============================================
2 days, 23:59:15.148734 INFO: Starting optimization step 2.
2 days, 23:59:15.148806 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:15.148874 INFO: Using python extraction backend
2 days, 23:59:15.148983 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:15.149058 INFO: === Search parameters used ===
2 days, 23:59:15.149119 INFO: rt_error       : 166.80496892020633
2 days, 23:59:15.149175 INFO: mobility_error : 0.1
2 days, 23:59:15.149228 INFO: num_candidates : 3
2 days, 23:59:15.149284 INFO: ms1_error      : 15.0
2 days, 23:59:15.149337 INFO: ms2_error      : 15.0
2 days, 23:59:15.149388 INFO: fwhm_rt        : 2.6936583518981934
2 days, 23:59:15.149439 INFO: quant_window   : 3
2 days, 23:59:15.149490 INFO: ==============================================
2 days, 23:59:15.150437 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:15.150494 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:15.150536 INFO: FWHM in RT is 2.69 seconds, sigma is 0.45
2 days, 23:59:15.150566 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.58
2 days, 23:59:15.155843 INFO: Starting candidate selection
2 days, 23:59:17.508190 INFO: Starting candidate scoring
2 days, 23:59:17.614391 INFO: Finished candidate processing
2 days, 23:59:17.614506 INFO: Collecting candidate features
2 days, 23:59:17.625028 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3337)
2 days, 23:59:17.625278 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3337)
2 days, 23:59:17.629636 INFO: Collecting fragment features
2 days, 23:59:17.633790 INFO: Finished candidate scoring
2 days, 23:59:17.636095 INFO: performing precursor FDR with 47 features
2 days, 23:59:17.636168 INFO: Decoy channel: -1
2 days, 23:59:17.636201 INFO: competitive: True
2 days, 23:59:17.639754 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:17.641478 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:59:17.641535 WARNING: dropped 4 decoy PSMs due to missing features
2 days, 23:59:17.642628 INFO: Estimating optimal hyperparameters - samples: 2,665, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:17.642725 INFO: Using random state 324173 for train-test-split
2 days, 23:59:17.956961 INFO: Test AUC: 0.790
2 days, 23:59:17.957087 INFO: Train AUC: 0.807
2 days, 23:59:17.957132 INFO: AUC difference: 2.11%
2 days, 23:59:18.244665 INFO: Resetting torch num_threads to 80
2 days, 23:59:18.245482 PROGRESS: === Extracted 3337 precursors and 26082 fragments ===
2 days, 23:59:18.246122 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:59:18.247066 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:18.247195 PROGRESS: Total precursors accumulated: 600
2 days, 23:59:18.247300 PROGRESS: Target precursors: 559 (93.17%)
2 days, 23:59:18.247395 PROGRESS: Decoy precursors: 41 (6.83%)
2 days, 23:59:18.247478 PROGRESS: 
2 days, 23:59:18.247577 PROGRESS: Precursor Summary:
2 days, 23:59:18.249544 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   512; 0.001 FDR:   495
2 days, 23:59:18.249678 PROGRESS: 
2 days, 23:59:18.249775 PROGRESS: Protein Summary:
2 days, 23:59:18.252059 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   379; 0.001 FDR:   371
2 days, 23:59:18.252202 PROGRESS: =========================================================================
2 days, 23:59:18.252426 INFO: Target number of precursors reached.
2 days, 23:59:18.262706 INFO: fragments_df: keeping 5000 of 26082 [sum(precursor_idx_mask)=12890 sum(mass_error_mask)=26082 stop_rank=5000
2 days, 23:59:18.268121 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:18.499329 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:18.674172 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:18.849649 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:19.817961 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:19.818456 INFO: Using score_cutoff 20.360658839035032 (fac=0.99, q=1)
2 days, 23:59:19.818807 INFO: Updating optimization_manager: fwhm_rt             : 2.6936583518981934 -> 2.666942596435547
2 days, 23:59:19.818901 INFO: Updating optimization_manager: fwhm_mobility       : 0.004753990098834038 -> 0.00438359659165144
2 days, 23:59:19.818973 INFO: Updating optimization_manager: score_cutoff        : 25.01571430206299 -> 20.360658839035032
2 days, 23:59:19.819045 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:19.820166 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:19.821620 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:19.822452 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:19.824451 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:19.824572 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:59:19.826501 INFO: Updating optimization_manager: rt_error            : 166.80496892020633 -> 116.05706501774041
2 days, 23:59:19.826618 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 116.0571.
2 days, 23:59:19.826700 INFO: ==============================================
2 days, 23:59:19.826787 INFO: Starting optimization step 3.
2 days, 23:59:19.826866 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:19.826941 INFO: Using python extraction backend
2 days, 23:59:19.827055 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:19.827134 INFO: === Search parameters used ===
2 days, 23:59:19.827198 INFO: rt_error       : 116.05706501774041
2 days, 23:59:19.827260 INFO: mobility_error : 0.1
2 days, 23:59:19.827317 INFO: num_candidates : 3
2 days, 23:59:19.827371 INFO: ms1_error      : 15.0
2 days, 23:59:19.827423 INFO: ms2_error      : 15.0
2 days, 23:59:19.827476 INFO: fwhm_rt        : 2.666942596435547
2 days, 23:59:19.827528 INFO: quant_window   : 3
2 days, 23:59:19.827580 INFO: ==============================================
2 days, 23:59:19.828419 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:19.828473 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:19.828513 INFO: FWHM in RT is 2.67 seconds, sigma is 0.44
2 days, 23:59:19.828544 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.38
2 days, 23:59:19.835518 INFO: Starting candidate selection
2 days, 23:59:21.357284 INFO: Starting candidate scoring
2 days, 23:59:21.467192 INFO: Finished candidate processing
2 days, 23:59:21.467330 INFO: Collecting candidate features
2 days, 23:59:21.483995 WARNING: intensity_correlation has 9 NaNs ( 0.27 % out of 3309)
2 days, 23:59:21.484368 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3309)
2 days, 23:59:21.492021 INFO: Collecting fragment features
2 days, 23:59:21.498073 INFO: Finished candidate scoring
2 days, 23:59:21.501178 INFO: performing precursor FDR with 47 features
2 days, 23:59:21.501273 INFO: Decoy channel: -1
2 days, 23:59:21.501308 INFO: competitive: True
2 days, 23:59:21.504780 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:21.506583 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:59:21.506648 WARNING: dropped 8 decoy PSMs due to missing features
2 days, 23:59:21.507737 INFO: Estimating optimal hyperparameters - samples: 2,639, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:21.507842 INFO: Using random state 324173 for train-test-split
2 days, 23:59:21.882463 INFO: Test AUC: 0.807
2 days, 23:59:21.882609 INFO: Train AUC: 0.834
2 days, 23:59:21.882677 INFO: AUC difference: 3.27%
2 days, 23:59:22.244933 INFO: Resetting torch num_threads to 80
2 days, 23:59:22.245556 PROGRESS: === Extracted 3309 precursors and 25441 fragments ===
2 days, 23:59:22.246056 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:59:22.246735 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:22.246849 PROGRESS: Total precursors accumulated: 600
2 days, 23:59:22.246944 PROGRESS: Target precursors: 569 (94.83%)
2 days, 23:59:22.247033 PROGRESS: Decoy precursors: 31 (5.17%)
2 days, 23:59:22.247111 PROGRESS: 
2 days, 23:59:22.247189 PROGRESS: Precursor Summary:
2 days, 23:59:22.248381 PROGRESS: Channel   0:	 0.050 FDR:   565; 0.010 FDR:   526; 0.001 FDR:   503
2 days, 23:59:22.248495 PROGRESS: 
2 days, 23:59:22.248581 PROGRESS: Protein Summary:
2 days, 23:59:22.249980 PROGRESS: Channel   0:	 0.050 FDR:   415; 0.010 FDR:   388; 0.001 FDR:   373
2 days, 23:59:22.250086 PROGRESS: =========================================================================
2 days, 23:59:22.250243 INFO: Target number of precursors reached.
2 days, 23:59:22.256936 INFO: fragments_df: keeping 5000 of 25441 [sum(precursor_idx_mask)=13113 sum(mass_error_mask)=25441 stop_rank=5000
2 days, 23:59:22.260691 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:22.452558 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:22.658744 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:22.846338 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:23.741552 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:23.742049 INFO: Using score_cutoff 19.849350543022155 (fac=0.99, q=1)
2 days, 23:59:23.742425 INFO: Updating optimization_manager: fwhm_rt             : 2.666942596435547 -> 2.6419010162353516
2 days, 23:59:23.742527 INFO: Updating optimization_manager: fwhm_mobility       : 0.00438359659165144 -> 0.004290818236768246
2 days, 23:59:23.742601 INFO: Updating optimization_manager: score_cutoff        : 20.360658839035032 -> 19.849350543022155
2 days, 23:59:23.742673 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:23.743819 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:23.745278 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:23.746142 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:23.748249 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:23.748374 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2 days, 23:59:23.750380 INFO: Updating optimization_manager: rt_error            : 116.05706501774041 -> 58.477626824647565
2 days, 23:59:23.750498 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 58.4776.
2 days, 23:59:23.750577 INFO: ==============================================
2 days, 23:59:23.750658 INFO: Starting optimization step 4.
2 days, 23:59:23.750728 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:23.750803 INFO: Using python extraction backend
2 days, 23:59:23.750918 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:23.750992 INFO: === Search parameters used ===
2 days, 23:59:23.751050 INFO: rt_error       : 58.477626824647565
2 days, 23:59:23.751102 INFO: mobility_error : 0.1
2 days, 23:59:23.751164 INFO: num_candidates : 3
2 days, 23:59:23.751216 INFO: ms1_error      : 15.0
2 days, 23:59:23.751267 INFO: ms2_error      : 15.0
2 days, 23:59:23.751318 INFO: fwhm_rt        : 2.6419010162353516
2 days, 23:59:23.751368 INFO: quant_window   : 3
2 days, 23:59:23.751418 INFO: ==============================================
2 days, 23:59:23.752314 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:23.752367 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:23.752407 INFO: FWHM in RT is 2.64 seconds, sigma is 0.44
2 days, 23:59:23.752436 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.33
2 days, 23:59:23.762088 INFO: Starting candidate selection
2 days, 23:59:24.767281 INFO: Starting candidate scoring
2 days, 23:59:24.864712 INFO: Finished candidate processing
2 days, 23:59:24.864852 INFO: Collecting candidate features
2 days, 23:59:24.881168 WARNING: intensity_correlation has 10 NaNs ( 0.31 % out of 3260)
2 days, 23:59:24.889421 INFO: Collecting fragment features
2 days, 23:59:24.895697 INFO: Finished candidate scoring
2 days, 23:59:24.899472 INFO: performing precursor FDR with 47 features
2 days, 23:59:24.899734 INFO: Decoy channel: -1
2 days, 23:59:24.899892 INFO: competitive: True
2 days, 23:59:24.905035 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:24.907547 WARNING: dropped 1 target PSMs due to missing features
2 days, 23:59:24.907646 WARNING: dropped 9 decoy PSMs due to missing features
2 days, 23:59:24.908967 INFO: Estimating optimal hyperparameters - samples: 2,600, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:24.909080 INFO: Using random state 324173 for train-test-split
2 days, 23:59:25.234834 INFO: Test AUC: 0.825
2 days, 23:59:25.234986 INFO: Train AUC: 0.857
2 days, 23:59:25.235044 INFO: AUC difference: 3.75%
2 days, 23:59:25.566339 INFO: Resetting torch num_threads to 80
2 days, 23:59:25.567143 PROGRESS: === Extracted 3260 precursors and 24507 fragments ===
2 days, 23:59:25.567747 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:59:25.568558 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:25.568670 PROGRESS: Total precursors accumulated: 600
2 days, 23:59:25.568752 PROGRESS: Target precursors: 580 (96.67%)
2 days, 23:59:25.568825 PROGRESS: Decoy precursors: 20 (3.33%)
2 days, 23:59:25.568893 PROGRESS: 
2 days, 23:59:25.568958 PROGRESS: Precursor Summary:
2 days, 23:59:25.570596 PROGRESS: Channel   0:	 0.050 FDR:   580; 0.010 FDR:   538; 0.001 FDR:   515
2 days, 23:59:25.570717 PROGRESS: 
2 days, 23:59:25.570809 PROGRESS: Protein Summary:
2 days, 23:59:25.572559 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   400; 0.001 FDR:   385
2 days, 23:59:25.572677 PROGRESS: =========================================================================
2 days, 23:59:25.572885 INFO: Target number of precursors reached.
2 days, 23:59:25.580717 INFO: fragments_df: keeping 5000 of 24507 [sum(precursor_idx_mask)=13292 sum(mass_error_mask)=24507 stop_rank=5000
2 days, 23:59:25.584897 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:25.804788 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:26.015303 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:26.274495 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:27.027446 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:27.028044 INFO: Using score_cutoff 19.43177273197174 (fac=0.99, q=1)
2 days, 23:59:27.028536 INFO: Updating optimization_manager: fwhm_rt             : 2.6419010162353516 -> 2.6299586296081543
2 days, 23:59:27.028658 INFO: Updating optimization_manager: fwhm_mobility       : 0.004290818236768246 -> 0.004202079959213734
2 days, 23:59:27.028761 INFO: Updating optimization_manager: score_cutoff        : 19.849350543022155 -> 19.43177273197174
2 days, 23:59:27.028868 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:27.030408 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:27.032255 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:27.033387 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:27.036004 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:27.036143 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2 days, 23:59:27.038877 INFO: Updating optimization_manager: rt_error            : 58.477626824647565 -> 7.264645775948358
2 days, 23:59:27.039041 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 7.2646.
2 days, 23:59:27.039156 INFO: ==============================================
2 days, 23:59:27.039289 INFO: Starting optimization step 5.
2 days, 23:59:27.039395 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:27.039496 INFO: Using python extraction backend
2 days, 23:59:27.039659 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:27.039766 INFO: === Search parameters used ===
2 days, 23:59:27.039837 INFO: rt_error       : 7.264645775948358
2 days, 23:59:27.039905 INFO: mobility_error : 0.1
2 days, 23:59:27.039970 INFO: num_candidates : 3
2 days, 23:59:27.040034 INFO: ms1_error      : 15.0
2 days, 23:59:27.040094 INFO: ms2_error      : 15.0
2 days, 23:59:27.040155 INFO: fwhm_rt        : 2.6299586296081543
2 days, 23:59:27.040215 INFO: quant_window   : 3
2 days, 23:59:27.040278 INFO: ==============================================
2 days, 23:59:27.041513 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:27.041581 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:27.041635 INFO: FWHM in RT is 2.63 seconds, sigma is 0.44
2 days, 23:59:27.041695 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.28
2 days, 23:59:27.046865 INFO: Starting candidate selection
2 days, 23:59:27.718998 INFO: Starting candidate scoring
2 days, 23:59:27.842690 INFO: Finished candidate processing
2 days, 23:59:27.842808 INFO: Collecting candidate features
2 days, 23:59:27.855673 WARNING: intensity_correlation has 26 NaNs ( 0.81 % out of 3208)
2 days, 23:59:27.860994 INFO: Collecting fragment features
2 days, 23:59:27.865533 INFO: Finished candidate scoring
2 days, 23:59:27.868005 INFO: performing precursor FDR with 47 features
2 days, 23:59:27.868084 INFO: Decoy channel: -1
2 days, 23:59:27.868119 INFO: competitive: True
2 days, 23:59:27.871807 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:27.873676 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:59:27.873735 WARNING: dropped 22 decoy PSMs due to missing features
2 days, 23:59:27.874969 INFO: Estimating optimal hyperparameters - samples: 2,545, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:27.875067 INFO: Using random state 324173 for train-test-split
2 days, 23:59:28.182151 INFO: Test AUC: 0.872
2 days, 23:59:28.182270 INFO: Train AUC: 0.884
2 days, 23:59:28.182325 INFO: AUC difference: 1.40%
2 days, 23:59:28.447825 INFO: Resetting torch num_threads to 80
2 days, 23:59:28.448542 PROGRESS: === Extracted 3208 precursors and 23068 fragments ===
2 days, 23:59:28.449086 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:59:28.449930 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:28.450050 PROGRESS: Total precursors accumulated: 599
2 days, 23:59:28.450139 PROGRESS: Target precursors: 587 (98.00%)
2 days, 23:59:28.450221 PROGRESS: Decoy precursors: 12 (2.00%)
2 days, 23:59:28.450298 PROGRESS: 
2 days, 23:59:28.450370 PROGRESS: Precursor Summary:
2 days, 23:59:28.452083 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   566; 0.001 FDR:   555
2 days, 23:59:28.452204 PROGRESS: 
2 days, 23:59:28.452287 PROGRESS: Protein Summary:
2 days, 23:59:28.454338 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   416; 0.001 FDR:   410
2 days, 23:59:28.454458 PROGRESS: =========================================================================
2 days, 23:59:28.454656 INFO: Target number of precursors reached.
2 days, 23:59:28.463759 INFO: fragments_df: keeping 5000 of 23068 [sum(precursor_idx_mask)=13604 sum(mass_error_mask)=23068 stop_rank=5000
2 days, 23:59:28.468318 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:28.652004 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:28.905959 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:29.084709 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:29.923325 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:29.923790 INFO: Using score_cutoff 17.404328988075257 (fac=0.99, q=1)
2 days, 23:59:29.924140 INFO: Updating optimization_manager: fwhm_rt             : 2.6299586296081543 -> 2.6241328716278076
2 days, 23:59:29.924246 INFO: Updating optimization_manager: fwhm_mobility       : 0.004202079959213734 -> 0.004045499488711357
2 days, 23:59:29.924316 INFO: Updating optimization_manager: score_cutoff        : 19.43177273197174 -> 17.404328988075257
2 days, 23:59:29.924385 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:29.925495 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:29.926905 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:29.927739 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:29.929768 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:29.929901 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2 days, 23:59:29.931927 INFO: Updating optimization_manager: rt_error            : 7.264645775948358 -> 8.496861912878897
2 days, 23:59:29.932044 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 8.4969.
2 days, 23:59:29.932129 INFO: ==============================================
2 days, 23:59:29.932215 INFO: Starting optimization step 6.
2 days, 23:59:29.932291 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:29.932364 INFO: Using python extraction backend
2 days, 23:59:29.932479 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:29.932559 INFO: === Search parameters used ===
2 days, 23:59:29.932627 INFO: rt_error       : 8.496861912878897
2 days, 23:59:29.932687 INFO: mobility_error : 0.1
2 days, 23:59:29.932742 INFO: num_candidates : 3
2 days, 23:59:29.932795 INFO: ms1_error      : 15.0
2 days, 23:59:29.932847 INFO: ms2_error      : 15.0
2 days, 23:59:29.932900 INFO: fwhm_rt        : 2.6241328716278076
2 days, 23:59:29.932952 INFO: quant_window   : 3
2 days, 23:59:29.933003 INFO: ==============================================
2 days, 23:59:29.933898 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:29.933956 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:29.933999 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:59:29.934027 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.19
2 days, 23:59:29.943566 INFO: Starting candidate selection
2 days, 23:59:30.478215 INFO: Starting candidate scoring
2 days, 23:59:30.590378 INFO: Finished candidate processing
2 days, 23:59:30.590488 INFO: Collecting candidate features
2 days, 23:59:30.600868 WARNING: intensity_correlation has 21 NaNs ( 0.66 % out of 3204)
2 days, 23:59:30.605077 INFO: Collecting fragment features
2 days, 23:59:30.608865 INFO: Finished candidate scoring
2 days, 23:59:30.611108 INFO: performing precursor FDR with 47 features
2 days, 23:59:30.611181 INFO: Decoy channel: -1
2 days, 23:59:30.611241 INFO: competitive: True
2 days, 23:59:30.614428 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:30.616026 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:59:30.616091 WARNING: dropped 19 decoy PSMs due to missing features
2 days, 23:59:30.617143 INFO: Estimating optimal hyperparameters - samples: 2,546, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:30.617286 INFO: Using random state 324173 for train-test-split
2 days, 23:59:30.965176 INFO: Test AUC: 0.884
2 days, 23:59:30.965308 INFO: Train AUC: 0.884
2 days, 23:59:30.965357 INFO: AUC difference: 0.02%
2 days, 23:59:31.318819 INFO: Resetting torch num_threads to 80
2 days, 23:59:31.319495 PROGRESS: === Extracted 3204 precursors and 23067 fragments ===
2 days, 23:59:31.320013 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:59:31.320662 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:31.320785 PROGRESS: Total precursors accumulated: 600
2 days, 23:59:31.320868 PROGRESS: Target precursors: 587 (97.83%)
2 days, 23:59:31.320938 PROGRESS: Decoy precursors: 13 (2.17%)
2 days, 23:59:31.321003 PROGRESS: 
2 days, 23:59:31.321069 PROGRESS: Precursor Summary:
2 days, 23:59:31.322748 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   568; 0.001 FDR:   559
2 days, 23:59:31.322875 PROGRESS: 
2 days, 23:59:31.322958 PROGRESS: Protein Summary:
2 days, 23:59:31.325044 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   418; 0.001 FDR:   412
2 days, 23:59:31.325181 PROGRESS: =========================================================================
2 days, 23:59:31.325381 INFO: Target number of precursors reached.
2 days, 23:59:31.335003 INFO: fragments_df: keeping 5000 of 23067 [sum(precursor_idx_mask)=13625 sum(mass_error_mask)=23067 stop_rank=5000
2 days, 23:59:31.339866 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:31.518836 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:31.784720 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:31.983498 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:32.814844 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:32.815429 INFO: Using score_cutoff 16.605557142448426 (fac=0.99, q=1)
2 days, 23:59:32.815900 INFO: Updating optimization_manager: fwhm_rt             : 2.6241328716278076 -> 2.629958152770996
2 days, 23:59:32.816023 INFO: Updating optimization_manager: fwhm_mobility       : 0.004045499488711357 -> 0.004038740880787373
2 days, 23:59:32.816128 INFO: Updating optimization_manager: score_cutoff        : 17.404328988075257 -> 16.605557142448426
2 days, 23:59:32.816227 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:32.817774 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:32.819571 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:32.820751 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:32.823330 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:32.823474 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2 days, 23:59:32.826220 INFO: Updating optimization_manager: rt_error            : 8.496861912878897 -> 8.708349878149996
2 days, 23:59:32.826367 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 8.7083.
2 days, 23:59:32.826467 INFO: ==============================================
2 days, 23:59:32.826586 INFO: Starting optimization step 7.
2 days, 23:59:32.826690 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:32.826797 INFO: Using python extraction backend
2 days, 23:59:32.826965 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:32.827069 INFO: === Search parameters used ===
2 days, 23:59:32.827163 INFO: rt_error       : 8.708349878149996
2 days, 23:59:32.827255 INFO: mobility_error : 0.1
2 days, 23:59:32.827348 INFO: num_candidates : 3
2 days, 23:59:32.827435 INFO: ms1_error      : 15.0
2 days, 23:59:32.827531 INFO: ms2_error      : 15.0
2 days, 23:59:32.827623 INFO: fwhm_rt        : 2.629958152770996
2 days, 23:59:32.827712 INFO: quant_window   : 3
2 days, 23:59:32.827799 INFO: ==============================================
2 days, 23:59:32.829016 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:32.829085 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:32.829139 INFO: FWHM in RT is 2.63 seconds, sigma is 0.44
2 days, 23:59:32.829190 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.19
2 days, 23:59:32.842116 INFO: Starting candidate selection
2 days, 23:59:33.370200 INFO: Starting candidate scoring
2 days, 23:59:33.469476 INFO: Finished candidate processing
2 days, 23:59:33.469608 INFO: Collecting candidate features
2 days, 23:59:33.485159 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3206)
2 days, 23:59:33.493331 INFO: Collecting fragment features
2 days, 23:59:33.499387 INFO: Finished candidate scoring
2 days, 23:59:33.502672 INFO: performing precursor FDR with 47 features
2 days, 23:59:33.502781 INFO: Decoy channel: -1
2 days, 23:59:33.502834 INFO: competitive: True
2 days, 23:59:33.507750 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:33.510363 WARNING: dropped 2 target PSMs due to missing features
2 days, 23:59:33.510453 WARNING: dropped 17 decoy PSMs due to missing features
2 days, 23:59:33.511919 INFO: Estimating optimal hyperparameters - samples: 2,549, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:33.512044 INFO: Using random state 324173 for train-test-split
2 days, 23:59:33.791830 INFO: Test AUC: 0.884
2 days, 23:59:33.791966 INFO: Train AUC: 0.888
2 days, 23:59:33.792012 INFO: AUC difference: 0.53%
2 days, 23:59:34.135381 INFO: Resetting torch num_threads to 80
2 days, 23:59:34.136135 PROGRESS: === Extracted 3206 precursors and 23089 fragments ===
2 days, 23:59:34.136745 INFO: === FDR correction performed with classifier version 3 ===
2 days, 23:59:34.137599 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:34.137722 PROGRESS: Total precursors accumulated: 600
2 days, 23:59:34.137816 PROGRESS: Target precursors: 588 (98.00%)
2 days, 23:59:34.137918 PROGRESS: Decoy precursors: 12 (2.00%)
2 days, 23:59:34.138014 PROGRESS: 
2 days, 23:59:34.138102 PROGRESS: Precursor Summary:
2 days, 23:59:34.140075 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   577; 0.001 FDR:   559
2 days, 23:59:34.140195 PROGRESS: 
2 days, 23:59:34.140278 PROGRESS: Protein Summary:
2 days, 23:59:34.142381 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   423; 0.001 FDR:   411
2 days, 23:59:34.142513 PROGRESS: =========================================================================
2 days, 23:59:34.142713 INFO: Target number of precursors reached.
2 days, 23:59:34.150082 INFO: fragments_df: keeping 5000 of 23089 [sum(precursor_idx_mask)=13788 sum(mass_error_mask)=23089 stop_rank=5000
2 days, 23:59:34.153527 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:34.355682 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:34.543578 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:34.740369 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:35.630482 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:35.631084 INFO: Using score_cutoff 16.74397992782593 (fac=0.99, q=1)
2 days, 23:59:35.631583 INFO: Updating optimization_manager: fwhm_rt             : 2.629958152770996 -> 2.605839967727661
2 days, 23:59:35.631706 INFO: Updating optimization_manager: fwhm_mobility       : 0.004038740880787373 -> 0.004001609981060028
2 days, 23:59:35.631809 INFO: Updating optimization_manager: score_cutoff        : 16.605557142448426 -> 16.74397992782593
2 days, 23:59:35.631913 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:35.633451 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:35.635321 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:35.636507 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:35.639099 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:35.639244 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2 days, 23:59:35.640804 INFO: Updating optimization_manager: rt_error            : 8.708349878149996 -> 7.264645775948358
2 days, 23:59:35.640991 INFO: Updating optimization_manager: classifier_version  : 3 -> 9
2 days, 23:59:35.641157 INFO: Updating optimization_manager: score_cutoff        : 16.74397992782593 -> 17.404328988075257
2 days, 23:59:35.641317 INFO: Updating optimization_manager: fwhm_rt             : 2.605839967727661 -> 2.6241328716278076
2 days, 23:59:35.641490 INFO: Updating optimization_manager: fwhm_mobility       : 0.004001609981060028 -> 0.004045499488711357
2 days, 23:59:35.641671 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 7.2646 found after 8 searches.
2 days, 23:59:35.641776 INFO: ==============================================
2 days, 23:59:35.641901 PROGRESS: Optimization finished for rt_error.
2 days, 23:59:35.646307 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:35.647631 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:35.649413 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:35.650566 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:35.653129 INFO: Starting optimization step 0.
2 days, 23:59:35.653266 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:35.653370 INFO: Using python extraction backend
2 days, 23:59:35.653534 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:35.653656 INFO: === Search parameters used ===
2 days, 23:59:35.653774 INFO: rt_error       : 7.264645775948358
2 days, 23:59:35.653902 INFO: mobility_error : 0.1
2 days, 23:59:35.654015 INFO: num_candidates : 3
2 days, 23:59:35.654113 INFO: ms1_error      : 15.0
2 days, 23:59:35.654214 INFO: ms2_error      : 15.0
2 days, 23:59:35.654322 INFO: fwhm_rt        : 2.6241328716278076
2 days, 23:59:35.654425 INFO: quant_window   : 3
2 days, 23:59:35.654527 INFO: ==============================================
2 days, 23:59:35.655760 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:35.655847 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:35.655924 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
2 days, 23:59:35.655982 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.19
2 days, 23:59:35.666082 INFO: Starting candidate selection
2 days, 23:59:36.246721 INFO: Starting candidate scoring
2 days, 23:59:36.366856 INFO: Finished candidate processing
2 days, 23:59:36.366994 INFO: Collecting candidate features
2 days, 23:59:36.380066 WARNING: intensity_correlation has 26 NaNs ( 0.81 % out of 3198)
2 days, 23:59:36.384171 INFO: Collecting fragment features
2 days, 23:59:36.388130 INFO: Finished candidate scoring
2 days, 23:59:36.390002 INFO: performing precursor FDR with 47 features
2 days, 23:59:36.390065 INFO: Decoy channel: -1
2 days, 23:59:36.390091 INFO: competitive: True
2 days, 23:59:36.393104 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:36.394814 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:59:36.394877 WARNING: dropped 22 decoy PSMs due to missing features
2 days, 23:59:36.395908 INFO: Estimating optimal hyperparameters - samples: 2,537, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:36.395990 INFO: Using random state 322159 for train-test-split
2 days, 23:59:36.613837 INFO: Test AUC: 0.878
2 days, 23:59:36.613990 INFO: Train AUC: 0.899
2 days, 23:59:36.614035 INFO: AUC difference: 2.38%
2 days, 23:59:36.946017 INFO: Resetting torch num_threads to 80
2 days, 23:59:36.946546 PROGRESS: === Extracted 3198 precursors and 23010 fragments ===
2 days, 23:59:36.946992 INFO: === FDR correction performed with classifier version 9 ===
2 days, 23:59:36.947613 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:36.947704 PROGRESS: Total precursors accumulated: 599
2 days, 23:59:36.947765 PROGRESS: Target precursors: 587 (98.00%)
2 days, 23:59:36.947818 PROGRESS: Decoy precursors: 12 (2.00%)
2 days, 23:59:36.947867 PROGRESS: 
2 days, 23:59:36.947913 PROGRESS: Precursor Summary:
2 days, 23:59:36.949052 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   575; 0.001 FDR:   564
2 days, 23:59:36.949144 PROGRESS: 
2 days, 23:59:36.949202 PROGRESS: Protein Summary:
2 days, 23:59:36.950566 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   423; 0.001 FDR:   415
2 days, 23:59:36.950670 PROGRESS: =========================================================================
2 days, 23:59:36.950809 INFO: Target number of precursors reached.
2 days, 23:59:36.956957 INFO: fragments_df: keeping 5000 of 23010 [sum(precursor_idx_mask)=13717 sum(mass_error_mask)=23010 stop_rank=5000
2 days, 23:59:36.960288 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:37.145204 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:37.331683 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:37.507051 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:38.331292 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:38.331747 INFO: Using score_cutoff 15.52882715435028 (fac=0.99, q=1)
2 days, 23:59:38.332085 INFO: Updating optimization_manager: fwhm_rt             : 2.6241328716278076 -> 2.6010794639587402
2 days, 23:59:38.332171 INFO: Updating optimization_manager: fwhm_mobility       : 0.004045499488711357 -> 0.0039988174103200436
2 days, 23:59:38.332229 INFO: Updating optimization_manager: score_cutoff        : 17.404328988075257 -> 15.52882715435028
2 days, 23:59:38.332287 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:38.333431 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:38.334894 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:38.335730 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:38.337793 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:38.337928 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2 days, 23:59:38.339623 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07092523165805102
2 days, 23:59:38.339745 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0709.
2 days, 23:59:38.339828 INFO: ==============================================
2 days, 23:59:38.339924 INFO: Starting optimization step 1.
