0:00:00.000028 INFO: Moved old log file ./run_output/alphadia_1.12.1_rs_benchmark_MBR/log.txt to run_output/alphadia_1.12.1_rs_benchmark_MBR/log.txt
0:00:00.000155 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/run_output/alphadia_1.12.1_rs_benchmark_MBR, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000192 INFO: User provided config file: config_alphadia112_rs_diaPASEF.yaml.
0:00:00.000219 INFO: User provided config dict: {}.
0:00:00.013415 PROGRESS:           _      _         ___ ___   _   
0:00:00.013478 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.013504 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013531 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013556 PROGRESS:            |_|                           
0:00:00.013576 PROGRESS: 
0:00:00.013596 PROGRESS: version: 1.12.1
0:00:00.013625 INFO: hostname: thestral
0:00:00.013677 INFO: date: 2025-10-19 18:09:37
0:00:00.013700 INFO: ================ AlphaX Environment ===============
0:00:00.013722 INFO: alphatims       : 1.0.9
0:00:00.013740 INFO: alpharaw        : 0.4.7
0:00:00.013759 INFO: alphabase       : 1.7.1
0:00:00.013777 INFO: alphapeptdeep   : 1.3.2
0:00:00.013795 INFO: directlfq       : 0.3.1
0:00:00.013815 INFO: ===================================================
0:00:00.013833 INFO: ================= Pip Environment =================
0:00:00.075742 INFO: peptdeep==1.3.2 pytz==2025.2 click==8.1.8 partd==1.4.2 wget==3.2 uri-template==1.3.0 nvidia-nvjitlink-cu12==12.4.127 huggingface-hub==0.30.2 fqdn==1.5.1 jsonref==1.1.0 rdkit==2024.9.6 simplejson==3.20.1 alphabase==1.7.1 tornado==6.4.2 s3transfer==0.11.4 tqdm==4.67.1 psutil==7.0.0 arrow==1.3.0 dask==2024.11.2 torchmetrics==1.7.1 numpy==1.26.4 directlfq==0.3.1 gitdb==4.0.12 contextlib2==21.6.0 future==1.0.0 toolz==1.0.0 monotonic==1.6 argparse==1.4.0 nvidia-cuda-cupti-cu12==12.4.127 importlib_resources==6.5.2 packaging==24.2 SQLAlchemy==2.0.39 pyarrow==19.0.1 alphadia-search-rs==0.2.0 joblib==1.4.2 requests-oauthlib==2.0.0 transformers==4.51.2 webcolors==24.11.1 cffi==1.17.1 nvidia-cuda-nvrtc-cu12==12.4.127 numba==0.61.2 protobuf==5.29.3 pyteomics==4.7.5 alphadia==1.12.1 mpmath==1.3.0 multiprocess==0.70.17 lightning-utilities==0.14.3 MarkupSafe==3.0.2 pyzstd==0.16.2 six==1.17.0 cycler==0.12.1 charset-normalizer==3.4.1 tenacity==9.0.0 fsspec==2025.3.2 xxhash==3.5.0 attrs==25.2.0 pip==23.0.1 threadpoolctl==3.6.0 pythonnet==3.0.5 requests==2.32.3 triton==3.2.0 alphatims==1.0.9 h5py==3.13.0 oauthlib==3.2.2 zstandard==0.22.0 pyahocorasick==2.1.0 swagger-spec-validator==3.0.4 blinker==1.9.0 pycparser==2.22 regex==2024.11.6 streamlit-aggrid==1.1.1 streamlit==1.43.2 websocket-client==1.8.0 certifi==2025.1.31 narwhals==1.30.0 isoduration==20.11.0 python-dateutil==2.9.0.post0 botocore==1.37.11 locket==1.0.0 alpharaw==0.4.7 referencing==0.36.2 torch==2.6.0 setuptools==78.1.0 nvidia-cusparse-cu12==12.3.1.170 rocket-fft==0.2.5 neptune==1.10.4 importlib_metadata==8.6.1 cloudpickle==3.1.1 clr_loader==0.2.7.post0 pandas==2.2.3 dill==0.3.9 pyparsing==3.2.3 typing_extensions==4.13.2 jsonschema-specifications==2024.10.1 networkx==3.4.2 biopython==1.85 urllib3==2.4.0 types-python-dateutil==2.9.0.20241206 seaborn==0.13.2 toml==0.10.2 zipp==3.21.0 rfc3339-validator==0.1.4 altair==5.5.0 llvmlite==0.44.0 greenlet==3.1.1 fonttools==4.57.0 scipy==1.12.0 tzdata==2025.2 filelock==3.18.0 matplotlib==3.10.1 contourpy==1.3.1 pydeck==0.9.1 lxml==5.3.2 Jinja2==3.1.6 bravado-core==6.1.1 msgpack==1.1.0 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 safetensors==0.5.3 idna==3.10 cachetools==5.5.2 jsonpointer==3.0.0 rpds-py==0.23.1 nvidia-cufft-cu12==11.2.1.3 jsonschema==4.23.0 watchdog==6.0.0 python-decouple==3.8 sympy==1.13.1 boto3==1.37.11 dask-expr==1.1.19 pillow==11.1.0 plotly==6.0.0 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 tokenizers==0.21.1 smmap==5.0.2 nvidia-curand-cu12==10.3.5.147 GitPython==3.1.44 progressbar==2.5 PyJWT==2.10.1 kiwisolver==1.4.8 nvidia-cuda-runtime-cu12==12.4.127 scikit-learn==1.6.1 nvidia-nccl-cu12==2.21.5 jmespath==1.0.1 rfc3986-validator==0.1.1 bravado==11.1.0 nvidia-cusparselt-cu12==0.6.2 PyYAML==6.0.2 more-itertools==10.3.0 wheel==0.45.1 autocommand==2.2.2 packaging==24.2 typing_extensions==4.12.2 tomli==2.0.1 backports.tarfile==1.2.0 jaraco.functools==4.0.1 jaraco.text==3.12.1 platformdirs==4.2.2 jaraco.collections==5.1.0 typeguard==4.3.0 jaraco.context==5.3.0 importlib_metadata==8.0.0 inflect==7.3.1 zipp==3.19.2
0:00:00.075847 INFO: ===================================================
0:00:00.075880 INFO: Running step 'library'
0:00:00.075992 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.087233 INFO: loading additional config provided via CLI
0:00:00.087296 INFO: loading additional config provided via CLI parameters
0:00:00.087681 INFO: Updating config with 'user defined'
0:00:00.087820 INFO: Updating config with 'user defined (cli)'
0:00:00.087925 INFO: updating config with user defined values: [{'version': 1, 'workflow_name': None, 'output_directory': None, 'library_path': None, 'raw_paths': ['./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.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': False, 'save_figures': True, 'save_library': True, 'save_flat_library': False, 'input_library_type': 'base', 'save_mbr_library': True, 'random_state': None}, 'library_loading': {'rt_heuristic': 180}, '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': 'classic', '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': {'initial_num_candidates': 1, 'initial_ms1_tolerance': 30, 'initial_ms2_tolerance': 30, 'initial_mobility_tolerance': 0.1, 'initial_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, 'competetive_scoring': True}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins', 'inference_strategy': 'heuristic', 'competetive_scoring': True, 'keep_decoys': False, 'channel_wise_fdr': False, 'enable_two_step_classifier': False, 'two_step_classifier_max_iterations': 5, 'enable_nn_hyperparameter_tuning': False}, 'search_output': {'file_format': 'tsv', 'peptide_level_lfq': False, 'precursor_level_lfq': True, 'save_fragment_quant_matrix': False, 'min_k_fragments': 12, 'min_correlation': 0.9, 'num_samples_quadratic': 50, 'min_nonnan': 3, 'normalize_lfq': True}, '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': 'timsTOF'}}, {'raw_paths': ['./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d'], 'library_path': '/home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf', 'fasta_paths': ['./ProteoBenchFASTA_DDAQuantification.fasta']}, {'quant_directory': None, 'general': {'save_mbr_library': True, 'save_library': False, 'reuse_quant': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'output_directory': 'run_output/alphadia_1.12.1_rs_benchmark_MBR/library'}]
0:00:00.088182 INFO: Updating config with 'user defined'
0:00:00.088294 INFO: Updating config with 'user defined (cli)'
0:00:00.088317 INFO: Updating config with 'multistep search'
0:00:00.088355 INFO: ├──version: 1
0:00:00.088380 INFO: ├──workflow_name: None
0:00:00.088402 INFO: [32;20m├──output_directory: run_output/alphadia_1.12.1_rs_benchmark_MBR/library [multistep search, default: None][0m
0:00:00.088431 INFO: [32;20m├──library_path: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf [user defined (cli), default: None][0m
0:00:00.088452 INFO: ├──raw_paths:
0:00:00.088472 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
0:00:00.088491 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
0:00:00.088510 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
0:00:00.088532 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
0:00:00.088551 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
0:00:00.088568 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
0:00:00.088587 INFO: ├──fasta_paths:
0:00:00.088607 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.088627 INFO: ├──quant_directory: None
0:00:00.088646 INFO: ├──general
0:00:00.088666 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:00:00.088685 INFO: │   ├──transfer_step_enabled: False
0:00:00.088705 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.088724 INFO: │   ├──reuse_calibration: False
0:00:00.088743 INFO: │   ├──reuse_quant: False
0:00:00.088764 INFO: │   ├──astral_ms1: False
0:00:00.088783 INFO: │   ├──log_level: INFO
0:00:00.088802 INFO: │   ├──mmap_detector_events: False
0:00:00.088822 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.088842 INFO: │   ├──save_figures: True
0:00:00.088862 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.088881 INFO: │   ├──save_flat_library: False
0:00:00.088899 INFO: │   ├──input_library_type: base
0:00:00.088917 INFO: │   ├──save_mbr_library: True
0:00:00.088936 INFO: │   └──random_state: None
0:00:00.088954 INFO: ├──library_loading
0:00:00.088974 INFO: │   └──rt_heuristic: 180
0:00:00.088992 INFO: ├──library_prediction
0:00:00.089010 INFO: │   ├──enabled: False
0:00:00.089029 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.089049 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.089068 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.089086 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.089104 INFO: │   ├──missed_cleavages: 1
0:00:00.089123 INFO: │   ├──precursor_len:
0:00:00.089143 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.089162 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.089180 INFO: │   ├──precursor_charge:
0:00:00.089198 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.089216 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.089233 INFO: │   ├──precursor_mz:
0:00:00.089252 INFO: │   │   - 400
0:00:00.089270 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.089290 INFO: │   ├──fragment_mz:
0:00:00.089307 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.089326 INFO: │   │   - 2000
0:00:00.089344 INFO: │   ├──nce: 25.0
0:00:00.089360 INFO: │   ├──fragment_types:
0:00:00.089378 INFO: │   │   - b
0:00:00.089396 INFO: │   │   - y
0:00:00.089414 INFO: │   ├──max_fragment_charge: 2
0:00:00.089432 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.089456 INFO: │   ├──peptdeep_model_path: None
0:00:00.089475 INFO: │   └──peptdeep_model_type: generic
0:00:00.089493 INFO: ├──custom_modifications:
0:00:00.089512 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.089530 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.089548 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.089566 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.089586 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.089604 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.089622 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.089639 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.089659 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.089677 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.089694 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.089713 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.089731 INFO: │   ├──name: Label:13C(12)@K
0:00:00.089748 INFO: │   └──composition: C(12)
0:00:00.089766 INFO: ├──search
0:00:00.089784 INFO: │   ├──extraction_backend: classic
0:00:00.089802 INFO: │   [32;20m├──target_ms1_tolerance: 15 [user defined, default: 5][0m
0:00:00.089820 INFO: │   [32;20m├──target_ms2_tolerance: 15 [user defined, default: 10][0m
0:00:00.089839 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.089858 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.089875 INFO: │   ├──quant_window: 3
0:00:00.089893 INFO: │   ├──target_num_candidates: 3
0:00:00.089911 INFO: │   ├──channel_filter: 
0:00:00.089930 INFO: │   ├──exclude_shared_ions: True
0:00:00.089948 INFO: │   ├──compete_for_fragments: True
0:00:00.089966 INFO: │   ├──quant_all: True
0:00:00.089984 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.090002 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.090020 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.090037 INFO: │   ├──experimental_xic: True
0:00:00.090073 INFO: │   └──optimized_peak_group_score: False
0:00:00.090090 INFO: ├──calibration
0:00:00.090109 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.090130 INFO: │   ├──optimization_lock_target: 200
0:00:00.090148 INFO: │   ├──max_steps: 20
0:00:00.090167 INFO: │   ├──min_steps: 2
0:00:00.090185 INFO: │   ├──max_skips: 1
0:00:00.090204 INFO: │   ├──max_fragments: 5000
0:00:00.090223 INFO: │   └──min_correlation: 0.7
0:00:00.090241 INFO: ├──search_initial
0:00:00.090260 INFO: │   ├──initial_num_candidates: 1
0:00:00.090278 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.090297 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.090315 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.090334 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.090351 INFO: ├──selection_config
0:00:00.090370 INFO: │   ├──peak_len_rt: 10.0
0:00:00.090389 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.090409 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.090429 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.090448 INFO: │   ├──top_k_precursors: 3
0:00:00.090469 INFO: │   ├──kernel_size: 30
0:00:00.090488 INFO: │   ├──f_mobility: 1.0
0:00:00.090506 INFO: │   ├──f_rt: 0.99
0:00:00.090524 INFO: │   ├──center_fraction: 0.5
0:00:00.090541 INFO: │   ├──min_size_mobility: 8
0:00:00.090559 INFO: │   ├──min_size_rt: 3
0:00:00.090577 INFO: │   ├──max_size_mobility: 20
0:00:00.090596 INFO: │   ├──max_size_rt: 15
0:00:00.090614 INFO: │   ├──group_channels: False
0:00:00.090631 INFO: │   ├──use_weighted_score: True
0:00:00.090649 INFO: │   ├──join_close_candidates: False
0:00:00.090667 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.090692 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.090710 INFO: ├──scoring_config
0:00:00.090729 INFO: │   ├──score_grouped: False
0:00:00.090746 INFO: │   ├──top_k_isotopes: 3
0:00:00.090764 INFO: │   ├──reference_channel: -1
0:00:00.090782 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.090800 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.090816 INFO: ├──library_multiplexing
0:00:00.090834 INFO: │   ├──enabled: False
0:00:00.090852 INFO: │   ├──input_channel: 0
0:00:00.090869 INFO: │   └──multiplex_mapping:
0:00:00.090887 INFO: ├──multiplexing
0:00:00.090905 INFO: │   ├──enabled: False
0:00:00.090923 INFO: │   ├──target_channels: 4,8
0:00:00.090941 INFO: │   ├──decoy_channel: 12
0:00:00.090960 INFO: │   ├──reference_channel: 0
0:00:00.090979 INFO: │   └──competetive_scoring: True
0:00:00.090998 INFO: ├──fdr
0:00:00.091016 INFO: │   ├──fdr: 0.01
0:00:00.091035 INFO: │   ├──group_level: proteins
0:00:00.091054 INFO: │   ├──inference_strategy: heuristic
0:00:00.091072 INFO: │   ├──competetive_scoring: True
0:00:00.091089 INFO: │   ├──keep_decoys: False
0:00:00.091108 INFO: │   ├──channel_wise_fdr: False
0:00:00.091126 INFO: │   ├──enable_two_step_classifier: False
0:00:00.091144 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.091161 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.091179 INFO: ├──search_output
0:00:00.091197 INFO: │   ├──file_format: tsv
0:00:00.091216 INFO: │   ├──peptide_level_lfq: False
0:00:00.091234 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.091254 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.091272 INFO: │   ├──min_k_fragments: 12
0:00:00.091290 INFO: │   ├──min_correlation: 0.9
0:00:00.091309 INFO: │   ├──num_samples_quadratic: 50
0:00:00.091329 INFO: │   ├──min_nonnan: 3
0:00:00.091347 INFO: │   └──normalize_lfq: True
0:00:00.091364 INFO: ├──optimization
0:00:00.091384 INFO: │   ├──order_of_optimization: None
0:00:00.091402 INFO: │   ├──ms2_error
0:00:00.091422 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.091443 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.091462 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.091480 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.091498 INFO: │   │   ├──try_narrower_values: True
0:00:00.091517 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.091536 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.091554 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.091574 INFO: │   ├──ms1_error
0:00:00.091593 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.091613 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.091633 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.091654 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.091672 INFO: │   │   ├──try_narrower_values: False
0:00:00.091691 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.091711 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.091731 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.091750 INFO: │   ├──mobility_error
0:00:00.091769 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.091788 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.091807 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.091825 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.091844 INFO: │   │   ├──try_narrower_values: False
0:00:00.091862 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.091880 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.092218 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.092241 INFO: │   └──rt_error
0:00:00.092260 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.092278 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.092296 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.092314 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.092331 INFO: │       ├──try_narrower_values: True
0:00:00.092350 INFO: │       ├──maximal_decrease: 0.2
0:00:00.092367 INFO: │       ├──favour_narrower_optimum: True
0:00:00.092385 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.092402 INFO: ├──optimization_manager
0:00:00.092420 INFO: │   ├──fwhm_rt: 5
0:00:00.092438 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.092455 INFO: │   └──score_cutoff: 0
0:00:00.092472 INFO: ├──transfer_library
0:00:00.092491 INFO: │   ├──enabled: False
0:00:00.092508 INFO: │   ├──fragment_types:
0:00:00.092525 INFO: │   │   - b
0:00:00.092543 INFO: │   │   - y
0:00:00.092561 INFO: │   ├──max_charge: 2
0:00:00.092579 INFO: │   ├──top_k_samples: 3
0:00:00.092596 INFO: │   ├──norm_delta_max: True
0:00:00.092614 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.092633 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.092650 INFO: └──transfer_learning
0:00:00.092668 INFO:     ├──enabled: False
0:00:00.092686 INFO:     ├──batch_size: 2000
0:00:00.092704 INFO:     ├──max_lr: 0.0001
0:00:00.092721 INFO:     ├──train_fraction: 0.7
0:00:00.092739 INFO:     ├──validation_fraction: 0.2
0:00:00.092757 INFO:     ├──test_fraction: 0.1
0:00:00.092775 INFO:     ├──test_interval: 1
0:00:00.092792 INFO:     ├──lr_patience: 3
0:00:00.092810 INFO:     ├──epochs: 51
0:00:00.092829 INFO:     ├──warmup_epochs: 5
0:00:00.092847 INFO:     ├──nce: 25
0:00:00.092865 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.097662 INFO: Moved existing config file run_output/alphadia_1.12.1_rs_benchmark_MBR/library/frozen_config.yaml to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/frozen_config.yaml
0:00:00.097869 INFO: Registering 7 custom modifications
0:00:00.125634 INFO: Searching 6 files:
0:00:00.125711 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:00:00.125737 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
0:00:00.125758 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
0:00:00.125778 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
0:00:00.125796 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
0:00:00.125813 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
0:00:00.125830 INFO: Using 1 fasta files:
0:00:00.125848 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:00:00.125868 INFO: Using library: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:00.125886 INFO: Saving output to: run_output/alphadia_1.12.1_rs_benchmark_MBR/library
0:00:00.125912 PROGRESS: Loading spectral library
0:00:00.125938 PROGRESS: Loading library (type: base) from disk..