2 days, 23:59:38.340013 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:38.340102 INFO: Using python extraction backend
2 days, 23:59:38.340253 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:38.340351 INFO: === Search parameters used ===
2 days, 23:59:38.340429 INFO: rt_error       : 7.264645775948358
2 days, 23:59:38.340502 INFO: mobility_error : 0.07092523165805102
2 days, 23:59:38.340578 INFO: num_candidates : 3
2 days, 23:59:38.340649 INFO: ms1_error      : 15.0
2 days, 23:59:38.340720 INFO: ms2_error      : 15.0
2 days, 23:59:38.340786 INFO: fwhm_rt        : 2.6010794639587402
2 days, 23:59:38.340852 INFO: quant_window   : 3
2 days, 23:59:38.340919 INFO: ==============================================
2 days, 23:59:38.341779 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:38.341835 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:38.341906 INFO: FWHM in RT is 2.60 seconds, sigma is 0.43
2 days, 23:59:38.341954 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.17
2 days, 23:59:38.354048 INFO: Starting candidate selection
2 days, 23:59:38.868694 INFO: Starting candidate scoring
2 days, 23:59:38.979090 INFO: Finished candidate processing
2 days, 23:59:38.979199 INFO: Collecting candidate features
2 days, 23:59:38.989122 WARNING: intensity_correlation has 27 NaNs ( 0.84 % out of 3199)
2 days, 23:59:38.994015 INFO: Collecting fragment features
2 days, 23:59:38.999743 INFO: Finished candidate scoring
2 days, 23:59:39.002883 INFO: performing precursor FDR with 47 features
2 days, 23:59:39.002971 INFO: Decoy channel: -1
2 days, 23:59:39.003014 INFO: competitive: True
2 days, 23:59:39.007781 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:39.010178 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:59:39.010256 WARNING: dropped 23 decoy PSMs due to missing features
2 days, 23:59:39.010328 WARNING: FDR calculation for 1666 target and 1506 decoy PSMs
2 days, 23:59:39.010364 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:59:39.011831 INFO: Estimating optimal hyperparameters - samples: 2,537, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:39.011947 INFO: Using random state 322159 for train-test-split
2 days, 23:59:39.317883 INFO: Test AUC: 0.904
2 days, 23:59:39.318106 INFO: Train AUC: 0.894
2 days, 23:59:39.318187 INFO: AUC difference: 1.14%
2 days, 23:59:39.619342 INFO: Resetting torch num_threads to 80
2 days, 23:59:39.620005 PROGRESS: === Extracted 3199 precursors and 22890 fragments ===
2 days, 23:59:39.620494 INFO: === FDR correction performed with classifier version 9 ===
2 days, 23:59:39.621203 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:39.621305 PROGRESS: Total precursors accumulated: 599
2 days, 23:59:39.621374 PROGRESS: Target precursors: 587 (98.00%)
2 days, 23:59:39.621435 PROGRESS: Decoy precursors: 12 (2.00%)
2 days, 23:59:39.621493 PROGRESS: 
2 days, 23:59:39.621548 PROGRESS: Precursor Summary:
2 days, 23:59:39.622954 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   578; 0.001 FDR:   572
2 days, 23:59:39.623063 PROGRESS: 
2 days, 23:59:39.623131 PROGRESS: Protein Summary:
2 days, 23:59:39.624793 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   422; 0.001 FDR:   420
2 days, 23:59:39.624897 PROGRESS: =========================================================================
2 days, 23:59:39.625060 INFO: Target number of precursors reached.
2 days, 23:59:39.633430 INFO: fragments_df: keeping 5000 of 22890 [sum(precursor_idx_mask)=13770 sum(mass_error_mask)=22890 stop_rank=5000
2 days, 23:59:39.637484 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:39.853436 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:40.057122 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:40.240871 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:41.046931 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:41.047385 INFO: Using score_cutoff 15.529540988445282 (fac=0.99, q=1)
2 days, 23:59:41.047723 INFO: Updating optimization_manager: fwhm_rt             : 2.6010794639587402 -> 2.5876615047454834
2 days, 23:59:41.047810 INFO: Updating optimization_manager: fwhm_mobility       : 0.0039988174103200436 -> 0.00399762112647295
2 days, 23:59:41.047873 INFO: Updating optimization_manager: score_cutoff        : 15.52882715435028 -> 15.529540988445282
2 days, 23:59:41.047935 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:41.049032 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:41.050431 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:41.051239 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:41.053232 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:41.053337 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2 days, 23:59:41.054936 INFO: Updating optimization_manager: mobility_error      : 0.07092523165805102 -> 0.05674328063822852
2 days, 23:59:41.055051 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0567.
2 days, 23:59:41.055121 INFO: ==============================================
2 days, 23:59:41.055219 INFO: Starting optimization step 2.
2 days, 23:59:41.055285 PROGRESS: === Extracting elution groups 0 to 600 ===
2 days, 23:59:41.055347 INFO: Using python extraction backend
2 days, 23:59:41.055448 PROGRESS: Extracting batch of 1197 precursors
2 days, 23:59:41.055520 INFO: === Search parameters used ===
2 days, 23:59:41.055574 INFO: rt_error       : 7.264645775948358
2 days, 23:59:41.055624 INFO: mobility_error : 0.05674328063822852
2 days, 23:59:41.055680 INFO: num_candidates : 3
2 days, 23:59:41.055728 INFO: ms1_error      : 15.0
2 days, 23:59:41.055772 INFO: ms2_error      : 15.0
2 days, 23:59:41.055816 INFO: fwhm_rt        : 2.5876615047454834
2 days, 23:59:41.055861 INFO: quant_window   : 3
2 days, 23:59:41.055904 INFO: ==============================================
2 days, 23:59:41.056715 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:41.056764 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:41.056799 INFO: FWHM in RT is 2.59 seconds, sigma is 0.43
2 days, 23:59:41.056822 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.17
2 days, 23:59:41.064525 INFO: Starting candidate selection
2 days, 23:59:41.584497 INFO: Starting candidate scoring
2 days, 23:59:41.690750 INFO: Finished candidate processing
2 days, 23:59:41.691077 INFO: Collecting candidate features
2 days, 23:59:41.704659 WARNING: intensity_correlation has 29 NaNs ( 0.91 % out of 3187)
2 days, 23:59:41.704889 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3187)
2 days, 23:59:41.708839 INFO: Collecting fragment features
2 days, 23:59:41.712895 INFO: Finished candidate scoring
2 days, 23:59:41.715843 INFO: performing precursor FDR with 47 features
2 days, 23:59:41.715921 INFO: Decoy channel: -1
2 days, 23:59:41.715962 INFO: competitive: True
2 days, 23:59:41.720824 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:41.723220 WARNING: dropped 4 target PSMs due to missing features
2 days, 23:59:41.723300 WARNING: dropped 26 decoy PSMs due to missing features
2 days, 23:59:41.723367 WARNING: FDR calculation for 1668 target and 1489 decoy PSMs
2 days, 23:59:41.723413 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:59:41.724878 INFO: Estimating optimal hyperparameters - samples: 2,525, batch_size: 128, learning_rate: 1.77e-04
2 days, 23:59:41.724991 INFO: Using random state 322159 for train-test-split
2 days, 23:59:42.013912 INFO: Test AUC: 0.880
2 days, 23:59:42.014062 INFO: Train AUC: 0.898
2 days, 23:59:42.014119 INFO: AUC difference: 1.97%
2 days, 23:59:42.318916 INFO: Resetting torch num_threads to 80
2 days, 23:59:42.319453 PROGRESS: === Extracted 3187 precursors and 22638 fragments ===
2 days, 23:59:42.319906 INFO: === FDR correction performed with classifier version 9 ===
2 days, 23:59:42.320528 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:42.320630 PROGRESS: Total precursors accumulated: 600
2 days, 23:59:42.320704 PROGRESS: Target precursors: 590 (98.33%)
2 days, 23:59:42.320771 PROGRESS: Decoy precursors: 10 (1.67%)
2 days, 23:59:42.320832 PROGRESS: 
2 days, 23:59:42.320892 PROGRESS: Precursor Summary:
2 days, 23:59:42.322071 PROGRESS: Channel   0:	 0.050 FDR:   590; 0.010 FDR:   582; 0.001 FDR:   563
2 days, 23:59:42.322192 PROGRESS: 
2 days, 23:59:42.322262 PROGRESS: Protein Summary:
2 days, 23:59:42.323623 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   429; 0.001 FDR:   418
2 days, 23:59:42.323732 PROGRESS: =========================================================================
2 days, 23:59:42.323909 INFO: Target number of precursors reached.
2 days, 23:59:42.330448 INFO: fragments_df: keeping 5000 of 22638 [sum(precursor_idx_mask)=13779 sum(mass_error_mask)=22638 stop_rank=5000
2 days, 23:59:42.333851 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:42.618461 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:42.856579 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:43.067551 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:43.889883 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2 days, 23:59:43.890385 INFO: Using score_cutoff 15.304763349151612 (fac=0.99, q=1)
2 days, 23:59:43.890756 INFO: Updating optimization_manager: fwhm_rt             : 2.5876615047454834 -> 2.576237201690674
2 days, 23:59:43.890862 INFO: Updating optimization_manager: fwhm_mobility       : 0.00399762112647295 -> 0.003931111190468073
2 days, 23:59:43.890946 INFO: Updating optimization_manager: score_cutoff        : 15.529540988445282 -> 15.304763349151612
2 days, 23:59:43.891029 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:43.892378 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:43.894117 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:43.895216 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:43.897720 INFO: === checking if optimization conditions were reached ===
2 days, 23:59:43.897876 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2 days, 23:59:43.899005 INFO: Updating optimization_manager: mobility_error      : 0.05674328063822852 -> 0.05674328063822852
2 days, 23:59:43.899181 INFO: Updating optimization_manager: classifier_version  : 9 -> 14
2 days, 23:59:43.899336 INFO: Updating optimization_manager: score_cutoff        : 15.304763349151612 -> 15.304763349151612
2 days, 23:59:43.899492 INFO: Updating optimization_manager: fwhm_rt             : 2.576237201690674 -> 2.576237201690674
2 days, 23:59:43.899651 INFO: Updating optimization_manager: fwhm_mobility       : 0.003931111190468073 -> 0.003931111190468073
2 days, 23:59:43.899807 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0567 found after 3 searches.
2 days, 23:59:43.899921 INFO: ==============================================
2 days, 23:59:43.900046 PROGRESS: Optimization finished for mobility_error.
2 days, 23:59:43.904463 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:43.905766 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:43.907555 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:43.908715 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:43.911209 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2 days, 23:59:43.911344 PROGRESS: ==============================================
2 days, 23:59:43.911461 PROGRESS: ms2_error      : 15.0000
2 days, 23:59:43.911565 PROGRESS: ms1_error      : 15.0000
2 days, 23:59:43.911674 PROGRESS: rt_error       : 7.2646
2 days, 23:59:43.911771 PROGRESS: mobility_error : 0.0567
2 days, 23:59:43.911864 PROGRESS: ==============================================
2 days, 23:59:43.912672 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2 days, 23:59:43.917145 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2 days, 23:59:43.934898 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2 days, 23:59:43.939487 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2 days, 23:59:43.984832 INFO: Using python extraction backend
2 days, 23:59:43.985152 PROGRESS: Extracting batch of 27494 precursors
2 days, 23:59:43.985260 INFO: === Search parameters used ===
2 days, 23:59:43.985330 INFO: rt_error       : 7.264645775948358
2 days, 23:59:43.985396 INFO: mobility_error : 0.05674328063822852
2 days, 23:59:43.985457 INFO: num_candidates : 3
2 days, 23:59:43.985516 INFO: ms1_error      : 15.0
2 days, 23:59:43.985573 INFO: ms2_error      : 15.0
2 days, 23:59:43.985631 INFO: fwhm_rt        : 2.576237201690674
2 days, 23:59:43.985688 INFO: quant_window   : 3
2 days, 23:59:43.985743 INFO: ==============================================
2 days, 23:59:43.991873 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:43.991989 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:43.992040 INFO: FWHM in RT is 2.58 seconds, sigma is 0.43
2 days, 23:59:43.992072 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.13
2 days, 23:59:44.030100 INFO: Starting candidate selection
2 days, 23:59:45.826951 INFO: Removed 21270 precursors with score below cutoff 15.304763349151612
2 days, 23:59:46.190215 INFO: Starting candidate scoring
2 days, 23:59:47.065643 INFO: Finished candidate processing
2 days, 23:59:47.065772 INFO: Collecting candidate features
2 days, 23:59:47.144650 WARNING: intensity_correlation has 147 NaNs ( 0.26 % out of 55541)
2 days, 23:59:47.145001 WARNING: height_correlation has 3 NaNs ( 0.01 % out of 55541)
2 days, 23:59:47.151237 INFO: Collecting fragment features
2 days, 23:59:47.189301 INFO: Finished candidate scoring
2 days, 23:59:47.218433 INFO: === Performing FDR correction with classifier version 14 ===
2 days, 23:59:47.218807 INFO: performing precursor FDR with 47 features
2 days, 23:59:47.218850 INFO: Decoy channel: -1
2 days, 23:59:47.218885 INFO: competitive: True
2 days, 23:59:47.234133 INFO: Setting torch num_threads to 2 for FDR classification task
2 days, 23:59:47.242846 WARNING: dropped 33 target PSMs due to missing features
2 days, 23:59:47.242968 WARNING: dropped 116 decoy PSMs due to missing features
2 days, 23:59:47.243025 WARNING: FDR calculation for 33965 target and 21427 decoy PSMs
2 days, 23:59:47.243057 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2 days, 23:59:47.251428 INFO: Estimating optimal hyperparameters - samples: 44,313, batch_size: 181, learning_rate: 2.10e-04
2 days, 23:59:47.251658 INFO: Using random state 538290 for train-test-split
2 days, 23:59:50.569613 INFO: Test AUC: 0.908
2 days, 23:59:50.569745 INFO: Train AUC: 0.912
2 days, 23:59:50.569786 INFO: AUC difference: 0.47%
2 days, 23:59:50.923852 INFO: Resetting torch num_threads to 80
2 days, 23:59:50.927928 INFO: Removing fragments below FDR threshold
2 days, 23:59:50.939085 PROGRESS: ============================= Precursor FDR =============================
2 days, 23:59:50.939286 PROGRESS: Total precursors accumulated: 13,146
2 days, 23:59:50.939363 PROGRESS: Target precursors: 13,016 (99.01%)
2 days, 23:59:50.939420 PROGRESS: Decoy precursors: 130 (0.99%)
2 days, 23:59:50.939474 PROGRESS: 
2 days, 23:59:50.939523 PROGRESS: Precursor Summary:
2 days, 23:59:50.944041 PROGRESS: Channel   0:	 0.050 FDR: 13,016; 0.010 FDR: 13,016; 0.001 FDR: 12,379
2 days, 23:59:50.944185 PROGRESS: 
2 days, 23:59:50.944265 PROGRESS: Protein Summary:
2 days, 23:59:50.950588 PROGRESS: Channel   0:	 0.050 FDR: 1,683; 0.010 FDR: 1,683; 0.001 FDR: 1,683
2 days, 23:59:50.950763 PROGRESS: =========================================================================
2 days, 23:59:50.951823 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R4/psm.parquet
2 days, 23:59:51.019928 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R4/frag.parquet
2 days, 23:59:51.086060 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R4
2 days, 23:59:51.090658 PROGRESS: Loading raw file 11/12: B9_G_DIA_nLC_tTOF_R5 
2 days, 23:59:51.090785 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
2 days, 23:59:51.090870 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R5/figures
2 days, 23:59:51.091086 INFO: Initializing TimingManager
2 days, 23:59:51.091581 INFO: Initializing RawFileManager
2 days, 23:59:51.091740 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:51.091810 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:51.091863 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:51.297977 INFO: Reading 22,623 frames with 399,194,214 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:55.175193 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d...
2 days, 23:59:55.176467 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:55.181907 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:55.182205 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:55.182830 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:55.185030 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:55.205424 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:55.210253 INFO: Indexing quadrupole dimension
2 days, 23:59:55.338354 INFO: Transposing detector events
2 days, 23:59:57.283999 INFO: Finished transposing data
2 days, 23:59:57.284194 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
2 days, 23:59:57.284593 INFO: RT (min)            : 0.0 - 40.0
2 days, 23:59:57.284650 INFO: RT duration (sec)   : 2400.0
2 days, 23:59:57.284697 INFO: RT duration (min)   : 40.0
2 days, 23:59:57.284737 INFO: Cycle len (scans)   : 12
2 days, 23:59:57.284775 INFO: Cycle len (sec)     : 1.27
2 days, 23:59:57.284810 INFO: Number of cycles    : 1885
2 days, 23:59:57.284841 INFO: MS2 range (m/z)     : 374.4 - 1151.9
2 days, 23:59:57.284881 INFO: Creating DIA data object took: 6.1931445598602295
2 days, 23:59:57.290366 INFO: Initializing CalibrationManager
2 days, 23:59:57.290642 INFO: Setting up calibration estimators ..
2 days, 23:59:57.290722 INFO: Found 1 estimator(s) in calibration group 'fragment'
2 days, 23:59:57.290812 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:59:57.290903 INFO: Found 3 estimator(s) in calibration group 'precursor'
2 days, 23:59:57.290984 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2 days, 23:59:57.291068 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2 days, 23:59:57.291156 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
2 days, 23:59:57.291236 INFO: Done setting up calibration estimators.
2 days, 23:59:57.291367 INFO: Initializing OptimizationManager
2 days, 23:59:57.291483 INFO: initial parameter: ms1_error = 30
2 days, 23:59:57.291557 INFO: initial parameter: ms2_error = 30
2 days, 23:59:57.291630 INFO: initial parameter: rt_error = 1199.9910355
2 days, 23:59:57.291701 INFO: initial parameter: mobility_error = 0.1
2 days, 23:59:57.291772 INFO: initial parameter: num_candidates = 1
2 days, 23:59:57.291841 INFO: initial parameter: fwhm_rt = 5
2 days, 23:59:57.291911 INFO: initial parameter: fwhm_mobility = 0.01
2 days, 23:59:57.291979 INFO: initial parameter: score_cutoff = 0
2 days, 23:59:57.292043 INFO: initial parameter: classifier_version = -1
2 days, 23:59:57.292149 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R5
2 days, 23:59:57.292334 INFO: FDRManager: loading saved state not requested, will be initialized.
2 days, 23:59:57.292375 INFO: Initializing FDRManager
2 days, 23:59:57.292425 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2 days, 23:59:57.299428 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
2 days, 23:59:57.304025 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2 days, 23:59:57.304416 INFO: Updating optimization_manager: rt_error            : 1199.9910355 -> 1199.9910355
2 days, 23:59:57.304553 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2 days, 23:59:57.304812 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2 days, 23:59:57.304949 PROGRESS: Starting initial search for precursors.
2 days, 23:59:57.305104 INFO: Starting optimization step 0.
2 days, 23:59:57.305204 PROGRESS: === Extracting elution groups 0 to 200 ===
2 days, 23:59:57.305303 INFO: Using python extraction backend
2 days, 23:59:57.305447 PROGRESS: Extracting batch of 399 precursors
2 days, 23:59:57.305549 INFO: === Search parameters used ===
2 days, 23:59:57.305634 INFO: rt_error       : 1199.9910355
2 days, 23:59:57.305710 INFO: mobility_error : 0.1
2 days, 23:59:57.305775 INFO: num_candidates : 1
2 days, 23:59:57.305837 INFO: ms1_error      : 30
2 days, 23:59:57.305918 INFO: ms2_error      : 30
2 days, 23:59:57.306003 INFO: fwhm_rt        : 5
2 days, 23:59:57.306080 INFO: quant_window   : 3
2 days, 23:59:57.306155 INFO: ==============================================
2 days, 23:59:57.306912 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
2 days, 23:59:57.306973 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
2 days, 23:59:57.307013 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
2 days, 23:59:57.307049 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
2 days, 23:59:57.318114 INFO: Starting candidate selection
3 days, 0:00:00.781049 INFO: Starting candidate scoring
3 days, 0:00:00.831857 INFO: Finished candidate processing
3 days, 0:00:00.832001 INFO: Collecting candidate features
3 days, 0:00:00.850219 INFO: Collecting fragment features
3 days, 0:00:00.854177 INFO: Finished candidate scoring
3 days, 0:00:00.855443 INFO: performing precursor FDR with 47 features
3 days, 0:00:00.855509 INFO: Decoy channel: -1
3 days, 0:00:00.855555 INFO: competitive: True
3 days, 0:00:00.857489 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:00:00.860100 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:00:00.861251 INFO: Using random state 489099 for train-test-split
3 days, 0:00:00.896770 INFO: Test AUC: 0.582
3 days, 0:00:00.896909 INFO: Train AUC: 0.515
3 days, 0:00:00.896965 INFO: AUC difference: 12.98%
3 days, 0:00:00.897007 WARNING: AUC difference > 5%. This may indicate overfitting.
3 days, 0:00:01.250932 INFO: Resetting torch num_threads to 80
3 days, 0:00:01.251464 PROGRESS: === Extracted 399 precursors and 3729 fragments ===
3 days, 0:00:01.251983 INFO: === FDR correction performed with classifier version -1 ===
3 days, 0:00:01.252682 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:00:01.252796 PROGRESS: Total precursors accumulated: 200
3 days, 0:00:01.252881 PROGRESS: Target precursors: 113 (56.50%)
3 days, 0:00:01.252959 PROGRESS: Decoy precursors: 87 (43.50%)
3 days, 0:00:01.253035 PROGRESS: 
3 days, 0:00:01.253108 PROGRESS: Precursor Summary:
3 days, 0:00:01.254281 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
3 days, 0:00:01.254402 PROGRESS: 
3 days, 0:00:01.254483 PROGRESS: Protein Summary:
3 days, 0:00:01.255772 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
3 days, 0:00:01.255886 PROGRESS: =========================================================================
3 days, 0:00:01.256052 INFO: Target number of precursors not reached yet.
3 days, 0:00:01.259841 INFO: Starting optimization step 1.
3 days, 0:00:01.259969 PROGRESS: === Extracting elution groups 200 to 600 ===
3 days, 0:00:01.260065 INFO: Using python extraction backend
3 days, 0:00:01.260198 PROGRESS: Extracting batch of 798 precursors
3 days, 0:00:01.260291 INFO: === Search parameters used ===
3 days, 0:00:01.260365 INFO: rt_error       : 1199.9910355
3 days, 0:00:01.260433 INFO: mobility_error : 0.1
3 days, 0:00:01.260499 INFO: num_candidates : 1
3 days, 0:00:01.260583 INFO: ms1_error      : 30
3 days, 0:00:01.260657 INFO: ms2_error      : 30
3 days, 0:00:01.260719 INFO: fwhm_rt        : 5
3 days, 0:00:01.260784 INFO: quant_window   : 3
3 days, 0:00:01.260883 INFO: ==============================================
3 days, 0:00:01.261611 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:00:01.261668 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:00:01.261715 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
3 days, 0:00:01.261759 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
3 days, 0:00:01.268235 INFO: Starting candidate selection
3 days, 0:00:06.326427 INFO: Starting candidate scoring
3 days, 0:00:06.387940 INFO: Finished candidate processing
3 days, 0:00:06.388084 INFO: Collecting candidate features
3 days, 0:00:06.407096 INFO: Collecting fragment features
3 days, 0:00:06.411350 INFO: Finished candidate scoring
3 days, 0:00:06.414994 INFO: performing precursor FDR with 47 features
3 days, 0:00:06.415121 INFO: Decoy channel: -1
3 days, 0:00:06.415251 INFO: competitive: True
3 days, 0:00:06.420009 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:00:06.422350 INFO: Estimating optimal hyperparameters - samples: 957, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:00:06.422468 INFO: Using random state 792214 for train-test-split
3 days, 0:00:06.529288 INFO: Test AUC: 0.826
3 days, 0:00:06.529403 INFO: Train AUC: 0.777
3 days, 0:00:06.529442 INFO: AUC difference: 6.43%
3 days, 0:00:06.529473 WARNING: AUC difference > 5%. This may indicate overfitting.
3 days, 0:00:06.824766 INFO: Resetting torch num_threads to 80
3 days, 0:00:06.826599 PROGRESS: === Extracted 1197 precursors and 11451 fragments ===
3 days, 0:00:06.827214 INFO: === FDR correction performed with classifier version -1 ===
3 days, 0:00:06.828092 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:00:06.828229 PROGRESS: Total precursors accumulated: 600
3 days, 0:00:06.828346 PROGRESS: Target precursors: 482 (80.33%)
3 days, 0:00:06.828463 PROGRESS: Decoy precursors: 118 (19.67%)
3 days, 0:00:06.828570 PROGRESS: 
3 days, 0:00:06.828666 PROGRESS: Precursor Summary:
3 days, 0:00:06.830549 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:   217; 0.001 FDR:   217
3 days, 0:00:06.830689 PROGRESS: 
3 days, 0:00:06.830787 PROGRESS: Protein Summary:
3 days, 0:00:06.832815 PROGRESS: Channel   0:	 0.050 FDR:   203; 0.010 FDR:   167; 0.001 FDR:   167
3 days, 0:00:06.832947 PROGRESS: =========================================================================
3 days, 0:00:06.833180 INFO: Target number of precursors reached.
3 days, 0:00:06.838310 INFO: fragments_df: keeping 1814 of 11451 [sum(precursor_idx_mask)=2240 sum(mass_error_mask)=11451 stop_rank=1814
3 days, 0:00:06.843258 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:07.001156 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:07.153691 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:07.329162 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:07.645198 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
3 days, 0:00:07.645682 INFO: Using score_cutoff 37.04205487060547 (fac=0.99, q=1)
3 days, 0:00:07.646105 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1536307334899902
3 days, 0:00:07.646222 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007584692910313606
3 days, 0:00:07.646329 INFO: Updating optimization_manager: score_cutoff        : 0 -> 37.04205487060547
3 days, 0:00:07.646419 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:07.647614 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:07.649139 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:07.650064 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:07.652210 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
3 days, 0:00:07.652318 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3 days, 0:00:07.652417 INFO: Starting optimization step 2.
3 days, 0:00:07.652504 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:00:07.652577 INFO: Using python extraction backend
3 days, 0:00:07.652687 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:00:07.652760 INFO: === Search parameters used ===
3 days, 0:00:07.652820 INFO: rt_error       : 1199.9910355
3 days, 0:00:07.652873 INFO: mobility_error : 0.1
3 days, 0:00:07.652924 INFO: num_candidates : 3
3 days, 0:00:07.652975 INFO: ms1_error      : 30
3 days, 0:00:07.653026 INFO: ms2_error      : 30
3 days, 0:00:07.653076 INFO: fwhm_rt        : 3.1536307334899902
3 days, 0:00:07.653126 INFO: quant_window   : 3
3 days, 0:00:07.653177 INFO: ==============================================
3 days, 0:00:07.654130 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:00:07.654187 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:00:07.654227 INFO: FWHM in RT is 3.15 seconds, sigma is 0.53
3 days, 0:00:07.654253 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.11
3 days, 0:00:07.658428 INFO: Starting candidate selection
3 days, 0:00:16.202202 INFO: Starting candidate scoring
3 days, 0:00:16.353954 INFO: Finished candidate processing
3 days, 0:00:16.354090 INFO: Collecting candidate features
3 days, 0:00:16.378356 INFO: Collecting fragment features
3 days, 0:00:16.384493 INFO: Finished candidate scoring
3 days, 0:00:16.387911 INFO: performing precursor FDR with 47 features
3 days, 0:00:16.388022 INFO: Decoy channel: -1
3 days, 0:00:16.388066 INFO: competitive: True
3 days, 0:00:16.392707 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:00:16.395186 INFO: Estimating optimal hyperparameters - samples: 2,746, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:00:16.395288 INFO: Using random state 996498 for train-test-split
3 days, 0:00:16.651298 INFO: Test AUC: 0.679
3 days, 0:00:16.651413 INFO: Train AUC: 0.703
3 days, 0:00:16.651447 INFO: AUC difference: 3.40%
3 days, 0:00:16.896365 INFO: Resetting torch num_threads to 80
3 days, 0:00:16.896932 PROGRESS: === Extracted 3433 precursors and 31779 fragments ===
3 days, 0:00:16.897374 INFO: === FDR correction performed with classifier version 1 ===
3 days, 0:00:16.898005 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:00:16.898107 PROGRESS: Total precursors accumulated: 600
3 days, 0:00:16.898173 PROGRESS: Target precursors: 510 (85.00%)
3 days, 0:00:16.898231 PROGRESS: Decoy precursors: 90 (15.00%)
3 days, 0:00:16.898283 PROGRESS: 
3 days, 0:00:16.898333 PROGRESS: Precursor Summary:
3 days, 0:00:16.899401 PROGRESS: Channel   0:	 0.050 FDR:   437; 0.010 FDR:   437; 0.001 FDR:   437
3 days, 0:00:16.899507 PROGRESS: 
3 days, 0:00:16.899583 PROGRESS: Protein Summary:
3 days, 0:00:16.900930 PROGRESS: Channel   0:	 0.050 FDR:   329; 0.010 FDR:   329; 0.001 FDR:   329
3 days, 0:00:16.901044 PROGRESS: =========================================================================
3 days, 0:00:16.901238 INFO: Target number of precursors reached.
3 days, 0:00:16.908781 INFO: fragments_df: keeping 5000 of 31779 [sum(precursor_idx_mask)=12246 sum(mass_error_mask)=31779 stop_rank=5000
3 days, 0:00:16.912703 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:17.100939 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:17.280190 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:17.508602 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:18.471061 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:00:18.471556 INFO: Using score_cutoff 29.304863470458983 (fac=0.99, q=1)
3 days, 0:00:18.471975 INFO: Updating optimization_manager: fwhm_rt             : 3.1536307334899902 -> 2.9159321784973145
3 days, 0:00:18.472098 INFO: Updating optimization_manager: fwhm_mobility       : 0.007584692910313606 -> 0.006330292671918869
3 days, 0:00:18.472178 INFO: Updating optimization_manager: score_cutoff        : 37.04205487060547 -> 29.304863470458983
3 days, 0:00:18.472263 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:18.473502 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:18.475103 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:18.476052 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:18.478185 INFO: === checking if optimization conditions were reached ===
3 days, 0:00:18.479966 INFO: Updating optimization_manager: ms2_error           : 30 -> 18.627296241051106
3 days, 0:00:18.480099 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
3 days, 0:00:18.480198 PROGRESS: ❌ ms2_error      : 18.6273 > 15.0000 or insufficient steps taken.
3 days, 0:00:18.481314 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
3 days, 0:00:18.481438 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
3 days, 0:00:18.481533 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
3 days, 0:00:18.481624 INFO: ==============================================
3 days, 0:00:18.481725 INFO: Starting optimization step 3.
3 days, 0:00:18.481833 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:00:18.481937 INFO: Using python extraction backend
3 days, 0:00:18.482080 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:00:18.482177 INFO: === Search parameters used ===
3 days, 0:00:18.482271 INFO: rt_error       : 1199.9910355
3 days, 0:00:18.482352 INFO: mobility_error : 0.1
3 days, 0:00:18.482427 INFO: num_candidates : 3
3 days, 0:00:18.482502 INFO: ms1_error      : 15.0
3 days, 0:00:18.482572 INFO: ms2_error      : 18.627296241051106
3 days, 0:00:18.482640 INFO: fwhm_rt        : 2.9159321784973145
3 days, 0:00:18.482711 INFO: quant_window   : 3
3 days, 0:00:18.482803 INFO: ==============================================
3 days, 0:00:18.483800 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:00:18.483860 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:00:18.483914 INFO: FWHM in RT is 2.92 seconds, sigma is 0.49
3 days, 0:00:18.483949 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.43
3 days, 0:00:18.509225 INFO: Starting candidate selection
3 days, 0:00:26.660417 INFO: Starting candidate scoring
3 days, 0:00:26.801806 INFO: Finished candidate processing
3 days, 0:00:26.801952 INFO: Collecting candidate features
3 days, 0:00:26.818762 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3425)
3 days, 0:00:26.827170 INFO: Collecting fragment features
3 days, 0:00:26.833428 INFO: Finished candidate scoring
3 days, 0:00:26.836765 INFO: performing precursor FDR with 47 features
3 days, 0:00:26.836878 INFO: Decoy channel: -1
3 days, 0:00:26.836928 INFO: competitive: True
3 days, 0:00:26.841969 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:00:26.844178 WARNING: dropped 1 target PSMs due to missing features
3 days, 0:00:26.845690 INFO: Estimating optimal hyperparameters - samples: 2,739, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:00:26.845886 INFO: Using random state 666599 for train-test-split
3 days, 0:00:27.140572 INFO: Test AUC: 0.724
3 days, 0:00:27.140716 INFO: Train AUC: 0.745
3 days, 0:00:27.140764 INFO: AUC difference: 2.77%
3 days, 0:00:27.480489 INFO: Resetting torch num_threads to 80
3 days, 0:00:27.481060 PROGRESS: === Extracted 3425 precursors and 29145 fragments ===
3 days, 0:00:27.481536 INFO: === FDR correction performed with classifier version 2 ===
3 days, 0:00:27.482221 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:00:27.482340 PROGRESS: Total precursors accumulated: 600
3 days, 0:00:27.482435 PROGRESS: Target precursors: 545 (90.83%)
3 days, 0:00:27.482521 PROGRESS: Decoy precursors: 55 (9.17%)
3 days, 0:00:27.482600 PROGRESS: 
3 days, 0:00:27.482674 PROGRESS: Precursor Summary:
3 days, 0:00:27.483832 PROGRESS: Channel   0:	 0.050 FDR:   481; 0.010 FDR:   481; 0.001 FDR:   481
3 days, 0:00:27.483947 PROGRESS: 
3 days, 0:00:27.484043 PROGRESS: Protein Summary:
3 days, 0:00:27.485429 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   365; 0.001 FDR:   365
3 days, 0:00:27.485542 PROGRESS: =========================================================================
3 days, 0:00:27.485726 INFO: Target number of precursors reached.
3 days, 0:00:27.492707 INFO: fragments_df: keeping 5000 of 29145 [sum(precursor_idx_mask)=12806 sum(mass_error_mask)=29145 stop_rank=5000
3 days, 0:00:27.497092 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:27.692166 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:27.918523 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:28.088261 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:29.029738 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:00:29.030346 INFO: Using score_cutoff 26.924558807373046 (fac=0.99, q=1)
3 days, 0:00:29.030845 INFO: Updating optimization_manager: fwhm_rt             : 2.9159321784973145 -> 2.803256034851074
3 days, 0:00:29.030971 INFO: Updating optimization_manager: fwhm_mobility       : 0.006330292671918869 -> 0.005267359782010317
3 days, 0:00:29.031074 INFO: Updating optimization_manager: score_cutoff        : 29.304863470458983 -> 26.924558807373046
3 days, 0:00:29.031165 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:29.032689 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:29.034513 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:29.035649 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:29.038182 INFO: === checking if optimization conditions were reached ===
3 days, 0:00:29.040412 INFO: Updating optimization_manager: ms2_error           : 18.627296241051106 -> 15.0
3 days, 0:00:29.040561 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
3 days, 0:00:29.040677 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3 days, 0:00:29.042248 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
3 days, 0:00:29.042387 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
3 days, 0:00:29.042482 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
3 days, 0:00:29.042571 INFO: ==============================================
3 days, 0:00:29.042677 PROGRESS: Optimization finished for ms2_error, ms1_error.
3 days, 0:00:29.046954 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:29.048112 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:29.049613 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:29.050574 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:29.052587 INFO: Starting optimization step 0.
3 days, 0:00:29.052707 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:00:29.052823 INFO: Using python extraction backend
3 days, 0:00:29.052983 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:00:29.053105 INFO: === Search parameters used ===
3 days, 0:00:29.053291 INFO: rt_error       : 1199.9910355
3 days, 0:00:29.053379 INFO: mobility_error : 0.1
3 days, 0:00:29.053457 INFO: num_candidates : 3
3 days, 0:00:29.053530 INFO: ms1_error      : 15.0
3 days, 0:00:29.053598 INFO: ms2_error      : 15.0
3 days, 0:00:29.053667 INFO: fwhm_rt        : 2.803256034851074
3 days, 0:00:29.053734 INFO: quant_window   : 3
3 days, 0:00:29.053814 INFO: ==============================================
3 days, 0:00:29.054836 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:00:29.054899 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:00:29.054954 INFO: FWHM in RT is 2.80 seconds, sigma is 0.47
3 days, 0:00:29.054993 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.85
3 days, 0:00:29.086052 INFO: Starting candidate selection
3 days, 0:00:37.479332 INFO: Starting candidate scoring
3 days, 0:00:37.591121 INFO: Finished candidate processing
3 days, 0:00:37.591244 INFO: Collecting candidate features
3 days, 0:00:37.608456 INFO: Collecting fragment features
3 days, 0:00:37.612918 INFO: Finished candidate scoring
3 days, 0:00:37.614957 INFO: performing precursor FDR with 47 features
3 days, 0:00:37.615010 INFO: Decoy channel: -1
3 days, 0:00:37.615042 INFO: competitive: True
3 days, 0:00:37.618645 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:00:37.621145 INFO: Estimating optimal hyperparameters - samples: 2,739, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:00:37.621238 INFO: Using random state 224957 for train-test-split
3 days, 0:00:37.866854 INFO: Test AUC: 0.766
3 days, 0:00:37.866970 INFO: Train AUC: 0.749
3 days, 0:00:37.867008 INFO: AUC difference: 2.31%
3 days, 0:00:38.183341 INFO: Resetting torch num_threads to 80
3 days, 0:00:38.183882 PROGRESS: === Extracted 3424 precursors and 27990 fragments ===
3 days, 0:00:38.184327 INFO: === FDR correction performed with classifier version 3 ===
3 days, 0:00:38.184937 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:00:38.185038 PROGRESS: Total precursors accumulated: 600
3 days, 0:00:38.185116 PROGRESS: Target precursors: 544 (90.67%)
3 days, 0:00:38.185180 PROGRESS: Decoy precursors: 56 (9.33%)
3 days, 0:00:38.185236 PROGRESS: 
3 days, 0:00:38.185290 PROGRESS: Precursor Summary:
3 days, 0:00:38.186433 PROGRESS: Channel   0:	 0.050 FDR:   480; 0.010 FDR:   480; 0.001 FDR:   480
3 days, 0:00:38.186542 PROGRESS: 
3 days, 0:00:38.186614 PROGRESS: Protein Summary:
3 days, 0:00:38.187931 PROGRESS: Channel   0:	 0.050 FDR:   364; 0.010 FDR:   364; 0.001 FDR:   364
3 days, 0:00:38.188034 PROGRESS: =========================================================================
3 days, 0:00:38.188192 INFO: Target number of precursors reached.
3 days, 0:00:38.194799 INFO: fragments_df: keeping 5000 of 27990 [sum(precursor_idx_mask)=12354 sum(mass_error_mask)=27990 stop_rank=5000
3 days, 0:00:38.198148 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:38.386280 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:38.596463 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:38.822797 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:39.625194 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:00:39.625657 INFO: Using score_cutoff 25.881644560432434 (fac=0.99, q=1)
3 days, 0:00:39.626039 INFO: Updating optimization_manager: fwhm_rt             : 2.803256034851074 -> 2.7133383750915527
3 days, 0:00:39.626148 INFO: Updating optimization_manager: fwhm_mobility       : 0.005267359782010317 -> 0.005042281001806259
3 days, 0:00:39.626234 INFO: Updating optimization_manager: score_cutoff        : 26.924558807373046 -> 25.881644560432434
3 days, 0:00:39.626321 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:39.627439 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:39.628848 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:39.629678 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:39.631716 INFO: === checking if optimization conditions were reached ===
3 days, 0:00:39.631837 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3 days, 0:00:39.633514 INFO: Updating optimization_manager: rt_error            : 1199.9910355 -> 745.6878214096257
3 days, 0:00:39.633637 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 745.6878.
3 days, 0:00:39.633726 INFO: ==============================================
3 days, 0:00:39.633822 INFO: Starting optimization step 1.
3 days, 0:00:39.633926 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:00:39.634020 INFO: Using python extraction backend
3 days, 0:00:39.634145 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:00:39.634244 INFO: === Search parameters used ===
3 days, 0:00:39.634322 INFO: rt_error       : 745.6878214096257
3 days, 0:00:39.634393 INFO: mobility_error : 0.1
3 days, 0:00:39.634460 INFO: num_candidates : 3
3 days, 0:00:39.634525 INFO: ms1_error      : 15.0
3 days, 0:00:39.634590 INFO: ms2_error      : 15.0
3 days, 0:00:39.634655 INFO: fwhm_rt        : 2.7133383750915527
3 days, 0:00:39.634723 INFO: quant_window   : 3
3 days, 0:00:39.634786 INFO: ==============================================
3 days, 0:00:39.635618 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:00:39.635675 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:00:39.635732 INFO: FWHM in RT is 2.71 seconds, sigma is 0.45
3 days, 0:00:39.635769 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.73
3 days, 0:00:39.646073 INFO: Starting candidate selection
3 days, 0:00:46.467688 INFO: Starting candidate scoring
3 days, 0:00:46.577626 INFO: Finished candidate processing
3 days, 0:00:46.577797 INFO: Collecting candidate features
3 days, 0:00:46.592708 INFO: Collecting fragment features
3 days, 0:00:46.596548 INFO: Finished candidate scoring
3 days, 0:00:46.598364 INFO: performing precursor FDR with 47 features
3 days, 0:00:46.598428 INFO: Decoy channel: -1
3 days, 0:00:46.598464 INFO: competitive: True
3 days, 0:00:46.601629 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:00:46.603862 INFO: Estimating optimal hyperparameters - samples: 2,720, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:00:46.603981 INFO: Using random state 224957 for train-test-split
3 days, 0:00:46.936962 INFO: Test AUC: 0.730
3 days, 0:00:46.937081 INFO: Train AUC: 0.774
3 days, 0:00:46.937130 INFO: AUC difference: 5.72%
3 days, 0:00:46.937168 WARNING: AUC difference > 5%. This may indicate overfitting.
3 days, 0:00:47.197374 INFO: Resetting torch num_threads to 80
3 days, 0:00:47.198063 PROGRESS: === Extracted 3401 precursors and 27746 fragments ===
3 days, 0:00:47.198612 INFO: === FDR correction performed with classifier version 3 ===
3 days, 0:00:47.199463 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:00:47.199584 PROGRESS: Total precursors accumulated: 600
3 days, 0:00:47.199675 PROGRESS: Target precursors: 535 (89.17%)
3 days, 0:00:47.199754 PROGRESS: Decoy precursors: 65 (10.83%)
3 days, 0:00:47.199833 PROGRESS: 
3 days, 0:00:47.199907 PROGRESS: Precursor Summary:
3 days, 0:00:47.201572 PROGRESS: Channel   0:	 0.050 FDR:   469; 0.010 FDR:   469; 0.001 FDR:   469
3 days, 0:00:47.201709 PROGRESS: 
3 days, 0:00:47.201803 PROGRESS: Protein Summary:
3 days, 0:00:47.203967 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   355
3 days, 0:00:47.204099 PROGRESS: =========================================================================
3 days, 0:00:47.204315 INFO: Target number of precursors reached.
3 days, 0:00:47.214650 INFO: fragments_df: keeping 5000 of 27746 [sum(precursor_idx_mask)=12112 sum(mass_error_mask)=27746 stop_rank=5000
3 days, 0:00:47.219663 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:47.451791 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:47.626738 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:47.794831 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:48.647927 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:00:48.648512 INFO: Using score_cutoff 25.145267047119138 (fac=0.99, q=1)
3 days, 0:00:48.648977 INFO: Updating optimization_manager: fwhm_rt             : 2.7133383750915527 -> 2.737022876739502
3 days, 0:00:48.649094 INFO: Updating optimization_manager: fwhm_mobility       : 0.005042281001806259 -> 0.00504231546074152
3 days, 0:00:48.649185 INFO: Updating optimization_manager: score_cutoff        : 25.881644560432434 -> 25.145267047119138
3 days, 0:00:48.649275 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:48.650810 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:48.652616 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:48.653795 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:48.656332 INFO: === checking if optimization conditions were reached ===
3 days, 0:00:48.656473 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3 days, 0:00:48.659074 INFO: Updating optimization_manager: rt_error            : 745.6878214096257 -> 612.1901890917136
3 days, 0:00:48.659215 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 612.1902.
3 days, 0:00:48.659335 INFO: ==============================================
3 days, 0:00:48.659461 INFO: Starting optimization step 2.
3 days, 0:00:48.659565 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:00:48.659674 INFO: Using python extraction backend
3 days, 0:00:48.659839 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:00:48.659962 INFO: === Search parameters used ===
3 days, 0:00:48.660059 INFO: rt_error       : 612.1901890917136
3 days, 0:00:48.660147 INFO: mobility_error : 0.1
3 days, 0:00:48.660238 INFO: num_candidates : 3
3 days, 0:00:48.660333 INFO: ms1_error      : 15.0
3 days, 0:00:48.660421 INFO: ms2_error      : 15.0
3 days, 0:00:48.660511 INFO: fwhm_rt        : 2.737022876739502
3 days, 0:00:48.660598 INFO: quant_window   : 3
3 days, 0:00:48.660684 INFO: ==============================================
3 days, 0:00:48.661884 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:00:48.661963 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:00:48.662051 INFO: FWHM in RT is 2.74 seconds, sigma is 0.46
3 days, 0:00:48.662095 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.73
3 days, 0:00:48.668445 INFO: Starting candidate selection
3 days, 0:00:54.780161 INFO: Starting candidate scoring
3 days, 0:00:54.905239 INFO: Finished candidate processing
3 days, 0:00:54.905373 INFO: Collecting candidate features
3 days, 0:00:54.929047 INFO: Collecting fragment features
3 days, 0:00:54.934102 INFO: Finished candidate scoring
3 days, 0:00:54.937158 INFO: performing precursor FDR with 47 features
3 days, 0:00:54.937271 INFO: Decoy channel: -1
3 days, 0:00:54.937316 INFO: competitive: True
3 days, 0:00:54.942467 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:00:54.945972 INFO: Estimating optimal hyperparameters - samples: 2,724, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:00:54.946134 INFO: Using random state 224957 for train-test-split
3 days, 0:00:55.276197 INFO: Test AUC: 0.772
3 days, 0:00:55.276342 INFO: Train AUC: 0.755
3 days, 0:00:55.276392 INFO: AUC difference: 2.23%
3 days, 0:00:55.656487 INFO: Resetting torch num_threads to 80
3 days, 0:00:55.657111 PROGRESS: === Extracted 3406 precursors and 27753 fragments ===
3 days, 0:00:55.657595 INFO: === FDR correction performed with classifier version 3 ===
3 days, 0:00:55.658275 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:00:55.658392 PROGRESS: Total precursors accumulated: 600
3 days, 0:00:55.658495 PROGRESS: Target precursors: 559 (93.17%)
3 days, 0:00:55.658586 PROGRESS: Decoy precursors: 41 (6.83%)
3 days, 0:00:55.658670 PROGRESS: 
3 days, 0:00:55.658755 PROGRESS: Precursor Summary:
3 days, 0:00:55.659916 PROGRESS: Channel   0:	 0.050 FDR:   504; 0.010 FDR:   504; 0.001 FDR:   504
3 days, 0:00:55.660026 PROGRESS: 
3 days, 0:00:55.660107 PROGRESS: Protein Summary:
3 days, 0:00:55.661518 PROGRESS: Channel   0:	 0.050 FDR:   376; 0.010 FDR:   376; 0.001 FDR:   376
3 days, 0:00:55.661634 PROGRESS: =========================================================================
3 days, 0:00:55.661802 INFO: Target number of precursors reached.
3 days, 0:00:55.668656 INFO: fragments_df: keeping 5000 of 27753 [sum(precursor_idx_mask)=12919 sum(mass_error_mask)=27753 stop_rank=5000
3 days, 0:00:55.672153 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:55.861289 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:56.079009 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:56.243910 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:57.185730 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:00:57.186247 INFO: Using score_cutoff 24.91114281406403 (fac=0.99, q=1)
3 days, 0:00:57.186669 INFO: Updating optimization_manager: fwhm_rt             : 2.737022876739502 -> 2.6994729042053223
3 days, 0:00:57.186774 INFO: Updating optimization_manager: fwhm_mobility       : 0.00504231546074152 -> 0.004709890112280846
3 days, 0:00:57.186853 INFO: Updating optimization_manager: score_cutoff        : 25.145267047119138 -> 24.91114281406403
3 days, 0:00:57.186934 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:00:57.188113 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:00:57.189649 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:00:57.190546 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:00:57.192651 INFO: === checking if optimization conditions were reached ===
3 days, 0:00:57.192774 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3 days, 0:00:57.194880 INFO: Updating optimization_manager: rt_error            : 612.1901890917136 -> 547.3178097960327
3 days, 0:00:57.195013 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 547.3178.
3 days, 0:00:57.195113 INFO: ==============================================
3 days, 0:00:57.195216 INFO: Starting optimization step 3.
3 days, 0:00:57.195308 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:00:57.195397 INFO: Using python extraction backend
3 days, 0:00:57.195527 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:00:57.195623 INFO: === Search parameters used ===
3 days, 0:00:57.195706 INFO: rt_error       : 547.3178097960327
3 days, 0:00:57.195780 INFO: mobility_error : 0.1
3 days, 0:00:57.195848 INFO: num_candidates : 3
3 days, 0:00:57.195915 INFO: ms1_error      : 15.0
3 days, 0:00:57.195982 INFO: ms2_error      : 15.0
3 days, 0:00:57.196048 INFO: fwhm_rt        : 2.6994729042053223
3 days, 0:00:57.196115 INFO: quant_window   : 3
3 days, 0:00:57.196181 INFO: ==============================================
3 days, 0:00:57.197079 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:00:57.197134 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:00:57.197190 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
3 days, 0:00:57.197226 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
3 days, 0:00:57.202558 INFO: Starting candidate selection
3 days, 0:01:01.998606 INFO: Starting candidate scoring
3 days, 0:01:02.102004 INFO: Finished candidate processing
3 days, 0:01:02.102143 INFO: Collecting candidate features
3 days, 0:01:02.114926 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3387)
3 days, 0:01:02.120453 INFO: Collecting fragment features
3 days, 0:01:02.125481 INFO: Finished candidate scoring
3 days, 0:01:02.127973 INFO: performing precursor FDR with 47 features
3 days, 0:01:02.128087 INFO: Decoy channel: -1
3 days, 0:01:02.128135 INFO: competitive: True
3 days, 0:01:02.132190 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:01:02.134202 WARNING: dropped 1 target PSMs due to missing features
3 days, 0:01:02.134276 WARNING: dropped 1 decoy PSMs due to missing features
3 days, 0:01:02.135551 INFO: Estimating optimal hyperparameters - samples: 2,708, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:01:02.135655 INFO: Using random state 224957 for train-test-split
3 days, 0:01:02.512897 INFO: Test AUC: 0.717
3 days, 0:01:02.513026 INFO: Train AUC: 0.766
3 days, 0:01:02.513072 INFO: AUC difference: 6.35%
3 days, 0:01:02.513110 WARNING: AUC difference > 5%. This may indicate overfitting.
3 days, 0:01:02.778754 INFO: Resetting torch num_threads to 80
3 days, 0:01:02.779341 PROGRESS: === Extracted 3387 precursors and 27452 fragments ===
3 days, 0:01:02.779783 INFO: === FDR correction performed with classifier version 3 ===
3 days, 0:01:02.780412 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:01:02.780508 PROGRESS: Total precursors accumulated: 599
3 days, 0:01:02.780584 PROGRESS: Target precursors: 554 (92.49%)
3 days, 0:01:02.780648 PROGRESS: Decoy precursors: 45 (7.51%)
3 days, 0:01:02.780704 PROGRESS: 
3 days, 0:01:02.780759 PROGRESS: Precursor Summary:
3 days, 0:01:02.781925 PROGRESS: Channel   0:	 0.050 FDR:   513; 0.010 FDR:   509; 0.001 FDR:   509
3 days, 0:01:02.782036 PROGRESS: 
3 days, 0:01:02.782113 PROGRESS: Protein Summary:
3 days, 0:01:02.783469 PROGRESS: Channel   0:	 0.050 FDR:   386; 0.010 FDR:   382; 0.001 FDR:   382
3 days, 0:01:02.783574 PROGRESS: =========================================================================
3 days, 0:01:02.783728 INFO: Target number of precursors reached.
3 days, 0:01:02.790637 INFO: fragments_df: keeping 5000 of 27452 [sum(precursor_idx_mask)=13109 sum(mass_error_mask)=27452 stop_rank=5000
3 days, 0:01:02.794003 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:03.049166 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:03.237938 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:03.449697 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:04.329352 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:01:04.329826 INFO: Using score_cutoff 24.827763777923582 (fac=0.99, q=1)
3 days, 0:01:04.330215 INFO: Updating optimization_manager: fwhm_rt             : 2.6994729042053223 -> 2.697737216949463
3 days, 0:01:04.330314 INFO: Updating optimization_manager: fwhm_mobility       : 0.004709890112280846 -> 0.004778140690177679
3 days, 0:01:04.330394 INFO: Updating optimization_manager: score_cutoff        : 24.91114281406403 -> 24.827763777923582
3 days, 0:01:04.330477 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:04.331620 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:04.333013 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:04.333841 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:04.335915 INFO: === checking if optimization conditions were reached ===
3 days, 0:01:04.336030 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3 days, 0:01:04.338006 INFO: Updating optimization_manager: rt_error            : 547.3178097960327 -> 493.16578355076507
3 days, 0:01:04.338127 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 493.1658.
3 days, 0:01:04.338239 INFO: ==============================================
3 days, 0:01:04.338361 INFO: Starting optimization step 4.
3 days, 0:01:04.338458 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:01:04.338555 INFO: Using python extraction backend
3 days, 0:01:04.338698 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:01:04.338799 INFO: === Search parameters used ===
3 days, 0:01:04.338881 INFO: rt_error       : 493.16578355076507
3 days, 0:01:04.338954 INFO: mobility_error : 0.1
3 days, 0:01:04.339039 INFO: num_candidates : 3
3 days, 0:01:04.339114 INFO: ms1_error      : 15.0
3 days, 0:01:04.339184 INFO: ms2_error      : 15.0
3 days, 0:01:04.339251 INFO: fwhm_rt        : 2.697737216949463
3 days, 0:01:04.339321 INFO: quant_window   : 3
3 days, 0:01:04.339390 INFO: ==============================================
3 days, 0:01:04.340253 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:01:04.340309 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:01:04.340367 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
3 days, 0:01:04.340417 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.59
3 days, 0:01:04.359804 INFO: Starting candidate selection
3 days, 0:01:09.459267 INFO: Starting candidate scoring
3 days, 0:01:09.562515 INFO: Finished candidate processing
3 days, 0:01:09.562650 INFO: Collecting candidate features
3 days, 0:01:09.578992 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3390)
3 days, 0:01:09.586813 INFO: Collecting fragment features
3 days, 0:01:09.592660 INFO: Finished candidate scoring
3 days, 0:01:09.595515 INFO: performing precursor FDR with 47 features
3 days, 0:01:09.595618 INFO: Decoy channel: -1
3 days, 0:01:09.595657 INFO: competitive: True
3 days, 0:01:09.600528 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:01:09.603075 WARNING: dropped 1 target PSMs due to missing features
3 days, 0:01:09.603159 WARNING: dropped 1 decoy PSMs due to missing features
3 days, 0:01:09.604621 INFO: Estimating optimal hyperparameters - samples: 2,710, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:01:09.604756 INFO: Using random state 224957 for train-test-split
3 days, 0:01:09.835127 INFO: Test AUC: 0.761
3 days, 0:01:09.835247 INFO: Train AUC: 0.764
3 days, 0:01:09.835282 INFO: AUC difference: 0.38%
3 days, 0:01:10.114766 INFO: Resetting torch num_threads to 80
3 days, 0:01:10.115352 PROGRESS: === Extracted 3390 precursors and 27419 fragments ===
3 days, 0:01:10.116103 INFO: === FDR correction performed with classifier version 3 ===
3 days, 0:01:10.116853 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:01:10.116972 PROGRESS: Total precursors accumulated: 599
3 days, 0:01:10.117071 PROGRESS: Target precursors: 555 (92.65%)
3 days, 0:01:10.117157 PROGRESS: Decoy precursors: 44 (7.35%)
3 days, 0:01:10.117234 PROGRESS: 
3 days, 0:01:10.117308 PROGRESS: Precursor Summary:
3 days, 0:01:10.121952 PROGRESS: Channel   0:	 0.050 FDR:   520; 0.010 FDR:   508; 0.001 FDR:   508
3 days, 0:01:10.122080 PROGRESS: 
3 days, 0:01:10.122187 PROGRESS: Protein Summary:
3 days, 0:01:10.123817 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   379; 0.001 FDR:   379
3 days, 0:01:10.124001 PROGRESS: =========================================================================
3 days, 0:01:10.124274 INFO: Target number of precursors reached.
3 days, 0:01:10.132049 INFO: fragments_df: keeping 5000 of 27419 [sum(precursor_idx_mask)=13100 sum(mass_error_mask)=27419 stop_rank=5000
3 days, 0:01:10.136632 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:10.347761 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:10.576252 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:10.757442 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:11.728062 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:01:11.728534 INFO: Using score_cutoff 24.835293766021728 (fac=0.99, q=1)
3 days, 0:01:11.728929 INFO: Updating optimization_manager: fwhm_rt             : 2.697737216949463 -> 2.6994729042053223
3 days, 0:01:11.729035 INFO: Updating optimization_manager: fwhm_mobility       : 0.004778140690177679 -> 0.004709890112280846
3 days, 0:01:11.729118 INFO: Updating optimization_manager: score_cutoff        : 24.827763777923582 -> 24.835293766021728
3 days, 0:01:11.729199 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:11.730397 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:11.731884 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:11.732743 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:11.734805 INFO: === checking if optimization conditions were reached ===
3 days, 0:01:11.734926 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3 days, 0:01:11.736865 INFO: Updating optimization_manager: rt_error            : 493.16578355076507 -> 473.6294633073676
3 days, 0:01:11.736983 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 473.6295.
3 days, 0:01:11.737077 INFO: ==============================================
3 days, 0:01:11.737178 INFO: Starting optimization step 5.
3 days, 0:01:11.737255 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:01:11.737326 INFO: Using python extraction backend
3 days, 0:01:11.737435 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:01:11.737512 INFO: === Search parameters used ===
3 days, 0:01:11.737574 INFO: rt_error       : 473.6294633073676
3 days, 0:01:11.737631 INFO: mobility_error : 0.1
3 days, 0:01:11.737685 INFO: num_candidates : 3
3 days, 0:01:11.737739 INFO: ms1_error      : 15.0
3 days, 0:01:11.737792 INFO: ms2_error      : 15.0
3 days, 0:01:11.737842 INFO: fwhm_rt        : 2.6994729042053223
3 days, 0:01:11.737920 INFO: quant_window   : 3
3 days, 0:01:11.737980 INFO: ==============================================
3 days, 0:01:11.738875 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:01:11.738931 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:01:11.738972 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
3 days, 0:01:11.739001 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
3 days, 0:01:11.754049 INFO: Starting candidate selection
3 days, 0:01:17.011397 INFO: Starting candidate scoring
3 days, 0:01:17.147513 INFO: Finished candidate processing
3 days, 0:01:17.147645 INFO: Collecting candidate features
3 days, 0:01:17.164289 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3382)
3 days, 0:01:17.172960 INFO: Collecting fragment features
3 days, 0:01:17.178216 INFO: Finished candidate scoring
3 days, 0:01:17.181230 INFO: performing precursor FDR with 47 features
3 days, 0:01:17.181306 INFO: Decoy channel: -1
3 days, 0:01:17.181349 INFO: competitive: True
3 days, 0:01:17.186046 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:01:17.188479 WARNING: dropped 1 target PSMs due to missing features
3 days, 0:01:17.188555 WARNING: dropped 1 decoy PSMs due to missing features
3 days, 0:01:17.190047 INFO: Estimating optimal hyperparameters - samples: 2,704, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:01:17.190172 INFO: Using random state 224957 for train-test-split
3 days, 0:01:17.444155 INFO: Test AUC: 0.744
3 days, 0:01:17.444298 INFO: Train AUC: 0.762
3 days, 0:01:17.444357 INFO: AUC difference: 2.41%
3 days, 0:01:17.812821 INFO: Resetting torch num_threads to 80
3 days, 0:01:17.813507 PROGRESS: === Extracted 3382 precursors and 27321 fragments ===
3 days, 0:01:17.813977 INFO: === FDR correction performed with classifier version 3 ===
3 days, 0:01:17.814635 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:01:17.814755 PROGRESS: Total precursors accumulated: 600
3 days, 0:01:17.814851 PROGRESS: Target precursors: 549 (91.50%)
3 days, 0:01:17.814935 PROGRESS: Decoy precursors: 51 (8.50%)
3 days, 0:01:17.815015 PROGRESS: 
3 days, 0:01:17.815089 PROGRESS: Precursor Summary:
3 days, 0:01:17.816246 PROGRESS: Channel   0:	 0.050 FDR:   493; 0.010 FDR:   493; 0.001 FDR:   493
3 days, 0:01:17.816367 PROGRESS: 
3 days, 0:01:17.816461 PROGRESS: Protein Summary:
3 days, 0:01:17.817827 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   368; 0.001 FDR:   368
3 days, 0:01:17.817963 PROGRESS: =========================================================================
3 days, 0:01:17.818177 INFO: Target number of precursors reached.
3 days, 0:01:17.825108 INFO: fragments_df: keeping 5000 of 27321 [sum(precursor_idx_mask)=12732 sum(mass_error_mask)=27321 stop_rank=5000
3 days, 0:01:17.829973 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:18.061322 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:18.257161 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:18.465011 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:19.345072 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:01:19.345544 INFO: Using score_cutoff 24.793382064056395 (fac=0.99, q=1)
3 days, 0:01:19.345900 INFO: Updating optimization_manager: fwhm_rt             : 2.6994729042053223 -> 2.723207712173462
3 days, 0:01:19.346062 INFO: Updating optimization_manager: fwhm_mobility       : 0.004709890112280846 -> 0.0048581804148852825
3 days, 0:01:19.346154 INFO: Updating optimization_manager: score_cutoff        : 24.835293766021728 -> 24.793382064056395
3 days, 0:01:19.346244 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:19.347419 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:19.348824 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:19.349658 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:19.351810 INFO: === checking if optimization conditions were reached ===
3 days, 0:01:19.351935 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3 days, 0:01:19.353174 INFO: Updating optimization_manager: rt_error            : 473.6294633073676 -> 473.6294633073676
3 days, 0:01:19.353335 INFO: Updating optimization_manager: classifier_version  : 3 -> 9
3 days, 0:01:19.353466 INFO: Updating optimization_manager: score_cutoff        : 24.793382064056395 -> 24.793382064056395
3 days, 0:01:19.353586 INFO: Updating optimization_manager: fwhm_rt             : 2.723207712173462 -> 2.723207712173462
3 days, 0:01:19.353698 INFO: Updating optimization_manager: fwhm_mobility       : 0.0048581804148852825 -> 0.0048581804148852825
3 days, 0:01:19.353812 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 473.6295 found after 6 searches.
3 days, 0:01:19.353909 INFO: ==============================================
3 days, 0:01:19.354001 PROGRESS: Optimization finished for rt_error.
3 days, 0:01:19.356971 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:19.357913 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:19.359371 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:19.360240 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:19.362282 INFO: Starting optimization step 0.
3 days, 0:01:19.362395 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:01:19.362481 INFO: Using python extraction backend
3 days, 0:01:19.362601 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:01:19.362688 INFO: === Search parameters used ===
3 days, 0:01:19.362766 INFO: rt_error       : 473.6294633073676
3 days, 0:01:19.362826 INFO: mobility_error : 0.1
3 days, 0:01:19.362881 INFO: num_candidates : 3
3 days, 0:01:19.362936 INFO: ms1_error      : 15.0
3 days, 0:01:19.362987 INFO: ms2_error      : 15.0
3 days, 0:01:19.363040 INFO: fwhm_rt        : 2.723207712173462
3 days, 0:01:19.363119 INFO: quant_window   : 3
3 days, 0:01:19.363192 INFO: ==============================================
3 days, 0:01:19.363963 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:01:19.364016 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:01:19.364056 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
3 days, 0:01:19.364084 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.63
3 days, 0:01:19.374365 INFO: Starting candidate selection
3 days, 0:01:24.514054 INFO: Starting candidate scoring
3 days, 0:01:24.619122 INFO: Finished candidate processing
3 days, 0:01:24.619267 INFO: Collecting candidate features
3 days, 0:01:24.635716 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3394)
3 days, 0:01:24.643033 INFO: Collecting fragment features
3 days, 0:01:24.647970 INFO: Finished candidate scoring
3 days, 0:01:24.650146 INFO: performing precursor FDR with 47 features
3 days, 0:01:24.650233 INFO: Decoy channel: -1
3 days, 0:01:24.650264 INFO: competitive: True
3 days, 0:01:24.653601 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:01:24.655177 WARNING: dropped 1 target PSMs due to missing features
3 days, 0:01:24.656337 INFO: Estimating optimal hyperparameters - samples: 2,714, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:01:24.656438 INFO: Using random state 832165 for train-test-split
3 days, 0:01:25.009600 INFO: Test AUC: 0.763
3 days, 0:01:25.009743 INFO: Train AUC: 0.801
3 days, 0:01:25.009793 INFO: AUC difference: 4.84%
3 days, 0:01:25.346646 INFO: Resetting torch num_threads to 80
3 days, 0:01:25.347340 PROGRESS: === Extracted 3394 precursors and 27384 fragments ===
3 days, 0:01:25.347903 INFO: === FDR correction performed with classifier version 9 ===
3 days, 0:01:25.348763 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:01:25.348887 PROGRESS: Total precursors accumulated: 600
3 days, 0:01:25.348981 PROGRESS: Target precursors: 525 (87.50%)
3 days, 0:01:25.349064 PROGRESS: Decoy precursors: 75 (12.50%)
3 days, 0:01:25.349138 PROGRESS: 
3 days, 0:01:25.349208 PROGRESS: Precursor Summary:
3 days, 0:01:25.350886 PROGRESS: Channel   0:	 0.050 FDR:   234; 0.010 FDR:   136; 0.001 FDR:   132
3 days, 0:01:25.351027 PROGRESS: 
3 days, 0:01:25.351124 PROGRESS: Protein Summary:
3 days, 0:01:25.353092 PROGRESS: Channel   0:	 0.050 FDR:   185; 0.010 FDR:   115; 0.001 FDR:   112
3 days, 0:01:25.353358 PROGRESS: =========================================================================
3 days, 0:01:25.353713 INFO: Target number of precursors not reached yet.
3 days, 0:01:25.358827 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:25.360373 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:25.362458 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:25.363658 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:25.366739 INFO: === skipping optimization until target number of precursors are found ===
3 days, 0:01:25.366893 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
3 days, 0:01:25.367041 INFO: Starting optimization step 1.