0:00:00.125964 INFO: Running DynamicLoader
0:00:00.126016 INFO: Loading .hdf library from /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:26.869155 INFO: Running PrecursorInitializer
0:00:26.869526 INFO: Running AnnotateFasta
0:00:27.000068 INFO: Dropping decoys from input library before annotation
0:00:47.082863 INFO: Running IsotopeGenerator
0:00:47.083170 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
0:00:47.083212 INFO: Running RTNormalization
0:00:47.083269 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:00:47.083308 INFO: Saving library to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/speclib.hdf
0:01:19.937265 INFO: Running DecoyGenerator
0:02:58.932874 INFO: Running FlattenLibrary
0:03:37.013319 INFO: Running InitFlatColumns
0:03:37.318971 INFO: Running LogFlatLibraryStats
0:03:37.319146 INFO: ============ Library Stats ============
0:03:37.319191 INFO: Number of precursors: 12,218,312
0:03:39.213423 INFO: 	thereof targets:6,124,046
0:03:39.213595 INFO: 	thereof decoys: 6,094,266
0:03:39.307917 INFO: Number of elution groups: 6,124,046
0:03:39.308080 INFO: 	average size: 2.00
0:03:39.598884 INFO: Number of proteins: 117,993
0:03:39.628787 INFO: Number of channels: 1 ([0])
0:03:39.629009 INFO: Isotopes Distribution for 4 isotopes
0:03:39.629040 INFO: =======================================
0:03:39.637964 PROGRESS: Starting Search Workflows
0:03:39.638188 PROGRESS: 
0:03:39.638273 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant
0:03:39.638357 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/figures
0:03:39.638621 INFO: Initializing TimingManager
0:03:39.639126 INFO: Initializing RawFileManager
0:03:39.639253 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:39.639320 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:39.639368 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:39.849375 INFO: Reading 39,128 frames with 2,835,410,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:49.316522 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
0:03:49.323240 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:49.327372 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:49.327657 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:49.327982 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:49.329565 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:49.348806 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:49.349174 INFO: Indexing quadrupole dimension
0:03:49.844759 INFO: Transposing detector events
0:03:59.497037 INFO: Finished transposing data
0:03:59.534785 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:59.536755 INFO: RT (min)            : 0.0 - 70.0
0:03:59.536867 INFO: RT duration (sec)   : 4199.9
0:03:59.536922 INFO: RT duration (min)   : 70.0
0:03:59.536971 INFO: Cycle len (scans)   : 9
0:03:59.537016 INFO: Cycle len (sec)     : 0.97
0:03:59.537060 INFO: Number of cycles    : 4347
0:03:59.537105 INFO: MS2 range (m/z)     : 400.0 - 1000.0
0:03:59.537230 INFO: Creating DIA data object took: 19.8979811668396
0:04:01.104566 INFO: Initializing CalibrationManager
0:04:01.104876 INFO: Setting up calibration estimators ..
0:04:01.104938 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:04:01.105021 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'}' ..
0:04:01.105146 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:04:01.105212 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'}' ..
0:04:01.105274 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}}' ..
0:04:01.105355 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}}' ..
0:04:01.105406 INFO: Done setting up calibration estimators.
0:04:01.105535 INFO: Initializing OptimizationManager
0:04:01.105630 INFO: initial parameter: ms1_error = 30
0:04:01.105681 INFO: initial parameter: ms2_error = 30
0:04:01.105728 INFO: initial parameter: rt_error = 2099.928159
0:04:01.105770 INFO: initial parameter: mobility_error = 0.1
0:04:01.105811 INFO: initial parameter: num_candidates = 1
0:04:01.105852 INFO: initial parameter: fwhm_rt = 5
0:04:01.105895 INFO: initial parameter: fwhm_mobility = 0.01
0:04:01.105937 INFO: initial parameter: score_cutoff = 0
0:04:01.105977 INFO: initial parameter: classifier_version = -1
0:04:01.106062 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:04:01.106439 INFO: FDRManager: loading saved state not requested, will be initialized.
0:04:01.106479 INFO: Initializing FDRManager
0:04:01.106527 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:04:02.305407 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
0:04:03.492238 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:04:03.492714 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 2099.928159
0:04:03.492813 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
0:04:03.492990 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
0:04:03.493088 PROGRESS: Starting initial search for precursors.
0:04:03.493171 INFO: Starting optimization step 0.
0:04:03.493232 PROGRESS: === Extracting elution groups 0 to 200 ===
0:04:03.493307 INFO: Using classic extraction backend
0:04:03.493486 PROGRESS: Extracting batch of 390 precursors
0:04:03.493554 INFO: === Search parameters used ===
0:04:03.493605 INFO: rt_error       : 2099.928159
0:04:03.493650 INFO: mobility_error : 0.1
0:04:03.493691 INFO: num_candidates : 1
0:04:03.493734 INFO: ms1_error      : 30
0:04:03.493773 INFO: ms2_error      : 30
0:04:03.493811 INFO: fwhm_rt        : 5
0:04:03.493850 INFO: quant_window   : 3
0:04:03.493888 INFO: ==============================================
0:04:05.417636 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:04:05.417765 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:04:05.417798 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:04:05.417820 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:04:07.398235 INFO: Starting candidate selection
0:05:13.438895 INFO: Starting candidate scoring
0:09:49.403391 INFO: Finished candidate processing
0:09:49.403698 INFO: Collecting candidate features
0:09:49.793432 INFO: Collecting fragment features
0:09:51.028821 INFO: Finished candidate scoring
0:09:51.031468 INFO: performing precursor FDR with 47 features
0:09:51.031522 INFO: Decoy channel: -1
0:09:51.031550 INFO: Competetive: True
0:09:51.033074 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:51.036633 INFO: Using random state 732719 for train-test-split
0:09:51.048087 INFO: Test AUC: 0.468
0:09:51.048150 INFO: Train AUC: 0.508
0:09:51.048184 INFO: AUC difference: 7.82%
0:09:51.048208 WARNING: AUC difference > 5%. This may indicate overfitting.
0:09:51.281136 INFO: Resetting torch num_threads to 80
0:09:51.281633 PROGRESS: === Extracted 364 precursors and 3956 fragments ===
0:09:51.282127 INFO: === FDR correction performed with classifier version -1 ===
0:09:51.282679 PROGRESS: ============================= Precursor FDR =============================
0:09:51.282767 PROGRESS: Total precursors accumulated: 188
0:09:51.282826 PROGRESS: Target precursors: 137 (72.87%)
0:09:51.282888 PROGRESS: Decoy precursors: 51 (27.13%)
0:09:51.282933 PROGRESS: 
0:09:51.282979 PROGRESS: Precursor Summary:
0:09:51.283882 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
0:09:51.283967 PROGRESS: 
0:09:51.284028 PROGRESS: Protein Summary:
0:09:51.285004 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
0:09:51.285098 PROGRESS: =========================================================================
0:09:51.285455 INFO: Target number of precursors not reached yet.
0:09:51.371912 INFO: Starting optimization step 1.
0:09:51.372162 PROGRESS: === Extracting elution groups 200 to 600 ===
0:09:51.372275 INFO: Using classic extraction backend
0:09:51.372467 PROGRESS: Extracting batch of 783 precursors
0:09:51.372547 INFO: === Search parameters used ===
0:09:51.372596 INFO: rt_error       : 2099.928159
0:09:51.372640 INFO: mobility_error : 0.1
0:09:51.372683 INFO: num_candidates : 1
0:09:51.372723 INFO: ms1_error      : 30
0:09:51.372762 INFO: ms2_error      : 30
0:09:51.372800 INFO: fwhm_rt        : 5
0:09:51.372838 INFO: quant_window   : 3
0:09:51.372876 INFO: ==============================================
0:09:51.373885 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:09:51.373930 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:09:51.373964 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:09:51.373985 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:09:51.375120 INFO: Starting candidate selection
0:09:57.252830 INFO: Starting candidate scoring
0:09:57.373573 INFO: Finished candidate processing
0:09:57.373687 INFO: Collecting candidate features
0:09:57.383372 INFO: Collecting fragment features
0:09:57.385763 INFO: Finished candidate scoring
0:09:57.387619 INFO: performing precursor FDR with 47 features
0:09:57.387667 INFO: Decoy channel: -1
0:09:57.387692 INFO: Competetive: True
0:09:57.390726 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:57.392481 INFO: Using random state 93766 for train-test-split
0:09:57.400169 INFO: Test AUC: 0.509
0:09:57.400224 INFO: Train AUC: 0.501
0:09:57.400254 INFO: AUC difference: 1.50%
0:09:57.613723 INFO: Resetting torch num_threads to 80
0:09:57.614943 PROGRESS: === Extracted 1120 precursors and 12173 fragments ===
0:09:57.615357 INFO: === FDR correction performed with classifier version -1 ===
0:09:57.615921 PROGRESS: ============================= Precursor FDR =============================
0:09:57.616009 PROGRESS: Total precursors accumulated: 577
0:09:57.616068 PROGRESS: Target precursors: 432 (74.87%)
0:09:57.616127 PROGRESS: Decoy precursors: 145 (25.13%)
0:09:57.616176 PROGRESS: 
0:09:57.616220 PROGRESS: Precursor Summary:
0:09:57.617098 PROGRESS: Channel   0:	 0.050 FDR:    48; 0.010 FDR:    48; 0.001 FDR:    48
0:09:57.617188 PROGRESS: 
0:09:57.617244 PROGRESS: Protein Summary:
0:09:57.618219 PROGRESS: Channel   0:	 0.050 FDR:    48; 0.010 FDR:    48; 0.001 FDR:    48
0:09:57.618312 PROGRESS: =========================================================================
0:09:57.618442 INFO: Target number of precursors not reached yet.
0:09:57.693254 INFO: Starting optimization step 2.
0:09:57.693492 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:09:57.693570 INFO: Using classic extraction backend
0:09:57.693695 PROGRESS: Extracting batch of 1576 precursors
0:09:57.693766 INFO: === Search parameters used ===
0:09:57.693815 INFO: rt_error       : 2099.928159
0:09:57.693859 INFO: mobility_error : 0.1
0:09:57.693901 INFO: num_candidates : 1
0:09:57.693943 INFO: ms1_error      : 30
0:09:57.693984 INFO: ms2_error      : 30
0:09:57.694024 INFO: fwhm_rt        : 5
0:09:57.694088 INFO: quant_window   : 3
0:09:57.694135 INFO: ==============================================
0:09:57.694938 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:09:57.694983 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:09:57.695013 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:09:57.695035 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:09:57.695706 INFO: Starting candidate selection
0:10:09.385620 INFO: Starting candidate scoring
0:10:09.551500 INFO: Finished candidate processing
0:10:09.551624 INFO: Collecting candidate features
0:10:09.564529 INFO: Collecting fragment features
0:10:09.567910 INFO: Finished candidate scoring
0:10:09.570889 INFO: performing precursor FDR with 47 features
0:10:09.570940 INFO: Decoy channel: -1
0:10:09.570965 INFO: Competetive: True
0:10:09.574514 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:09.576655 INFO: Using random state 706484 for train-test-split
0:10:09.587191 INFO: Test AUC: 0.510
0:10:09.587250 INFO: Train AUC: 0.500
0:10:09.587280 INFO: AUC difference: 1.91%
0:10:09.794778 INFO: Resetting torch num_threads to 80
0:10:09.796391 PROGRESS: === Extracted 2644 precursors and 28607 fragments ===
0:10:09.796811 INFO: === FDR correction performed with classifier version -1 ===
0:10:09.797458 PROGRESS: ============================= Precursor FDR =============================
0:10:09.797544 PROGRESS: Total precursors accumulated: 1,357
0:10:09.797603 PROGRESS: Target precursors: 1,003 (73.91%)
0:10:09.797654 PROGRESS: Decoy precursors: 354 (26.09%)
0:10:09.797700 PROGRESS: 
0:10:09.797743 PROGRESS: Precursor Summary:
0:10:09.798659 PROGRESS: Channel   0:	 0.050 FDR:   108; 0.010 FDR:   108; 0.001 FDR:   108
0:10:09.798748 PROGRESS: 
0:10:09.798803 PROGRESS: Protein Summary:
0:10:09.799794 PROGRESS: Channel   0:	 0.050 FDR:   108; 0.010 FDR:   108; 0.001 FDR:   108
0:10:09.799879 PROGRESS: =========================================================================
0:10:09.800014 INFO: Target number of precursors not reached yet.
0:10:09.883255 INFO: Starting optimization step 3.
0:10:09.883476 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:10:09.883562 INFO: Using classic extraction backend
0:10:09.883704 PROGRESS: Extracting batch of 3162 precursors
0:10:09.883775 INFO: === Search parameters used ===
0:10:09.883821 INFO: rt_error       : 2099.928159
0:10:09.883863 INFO: mobility_error : 0.1
0:10:09.884732 INFO: num_candidates : 1
0:10:09.884786 INFO: ms1_error      : 30
0:10:09.884824 INFO: ms2_error      : 30
0:10:09.884863 INFO: fwhm_rt        : 5
0:10:09.884900 INFO: quant_window   : 3
0:10:09.884939 INFO: ==============================================
0:10:09.885930 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:10:09.885975 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:10:09.886003 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:10:09.886024 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:10:09.886801 INFO: Starting candidate selection
0:10:31.442023 INFO: Starting candidate scoring
0:10:31.745886 INFO: Finished candidate processing
0:10:31.746002 INFO: Collecting candidate features
0:10:31.759658 INFO: Collecting fragment features
0:10:31.764224 INFO: Finished candidate scoring
0:10:31.773243 INFO: performing precursor FDR with 47 features
0:10:31.773295 INFO: Decoy channel: -1
0:10:31.773319 INFO: Competetive: True
0:10:31.778908 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:31.782105 INFO: Using random state 664442 for train-test-split
0:10:31.799623 INFO: Test AUC: 0.506
0:10:31.799697 INFO: Train AUC: 0.502
0:10:31.799727 INFO: AUC difference: 0.90%
0:10:32.665328 INFO: Resetting torch num_threads to 80
0:10:32.667505 PROGRESS: === Extracted 5675 precursors and 61258 fragments ===
0:10:32.667938 INFO: === FDR correction performed with classifier version -1 ===
0:10:32.668779 PROGRESS: ============================= Precursor FDR =============================
0:10:32.668867 PROGRESS: Total precursors accumulated: 2,903
0:10:32.668926 PROGRESS: Target precursors: 2,140 (73.72%)
0:10:32.668973 PROGRESS: Decoy precursors: 763 (26.28%)
0:10:32.669018 PROGRESS: 
0:10:32.669060 PROGRESS: Precursor Summary:
0:10:32.670029 PROGRESS: Channel   0:	 0.050 FDR:   234; 0.010 FDR:   234; 0.001 FDR:   234
0:10:32.670129 PROGRESS: 
0:10:32.670186 PROGRESS: Protein Summary:
0:10:32.671280 PROGRESS: Channel   0:	 0.050 FDR:   232; 0.010 FDR:   232; 0.001 FDR:   232
0:10:32.671384 PROGRESS: =========================================================================
0:10:32.671563 INFO: Target number of precursors reached.
0:10:32.677545 INFO: fragments_df: keeping 407 of 61258 [sum(precursor_idx_mask)=2572 sum(mass_error_mask)=61258 stop_rank=407
0:10:32.835916 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:10:32.952005 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:33.071861 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:10:33.191155 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:33.295117 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:10:33.295569 INFO: Using score_cutoff 32.142118936157225 (fac=0.99, q=1)
0:10:33.295951 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.5219810009002686
0:10:33.296036 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008113141171634197
0:10:33.296096 INFO: Updating optimization_manager: score_cutoff        : 0 -> 32.142118936157225
0:10:33.296160 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:10:33.297876 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:33.303968 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:10:33.305398 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:33.313744 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
0:10:33.313865 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:10:33.313947 INFO: Starting optimization step 4.
0:10:33.314011 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:10:33.314086 INFO: Using classic extraction backend
0:10:33.314210 PROGRESS: Extracting batch of 5911 precursors
0:10:33.314292 INFO: === Search parameters used ===
0:10:33.314348 INFO: rt_error       : 2099.928159
0:10:33.314396 INFO: mobility_error : 0.1
0:10:33.314442 INFO: num_candidates : 3
0:10:33.314485 INFO: ms1_error      : 30
0:10:33.314530 INFO: ms2_error      : 30
0:10:33.314574 INFO: fwhm_rt        : 3.5219810009002686
0:10:33.314619 INFO: quant_window   : 3
0:10:33.314665 INFO: ==============================================
0:10:33.316435 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:10:33.316487 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:10:33.316531 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
0:10:33.316558 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
0:10:33.317190 INFO: Starting candidate selection
0:11:15.951245 INFO: Starting candidate scoring
0:11:17.352912 INFO: Finished candidate processing
0:11:17.353141 INFO: Collecting candidate features
0:11:17.379151 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 16464)
0:11:17.382970 INFO: Collecting fragment features
0:11:17.393429 INFO: Finished candidate scoring
0:11:17.400843 INFO: performing precursor FDR with 47 features
0:11:17.400926 INFO: Decoy channel: -1
0:11:17.400950 INFO: Competetive: True
0:11:17.407225 INFO: Setting torch num_threads to 2 for FDR classification task
0:11:17.409863 WARNING: dropped 1 decoy PSMs due to missing features
0:11:17.412421 INFO: Using random state 242892 for train-test-split
0:11:17.546271 INFO: Test AUC: 0.535
0:11:17.546397 INFO: Train AUC: 0.543
0:11:17.546429 INFO: AUC difference: 1.48%
0:11:17.771748 INFO: Resetting torch num_threads to 80
0:11:17.772660 PROGRESS: === Extracted 16464 precursors and 179501 fragments ===
0:11:17.773164 INFO: === FDR correction performed with classifier version 3 ===
0:11:17.774024 PROGRESS: ============================= Precursor FDR =============================
0:11:17.774136 PROGRESS: Total precursors accumulated: 2,954
0:11:17.774196 PROGRESS: Target precursors: 1,675 (56.70%)
0:11:17.774246 PROGRESS: Decoy precursors: 1,279 (43.30%)
0:11:17.774291 PROGRESS: 
0:11:17.774334 PROGRESS: Precursor Summary:
0:11:17.775234 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:11:17.775336 PROGRESS: 
0:11:17.775393 PROGRESS: Protein Summary:
0:11:17.776361 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:11:17.776448 PROGRESS: =========================================================================
0:11:17.776785 INFO: Target number of precursors not reached yet.