3 days, 0:01:25.367154 PROGRESS: === Extracting elution groups 600 to 1400 ===
3 days, 0:01:25.367270 INFO: Using python extraction backend
3 days, 0:01:25.367440 PROGRESS: Extracting batch of 1599 precursors
3 days, 0:01:25.367569 INFO: === Search parameters used ===
3 days, 0:01:25.367663 INFO: rt_error       : 473.6294633073676
3 days, 0:01:25.367756 INFO: mobility_error : 0.1
3 days, 0:01:25.367846 INFO: num_candidates : 3
3 days, 0:01:25.367935 INFO: ms1_error      : 15.0
3 days, 0:01:25.368021 INFO: ms2_error      : 15.0
3 days, 0:01:25.368107 INFO: fwhm_rt        : 2.723207712173462
3 days, 0:01:25.368193 INFO: quant_window   : 3
3 days, 0:01:25.368280 INFO: ==============================================
3 days, 0:01:25.369622 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:01:25.369693 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:01:25.369775 INFO: FWHM in RT is 2.72 seconds, sigma is 0.45
3 days, 0:01:25.369820 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.63
3 days, 0:01:25.390632 INFO: Starting candidate selection
3 days, 0:01:30.628380 INFO: Starting candidate scoring
3 days, 0:01:30.765186 INFO: Finished candidate processing
3 days, 0:01:30.765293 INFO: Collecting candidate features
3 days, 0:01:30.776722 WARNING: intensity_correlation has 3 NaNs ( 0.07 % out of 4499)
3 days, 0:01:30.781008 INFO: Collecting fragment features
3 days, 0:01:30.785541 INFO: Finished candidate scoring
3 days, 0:01:30.790116 INFO: performing precursor FDR with 47 features
3 days, 0:01:30.790217 INFO: Decoy channel: -1
3 days, 0:01:30.790255 INFO: competitive: True
3 days, 0:01:30.795146 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:01:30.797392 WARNING: dropped 2 target PSMs due to missing features
3 days, 0:01:30.797468 WARNING: dropped 2 decoy PSMs due to missing features
3 days, 0:01:30.799204 INFO: Estimating optimal hyperparameters - samples: 6,311, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:01:30.799325 INFO: Using random state 832165 for train-test-split
3 days, 0:01:31.487868 INFO: Test AUC: 0.769
3 days, 0:01:31.488015 INFO: Train AUC: 0.796
3 days, 0:01:31.488071 INFO: AUC difference: 3.39%
3 days, 0:01:31.805084 INFO: Resetting torch num_threads to 80
3 days, 0:01:31.807189 PROGRESS: === Extracted 7893 precursors and 64357 fragments ===
3 days, 0:01:31.807740 INFO: === FDR correction performed with classifier version 9 ===
3 days, 0:01:31.808480 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:01:31.808599 PROGRESS: Total precursors accumulated: 1,400
3 days, 0:01:31.808690 PROGRESS: Target precursors: 1,270 (90.71%)
3 days, 0:01:31.808757 PROGRESS: Decoy precursors: 130 (9.29%)
3 days, 0:01:31.808818 PROGRESS: 
3 days, 0:01:31.808874 PROGRESS: Precursor Summary:
3 days, 0:01:31.810178 PROGRESS: Channel   0:	 0.050 FDR: 1,075; 0.010 FDR:   896; 0.001 FDR:   486
3 days, 0:01:31.810296 PROGRESS: 
3 days, 0:01:31.810384 PROGRESS: Protein Summary:
3 days, 0:01:31.812026 PROGRESS: Channel   0:	 0.050 FDR:   634; 0.010 FDR:   520; 0.001 FDR:   301
3 days, 0:01:31.812142 PROGRESS: =========================================================================
3 days, 0:01:31.812333 INFO: Target number of precursors reached.
3 days, 0:01:31.825989 INFO: fragments_df: keeping 5000 of 64357 [sum(precursor_idx_mask)=23962 sum(mass_error_mask)=64357 stop_rank=5000
3 days, 0:01:31.830147 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:32.096820 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:32.367079 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:32.622129 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:33.450062 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:01:33.450559 INFO: Using score_cutoff 27.09458221721649 (fac=0.99, q=1)
3 days, 0:01:33.450981 INFO: Updating optimization_manager: fwhm_rt             : 2.723207712173462 -> 2.8282856941223145
3 days, 0:01:33.451094 INFO: Updating optimization_manager: fwhm_mobility       : 0.0048581804148852825 -> 0.005526394117623568
3 days, 0:01:33.451185 INFO: Updating optimization_manager: score_cutoff        : 24.793382064056395 -> 27.09458221721649
3 days, 0:01:33.451272 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:33.452458 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:33.454026 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:33.454977 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:33.457136 INFO: === checking if optimization conditions were reached ===
3 days, 0:01:33.457277 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
3 days, 0:01:33.458900 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06132821648063777
3 days, 0:01:33.459040 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0613.
3 days, 0:01:33.459143 INFO: ==============================================
3 days, 0:01:33.459259 INFO: Starting optimization step 2.
3 days, 0:01:33.459358 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:01:33.459458 INFO: Using python extraction backend
3 days, 0:01:33.459610 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:01:33.459711 INFO: === Search parameters used ===
3 days, 0:01:33.459776 INFO: rt_error       : 473.6294633073676
3 days, 0:01:33.459826 INFO: mobility_error : 0.06132821648063777
3 days, 0:01:33.459884 INFO: num_candidates : 3
3 days, 0:01:33.459931 INFO: ms1_error      : 15.0
3 days, 0:01:33.459976 INFO: ms2_error      : 15.0
3 days, 0:01:33.460020 INFO: fwhm_rt        : 2.8282856941223145
3 days, 0:01:33.460063 INFO: quant_window   : 3
3 days, 0:01:33.460105 INFO: ==============================================
3 days, 0:01:33.461038 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:01:33.461104 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:01:33.461185 INFO: FWHM in RT is 2.83 seconds, sigma is 0.47
3 days, 0:01:33.461228 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.00
3 days, 0:01:33.466841 INFO: Starting candidate selection
3 days, 0:01:36.843977 INFO: Starting candidate scoring
3 days, 0:01:36.956981 INFO: Finished candidate processing
3 days, 0:01:36.957124 INFO: Collecting candidate features
3 days, 0:01:36.971013 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3377)
3 days, 0:01:36.976164 INFO: Collecting fragment features
3 days, 0:01:36.980709 INFO: Finished candidate scoring
3 days, 0:01:36.982923 INFO: performing precursor FDR with 47 features
3 days, 0:01:36.982982 INFO: Decoy channel: -1
3 days, 0:01:36.983014 INFO: competitive: True
3 days, 0:01:36.986951 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:01:36.988658 WARNING: dropped 1 target PSMs due to missing features
3 days, 0:01:36.989963 INFO: Estimating optimal hyperparameters - samples: 2,700, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:01:36.990062 INFO: Using random state 832165 for train-test-split
3 days, 0:01:37.235539 INFO: Test AUC: 0.760
3 days, 0:01:37.235651 INFO: Train AUC: 0.775
3 days, 0:01:37.235686 INFO: AUC difference: 2.02%
3 days, 0:01:37.603990 INFO: Resetting torch num_threads to 80
3 days, 0:01:37.604681 PROGRESS: === Extracted 3377 precursors and 27083 fragments ===
3 days, 0:01:37.605312 INFO: === FDR correction performed with classifier version 9 ===
3 days, 0:01:37.606297 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:01:37.606424 PROGRESS: Total precursors accumulated: 600
3 days, 0:01:37.606519 PROGRESS: Target precursors: 561 (93.50%)
3 days, 0:01:37.606604 PROGRESS: Decoy precursors: 39 (6.50%)
3 days, 0:01:37.606680 PROGRESS: 
3 days, 0:01:37.606755 PROGRESS: Precursor Summary:
3 days, 0:01:37.608524 PROGRESS: Channel   0:	 0.050 FDR:   534; 0.010 FDR:   507; 0.001 FDR:   507
3 days, 0:01:37.608649 PROGRESS: 
3 days, 0:01:37.608743 PROGRESS: Protein Summary:
3 days, 0:01:37.610816 PROGRESS: Channel   0:	 0.050 FDR:   397; 0.010 FDR:   381; 0.001 FDR:   381
3 days, 0:01:37.610947 PROGRESS: =========================================================================
3 days, 0:01:37.611195 INFO: Target number of precursors reached.
3 days, 0:01:37.618263 INFO: fragments_df: keeping 5000 of 27083 [sum(precursor_idx_mask)=12908 sum(mass_error_mask)=27083 stop_rank=5000
3 days, 0:01:37.621564 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:37.823988 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:38.005441 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:38.184853 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:39.039006 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:01:39.039466 INFO: Using score_cutoff 23.782319110107423 (fac=0.99, q=1)
3 days, 0:01:39.039847 INFO: Updating optimization_manager: fwhm_rt             : 2.8282856941223145 -> 2.6957180500030518
3 days, 0:01:39.039943 INFO: Updating optimization_manager: fwhm_mobility       : 0.005526394117623568 -> 0.004690541885793209
3 days, 0:01:39.040015 INFO: Updating optimization_manager: score_cutoff        : 27.09458221721649 -> 23.782319110107423
3 days, 0:01:39.040085 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:39.041218 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:39.042634 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:39.043559 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:39.045570 INFO: === checking if optimization conditions were reached ===
3 days, 0:01:39.045681 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
3 days, 0:01:39.047461 INFO: Updating optimization_manager: mobility_error      : 0.06132821648063777 -> 0.05343267787517096
3 days, 0:01:39.047577 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0534.
3 days, 0:01:39.047657 INFO: ==============================================
3 days, 0:01:39.047744 INFO: Starting optimization step 3.
3 days, 0:01:39.047819 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:01:39.047888 INFO: Using python extraction backend
3 days, 0:01:39.047999 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:01:39.048077 INFO: === Search parameters used ===
3 days, 0:01:39.048135 INFO: rt_error       : 473.6294633073676
3 days, 0:01:39.048188 INFO: mobility_error : 0.05343267787517096
3 days, 0:01:39.048239 INFO: num_candidates : 3
3 days, 0:01:39.048290 INFO: ms1_error      : 15.0
3 days, 0:01:39.048341 INFO: ms2_error      : 15.0
3 days, 0:01:39.048394 INFO: fwhm_rt        : 2.6957180500030518
3 days, 0:01:39.048445 INFO: quant_window   : 3
3 days, 0:01:39.048495 INFO: ==============================================
3 days, 0:01:39.049327 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:01:39.049380 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:01:39.049419 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
3 days, 0:01:39.049447 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.54
3 days, 0:01:39.066038 INFO: Starting candidate selection
3 days, 0:01:42.000827 INFO: Starting candidate scoring
3 days, 0:01:42.123179 INFO: Finished candidate processing
3 days, 0:01:42.123307 INFO: Collecting candidate features
3 days, 0:01:42.135669 WARNING: intensity_correlation has 3 NaNs ( 0.09 % out of 3373)
3 days, 0:01:42.140839 INFO: Collecting fragment features
3 days, 0:01:42.145342 INFO: Finished candidate scoring
3 days, 0:01:42.147553 INFO: performing precursor FDR with 47 features
3 days, 0:01:42.147649 INFO: Decoy channel: -1
3 days, 0:01:42.147784 INFO: competitive: True
3 days, 0:01:42.151619 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:01:42.153515 WARNING: dropped 1 target PSMs due to missing features
3 days, 0:01:42.153585 WARNING: dropped 2 decoy PSMs due to missing features
3 days, 0:01:42.154834 INFO: Estimating optimal hyperparameters - samples: 2,696, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:01:42.154937 INFO: Using random state 832165 for train-test-split
3 days, 0:01:42.512705 INFO: Test AUC: 0.787
3 days, 0:01:42.512827 INFO: Train AUC: 0.803
3 days, 0:01:42.512866 INFO: AUC difference: 2.03%
3 days, 0:01:42.831798 INFO: Resetting torch num_threads to 80
3 days, 0:01:42.832526 PROGRESS: === Extracted 3373 precursors and 26971 fragments ===
3 days, 0:01:42.833153 INFO: === FDR correction performed with classifier version 9 ===
3 days, 0:01:42.834095 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:01:42.834236 PROGRESS: Total precursors accumulated: 599
3 days, 0:01:42.834337 PROGRESS: Target precursors: 541 (90.32%)
3 days, 0:01:42.834434 PROGRESS: Decoy precursors: 58 (9.68%)
3 days, 0:01:42.834518 PROGRESS: 
3 days, 0:01:42.834598 PROGRESS: Precursor Summary:
3 days, 0:01:42.836322 PROGRESS: Channel   0:	 0.050 FDR:   422; 0.010 FDR:   221; 0.001 FDR:   151
3 days, 0:01:42.836467 PROGRESS: 
3 days, 0:01:42.836575 PROGRESS: Protein Summary:
3 days, 0:01:42.838600 PROGRESS: Channel   0:	 0.050 FDR:   319; 0.010 FDR:   181; 0.001 FDR:   129
3 days, 0:01:42.838735 PROGRESS: =========================================================================
3 days, 0:01:42.838941 INFO: Target number of precursors reached.
3 days, 0:01:42.846112 INFO: fragments_df: keeping 3790 of 26971 [sum(precursor_idx_mask)=6138 sum(mass_error_mask)=26971 stop_rank=3790
3 days, 0:01:42.849437 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:43.012081 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:43.161411 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:43.312116 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:43.983271 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:01:43.983712 INFO: Using score_cutoff 27.741115070343017 (fac=0.99, q=1)
3 days, 0:01:43.984064 INFO: Updating optimization_manager: fwhm_rt             : 2.6957180500030518 -> 2.8796944618225098
3 days, 0:01:43.984153 INFO: Updating optimization_manager: fwhm_mobility       : 0.004690541885793209 -> 0.0056420196779072285
3 days, 0:01:43.984212 INFO: Updating optimization_manager: score_cutoff        : 23.782319110107423 -> 27.741115070343017
3 days, 0:01:43.984270 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:43.985419 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:43.986894 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:43.987775 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:43.989723 INFO: === checking if optimization conditions were reached ===
3 days, 0:01:43.989827 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
3 days, 0:01:43.990649 INFO: Updating optimization_manager: mobility_error      : 0.05343267787517096 -> 0.06132821648063777
3 days, 0:01:43.990829 INFO: Updating optimization_manager: classifier_version  : 9 -> 12
3 days, 0:01:43.990944 INFO: Updating optimization_manager: score_cutoff        : 27.741115070343017 -> 23.782319110107423
3 days, 0:01:43.991073 INFO: Updating optimization_manager: fwhm_rt             : 2.8796944618225098 -> 2.6957180500030518
3 days, 0:01:43.991199 INFO: Updating optimization_manager: fwhm_mobility       : 0.0056420196779072285 -> 0.004690541885793209
3 days, 0:01:43.991320 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0613 found after 3 searches.
3 days, 0:01:43.991407 INFO: ==============================================
3 days, 0:01:43.991499 PROGRESS: Optimization finished for mobility_error.
3 days, 0:01:43.994713 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:43.995677 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:43.997139 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:43.998014 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:44.000149 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3 days, 0:01:44.000257 PROGRESS: ==============================================
3 days, 0:01:44.000337 PROGRESS: ms2_error      : 15.0000
3 days, 0:01:44.000419 PROGRESS: ms1_error      : 15.0000
3 days, 0:01:44.000633 PROGRESS: rt_error       : 473.6295
3 days, 0:01:44.000749 PROGRESS: mobility_error : 0.0613
3 days, 0:01:44.000816 PROGRESS: ==============================================
3 days, 0:01:44.001350 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:01:44.005796 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:01:44.023693 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:01:44.028774 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:01:44.070822 INFO: Using python extraction backend
3 days, 0:01:44.071126 PROGRESS: Extracting batch of 27494 precursors
3 days, 0:01:44.071231 INFO: === Search parameters used ===
3 days, 0:01:44.071305 INFO: rt_error       : 473.6294633073676
3 days, 0:01:44.071370 INFO: mobility_error : 0.06132821648063777
3 days, 0:01:44.071433 INFO: num_candidates : 3
3 days, 0:01:44.071494 INFO: ms1_error      : 15.0
3 days, 0:01:44.071554 INFO: ms2_error      : 15.0
3 days, 0:01:44.071614 INFO: fwhm_rt        : 2.6957180500030518
3 days, 0:01:44.071673 INFO: quant_window   : 3
3 days, 0:01:44.071731 INFO: ==============================================
3 days, 0:01:44.077600 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:01:44.077725 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:01:44.077780 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
3 days, 0:01:44.077817 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.54
3 days, 0:01:44.094094 INFO: Starting candidate selection
3 days, 0:02:23.580484 INFO: Removed 11656 precursors with score below cutoff 23.782319110107423
3 days, 0:02:23.972097 INFO: Starting candidate scoring
3 days, 0:02:25.195395 INFO: Finished candidate processing
3 days, 0:02:25.195509 INFO: Collecting candidate features
3 days, 0:02:25.354220 WARNING: intensity_correlation has 9 NaNs ( 0.01 % out of 66392)
3 days, 0:02:25.354579 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 66392)
3 days, 0:02:25.362592 INFO: Collecting fragment features
3 days, 0:02:25.401345 INFO: Finished candidate scoring
3 days, 0:02:25.434172 INFO: === Performing FDR correction with classifier version 12 ===
3 days, 0:02:25.434548 INFO: performing precursor FDR with 47 features
3 days, 0:02:25.434596 INFO: Decoy channel: -1
3 days, 0:02:25.434640 INFO: competitive: True
3 days, 0:02:25.454198 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:02:25.464131 WARNING: dropped 2 target PSMs due to missing features
3 days, 0:02:25.464263 WARNING: dropped 8 decoy PSMs due to missing features
3 days, 0:02:25.464340 WARNING: FDR calculation for 35932 target and 30450 decoy PSMs
3 days, 0:02:25.464376 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3 days, 0:02:25.475655 INFO: Estimating optimal hyperparameters - samples: 53,105, batch_size: 217, learning_rate: 2.30e-04
3 days, 0:02:25.475939 INFO: Using random state 810637 for train-test-split
3 days, 0:02:29.209934 INFO: Test AUC: 0.781
3 days, 0:02:29.210109 INFO: Train AUC: 0.792
3 days, 0:02:29.210166 INFO: AUC difference: 1.41%
3 days, 0:02:29.513731 INFO: Resetting torch num_threads to 80
3 days, 0:02:29.516887 INFO: Removing fragments below FDR threshold
3 days, 0:02:29.529432 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:02:29.529632 PROGRESS: Total precursors accumulated: 10,615
3 days, 0:02:29.529701 PROGRESS: Target precursors: 10,510 (99.01%)
3 days, 0:02:29.529758 PROGRESS: Decoy precursors: 105 (0.99%)
3 days, 0:02:29.529812 PROGRESS: 
3 days, 0:02:29.529876 PROGRESS: Precursor Summary:
3 days, 0:02:29.533601 PROGRESS: Channel   0:	 0.050 FDR: 10,510; 0.010 FDR: 10,510; 0.001 FDR: 9,545
3 days, 0:02:29.533721 PROGRESS: 
3 days, 0:02:29.533785 PROGRESS: Protein Summary:
3 days, 0:02:29.538830 PROGRESS: Channel   0:	 0.050 FDR: 1,635; 0.010 FDR: 1,635; 0.001 FDR: 1,591
3 days, 0:02:29.538960 PROGRESS: =========================================================================
3 days, 0:02:29.540063 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R5/psm.parquet
3 days, 0:02:29.614194 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R5/frag.parquet
3 days, 0:02:29.667590 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R5
3 days, 0:02:29.672465 PROGRESS: Loading raw file 12/12: B9_G_DIA_nLC_tTOF_R6 
3 days, 0:02:29.672595 INFO: Quantification results path: plasma_output/alphadia_2.1.0/quant
3 days, 0:02:29.672676 INFO: Creating folder plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R6/figures
3 days, 0:02:29.672875 INFO: Initializing TimingManager
3 days, 0:02:29.673311 INFO: Initializing RawFileManager
3 days, 0:02:29.673456 INFO: Importing data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:29.673535 INFO: Using .d import for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:29.673577 INFO: Reading frame metadata for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:29.916856 INFO: Reading 22,623 frames with 408,184,843 detector events for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:33.788668 INFO: Indexing /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d...
3 days, 0:02:33.789905 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:33.791901 INFO: Fetching mobility values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:33.792154 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:33.792709 INFO: Opening handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:33.794359 INFO: Fetching mz values from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:33.818108 INFO: Closing handle for /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:33.818363 INFO: Indexing quadrupole dimension
3 days, 0:02:33.951147 INFO: Transposing detector events
3 days, 0:02:35.952484 INFO: Finished transposing data
3 days, 0:02:35.952631 INFO: Successfully imported data from /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
3 days, 0:02:35.952977 INFO: RT (min)            : 0.0 - 40.0
3 days, 0:02:35.953027 INFO: RT duration (sec)   : 2400.0
3 days, 0:02:35.953058 INFO: RT duration (min)   : 40.0
3 days, 0:02:35.953090 INFO: Cycle len (scans)   : 12
3 days, 0:02:35.953117 INFO: Cycle len (sec)     : 1.27
3 days, 0:02:35.953144 INFO: Number of cycles    : 1885
3 days, 0:02:35.953171 INFO: MS2 range (m/z)     : 374.4 - 1151.9
3 days, 0:02:35.953210 INFO: Creating DIA data object took: 6.279756784439087
3 days, 0:02:35.959236 INFO: Initializing CalibrationManager
3 days, 0:02:35.959508 INFO: Setting up calibration estimators ..
3 days, 0:02:35.959594 INFO: Found 1 estimator(s) in calibration group 'fragment'
3 days, 0:02:35.959678 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
3 days, 0:02:35.959760 INFO: Found 3 estimator(s) in calibration group 'precursor'
3 days, 0:02:35.959829 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
3 days, 0:02:35.959900 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
3 days, 0:02:35.959974 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
3 days, 0:02:35.960038 INFO: Done setting up calibration estimators.
3 days, 0:02:35.960160 INFO: Initializing OptimizationManager
3 days, 0:02:35.960268 INFO: initial parameter: ms1_error = 30
3 days, 0:02:35.960328 INFO: initial parameter: ms2_error = 30
3 days, 0:02:35.960387 INFO: initial parameter: rt_error = 1199.986106
3 days, 0:02:35.960444 INFO: initial parameter: mobility_error = 0.1
3 days, 0:02:35.960498 INFO: initial parameter: num_candidates = 1
3 days, 0:02:35.960553 INFO: initial parameter: fwhm_rt = 5
3 days, 0:02:35.960611 INFO: initial parameter: fwhm_mobility = 0.01
3 days, 0:02:35.960666 INFO: initial parameter: score_cutoff = 0
3 days, 0:02:35.960720 INFO: initial parameter: classifier_version = -1
3 days, 0:02:35.960811 PROGRESS: Initializing workflow B9_G_DIA_nLC_tTOF_R6
3 days, 0:02:35.961011 INFO: FDRManager: loading saved state not requested, will be initialized.
3 days, 0:02:35.961051 INFO: Initializing FDRManager
3 days, 0:02:35.961089 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
3 days, 0:02:35.968922 PROGRESS: Initializing spectral library: 13,761 target precursors potentially observable (0 removed)
3 days, 0:02:35.973893 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
3 days, 0:02:35.974232 INFO: Updating optimization_manager: rt_error            : 1199.986106 -> 1199.986106
3 days, 0:02:35.974346 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
3 days, 0:02:35.974551 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
3 days, 0:02:35.974645 PROGRESS: Starting initial search for precursors.
3 days, 0:02:35.974731 INFO: Starting optimization step 0.
3 days, 0:02:35.974797 PROGRESS: === Extracting elution groups 0 to 200 ===
3 days, 0:02:35.974869 INFO: Using python extraction backend
3 days, 0:02:35.974982 PROGRESS: Extracting batch of 399 precursors
3 days, 0:02:35.975053 INFO: === Search parameters used ===
3 days, 0:02:35.975110 INFO: rt_error       : 1199.986106
3 days, 0:02:35.975163 INFO: mobility_error : 0.1
3 days, 0:02:35.975215 INFO: num_candidates : 1
3 days, 0:02:35.975266 INFO: ms1_error      : 30
3 days, 0:02:35.975317 INFO: ms2_error      : 30
3 days, 0:02:35.975367 INFO: fwhm_rt        : 5
3 days, 0:02:35.975418 INFO: quant_window   : 3
3 days, 0:02:35.975468 INFO: ==============================================
3 days, 0:02:35.976214 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:02:35.976266 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:02:35.976298 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
3 days, 0:02:35.976325 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
3 days, 0:02:35.989975 INFO: Starting candidate selection
3 days, 0:02:39.216897 INFO: Starting candidate scoring
3 days, 0:02:39.263120 INFO: Finished candidate processing
3 days, 0:02:39.263256 INFO: Collecting candidate features
3 days, 0:02:39.275616 INFO: Collecting fragment features
3 days, 0:02:39.278029 INFO: Finished candidate scoring
3 days, 0:02:39.278849 INFO: performing precursor FDR with 47 features
3 days, 0:02:39.278896 INFO: Decoy channel: -1
3 days, 0:02:39.278921 INFO: competitive: True
3 days, 0:02:39.280157 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:02:39.281879 INFO: Estimating optimal hyperparameters - samples: 319, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:02:39.282665 INFO: Using random state 822507 for train-test-split
3 days, 0:02:39.307735 INFO: Test AUC: 0.476
3 days, 0:02:39.307852 INFO: Train AUC: 0.468
3 days, 0:02:39.307898 INFO: AUC difference: 1.62%
3 days, 0:02:39.611771 INFO: Resetting torch num_threads to 80
3 days, 0:02:39.612309 PROGRESS: === Extracted 399 precursors and 3740 fragments ===
3 days, 0:02:39.612755 INFO: === FDR correction performed with classifier version -1 ===
3 days, 0:02:39.613341 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:02:39.613445 PROGRESS: Total precursors accumulated: 200
3 days, 0:02:39.613516 PROGRESS: Target precursors: 94 (47.00%)
3 days, 0:02:39.613570 PROGRESS: Decoy precursors: 106 (53.00%)
3 days, 0:02:39.613622 PROGRESS: 
3 days, 0:02:39.613672 PROGRESS: Precursor Summary:
3 days, 0:02:39.614653 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
3 days, 0:02:39.614775 PROGRESS: 
3 days, 0:02:39.614843 PROGRESS: Protein Summary:
3 days, 0:02:39.615899 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
3 days, 0:02:39.616008 PROGRESS: =========================================================================
3 days, 0:02:39.616137 INFO: Target number of precursors not reached yet.
3 days, 0:02:39.618936 INFO: Starting optimization step 1.
3 days, 0:02:39.619051 PROGRESS: === Extracting elution groups 200 to 600 ===
3 days, 0:02:39.619169 INFO: Using python extraction backend
3 days, 0:02:39.619298 PROGRESS: Extracting batch of 798 precursors
3 days, 0:02:39.619391 INFO: === Search parameters used ===
3 days, 0:02:39.619467 INFO: rt_error       : 1199.986106
3 days, 0:02:39.619534 INFO: mobility_error : 0.1
3 days, 0:02:39.619600 INFO: num_candidates : 1
3 days, 0:02:39.619666 INFO: ms1_error      : 30
3 days, 0:02:39.619746 INFO: ms2_error      : 30
3 days, 0:02:39.619812 INFO: fwhm_rt        : 5
3 days, 0:02:39.619876 INFO: quant_window   : 3
3 days, 0:02:39.619942 INFO: ==============================================
3 days, 0:02:39.620619 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:02:39.620673 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:02:39.620718 INFO: FWHM in RT is 5.00 seconds, sigma is 0.83
3 days, 0:02:39.620747 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 5.42
3 days, 0:02:39.637998 INFO: Starting candidate selection
3 days, 0:02:44.512119 INFO: Starting candidate scoring
3 days, 0:02:44.582592 INFO: Finished candidate processing
3 days, 0:02:44.582728 INFO: Collecting candidate features
3 days, 0:02:44.601664 INFO: Collecting fragment features
3 days, 0:02:44.605832 INFO: Finished candidate scoring
3 days, 0:02:44.609111 INFO: performing precursor FDR with 47 features
3 days, 0:02:44.609201 INFO: Decoy channel: -1
3 days, 0:02:44.609239 INFO: competitive: True
3 days, 0:02:44.614094 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:02:44.617013 INFO: Estimating optimal hyperparameters - samples: 957, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:02:44.617138 INFO: Using random state 109981 for train-test-split
3 days, 0:02:44.712142 INFO: Test AUC: 0.775
3 days, 0:02:44.712248 INFO: Train AUC: 0.809
3 days, 0:02:44.712281 INFO: AUC difference: 4.21%
3 days, 0:02:45.028919 INFO: Resetting torch num_threads to 80
3 days, 0:02:45.030720 PROGRESS: === Extracted 1197 precursors and 11505 fragments ===
3 days, 0:02:45.031309 INFO: === FDR correction performed with classifier version -1 ===
3 days, 0:02:45.032254 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:02:45.032371 PROGRESS: Total precursors accumulated: 600
3 days, 0:02:45.032455 PROGRESS: Target precursors: 484 (80.67%)
3 days, 0:02:45.032536 PROGRESS: Decoy precursors: 116 (19.33%)
3 days, 0:02:45.032607 PROGRESS: 
3 days, 0:02:45.032676 PROGRESS: Precursor Summary:
3 days, 0:02:45.034550 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   213; 0.001 FDR:   147
3 days, 0:02:45.034681 PROGRESS: 
3 days, 0:02:45.034807 PROGRESS: Protein Summary:
3 days, 0:02:45.036849 PROGRESS: Channel   0:	 0.050 FDR:   226; 0.010 FDR:   161; 0.001 FDR:   109
3 days, 0:02:45.036980 PROGRESS: =========================================================================
3 days, 0:02:45.037207 INFO: Target number of precursors reached.
3 days, 0:02:45.042349 INFO: fragments_df: keeping 1836 of 11505 [sum(precursor_idx_mask)=2167 sum(mass_error_mask)=11505 stop_rank=1836
3 days, 0:02:45.047218 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:02:45.241935 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:02:45.452852 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:02:45.651313 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:02:46.102219 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
3 days, 0:02:46.102770 INFO: Using score_cutoff 34.14782349700928 (fac=0.99, q=1)
3 days, 0:02:46.103235 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.9136712551116943
3 days, 0:02:46.103360 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.00780184892937541
3 days, 0:02:46.103461 INFO: Updating optimization_manager: score_cutoff        : 0 -> 34.14782349700928
3 days, 0:02:46.103562 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:02:46.105100 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:02:46.106903 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:02:46.108109 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:02:46.110692 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
3 days, 0:02:46.110831 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3 days, 0:02:46.110976 INFO: Starting optimization step 2.
3 days, 0:02:46.111077 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:02:46.111182 INFO: Using python extraction backend
3 days, 0:02:46.111348 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:02:46.111463 INFO: === Search parameters used ===
3 days, 0:02:46.111557 INFO: rt_error       : 1199.986106
3 days, 0:02:46.111638 INFO: mobility_error : 0.1
3 days, 0:02:46.111713 INFO: num_candidates : 3
3 days, 0:02:46.111789 INFO: ms1_error      : 30
3 days, 0:02:46.111871 INFO: ms2_error      : 30
3 days, 0:02:46.111953 INFO: fwhm_rt        : 2.9136712551116943
3 days, 0:02:46.112034 INFO: quant_window   : 3
3 days, 0:02:46.112118 INFO: ==============================================
3 days, 0:02:46.113347 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:02:46.113413 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:02:46.113475 INFO: FWHM in RT is 2.91 seconds, sigma is 0.49
3 days, 0:02:46.113523 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.23
3 days, 0:02:46.118748 INFO: Starting candidate selection
3 days, 0:02:53.747207 INFO: Starting candidate scoring
3 days, 0:02:53.892272 INFO: Finished candidate processing
3 days, 0:02:53.892513 INFO: Collecting candidate features
3 days, 0:02:53.914444 INFO: Collecting fragment features
3 days, 0:02:53.918658 INFO: Finished candidate scoring
3 days, 0:02:53.920695 INFO: performing precursor FDR with 47 features
3 days, 0:02:53.920771 INFO: Decoy channel: -1
3 days, 0:02:53.920804 INFO: competitive: True
3 days, 0:02:53.923985 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:02:53.926372 INFO: Estimating optimal hyperparameters - samples: 2,740, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:02:53.926487 INFO: Using random state 892506 for train-test-split
3 days, 0:02:54.179352 INFO: Test AUC: 0.689
3 days, 0:02:54.179467 INFO: Train AUC: 0.728
3 days, 0:02:54.179503 INFO: AUC difference: 5.44%
3 days, 0:02:54.179526 WARNING: AUC difference > 5%. This may indicate overfitting.
3 days, 0:02:54.427448 INFO: Resetting torch num_threads to 80
3 days, 0:02:54.428035 PROGRESS: === Extracted 3425 precursors and 31911 fragments ===
3 days, 0:02:54.428499 INFO: === FDR correction performed with classifier version 1 ===
3 days, 0:02:54.429160 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:02:54.429287 PROGRESS: Total precursors accumulated: 600
3 days, 0:02:54.429384 PROGRESS: Target precursors: 498 (83.00%)
3 days, 0:02:54.429469 PROGRESS: Decoy precursors: 102 (17.00%)
3 days, 0:02:54.429542 PROGRESS: 
3 days, 0:02:54.429616 PROGRESS: Precursor Summary:
3 days, 0:02:54.430740 PROGRESS: Channel   0:	 0.050 FDR:   249; 0.010 FDR:     3; 0.001 FDR:     3
3 days, 0:02:54.430857 PROGRESS: 
3 days, 0:02:54.430951 PROGRESS: Protein Summary:
3 days, 0:02:54.432112 PROGRESS: Channel   0:	 0.050 FDR:   188; 0.010 FDR:     3; 0.001 FDR:     3
3 days, 0:02:54.432225 PROGRESS: =========================================================================
3 days, 0:02:54.432414 INFO: Target number of precursors not reached yet.
3 days, 0:02:54.435894 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:02:54.436982 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:02:54.438708 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:02:54.439615 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:02:54.442201 INFO: === skipping optimization until target number of precursors are found ===
3 days, 0:02:54.442351 INFO: Starting optimization step 3.
3 days, 0:02:54.442449 PROGRESS: === Extracting elution groups 600 to 1400 ===
3 days, 0:02:54.442552 INFO: Using python extraction backend
3 days, 0:02:54.442744 PROGRESS: Extracting batch of 1599 precursors
3 days, 0:02:54.442870 INFO: === Search parameters used ===
3 days, 0:02:54.442951 INFO: rt_error       : 1199.986106
3 days, 0:02:54.443047 INFO: mobility_error : 0.1
3 days, 0:02:54.443128 INFO: num_candidates : 3
3 days, 0:02:54.443208 INFO: ms1_error      : 30
3 days, 0:02:54.443282 INFO: ms2_error      : 30
3 days, 0:02:54.443361 INFO: fwhm_rt        : 2.9136712551116943
3 days, 0:02:54.443435 INFO: quant_window   : 3
3 days, 0:02:54.443491 INFO: ==============================================
3 days, 0:02:54.444390 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:02:54.444448 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:02:54.444490 INFO: FWHM in RT is 2.91 seconds, sigma is 0.49
3 days, 0:02:54.444521 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 4.23
3 days, 0:02:54.464582 INFO: Starting candidate selection
3 days, 0:03:04.909695 INFO: Starting candidate scoring
3 days, 0:03:05.100297 INFO: Finished candidate processing
3 days, 0:03:05.100441 INFO: Collecting candidate features
3 days, 0:03:05.127551 INFO: Collecting fragment features
3 days, 0:03:05.134150 INFO: Finished candidate scoring
3 days, 0:03:05.140101 INFO: performing precursor FDR with 47 features
3 days, 0:03:05.140212 INFO: Decoy channel: -1
3 days, 0:03:05.140249 INFO: competitive: True
3 days, 0:03:05.144821 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:05.147969 INFO: Estimating optimal hyperparameters - samples: 6,405, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:05.148101 INFO: Using random state 892506 for train-test-split
3 days, 0:03:06.049766 INFO: Test AUC: 0.714
3 days, 0:03:06.049927 INFO: Train AUC: 0.733
3 days, 0:03:06.049987 INFO: AUC difference: 2.60%
3 days, 0:03:06.397377 INFO: Resetting torch num_threads to 80
3 days, 0:03:06.400324 PROGRESS: === Extracted 8007 precursors and 74980 fragments ===
3 days, 0:03:06.400956 INFO: === FDR correction performed with classifier version 1 ===
3 days, 0:03:06.402007 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:06.402140 PROGRESS: Total precursors accumulated: 1,400
3 days, 0:03:06.402243 PROGRESS: Target precursors: 1,179 (84.21%)
3 days, 0:03:06.402339 PROGRESS: Decoy precursors: 221 (15.79%)
3 days, 0:03:06.402432 PROGRESS: 
3 days, 0:03:06.402527 PROGRESS: Precursor Summary:
3 days, 0:03:06.404582 PROGRESS: Channel   0:	 0.050 FDR:   884; 0.010 FDR:   741; 0.001 FDR:   562
3 days, 0:03:06.404711 PROGRESS: 
3 days, 0:03:06.404813 PROGRESS: Protein Summary:
3 days, 0:03:06.407234 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:   435; 0.001 FDR:   330
3 days, 0:03:06.407371 PROGRESS: =========================================================================
3 days, 0:03:06.407637 INFO: Target number of precursors reached.
3 days, 0:03:06.430281 INFO: fragments_df: keeping 5000 of 74980 [sum(precursor_idx_mask)=21245 sum(mass_error_mask)=74980 stop_rank=5000
3 days, 0:03:06.436194 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:06.713893 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:06.965782 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:07.220867 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:08.071961 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:08.072403 INFO: Using score_cutoff 32.87235813903809 (fac=0.99, q=1)
3 days, 0:03:08.072742 INFO: Updating optimization_manager: fwhm_rt             : 2.9136712551116943 -> 2.963731050491333
3 days, 0:03:08.072830 INFO: Updating optimization_manager: fwhm_mobility       : 0.00780184892937541 -> 0.0066536301746964455
3 days, 0:03:08.072891 INFO: Updating optimization_manager: score_cutoff        : 34.14782349700928 -> 32.87235813903809
3 days, 0:03:08.072952 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:08.074059 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:08.075459 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:08.076250 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:08.078210 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:08.079836 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.061591994505577
3 days, 0:03:08.079941 INFO: Updating optimization_manager: classifier_version  : 1 -> 3
3 days, 0:03:08.080024 PROGRESS: ❌ ms2_error      : 15.0616 > 15.0000 or insufficient steps taken.
3 days, 0:03:08.081074 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
3 days, 0:03:08.081172 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
3 days, 0:03:08.081242 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
3 days, 0:03:08.081300 INFO: ==============================================
3 days, 0:03:08.081368 INFO: Starting optimization step 4.
3 days, 0:03:08.081429 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:08.081487 INFO: Using python extraction backend
3 days, 0:03:08.081583 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:08.081649 INFO: === Search parameters used ===
3 days, 0:03:08.081701 INFO: rt_error       : 1199.986106
3 days, 0:03:08.081747 INFO: mobility_error : 0.1
3 days, 0:03:08.081791 INFO: num_candidates : 3
3 days, 0:03:08.081836 INFO: ms1_error      : 15.0
3 days, 0:03:08.081897 INFO: ms2_error      : 15.061591994505577
3 days, 0:03:08.081949 INFO: fwhm_rt        : 2.963731050491333
3 days, 0:03:08.081994 INFO: quant_window   : 3
3 days, 0:03:08.082036 INFO: ==============================================
3 days, 0:03:08.082891 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:08.082942 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:08.082977 INFO: FWHM in RT is 2.96 seconds, sigma is 0.49
3 days, 0:03:08.083002 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.61
3 days, 0:03:08.094010 INFO: Starting candidate selection
3 days, 0:03:16.248804 INFO: Starting candidate scoring
3 days, 0:03:16.358169 INFO: Finished candidate processing
3 days, 0:03:16.358311 INFO: Collecting candidate features
3 days, 0:03:16.370803 WARNING: intensity_correlation has 4 NaNs ( 0.12 % out of 3412)
3 days, 0:03:16.377016 INFO: Collecting fragment features
3 days, 0:03:16.381773 INFO: Finished candidate scoring
3 days, 0:03:16.384129 INFO: performing precursor FDR with 47 features
3 days, 0:03:16.384200 INFO: Decoy channel: -1
3 days, 0:03:16.384233 INFO: competitive: True
3 days, 0:03:16.388104 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:16.390070 WARNING: dropped 3 target PSMs due to missing features
3 days, 0:03:16.390142 WARNING: dropped 1 decoy PSMs due to missing features
3 days, 0:03:16.391402 INFO: Estimating optimal hyperparameters - samples: 2,726, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:16.391501 INFO: Using random state 608593 for train-test-split
3 days, 0:03:16.744517 INFO: Test AUC: 0.744
3 days, 0:03:16.744658 INFO: Train AUC: 0.778
3 days, 0:03:16.744721 INFO: AUC difference: 4.29%
3 days, 0:03:17.131819 INFO: Resetting torch num_threads to 80
3 days, 0:03:17.132394 PROGRESS: === Extracted 3412 precursors and 28315 fragments ===
3 days, 0:03:17.132859 INFO: === FDR correction performed with classifier version 3 ===
3 days, 0:03:17.133524 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:17.133645 PROGRESS: Total precursors accumulated: 600
3 days, 0:03:17.133738 PROGRESS: Target precursors: 539 (89.83%)
3 days, 0:03:17.133819 PROGRESS: Decoy precursors: 61 (10.17%)
3 days, 0:03:17.133901 PROGRESS: 
3 days, 0:03:17.133974 PROGRESS: Precursor Summary:
3 days, 0:03:17.135120 PROGRESS: Channel   0:	 0.050 FDR:   472; 0.010 FDR:   414; 0.001 FDR:   259
3 days, 0:03:17.135231 PROGRESS: 
3 days, 0:03:17.135316 PROGRESS: Protein Summary:
3 days, 0:03:17.136645 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   311; 0.001 FDR:   197
3 days, 0:03:17.136756 PROGRESS: =========================================================================
3 days, 0:03:17.136991 INFO: Target number of precursors reached.
3 days, 0:03:17.143483 INFO: fragments_df: keeping 5000 of 28315 [sum(precursor_idx_mask)=10879 sum(mass_error_mask)=28315 stop_rank=5000
3 days, 0:03:17.147490 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:17.355924 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:17.553754 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:17.755177 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:18.693127 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:18.693981 INFO: Using score_cutoff 25.54223563785553 (fac=0.99, q=1)
3 days, 0:03:18.694657 INFO: Updating optimization_manager: fwhm_rt             : 2.963731050491333 -> 2.754840135574341
3 days, 0:03:18.694907 INFO: Updating optimization_manager: fwhm_mobility       : 0.0066536301746964455 -> 0.005206970497965813
3 days, 0:03:18.695085 INFO: Updating optimization_manager: score_cutoff        : 32.87235813903809 -> 25.54223563785553
3 days, 0:03:18.695265 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:18.696870 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:18.699383 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:18.700819 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:18.703396 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:18.705728 INFO: Updating optimization_manager: ms2_error           : 15.061591994505577 -> 15.0
3 days, 0:03:18.705915 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
3 days, 0:03:18.706169 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3 days, 0:03:18.707915 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
3 days, 0:03:18.708083 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
3 days, 0:03:18.708203 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
3 days, 0:03:18.708409 INFO: ==============================================
3 days, 0:03:18.708624 PROGRESS: Optimization finished for ms2_error, ms1_error.
3 days, 0:03:18.713342 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:18.714813 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:18.716637 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:18.717990 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:18.720538 INFO: Starting optimization step 0.
3 days, 0:03:18.720784 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:18.721011 INFO: Using python extraction backend
3 days, 0:03:18.721272 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:18.721468 INFO: === Search parameters used ===
3 days, 0:03:18.721662 INFO: rt_error       : 1199.986106
3 days, 0:03:18.721845 INFO: mobility_error : 0.1
3 days, 0:03:18.722043 INFO: num_candidates : 3
3 days, 0:03:18.722215 INFO: ms1_error      : 15.0
3 days, 0:03:18.722395 INFO: ms2_error      : 15.0
3 days, 0:03:18.722558 INFO: fwhm_rt        : 2.754840135574341
3 days, 0:03:18.722723 INFO: quant_window   : 3
3 days, 0:03:18.722889 INFO: ==============================================
3 days, 0:03:18.724305 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:18.724441 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:18.724557 INFO: FWHM in RT is 2.75 seconds, sigma is 0.46
3 days, 0:03:18.724648 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.82
3 days, 0:03:18.731557 INFO: Starting candidate selection
3 days, 0:03:26.756994 INFO: Starting candidate scoring
3 days, 0:03:26.866369 INFO: Finished candidate processing
3 days, 0:03:26.866510 INFO: Collecting candidate features
3 days, 0:03:26.882520 WARNING: intensity_correlation has 3 NaNs ( 0.09 % out of 3399)
3 days, 0:03:26.888932 INFO: Collecting fragment features
3 days, 0:03:26.893179 INFO: Finished candidate scoring
3 days, 0:03:26.895191 INFO: performing precursor FDR with 47 features
3 days, 0:03:26.895269 INFO: Decoy channel: -1
3 days, 0:03:26.895307 INFO: competitive: True
3 days, 0:03:26.898554 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:26.900019 WARNING: dropped 3 target PSMs due to missing features
3 days, 0:03:26.901130 INFO: Estimating optimal hyperparameters - samples: 2,716, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:26.901224 INFO: Using random state 114982 for train-test-split
3 days, 0:03:27.136249 INFO: Test AUC: 0.771
3 days, 0:03:27.136363 INFO: Train AUC: 0.801
3 days, 0:03:27.136409 INFO: AUC difference: 3.76%
3 days, 0:03:27.437491 INFO: Resetting torch num_threads to 80
3 days, 0:03:27.438037 PROGRESS: === Extracted 3399 precursors and 28037 fragments ===
3 days, 0:03:27.438492 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:03:27.439171 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:27.439277 PROGRESS: Total precursors accumulated: 600
3 days, 0:03:27.439344 PROGRESS: Target precursors: 532 (88.67%)
3 days, 0:03:27.439403 PROGRESS: Decoy precursors: 68 (11.33%)
3 days, 0:03:27.439457 PROGRESS: 
3 days, 0:03:27.439511 PROGRESS: Precursor Summary:
3 days, 0:03:27.440669 PROGRESS: Channel   0:	 0.050 FDR:   450; 0.010 FDR:   421; 0.001 FDR:   294
3 days, 0:03:27.440781 PROGRESS: 
3 days, 0:03:27.440845 PROGRESS: Protein Summary:
3 days, 0:03:27.442178 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   316; 0.001 FDR:   225
3 days, 0:03:27.442279 PROGRESS: =========================================================================
3 days, 0:03:27.442426 INFO: Target number of precursors reached.
3 days, 0:03:27.448885 INFO: fragments_df: keeping 5000 of 28037 [sum(precursor_idx_mask)=11033 sum(mass_error_mask)=28037 stop_rank=5000
3 days, 0:03:27.452363 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:27.637349 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:27.803017 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:28.006341 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:28.816981 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:28.817530 INFO: Using score_cutoff 24.88585648727417 (fac=0.99, q=1)
3 days, 0:03:28.818015 INFO: Updating optimization_manager: fwhm_rt             : 2.754840135574341 -> 2.7293741703033447
3 days, 0:03:28.818147 INFO: Updating optimization_manager: fwhm_mobility       : 0.005206970497965813 -> 0.004970097448676825
3 days, 0:03:28.818237 INFO: Updating optimization_manager: score_cutoff        : 25.54223563785553 -> 24.88585648727417
3 days, 0:03:28.818324 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:28.819513 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:28.821043 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:28.821967 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:28.824230 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:28.824362 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3 days, 0:03:28.826105 INFO: Updating optimization_manager: rt_error            : 1199.986106 -> 289.07937108536925
3 days, 0:03:28.826238 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 289.0794.
3 days, 0:03:28.826335 INFO: ==============================================
3 days, 0:03:28.826441 INFO: Starting optimization step 1.
3 days, 0:03:28.826534 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:28.826626 INFO: Using python extraction backend
3 days, 0:03:28.826762 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:28.826859 INFO: === Search parameters used ===
3 days, 0:03:28.826940 INFO: rt_error       : 289.07937108536925
3 days, 0:03:28.827027 INFO: mobility_error : 0.1
3 days, 0:03:28.827098 INFO: num_candidates : 3
3 days, 0:03:28.827170 INFO: ms1_error      : 15.0
3 days, 0:03:28.827238 INFO: ms2_error      : 15.0
3 days, 0:03:28.827306 INFO: fwhm_rt        : 2.7293741703033447
3 days, 0:03:28.827375 INFO: quant_window   : 3
3 days, 0:03:28.827442 INFO: ==============================================
3 days, 0:03:28.828364 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:28.828424 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:28.828481 INFO: FWHM in RT is 2.73 seconds, sigma is 0.46
3 days, 0:03:28.828520 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.69
3 days, 0:03:28.835205 INFO: Starting candidate selection
3 days, 0:03:31.965317 INFO: Starting candidate scoring
3 days, 0:03:32.085765 INFO: Finished candidate processing
3 days, 0:03:32.085938 INFO: Collecting candidate features
3 days, 0:03:32.102185 WARNING: intensity_correlation has 10 NaNs ( 0.30 % out of 3349)
3 days, 0:03:32.102501 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3349)
3 days, 0:03:32.109588 INFO: Collecting fragment features
3 days, 0:03:32.114059 INFO: Finished candidate scoring
3 days, 0:03:32.115962 INFO: performing precursor FDR with 47 features
3 days, 0:03:32.116023 INFO: Decoy channel: -1
3 days, 0:03:32.116049 INFO: competitive: True
3 days, 0:03:32.119185 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:32.120783 WARNING: dropped 6 target PSMs due to missing features
3 days, 0:03:32.120836 WARNING: dropped 4 decoy PSMs due to missing features
3 days, 0:03:32.121893 INFO: Estimating optimal hyperparameters - samples: 2,671, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:32.121984 INFO: Using random state 114982 for train-test-split
3 days, 0:03:32.426602 INFO: Test AUC: 0.777
3 days, 0:03:32.426723 INFO: Train AUC: 0.822
3 days, 0:03:32.426774 INFO: AUC difference: 5.46%
3 days, 0:03:32.426813 WARNING: AUC difference > 5%. This may indicate overfitting.
3 days, 0:03:32.767088 INFO: Resetting torch num_threads to 80
3 days, 0:03:32.767840 PROGRESS: === Extracted 3349 precursors and 27008 fragments ===
3 days, 0:03:32.768443 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:03:32.769398 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:32.769540 PROGRESS: Total precursors accumulated: 600
3 days, 0:03:32.769657 PROGRESS: Target precursors: 556 (92.67%)
3 days, 0:03:32.769767 PROGRESS: Decoy precursors: 44 (7.33%)
3 days, 0:03:32.769879 PROGRESS: 
3 days, 0:03:32.769982 PROGRESS: Precursor Summary:
3 days, 0:03:32.771820 PROGRESS: Channel   0:	 0.050 FDR:   532; 0.010 FDR:   471; 0.001 FDR:   417
3 days, 0:03:32.771948 PROGRESS: 
3 days, 0:03:32.772043 PROGRESS: Protein Summary:
3 days, 0:03:32.774262 PROGRESS: Channel   0:	 0.050 FDR:   392; 0.010 FDR:   350; 0.001 FDR:   308
3 days, 0:03:32.774388 PROGRESS: =========================================================================
3 days, 0:03:32.774594 INFO: Target number of precursors reached.
3 days, 0:03:32.784851 INFO: fragments_df: keeping 5000 of 27008 [sum(precursor_idx_mask)=12294 sum(mass_error_mask)=27008 stop_rank=5000
3 days, 0:03:32.789989 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:32.995267 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:33.177965 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:33.393543 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:34.375893 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:34.376481 INFO: Using score_cutoff 23.89686784744263 (fac=0.99, q=1)
3 days, 0:03:34.376937 INFO: Updating optimization_manager: fwhm_rt             : 2.7293741703033447 -> 2.704671621322632
3 days, 0:03:34.377062 INFO: Updating optimization_manager: fwhm_mobility       : 0.004970097448676825 -> 0.004670589230954647
3 days, 0:03:34.377172 INFO: Updating optimization_manager: score_cutoff        : 24.88585648727417 -> 23.89686784744263
3 days, 0:03:34.377274 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:34.378833 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:34.380638 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:34.381719 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:34.384179 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:34.384319 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3 days, 0:03:34.386768 INFO: Updating optimization_manager: rt_error            : 289.07937108536925 -> 21.455832851158544
3 days, 0:03:34.386900 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 21.4558.
3 days, 0:03:34.387002 INFO: ==============================================
3 days, 0:03:34.387106 INFO: Starting optimization step 2.
3 days, 0:03:34.387194 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:34.387284 INFO: Using python extraction backend
3 days, 0:03:34.387433 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:34.387531 INFO: === Search parameters used ===
3 days, 0:03:34.387609 INFO: rt_error       : 21.455832851158544
3 days, 0:03:34.387680 INFO: mobility_error : 0.1
3 days, 0:03:34.387750 INFO: num_candidates : 3
3 days, 0:03:34.387822 INFO: ms1_error      : 15.0
3 days, 0:03:34.387901 INFO: ms2_error      : 15.0
3 days, 0:03:34.387972 INFO: fwhm_rt        : 2.704671621322632
3 days, 0:03:34.388042 INFO: quant_window   : 3
3 days, 0:03:34.388109 INFO: ==============================================
3 days, 0:03:34.389271 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:34.389332 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:34.389375 INFO: FWHM in RT is 2.70 seconds, sigma is 0.45
3 days, 0:03:34.389405 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
3 days, 0:03:34.395478 INFO: Starting candidate selection
3 days, 0:03:35.020375 INFO: Starting candidate scoring
3 days, 0:03:35.128093 INFO: Finished candidate processing
3 days, 0:03:35.128236 INFO: Collecting candidate features
3 days, 0:03:35.141236 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3235)
3 days, 0:03:35.141477 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3235)
3 days, 0:03:35.147334 INFO: Collecting fragment features
3 days, 0:03:35.151775 INFO: Finished candidate scoring
3 days, 0:03:35.153947 INFO: performing precursor FDR with 47 features
3 days, 0:03:35.154005 INFO: Decoy channel: -1
3 days, 0:03:35.154058 INFO: competitive: True
3 days, 0:03:35.157773 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:35.159652 WARNING: dropped 4 target PSMs due to missing features
3 days, 0:03:35.159716 WARNING: dropped 15 decoy PSMs due to missing features
3 days, 0:03:35.160915 INFO: Estimating optimal hyperparameters - samples: 2,572, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:35.161006 INFO: Using random state 114982 for train-test-split
3 days, 0:03:35.466244 INFO: Test AUC: 0.851
3 days, 0:03:35.466365 INFO: Train AUC: 0.871
3 days, 0:03:35.466403 INFO: AUC difference: 2.29%
3 days, 0:03:35.766699 INFO: Resetting torch num_threads to 80
3 days, 0:03:35.767325 PROGRESS: === Extracted 3235 precursors and 23945 fragments ===
3 days, 0:03:35.767820 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:03:35.768533 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:35.768638 PROGRESS: Total precursors accumulated: 600
3 days, 0:03:35.768712 PROGRESS: Target precursors: 582 (97.00%)
3 days, 0:03:35.768797 PROGRESS: Decoy precursors: 18 (3.00%)
3 days, 0:03:35.768872 PROGRESS: 
3 days, 0:03:35.768943 PROGRESS: Precursor Summary:
3 days, 0:03:35.770349 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   545; 0.001 FDR:   510
3 days, 0:03:35.770493 PROGRESS: 
3 days, 0:03:35.770577 PROGRESS: Protein Summary:
3 days, 0:03:35.772226 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   406; 0.001 FDR:   382
3 days, 0:03:35.772352 PROGRESS: =========================================================================
3 days, 0:03:35.772530 INFO: Target number of precursors reached.
3 days, 0:03:35.781064 INFO: fragments_df: keeping 5000 of 23945 [sum(precursor_idx_mask)=13324 sum(mass_error_mask)=23945 stop_rank=5000
3 days, 0:03:35.785103 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:36.041536 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:36.209067 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:36.425633 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:37.184484 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:37.184960 INFO: Using score_cutoff 19.481773219299317 (fac=0.99, q=1)
3 days, 0:03:37.185318 INFO: Updating optimization_manager: fwhm_rt             : 2.704671621322632 -> 2.6195383071899414
3 days, 0:03:37.185418 INFO: Updating optimization_manager: fwhm_mobility       : 0.004670589230954647 -> 0.004206835757941008
3 days, 0:03:37.185499 INFO: Updating optimization_manager: score_cutoff        : 23.89686784744263 -> 19.481773219299317
3 days, 0:03:37.185576 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:37.186722 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:37.188152 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:37.188973 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:37.191221 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:37.191343 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3 days, 0:03:37.193321 INFO: Updating optimization_manager: rt_error            : 21.455832851158544 -> 9.983242759283742
3 days, 0:03:37.193436 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 9.9832.
3 days, 0:03:37.193515 INFO: ==============================================
3 days, 0:03:37.193594 INFO: Starting optimization step 3.
3 days, 0:03:37.193667 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:37.193737 INFO: Using python extraction backend
3 days, 0:03:37.193859 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:37.193960 INFO: === Search parameters used ===
3 days, 0:03:37.194023 INFO: rt_error       : 9.983242759283742
3 days, 0:03:37.194080 INFO: mobility_error : 0.1
3 days, 0:03:37.194133 INFO: num_candidates : 3
3 days, 0:03:37.194188 INFO: ms1_error      : 15.0
3 days, 0:03:37.194239 INFO: ms2_error      : 15.0
3 days, 0:03:37.194292 INFO: fwhm_rt        : 2.6195383071899414
3 days, 0:03:37.194343 INFO: quant_window   : 3
3 days, 0:03:37.194394 INFO: ==============================================
3 days, 0:03:37.195222 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:37.195275 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:37.195314 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:03:37.195343 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.28
3 days, 0:03:37.198710 INFO: Starting candidate selection
3 days, 0:03:37.772615 INFO: Starting candidate scoring
3 days, 0:03:37.893743 INFO: Finished candidate processing
3 days, 0:03:37.893847 INFO: Collecting candidate features
3 days, 0:03:37.903399 WARNING: intensity_correlation has 18 NaNs ( 0.56 % out of 3213)
3 days, 0:03:37.903613 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3213)
3 days, 0:03:37.907614 INFO: Collecting fragment features
3 days, 0:03:37.911420 INFO: Finished candidate scoring
3 days, 0:03:37.913254 INFO: performing precursor FDR with 47 features
3 days, 0:03:37.913314 INFO: Decoy channel: -1
3 days, 0:03:37.913342 INFO: competitive: True
3 days, 0:03:37.916476 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:37.918076 WARNING: dropped 3 target PSMs due to missing features
3 days, 0:03:37.918140 WARNING: dropped 15 decoy PSMs due to missing features
3 days, 0:03:37.919186 INFO: Estimating optimal hyperparameters - samples: 2,556, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:37.919277 INFO: Using random state 114982 for train-test-split
3 days, 0:03:38.217950 INFO: Test AUC: 0.852
3 days, 0:03:38.218072 INFO: Train AUC: 0.887
3 days, 0:03:38.218116 INFO: AUC difference: 3.88%
3 days, 0:03:38.551881 INFO: Resetting torch num_threads to 80
3 days, 0:03:38.552476 PROGRESS: === Extracted 3213 precursors and 23522 fragments ===
3 days, 0:03:38.552924 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:03:38.553553 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:38.553659 PROGRESS: Total precursors accumulated: 600
3 days, 0:03:38.553733 PROGRESS: Target precursors: 587 (97.83%)
3 days, 0:03:38.553798 PROGRESS: Decoy precursors: 13 (2.17%)
3 days, 0:03:38.553858 PROGRESS: 
3 days, 0:03:38.553938 PROGRESS: Precursor Summary:
3 days, 0:03:38.555097 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   558; 0.001 FDR:   538
3 days, 0:03:38.555201 PROGRESS: 
3 days, 0:03:38.555270 PROGRESS: Protein Summary:
3 days, 0:03:38.556639 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   419; 0.001 FDR:   403
3 days, 0:03:38.556738 PROGRESS: =========================================================================
3 days, 0:03:38.556884 INFO: Target number of precursors reached.
3 days, 0:03:38.563339 INFO: fragments_df: keeping 5000 of 23522 [sum(precursor_idx_mask)=13596 sum(mass_error_mask)=23522 stop_rank=5000
3 days, 0:03:38.567975 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:38.771459 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:39.020682 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:39.258776 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:40.198941 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:40.199393 INFO: Using score_cutoff 16.798719154930115 (fac=0.99, q=1)
3 days, 0:03:40.199729 INFO: Updating optimization_manager: fwhm_rt             : 2.6195383071899414 -> 2.618713140487671
3 days, 0:03:40.199814 INFO: Updating optimization_manager: fwhm_mobility       : 0.004206835757941008 -> 0.004122075159102678
3 days, 0:03:40.199874 INFO: Updating optimization_manager: score_cutoff        : 19.481773219299317 -> 16.798719154930115
3 days, 0:03:40.199934 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:40.201043 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:40.202430 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:40.203242 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:40.205156 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:40.205256 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3 days, 0:03:40.207274 INFO: Updating optimization_manager: rt_error            : 9.983242759283742 -> 9.140629962898418
3 days, 0:03:40.207390 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 9.1406.
3 days, 0:03:40.207463 INFO: ==============================================
3 days, 0:03:40.207541 INFO: Starting optimization step 4.
3 days, 0:03:40.207605 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:40.207669 INFO: Using python extraction backend
3 days, 0:03:40.207769 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:40.207838 INFO: === Search parameters used ===
3 days, 0:03:40.207891 INFO: rt_error       : 9.140629962898418
3 days, 0:03:40.207941 INFO: mobility_error : 0.1
3 days, 0:03:40.207989 INFO: num_candidates : 3
3 days, 0:03:40.208047 INFO: ms1_error      : 15.0
3 days, 0:03:40.208096 INFO: ms2_error      : 15.0
3 days, 0:03:40.208142 INFO: fwhm_rt        : 2.618713140487671
3 days, 0:03:40.208188 INFO: quant_window   : 3
3 days, 0:03:40.208233 INFO: ==============================================
3 days, 0:03:40.209044 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:40.209095 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:40.209131 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:03:40.209158 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.23
3 days, 0:03:40.216957 INFO: Starting candidate selection
3 days, 0:03:40.856045 INFO: Starting candidate scoring
3 days, 0:03:40.959748 INFO: Finished candidate processing
3 days, 0:03:40.959884 INFO: Collecting candidate features
3 days, 0:03:40.970554 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3214)
3 days, 0:03:40.970773 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3214)
3 days, 0:03:40.974778 INFO: Collecting fragment features
3 days, 0:03:40.978555 INFO: Finished candidate scoring
3 days, 0:03:40.980560 INFO: performing precursor FDR with 47 features
3 days, 0:03:40.980622 INFO: Decoy channel: -1
3 days, 0:03:40.980649 INFO: competitive: True
3 days, 0:03:40.983674 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:40.985240 WARNING: dropped 2 target PSMs due to missing features
3 days, 0:03:40.985296 WARNING: dropped 17 decoy PSMs due to missing features
3 days, 0:03:40.986331 INFO: Estimating optimal hyperparameters - samples: 2,556, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:40.986430 INFO: Using random state 114982 for train-test-split
3 days, 0:03:41.269018 INFO: Test AUC: 0.866
3 days, 0:03:41.269135 INFO: Train AUC: 0.887
3 days, 0:03:41.269177 INFO: AUC difference: 2.44%
3 days, 0:03:49.435769 INFO: Resetting torch num_threads to 80
3 days, 0:03:49.436667 PROGRESS: === Extracted 3214 precursors and 23547 fragments ===
3 days, 0:03:49.437269 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:03:49.438347 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:49.438487 PROGRESS: Total precursors accumulated: 600
3 days, 0:03:49.438594 PROGRESS: Target precursors: 584 (97.33%)
3 days, 0:03:49.438705 PROGRESS: Decoy precursors: 16 (2.67%)
3 days, 0:03:49.438809 PROGRESS: 
3 days, 0:03:49.438910 PROGRESS: Precursor Summary:
3 days, 0:03:49.440981 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   548; 0.001 FDR:   534
3 days, 0:03:49.441126 PROGRESS: 
3 days, 0:03:49.441234 PROGRESS: Protein Summary:
3 days, 0:03:49.443642 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   410; 0.001 FDR:   400
3 days, 0:03:49.443784 PROGRESS: =========================================================================
3 days, 0:03:49.444010 INFO: Target number of precursors reached.
3 days, 0:03:49.454378 INFO: fragments_df: keeping 5000 of 23547 [sum(precursor_idx_mask)=13435 sum(mass_error_mask)=23547 stop_rank=5000
3 days, 0:03:49.459765 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:49.704056 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:49.959178 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:50.189965 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:51.025523 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:51.026004 INFO: Using score_cutoff 18.59993828372955 (fac=0.99, q=1)
3 days, 0:03:51.026345 INFO: Updating optimization_manager: fwhm_rt             : 2.618713140487671 -> 2.6204147338867188
3 days, 0:03:51.026438 INFO: Updating optimization_manager: fwhm_mobility       : 0.004122075159102678 -> 0.004159810487180948
3 days, 0:03:51.026506 INFO: Updating optimization_manager: score_cutoff        : 16.798719154930115 -> 18.59993828372955
3 days, 0:03:51.026592 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:51.027847 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:51.029308 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:51.030185 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:51.032299 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:51.032421 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3 days, 0:03:51.034460 INFO: Updating optimization_manager: rt_error            : 9.140629962898418 -> 8.483719760328377
3 days, 0:03:51.034588 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 8.4837.
3 days, 0:03:51.034675 INFO: ==============================================
3 days, 0:03:51.034767 INFO: Starting optimization step 5.
3 days, 0:03:51.034860 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:51.034944 INFO: Using python extraction backend
3 days, 0:03:51.035061 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:51.035142 INFO: === Search parameters used ===
3 days, 0:03:51.035205 INFO: rt_error       : 8.483719760328377
3 days, 0:03:51.035260 INFO: mobility_error : 0.1
3 days, 0:03:51.035311 INFO: num_candidates : 3
3 days, 0:03:51.035362 INFO: ms1_error      : 15.0
3 days, 0:03:51.035413 INFO: ms2_error      : 15.0
3 days, 0:03:51.035462 INFO: fwhm_rt        : 2.6204147338867188
3 days, 0:03:51.035521 INFO: quant_window   : 3
3 days, 0:03:51.035574 INFO: ==============================================
3 days, 0:03:51.036512 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:51.036565 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:51.036608 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:03:51.036643 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.25
3 days, 0:03:51.049993 INFO: Starting candidate selection
3 days, 0:03:51.820708 INFO: Starting candidate scoring
3 days, 0:03:51.935938 INFO: Finished candidate processing
3 days, 0:03:51.936676 INFO: Collecting candidate features
3 days, 0:03:51.952616 WARNING: intensity_correlation has 20 NaNs ( 0.62 % out of 3220)
3 days, 0:03:51.952859 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3220)
3 days, 0:03:51.957321 INFO: Collecting fragment features
3 days, 0:03:51.961717 INFO: Finished candidate scoring
3 days, 0:03:51.967350 INFO: performing precursor FDR with 47 features
3 days, 0:03:51.967415 INFO: Decoy channel: -1
3 days, 0:03:51.967448 INFO: competitive: True
3 days, 0:03:51.970933 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:51.972797 WARNING: dropped 2 target PSMs due to missing features
3 days, 0:03:51.972856 WARNING: dropped 19 decoy PSMs due to missing features
3 days, 0:03:51.974043 INFO: Estimating optimal hyperparameters - samples: 2,559, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:51.974161 INFO: Using random state 114982 for train-test-split
3 days, 0:03:52.288813 INFO: Test AUC: 0.869
3 days, 0:03:52.288938 INFO: Train AUC: 0.883
3 days, 0:03:52.288977 INFO: AUC difference: 1.62%
3 days, 0:03:52.628406 INFO: Resetting torch num_threads to 80
3 days, 0:03:52.629138 PROGRESS: === Extracted 3220 precursors and 23536 fragments ===
3 days, 0:03:52.629609 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:03:52.630335 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:52.630448 PROGRESS: Total precursors accumulated: 600
3 days, 0:03:52.630535 PROGRESS: Target precursors: 583 (97.17%)
3 days, 0:03:52.630617 PROGRESS: Decoy precursors: 17 (2.83%)
3 days, 0:03:52.630689 PROGRESS: 
3 days, 0:03:52.630754 PROGRESS: Precursor Summary:
3 days, 0:03:52.632004 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   560; 0.001 FDR:   536
3 days, 0:03:52.632112 PROGRESS: 
3 days, 0:03:52.632184 PROGRESS: Protein Summary:
3 days, 0:03:52.633672 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   421; 0.001 FDR:   401
3 days, 0:03:52.633787 PROGRESS: =========================================================================
3 days, 0:03:52.633983 INFO: Target number of precursors reached.