0:11:17.890399 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:11:17.892481 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:11:17.897462 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:11:17.898965 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:11:17.908050 INFO: === skipping optimization until target number of precursors are found ===
0:11:17.908192 INFO: Starting optimization step 5.
0:11:17.908262 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:11:17.908337 INFO: Using classic extraction backend
0:11:17.908489 PROGRESS: Extracting batch of 6312 precursors
0:11:17.908570 INFO: === Search parameters used ===
0:11:17.908620 INFO: rt_error       : 2099.928159
0:11:17.908664 INFO: mobility_error : 0.1
0:11:17.908706 INFO: num_candidates : 3
0:11:17.908747 INFO: ms1_error      : 30
0:11:17.908787 INFO: ms2_error      : 30
0:11:17.908827 INFO: fwhm_rt        : 3.5219810009002686
0:11:17.908866 INFO: quant_window   : 3
0:11:17.908909 INFO: ==============================================
0:11:17.910671 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:11:17.910721 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:11:17.910766 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
0:11:17.910790 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
0:11:17.911626 INFO: Starting candidate selection
0:12:07.272002 INFO: Starting candidate scoring
0:12:08.768979 INFO: Finished candidate processing
0:12:08.769097 INFO: Collecting candidate features
0:12:08.800901 INFO: Collecting fragment features
0:12:08.812186 INFO: Finished candidate scoring
0:12:08.833895 INFO: performing precursor FDR with 47 features
0:12:08.834029 INFO: Decoy channel: -1
0:12:08.834070 INFO: Competetive: True
0:12:08.846608 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:08.851320 WARNING: dropped 1 decoy PSMs due to missing features
0:12:08.857950 INFO: Using random state 242892 for train-test-split
0:12:09.320056 INFO: Test AUC: 0.545
0:12:09.320196 INFO: Train AUC: 0.565
0:12:09.320233 INFO: AUC difference: 3.57%
0:12:09.558753 INFO: Resetting torch num_threads to 80
0:12:09.564014 PROGRESS: === Extracted 33976 precursors and 369824 fragments ===
0:12:09.564587 INFO: === FDR correction performed with classifier version 3 ===
0:12:09.565998 PROGRESS: ============================= Precursor FDR =============================
0:12:09.566125 PROGRESS: Total precursors accumulated: 6,103
0:12:09.566191 PROGRESS: Target precursors: 3,700 (60.63%)
0:12:09.566248 PROGRESS: Decoy precursors: 2,403 (39.37%)
0:12:09.566296 PROGRESS: 
0:12:09.566341 PROGRESS: Precursor Summary:
0:12:09.567299 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:12:09.567391 PROGRESS: 
0:12:09.567450 PROGRESS: Protein Summary:
0:12:09.568440 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:12:09.568529 PROGRESS: =========================================================================
0:12:09.568806 INFO: Target number of precursors not reached yet.
0:12:09.708615 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:12:09.711616 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:12:09.720046 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:12:09.722346 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:12:09.739479 INFO: === skipping optimization until target number of precursors are found ===
0:12:09.739663 INFO: Starting optimization step 6.
0:12:09.739731 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:12:09.739808 INFO: Using classic extraction backend
0:12:09.739979 PROGRESS: Extracting batch of 12615 precursors
0:12:09.740236 INFO: === Search parameters used ===
0:12:09.740287 INFO: rt_error       : 2099.928159
0:12:09.740331 INFO: mobility_error : 0.1
0:12:09.740372 INFO: num_candidates : 3
0:12:09.740411 INFO: ms1_error      : 30
0:12:09.740451 INFO: ms2_error      : 30
0:12:09.740489 INFO: fwhm_rt        : 3.5219810009002686
0:12:09.740528 INFO: quant_window   : 3
0:12:09.740567 INFO: ==============================================
0:12:09.743925 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:12:09.743993 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:12:09.744041 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
0:12:09.744065 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
0:12:09.744790 INFO: Starting candidate selection
0:13:42.876797 INFO: Starting candidate scoring
0:13:45.787618 INFO: Finished candidate processing
0:13:45.787739 INFO: Collecting candidate features
0:13:45.835412 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 35065)
0:13:45.840236 INFO: Collecting fragment features
0:13:45.861274 INFO: Finished candidate scoring
0:13:45.906994 INFO: performing precursor FDR with 47 features
0:13:45.907137 INFO: Decoy channel: -1
0:13:45.907164 INFO: Competetive: True
0:13:45.931342 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:45.941463 WARNING: dropped 2 decoy PSMs due to missing features
0:13:45.951707 INFO: Using random state 242892 for train-test-split
0:13:47.056209 INFO: Test AUC: 0.554
0:13:47.056346 INFO: Train AUC: 0.584
0:13:47.056381 INFO: AUC difference: 5.18%
0:13:47.056403 WARNING: AUC difference > 5%. This may indicate overfitting.
0:13:47.310384 INFO: Resetting torch num_threads to 80
0:13:47.324320 PROGRESS: === Extracted 69041 precursors and 750839 fragments ===
0:13:47.325068 INFO: === FDR correction performed with classifier version 3 ===
0:13:47.327750 PROGRESS: ============================= Precursor FDR =============================
0:13:47.327857 PROGRESS: Total precursors accumulated: 12,415
0:13:47.327914 PROGRESS: Target precursors: 7,758 (62.49%)
0:13:47.327962 PROGRESS: Decoy precursors: 4,657 (37.51%)
0:13:47.328004 PROGRESS: 
0:13:47.328046 PROGRESS: Precursor Summary:
0:13:47.329001 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
0:13:47.329087 PROGRESS: 
0:13:47.329139 PROGRESS: Protein Summary:
0:13:47.330165 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
0:13:47.330267 PROGRESS: =========================================================================
0:13:47.330667 INFO: Target number of precursors not reached yet.
0:13:47.523224 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:13:47.528194 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:47.542601 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:13:47.546586 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:47.584543 INFO: === skipping optimization until target number of precursors are found ===
0:13:47.584862 INFO: Starting optimization step 7.
0:13:47.584937 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:13:47.585016 INFO: Using classic extraction backend
0:13:47.585184 PROGRESS: Extracting batch of 25223 precursors
0:13:47.585263 INFO: === Search parameters used ===
0:13:47.585312 INFO: rt_error       : 2099.928159
0:13:47.585355 INFO: mobility_error : 0.1
0:13:47.585396 INFO: num_candidates : 3
0:13:47.585435 INFO: ms1_error      : 30
0:13:47.585475 INFO: ms2_error      : 30
0:13:47.585513 INFO: fwhm_rt        : 3.5219810009002686
0:13:47.585553 INFO: quant_window   : 3
0:13:47.585595 INFO: ==============================================
0:13:47.595291 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:13:47.595376 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:13:47.596140 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
0:13:47.596166 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
0:13:47.597119 INFO: Starting candidate selection
0:16:50.387709 INFO: Starting candidate scoring
0:16:55.860429 INFO: Finished candidate processing
0:16:55.860556 INFO: Collecting candidate features
0:16:55.978875 INFO: Collecting fragment features
0:16:56.023438 INFO: Finished candidate scoring
0:16:56.139120 INFO: performing precursor FDR with 47 features
0:16:56.139271 INFO: Decoy channel: -1
0:16:56.139298 INFO: Competetive: True
0:16:56.190853 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:56.211029 WARNING: dropped 2 decoy PSMs due to missing features
0:16:56.232468 INFO: Using random state 242892 for train-test-split
0:16:58.463131 INFO: Test AUC: 0.565
0:16:58.463385 INFO: Train AUC: 0.585
0:16:58.463419 INFO: AUC difference: 3.38%
0:16:58.735073 INFO: Resetting torch num_threads to 80
0:16:58.765479 PROGRESS: === Extracted 138954 precursors and 1511337 fragments ===
0:16:58.766314 INFO: === FDR correction performed with classifier version 3 ===
0:16:58.771660 PROGRESS: ============================= Precursor FDR =============================
0:16:58.771789 PROGRESS: Total precursors accumulated: 25,015
0:16:58.771848 PROGRESS: Target precursors: 15,810 (63.20%)
0:16:58.771897 PROGRESS: Decoy precursors: 9,205 (36.80%)
0:16:58.771941 PROGRESS: 
0:16:58.771983 PROGRESS: Precursor Summary:
0:16:58.773084 PROGRESS: Channel   0:	 0.050 FDR:   113; 0.010 FDR:    87; 0.001 FDR:    87
0:16:58.773174 PROGRESS: 
0:16:58.773230 PROGRESS: Protein Summary:
0:16:58.774383 PROGRESS: Channel   0:	 0.050 FDR:   111; 0.010 FDR:    86; 0.001 FDR:    86
0:16:58.774473 PROGRESS: =========================================================================
0:16:58.775043 INFO: Target number of precursors not reached yet.
0:16:59.049060 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:16:59.057582 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:16:59.085863 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:16:59.093318 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:16:59.162704 INFO: === skipping optimization until target number of precursors are found ===
0:16:59.163040 INFO: Starting optimization step 8.
0:16:59.163122 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:16:59.163249 INFO: Using classic extraction backend
0:16:59.163471 PROGRESS: Extracting batch of 50469 precursors
0:16:59.163567 INFO: === Search parameters used ===
0:16:59.163623 INFO: rt_error       : 2099.928159
0:16:59.163675 INFO: mobility_error : 0.1
0:16:59.163726 INFO: num_candidates : 3
0:16:59.163776 INFO: ms1_error      : 30
0:16:59.163824 INFO: ms2_error      : 30
0:16:59.163871 INFO: fwhm_rt        : 3.5219810009002686
0:16:59.163923 INFO: quant_window   : 3
0:16:59.163971 INFO: ==============================================
0:16:59.183323 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:16:59.183463 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:16:59.183522 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
0:16:59.183551 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
0:16:59.184453 INFO: Starting candidate selection
0:22:51.119359 INFO: Starting candidate scoring
0:23:01.413123 INFO: Finished candidate processing
0:23:01.413311 INFO: Collecting candidate features
0:23:01.650014 INFO: Collecting fragment features
0:23:01.746599 INFO: Finished candidate scoring
0:23:01.932660 INFO: performing precursor FDR with 47 features
0:23:01.932813 INFO: Decoy channel: -1
0:23:01.932842 INFO: Competetive: True
0:23:02.038494 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:02.079825 WARNING: dropped 2 decoy PSMs due to missing features
0:23:02.155149 INFO: Using random state 242892 for train-test-split
0:23:07.021438 INFO: Test AUC: 0.567
0:23:07.021686 INFO: Train AUC: 0.586
0:23:07.021723 INFO: AUC difference: 3.32%
0:23:07.342119 INFO: Resetting torch num_threads to 80
0:23:07.407936 PROGRESS: === Extracted 279268 precursors and 3037402 fragments ===
0:23:07.408814 INFO: === FDR correction performed with classifier version 3 ===
0:23:07.418270 PROGRESS: ============================= Precursor FDR =============================
0:23:07.418477 PROGRESS: Total precursors accumulated: 50,242
0:23:07.418541 PROGRESS: Target precursors: 31,612 (62.92%)
0:23:07.418592 PROGRESS: Decoy precursors: 18,630 (37.08%)
0:23:07.418637 PROGRESS: 
0:23:07.418680 PROGRESS: Precursor Summary:
0:23:07.420031 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   168; 0.001 FDR:   106
0:23:07.420123 PROGRESS: 
0:23:07.420193 PROGRESS: Protein Summary:
0:23:07.421541 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   162; 0.001 FDR:   104
0:23:07.421629 PROGRESS: =========================================================================
0:23:07.422450 INFO: Target number of precursors not reached yet.
0:23:07.834478 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:23:07.849749 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:07.908866 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:23:07.926423 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:08.083512 INFO: === skipping optimization until target number of precursors are found ===
0:23:08.083827 INFO: Starting optimization step 9.
0:23:08.083907 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:23:08.084017 INFO: Using classic extraction backend
0:23:08.084248 PROGRESS: Extracting batch of 100931 precursors
0:23:08.084334 INFO: === Search parameters used ===
0:23:08.084383 INFO: rt_error       : 2099.928159
0:23:08.084427 INFO: mobility_error : 0.1
0:23:08.084470 INFO: num_candidates : 3
0:23:08.084513 INFO: ms1_error      : 30
0:23:08.084556 INFO: ms2_error      : 30
0:23:08.084596 INFO: fwhm_rt        : 3.5219810009002686
0:23:08.084636 INFO: quant_window   : 3
0:23:08.084687 INFO: ==============================================
0:23:08.119705 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:23:08.119849 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:23:08.119908 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
0:23:08.119932 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
0:23:08.120970 INFO: Starting candidate selection
0:34:36.183814 INFO: Starting candidate scoring
0:34:54.906767 INFO: Finished candidate processing
0:34:54.907184 INFO: Collecting candidate features
0:34:55.430876 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 280140)
0:34:55.444161 INFO: Collecting fragment features
0:34:55.617823 INFO: Finished candidate scoring
0:34:56.023342 INFO: performing precursor FDR with 47 features
0:34:56.023500 INFO: Decoy channel: -1
0:34:56.023528 INFO: Competetive: True
0:34:56.236790 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:56.337633 WARNING: dropped 2 target PSMs due to missing features
0:34:56.337791 WARNING: dropped 4 decoy PSMs due to missing features
0:34:56.509181 INFO: Using random state 242892 for train-test-split
0:35:05.751893 INFO: Test AUC: 0.570
0:35:05.752052 INFO: Train AUC: 0.583
0:35:05.752086 INFO: AUC difference: 2.16%
0:35:06.167756 INFO: Resetting torch num_threads to 80
0:35:06.264445 PROGRESS: === Extracted 559408 precursors and 6080923 fragments ===
0:35:06.265301 INFO: === FDR correction performed with classifier version 3 ===
0:35:06.282387 PROGRESS: ============================= Precursor FDR =============================
0:35:06.282688 PROGRESS: Total precursors accumulated: 100,599
0:35:06.282758 PROGRESS: Target precursors: 62,570 (62.20%)
0:35:06.282813 PROGRESS: Decoy precursors: 38,029 (37.80%)
0:35:06.282863 PROGRESS: 
0:35:06.282908 PROGRESS: Precursor Summary:
0:35:06.284667 PROGRESS: Channel   0:	 0.050 FDR:   772; 0.010 FDR:   544; 0.001 FDR:   209
0:35:06.284763 PROGRESS: 
0:35:06.284820 PROGRESS: Protein Summary:
0:35:06.286582 PROGRESS: Channel   0:	 0.050 FDR:   708; 0.010 FDR:   509; 0.001 FDR:   205
0:35:06.286711 PROGRESS: =========================================================================
0:35:06.288323 INFO: Target number of precursors reached.
0:35:06.716826 INFO: fragments_df: keeping 5000 of 6080923 [sum(precursor_idx_mask)=17920 sum(mass_error_mask)=6080919 stop_rank=5000
0:35:07.041269 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:35:07.187181 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:07.324997 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:35:07.467489 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:08.141361 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:35:08.141814 INFO: Using score_cutoff 51.81134817810059 (fac=0.99, q=1)
0:35:08.142190 INFO: Updating optimization_manager: fwhm_rt             : 3.5219810009002686 -> 2.925692081451416
0:35:08.142268 INFO: Updating optimization_manager: fwhm_mobility       : 0.008113141171634197 -> 0.01075603999197483
0:35:08.142321 INFO: Updating optimization_manager: score_cutoff        : 32.142118936157225 -> 51.81134817810059
0:35:08.142382 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:35:08.156442 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:08.215852 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:35:08.230719 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:08.356547 INFO: === checking if optimization conditions were reached ===
0:35:08.358727 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
0:35:08.358837 INFO: Updating optimization_manager: classifier_version  : 3 -> 9
0:35:08.358904 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
0:35:08.359914 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
0:35:08.360006 INFO: Updating optimization_manager: classifier_version  : 9 -> 9
0:35:08.360067 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
0:35:08.360120 INFO: ==============================================
0:35:08.360192 INFO: Starting optimization step 10.