3 days, 0:03:52.640767 INFO: fragments_df: keeping 5000 of 23536 [sum(precursor_idx_mask)=13647 sum(mass_error_mask)=23536 stop_rank=5000
3 days, 0:03:52.644735 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:52.826495 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:53.015872 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:53.194583 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:54.187002 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:54.187622 INFO: Using score_cutoff 17.462663547706605 (fac=0.99, q=1)
3 days, 0:03:54.188138 INFO: Updating optimization_manager: fwhm_rt             : 2.6204147338867188 -> 2.617318868637085
3 days, 0:03:54.188264 INFO: Updating optimization_manager: fwhm_mobility       : 0.004159810487180948 -> 0.004055087920278311
3 days, 0:03:54.188355 INFO: Updating optimization_manager: score_cutoff        : 18.59993828372955 -> 17.462663547706605
3 days, 0:03:54.188452 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:54.190166 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:54.192101 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:54.193325 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:54.195943 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:54.196100 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3 days, 0:03:54.199031 INFO: Updating optimization_manager: rt_error            : 8.483719760328377 -> 10.272713699097517
3 days, 0:03:54.199186 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 10.2727.
3 days, 0:03:54.199305 INFO: ==============================================
3 days, 0:03:54.199436 INFO: Starting optimization step 6.
3 days, 0:03:54.199577 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:54.199697 INFO: Using python extraction backend
3 days, 0:03:54.199890 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:54.200029 INFO: === Search parameters used ===
3 days, 0:03:54.200127 INFO: rt_error       : 10.272713699097517
3 days, 0:03:54.200221 INFO: mobility_error : 0.1
3 days, 0:03:54.200317 INFO: num_candidates : 3
3 days, 0:03:54.200413 INFO: ms1_error      : 15.0
3 days, 0:03:54.200507 INFO: ms2_error      : 15.0
3 days, 0:03:54.200593 INFO: fwhm_rt        : 2.617318868637085
3 days, 0:03:54.200686 INFO: quant_window   : 3
3 days, 0:03:54.200773 INFO: ==============================================
3 days, 0:03:54.202098 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:54.202274 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:54.202430 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:03:54.202543 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.20
3 days, 0:03:54.207553 INFO: Starting candidate selection
3 days, 0:03:54.863249 INFO: Starting candidate scoring
3 days, 0:03:54.979784 INFO: Finished candidate processing
3 days, 0:03:54.979916 INFO: Collecting candidate features
3 days, 0:03:54.996469 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3214)
3 days, 0:03:54.996803 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3214)
3 days, 0:03:55.004608 INFO: Collecting fragment features
3 days, 0:03:55.010444 INFO: Finished candidate scoring
3 days, 0:03:55.016497 INFO: performing precursor FDR with 47 features
3 days, 0:03:55.016586 INFO: Decoy channel: -1
3 days, 0:03:55.016616 INFO: competitive: True
3 days, 0:03:55.020145 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:55.021913 WARNING: dropped 3 target PSMs due to missing features
3 days, 0:03:55.021974 WARNING: dropped 16 decoy PSMs due to missing features
3 days, 0:03:55.023113 INFO: Estimating optimal hyperparameters - samples: 2,556, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:55.023204 INFO: Using random state 114982 for train-test-split
3 days, 0:03:55.270874 INFO: Test AUC: 0.881
3 days, 0:03:55.271005 INFO: Train AUC: 0.881
3 days, 0:03:55.271056 INFO: AUC difference: 0.07%
3 days, 0:03:55.597510 INFO: Resetting torch num_threads to 80
3 days, 0:03:55.598235 PROGRESS: === Extracted 3214 precursors and 23519 fragments ===
3 days, 0:03:55.598752 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:03:55.599484 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:55.599603 PROGRESS: Total precursors accumulated: 600
3 days, 0:03:55.599700 PROGRESS: Target precursors: 583 (97.17%)
3 days, 0:03:55.599795 PROGRESS: Decoy precursors: 17 (2.83%)
3 days, 0:03:55.599873 PROGRESS: 
3 days, 0:03:55.599951 PROGRESS: Precursor Summary:
3 days, 0:03:55.601644 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   561; 0.001 FDR:   530
3 days, 0:03:55.601896 PROGRESS: 
3 days, 0:03:55.602120 PROGRESS: Protein Summary:
3 days, 0:03:55.604297 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   420; 0.001 FDR:   396
3 days, 0:03:55.604422 PROGRESS: =========================================================================
3 days, 0:03:55.604658 INFO: Target number of precursors reached.
3 days, 0:03:55.614960 INFO: fragments_df: keeping 5000 of 23519 [sum(precursor_idx_mask)=13683 sum(mass_error_mask)=23519 stop_rank=5000
3 days, 0:03:55.620252 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:55.854639 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:56.035461 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:56.228739 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:57.113087 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:57.113589 INFO: Using score_cutoff 17.078162784576417 (fac=0.99, q=1)
3 days, 0:03:57.113968 INFO: Updating optimization_manager: fwhm_rt             : 2.617318868637085 -> 2.622786521911621
3 days, 0:03:57.114073 INFO: Updating optimization_manager: fwhm_mobility       : 0.004055087920278311 -> 0.004061401356011629
3 days, 0:03:57.114156 INFO: Updating optimization_manager: score_cutoff        : 17.462663547706605 -> 17.078162784576417
3 days, 0:03:57.114236 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:57.115503 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:57.117021 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:57.117940 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:57.120058 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:57.120188 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3 days, 0:03:57.122299 INFO: Updating optimization_manager: rt_error            : 10.272713699097517 -> 14.088610798769498
3 days, 0:03:57.122446 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 14.0886.
3 days, 0:03:57.122546 INFO: ==============================================
3 days, 0:03:57.122650 INFO: Starting optimization step 7.
3 days, 0:03:57.122741 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:57.122829 INFO: Using python extraction backend
3 days, 0:03:57.122974 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:57.123078 INFO: === Search parameters used ===
3 days, 0:03:57.123161 INFO: rt_error       : 14.088610798769498
3 days, 0:03:57.123234 INFO: mobility_error : 0.1
3 days, 0:03:57.123299 INFO: num_candidates : 3
3 days, 0:03:57.123360 INFO: ms1_error      : 15.0
3 days, 0:03:57.123420 INFO: ms2_error      : 15.0
3 days, 0:03:57.123479 INFO: fwhm_rt        : 2.622786521911621
3 days, 0:03:57.123538 INFO: quant_window   : 3
3 days, 0:03:57.123606 INFO: ==============================================
3 days, 0:03:57.124647 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:57.124711 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:57.124761 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:03:57.124797 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.20
3 days, 0:03:57.138034 INFO: Starting candidate selection
3 days, 0:03:57.664100 INFO: Starting candidate scoring
3 days, 0:03:57.776857 INFO: Finished candidate processing
3 days, 0:03:57.776983 INFO: Collecting candidate features
3 days, 0:03:57.789972 WARNING: intensity_correlation has 23 NaNs ( 0.72 % out of 3202)
3 days, 0:03:57.790233 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3202)
3 days, 0:03:57.796302 INFO: Collecting fragment features
3 days, 0:03:57.801090 INFO: Finished candidate scoring
3 days, 0:03:57.806239 INFO: performing precursor FDR with 47 features
3 days, 0:03:57.806314 INFO: Decoy channel: -1
3 days, 0:03:57.806346 INFO: competitive: True
3 days, 0:03:57.810374 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:03:57.812373 WARNING: dropped 5 target PSMs due to missing features
3 days, 0:03:57.812427 WARNING: dropped 18 decoy PSMs due to missing features
3 days, 0:03:57.812475 WARNING: FDR calculation for 1671 target and 1508 decoy PSMs
3 days, 0:03:57.812505 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3 days, 0:03:57.813747 INFO: Estimating optimal hyperparameters - samples: 2,543, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:03:57.813856 INFO: Using random state 114982 for train-test-split
3 days, 0:03:58.060076 INFO: Test AUC: 0.876
3 days, 0:03:58.060204 INFO: Train AUC: 0.884
3 days, 0:03:58.060240 INFO: AUC difference: 0.86%
3 days, 0:03:58.363754 INFO: Resetting torch num_threads to 80
3 days, 0:03:58.364442 PROGRESS: === Extracted 3202 precursors and 23447 fragments ===
3 days, 0:03:58.364917 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:03:58.365688 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:03:58.365790 PROGRESS: Total precursors accumulated: 600
3 days, 0:03:58.365878 PROGRESS: Target precursors: 584 (97.33%)
3 days, 0:03:58.365949 PROGRESS: Decoy precursors: 16 (2.67%)
3 days, 0:03:58.366014 PROGRESS: 
3 days, 0:03:58.366072 PROGRESS: Precursor Summary:
3 days, 0:03:58.367522 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   567; 0.001 FDR:   534
3 days, 0:03:58.367632 PROGRESS: 
3 days, 0:03:58.367701 PROGRESS: Protein Summary:
3 days, 0:03:58.369401 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   421; 0.001 FDR:   399
3 days, 0:03:58.369508 PROGRESS: =========================================================================
3 days, 0:03:58.369682 INFO: Target number of precursors reached.
3 days, 0:03:58.378477 INFO: fragments_df: keeping 5000 of 23447 [sum(precursor_idx_mask)=13813 sum(mass_error_mask)=23447 stop_rank=5000
3 days, 0:03:58.382686 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:58.597821 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:58.810366 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:59.024026 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:59.811986 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:03:59.812478 INFO: Using score_cutoff 17.246275467681883 (fac=0.99, q=1)
3 days, 0:03:59.812820 INFO: Updating optimization_manager: fwhm_rt             : 2.622786521911621 -> 2.6137924194335938
3 days, 0:03:59.812911 INFO: Updating optimization_manager: fwhm_mobility       : 0.004061401356011629 -> 0.004027172923088074
3 days, 0:03:59.812980 INFO: Updating optimization_manager: score_cutoff        : 17.078162784576417 -> 17.246275467681883
3 days, 0:03:59.813048 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:03:59.814270 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:03:59.815734 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:03:59.816582 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:03:59.818686 INFO: === checking if optimization conditions were reached ===
3 days, 0:03:59.818804 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
3 days, 0:03:59.820962 INFO: Updating optimization_manager: rt_error            : 14.088610798769498 -> 10.131665007384342
3 days, 0:03:59.821084 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 10.1317.
3 days, 0:03:59.821166 INFO: ==============================================
3 days, 0:03:59.821252 INFO: Starting optimization step 8.
3 days, 0:03:59.821339 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:03:59.821430 INFO: Using python extraction backend
3 days, 0:03:59.821567 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:03:59.821663 INFO: === Search parameters used ===
3 days, 0:03:59.821745 INFO: rt_error       : 10.131665007384342
3 days, 0:03:59.821818 INFO: mobility_error : 0.1
3 days, 0:03:59.821907 INFO: num_candidates : 3
3 days, 0:03:59.821984 INFO: ms1_error      : 15.0
3 days, 0:03:59.822054 INFO: ms2_error      : 15.0
3 days, 0:03:59.822121 INFO: fwhm_rt        : 2.6137924194335938
3 days, 0:03:59.822187 INFO: quant_window   : 3
3 days, 0:03:59.822253 INFO: ==============================================
3 days, 0:03:59.823213 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:03:59.823266 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:03:59.823317 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
3 days, 0:03:59.823359 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.18
3 days, 0:03:59.834264 INFO: Starting candidate selection
3 days, 0:04:00.484845 INFO: Starting candidate scoring
3 days, 0:04:00.600498 INFO: Finished candidate processing
3 days, 0:04:00.600631 INFO: Collecting candidate features
3 days, 0:04:00.613190 WARNING: intensity_correlation has 20 NaNs ( 0.62 % out of 3218)
3 days, 0:04:00.613471 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3218)
3 days, 0:04:00.617507 INFO: Collecting fragment features
3 days, 0:04:00.621798 INFO: Finished candidate scoring
3 days, 0:04:00.626272 INFO: performing precursor FDR with 47 features
3 days, 0:04:00.626350 INFO: Decoy channel: -1
3 days, 0:04:00.626388 INFO: competitive: True
3 days, 0:04:00.630021 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:00.631843 WARNING: dropped 3 target PSMs due to missing features
3 days, 0:04:00.631908 WARNING: dropped 17 decoy PSMs due to missing features
3 days, 0:04:00.633035 INFO: Estimating optimal hyperparameters - samples: 2,558, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:00.633145 INFO: Using random state 114982 for train-test-split
3 days, 0:04:00.877974 INFO: Test AUC: 0.868
3 days, 0:04:00.878080 INFO: Train AUC: 0.882
3 days, 0:04:00.878112 INFO: AUC difference: 1.54%
3 days, 0:04:01.191052 INFO: Resetting torch num_threads to 80
3 days, 0:04:01.191704 PROGRESS: === Extracted 3218 precursors and 23546 fragments ===
3 days, 0:04:01.192142 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:04:01.192826 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:01.192922 PROGRESS: Total precursors accumulated: 600
3 days, 0:04:01.192987 PROGRESS: Target precursors: 580 (96.67%)
3 days, 0:04:01.193043 PROGRESS: Decoy precursors: 20 (3.33%)
3 days, 0:04:01.193094 PROGRESS: 
3 days, 0:04:01.193143 PROGRESS: Precursor Summary:
3 days, 0:04:01.194395 PROGRESS: Channel   0:	 0.050 FDR:   580; 0.010 FDR:   560; 0.001 FDR:   514
3 days, 0:04:01.194509 PROGRESS: 
3 days, 0:04:01.194572 PROGRESS: Protein Summary:
3 days, 0:04:01.195975 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   419; 0.001 FDR:   387
3 days, 0:04:01.196083 PROGRESS: =========================================================================
3 days, 0:04:01.196229 INFO: Target number of precursors reached.
3 days, 0:04:01.202780 INFO: fragments_df: keeping 5000 of 23546 [sum(precursor_idx_mask)=13690 sum(mass_error_mask)=23546 stop_rank=5000
3 days, 0:04:01.206499 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:01.397601 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:01.591617 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:01.806531 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:02.571122 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:02.571643 INFO: Using score_cutoff 17.22268955154419 (fac=0.99, q=1)
3 days, 0:04:02.572002 INFO: Updating optimization_manager: fwhm_rt             : 2.6137924194335938 -> 2.6160364151000977
3 days, 0:04:02.572097 INFO: Updating optimization_manager: fwhm_mobility       : 0.004027172923088074 -> 0.004082782194018364
3 days, 0:04:02.572167 INFO: Updating optimization_manager: score_cutoff        : 17.246275467681883 -> 17.22268955154419
3 days, 0:04:02.572253 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:02.573622 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:02.575130 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:02.576021 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:02.578167 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:02.578302 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
3 days, 0:04:02.580387 INFO: Updating optimization_manager: rt_error            : 10.131665007384342 -> 8.871952367421088
3 days, 0:04:02.580517 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 8.8720.
3 days, 0:04:02.580615 INFO: ==============================================
3 days, 0:04:02.580700 INFO: Starting optimization step 9.
3 days, 0:04:02.580788 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:02.580880 INFO: Using python extraction backend
3 days, 0:04:02.581017 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:02.581111 INFO: === Search parameters used ===
3 days, 0:04:02.581191 INFO: rt_error       : 8.871952367421088
3 days, 0:04:02.581272 INFO: mobility_error : 0.1
3 days, 0:04:02.581343 INFO: num_candidates : 3
3 days, 0:04:02.581408 INFO: ms1_error      : 15.0
3 days, 0:04:02.581471 INFO: ms2_error      : 15.0
3 days, 0:04:02.581531 INFO: fwhm_rt        : 2.6160364151000977
3 days, 0:04:02.581593 INFO: quant_window   : 3
3 days, 0:04:02.581653 INFO: ==============================================
3 days, 0:04:02.582619 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:02.582675 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:02.582724 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:04:02.582758 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.21
3 days, 0:04:02.587042 INFO: Starting candidate selection
3 days, 0:04:03.214831 INFO: Starting candidate scoring
3 days, 0:04:03.333367 INFO: Finished candidate processing
3 days, 0:04:03.333480 INFO: Collecting candidate features
3 days, 0:04:03.346938 WARNING: intensity_correlation has 21 NaNs ( 0.65 % out of 3215)
3 days, 0:04:03.347186 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3215)
3 days, 0:04:03.352257 INFO: Collecting fragment features
3 days, 0:04:03.356848 INFO: Finished candidate scoring
3 days, 0:04:03.360625 INFO: performing precursor FDR with 47 features
3 days, 0:04:03.360696 INFO: Decoy channel: -1
3 days, 0:04:03.360724 INFO: competitive: True
3 days, 0:04:03.363912 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:03.365539 WARNING: dropped 2 target PSMs due to missing features
3 days, 0:04:03.365591 WARNING: dropped 19 decoy PSMs due to missing features
3 days, 0:04:03.366645 INFO: Estimating optimal hyperparameters - samples: 2,555, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:03.366740 INFO: Using random state 114982 for train-test-split
3 days, 0:04:03.714683 INFO: Test AUC: 0.868
3 days, 0:04:03.714794 INFO: Train AUC: 0.884
3 days, 0:04:03.714827 INFO: AUC difference: 1.90%
3 days, 0:04:04.026634 INFO: Resetting torch num_threads to 80
3 days, 0:04:04.027426 PROGRESS: === Extracted 3215 precursors and 23501 fragments ===
3 days, 0:04:04.027978 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:04:04.028909 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:04.029038 PROGRESS: Total precursors accumulated: 600
3 days, 0:04:04.029136 PROGRESS: Target precursors: 585 (97.50%)
3 days, 0:04:04.029227 PROGRESS: Decoy precursors: 15 (2.50%)
3 days, 0:04:04.029310 PROGRESS: 
3 days, 0:04:04.029397 PROGRESS: Precursor Summary:
3 days, 0:04:04.031374 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   570; 0.001 FDR:   528
3 days, 0:04:04.031541 PROGRESS: 
3 days, 0:04:04.031647 PROGRESS: Protein Summary:
3 days, 0:04:04.034001 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   423; 0.001 FDR:   395
3 days, 0:04:04.034148 PROGRESS: =========================================================================
3 days, 0:04:04.034367 INFO: Target number of precursors reached.
3 days, 0:04:04.044297 INFO: fragments_df: keeping 5000 of 23501 [sum(precursor_idx_mask)=13852 sum(mass_error_mask)=23501 stop_rank=5000
3 days, 0:04:04.049452 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:04.271762 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:04.497755 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:04.694163 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:05.572536 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:05.573144 INFO: Using score_cutoff 15.903597239112855 (fac=0.99, q=1)
3 days, 0:04:05.573635 INFO: Updating optimization_manager: fwhm_rt             : 2.6160364151000977 -> 2.607738494873047
3 days, 0:04:05.573749 INFO: Updating optimization_manager: fwhm_mobility       : 0.004082782194018364 -> 0.00401970325037837
3 days, 0:04:05.573828 INFO: Updating optimization_manager: score_cutoff        : 17.22268955154419 -> 15.903597239112855
3 days, 0:04:05.573924 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:05.575569 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:05.577509 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:05.578780 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:05.581379 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:05.581529 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
3 days, 0:04:05.584523 INFO: Updating optimization_manager: rt_error            : 8.871952367421088 -> 16.141454212720998
3 days, 0:04:05.584675 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 16.1415.
3 days, 0:04:05.584789 INFO: ==============================================
3 days, 0:04:05.584929 INFO: Starting optimization step 10.
3 days, 0:04:05.585050 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:05.585166 INFO: Using python extraction backend
3 days, 0:04:05.585333 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:05.585452 INFO: === Search parameters used ===
3 days, 0:04:05.585556 INFO: rt_error       : 16.141454212720998
3 days, 0:04:05.585660 INFO: mobility_error : 0.1
3 days, 0:04:05.585754 INFO: num_candidates : 3
3 days, 0:04:05.585841 INFO: ms1_error      : 15.0
3 days, 0:04:05.585932 INFO: ms2_error      : 15.0
3 days, 0:04:05.586011 INFO: fwhm_rt        : 2.607738494873047
3 days, 0:04:05.586105 INFO: quant_window   : 3
3 days, 0:04:05.586199 INFO: ==============================================
3 days, 0:04:05.587557 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:05.587625 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:05.587684 INFO: FWHM in RT is 2.61 seconds, sigma is 0.43
3 days, 0:04:05.587728 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.18
3 days, 0:04:05.599376 INFO: Starting candidate selection
3 days, 0:04:06.197575 INFO: Starting candidate scoring
3 days, 0:04:06.306388 INFO: Finished candidate processing
3 days, 0:04:06.306506 INFO: Collecting candidate features
3 days, 0:04:06.319397 WARNING: intensity_correlation has 26 NaNs ( 0.81 % out of 3199)
3 days, 0:04:06.319648 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3199)
3 days, 0:04:06.324670 INFO: Collecting fragment features
3 days, 0:04:06.329552 INFO: Finished candidate scoring
3 days, 0:04:06.333801 INFO: performing precursor FDR with 47 features
3 days, 0:04:06.333894 INFO: Decoy channel: -1
3 days, 0:04:06.333929 INFO: competitive: True
3 days, 0:04:06.338121 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:06.340165 WARNING: dropped 7 target PSMs due to missing features
3 days, 0:04:06.340227 WARNING: dropped 19 decoy PSMs due to missing features
3 days, 0:04:06.340275 WARNING: FDR calculation for 1669 target and 1504 decoy PSMs
3 days, 0:04:06.340302 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3 days, 0:04:06.341538 INFO: Estimating optimal hyperparameters - samples: 2,538, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:06.341647 INFO: Using random state 114982 for train-test-split
3 days, 0:04:06.650738 INFO: Test AUC: 0.868
3 days, 0:04:06.650860 INFO: Train AUC: 0.892
3 days, 0:04:06.650899 INFO: AUC difference: 2.63%
3 days, 0:04:06.954725 INFO: Resetting torch num_threads to 80
3 days, 0:04:06.955482 PROGRESS: === Extracted 3199 precursors and 23437 fragments ===
3 days, 0:04:06.955967 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:04:06.956764 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:06.956867 PROGRESS: Total precursors accumulated: 600
3 days, 0:04:06.956938 PROGRESS: Target precursors: 588 (98.00%)
3 days, 0:04:06.956999 PROGRESS: Decoy precursors: 12 (2.00%)
3 days, 0:04:06.957056 PROGRESS: 
3 days, 0:04:06.957111 PROGRESS: Precursor Summary:
3 days, 0:04:06.958617 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   574; 0.001 FDR:   531
3 days, 0:04:06.958745 PROGRESS: 
3 days, 0:04:06.958814 PROGRESS: Protein Summary:
3 days, 0:04:06.960508 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   425; 0.001 FDR:   397
3 days, 0:04:06.960615 PROGRESS: =========================================================================
3 days, 0:04:06.960786 INFO: Target number of precursors reached.
3 days, 0:04:06.969642 INFO: fragments_df: keeping 5000 of 23437 [sum(precursor_idx_mask)=14020 sum(mass_error_mask)=23437 stop_rank=5000
3 days, 0:04:06.974046 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:07.143595 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:07.408713 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:07.621824 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:08.433251 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:08.433706 INFO: Using score_cutoff 16.760726756858826 (fac=0.99, q=1)
3 days, 0:04:08.434047 INFO: Updating optimization_manager: fwhm_rt             : 2.607738494873047 -> 2.607738494873047
3 days, 0:04:08.434138 INFO: Updating optimization_manager: fwhm_mobility       : 0.00401970325037837 -> 0.004013802856206894
3 days, 0:04:08.434198 INFO: Updating optimization_manager: score_cutoff        : 15.903597239112855 -> 16.760726756858826
3 days, 0:04:08.434258 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:08.435446 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:08.436892 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:08.437733 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:08.439781 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:08.439894 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
3 days, 0:04:08.441899 INFO: Updating optimization_manager: rt_error            : 16.141454212720998 -> 11.485611523914736
3 days, 0:04:08.442019 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 11.4856.
3 days, 0:04:08.442087 INFO: ==============================================
3 days, 0:04:08.442164 INFO: Starting optimization step 11.
3 days, 0:04:08.442228 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:08.442290 INFO: Using python extraction backend
3 days, 0:04:08.442389 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:08.442456 INFO: === Search parameters used ===
3 days, 0:04:08.442508 INFO: rt_error       : 11.485611523914736
3 days, 0:04:08.442555 INFO: mobility_error : 0.1
3 days, 0:04:08.442602 INFO: num_candidates : 3
3 days, 0:04:08.442649 INFO: ms1_error      : 15.0
3 days, 0:04:08.442693 INFO: ms2_error      : 15.0
3 days, 0:04:08.442737 INFO: fwhm_rt        : 2.607738494873047
3 days, 0:04:08.442780 INFO: quant_window   : 3
3 days, 0:04:08.442824 INFO: ==============================================
3 days, 0:04:08.443705 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:08.443756 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:08.443792 INFO: FWHM in RT is 2.61 seconds, sigma is 0.43
3 days, 0:04:08.443817 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.18
3 days, 0:04:08.454155 INFO: Starting candidate selection
3 days, 0:04:09.128428 INFO: Starting candidate scoring
3 days, 0:04:09.255725 INFO: Finished candidate processing
3 days, 0:04:09.255857 INFO: Collecting candidate features
3 days, 0:04:09.272314 WARNING: intensity_correlation has 16 NaNs ( 0.50 % out of 3212)
3 days, 0:04:09.272636 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3212)
3 days, 0:04:09.280693 INFO: Collecting fragment features
3 days, 0:04:09.286878 INFO: Finished candidate scoring
3 days, 0:04:09.292006 INFO: performing precursor FDR with 47 features
3 days, 0:04:09.292090 INFO: Decoy channel: -1
3 days, 0:04:09.292140 INFO: competitive: True
3 days, 0:04:09.297100 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:09.299585 WARNING: dropped 2 target PSMs due to missing features
3 days, 0:04:09.299658 WARNING: dropped 14 decoy PSMs due to missing features
3 days, 0:04:09.299726 WARNING: FDR calculation for 1681 target and 1515 decoy PSMs
3 days, 0:04:09.299767 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3 days, 0:04:09.301211 INFO: Estimating optimal hyperparameters - samples: 2,556, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:09.301325 INFO: Using random state 114982 for train-test-split
3 days, 0:04:09.528851 INFO: Test AUC: 0.867
3 days, 0:04:09.528964 INFO: Train AUC: 0.885
3 days, 0:04:09.529005 INFO: AUC difference: 2.10%
3 days, 0:04:09.868491 INFO: Resetting torch num_threads to 80
3 days, 0:04:09.869309 PROGRESS: === Extracted 3212 precursors and 23602 fragments ===
3 days, 0:04:09.869929 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:04:09.870968 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:09.871099 PROGRESS: Total precursors accumulated: 600
3 days, 0:04:09.871205 PROGRESS: Target precursors: 585 (97.50%)
3 days, 0:04:09.871309 PROGRESS: Decoy precursors: 15 (2.50%)
3 days, 0:04:09.871405 PROGRESS: 
3 days, 0:04:09.871500 PROGRESS: Precursor Summary:
3 days, 0:04:09.873502 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   561; 0.001 FDR:   527
3 days, 0:04:09.873647 PROGRESS: 
3 days, 0:04:09.873744 PROGRESS: Protein Summary:
3 days, 0:04:09.876127 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   417; 0.001 FDR:   393
3 days, 0:04:09.876267 PROGRESS: =========================================================================
3 days, 0:04:09.876487 INFO: Target number of precursors reached.
3 days, 0:04:09.886652 INFO: fragments_df: keeping 5000 of 23602 [sum(precursor_idx_mask)=13799 sum(mass_error_mask)=23602 stop_rank=5000
3 days, 0:04:09.891985 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:10.059781 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:10.339073 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:10.517359 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:11.349126 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:11.349732 INFO: Using score_cutoff 17.331371417999264 (fac=0.99, q=1)
3 days, 0:04:11.350192 INFO: Updating optimization_manager: fwhm_rt             : 2.607738494873047 -> 2.615323305130005
3 days, 0:04:11.350327 INFO: Updating optimization_manager: fwhm_mobility       : 0.004013802856206894 -> 0.004061401356011629
3 days, 0:04:11.350435 INFO: Updating optimization_manager: score_cutoff        : 16.760726756858826 -> 17.331371417999264
3 days, 0:04:11.350542 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:11.352194 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:11.354129 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:11.355347 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:11.358031 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:11.358183 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
3 days, 0:04:11.361134 INFO: Updating optimization_manager: rt_error            : 11.485611523914736 -> 9.622378756646835
3 days, 0:04:11.361275 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 9.6224.
3 days, 0:04:11.361389 INFO: ==============================================
3 days, 0:04:11.361510 INFO: Starting optimization step 12.
3 days, 0:04:11.361620 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:11.361725 INFO: Using python extraction backend
3 days, 0:04:11.361896 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:11.362018 INFO: === Search parameters used ===
3 days, 0:04:11.362111 INFO: rt_error       : 9.622378756646835
3 days, 0:04:11.362200 INFO: mobility_error : 0.1
3 days, 0:04:11.362282 INFO: num_candidates : 3
3 days, 0:04:11.362381 INFO: ms1_error      : 15.0
3 days, 0:04:11.362468 INFO: ms2_error      : 15.0
3 days, 0:04:11.362557 INFO: fwhm_rt        : 2.615323305130005
3 days, 0:04:11.362642 INFO: quant_window   : 3
3 days, 0:04:11.362729 INFO: ==============================================
3 days, 0:04:11.364106 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:11.364175 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:11.364232 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:04:11.364271 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.20
3 days, 0:04:11.378323 INFO: Starting candidate selection
3 days, 0:04:11.946507 INFO: Starting candidate scoring
3 days, 0:04:12.062802 INFO: Finished candidate processing
3 days, 0:04:12.062933 INFO: Collecting candidate features
3 days, 0:04:12.079628 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3215)
3 days, 0:04:12.079985 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3215)
3 days, 0:04:12.087988 INFO: Collecting fragment features
3 days, 0:04:12.094213 INFO: Finished candidate scoring
3 days, 0:04:12.099016 INFO: performing precursor FDR with 47 features
3 days, 0:04:12.099124 INFO: Decoy channel: -1
3 days, 0:04:12.099181 INFO: competitive: True
3 days, 0:04:12.104327 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:12.106766 WARNING: dropped 2 target PSMs due to missing features
3 days, 0:04:12.106839 WARNING: dropped 17 decoy PSMs due to missing features
3 days, 0:04:12.108302 INFO: Estimating optimal hyperparameters - samples: 2,556, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:12.108419 INFO: Using random state 114982 for train-test-split
3 days, 0:04:12.337365 INFO: Test AUC: 0.860
3 days, 0:04:12.337473 INFO: Train AUC: 0.886
3 days, 0:04:12.337507 INFO: AUC difference: 2.94%
3 days, 0:04:12.632045 INFO: Resetting torch num_threads to 80
3 days, 0:04:12.632676 PROGRESS: === Extracted 3215 precursors and 23541 fragments ===
3 days, 0:04:12.633102 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:04:12.633763 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:12.633858 PROGRESS: Total precursors accumulated: 600
3 days, 0:04:12.633946 PROGRESS: Target precursors: 585 (97.50%)
3 days, 0:04:12.634006 PROGRESS: Decoy precursors: 15 (2.50%)
3 days, 0:04:12.634060 PROGRESS: 
3 days, 0:04:12.634113 PROGRESS: Precursor Summary:
3 days, 0:04:12.635339 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   568; 0.001 FDR:   524
3 days, 0:04:12.635452 PROGRESS: 
3 days, 0:04:12.635515 PROGRESS: Protein Summary:
3 days, 0:04:12.636890 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   425; 0.001 FDR:   392
3 days, 0:04:12.636991 PROGRESS: =========================================================================
3 days, 0:04:12.637145 INFO: Target number of precursors reached.