0:35:08.360247 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:35:08.360325 INFO: Using classic extraction backend
0:35:08.360486 PROGRESS: Extracting batch of 100530 precursors
0:35:08.360554 INFO: === Search parameters used ===
0:35:08.360604 INFO: rt_error       : 2099.928159
0:35:08.360646 INFO: mobility_error : 0.1
0:35:08.360686 INFO: num_candidates : 3
0:35:08.360726 INFO: ms1_error      : 15.0
0:35:08.360765 INFO: ms2_error      : 15.0
0:35:08.360803 INFO: fwhm_rt        : 2.925692081451416
0:35:08.360841 INFO: quant_window   : 3
0:35:08.360878 INFO: ==============================================
0:35:08.385775 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:35:08.385916 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:35:08.385966 INFO: FWHM in RT is 2.93 seconds, sigma is 0.64
0:35:08.385988 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.99
0:35:08.392963 INFO: Starting candidate selection
0:44:14.003055 INFO: Starting candidate scoring
0:44:24.549230 INFO: Finished candidate processing
0:44:24.549465 INFO: Collecting candidate features
0:44:25.041218 WARNING: intensity_correlation has 12 NaNs ( 0.00 % out of 279090)
0:44:25.041691 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 279090)
0:44:25.055991 INFO: Collecting fragment features
0:44:25.219830 INFO: Finished candidate scoring
0:44:25.462847 INFO: performing precursor FDR with 47 features
0:44:25.462974 INFO: Decoy channel: -1
0:44:25.462999 INFO: Competetive: True
0:44:25.550702 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:25.595353 WARNING: dropped 11 target PSMs due to missing features
0:44:25.595499 WARNING: dropped 4 decoy PSMs due to missing features
0:44:25.667201 INFO: Using random state 481581 for train-test-split
0:44:30.195765 INFO: Test AUC: 0.566
0:44:30.195907 INFO: Train AUC: 0.593
0:44:30.195940 INFO: AUC difference: 4.56%
0:44:30.512656 INFO: Resetting torch num_threads to 80
0:44:30.518285 PROGRESS: === Extracted 279090 precursors and 2898817 fragments ===
0:44:30.518870 INFO: === FDR correction performed with classifier version 9 ===
0:44:30.526990 PROGRESS: ============================= Precursor FDR =============================
0:44:30.527201 PROGRESS: Total precursors accumulated: 50,047
0:44:30.527261 PROGRESS: Target precursors: 31,399 (62.74%)
0:44:30.527307 PROGRESS: Decoy precursors: 18,648 (37.26%)
0:44:30.527349 PROGRESS: 
0:44:30.527389 PROGRESS: Precursor Summary:
0:44:30.528753 PROGRESS: Channel   0:	 0.050 FDR:   607; 0.010 FDR:   334; 0.001 FDR:   202
0:44:30.528843 PROGRESS: 
0:44:30.528909 PROGRESS: Protein Summary:
0:44:30.530339 PROGRESS: Channel   0:	 0.050 FDR:   570; 0.010 FDR:   318; 0.001 FDR:   192
0:44:30.530429 PROGRESS: =========================================================================
0:44:30.571462 INFO: Target number of precursors reached.
0:44:30.761685 INFO: fragments_df: keeping 4996 of 2898817 [sum(precursor_idx_mask)=10746 sum(mass_error_mask)=2898817 stop_rank=4996
0:44:31.044140 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:44:31.154391 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:31.262952 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:44:31.371025 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:31.984598 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:31.985061 INFO: Using score_cutoff 49.79722765045166 (fac=0.99, q=1)
0:44:31.985399 INFO: Updating optimization_manager: fwhm_rt             : 2.925692081451416 -> 2.7547390460968018
0:44:31.985478 INFO: Updating optimization_manager: fwhm_mobility       : 0.01075603999197483 -> 0.009407548233866692
0:44:31.985531 INFO: Updating optimization_manager: score_cutoff        : 51.81134817810059 -> 49.79722765045166
0:44:31.985591 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:44:31.999561 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:32.060075 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:44:32.076712 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:32.219728 INFO: === checking if optimization conditions were reached ===
0:44:32.222283 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
0:44:32.222403 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:44:32.222481 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
0:44:32.223637 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
0:44:32.223741 INFO: Updating optimization_manager: classifier_version  : 10 -> 10
0:44:32.223810 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
0:44:32.223872 INFO: ==============================================
0:44:32.223960 PROGRESS: Optimization finished for ms2_error, ms1_error.
0:44:32.433515 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:44:32.447881 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:32.508071 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:44:32.525475 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:32.668492 INFO: Starting optimization step 0.
0:44:32.668804 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:44:32.668901 INFO: Using classic extraction backend
0:44:32.669110 PROGRESS: Extracting batch of 100530 precursors
0:44:32.669200 INFO: === Search parameters used ===
0:44:32.669260 INFO: rt_error       : 2099.928159
0:44:32.669313 INFO: mobility_error : 0.1
0:44:32.669363 INFO: num_candidates : 3
0:44:32.669433 INFO: ms1_error      : 15.0
0:44:32.669484 INFO: ms2_error      : 15.0
0:44:32.669532 INFO: fwhm_rt        : 2.7547390460968018
0:44:32.669581 INFO: quant_window   : 3
0:44:32.669628 INFO: ==============================================
0:44:32.710249 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:44:32.710388 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:44:32.710443 INFO: FWHM in RT is 2.75 seconds, sigma is 0.61
0:44:32.710470 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.36
0:44:32.714546 INFO: Starting candidate selection
0:53:30.260354 INFO: Starting candidate scoring
0:53:40.742121 INFO: Finished candidate processing
0:53:40.742273 INFO: Collecting candidate features
0:53:41.158328 WARNING: intensity_correlation has 11 NaNs ( 0.00 % out of 278736)
0:53:41.158803 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 278736)
0:53:41.171164 INFO: Collecting fragment features
0:53:41.338455 INFO: Finished candidate scoring
0:53:41.504833 INFO: performing precursor FDR with 47 features
0:53:41.504964 INFO: Decoy channel: -1
0:53:41.504990 INFO: Competetive: True
0:53:41.581366 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:41.625063 WARNING: dropped 9 target PSMs due to missing features
0:53:41.625213 WARNING: dropped 4 decoy PSMs due to missing features
0:53:41.698663 INFO: Using random state 686047 for train-test-split
0:53:46.138568 INFO: Test AUC: 0.577
0:53:46.138817 INFO: Train AUC: 0.605
0:53:46.138852 INFO: AUC difference: 4.54%
0:53:46.454174 INFO: Resetting torch num_threads to 80
0:53:46.459800 PROGRESS: === Extracted 278736 precursors and 2888539 fragments ===
0:53:46.460414 INFO: === FDR correction performed with classifier version 10 ===
0:53:46.468738 PROGRESS: ============================= Precursor FDR =============================
0:53:46.468889 PROGRESS: Total precursors accumulated: 50,021
0:53:46.468952 PROGRESS: Target precursors: 31,986 (63.95%)
0:53:46.469000 PROGRESS: Decoy precursors: 18,035 (36.05%)
0:53:46.469047 PROGRESS: 
0:53:46.469088 PROGRESS: Precursor Summary:
0:53:46.470520 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   371; 0.001 FDR:   208
0:53:46.470621 PROGRESS: 
0:53:46.470677 PROGRESS: Protein Summary:
0:53:46.472179 PROGRESS: Channel   0:	 0.050 FDR:   552; 0.010 FDR:   350; 0.001 FDR:   199
0:53:46.472274 PROGRESS: =========================================================================
0:53:46.473808 INFO: Target number of precursors reached.
0:53:46.665846 INFO: fragments_df: keeping 5000 of 2888539 [sum(precursor_idx_mask)=12010 sum(mass_error_mask)=2888539 stop_rank=5000
0:53:47.017839 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:53:47.143177 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:53:47.252491 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:53:47.362329 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:53:47.985589 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:53:47.986088 INFO: Using score_cutoff 46.865452835083005 (fac=0.99, q=1)
0:53:47.986446 INFO: Updating optimization_manager: fwhm_rt             : 2.7547390460968018 -> 2.756852388381958
0:53:47.986524 INFO: Updating optimization_manager: fwhm_mobility       : 0.009407548233866692 -> 0.009130029939115047
0:53:47.986577 INFO: Updating optimization_manager: score_cutoff        : 49.79722765045166 -> 46.865452835083005
0:53:47.986632 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:53:47.999543 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:48.059623 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:53:48.074499 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:48.200587 INFO: === checking if optimization conditions were reached ===
0:53:48.200901 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:53:48.202993 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 379.7799705721328
0:53:48.203095 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 379.7800.
0:53:48.203162 INFO: ==============================================
0:53:48.203239 INFO: Starting optimization step 1.
0:53:48.203309 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:53:48.203382 INFO: Using classic extraction backend
0:53:48.203551 PROGRESS: Extracting batch of 100530 precursors
0:53:48.203618 INFO: === Search parameters used ===
0:53:48.203664 INFO: rt_error       : 379.7799705721328
0:53:48.203714 INFO: mobility_error : 0.1
0:53:48.203756 INFO: num_candidates : 3
0:53:48.203797 INFO: ms1_error      : 15.0
0:53:48.203835 INFO: ms2_error      : 15.0
0:53:48.203873 INFO: fwhm_rt        : 2.756852388381958
0:53:48.203909 INFO: quant_window   : 3
0:53:48.203945 INFO: ==============================================
0:53:48.228905 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:53:48.229046 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:53:48.229097 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
0:53:48.229119 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.23
0:53:48.234821 INFO: Starting candidate selection
0:55:29.082047 INFO: Starting candidate scoring
0:55:39.171247 INFO: Finished candidate processing
0:55:39.171670 INFO: Collecting candidate features
0:55:39.677203 WARNING: intensity_correlation has 70 NaNs ( 0.03 % out of 268656)
0:55:39.677671 WARNING: height_correlation has 15 NaNs ( 0.01 % out of 268656)
0:55:39.689880 INFO: Collecting fragment features
0:55:39.853048 INFO: Finished candidate scoring
0:55:40.080846 INFO: performing precursor FDR with 47 features
0:55:40.080985 INFO: Decoy channel: -1
0:55:40.081012 INFO: Competetive: True
0:55:40.152951 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:40.195454 WARNING: dropped 48 target PSMs due to missing features
0:55:40.195590 WARNING: dropped 33 decoy PSMs due to missing features
0:55:40.263775 INFO: Using random state 686047 for train-test-split
0:55:44.453572 INFO: Test AUC: 0.562
0:55:44.453716 INFO: Train AUC: 0.585
0:55:44.453748 INFO: AUC difference: 4.02%
0:55:44.762738 INFO: Resetting torch num_threads to 80
0:55:44.768097 PROGRESS: === Extracted 268656 precursors and 2709500 fragments ===
0:55:44.768680 INFO: === FDR correction performed with classifier version 10 ===
0:55:44.776781 PROGRESS: ============================= Precursor FDR =============================
0:55:44.776924 PROGRESS: Total precursors accumulated: 49,035
0:55:44.776987 PROGRESS: Target precursors: 30,048 (61.28%)
0:55:44.777036 PROGRESS: Decoy precursors: 18,987 (38.72%)
0:55:44.777080 PROGRESS: 
0:55:44.777124 PROGRESS: Precursor Summary:
0:55:44.778567 PROGRESS: Channel   0:	 0.050 FDR:   663; 0.010 FDR:   399; 0.001 FDR:   293
0:55:44.778668 PROGRESS: 
0:55:44.778733 PROGRESS: Protein Summary:
0:55:44.780250 PROGRESS: Channel   0:	 0.050 FDR:   623; 0.010 FDR:   380; 0.001 FDR:   279
0:55:44.780341 PROGRESS: =========================================================================
0:55:44.781785 INFO: Target number of precursors reached.
0:55:44.960169 INFO: fragments_df: keeping 5000 of 2709500 [sum(precursor_idx_mask)=12716 sum(mass_error_mask)=2709498 stop_rank=5000
0:55:45.245920 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:55:46.027423 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:46.160309 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:55:46.292808 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:46.908564 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:55:46.909024 INFO: Using score_cutoff 47.72165252838135 (fac=0.99, q=1)
0:55:46.909329 INFO: Updating optimization_manager: fwhm_rt             : 2.756852388381958 -> 2.8218278884887695
0:55:46.909409 INFO: Updating optimization_manager: fwhm_mobility       : 0.009130029939115047 -> 0.009205679409205914
0:55:46.909466 INFO: Updating optimization_manager: score_cutoff        : 46.865452835083005 -> 47.72165252838135
0:55:46.909521 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:55:46.922712 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:46.982758 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:55:46.999725 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:47.140032 INFO: === checking if optimization conditions were reached ===
0:55:47.140365 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:55:47.142843 INFO: Updating optimization_manager: rt_error            : 379.7799705721328 -> 334.90268577222383
0:55:47.142961 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 334.9027.
0:55:47.143038 INFO: ==============================================
0:55:47.143115 INFO: Starting optimization step 2.
0:55:47.143179 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:55:47.143245 INFO: Using classic extraction backend
0:55:47.143381 PROGRESS: Extracting batch of 100530 precursors
0:55:47.143456 INFO: === Search parameters used ===
0:55:47.143511 INFO: rt_error       : 334.90268577222383
0:55:47.143562 INFO: mobility_error : 0.1
0:55:47.143613 INFO: num_candidates : 3
0:55:47.143662 INFO: ms1_error      : 15.0
0:55:47.143711 INFO: ms2_error      : 15.0
0:55:47.143759 INFO: fwhm_rt        : 2.8218278884887695
0:55:47.143806 INFO: quant_window   : 3
0:55:47.143855 INFO: ==============================================
0:55:47.183988 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:55:47.184164 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:55:47.184217 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
0:55:47.184246 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.27
0:55:47.187912 INFO: Starting candidate selection
0:57:23.300515 INFO: Starting candidate scoring
0:57:33.658337 INFO: Finished candidate processing
0:57:33.658758 INFO: Collecting candidate features
0:57:34.168514 WARNING: intensity_correlation has 79 NaNs ( 0.03 % out of 267885)
0:57:34.168995 WARNING: height_correlation has 15 NaNs ( 0.01 % out of 267885)
0:57:34.181329 INFO: Collecting fragment features
0:57:34.338671 INFO: Finished candidate scoring
0:57:34.562446 INFO: performing precursor FDR with 47 features
0:57:34.562578 INFO: Decoy channel: -1
0:57:34.562603 INFO: Competetive: True
0:57:34.632481 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:34.674014 WARNING: dropped 54 target PSMs due to missing features
0:57:34.674197 WARNING: dropped 33 decoy PSMs due to missing features
0:57:34.741900 INFO: Using random state 686047 for train-test-split
0:57:38.810552 INFO: Test AUC: 0.564
0:57:38.810701 INFO: Train AUC: 0.583
0:57:38.810733 INFO: AUC difference: 3.21%
0:57:39.117483 INFO: Resetting torch num_threads to 80
0:57:39.122840 PROGRESS: === Extracted 267885 precursors and 2691611 fragments ===
0:57:39.123417 INFO: === FDR correction performed with classifier version 10 ===
0:57:39.131195 PROGRESS: ============================= Precursor FDR =============================
0:57:39.131350 PROGRESS: Total precursors accumulated: 48,906
0:57:39.131414 PROGRESS: Target precursors: 29,780 (60.89%)
0:57:39.131464 PROGRESS: Decoy precursors: 19,126 (39.11%)
0:57:39.131506 PROGRESS: 
0:57:39.131548 PROGRESS: Precursor Summary:
0:57:39.132990 PROGRESS: Channel   0:	 0.050 FDR:   681; 0.010 FDR:   431; 0.001 FDR:   214
0:57:39.133088 PROGRESS: 
0:57:39.133144 PROGRESS: Protein Summary:
0:57:39.134682 PROGRESS: Channel   0:	 0.050 FDR:   640; 0.010 FDR:   409; 0.001 FDR:   205
0:57:39.134781 PROGRESS: =========================================================================
0:57:39.136159 INFO: Target number of precursors reached.
0:57:39.311718 INFO: fragments_df: keeping 5000 of 2691611 [sum(precursor_idx_mask)=13712 sum(mass_error_mask)=2691607 stop_rank=5000
0:57:39.519369 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:57:39.656468 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:57:39.793864 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:57:39.917051 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:57:40.531613 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:57:40.532082 INFO: Using score_cutoff 41.5632898979187 (fac=0.99, q=1)
0:57:40.532422 INFO: Updating optimization_manager: fwhm_rt             : 2.8218278884887695 -> 2.7740821838378906
0:57:40.532502 INFO: Updating optimization_manager: fwhm_mobility       : 0.009205679409205914 -> 0.009010378271341324
0:57:40.532573 INFO: Updating optimization_manager: score_cutoff        : 47.72165252838135 -> 41.5632898979187
0:57:40.532633 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:57:40.539964 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:40.569886 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:57:40.577252 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:40.638172 INFO: === checking if optimization conditions were reached ===
0:57:40.638515 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:57:40.641167 INFO: Updating optimization_manager: rt_error            : 334.90268577222383 -> 265.9491807039095
0:57:40.641286 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 265.9492.
0:57:40.641363 INFO: ==============================================
0:57:40.641448 INFO: Starting optimization step 3.
0:57:40.641512 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:57:40.641591 INFO: Using classic extraction backend
0:57:40.641784 PROGRESS: Extracting batch of 50061 precursors
0:57:40.641863 INFO: === Search parameters used ===
0:57:40.641919 INFO: rt_error       : 265.9491807039095
0:57:40.641972 INFO: mobility_error : 0.1
0:57:40.642024 INFO: num_candidates : 3
0:57:40.642087 INFO: ms1_error      : 15.0
0:57:40.642160 INFO: ms2_error      : 15.0
0:57:40.642213 INFO: fwhm_rt        : 2.7740821838378906
0:57:40.642262 INFO: quant_window   : 3
0:57:40.642311 INFO: ==============================================
0:57:40.660517 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:57:40.660650 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:57:40.660709 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
0:57:40.660738 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.18
0:57:40.674479 INFO: Starting candidate selection
0:58:19.052014 INFO: Starting candidate scoring
0:58:25.047271 INFO: Finished candidate processing
0:58:25.047519 INFO: Collecting candidate features
0:58:25.260065 WARNING: intensity_correlation has 48 NaNs ( 0.04 % out of 133962)
0:58:25.260428 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 133962)
0:58:25.268604 INFO: Collecting fragment features
0:58:25.346609 INFO: Finished candidate scoring
0:58:25.418467 INFO: performing precursor FDR with 47 features
0:58:25.418597 INFO: Decoy channel: -1
0:58:25.418622 INFO: Competetive: True
0:58:25.455933 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:25.477876 WARNING: dropped 26 target PSMs due to missing features
0:58:25.478026 WARNING: dropped 25 decoy PSMs due to missing features
0:58:25.497526 INFO: Using random state 686047 for train-test-split
0:58:27.532670 INFO: Test AUC: 0.561
0:58:27.533221 INFO: Train AUC: 0.587
0:58:27.533261 INFO: AUC difference: 4.42%
0:58:27.804368 INFO: Resetting torch num_threads to 80
0:58:27.807496 PROGRESS: === Extracted 133962 precursors and 1339097 fragments ===
0:58:27.808026 INFO: === FDR correction performed with classifier version 10 ===
0:58:27.811652 PROGRESS: ============================= Precursor FDR =============================
0:58:27.811785 PROGRESS: Total precursors accumulated: 24,453
0:58:27.811845 PROGRESS: Target precursors: 15,003 (61.35%)
0:58:27.811893 PROGRESS: Decoy precursors: 9,450 (38.65%)
0:58:27.811937 PROGRESS: 
0:58:27.811978 PROGRESS: Precursor Summary:
0:58:27.813130 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   219; 0.001 FDR:   111
0:58:27.813220 PROGRESS: 
0:58:27.813274 PROGRESS: Protein Summary:
0:58:27.814520 PROGRESS: Channel   0:	 0.050 FDR:   332; 0.010 FDR:   214; 0.001 FDR:   108
0:58:27.814614 PROGRESS: =========================================================================
0:58:27.842393 INFO: Target number of precursors reached.