3 days, 0:04:12.643722 INFO: fragments_df: keeping 5000 of 23541 [sum(precursor_idx_mask)=13852 sum(mass_error_mask)=23541 stop_rank=5000
3 days, 0:04:12.647450 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:12.830189 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:13.066134 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:13.297273 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:14.157159 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:14.157613 INFO: Using score_cutoff 16.69681870765686 (fac=0.99, q=1)
3 days, 0:04:14.157984 INFO: Updating optimization_manager: fwhm_rt             : 2.615323305130005 -> 2.6104559898376465
3 days, 0:04:14.158082 INFO: Updating optimization_manager: fwhm_mobility       : 0.004061401356011629 -> 0.0040396954864263535
3 days, 0:04:14.158145 INFO: Updating optimization_manager: score_cutoff        : 17.331371417999264 -> 16.69681870765686
3 days, 0:04:14.158207 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:14.159437 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:14.160905 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:14.161759 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:14.163839 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:14.163956 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 2 ===
3 days, 0:04:14.166065 INFO: Updating optimization_manager: rt_error            : 9.622378756646835 -> 13.949045733347074
3 days, 0:04:14.166180 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 13.9490.
3 days, 0:04:14.166250 INFO: ==============================================
3 days, 0:04:14.166324 INFO: Starting optimization step 13.
3 days, 0:04:14.166399 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:14.166466 INFO: Using python extraction backend
3 days, 0:04:14.166569 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:14.166639 INFO: === Search parameters used ===
3 days, 0:04:14.166692 INFO: rt_error       : 13.949045733347074
3 days, 0:04:14.166739 INFO: mobility_error : 0.1
3 days, 0:04:14.166791 INFO: num_candidates : 3
3 days, 0:04:14.166838 INFO: ms1_error      : 15.0
3 days, 0:04:14.166883 INFO: ms2_error      : 15.0
3 days, 0:04:14.166927 INFO: fwhm_rt        : 2.6104559898376465
3 days, 0:04:14.166971 INFO: quant_window   : 3
3 days, 0:04:14.167015 INFO: ==============================================
3 days, 0:04:14.167951 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:14.168001 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:14.168037 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
3 days, 0:04:14.168060 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.19
3 days, 0:04:14.178288 INFO: Starting candidate selection
3 days, 0:04:14.771544 INFO: Starting candidate scoring
3 days, 0:04:14.881451 INFO: Finished candidate processing
3 days, 0:04:14.881645 INFO: Collecting candidate features
3 days, 0:04:14.893765 WARNING: intensity_correlation has 21 NaNs ( 0.66 % out of 3204)
3 days, 0:04:14.894280 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3204)
3 days, 0:04:14.901711 INFO: Collecting fragment features
3 days, 0:04:14.907919 INFO: Finished candidate scoring
3 days, 0:04:14.912665 INFO: performing precursor FDR with 47 features
3 days, 0:04:14.912764 INFO: Decoy channel: -1
3 days, 0:04:14.912808 INFO: competitive: True
3 days, 0:04:14.917899 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:14.920488 WARNING: dropped 3 target PSMs due to missing features
3 days, 0:04:14.920585 WARNING: dropped 18 decoy PSMs due to missing features
3 days, 0:04:14.920671 WARNING: FDR calculation for 1675 target and 1508 decoy PSMs
3 days, 0:04:14.920737 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3 days, 0:04:14.922314 INFO: Estimating optimal hyperparameters - samples: 2,546, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:14.922480 INFO: Using random state 114982 for train-test-split
3 days, 0:04:15.197999 INFO: Test AUC: 0.897
3 days, 0:04:15.198174 INFO: Train AUC: 0.879
3 days, 0:04:15.198344 INFO: AUC difference: 1.96%
3 days, 0:04:15.542228 INFO: Resetting torch num_threads to 80
3 days, 0:04:15.543051 PROGRESS: === Extracted 3204 precursors and 23481 fragments ===
3 days, 0:04:15.543650 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:04:15.544656 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:15.544786 PROGRESS: Total precursors accumulated: 600
3 days, 0:04:15.544889 PROGRESS: Target precursors: 582 (97.00%)
3 days, 0:04:15.544979 PROGRESS: Decoy precursors: 18 (3.00%)
3 days, 0:04:15.545055 PROGRESS: 
3 days, 0:04:15.545129 PROGRESS: Precursor Summary:
3 days, 0:04:15.547098 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   561; 0.001 FDR:   532
3 days, 0:04:15.547245 PROGRESS: 
3 days, 0:04:15.547357 PROGRESS: Protein Summary:
3 days, 0:04:15.549470 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   419; 0.001 FDR:   398
3 days, 0:04:15.549607 PROGRESS: =========================================================================
3 days, 0:04:15.549810 INFO: Target number of precursors reached.
3 days, 0:04:15.557341 INFO: fragments_df: keeping 5000 of 23481 [sum(precursor_idx_mask)=13729 sum(mass_error_mask)=23481 stop_rank=5000
3 days, 0:04:15.560986 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:15.747398 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:15.995700 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:16.227472 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:17.133633 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:17.134118 INFO: Using score_cutoff 18.026741203308106 (fac=0.99, q=1)
3 days, 0:04:17.134492 INFO: Updating optimization_manager: fwhm_rt             : 2.6104559898376465 -> 2.620155096054077
3 days, 0:04:17.134587 INFO: Updating optimization_manager: fwhm_mobility       : 0.0040396954864263535 -> 0.0040556201711297035
3 days, 0:04:17.134670 INFO: Updating optimization_manager: score_cutoff        : 16.69681870765686 -> 18.026741203308106
3 days, 0:04:17.134741 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:17.136013 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:17.137593 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:17.138543 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:17.140776 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:17.140894 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 2 ===
3 days, 0:04:17.142983 INFO: Updating optimization_manager: rt_error            : 13.949045733347074 -> 10.45663876551177
3 days, 0:04:17.143108 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 10.4566.
3 days, 0:04:17.143189 INFO: ==============================================
3 days, 0:04:17.143273 INFO: Starting optimization step 14.
3 days, 0:04:17.143346 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:17.143418 INFO: Using python extraction backend
3 days, 0:04:17.143532 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:17.143613 INFO: === Search parameters used ===
3 days, 0:04:17.143676 INFO: rt_error       : 10.45663876551177
3 days, 0:04:17.143734 INFO: mobility_error : 0.1
3 days, 0:04:17.143789 INFO: num_candidates : 3
3 days, 0:04:17.143844 INFO: ms1_error      : 15.0
3 days, 0:04:17.143898 INFO: ms2_error      : 15.0
3 days, 0:04:17.143949 INFO: fwhm_rt        : 2.620155096054077
3 days, 0:04:17.144000 INFO: quant_window   : 3
3 days, 0:04:17.144050 INFO: ==============================================
3 days, 0:04:17.145123 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:17.145177 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:17.145215 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:04:17.145242 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.20
3 days, 0:04:17.150839 INFO: Starting candidate selection
3 days, 0:04:17.756376 INFO: Starting candidate scoring
3 days, 0:04:17.873812 INFO: Finished candidate processing
3 days, 0:04:17.873957 INFO: Collecting candidate features
3 days, 0:04:17.887374 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3216)
3 days, 0:04:17.887652 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3216)
3 days, 0:04:17.893433 INFO: Collecting fragment features
3 days, 0:04:17.899843 INFO: Finished candidate scoring
3 days, 0:04:17.904601 INFO: performing precursor FDR with 47 features
3 days, 0:04:17.904715 INFO: Decoy channel: -1
3 days, 0:04:17.904763 INFO: competitive: True
3 days, 0:04:17.910866 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:17.913570 WARNING: dropped 3 target PSMs due to missing features
3 days, 0:04:17.913649 WARNING: dropped 16 decoy PSMs due to missing features
3 days, 0:04:17.917210 INFO: Estimating optimal hyperparameters - samples: 2,557, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:17.917349 INFO: Using random state 114982 for train-test-split
3 days, 0:04:18.228398 INFO: Test AUC: 0.880
3 days, 0:04:18.228521 INFO: Train AUC: 0.885
3 days, 0:04:18.228568 INFO: AUC difference: 0.58%
3 days, 0:04:18.531806 INFO: Resetting torch num_threads to 80
3 days, 0:04:18.532606 PROGRESS: === Extracted 3216 precursors and 23549 fragments ===
3 days, 0:04:18.533200 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:04:18.534282 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:18.534428 PROGRESS: Total precursors accumulated: 600
3 days, 0:04:18.534537 PROGRESS: Target precursors: 582 (97.00%)
3 days, 0:04:18.534630 PROGRESS: Decoy precursors: 18 (3.00%)
3 days, 0:04:18.534722 PROGRESS: 
3 days, 0:04:18.534806 PROGRESS: Precursor Summary:
3 days, 0:04:18.536803 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   565; 0.001 FDR:   535
3 days, 0:04:18.536946 PROGRESS: 
3 days, 0:04:18.537045 PROGRESS: Protein Summary:
3 days, 0:04:18.539440 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   422; 0.001 FDR:   400
3 days, 0:04:18.539583 PROGRESS: =========================================================================
3 days, 0:04:18.539808 INFO: Target number of precursors reached.
3 days, 0:04:18.549723 INFO: fragments_df: keeping 5000 of 23549 [sum(precursor_idx_mask)=13801 sum(mass_error_mask)=23549 stop_rank=5000
3 days, 0:04:18.555364 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:18.794033 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:18.968322 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:19.139850 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:20.004802 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:20.005394 INFO: Using score_cutoff 17.08875555496216 (fac=0.99, q=1)
3 days, 0:04:20.005912 INFO: Updating optimization_manager: fwhm_rt             : 2.620155096054077 -> 2.615323305130005
3 days, 0:04:20.006047 INFO: Updating optimization_manager: fwhm_mobility       : 0.0040556201711297035 -> 0.004061401356011629
3 days, 0:04:20.006163 INFO: Updating optimization_manager: score_cutoff        : 18.026741203308106 -> 17.08875555496216
3 days, 0:04:20.006270 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:20.007890 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:20.009893 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:20.011161 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:20.013848 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:20.014011 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 2 ===
3 days, 0:04:20.016880 INFO: Updating optimization_manager: rt_error            : 10.45663876551177 -> 10.708107589256194
3 days, 0:04:20.017028 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 10.7081.
3 days, 0:04:20.017137 INFO: ==============================================
3 days, 0:04:20.017262 INFO: Starting optimization step 15.
3 days, 0:04:20.017371 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:20.017480 INFO: Using python extraction backend
3 days, 0:04:20.017642 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:20.017765 INFO: === Search parameters used ===
3 days, 0:04:20.017876 INFO: rt_error       : 10.708107589256194
3 days, 0:04:20.017973 INFO: mobility_error : 0.1
3 days, 0:04:20.018063 INFO: num_candidates : 3
3 days, 0:04:20.018157 INFO: ms1_error      : 15.0
3 days, 0:04:20.018258 INFO: ms2_error      : 15.0
3 days, 0:04:20.018353 INFO: fwhm_rt        : 2.615323305130005
3 days, 0:04:20.018443 INFO: quant_window   : 3
3 days, 0:04:20.018535 INFO: ==============================================
3 days, 0:04:20.020185 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:20.020256 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:20.020316 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:04:20.020361 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.20
3 days, 0:04:20.034007 INFO: Starting candidate selection
3 days, 0:04:20.626915 INFO: Starting candidate scoring
3 days, 0:04:20.736964 INFO: Finished candidate processing
3 days, 0:04:20.737066 INFO: Collecting candidate features
3 days, 0:04:20.751159 WARNING: intensity_correlation has 19 NaNs ( 0.59 % out of 3218)
3 days, 0:04:20.751517 WARNING: height_correlation has 1 NaNs ( 0.03 % out of 3218)
3 days, 0:04:20.760695 INFO: Collecting fragment features
3 days, 0:04:20.767028 INFO: Finished candidate scoring
3 days, 0:04:20.771353 INFO: performing precursor FDR with 47 features
3 days, 0:04:20.771460 INFO: Decoy channel: -1
3 days, 0:04:20.771508 INFO: competitive: True
3 days, 0:04:20.776675 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:20.779296 WARNING: dropped 3 target PSMs due to missing features
3 days, 0:04:20.779368 WARNING: dropped 16 decoy PSMs due to missing features
3 days, 0:04:20.780899 INFO: Estimating optimal hyperparameters - samples: 2,559, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:20.781022 INFO: Using random state 114982 for train-test-split
3 days, 0:04:21.117971 INFO: Test AUC: 0.878
3 days, 0:04:21.118086 INFO: Train AUC: 0.884
3 days, 0:04:21.118128 INFO: AUC difference: 0.68%
3 days, 0:04:21.387994 INFO: Resetting torch num_threads to 80
3 days, 0:04:21.388640 PROGRESS: === Extracted 3218 precursors and 23574 fragments ===
3 days, 0:04:21.389111 INFO: === FDR correction performed with classifier version 4 ===
3 days, 0:04:21.389833 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:21.389966 PROGRESS: Total precursors accumulated: 600
3 days, 0:04:21.390049 PROGRESS: Target precursors: 584 (97.33%)
3 days, 0:04:21.390115 PROGRESS: Decoy precursors: 16 (2.67%)
3 days, 0:04:21.390177 PROGRESS: 
3 days, 0:04:21.390239 PROGRESS: Precursor Summary:
3 days, 0:04:21.391441 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   556; 0.001 FDR:   536
3 days, 0:04:21.391545 PROGRESS: 
3 days, 0:04:21.391612 PROGRESS: Protein Summary:
3 days, 0:04:21.392995 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   415; 0.001 FDR:   401
3 days, 0:04:21.393106 PROGRESS: =========================================================================
3 days, 0:04:21.393286 INFO: Target number of precursors reached.
3 days, 0:04:21.399897 INFO: fragments_df: keeping 5000 of 23574 [sum(precursor_idx_mask)=13654 sum(mass_error_mask)=23574 stop_rank=5000
3 days, 0:04:21.403548 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:21.677299 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:21.955521 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:22.146682 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:22.985142 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:22.985598 INFO: Using score_cutoff 17.80066396808624 (fac=0.99, q=1)
3 days, 0:04:22.985948 INFO: Updating optimization_manager: fwhm_rt             : 2.615323305130005 -> 2.6204147338867188
3 days, 0:04:22.986045 INFO: Updating optimization_manager: fwhm_mobility       : 0.004061401356011629 -> 0.00406656926497817
3 days, 0:04:22.986107 INFO: Updating optimization_manager: score_cutoff        : 17.08875555496216 -> 17.80066396808624
3 days, 0:04:22.986168 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:22.987390 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:22.988880 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:22.989720 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:22.991810 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:22.991931 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 2 ===
3 days, 0:04:22.992978 INFO: Updating optimization_manager: rt_error            : 10.708107589256194 -> 8.483719760328377
3 days, 0:04:22.993112 INFO: Updating optimization_manager: classifier_version  : 4 -> 10
3 days, 0:04:22.993216 INFO: Updating optimization_manager: score_cutoff        : 17.80066396808624 -> 17.462663547706605
3 days, 0:04:22.993314 INFO: Updating optimization_manager: fwhm_rt             : 2.6204147338867188 -> 2.617318868637085
3 days, 0:04:22.993409 INFO: Updating optimization_manager: fwhm_mobility       : 0.00406656926497817 -> 0.004055087920278311
3 days, 0:04:22.993518 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 8.4837 found after 16 searches.
3 days, 0:04:22.993587 INFO: ==============================================
3 days, 0:04:22.993664 PROGRESS: Optimization finished for rt_error.
3 days, 0:04:22.996796 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:22.997726 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:22.999155 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:22.999986 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:23.002048 INFO: Starting optimization step 0.
3 days, 0:04:23.002159 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:23.002235 INFO: Using python extraction backend
3 days, 0:04:23.002342 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:23.002417 INFO: === Search parameters used ===
3 days, 0:04:23.002473 INFO: rt_error       : 8.483719760328377
3 days, 0:04:23.002527 INFO: mobility_error : 0.1
3 days, 0:04:23.002576 INFO: num_candidates : 3
3 days, 0:04:23.002623 INFO: ms1_error      : 15.0
3 days, 0:04:23.002669 INFO: ms2_error      : 15.0
3 days, 0:04:23.002712 INFO: fwhm_rt        : 2.617318868637085
3 days, 0:04:23.002756 INFO: quant_window   : 3
3 days, 0:04:23.002800 INFO: ==============================================
3 days, 0:04:23.003667 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:23.003718 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:23.003755 INFO: FWHM in RT is 2.62 seconds, sigma is 0.44
3 days, 0:04:23.003779 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.20
3 days, 0:04:23.007156 INFO: Starting candidate selection
3 days, 0:04:23.555794 INFO: Starting candidate scoring
3 days, 0:04:23.663234 INFO: Finished candidate processing
3 days, 0:04:23.663360 INFO: Collecting candidate features
3 days, 0:04:23.675291 WARNING: intensity_correlation has 22 NaNs ( 0.68 % out of 3214)
3 days, 0:04:23.675566 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3214)
3 days, 0:04:23.681291 INFO: Collecting fragment features
3 days, 0:04:23.687698 INFO: Finished candidate scoring
3 days, 0:04:23.692026 INFO: performing precursor FDR with 47 features
3 days, 0:04:23.692125 INFO: Decoy channel: -1
3 days, 0:04:23.692170 INFO: competitive: True
3 days, 0:04:23.697407 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:23.700047 WARNING: dropped 3 target PSMs due to missing features
3 days, 0:04:23.700125 WARNING: dropped 20 decoy PSMs due to missing features
3 days, 0:04:23.701697 INFO: Estimating optimal hyperparameters - samples: 2,552, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:23.701898 INFO: Using random state 547198 for train-test-split
3 days, 0:04:23.982503 INFO: Test AUC: 0.884
3 days, 0:04:23.982746 INFO: Train AUC: 0.893
3 days, 0:04:23.982852 INFO: AUC difference: 1.05%
3 days, 0:04:24.286029 INFO: Resetting torch num_threads to 80
3 days, 0:04:24.286621 PROGRESS: === Extracted 3214 precursors and 23452 fragments ===
3 days, 0:04:24.287082 INFO: === FDR correction performed with classifier version 10 ===
3 days, 0:04:24.287796 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:24.287895 PROGRESS: Total precursors accumulated: 600
3 days, 0:04:24.287971 PROGRESS: Target precursors: 585 (97.50%)
3 days, 0:04:24.288033 PROGRESS: Decoy precursors: 15 (2.50%)
3 days, 0:04:24.288093 PROGRESS: 
3 days, 0:04:24.288147 PROGRESS: Precursor Summary:
3 days, 0:04:24.289378 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   566; 0.001 FDR:   538
3 days, 0:04:24.289487 PROGRESS: 
3 days, 0:04:24.289560 PROGRESS: Protein Summary:
3 days, 0:04:24.290968 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   422; 0.001 FDR:   405
3 days, 0:04:24.291084 PROGRESS: =========================================================================
3 days, 0:04:24.291287 INFO: Target number of precursors reached.
3 days, 0:04:24.298243 INFO: fragments_df: keeping 5000 of 23452 [sum(precursor_idx_mask)=13735 sum(mass_error_mask)=23452 stop_rank=5000
3 days, 0:04:24.302013 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:24.518584 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:24.719229 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:24.950871 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:25.811562 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:25.812061 INFO: Using score_cutoff 16.697638332366942 (fac=0.99, q=1)
3 days, 0:04:25.812483 INFO: Updating optimization_manager: fwhm_rt             : 2.617318868637085 -> 2.6145577430725098
3 days, 0:04:25.812594 INFO: Updating optimization_manager: fwhm_mobility       : 0.004055087920278311 -> 0.003991531208157539
3 days, 0:04:25.812680 INFO: Updating optimization_manager: score_cutoff        : 17.462663547706605 -> 16.697638332366942
3 days, 0:04:25.812769 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:25.814061 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:25.815686 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:25.816628 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:25.818783 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:25.818923 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
3 days, 0:04:25.820482 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.05122545799952102
3 days, 0:04:25.820612 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0512.
3 days, 0:04:25.820709 INFO: ==============================================
3 days, 0:04:25.820811 INFO: Starting optimization step 1.
3 days, 0:04:25.820901 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:25.820992 INFO: Using python extraction backend
3 days, 0:04:25.821135 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:25.821230 INFO: === Search parameters used ===
3 days, 0:04:25.821311 INFO: rt_error       : 8.483719760328377
3 days, 0:04:25.821396 INFO: mobility_error : 0.05122545799952102
3 days, 0:04:25.821467 INFO: num_candidates : 3
3 days, 0:04:25.821531 INFO: ms1_error      : 15.0
3 days, 0:04:25.821596 INFO: ms2_error      : 15.0
3 days, 0:04:25.821658 INFO: fwhm_rt        : 2.6145577430725098
3 days, 0:04:25.821720 INFO: quant_window   : 3
3 days, 0:04:25.821781 INFO: ==============================================
3 days, 0:04:25.822775 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:25.822833 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:25.822886 INFO: FWHM in RT is 2.61 seconds, sigma is 0.44
3 days, 0:04:25.822922 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.16
3 days, 0:04:25.833999 INFO: Starting candidate selection
3 days, 0:04:26.319245 INFO: Starting candidate scoring
3 days, 0:04:26.432341 INFO: Finished candidate processing
3 days, 0:04:26.432491 INFO: Collecting candidate features
3 days, 0:04:26.447768 WARNING: intensity_correlation has 20 NaNs ( 0.62 % out of 3200)
3 days, 0:04:26.448013 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3200)
3 days, 0:04:26.452202 INFO: Collecting fragment features
3 days, 0:04:26.456830 INFO: Finished candidate scoring
3 days, 0:04:26.460027 INFO: performing precursor FDR with 47 features
3 days, 0:04:26.460096 INFO: Decoy channel: -1
3 days, 0:04:26.460139 INFO: competitive: True
3 days, 0:04:26.463595 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:26.465346 WARNING: dropped 2 target PSMs due to missing features
3 days, 0:04:26.465406 WARNING: dropped 19 decoy PSMs due to missing features
3 days, 0:04:26.466530 INFO: Estimating optimal hyperparameters - samples: 2,543, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:26.466649 INFO: Using random state 547198 for train-test-split
3 days, 0:04:26.732977 INFO: Test AUC: 0.904
3 days, 0:04:26.733116 INFO: Train AUC: 0.894
3 days, 0:04:26.733183 INFO: AUC difference: 1.12%
3 days, 0:04:27.060909 INFO: Resetting torch num_threads to 80
3 days, 0:04:27.061651 PROGRESS: === Extracted 3200 precursors and 23053 fragments ===
3 days, 0:04:27.062255 INFO: === FDR correction performed with classifier version 10 ===
3 days, 0:04:27.063275 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:27.063411 PROGRESS: Total precursors accumulated: 599
3 days, 0:04:27.063517 PROGRESS: Target precursors: 580 (96.83%)
3 days, 0:04:27.063609 PROGRESS: Decoy precursors: 19 (3.17%)
3 days, 0:04:27.063695 PROGRESS: 
3 days, 0:04:27.063788 PROGRESS: Precursor Summary:
3 days, 0:04:27.065798 PROGRESS: Channel   0:	 0.050 FDR:   580; 0.010 FDR:   558; 0.001 FDR:   531
3 days, 0:04:27.065950 PROGRESS: 
3 days, 0:04:27.066054 PROGRESS: Protein Summary:
3 days, 0:04:27.068308 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   417; 0.001 FDR:   399
3 days, 0:04:27.068441 PROGRESS: =========================================================================
3 days, 0:04:27.068672 INFO: Target number of precursors reached.
3 days, 0:04:27.078590 INFO: fragments_df: keeping 5000 of 23053 [sum(precursor_idx_mask)=13569 sum(mass_error_mask)=23053 stop_rank=5000
3 days, 0:04:27.083876 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:27.317930 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:27.574498 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:27.827260 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:28.700426 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:28.700887 INFO: Using score_cutoff 17.19207043361664 (fac=0.99, q=1)
3 days, 0:04:28.701223 INFO: Updating optimization_manager: fwhm_rt             : 2.6145577430725098 -> 2.6075100898742676
3 days, 0:04:28.701313 INFO: Updating optimization_manager: fwhm_mobility       : 0.003991531208157539 -> 0.004050876945257187
3 days, 0:04:28.701376 INFO: Updating optimization_manager: score_cutoff        : 16.697638332366942 -> 17.19207043361664
3 days, 0:04:28.701440 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:28.702593 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:28.704063 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:28.704892 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:28.706948 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:28.707065 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
3 days, 0:04:28.708651 INFO: Updating optimization_manager: mobility_error      : 0.05122545799952102 -> 0.04588621882369695
3 days, 0:04:28.708759 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0459.
3 days, 0:04:28.708833 INFO: ==============================================
3 days, 0:04:28.708916 INFO: Starting optimization step 2.
3 days, 0:04:28.708987 PROGRESS: === Extracting elution groups 0 to 600 ===
3 days, 0:04:28.709054 INFO: Using python extraction backend
3 days, 0:04:28.709159 PROGRESS: Extracting batch of 1197 precursors
3 days, 0:04:28.709235 INFO: === Search parameters used ===
3 days, 0:04:28.709293 INFO: rt_error       : 8.483719760328377
3 days, 0:04:28.709347 INFO: mobility_error : 0.04588621882369695
3 days, 0:04:28.709401 INFO: num_candidates : 3
3 days, 0:04:28.709453 INFO: ms1_error      : 15.0
3 days, 0:04:28.709504 INFO: ms2_error      : 15.0
3 days, 0:04:28.709554 INFO: fwhm_rt        : 2.6075100898742676
3 days, 0:04:28.709604 INFO: quant_window   : 3
3 days, 0:04:28.709654 INFO: ==============================================
3 days, 0:04:28.710569 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:28.710624 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:28.710664 INFO: FWHM in RT is 2.61 seconds, sigma is 0.43
3 days, 0:04:28.710696 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.20
3 days, 0:04:28.726085 INFO: Starting candidate selection
3 days, 0:04:29.256840 INFO: Starting candidate scoring
3 days, 0:04:29.382185 INFO: Finished candidate processing
3 days, 0:04:29.382306 INFO: Collecting candidate features
3 days, 0:04:29.395107 WARNING: intensity_correlation has 20 NaNs ( 0.63 % out of 3193)
3 days, 0:04:29.395358 WARNING: height_correlation has 2 NaNs ( 0.06 % out of 3193)
3 days, 0:04:29.400441 INFO: Collecting fragment features
3 days, 0:04:29.405237 INFO: Finished candidate scoring
3 days, 0:04:29.408559 INFO: performing precursor FDR with 47 features
3 days, 0:04:29.408618 INFO: Decoy channel: -1
3 days, 0:04:29.408649 INFO: competitive: True
3 days, 0:04:29.412584 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:29.414556 WARNING: dropped 2 target PSMs due to missing features
3 days, 0:04:29.414616 WARNING: dropped 19 decoy PSMs due to missing features
3 days, 0:04:29.414664 WARNING: FDR calculation for 1666 target and 1506 decoy PSMs
3 days, 0:04:29.414781 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3 days, 0:04:29.416040 INFO: Estimating optimal hyperparameters - samples: 2,537, batch_size: 128, learning_rate: 1.77e-04
3 days, 0:04:29.416140 INFO: Using random state 547198 for train-test-split
3 days, 0:04:29.668611 INFO: Test AUC: 0.878
3 days, 0:04:29.668752 INFO: Train AUC: 0.897
3 days, 0:04:29.668810 INFO: AUC difference: 2.10%
3 days, 0:04:30.029407 INFO: Resetting torch num_threads to 80
3 days, 0:04:30.030180 PROGRESS: === Extracted 3193 precursors and 22919 fragments ===
3 days, 0:04:30.030764 INFO: === FDR correction performed with classifier version 10 ===
3 days, 0:04:30.031749 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:30.031883 PROGRESS: Total precursors accumulated: 599
3 days, 0:04:30.031991 PROGRESS: Target precursors: 585 (97.66%)
3 days, 0:04:30.032094 PROGRESS: Decoy precursors: 14 (2.34%)
3 days, 0:04:30.032184 PROGRESS: 
3 days, 0:04:30.032280 PROGRESS: Precursor Summary:
3 days, 0:04:30.034244 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   569; 0.001 FDR:   547
3 days, 0:04:30.034388 PROGRESS: 
3 days, 0:04:30.034487 PROGRESS: Protein Summary:
3 days, 0:04:30.036851 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   423; 0.001 FDR:   408
3 days, 0:04:30.036990 PROGRESS: =========================================================================
3 days, 0:04:30.037202 INFO: Target number of precursors reached.
3 days, 0:04:30.046688 INFO: fragments_df: keeping 5000 of 22919 [sum(precursor_idx_mask)=13776 sum(mass_error_mask)=22919 stop_rank=5000
3 days, 0:04:30.050242 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:30.276366 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:30.463160 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:30.648938 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:31.518175 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3 days, 0:04:31.518839 INFO: Using score_cutoff 15.896624915313721 (fac=0.99, q=1)
3 days, 0:04:31.519371 INFO: Updating optimization_manager: fwhm_rt             : 2.6075100898742676 -> 2.590550661087036
3 days, 0:04:31.519512 INFO: Updating optimization_manager: fwhm_mobility       : 0.004050876945257187 -> 0.003993608057498932
3 days, 0:04:31.519638 INFO: Updating optimization_manager: score_cutoff        : 17.19207043361664 -> 15.896624915313721
3 days, 0:04:31.519771 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:31.521418 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:31.523451 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:31.524676 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:31.527297 INFO: === checking if optimization conditions were reached ===
3 days, 0:04:31.527447 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
3 days, 0:04:31.528604 INFO: Updating optimization_manager: mobility_error      : 0.04588621882369695 -> 0.04588621882369695
3 days, 0:04:31.528797 INFO: Updating optimization_manager: classifier_version  : 10 -> 23
3 days, 0:04:31.528965 INFO: Updating optimization_manager: score_cutoff        : 15.896624915313721 -> 15.896624915313721
3 days, 0:04:31.529135 INFO: Updating optimization_manager: fwhm_rt             : 2.590550661087036 -> 2.590550661087036
3 days, 0:04:31.529291 INFO: Updating optimization_manager: fwhm_mobility       : 0.003993608057498932 -> 0.003993608057498932
3 days, 0:04:31.529456 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0459 found after 3 searches.
3 days, 0:04:31.529564 INFO: ==============================================
3 days, 0:04:31.529675 PROGRESS: Optimization finished for mobility_error.
3 days, 0:04:31.534376 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:31.535713 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:31.537594 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:31.538793 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:31.541361 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3 days, 0:04:31.541506 PROGRESS: ==============================================
3 days, 0:04:31.541617 PROGRESS: ms2_error      : 15.0000
3 days, 0:04:31.541726 PROGRESS: ms1_error      : 15.0000
3 days, 0:04:31.541828 PROGRESS: rt_error       : 8.4837
3 days, 0:04:31.541935 PROGRESS: mobility_error : 0.0459
3 days, 0:04:31.542020 PROGRESS: ==============================================
3 days, 0:04:31.542908 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3 days, 0:04:31.548023 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3 days, 0:04:31.566046 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3 days, 0:04:31.570299 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3 days, 0:04:31.612267 INFO: Using python extraction backend
3 days, 0:04:31.619595 PROGRESS: Extracting batch of 27494 precursors
3 days, 0:04:31.619760 INFO: === Search parameters used ===
3 days, 0:04:31.619835 INFO: rt_error       : 8.483719760328377
3 days, 0:04:31.619895 INFO: mobility_error : 0.04588621882369695
3 days, 0:04:31.619953 INFO: num_candidates : 3
3 days, 0:04:31.620012 INFO: ms1_error      : 15.0
3 days, 0:04:31.620074 INFO: ms2_error      : 15.0
3 days, 0:04:31.620128 INFO: fwhm_rt        : 2.590550661087036
3 days, 0:04:31.620183 INFO: quant_window   : 3
3 days, 0:04:31.620238 INFO: ==============================================
3 days, 0:04:31.630299 INFO: Duty cycle consists of 12 frames, 1.27 seconds cycle time
3 days, 0:04:31.630470 INFO: Duty cycle consists of 928 scans, 0.00078 1/K_0 resolution
3 days, 0:04:31.630528 INFO: FWHM in RT is 2.59 seconds, sigma is 0.43
3 days, 0:04:31.630566 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.16
3 days, 0:04:31.650005 INFO: Starting candidate selection
3 days, 0:04:33.419930 INFO: Removed 23180 precursors with score below cutoff 15.896624915313721
3 days, 0:04:33.774003 INFO: Starting candidate scoring
3 days, 0:04:34.742570 INFO: Finished candidate processing
3 days, 0:04:34.742691 INFO: Collecting candidate features
3 days, 0:04:34.857104 WARNING: intensity_correlation has 121 NaNs ( 0.23 % out of 53671)
3 days, 0:04:34.857458 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 53671)
3 days, 0:04:34.865181 INFO: Collecting fragment features
3 days, 0:04:34.902268 INFO: Finished candidate scoring
3 days, 0:04:34.935136 INFO: === Performing FDR correction with classifier version 23 ===
3 days, 0:04:34.936057 INFO: performing precursor FDR with 47 features
3 days, 0:04:34.936123 INFO: Decoy channel: -1
3 days, 0:04:34.936164 INFO: competitive: True
3 days, 0:04:34.961811 INFO: Setting torch num_threads to 2 for FDR classification task
3 days, 0:04:34.974000 WARNING: dropped 29 target PSMs due to missing features
3 days, 0:04:34.974141 WARNING: dropped 93 decoy PSMs due to missing features
3 days, 0:04:34.974198 WARNING: FDR calculation for 33343 target and 20206 decoy PSMs
3 days, 0:04:34.974230 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3 days, 0:04:34.984797 INFO: Estimating optimal hyperparameters - samples: 42,839, batch_size: 175, learning_rate: 2.07e-04
3 days, 0:04:34.985076 INFO: Using random state 3055 for train-test-split
3 days, 0:04:38.770723 INFO: Test AUC: 0.909
3 days, 0:04:38.770873 INFO: Train AUC: 0.919
3 days, 0:04:38.770930 INFO: AUC difference: 1.04%
3 days, 0:04:39.112847 INFO: Resetting torch num_threads to 80
3 days, 0:04:39.115848 INFO: Removing fragments below FDR threshold
3 days, 0:04:39.125765 PROGRESS: ============================= Precursor FDR =============================
3 days, 0:04:39.126000 PROGRESS: Total precursors accumulated: 13,117
3 days, 0:04:39.126073 PROGRESS: Target precursors: 12,988 (99.02%)
3 days, 0:04:39.126131 PROGRESS: Decoy precursors: 129 (0.98%)
3 days, 0:04:39.126186 PROGRESS: 
3 days, 0:04:39.126237 PROGRESS: Precursor Summary:
3 days, 0:04:39.131134 PROGRESS: Channel   0:	 0.050 FDR: 12,988; 0.010 FDR: 12,988; 0.001 FDR: 12,498
3 days, 0:04:39.131340 PROGRESS: 
3 days, 0:04:39.131431 PROGRESS: Protein Summary:
3 days, 0:04:39.138187 PROGRESS: Channel   0:	 0.050 FDR: 1,683; 0.010 FDR: 1,683; 0.001 FDR: 1,682
3 days, 0:04:39.138414 PROGRESS: =========================================================================
3 days, 0:04:39.139533 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R6/psm.parquet
3 days, 0:04:39.210380 INFO: Saving results to plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R6/frag.parquet
3 days, 0:04:39.265845 INFO: Finished workflow for B9_G_DIA_nLC_tTOF_R6
3 days, 0:04:39.423872 PROGRESS: Processing search outputs
3 days, 0:04:39.424003 PROGRESS: Performing protein grouping and FDR
3 days, 0:04:39.424057 INFO: Building output for A9_G_DIA_nLC_tTOF_R1
3 days, 0:04:39.445318 INFO: Building output for A9_G_DIA_nLC_tTOF_R2
3 days, 0:04:39.463469 INFO: Building output for A9_G_DIA_nLC_tTOF_R3
3 days, 0:04:39.481635 INFO: Building output for A9_G_DIA_nLC_tTOF_R4
3 days, 0:04:39.503531 INFO: Building output for A9_G_DIA_nLC_tTOF_R5
3 days, 0:04:39.518952 INFO: Building output for A9_G_DIA_nLC_tTOF_R6
3 days, 0:04:39.534133 INFO: Building output for B9_G_DIA_nLC_tTOF_R1
3 days, 0:04:39.551658 INFO: Building output for B9_G_DIA_nLC_tTOF_R2
3 days, 0:04:39.565315 INFO: Building output for B9_G_DIA_nLC_tTOF_R3
3 days, 0:04:39.579108 INFO: Building output for B9_G_DIA_nLC_tTOF_R4
3 days, 0:04:39.594481 INFO: Building output for B9_G_DIA_nLC_tTOF_R5
3 days, 0:04:39.608586 INFO: Building output for B9_G_DIA_nLC_tTOF_R6
3 days, 0:04:39.624912 INFO: Building combined output
3 days, 0:04:39.649014 INFO: Performing protein inference
3 days, 0:04:39.984786 INFO: Inference strategy: library. Using library grouping for protein inference
3 days, 0:04:39.986636 INFO: Performing protein FDR
3 days, 0:04:41.197295 INFO: Normalizing q-values using 1,683 targets and 665 decoys
3 days, 0:04:41.199093 INFO: Test AUC: 1.000
3 days, 0:04:41.199158 INFO: Train AUC: 1.000
3 days, 0:04:41.199198 INFO: AUC difference: 0.00%
3 days, 0:04:41.789955 INFO: ================ Protein FDR =================
3 days, 0:04:41.790118 INFO: Unique protein groups in output
3 days, 0:04:41.790164 INFO:   1% protein FDR: 1,683
3 days, 0:04:41.790199 INFO: 
3 days, 0:04:41.790231 INFO: Unique precursor in output
3 days, 0:04:41.790263 INFO:   1% protein FDR: 13,756
3 days, 0:04:41.790299 INFO: ================================================
3 days, 0:04:41.828352 PROGRESS: Building search statistics
3 days, 0:04:41.896294 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R1/optimization_manager.pkl
3 days, 0:04:41.896494 INFO: Initializing OptimizationManager
3 days, 0:04:41.896760 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R1/calibration_manager.pkl
3 days, 0:04:41.896846 INFO: Initializing CalibrationManager
3 days, 0:04:41.897081 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R1/raw_file_manager.pkl
3 days, 0:04:41.897161 INFO: Initializing RawFileManager
3 days, 0:04:41.906530 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R2/optimization_manager.pkl
3 days, 0:04:41.906695 INFO: Initializing OptimizationManager
3 days, 0:04:41.906934 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R2/calibration_manager.pkl
3 days, 0:04:41.907010 INFO: Initializing CalibrationManager
3 days, 0:04:41.907236 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R2/raw_file_manager.pkl
3 days, 0:04:41.907316 INFO: Initializing RawFileManager
3 days, 0:04:41.915806 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R3/optimization_manager.pkl
3 days, 0:04:41.915953 INFO: Initializing OptimizationManager
3 days, 0:04:41.916182 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R3/calibration_manager.pkl
3 days, 0:04:41.916262 INFO: Initializing CalibrationManager
3 days, 0:04:41.916483 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R3/raw_file_manager.pkl
3 days, 0:04:41.916564 INFO: Initializing RawFileManager
3 days, 0:04:41.928372 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R4/optimization_manager.pkl
3 days, 0:04:41.928614 INFO: Initializing OptimizationManager
3 days, 0:04:41.928978 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R4/calibration_manager.pkl
3 days, 0:04:41.929101 INFO: Initializing CalibrationManager
3 days, 0:04:41.929457 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R4/raw_file_manager.pkl
3 days, 0:04:41.929590 INFO: Initializing RawFileManager
3 days, 0:04:41.946302 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R5/optimization_manager.pkl
3 days, 0:04:41.946538 INFO: Initializing OptimizationManager
3 days, 0:04:41.946944 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R5/calibration_manager.pkl
3 days, 0:04:41.947062 INFO: Initializing CalibrationManager
3 days, 0:04:41.947406 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R5/raw_file_manager.pkl
3 days, 0:04:41.947541 INFO: Initializing RawFileManager
3 days, 0:04:41.962783 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R6/optimization_manager.pkl
3 days, 0:04:41.963021 INFO: Initializing OptimizationManager
3 days, 0:04:41.963561 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R6/calibration_manager.pkl
3 days, 0:04:41.963673 INFO: Initializing CalibrationManager
3 days, 0:04:41.963970 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R6/raw_file_manager.pkl
3 days, 0:04:41.964083 INFO: Initializing RawFileManager
3 days, 0:04:41.976168 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R1/optimization_manager.pkl
3 days, 0:04:41.976362 INFO: Initializing OptimizationManager
3 days, 0:04:41.976603 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R1/calibration_manager.pkl
3 days, 0:04:41.976680 INFO: Initializing CalibrationManager
3 days, 0:04:41.977101 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R1/raw_file_manager.pkl
3 days, 0:04:41.977188 INFO: Initializing RawFileManager
3 days, 0:04:41.986119 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R2/optimization_manager.pkl
3 days, 0:04:41.986275 INFO: Initializing OptimizationManager
3 days, 0:04:41.986508 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R2/calibration_manager.pkl
3 days, 0:04:41.986585 INFO: Initializing CalibrationManager
3 days, 0:04:41.986814 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R2/raw_file_manager.pkl
3 days, 0:04:41.986892 INFO: Initializing RawFileManager
3 days, 0:04:41.995763 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R3/optimization_manager.pkl
3 days, 0:04:41.995914 INFO: Initializing OptimizationManager
3 days, 0:04:41.996137 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R3/calibration_manager.pkl
3 days, 0:04:41.996214 INFO: Initializing CalibrationManager
3 days, 0:04:41.996444 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R3/raw_file_manager.pkl
3 days, 0:04:41.996526 INFO: Initializing RawFileManager
3 days, 0:04:42.005529 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R4/optimization_manager.pkl
3 days, 0:04:42.005696 INFO: Initializing OptimizationManager
3 days, 0:04:42.005951 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R4/calibration_manager.pkl
3 days, 0:04:42.006033 INFO: Initializing CalibrationManager
3 days, 0:04:42.006260 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R4/raw_file_manager.pkl
3 days, 0:04:42.006339 INFO: Initializing RawFileManager
3 days, 0:04:42.014714 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R5/optimization_manager.pkl
3 days, 0:04:42.014864 INFO: Initializing OptimizationManager
3 days, 0:04:42.015106 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R5/calibration_manager.pkl
3 days, 0:04:42.015192 INFO: Initializing CalibrationManager
3 days, 0:04:42.015430 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R5/raw_file_manager.pkl
3 days, 0:04:42.015517 INFO: Initializing RawFileManager
3 days, 0:04:42.024331 INFO: Loaded OptimizationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R6/optimization_manager.pkl
3 days, 0:04:42.024493 INFO: Initializing OptimizationManager
3 days, 0:04:42.024719 INFO: Loaded CalibrationManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R6/calibration_manager.pkl
3 days, 0:04:42.024810 INFO: Initializing CalibrationManager
3 days, 0:04:42.025026 INFO: Loaded RawFileManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R6/raw_file_manager.pkl
3 days, 0:04:42.025101 INFO: Initializing RawFileManager
3 days, 0:04:42.026823 INFO: Writing stat output to disk
3 days, 0:04:42.026884 INFO: Saving plasma_output/alphadia_2.1.0/stat.tsv to disk
3 days, 0:04:42.031396 PROGRESS: Building internal statistics
3 days, 0:04:42.031591 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R1/timing_manager.pkl
3 days, 0:04:42.031634 INFO: Initializing TimingManager
3 days, 0:04:42.031975 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R2/timing_manager.pkl
3 days, 0:04:42.032019 INFO: Initializing TimingManager
3 days, 0:04:42.032229 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R3/timing_manager.pkl
3 days, 0:04:42.032269 INFO: Initializing TimingManager
3 days, 0:04:42.032467 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R4/timing_manager.pkl
3 days, 0:04:42.032509 INFO: Initializing TimingManager
3 days, 0:04:42.032701 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R5/timing_manager.pkl
3 days, 0:04:42.032740 INFO: Initializing TimingManager
3 days, 0:04:42.032942 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/A9_G_DIA_nLC_tTOF_R6/timing_manager.pkl
3 days, 0:04:42.032980 INFO: Initializing TimingManager
3 days, 0:04:42.033179 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R1/timing_manager.pkl
3 days, 0:04:42.033218 INFO: Initializing TimingManager
3 days, 0:04:42.033413 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R2/timing_manager.pkl
3 days, 0:04:42.033449 INFO: Initializing TimingManager
3 days, 0:04:42.033640 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R3/timing_manager.pkl
3 days, 0:04:42.033677 INFO: Initializing TimingManager
3 days, 0:04:42.033899 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R4/timing_manager.pkl
3 days, 0:04:42.033942 INFO: Initializing TimingManager
3 days, 0:04:42.034144 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R5/timing_manager.pkl
3 days, 0:04:42.034182 INFO: Initializing TimingManager
3 days, 0:04:42.034392 INFO: Loaded TimingManager from plasma_output/alphadia_2.1.0/quant/B9_G_DIA_nLC_tTOF_R6/timing_manager.pkl
3 days, 0:04:42.034431 INFO: Initializing TimingManager
3 days, 0:04:42.034986 INFO: Writing internal output to disk
3 days, 0:04:42.035036 INFO: Saving plasma_output/alphadia_2.1.0/internal.tsv to disk
3 days, 0:04:42.076146 INFO: Performing label free quantification
3 days, 0:04:42.076314 INFO: Accumulating fragment data
3 days, 0:04:42.076384 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R1
3 days, 0:04:42.091275 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R2
3 days, 0:04:42.259092 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R3
3 days, 0:04:42.403062 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R4
3 days, 0:04:42.573120 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R5
3 days, 0:04:42.736637 INFO: reading frag file for A9_G_DIA_nLC_tTOF_R6
3 days, 0:04:42.910144 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R1
3 days, 0:04:43.089712 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R2
3 days, 0:04:43.270437 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R3
3 days, 0:04:43.441605 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R4
3 days, 0:04:43.619341 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R5
3 days, 0:04:43.808224 INFO: reading frag file for B9_G_DIA_nLC_tTOF_R6
3 days, 0:04:44.054931 INFO: Performing label free quantification on the precursor level
3 days, 0:04:44.055102 INFO: Filtering fragments by quality
3 days, 0:04:44.095112 INFO: Performing label-free quantification with directlfq normalization
3 days, 0:04:44.162846 INFO: Applying directLFQ normalization
3 days, 0:04:44.358321 INFO: 13756 lfq-groups total
3 days, 0:06:17.194665 INFO: using 80 processes
3 days, 0:06:17.277838 INFO: lfq-object 0
3 days, 0:06:17.345526 INFO: lfq-object 100
3 days, 0:06:17.407483 INFO: lfq-object 200
3 days, 0:06:17.458521 INFO: lfq-object 400
3 days, 0:06:17.497752 INFO: lfq-object 300
3 days, 0:06:17.526495 INFO: lfq-object 500
3 days, 0:06:17.637284 INFO: lfq-object 600
3 days, 0:06:17.655135 INFO: lfq-object 700
3 days, 0:06:17.755691 INFO: lfq-object 800
3 days, 0:06:17.842175 INFO: lfq-object 1000
3 days, 0:06:17.847297 INFO: lfq-object 900
3 days, 0:06:17.896342 INFO: lfq-object 1100
3 days, 0:06:18.001435 INFO: lfq-object 1300
3 days, 0:06:18.013480 INFO: lfq-object 1200
3 days, 0:06:18.104620 INFO: lfq-object 1400
3 days, 0:06:18.199232 INFO: lfq-object 1600
3 days, 0:06:18.202483 INFO: lfq-object 1500
3 days, 0:06:18.275180 INFO: lfq-object 1700
3 days, 0:06:18.352570 INFO: lfq-object 1800
3 days, 0:06:18.388907 INFO: lfq-object 1900
3 days, 0:06:18.499104 INFO: lfq-object 2000
3 days, 0:06:18.578453 INFO: lfq-object 2200
3 days, 0:06:18.588642 INFO: lfq-object 2100
3 days, 0:06:18.639537 INFO: lfq-object 2300
3 days, 0:06:18.752155 INFO: lfq-object 2400
3 days, 0:06:18.781148 INFO: lfq-object 2500
3 days, 0:06:18.868678 INFO: lfq-object 2600
3 days, 0:06:18.947191 INFO: lfq-object 2800
3 days, 0:06:18.968829 INFO: lfq-object 2700
3 days, 0:06:19.045403 INFO: lfq-object 2900
3 days, 0:06:19.111340 INFO: lfq-object 3000
3 days, 0:06:19.148705 INFO: lfq-object 3100
3 days, 0:06:19.226470 INFO: lfq-object 3200
3 days, 0:06:19.315399 INFO: lfq-object 3300
3 days, 0:06:19.318228 INFO: lfq-object 3400
3 days, 0:06:19.381603 INFO: lfq-object 3500
3 days, 0:06:19.439276 INFO: lfq-object 3600
3 days, 0:06:19.482312 INFO: lfq-object 3700
3 days, 0:06:19.580063 INFO: lfq-object 3800
3 days, 0:06:19.662720 INFO: lfq-object 4000
3 days, 0:06:19.663919 INFO: lfq-object 3900
3 days, 0:06:19.750633 INFO: lfq-object 4100
3 days, 0:06:19.831051 INFO: lfq-object 4300
3 days, 0:06:19.839585 INFO: lfq-object 4200
3 days, 0:06:19.924410 INFO: lfq-object 4400
3 days, 0:06:20.028947 INFO: lfq-object 4500
3 days, 0:06:20.108820 INFO: lfq-object 4700
3 days, 0:06:20.118129 INFO: lfq-object 4600
3 days, 0:06:20.155437 INFO: lfq-object 4800
3 days, 0:06:20.231813 INFO: lfq-object 5000
3 days, 0:06:20.241827 INFO: lfq-object 4900
3 days, 0:06:20.322853 INFO: lfq-object 5100
3 days, 0:06:20.425780 INFO: lfq-object 5300
3 days, 0:06:20.430916 INFO: lfq-object 5200
3 days, 0:06:20.514663 INFO: lfq-object 5400
3 days, 0:06:20.568865 INFO: lfq-object 5500
3 days, 0:06:20.614127 INFO: lfq-object 5600
3 days, 0:06:20.687538 INFO: lfq-object 5700
3 days, 0:06:20.750001 INFO: lfq-object 5900
3 days, 0:06:20.764819 INFO: lfq-object 5800
3 days, 0:06:20.847876 INFO: lfq-object 6000
3 days, 0:06:20.951248 INFO: lfq-object 6200
3 days, 0:06:20.958160 INFO: lfq-object 6100
3 days, 0:06:21.027568 INFO: lfq-object 6300
3 days, 0:06:21.090474 INFO: lfq-object 6400
3 days, 0:06:21.120310 INFO: lfq-object 6500
3 days, 0:06:21.229532 INFO: lfq-object 6600
3 days, 0:06:21.287320 INFO: lfq-object 6800
3 days, 0:06:21.322056 INFO: lfq-object 6700
3 days, 0:06:21.364420 INFO: lfq-object 6900
3 days, 0:06:21.473950 INFO: lfq-object 7000
3 days, 0:06:21.488827 INFO: lfq-object 7100
3 days, 0:06:21.588450 INFO: lfq-object 7200
3 days, 0:06:21.642369 INFO: lfq-object 7400
3 days, 0:06:21.669135 INFO: lfq-object 7300
3 days, 0:06:21.712984 INFO: lfq-object 7500
3 days, 0:06:21.838833 INFO: lfq-object 7700
3 days, 0:06:21.848234 INFO: lfq-object 7600
3 days, 0:06:21.901145 INFO: lfq-object 7800
3 days, 0:06:21.995294 INFO: lfq-object 7900
3 days, 0:06:22.009008 INFO: lfq-object 8000
3 days, 0:06:22.098885 INFO: lfq-object 8100
3 days, 0:06:22.203574 INFO: lfq-object 8300
3 days, 0:06:22.227267 INFO: lfq-object 8200
3 days, 0:06:22.305025 INFO: lfq-object 8400
3 days, 0:06:22.366212 INFO: lfq-object 8600
3 days, 0:06:22.382541 INFO: lfq-object 8500
3 days, 0:06:22.474463 INFO: lfq-object 8700
3 days, 0:06:22.547335 INFO: lfq-object 8800
3 days, 0:06:22.622998 INFO: lfq-object 8900
3 days, 0:06:22.633567 INFO: lfq-object 9000
3 days, 0:06:22.737452 INFO: lfq-object 9100
3 days, 0:06:22.780102 INFO: lfq-object 9300
3 days, 0:06:22.793128 INFO: lfq-object 9200
3 days, 0:06:22.864639 INFO: lfq-object 9400
3 days, 0:06:22.945903 INFO: lfq-object 9500
3 days, 0:06:22.972141 INFO: lfq-object 9600
3 days, 0:06:23.057813 INFO: lfq-object 9700
3 days, 0:06:23.142769 INFO: lfq-object 9900
3 days, 0:06:23.159773 INFO: lfq-object 9800
3 days, 0:06:23.224610 INFO: lfq-object 10000
3 days, 0:06:23.297270 INFO: lfq-object 10100
3 days, 0:06:23.302322 INFO: lfq-object 10200
3 days, 0:06:23.370663 INFO: lfq-object 10300
3 days, 0:06:23.489036 INFO: lfq-object 10400
3 days, 0:06:23.498901 INFO: lfq-object 10500
3 days, 0:06:23.580774 INFO: lfq-object 10600
3 days, 0:06:23.636947 INFO: lfq-object 10700
3 days, 0:06:23.665301 INFO: lfq-object 10800
3 days, 0:06:23.739131 INFO: lfq-object 10900
3 days, 0:06:23.818693 INFO: lfq-object 11000
3 days, 0:06:23.869361 INFO: lfq-object 11100
3 days, 0:06:23.941340 INFO: lfq-object 11200
3 days, 0:06:23.996856 INFO: lfq-object 11300
3 days, 0:06:24.013601 INFO: lfq-object 11400
3 days, 0:06:24.093762 INFO: lfq-object 11500
3 days, 0:06:24.178926 INFO: lfq-object 11600
3 days, 0:06:24.194112 INFO: lfq-object 11700
3 days, 0:06:24.308229 INFO: lfq-object 11800
3 days, 0:06:24.374426 INFO: lfq-object 12000
3 days, 0:06:24.395030 INFO: lfq-object 11900
3 days, 0:06:24.440874 INFO: lfq-object 12100
3 days, 0:06:24.511546 INFO: lfq-object 12300
3 days, 0:06:24.517852 INFO: lfq-object 12200
3 days, 0:06:24.614142 INFO: lfq-object 12400
3 days, 0:06:24.687063 INFO: lfq-object 12500
3 days, 0:06:24.713293 INFO: lfq-object 12600
3 days, 0:06:24.783006 INFO: lfq-object 12700
3 days, 0:06:24.875691 INFO: lfq-object 12800
3 days, 0:06:24.886386 INFO: lfq-object 12900
3 days, 0:06:24.993287 INFO: lfq-object 13000
3 days, 0:06:25.088283 INFO: lfq-object 13100
3 days, 0:06:25.155182 INFO: lfq-object 13200
3 days, 0:06:25.164258 INFO: lfq-object 13300
3 days, 0:06:25.232797 INFO: lfq-object 13400
3 days, 0:06:25.292015 INFO: lfq-object 13500
3 days, 0:06:25.322055 INFO: lfq-object 13600
3 days, 0:06:25.411360 INFO: lfq-object 13700
3 days, 0:06:29.706882 INFO: Performing label free quantification on the peptide level
3 days, 0:06:29.707049 INFO: Filtering fragments by quality
3 days, 0:06:29.758270 INFO: Performing label-free quantification with directlfq normalization
3 days, 0:06:29.833752 INFO: Applying directLFQ normalization
3 days, 0:06:30.038353 INFO: 12844 lfq-groups total
3 days, 0:08:13.960520 INFO: using 80 processes
3 days, 0:08:14.036054 INFO: lfq-object 0
3 days, 0:08:14.151880 INFO: lfq-object 100
3 days, 0:08:14.244008 INFO: lfq-object 200
3 days, 0:08:14.262080 INFO: lfq-object 300
3 days, 0:08:14.366061 INFO: lfq-object 400
3 days, 0:08:14.373200 INFO: lfq-object 500
3 days, 0:08:14.474941 INFO: lfq-object 600
3 days, 0:08:14.521071 INFO: lfq-object 700
3 days, 0:08:14.622595 INFO: lfq-object 800
3 days, 0:08:14.769751 INFO: lfq-object 900
3 days, 0:08:14.772620 INFO: lfq-object 1000
3 days, 0:08:14.850676 INFO: lfq-object 1100
3 days, 0:08:14.870522 INFO: lfq-object 1200
3 days, 0:08:15.003384 INFO: lfq-object 1400
3 days, 0:08:15.004620 INFO: lfq-object 1300
3 days, 0:08:15.104530 INFO: lfq-object 1600
3 days, 0:08:15.118732 INFO: lfq-object 1500
3 days, 0:08:15.193492 INFO: lfq-object 1700
3 days, 0:08:15.327504 INFO: lfq-object 1800
3 days, 0:08:15.328617 INFO: lfq-object 1900
3 days, 0:08:15.443336 INFO: lfq-object 2000
3 days, 0:08:15.474291 INFO: lfq-object 2100
3 days, 0:08:15.570734 INFO: lfq-object 2300
3 days, 0:08:15.573974 INFO: lfq-object 2200
3 days, 0:08:15.641483 INFO: lfq-object 2400
3 days, 0:08:15.780874 INFO: lfq-object 2500
3 days, 0:08:15.801327 INFO: lfq-object 2600
3 days, 0:08:15.902995 INFO: lfq-object 2700
3 days, 0:08:15.912804 INFO: lfq-object 2800
3 days, 0:08:16.010082 INFO: lfq-object 2900
3 days, 0:08:16.022334 INFO: lfq-object 3000
3 days, 0:08:16.120065 INFO: lfq-object 3200
3 days, 0:08:16.121801 INFO: lfq-object 3100
3 days, 0:08:16.201307 INFO: lfq-object 3300
3 days, 0:08:16.268313 INFO: lfq-object 3400
3 days, 0:08:16.327870 INFO: lfq-object 3500
3 days, 0:08:16.387968 INFO: lfq-object 3600
3 days, 0:08:16.414140 INFO: lfq-object 3700
3 days, 0:08:16.493851 INFO: lfq-object 3800
3 days, 0:08:16.507241 INFO: lfq-object 3900
3 days, 0:08:16.602059 INFO: lfq-object 4100
3 days, 0:08:16.612753 INFO: lfq-object 4000
3 days, 0:08:16.691104 INFO: lfq-object 4200
3 days, 0:08:16.782491 INFO: lfq-object 4300
3 days, 0:08:16.790076 INFO: lfq-object 4400
3 days, 0:08:16.883261 INFO: lfq-object 4500
3 days, 0:08:16.902769 INFO: lfq-object 4600
3 days, 0:08:16.992414 INFO: lfq-object 4700
3 days, 0:08:17.030221 INFO: lfq-object 4800
3 days, 0:08:17.108466 INFO: lfq-object 4900
3 days, 0:08:17.232224 INFO: lfq-object 5000
3 days, 0:08:17.234722 INFO: lfq-object 5100
3 days, 0:08:17.318491 INFO: lfq-object 5200
3 days, 0:08:17.358696 INFO: lfq-object 5300
3 days, 0:08:17.420228 INFO: lfq-object 5400
3 days, 0:08:17.433967 INFO: lfq-object 5500
3 days, 0:08:17.520042 INFO: lfq-object 5600
3 days, 0:08:17.536438 INFO: lfq-object 5700
3 days, 0:08:17.625936 INFO: lfq-object 5800
3 days, 0:08:17.729119 INFO: lfq-object 5900
3 days, 0:08:17.774177 INFO: lfq-object 6000
3 days, 0:08:17.827359 INFO: lfq-object 6100
3 days, 0:08:17.841715 INFO: lfq-object 6200
3 days, 0:08:17.957085 INFO: lfq-object 6300
3 days, 0:08:17.957126 INFO: lfq-object 6400
3 days, 0:08:18.054329 INFO: lfq-object 6500
3 days, 0:08:18.184567 INFO: lfq-object 6600
3 days, 0:08:18.185813 INFO: lfq-object 6700
3 days, 0:08:18.285941 INFO: lfq-object 6800
3 days, 0:08:18.331285 INFO: lfq-object 6900
3 days, 0:08:18.417980 INFO: lfq-object 7000
3 days, 0:08:18.436907 INFO: lfq-object 7100
3 days, 0:08:18.541103 INFO: lfq-object 7200
3 days, 0:08:18.552524 INFO: lfq-object 7300
3 days, 0:08:18.624540 INFO: lfq-object 7400
3 days, 0:08:18.699225 INFO: lfq-object 7500
3 days, 0:08:18.743578 INFO: lfq-object 7600
3 days, 0:08:18.841251 INFO: lfq-object 7800
3 days, 0:08:18.848946 INFO: lfq-object 7700
3 days, 0:08:18.929110 INFO: lfq-object 7900
3 days, 0:08:18.946221 INFO: lfq-object 8000
3 days, 0:08:19.063703 INFO: lfq-object 8100
3 days, 0:08:19.085638 INFO: lfq-object 8200
3 days, 0:08:19.193307 INFO: lfq-object 8300
3 days, 0:08:19.282996 INFO: lfq-object 8400
3 days, 0:08:19.309654 INFO: lfq-object 8500
3 days, 0:08:19.389857 INFO: lfq-object 8600
3 days, 0:08:19.435005 INFO: lfq-object 8700
3 days, 0:08:19.547508 INFO: lfq-object 8900
3 days, 0:08:19.549433 INFO: lfq-object 8800
3 days, 0:08:19.642613 INFO: lfq-object 9000
3 days, 0:08:19.738475 INFO: lfq-object 9100
3 days, 0:08:19.758222 INFO: lfq-object 9200
3 days, 0:08:19.836447 INFO: lfq-object 9300
3 days, 0:08:19.882016 INFO: lfq-object 9400
3 days, 0:08:19.961735 INFO: lfq-object 9500
3 days, 0:08:19.995497 INFO: lfq-object 9600
3 days, 0:08:20.103142 INFO: lfq-object 9800
3 days, 0:08:20.107734 INFO: lfq-object 9700
3 days, 0:08:20.191876 INFO: lfq-object 9900
3 days, 0:08:20.298843 INFO: lfq-object 10100
3 days, 0:08:20.319578 INFO: lfq-object 10000
3 days, 0:08:20.390198 INFO: lfq-object 10300
3 days, 0:08:20.396690 INFO: lfq-object 10200
3 days, 0:08:20.478457 INFO: lfq-object 10400
3 days, 0:08:20.498306 INFO: lfq-object 10500
3 days, 0:08:20.606256 INFO: lfq-object 10600
3 days, 0:08:20.681457 INFO: lfq-object 10700
3 days, 0:08:20.717062 INFO: lfq-object 10800
3 days, 0:08:20.835353 INFO: lfq-object 10900
3 days, 0:08:20.842546 INFO: lfq-object 11000
3 days, 0:08:20.944042 INFO: lfq-object 11100
3 days, 0:08:20.953756 INFO: lfq-object 11200
3 days, 0:08:21.046382 INFO: lfq-object 11300
3 days, 0:08:21.067049 INFO: lfq-object 11400
3 days, 0:08:21.157784 INFO: lfq-object 11500
3 days, 0:08:21.239157 INFO: lfq-object 11600
3 days, 0:08:21.269516 INFO: lfq-object 11700
3 days, 0:08:21.358148 INFO: lfq-object 11800
3 days, 0:08:21.402107 INFO: lfq-object 11900
3 days, 0:08:21.483290 INFO: lfq-object 12000
3 days, 0:08:21.512685 INFO: lfq-object 12100
3 days, 0:08:21.638040 INFO: lfq-object 12200
3 days, 0:08:21.649449 INFO: lfq-object 12300
3 days, 0:08:21.709746 INFO: lfq-object 12400
3 days, 0:08:21.812543 INFO: lfq-object 12600
3 days, 0:08:21.822832 INFO: lfq-object 12500
3 days, 0:08:21.911118 INFO: lfq-object 12700
3 days, 0:08:21.921447 INFO: lfq-object 12800
3 days, 0:08:26.096753 INFO: Performing label free quantification on the pg level
3 days, 0:08:26.096961 INFO: Filtering fragments by quality
3 days, 0:08:26.140271 INFO: Performing label-free quantification with directlfq normalization
3 days, 0:08:26.176762 INFO: Applying directLFQ normalization
3 days, 0:08:26.284190 INFO: 1683 lfq-groups total
3 days, 0:10:00.971811 INFO: using 80 processes
3 days, 0:10:00.997837 INFO: lfq-object 0
3 days, 0:10:01.097623 INFO: lfq-object 100
3 days, 0:10:01.187618 INFO: lfq-object 200
3 days, 0:10:01.273246 INFO: lfq-object 300
3 days, 0:10:01.389983 INFO: lfq-object 400
3 days, 0:10:01.440545 INFO: lfq-object 500
3 days, 0:10:01.554388 INFO: lfq-object 600
3 days, 0:10:01.652836 INFO: lfq-object 700
3 days, 0:10:01.770593 INFO: lfq-object 800
3 days, 0:10:01.838257 INFO: lfq-object 900
3 days, 0:10:01.957202 INFO: lfq-object 1000
3 days, 0:10:02.040855 INFO: lfq-object 1100
3 days, 0:10:02.064213 INFO: lfq-object 1200
3 days, 0:10:02.152108 INFO: lfq-object 1300
3 days, 0:10:02.235381 INFO: lfq-object 1400
3 days, 0:10:02.303689 INFO: lfq-object 1500
3 days, 0:10:02.382762 INFO: lfq-object 1600
3 days, 0:10:06.764189 INFO: Writing psm output to disk
3 days, 0:10:06.799790 INFO: Saving plasma_output/alphadia_2.1.0/precursors.parquet to disk
3 days, 0:10:07.129132 INFO: Writing precursor output to disk
3 days, 0:10:07.130467 INFO: Saving plasma_output/alphadia_2.1.0/precursor.matrix.parquet to disk
3 days, 0:10:07.153302 INFO: Writing peptide output to disk
3 days, 0:10:07.155194 INFO: Saving plasma_output/alphadia_2.1.0/peptide.matrix.parquet to disk
3 days, 0:10:07.180352 INFO: Writing pg output to disk
3 days, 0:10:07.181545 INFO: Saving plasma_output/alphadia_2.1.0/pg.matrix.parquet to disk
3 days, 0:10:07.220851 PROGRESS: Building MBR spectral library
3 days, 0:10:07.221076 INFO: Running MbrLibraryBuilder
3 days, 0:10:07.359975 INFO: MBR spectral library contains 13,756 precursors, 1,683 proteins
3 days, 0:10:07.360124 INFO: Writing MBR spectral library to disk
3 days, 0:10:07.584310 PROGRESS: =================== Search step 'mbr' finished ===================
3 days, 0:10:07.592568 INFO: =================== Search Finished ===================