0:58:27.930958 INFO: fragments_df: keeping 3211 of 1339097 [sum(precursor_idx_mask)=7011 sum(mass_error_mask)=1339096 stop_rank=3211
0:58:28.137173 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:58:28.238319 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:58:28.335882 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:58:28.442601 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:58:28.796867 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:58:28.797328 INFO: Using score_cutoff 46.00235006103516 (fac=0.99, q=1)
0:58:28.797657 INFO: Updating optimization_manager: fwhm_rt             : 2.7740821838378906 -> 2.756723165512085
0:58:28.797733 INFO: Updating optimization_manager: fwhm_mobility       : 0.009010378271341324 -> 0.009183293208479881
0:58:28.797784 INFO: Updating optimization_manager: score_cutoff        : 41.5632898979187 -> 46.00235006103516
0:58:28.797838 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:58:28.805300 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:58:28.834831 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:58:28.842654 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:28.903641 INFO: === checking if optimization conditions were reached ===
0:58:28.903960 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:58:28.906515 INFO: Updating optimization_manager: rt_error            : 265.9491807039095 -> 175.07462176359905
0:58:28.906636 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 175.0746.
0:58:28.906712 INFO: ==============================================
0:58:28.906796 INFO: Starting optimization step 4.
0:58:28.906861 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:28.907839 INFO: Using classic extraction backend
0:58:28.908037 PROGRESS: Extracting batch of 50061 precursors
0:58:28.908116 INFO: === Search parameters used ===
0:58:28.908171 INFO: rt_error       : 175.07462176359905
0:58:28.908222 INFO: mobility_error : 0.1
0:58:28.908271 INFO: num_candidates : 3
0:58:28.908320 INFO: ms1_error      : 15.0
0:58:28.908367 INFO: ms2_error      : 15.0
0:58:28.908414 INFO: fwhm_rt        : 2.756723165512085
0:58:28.908460 INFO: quant_window   : 3
0:58:28.908507 INFO: ==============================================
0:58:28.927275 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:58:28.927420 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:58:28.927480 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
0:58:28.927507 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.26
0:58:28.936283 INFO: Starting candidate selection
0:58:56.137282 INFO: Starting candidate scoring
0:59:01.997205 INFO: Finished candidate processing
0:59:01.997623 INFO: Collecting candidate features
0:59:02.263652 WARNING: intensity_correlation has 44 NaNs ( 0.03 % out of 133675)
0:59:02.264002 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 133675)
0:59:02.272028 INFO: Collecting fragment features
0:59:02.349727 INFO: Finished candidate scoring
0:59:02.465055 INFO: performing precursor FDR with 47 features
0:59:02.465185 INFO: Decoy channel: -1
0:59:02.465209 INFO: Competetive: True
0:59:02.503857 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:02.525741 WARNING: dropped 30 target PSMs due to missing features
0:59:02.525886 WARNING: dropped 18 decoy PSMs due to missing features
0:59:02.545864 INFO: Using random state 686047 for train-test-split
0:59:04.535586 INFO: Test AUC: 0.559
0:59:04.535721 INFO: Train AUC: 0.585
0:59:04.535752 INFO: AUC difference: 4.49%
0:59:04.801983 INFO: Resetting torch num_threads to 80
0:59:04.805080 PROGRESS: === Extracted 133675 precursors and 1320247 fragments ===
0:59:04.805598 INFO: === FDR correction performed with classifier version 10 ===
0:59:04.809284 PROGRESS: ============================= Precursor FDR =============================
0:59:04.809411 PROGRESS: Total precursors accumulated: 24,430
0:59:04.809479 PROGRESS: Target precursors: 14,932 (61.12%)
0:59:04.809557 PROGRESS: Decoy precursors: 9,498 (38.88%)
0:59:04.809610 PROGRESS: 
0:59:04.809663 PROGRESS: Precursor Summary:
0:59:04.810843 PROGRESS: Channel   0:	 0.050 FDR:   375; 0.010 FDR:   290; 0.001 FDR:   180
0:59:04.810934 PROGRESS: 
0:59:04.810989 PROGRESS: Protein Summary:
0:59:04.812233 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   282; 0.001 FDR:   176
0:59:04.812330 PROGRESS: =========================================================================
0:59:04.813178 INFO: Target number of precursors reached.
0:59:04.904008 INFO: fragments_df: keeping 3898 of 1320247 [sum(precursor_idx_mask)=9119 sum(mass_error_mask)=1320245 stop_rank=3898
0:59:05.107914 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:59:05.206425 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:05.311811 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:59:05.414187 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:05.854192 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:05.854645 INFO: Using score_cutoff 39.893322886276245 (fac=0.99, q=1)
0:59:05.854982 INFO: Updating optimization_manager: fwhm_rt             : 2.756723165512085 -> 2.8154797554016113
0:59:05.855065 INFO: Updating optimization_manager: fwhm_mobility       : 0.009183293208479881 -> 0.0089154914021492
0:59:05.855122 INFO: Updating optimization_manager: score_cutoff        : 46.00235006103516 -> 39.893322886276245
0:59:05.855178 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:59:05.862555 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:05.892717 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:59:05.900446 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:05.964457 INFO: === checking if optimization conditions were reached ===
0:59:05.964803 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:59:05.967400 INFO: Updating optimization_manager: rt_error            : 175.07462176359905 -> 163.9499363620572
0:59:05.967522 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 163.9499.
0:59:05.967596 INFO: ==============================================
0:59:05.967676 INFO: Starting optimization step 5.
0:59:05.967739 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:59:05.967817 INFO: Using classic extraction backend
0:59:05.968005 PROGRESS: Extracting batch of 50061 precursors
0:59:05.968082 INFO: === Search parameters used ===
0:59:05.968136 INFO: rt_error       : 163.9499363620572
0:59:05.968184 INFO: mobility_error : 0.1
0:59:05.968232 INFO: num_candidates : 3
0:59:05.968278 INFO: ms1_error      : 15.0
0:59:05.968324 INFO: ms2_error      : 15.0
0:59:05.968369 INFO: fwhm_rt        : 2.8154797554016113
0:59:05.968415 INFO: quant_window   : 3
0:59:05.968460 INFO: ==============================================
0:59:05.987276 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:59:05.987431 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:59:05.987491 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
0:59:05.987516 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
0:59:05.996227 INFO: Starting candidate selection
0:59:31.597663 INFO: Starting candidate scoring
0:59:37.699553 INFO: Finished candidate processing
0:59:37.700348 INFO: Collecting candidate features
0:59:37.910682 WARNING: intensity_correlation has 45 NaNs ( 0.03 % out of 133361)
0:59:37.911048 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 133361)
0:59:37.918812 INFO: Collecting fragment features
0:59:37.996070 INFO: Finished candidate scoring
0:59:38.069672 INFO: performing precursor FDR with 47 features
0:59:38.069816 INFO: Decoy channel: -1
0:59:38.069844 INFO: Competetive: True
0:59:38.107937 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:38.129297 WARNING: dropped 23 target PSMs due to missing features
0:59:38.129456 WARNING: dropped 25 decoy PSMs due to missing features
0:59:38.147106 INFO: Using random state 686047 for train-test-split
0:59:40.145121 INFO: Test AUC: 0.553
0:59:40.145273 INFO: Train AUC: 0.583
0:59:40.145305 INFO: AUC difference: 5.10%
0:59:40.145329 WARNING: AUC difference > 5%. This may indicate overfitting.
0:59:40.412283 INFO: Resetting torch num_threads to 80
0:59:40.415312 PROGRESS: === Extracted 133361 precursors and 1316284 fragments ===
0:59:40.415834 INFO: === FDR correction performed with classifier version 10 ===
0:59:40.419725 PROGRESS: ============================= Precursor FDR =============================
0:59:40.419847 PROGRESS: Total precursors accumulated: 24,378
0:59:40.419914 PROGRESS: Target precursors: 14,770 (60.59%)
0:59:40.419964 PROGRESS: Decoy precursors: 9,608 (39.41%)
0:59:40.420009 PROGRESS: 
0:59:40.420052 PROGRESS: Precursor Summary:
0:59:40.421199 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   272; 0.001 FDR:   197
0:59:40.421299 PROGRESS: 
0:59:40.421359 PROGRESS: Protein Summary:
0:59:40.422632 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   265; 0.001 FDR:   192
0:59:40.422723 PROGRESS: =========================================================================
0:59:40.423711 INFO: Target number of precursors reached.
0:59:40.514067 INFO: fragments_df: keeping 3748 of 1316284 [sum(precursor_idx_mask)=8510 sum(mass_error_mask)=1316282 stop_rank=3748
0:59:40.718770 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:59:40.814532 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:40.917196 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:59:41.023508 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:41.447485 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:41.447991 INFO: Using score_cutoff 41.009613975906376 (fac=0.99, q=1)
0:59:41.448327 INFO: Updating optimization_manager: fwhm_rt             : 2.8154797554016113 -> 2.808483123779297
0:59:41.448413 INFO: Updating optimization_manager: fwhm_mobility       : 0.0089154914021492 -> 0.009024706669151783
0:59:41.448475 INFO: Updating optimization_manager: score_cutoff        : 39.893322886276245 -> 41.009613975906376
0:59:41.448544 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:59:41.456116 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:41.486605 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:59:41.494452 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:41.557714 INFO: === checking if optimization conditions were reached ===
0:59:41.558073 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:59:41.560606 INFO: Updating optimization_manager: rt_error            : 163.9499363620572 -> 144.78252977859194
0:59:41.560726 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 144.7825.
0:59:41.560802 INFO: ==============================================
0:59:41.560886 INFO: Starting optimization step 6.
0:59:41.560952 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:59:41.561019 INFO: Using classic extraction backend
0:59:41.561186 PROGRESS: Extracting batch of 50061 precursors
0:59:41.561262 INFO: === Search parameters used ===
0:59:41.561317 INFO: rt_error       : 144.78252977859194
0:59:41.561369 INFO: mobility_error : 0.1
0:59:41.561418 INFO: num_candidates : 3
0:59:41.561468 INFO: ms1_error      : 15.0
0:59:41.561517 INFO: ms2_error      : 15.0
0:59:41.561564 INFO: fwhm_rt        : 2.808483123779297
0:59:41.561630 INFO: quant_window   : 3
0:59:41.561680 INFO: ==============================================
0:59:41.587575 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:59:41.587727 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:59:41.587786 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
0:59:41.587815 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.19
0:59:41.596576 INFO: Starting candidate selection
1:00:03.564230 INFO: Starting candidate scoring
1:00:09.458539 INFO: Finished candidate processing
1:00:09.458678 INFO: Collecting candidate features
1:00:09.636523 WARNING: intensity_correlation has 55 NaNs ( 0.04 % out of 133057)
1:00:09.636876 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 133057)
1:00:09.644672 INFO: Collecting fragment features
1:00:09.721904 INFO: Finished candidate scoring
1:00:09.793388 INFO: performing precursor FDR with 47 features
1:00:09.793524 INFO: Decoy channel: -1
1:00:09.793549 INFO: Competetive: True
1:00:09.830343 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:09.851838 WARNING: dropped 22 target PSMs due to missing features
1:00:09.851993 WARNING: dropped 35 decoy PSMs due to missing features
1:00:09.870402 INFO: Using random state 686047 for train-test-split
1:00:11.884581 INFO: Test AUC: 0.555
1:00:11.884722 INFO: Train AUC: 0.585
1:00:11.884754 INFO: AUC difference: 5.18%
1:00:11.884777 WARNING: AUC difference > 5%. This may indicate overfitting.
1:00:12.153616 INFO: Resetting torch num_threads to 80
1:00:12.156696 PROGRESS: === Extracted 133057 precursors and 1309568 fragments ===
1:00:12.157230 INFO: === FDR correction performed with classifier version 10 ===
1:00:12.160796 PROGRESS: ============================= Precursor FDR =============================
1:00:12.160914 PROGRESS: Total precursors accumulated: 24,333
1:00:12.160973 PROGRESS: Target precursors: 14,690 (60.37%)
1:00:12.161025 PROGRESS: Decoy precursors: 9,643 (39.63%)
1:00:12.161076 PROGRESS: 
1:00:12.161119 PROGRESS: Precursor Summary:
1:00:12.162278 PROGRESS: Channel   0:	 0.050 FDR:   388; 0.010 FDR:   301; 0.001 FDR:   126
1:00:12.162369 PROGRESS: 
1:00:12.162423 PROGRESS: Protein Summary:
1:00:12.163675 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   293; 0.001 FDR:   124
1:00:12.163765 PROGRESS: =========================================================================
1:00:12.164476 INFO: Target number of precursors reached.
1:00:12.254803 INFO: fragments_df: keeping 3935 of 1309568 [sum(precursor_idx_mask)=9369 sum(mass_error_mask)=1309566 stop_rank=3935
1:00:12.458968 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:00:12.558162 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:00:12.658708 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:00:12.764231 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:00:13.211004 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:00:13.211473 INFO: Using score_cutoff 38.06627494812012 (fac=0.99, q=1)
1:00:13.211806 INFO: Updating optimization_manager: fwhm_rt             : 2.808483123779297 -> 2.7949740886688232
1:00:13.211886 INFO: Updating optimization_manager: fwhm_mobility       : 0.009024706669151783 -> 0.008665547706186771
1:00:13.211940 INFO: Updating optimization_manager: score_cutoff        : 41.009613975906376 -> 38.06627494812012
1:00:13.211997 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:00:13.220083 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:00:13.250401 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:00:13.257014 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:00:13.318318 INFO: === checking if optimization conditions were reached ===
1:00:13.318682 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:00:13.321265 INFO: Updating optimization_manager: rt_error            : 144.78252977859194 -> 138.10813277827842
1:00:13.321378 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 138.1081.
1:00:13.321452 INFO: ==============================================
1:00:13.321538 INFO: Starting optimization step 7.
1:00:13.321602 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:00:13.321668 INFO: Using classic extraction backend
1:00:13.321865 PROGRESS: Extracting batch of 50061 precursors
1:00:13.321944 INFO: === Search parameters used ===
1:00:13.322001 INFO: rt_error       : 138.10813277827842
1:00:13.322069 INFO: mobility_error : 0.1
1:00:13.322124 INFO: num_candidates : 3
1:00:13.322791 INFO: ms1_error      : 15.0
1:00:13.322842 INFO: ms2_error      : 15.0
1:00:13.322888 INFO: fwhm_rt        : 2.7949740886688232
1:00:13.322932 INFO: quant_window   : 3
1:00:13.322977 INFO: ==============================================
1:00:13.338774 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:00:13.338907 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:00:13.338969 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1:00:13.338996 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.02
1:00:13.345357 INFO: Starting candidate selection
1:00:34.078233 INFO: Starting candidate scoring
1:00:39.975352 INFO: Finished candidate processing
1:00:39.975476 INFO: Collecting candidate features
1:00:40.149151 WARNING: intensity_correlation has 61 NaNs ( 0.05 % out of 133035)
1:00:40.149517 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 133035)
1:00:40.157263 INFO: Collecting fragment features
1:00:40.232657 INFO: Finished candidate scoring
1:00:40.306982 INFO: performing precursor FDR with 47 features
1:00:40.307122 INFO: Decoy channel: -1
1:00:40.307147 INFO: Competetive: True
1:00:40.344150 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:40.365721 WARNING: dropped 26 target PSMs due to missing features
1:00:40.365876 WARNING: dropped 37 decoy PSMs due to missing features
1:00:40.385209 INFO: Using random state 686047 for train-test-split
1:00:42.472680 INFO: Test AUC: 0.557
1:00:42.472800 INFO: Train AUC: 0.581
1:00:42.472833 INFO: AUC difference: 4.16%
1:00:42.744828 INFO: Resetting torch num_threads to 80
1:00:42.747908 PROGRESS: === Extracted 133035 precursors and 1306956 fragments ===
1:00:42.748440 INFO: === FDR correction performed with classifier version 10 ===
1:00:42.752122 PROGRESS: ============================= Precursor FDR =============================
1:00:42.752242 PROGRESS: Total precursors accumulated: 24,335
1:00:42.752306 PROGRESS: Target precursors: 14,704 (60.42%)
1:00:42.752356 PROGRESS: Decoy precursors: 9,631 (39.58%)
1:00:42.752399 PROGRESS: 
1:00:42.752441 PROGRESS: Precursor Summary:
1:00:42.753589 PROGRESS: Channel   0:	 0.050 FDR:   373; 0.010 FDR:   252; 0.001 FDR:   126
1:00:42.753680 PROGRESS: 
1:00:42.753733 PROGRESS: Protein Summary:
1:00:42.754986 PROGRESS: Channel   0:	 0.050 FDR:   363; 0.010 FDR:   245; 0.001 FDR:   123
1:00:42.755087 PROGRESS: =========================================================================
1:00:42.755799 INFO: Target number of precursors reached.
1:00:42.844034 INFO: fragments_df: keeping 3509 of 1306956 [sum(precursor_idx_mask)=7791 sum(mass_error_mask)=1306954 stop_rank=3509
1:00:43.050974 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:00:43.146418 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:00:43.242784 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:00:43.341908 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:00:43.731389 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:00:43.731856 INFO: Using score_cutoff 41.37117995681763 (fac=0.99, q=1)
1:00:43.732184 INFO: Updating optimization_manager: fwhm_rt             : 2.7949740886688232 -> 2.7193679809570312
1:00:43.732262 INFO: Updating optimization_manager: fwhm_mobility       : 0.008665547706186771 -> 0.009038612246513367
1:00:43.732317 INFO: Updating optimization_manager: score_cutoff        : 38.06627494812012 -> 41.37117995681763
1:00:43.732374 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:00:43.739588 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:00:43.770236 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:00:43.776720 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:00:43.834805 INFO: === checking if optimization conditions were reached ===
1:00:43.835120 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1:00:43.836401 INFO: Updating optimization_manager: rt_error            : 138.10813277827842 -> 144.78252977859194
1:00:43.836532 INFO: Updating optimization_manager: classifier_version  : 10 -> 17
1:00:43.836626 INFO: Updating optimization_manager: score_cutoff        : 41.37117995681763 -> 38.06627494812012
1:00:43.836710 INFO: Updating optimization_manager: fwhm_rt             : 2.7193679809570312 -> 2.7949740886688232
1:00:43.836795 INFO: Updating optimization_manager: fwhm_mobility       : 0.009038612246513367 -> 0.008665547706186771
1:00:43.836880 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 144.7825 found after 8 searches.
1:00:43.836942 INFO: ==============================================
1:00:43.837014 PROGRESS: Optimization finished for rt_error.
1:00:43.992903 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:00:44.000548 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:00:44.031020 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:00:44.037633 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:00:44.122744 INFO: Starting optimization step 0.
1:00:44.122985 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:00:44.123064 INFO: Using classic extraction backend
1:00:44.123211 PROGRESS: Extracting batch of 50061 precursors
1:00:44.123289 INFO: === Search parameters used ===
1:00:44.123343 INFO: rt_error       : 144.78252977859194
1:00:44.123391 INFO: mobility_error : 0.1
1:00:44.123439 INFO: num_candidates : 3
1:00:44.123504 INFO: ms1_error      : 15.0
1:00:44.123552 INFO: ms2_error      : 15.0
1:00:44.123596 INFO: fwhm_rt        : 2.7949740886688232
1:00:44.123640 INFO: quant_window   : 3
1:00:44.123684 INFO: ==============================================
1:00:44.136792 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:00:44.136923 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:00:44.136976 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1:00:44.137001 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.02
1:00:44.145663 INFO: Starting candidate selection
1:01:06.004057 INFO: Starting candidate scoring
1:01:12.064949 INFO: Finished candidate processing
1:01:12.065069 INFO: Collecting candidate features
1:01:12.301037 WARNING: intensity_correlation has 47 NaNs ( 0.04 % out of 132912)
1:01:12.301383 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 132912)
1:01:12.311171 INFO: Collecting fragment features
1:01:12.394282 INFO: Finished candidate scoring
1:01:12.506032 INFO: performing precursor FDR with 47 features
1:01:12.506172 INFO: Decoy channel: -1
1:01:12.506205 INFO: Competetive: True
1:01:12.541331 INFO: Setting torch num_threads to 2 for FDR classification task
1:01:12.564356 WARNING: dropped 19 target PSMs due to missing features
1:01:12.564545 WARNING: dropped 31 decoy PSMs due to missing features
1:01:12.584961 INFO: Using random state 375450 for train-test-split
1:01:14.660249 INFO: Test AUC: 0.569
1:01:14.660393 INFO: Train AUC: 0.593
1:01:14.660429 INFO: AUC difference: 4.08%
1:01:14.921287 INFO: Resetting torch num_threads to 80
1:01:14.924343 PROGRESS: === Extracted 132912 precursors and 1306833 fragments ===
1:01:14.924881 INFO: === FDR correction performed with classifier version 17 ===
1:01:14.928437 PROGRESS: ============================= Precursor FDR =============================
1:01:14.928553 PROGRESS: Total precursors accumulated: 24,299
1:01:14.928611 PROGRESS: Target precursors: 14,934 (61.46%)
1:01:14.928658 PROGRESS: Decoy precursors: 9,365 (38.54%)
1:01:14.928702 PROGRESS: 
1:01:14.928743 PROGRESS: Precursor Summary:
1:01:14.929869 PROGRESS: Channel   0:	 0.050 FDR:   402; 0.010 FDR:   266; 0.001 FDR:   187
1:01:14.929964 PROGRESS: 
1:01:14.930022 PROGRESS: Protein Summary:
1:01:14.931280 PROGRESS: Channel   0:	 0.050 FDR:   391; 0.010 FDR:   258; 0.001 FDR:   182
1:01:14.931371 PROGRESS: =========================================================================
1:01:14.932074 INFO: Target number of precursors reached.
1:01:15.021134 INFO: fragments_df: keeping 3559 of 1306833 [sum(precursor_idx_mask)=8239 sum(mass_error_mask)=1306831 stop_rank=3559
1:01:15.221822 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:01:15.326707 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:01:15.426022 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:01:15.527159 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:01:15.924575 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:01:15.925030 INFO: Using score_cutoff 38.83805831909179 (fac=0.99, q=1)
1:01:15.925363 INFO: Updating optimization_manager: fwhm_rt             : 2.7949740886688232 -> 2.8237881660461426
1:01:15.925440 INFO: Updating optimization_manager: fwhm_mobility       : 0.008665547706186771 -> 0.008951196447014809
1:01:15.925494 INFO: Updating optimization_manager: score_cutoff        : 38.06627494812012 -> 38.83805831909179
1:01:15.925550 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:01:15.932946 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:01:15.963089 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:01:15.970150 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:01:16.031981 INFO: === checking if optimization conditions were reached ===
1:01:16.032285 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1:01:16.034072 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06591220341826418
1:01:16.034175 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0659.
1:01:16.034240 INFO: ==============================================
1:01:16.034312 INFO: Starting optimization step 1.
1:01:16.034384 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:01:16.034454 INFO: Using classic extraction backend
1:01:16.034618 PROGRESS: Extracting batch of 50061 precursors
1:01:16.034684 INFO: === Search parameters used ===
1:01:16.034730 INFO: rt_error       : 144.78252977859194
1:01:16.034770 INFO: mobility_error : 0.06591220341826418
1:01:16.034809 INFO: num_candidates : 3
1:01:16.034848 INFO: ms1_error      : 15.0
1:01:16.034885 INFO: ms2_error      : 15.0
1:01:16.034922 INFO: fwhm_rt        : 2.8237881660461426
1:01:16.034960 INFO: quant_window   : 3
1:01:16.034997 INFO: ==============================================
1:01:16.048125 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:01:16.048252 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:01:16.048304 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1:01:16.048328 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.15
1:01:16.049242 INFO: Starting candidate selection
1:01:30.644458 INFO: Starting candidate scoring
1:01:36.403511 INFO: Finished candidate processing
1:01:36.403680 INFO: Collecting candidate features
1:01:36.568043 WARNING: intensity_correlation has 56 NaNs ( 0.04 % out of 129433)
1:01:36.568391 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 129433)
1:01:36.575943 INFO: Collecting fragment features
1:01:36.650289 INFO: Finished candidate scoring
1:01:36.717278 INFO: performing precursor FDR with 47 features
1:01:36.717418 INFO: Decoy channel: -1
1:01:36.717444 INFO: Competetive: True
1:01:36.751949 INFO: Setting torch num_threads to 2 for FDR classification task
1:01:36.772764 WARNING: dropped 32 target PSMs due to missing features
1:01:36.772917 WARNING: dropped 26 decoy PSMs due to missing features
1:01:36.790265 INFO: Using random state 375450 for train-test-split
1:01:38.685632 INFO: Test AUC: 0.570
1:01:38.685777 INFO: Train AUC: 0.610
1:01:38.685811 INFO: AUC difference: 6.65%
1:01:38.685833 WARNING: AUC difference > 5%. This may indicate overfitting.
1:01:39.726591 INFO: Resetting torch num_threads to 80
1:01:39.739528 PROGRESS: === Extracted 129433 precursors and 1257772 fragments ===
1:01:39.740028 INFO: === FDR correction performed with classifier version 17 ===
1:01:39.744138 PROGRESS: ============================= Precursor FDR =============================
1:01:39.744255 PROGRESS: Total precursors accumulated: 23,764
1:01:39.744323 PROGRESS: Target precursors: 15,064 (63.39%)
1:01:39.744373 PROGRESS: Decoy precursors: 8,700 (36.61%)
1:01:39.744418 PROGRESS: 
1:01:39.744461 PROGRESS: Precursor Summary:
1:01:39.745643 PROGRESS: Channel   0:	 0.050 FDR:   423; 0.010 FDR:   311; 0.001 FDR:   212
1:01:39.745742 PROGRESS: 
1:01:39.745800 PROGRESS: Protein Summary:
1:01:39.747111 PROGRESS: Channel   0:	 0.050 FDR:   413; 0.010 FDR:   303; 0.001 FDR:   207
1:01:39.747204 PROGRESS: =========================================================================
1:01:39.748156 INFO: Target number of precursors reached.
1:01:39.835399 INFO: fragments_df: keeping 3938 of 1257772 [sum(precursor_idx_mask)=9520 sum(mass_error_mask)=1257769 stop_rank=3938
1:01:40.090942 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:01:40.203872 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:01:40.311697 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:01:40.418290 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:01:40.873134 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:01:40.873747 INFO: Using score_cutoff 36.5520013961792 (fac=0.99, q=1)
1:01:40.874146 INFO: Updating optimization_manager: fwhm_rt             : 2.8237881660461426 -> 2.7949740886688232
1:01:40.874228 INFO: Updating optimization_manager: fwhm_mobility       : 0.008951196447014809 -> 0.008718868717551231
1:01:40.874283 INFO: Updating optimization_manager: score_cutoff        : 38.83805831909179 -> 36.5520013961792
1:01:40.874340 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:01:40.881820 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:01:40.912096 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:01:40.918768 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:01:40.980984 INFO: === checking if optimization conditions were reached ===
1:01:40.981276 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1:01:40.983458 INFO: Updating optimization_manager: mobility_error      : 0.06591220341826418 -> 0.05922647010032181
1:01:40.983572 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0592.
1:01:40.983646 INFO: ==============================================
1:01:40.983728 INFO: Starting optimization step 2.
1:01:40.983797 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:01:40.983878 INFO: Using classic extraction backend
1:01:40.984082 PROGRESS: Extracting batch of 50061 precursors
1:01:40.984157 INFO: === Search parameters used ===
1:01:40.984214 INFO: rt_error       : 144.78252977859194
1:01:40.984259 INFO: mobility_error : 0.05922647010032181
1:01:40.984305 INFO: num_candidates : 3
1:01:40.984349 INFO: ms1_error      : 15.0
1:01:40.984388 INFO: ms2_error      : 15.0
1:01:40.984433 INFO: fwhm_rt        : 2.7949740886688232
1:01:40.984475 INFO: quant_window   : 3
1:01:40.984513 INFO: ==============================================
1:01:40.997946 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:01:40.998091 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:01:40.998150 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1:01:40.998176 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
1:01:41.007746 INFO: Starting candidate selection
1:01:55.126647 INFO: Starting candidate scoring
1:02:01.145306 INFO: Finished candidate processing
1:02:01.145432 INFO: Collecting candidate features
1:02:01.319544 WARNING: intensity_correlation has 66 NaNs ( 0.05 % out of 129033)
1:02:01.319898 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 129033)
1:02:01.327478 INFO: Collecting fragment features
1:02:01.403326 INFO: Finished candidate scoring
1:02:01.483382 INFO: performing precursor FDR with 47 features
1:02:01.483526 INFO: Decoy channel: -1
1:02:01.483551 INFO: Competetive: True
1:02:01.520223 INFO: Setting torch num_threads to 2 for FDR classification task
1:02:01.545888 WARNING: dropped 33 target PSMs due to missing features
1:02:01.546047 WARNING: dropped 36 decoy PSMs due to missing features
1:02:01.563665 INFO: Using random state 375450 for train-test-split
1:02:03.484688 INFO: Test AUC: 0.567
1:02:03.484928 INFO: Train AUC: 0.600
1:02:03.484965 INFO: AUC difference: 5.40%
1:02:03.484989 WARNING: AUC difference > 5%. This may indicate overfitting.
1:02:03.759086 INFO: Resetting torch num_threads to 80
1:02:03.762135 PROGRESS: === Extracted 129033 precursors and 1249633 fragments ===
1:02:03.762713 INFO: === FDR correction performed with classifier version 17 ===
1:02:03.766421 PROGRESS: ============================= Precursor FDR =============================
1:02:03.766546 PROGRESS: Total precursors accumulated: 23,676
1:02:03.766609 PROGRESS: Target precursors: 14,796 (62.49%)
1:02:03.766660 PROGRESS: Decoy precursors: 8,880 (37.51%)
1:02:03.766705 PROGRESS: 
1:02:03.766745 PROGRESS: Precursor Summary:
1:02:03.767962 PROGRESS: Channel   0:	 0.050 FDR:   391; 0.010 FDR:   267; 0.001 FDR:   187
1:02:03.768053 PROGRESS: 
1:02:03.768109 PROGRESS: Protein Summary:
1:02:03.769393 PROGRESS: Channel   0:	 0.050 FDR:   380; 0.010 FDR:   262; 0.001 FDR:   184
1:02:03.769480 PROGRESS: =========================================================================
1:02:03.770418 INFO: Target number of precursors reached.
1:02:03.853537 INFO: fragments_df: keeping 3564 of 1249633 [sum(precursor_idx_mask)=8341 sum(mass_error_mask)=1249629 stop_rank=3564
1:02:04.094954 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:02:04.192490 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:02:04.289988 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:02:04.386860 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:02:04.788203 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:02:04.788661 INFO: Using score_cutoff 39.11106574401855 (fac=0.99, q=1)
1:02:04.788993 INFO: Updating optimization_manager: fwhm_rt             : 2.7949740886688232 -> 2.7499570846557617
1:02:04.789078 INFO: Updating optimization_manager: fwhm_mobility       : 0.008718868717551231 -> 0.008713694289326668
1:02:04.789132 INFO: Updating optimization_manager: score_cutoff        : 36.5520013961792 -> 39.11106574401855
1:02:04.789187 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:02:04.796582 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:02:04.826767 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:02:04.833256 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:02:04.891782 INFO: === checking if optimization conditions were reached ===
1:02:04.892092 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1:02:04.893070 INFO: Updating optimization_manager: mobility_error      : 0.05922647010032181 -> 0.06591220341826418
1:02:04.893198 INFO: Updating optimization_manager: classifier_version  : 17 -> 20
1:02:04.893297 INFO: Updating optimization_manager: score_cutoff        : 39.11106574401855 -> 36.5520013961792
1:02:04.893390 INFO: Updating optimization_manager: fwhm_rt             : 2.7499570846557617 -> 2.7949740886688232
1:02:04.893481 INFO: Updating optimization_manager: fwhm_mobility       : 0.008713694289326668 -> 0.008718868717551231
1:02:04.893577 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0659 found after 3 searches.
1:02:04.893645 INFO: ==============================================
1:02:04.893724 PROGRESS: Optimization finished for mobility_error.
1:02:05.025382 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:02:05.033149 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:02:05.063607 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:02:05.070205 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:02:05.156024 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:02:05.156276 PROGRESS: ==============================================
1:02:05.156352 PROGRESS: ms2_error      : 15.0000
1:02:05.156411 PROGRESS: ms1_error      : 15.0000
1:02:05.156464 PROGRESS: rt_error       : 144.7825
1:02:05.156514 PROGRESS: mobility_error : 0.0659
1:02:05.156560 PROGRESS: ==============================================
1:02:05.158375 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:02:06.787129 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:02:14.360967 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:02:15.899964 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:02:31.410256 INFO: Using classic extraction backend
1:02:31.411058 PROGRESS: Extracting batch of 12073114 precursors
1:02:31.411190 INFO: === Search parameters used ===
1:02:31.411248 INFO: rt_error       : 144.78252977859194
1:02:31.411297 INFO: mobility_error : 0.06591220341826418
1:02:31.411343 INFO: num_candidates : 3
1:02:31.411386 INFO: ms1_error      : 15.0
1:02:31.411431 INFO: ms2_error      : 15.0
1:02:31.411487 INFO: fwhm_rt        : 2.7949740886688232
1:02:31.411530 INFO: quant_window   : 3
1:02:31.411576 INFO: ==============================================
1:02:34.033700 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:02:34.033891 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:02:34.033952 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1:02:34.033976 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
1:02:34.039385 INFO: Starting candidate selection
1:55:03.818715 INFO: Removed 14110125 precursors with score below cutoff 36.5520013961792
1:55:06.666099 INFO: Starting candidate scoring
2:07:57.005930 INFO: Finished candidate processing
2:07:57.006434 INFO: Collecting candidate features
2:08:54.131209 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 18947355)
2:08:54.785137 INFO: Collecting fragment features
2:09:10.519631 INFO: Finished candidate scoring
2:09:39.889674 INFO: === Performing FDR correction with classifier version 20 ===
2:09:40.026432 INFO: performing precursor FDR with 47 features
2:09:40.026551 INFO: Decoy channel: -1
2:09:40.026586 INFO: Competetive: True
2:09:45.955834 INFO: Setting torch num_threads to 2 for FDR classification task
2:09:48.934295 WARNING: dropped 3 target PSMs due to missing features
2:09:48.934498 WARNING: dropped 3 decoy PSMs due to missing features
2:09:58.257544 INFO: Using random state 885003 for train-test-split
2:16:05.270358 INFO: Test AUC: 0.569
2:16:05.270616 INFO: Train AUC: 0.570
2:16:05.270663 INFO: AUC difference: 0.23%
2:16:09.601695 INFO: Resetting torch num_threads to 80
2:16:10.147955 INFO: Removing fragments below FDR threshold
2:16:11.949331 PROGRESS: ============================= Precursor FDR =============================
2:16:11.949585 PROGRESS: Total precursors accumulated: 69,361
2:16:11.949655 PROGRESS: Target precursors: 68,675 (99.01%)
2:16:11.949709 PROGRESS: Decoy precursors: 686 (0.99%)
2:16:11.949759 PROGRESS: 
2:16:11.949816 PROGRESS: Precursor Summary:
2:16:11.975562 PROGRESS: Channel   0:	 0.050 FDR: 68,675; 0.010 FDR: 68,675; 0.001 FDR: 46,535
2:16:11.975809 PROGRESS: 
2:16:11.975873 PROGRESS: Protein Summary:
2:16:12.008734 PROGRESS: Channel   0:	 0.050 FDR: 11,189; 0.010 FDR: 11,189; 0.001 FDR: 8,615
2:16:12.008943 PROGRESS: =========================================================================
2:16:12.228626 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/psm.parquet
2:16:12.698367 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/frag.parquet
2:16:12.961351 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
2:16:13.610759 PROGRESS: 
2:16:13.610957 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant
2:16:13.611037 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/figures
2:16:13.611266 INFO: Initializing TimingManager
2:16:13.611928 INFO: Initializing RawFileManager
2:16:13.612092 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:13.612173 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:13.612250 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:13.841485 INFO: Reading 39,128 frames with 2,860,596,893 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:22.049253 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
2:16:22.052238 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:22.055734 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:22.055969 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:22.056409 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:22.057662 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:22.070781 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:22.071324 INFO: Indexing quadrupole dimension
2:16:22.532907 INFO: Transposing detector events
2:16:32.761420 INFO: Finished transposing data
2:16:32.800303 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:16:32.801806 INFO: RT (min)            : 0.0 - 70.0
2:16:32.801909 INFO: RT duration (sec)   : 4199.8
2:16:32.801969 INFO: RT duration (min)   : 70.0
2:16:32.802019 INFO: Cycle len (scans)   : 9
2:16:32.802084 INFO: Cycle len (sec)     : 0.97
2:16:32.802130 INFO: Number of cycles    : 4347
2:16:32.802176 INFO: MS2 range (m/z)     : 400.0 - 1000.0
2:16:32.802311 INFO: Creating DIA data object took: 19.19026207923889
2:16:34.900646 INFO: Initializing CalibrationManager
2:16:34.900956 INFO: Setting up calibration estimators ..
2:16:34.901023 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:16:34.901152 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'}' ..
2:16:34.901354 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:16:34.901418 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'}' ..
2:16:34.901496 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}}' ..
2:16:34.901565 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}}' ..
2:16:34.901625 INFO: Done setting up calibration estimators.
2:16:34.901774 INFO: Initializing OptimizationManager
2:16:34.901882 INFO: initial parameter: ms1_error = 30
2:16:34.901932 INFO: initial parameter: ms2_error = 30
2:16:34.901978 INFO: initial parameter: rt_error = 2099.894844
2:16:34.902020 INFO: initial parameter: mobility_error = 0.1
2:16:34.902073 INFO: initial parameter: num_candidates = 1
2:16:34.902115 INFO: initial parameter: fwhm_rt = 5
2:16:34.902158 INFO: initial parameter: fwhm_mobility = 0.01
2:16:34.902199 INFO: initial parameter: score_cutoff = 0
2:16:34.902241 INFO: initial parameter: classifier_version = -1
2:16:34.902328 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
2:16:34.902737 INFO: FDRManager: loading saved state not requested, will be initialized.
2:16:34.902777 INFO: Initializing FDRManager
2:16:34.902839 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:16:36.164316 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
2:16:36.960469 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:16:36.960938 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 2099.894844
2:16:36.961054 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2:16:36.961248 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
2:16:36.961373 PROGRESS: Starting initial search for precursors.
2:16:36.961488 INFO: Starting optimization step 0.
2:16:36.961560 PROGRESS: === Extracting elution groups 0 to 200 ===
2:16:36.961655 INFO: Using classic extraction backend
2:16:36.961948 PROGRESS: Extracting batch of 390 precursors
2:16:36.962029 INFO: === Search parameters used ===
2:16:36.962095 INFO: rt_error       : 2099.894844
2:16:36.962138 INFO: mobility_error : 0.1
2:16:36.962179 INFO: num_candidates : 1
2:16:36.962219 INFO: ms1_error      : 30
2:16:36.962258 INFO: ms2_error      : 30
2:16:36.962298 INFO: fwhm_rt        : 5
2:16:36.962336 INFO: quant_window   : 3
2:16:36.962374 INFO: ==============================================
2:16:36.963686 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:16:36.963731 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:16:36.963794 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:16:36.963816 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:16:36.969849 INFO: Starting candidate selection
2:16:41.030269 INFO: Starting candidate scoring
2:16:41.106520 INFO: Finished candidate processing
2:16:41.106660 INFO: Collecting candidate features
2:16:41.113831 WARNING: intensity_correlation has 1 NaNs ( 0.28 % out of 363)
2:16:41.116964 INFO: Collecting fragment features
2:16:41.119248 INFO: Finished candidate scoring
2:16:41.120280 INFO: performing precursor FDR with 47 features
2:16:41.120322 INFO: Decoy channel: -1
2:16:41.120347 INFO: Competetive: True
2:16:41.121616 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:41.122814 WARNING: dropped 1 decoy PSMs due to missing features
2:16:41.124674 INFO: Using random state 470346 for train-test-split
2:16:41.134068 INFO: Test AUC: 0.452
2:16:41.134128 INFO: Train AUC: 0.495
2:16:41.134162 INFO: AUC difference: 8.76%
2:16:41.134189 WARNING: AUC difference > 5%. This may indicate overfitting.
2:16:41.358865 INFO: Resetting torch num_threads to 80
2:16:41.359459 PROGRESS: === Extracted 363 precursors and 3948 fragments ===
2:16:41.359978 INFO: === FDR correction performed with classifier version -1 ===
2:16:41.360556 PROGRESS: ============================= Precursor FDR =============================
2:16:41.360640 PROGRESS: Total precursors accumulated: 187
2:16:41.360700 PROGRESS: Target precursors: 149 (79.68%)
2:16:41.360750 PROGRESS: Decoy precursors: 38 (20.32%)
2:16:41.360797 PROGRESS: 
2:16:41.360838 PROGRESS: Precursor Summary:
2:16:41.361729 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
2:16:41.361814 PROGRESS: 
2:16:41.361876 PROGRESS: Protein Summary:
2:16:41.362864 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
2:16:41.362952 PROGRESS: =========================================================================
2:16:41.363070 INFO: Target number of precursors not reached yet.
2:16:41.433879 INFO: Starting optimization step 1.
2:16:41.434169 PROGRESS: === Extracting elution groups 200 to 600 ===
2:16:41.434260 INFO: Using classic extraction backend
2:16:41.434397 PROGRESS: Extracting batch of 783 precursors
2:16:41.434472 INFO: === Search parameters used ===
2:16:41.434520 INFO: rt_error       : 2099.894844
2:16:41.434578 INFO: mobility_error : 0.1
2:16:41.434622 INFO: num_candidates : 1
2:16:41.434663 INFO: ms1_error      : 30
2:16:41.434703 INFO: ms2_error      : 30
2:16:41.434743 INFO: fwhm_rt        : 5
2:16:41.434782 INFO: quant_window   : 3
2:16:41.434820 INFO: ==============================================
2:16:41.435629 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:16:41.435675 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:16:41.435704 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:16:41.435725 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:16:41.437710 INFO: Starting candidate selection
2:16:47.607506 INFO: Starting candidate scoring
2:16:47.736559 INFO: Finished candidate processing
2:16:47.736691 INFO: Collecting candidate features
2:16:47.746902 INFO: Collecting fragment features
2:16:47.749491 INFO: Finished candidate scoring
2:16:47.752636 INFO: performing precursor FDR with 47 features
2:16:47.752684 INFO: Decoy channel: -1
2:16:47.752708 INFO: Competetive: True
2:16:47.755770 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:47.756898 WARNING: dropped 1 decoy PSMs due to missing features
2:16:47.757759 INFO: Using random state 734572 for train-test-split
2:16:47.766361 INFO: Test AUC: 0.512
2:16:47.766419 INFO: Train AUC: 0.496
2:16:47.766448 INFO: AUC difference: 3.27%
2:16:47.996621 INFO: Resetting torch num_threads to 80
2:16:47.998130 PROGRESS: === Extracted 1116 precursors and 12181 fragments ===
2:16:47.998636 INFO: === FDR correction performed with classifier version -1 ===
2:16:47.999253 PROGRESS: ============================= Precursor FDR =============================
2:16:47.999345 PROGRESS: Total precursors accumulated: 575
2:16:47.999404 PROGRESS: Target precursors: 452 (78.61%)
2:16:47.999462 PROGRESS: Decoy precursors: 123 (21.39%)
2:16:47.999509 PROGRESS: 
2:16:47.999554 PROGRESS: Precursor Summary:
2:16:48.000448 PROGRESS: Channel   0:	 0.050 FDR:    77; 0.010 FDR:    77; 0.001 FDR:    77
2:16:48.000536 PROGRESS: 
2:16:48.000593 PROGRESS: Protein Summary:
2:16:48.001572 PROGRESS: Channel   0:	 0.050 FDR:    77; 0.010 FDR:    77; 0.001 FDR:    77
2:16:48.001663 PROGRESS: =========================================================================
2:16:48.001830 INFO: Target number of precursors not reached yet.
2:16:48.071058 INFO: Starting optimization step 2.
2:16:48.071333 PROGRESS: === Extracting elution groups 600 to 1400 ===
2:16:48.071419 INFO: Using classic extraction backend
2:16:48.071557 PROGRESS: Extracting batch of 1576 precursors
2:16:48.071634 INFO: === Search parameters used ===
2:16:48.071683 INFO: rt_error       : 2099.894844
2:16:48.071726 INFO: mobility_error : 0.1
2:16:48.071770 INFO: num_candidates : 1
2:16:48.071812 INFO: ms1_error      : 30
2:16:48.071856 INFO: ms2_error      : 30
2:16:48.071896 INFO: fwhm_rt        : 5
2:16:48.071936 INFO: quant_window   : 3
2:16:48.071976 INFO: ==============================================
2:16:48.072882 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:16:48.072929 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:16:48.072959 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:16:48.072982 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:16:48.073714 INFO: Starting candidate selection
2:16:59.133342 INFO: Starting candidate scoring
2:16:59.323781 INFO: Finished candidate processing
2:16:59.324006 INFO: Collecting candidate features
2:16:59.351469 INFO: Collecting fragment features
2:16:59.359134 INFO: Finished candidate scoring
2:16:59.370194 INFO: performing precursor FDR with 47 features
2:16:59.370325 INFO: Decoy channel: -1
2:16:59.370414 INFO: Competetive: True
2:16:59.377101 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:59.379608 WARNING: dropped 1 decoy PSMs due to missing features
2:16:59.381254 INFO: Using random state 619172 for train-test-split
2:16:59.399216 INFO: Test AUC: 0.467
2:16:59.399296 INFO: Train AUC: 0.500
2:16:59.399334 INFO: AUC difference: 6.50%
2:16:59.399363 WARNING: AUC difference > 5%. This may indicate overfitting.
2:16:59.639060 INFO: Resetting torch num_threads to 80
2:16:59.643019 PROGRESS: === Extracted 2636 precursors and 28710 fragments ===
2:16:59.643694 INFO: === FDR correction performed with classifier version -1 ===
2:16:59.644600 PROGRESS: ============================= Precursor FDR =============================
2:16:59.644706 PROGRESS: Total precursors accumulated: 1,353
2:16:59.644783 PROGRESS: Target precursors: 1,056 (78.05%)
2:16:59.644852 PROGRESS: Decoy precursors: 297 (21.95%)
2:16:59.644927 PROGRESS: 
2:16:59.644992 PROGRESS: Precursor Summary:
2:16:59.645993 PROGRESS: Channel   0:	 0.050 FDR:   149; 0.010 FDR:   149; 0.001 FDR:   149
2:16:59.646108 PROGRESS: 
2:16:59.646187 PROGRESS: Protein Summary:
2:16:59.647303 PROGRESS: Channel   0:	 0.050 FDR:   148; 0.010 FDR:   148; 0.001 FDR:   148
2:16:59.647409 PROGRESS: =========================================================================
2:16:59.647853 INFO: Target number of precursors not reached yet.
2:16:59.728417 INFO: Starting optimization step 3.
2:16:59.728708 PROGRESS: === Extracting elution groups 1400 to 3000 ===
2:16:59.728798 INFO: Using classic extraction backend
2:16:59.728935 PROGRESS: Extracting batch of 3162 precursors
2:16:59.729019 INFO: === Search parameters used ===
2:16:59.729070 INFO: rt_error       : 2099.894844
2:16:59.729113 INFO: mobility_error : 0.1
2:16:59.729169 INFO: num_candidates : 1
2:16:59.729213 INFO: ms1_error      : 30
2:16:59.729257 INFO: ms2_error      : 30
2:16:59.729297 INFO: fwhm_rt        : 5
2:16:59.729336 INFO: quant_window   : 3
2:16:59.729372 INFO: ==============================================
2:16:59.730676 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:16:59.730727 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:16:59.730762 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:16:59.730783 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:16:59.732350 INFO: Starting candidate selection
2:17:23.624473 INFO: Starting candidate scoring
2:17:23.925624 INFO: Finished candidate processing
2:17:23.925805 INFO: Collecting candidate features
2:17:23.947004 INFO: Collecting fragment features
2:17:23.954032 INFO: Finished candidate scoring
2:17:23.959956 INFO: performing precursor FDR with 47 features
2:17:23.960020 INFO: Decoy channel: -1
2:17:23.960046 INFO: Competetive: True
2:17:23.965925 INFO: Setting torch num_threads to 2 for FDR classification task
2:17:23.967932 WARNING: dropped 1 decoy PSMs due to missing features
2:17:23.970468 INFO: Using random state 936894 for train-test-split
2:17:23.991928 INFO: Test AUC: 0.498
2:17:23.992027 INFO: Train AUC: 0.495
2:17:23.992058 INFO: AUC difference: 0.55%
2:17:24.228752 INFO: Resetting torch num_threads to 80
2:17:24.231196 PROGRESS: === Extracted 5666 precursors and 61386 fragments ===
2:17:24.231694 INFO: === FDR correction performed with classifier version -1 ===
2:17:24.232605 PROGRESS: ============================= Precursor FDR =============================
2:17:24.232702 PROGRESS: Total precursors accumulated: 2,897
2:17:24.232764 PROGRESS: Target precursors: 2,264 (78.15%)
2:17:24.232816 PROGRESS: Decoy precursors: 633 (21.85%)
2:17:24.232862 PROGRESS: 
2:17:24.232921 PROGRESS: Precursor Summary:
2:17:24.233939 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   350; 0.001 FDR:   350
2:17:24.234035 PROGRESS: 
2:17:24.234102 PROGRESS: Protein Summary:
2:17:24.235315 PROGRESS: Channel   0:	 0.050 FDR:   344; 0.010 FDR:   344; 0.001 FDR:   344
2:17:24.235407 PROGRESS: =========================================================================
2:17:24.235621 INFO: Target number of precursors reached.
2:17:24.242085 INFO: fragments_df: keeping 728 of 61386 [sum(precursor_idx_mask)=3909 sum(mass_error_mask)=61386 stop_rank=728
2:17:24.400090 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:17:24.531678 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:17:24.660400 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:17:24.789165 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:17:24.939806 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:17:24.940218 INFO: Using score_cutoff 36.7338261669159 (fac=0.99, q=1)
2:17:24.940569 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.4029855728149414
2:17:24.940651 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007905603386461735
2:17:24.940715 INFO: Updating optimization_manager: score_cutoff        : 0 -> 36.7338261669159
2:17:24.940780 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:17:24.942474 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:24.947307 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:17:24.948657 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:24.957013 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
2:17:24.957131 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:17:24.957220 INFO: Starting optimization step 4.
2:17:24.957281 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:17:24.957343 INFO: Using classic extraction backend
2:17:24.957484 PROGRESS: Extracting batch of 5911 precursors
2:17:24.958127 INFO: === Search parameters used ===
2:17:24.958189 INFO: rt_error       : 2099.894844
2:17:24.958232 INFO: mobility_error : 0.1
2:17:24.958272 INFO: num_candidates : 3
2:17:24.958312 INFO: ms1_error      : 30
2:17:24.958355 INFO: ms2_error      : 30
2:17:24.958394 INFO: fwhm_rt        : 3.4029855728149414
2:17:24.958432 INFO: quant_window   : 3
2:17:24.958469 INFO: ==============================================
2:17:24.960626 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:17:24.960674 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:17:24.960714 INFO: FWHM in RT is 3.40 seconds, sigma is 0.75
2:17:24.960737 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
2:17:24.961390 INFO: Starting candidate selection
2:18:14.071967 INFO: Starting candidate scoring
2:18:15.521889 INFO: Finished candidate processing
2:18:15.522123 INFO: Collecting candidate features
2:18:15.588089 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 16417)
2:18:15.594585 INFO: Collecting fragment features
2:18:15.612074 INFO: Finished candidate scoring
2:18:15.620817 INFO: performing precursor FDR with 47 features
2:18:15.620925 INFO: Decoy channel: -1
2:18:15.620952 INFO: Competetive: True
2:18:15.630805 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:15.634485 WARNING: dropped 1 decoy PSMs due to missing features
2:18:15.637600 INFO: Using random state 704532 for train-test-split
2:18:15.807517 INFO: Test AUC: 0.504
2:18:15.807661 INFO: Train AUC: 0.504
2:18:15.807698 INFO: AUC difference: 0.12%
2:18:16.043149 INFO: Resetting torch num_threads to 80
2:18:16.044327 PROGRESS: === Extracted 16417 precursors and 179317 fragments ===
2:18:16.044952 INFO: === FDR correction performed with classifier version 3 ===
2:18:16.045959 PROGRESS: ============================= Precursor FDR =============================
2:18:16.046059 PROGRESS: Total precursors accumulated: 2,951
2:18:16.046122 PROGRESS: Target precursors: 2,886 (97.80%)
2:18:16.046184 PROGRESS: Decoy precursors: 65 (2.20%)
2:18:16.046229 PROGRESS: 
2:18:16.046273 PROGRESS: Precursor Summary:
2:18:16.047515 PROGRESS: Channel   0:	 0.050 FDR: 2,886; 0.010 FDR:     3; 0.001 FDR:     3
2:18:16.047612 PROGRESS: 
2:18:16.047667 PROGRESS: Protein Summary:
2:18:16.049279 PROGRESS: Channel   0:	 0.050 FDR: 2,667; 0.010 FDR:     3; 0.001 FDR:     3
2:18:16.049375 PROGRESS: =========================================================================
2:18:16.050304 INFO: Target number of precursors not reached yet.
2:18:16.644523 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:18:16.647245 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:18:16.652531 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:18:16.653988 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:18:16.662763 INFO: === skipping optimization until target number of precursors are found ===
2:18:16.662943 INFO: Starting optimization step 5.
2:18:16.663018 PROGRESS: === Extracting elution groups 3000 to 6200 ===
2:18:16.663096 INFO: Using classic extraction backend
2:18:16.663263 PROGRESS: Extracting batch of 6312 precursors
2:18:16.663343 INFO: === Search parameters used ===
2:18:16.663392 INFO: rt_error       : 2099.894844
2:18:16.663436 INFO: mobility_error : 0.1
2:18:16.663479 INFO: num_candidates : 3
2:18:16.663521 INFO: ms1_error      : 30
2:18:16.663561 INFO: ms2_error      : 30
2:18:16.663599 INFO: fwhm_rt        : 3.4029855728149414
2:18:16.663638 INFO: quant_window   : 3
2:18:16.663676 INFO: ==============================================
2:18:16.666253 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:18:16.666310 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:18:16.666368 INFO: FWHM in RT is 3.40 seconds, sigma is 0.75
2:18:16.666392 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
2:18:16.667204 INFO: Starting candidate selection
2:19:12.696123 INFO: Starting candidate scoring
2:19:14.229850 INFO: Finished candidate processing
2:19:14.230020 INFO: Collecting candidate features
2:19:14.265143 INFO: Collecting fragment features
2:19:14.279098 INFO: Finished candidate scoring
2:19:14.325210 INFO: performing precursor FDR with 47 features
2:19:14.325375 INFO: Decoy channel: -1
2:19:14.325402 INFO: Competetive: True
2:19:14.341348 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:14.346954 WARNING: dropped 1 decoy PSMs due to missing features
2:19:14.353084 INFO: Using random state 704532 for train-test-split
2:19:14.910311 INFO: Test AUC: 0.548
2:19:14.910456 INFO: Train AUC: 0.550
2:19:14.910489 INFO: AUC difference: 0.48%
2:19:15.148760 INFO: Resetting torch num_threads to 80
2:19:15.154780 PROGRESS: === Extracted 33882 precursors and 369172 fragments ===
2:19:15.155634 INFO: === FDR correction performed with classifier version 3 ===
2:19:15.157091 PROGRESS: ============================= Precursor FDR =============================
2:19:15.157189 PROGRESS: Total precursors accumulated: 6,100
2:19:15.157255 PROGRESS: Target precursors: 3,519 (57.69%)
2:19:15.157308 PROGRESS: Decoy precursors: 2,581 (42.31%)
2:19:15.157351 PROGRESS: 
2:19:15.157394 PROGRESS: Precursor Summary:
2:19:15.158360 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2:19:15.158451 PROGRESS: 
2:19:15.158505 PROGRESS: Protein Summary:
2:19:15.159515 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2:19:15.159604 PROGRESS: =========================================================================
2:19:15.159992 INFO: Target number of precursors not reached yet.
2:19:15.321441 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:19:15.324842 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:19:15.342892 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:19:15.345513 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:19:15.360935 INFO: === skipping optimization until target number of precursors are found ===
2:19:15.361168 INFO: Starting optimization step 6.
2:19:15.361241 PROGRESS: === Extracting elution groups 6200 to 12600 ===
2:19:15.361336 INFO: Using classic extraction backend
2:19:15.361777 PROGRESS: Extracting batch of 12615 precursors
2:19:15.361870 INFO: === Search parameters used ===
2:19:15.361923 INFO: rt_error       : 2099.894844
2:19:15.361969 INFO: mobility_error : 0.1
2:19:15.362011 INFO: num_candidates : 3
2:19:15.362079 INFO: ms1_error      : 30
2:19:15.362124 INFO: ms2_error      : 30
2:19:15.362165 INFO: fwhm_rt        : 3.4029855728149414
2:19:15.362205 INFO: quant_window   : 3
2:19:15.362243 INFO: ==============================================
2:19:15.366838 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:19:15.366899 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:19:15.366972 INFO: FWHM in RT is 3.40 seconds, sigma is 0.75
2:19:15.366997 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
2:19:15.367898 INFO: Starting candidate selection
2:20:57.788589 INFO: Starting candidate scoring
2:21:00.746719 INFO: Finished candidate processing
2:21:00.746838 INFO: Collecting candidate features
2:21:00.798866 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 35034)
2:21:00.803690 INFO: Collecting fragment features
2:21:00.826207 INFO: Finished candidate scoring
2:21:00.876292 INFO: performing precursor FDR with 47 features
2:21:00.876420 INFO: Decoy channel: -1
2:21:00.876446 INFO: Competetive: True
2:21:00.905081 INFO: Setting torch num_threads to 2 for FDR classification task
2:21:00.916978 WARNING: dropped 2 decoy PSMs due to missing features
2:21:00.927585 INFO: Using random state 704532 for train-test-split
2:21:02.208943 INFO: Test AUC: 0.557
2:21:02.209065 INFO: Train AUC: 0.571
2:21:02.209098 INFO: AUC difference: 2.49%
2:21:02.466986 INFO: Resetting torch num_threads to 80
2:21:02.482935 PROGRESS: === Extracted 68916 precursors and 750049 fragments ===
2:21:02.483732 INFO: === FDR correction performed with classifier version 3 ===
2:21:02.487250 PROGRESS: ============================= Precursor FDR =============================
2:21:02.487379 PROGRESS: Total precursors accumulated: 12,416
2:21:02.487447 PROGRESS: Target precursors: 7,590 (61.13%)
2:21:02.487504 PROGRESS: Decoy precursors: 4,826 (38.87%)
2:21:02.487553 PROGRESS: 
2:21:02.487602 PROGRESS: Precursor Summary:
2:21:02.488620 PROGRESS: Channel   0:	 0.050 FDR:    25; 0.010 FDR:     2; 0.001 FDR:     2
2:21:02.488716 PROGRESS: 
2:21:02.488777 PROGRESS: Protein Summary:
2:21:02.489803 PROGRESS: Channel   0:	 0.050 FDR:    25; 0.010 FDR:     2; 0.001 FDR:     2
2:21:02.489908 PROGRESS: =========================================================================
2:21:02.490669 INFO: Target number of precursors not reached yet.
2:21:02.706123 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:21:02.711159 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:21:02.725540 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:21:02.729155 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:21:02.759387 INFO: === skipping optimization until target number of precursors are found ===
2:21:02.759640 INFO: Starting optimization step 7.
2:21:02.759718 PROGRESS: === Extracting elution groups 12600 to 25400 ===
2:21:02.759795 INFO: Using classic extraction backend
2:21:02.759968 PROGRESS: Extracting batch of 25223 precursors
2:21:02.760046 INFO: === Search parameters used ===
2:21:02.760096 INFO: rt_error       : 2099.894844
2:21:02.760141 INFO: mobility_error : 0.1
2:21:02.760183 INFO: num_candidates : 3
2:21:02.760223 INFO: ms1_error      : 30
2:21:02.760263 INFO: ms2_error      : 30
2:21:02.760303 INFO: fwhm_rt        : 3.4029855728149414
2:21:02.760342 INFO: quant_window   : 3
2:21:02.760380 INFO: ==============================================
2:21:02.769015 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:21:02.769088 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:21:02.769139 INFO: FWHM in RT is 3.40 seconds, sigma is 0.75
2:21:02.769163 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
2:21:02.785858 INFO: Starting candidate selection
2:24:17.101402 INFO: Starting candidate scoring
2:24:22.685291 INFO: Finished candidate processing
2:24:22.685491 INFO: Collecting candidate features
2:24:22.812121 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 70112)
2:24:22.820701 INFO: Collecting fragment features
2:24:22.867864 INFO: Finished candidate scoring
2:24:22.988571 INFO: performing precursor FDR with 47 features
2:24:22.988730 INFO: Decoy channel: -1
2:24:22.988758 INFO: Competetive: True
2:24:23.045570 INFO: Setting torch num_threads to 2 for FDR classification task
2:24:23.068518 WARNING: dropped 3 decoy PSMs due to missing features
2:24:23.095958 INFO: Using random state 704532 for train-test-split
2:24:25.402985 INFO: Test AUC: 0.564
2:24:25.403129 INFO: Train AUC: 0.577
2:24:25.403162 INFO: AUC difference: 2.35%
2:24:25.671783 INFO: Resetting torch num_threads to 80
2:24:25.697625 PROGRESS: === Extracted 139028 precursors and 1512873 fragments ===
2:24:25.698446 INFO: === FDR correction performed with classifier version 3 ===
2:24:25.704010 PROGRESS: ============================= Precursor FDR =============================
2:24:25.704148 PROGRESS: Total precursors accumulated: 25,026
2:24:25.704213 PROGRESS: Target precursors: 15,604 (62.35%)
2:24:25.704263 PROGRESS: Decoy precursors: 9,422 (37.65%)
2:24:25.704309 PROGRESS: 
2:24:25.704353 PROGRESS: Precursor Summary:
2:24:25.705441 PROGRESS: Channel   0:	 0.050 FDR:    86; 0.010 FDR:     1; 0.001 FDR:     1
2:24:25.705533 PROGRESS: 
2:24:25.705588 PROGRESS: Protein Summary:
2:24:25.706714 PROGRESS: Channel   0:	 0.050 FDR:    86; 0.010 FDR:     1; 0.001 FDR:     1
2:24:25.706816 PROGRESS: =========================================================================
2:24:25.707609 INFO: Target number of precursors not reached yet.
2:24:26.078053 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:24:26.086114 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:24:26.117729 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:24:26.124612 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:24:26.190013 INFO: === skipping optimization until target number of precursors are found ===
2:24:26.190386 INFO: Starting optimization step 8.
2:24:26.190475 PROGRESS: === Extracting elution groups 25400 to 51000 ===
2:24:26.190586 INFO: Using classic extraction backend
2:24:26.190793 PROGRESS: Extracting batch of 50469 precursors
2:24:26.190888 INFO: === Search parameters used ===
2:24:26.190946 INFO: rt_error       : 2099.894844
2:24:26.190998 INFO: mobility_error : 0.1
2:24:26.191048 INFO: num_candidates : 3
2:24:26.191099 INFO: ms1_error      : 30
2:24:26.191148 INFO: ms2_error      : 30
2:24:26.191196 INFO: fwhm_rt        : 3.4029855728149414
2:24:26.191246 INFO: quant_window   : 3
2:24:26.191293 INFO: ==============================================
2:24:26.214447 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:24:26.214592 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:24:26.214653 INFO: FWHM in RT is 3.40 seconds, sigma is 0.75
2:24:26.214680 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
2:24:26.234794 INFO: Starting candidate selection
2:30:50.098069 INFO: Starting candidate scoring
2:31:00.717739 INFO: Finished candidate processing
2:31:00.717938 INFO: Collecting candidate features
2:31:00.961634 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 140167)
2:31:00.970372 INFO: Collecting fragment features
2:31:01.078809 INFO: Finished candidate scoring
2:31:01.342510 INFO: performing precursor FDR with 47 features
2:31:01.342677 INFO: Decoy channel: -1
2:31:01.342703 INFO: Competetive: True
2:31:01.442518 INFO: Setting torch num_threads to 2 for FDR classification task
2:31:01.492081 WARNING: dropped 2 target PSMs due to missing features
2:31:01.492238 WARNING: dropped 4 decoy PSMs due to missing features
2:31:01.565880 INFO: Using random state 704532 for train-test-split
2:31:06.865657 INFO: Test AUC: 0.571
2:31:06.865906 INFO: Train AUC: 0.583
2:31:06.865942 INFO: AUC difference: 2.08%
2:31:07.189573 INFO: Resetting torch num_threads to 80
2:31:07.244194 PROGRESS: === Extracted 279195 precursors and 3038562 fragments ===
2:31:07.245057 INFO: === FDR correction performed with classifier version 3 ===
2:31:07.254818 PROGRESS: ============================= Precursor FDR =============================
2:31:07.255033 PROGRESS: Total precursors accumulated: 50,235
2:31:07.255098 PROGRESS: Target precursors: 31,395 (62.50%)
2:31:07.255155 PROGRESS: Decoy precursors: 18,840 (37.50%)
2:31:07.255201 PROGRESS: 
2:31:07.255243 PROGRESS: Precursor Summary:
2:31:07.256522 PROGRESS: Channel   0:	 0.050 FDR:   171; 0.010 FDR:     9; 0.001 FDR:     9
2:31:07.256628 PROGRESS: 
2:31:07.257004 PROGRESS: Protein Summary:
2:31:07.258291 PROGRESS: Channel   0:	 0.050 FDR:   167; 0.010 FDR:     9; 0.001 FDR:     9
2:31:07.258385 PROGRESS: =========================================================================
2:31:07.259245 INFO: Target number of precursors not reached yet.
2:31:07.899593 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:31:07.913822 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:31:07.970207 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:31:07.984045 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:31:08.125192 INFO: === skipping optimization until target number of precursors are found ===
2:31:08.125527 INFO: Starting optimization step 9.
2:31:08.125603 PROGRESS: === Extracting elution groups 51000 to 102200 ===
2:31:08.125705 INFO: Using classic extraction backend
2:31:08.125897 PROGRESS: Extracting batch of 100931 precursors
2:31:08.125981 INFO: === Search parameters used ===
2:31:08.126032 INFO: rt_error       : 2099.894844
2:31:08.126095 INFO: mobility_error : 0.1
2:31:08.126140 INFO: num_candidates : 3
2:31:08.126180 INFO: ms1_error      : 30
2:31:08.126222 INFO: ms2_error      : 30
2:31:08.126261 INFO: fwhm_rt        : 3.4029855728149414
2:31:08.126299 INFO: quant_window   : 3
2:31:08.126350 INFO: ==============================================
2:31:08.155506 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:31:08.155649 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:31:08.155702 INFO: FWHM in RT is 3.40 seconds, sigma is 0.75
2:31:08.155723 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
2:31:08.156889 INFO: Starting candidate selection
2:43:51.808996 INFO: Starting candidate scoring
2:44:11.151725 INFO: Finished candidate processing
2:44:11.152213 INFO: Collecting candidate features
2:44:11.809129 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 280326)
2:44:11.822994 INFO: Collecting fragment features
2:44:12.011424 INFO: Finished candidate scoring
2:44:12.507225 INFO: performing precursor FDR with 47 features
2:44:12.507373 INFO: Decoy channel: -1
2:44:12.507438 INFO: Competetive: True
2:44:12.793428 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:12.927027 WARNING: dropped 5 target PSMs due to missing features
2:44:12.927172 WARNING: dropped 4 decoy PSMs due to missing features
2:44:13.106404 INFO: Using random state 704532 for train-test-split
2:44:23.951094 INFO: Test AUC: 0.568
2:44:23.951250 INFO: Train AUC: 0.580
2:44:23.951285 INFO: AUC difference: 2.01%
2:44:25.229535 INFO: Resetting torch num_threads to 80
2:44:25.441407 PROGRESS: === Extracted 559521 precursors and 6086304 fragments ===
2:44:25.442405 INFO: === FDR correction performed with classifier version 3 ===
2:44:25.466555 PROGRESS: ============================= Precursor FDR =============================
2:44:25.466875 PROGRESS: Total precursors accumulated: 100,661
2:44:25.466960 PROGRESS: Target precursors: 62,448 (62.04%)
2:44:25.467016 PROGRESS: Decoy precursors: 38,213 (37.96%)
2:44:25.467062 PROGRESS: 
2:44:25.467106 PROGRESS: Precursor Summary:
2:44:25.468976 PROGRESS: Channel   0:	 0.050 FDR:   784; 0.010 FDR:   592; 0.001 FDR:     0
2:44:25.469073 PROGRESS: 
2:44:25.469132 PROGRESS: Protein Summary:
2:44:25.470915 PROGRESS: Channel   0:	 0.050 FDR:   719; 0.010 FDR:   551; 0.001 FDR:     0
2:44:25.471010 PROGRESS: =========================================================================
2:44:25.473426 INFO: Target number of precursors reached.
2:44:25.922164 INFO: fragments_df: keeping 5000 of 6086304 [sum(precursor_idx_mask)=19554 sum(mass_error_mask)=6086302 stop_rank=5000
2:44:26.428160 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:44:26.581175 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:26.728180 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:44:26.850725 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:27.466352 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:27.466834 INFO: Using score_cutoff 53.98703915748597 (fac=0.99, q=1)
2:44:27.467236 INFO: Updating optimization_manager: fwhm_rt             : 3.4029855728149414 -> 3.004304885864258
2:44:27.467317 INFO: Updating optimization_manager: fwhm_mobility       : 0.007905603386461735 -> 0.010516232810914516
2:44:27.467373 INFO: Updating optimization_manager: score_cutoff        : 36.7338261669159 -> 53.98703915748597
2:44:27.467434 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:44:27.481500 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:27.542542 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:44:27.558990 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:27.699342 INFO: === checking if optimization conditions were reached ===
2:44:27.702104 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
2:44:27.702235 INFO: Updating optimization_manager: classifier_version  : 3 -> 9
2:44:27.702319 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
2:44:27.703572 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
2:44:27.703679 INFO: Updating optimization_manager: classifier_version  : 9 -> 9
2:44:27.703748 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
2:44:27.703821 INFO: ==============================================
2:44:27.703913 INFO: Starting optimization step 10.
2:44:27.703982 PROGRESS: === Extracting elution groups 0 to 51000 ===
2:44:27.704080 INFO: Using classic extraction backend
2:44:27.704319 PROGRESS: Extracting batch of 100530 precursors
2:44:27.704402 INFO: === Search parameters used ===
2:44:27.704458 INFO: rt_error       : 2099.894844
2:44:27.704509 INFO: mobility_error : 0.1
2:44:27.704558 INFO: num_candidates : 3
2:44:27.704607 INFO: ms1_error      : 15.0
2:44:27.704655 INFO: ms2_error      : 15.0
2:44:27.704707 INFO: fwhm_rt        : 3.004304885864258
2:44:27.704756 INFO: quant_window   : 3
2:44:27.704803 INFO: ==============================================
2:44:27.741906 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:44:27.742080 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:44:27.742142 INFO: FWHM in RT is 3.00 seconds, sigma is 0.66
2:44:27.742171 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.88
2:44:27.747184 INFO: Starting candidate selection
2:54:01.592732 INFO: Starting candidate scoring
2:54:12.864445 INFO: Finished candidate processing
2:54:12.864990 INFO: Collecting candidate features
2:54:13.719939 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 278783)
2:54:13.736592 INFO: Collecting fragment features
2:54:13.942282 INFO: Finished candidate scoring
2:54:14.244080 INFO: performing precursor FDR with 47 features
2:54:14.244196 INFO: Decoy channel: -1
2:54:14.244221 INFO: Competetive: True
2:54:14.343972 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:14.390534 WARNING: dropped 2 target PSMs due to missing features
2:54:14.390657 WARNING: dropped 3 decoy PSMs due to missing features
2:54:14.477328 INFO: Using random state 411705 for train-test-split
2:54:19.432414 INFO: Test AUC: 0.564
2:54:19.433079 INFO: Train AUC: 0.584
2:54:19.433122 INFO: AUC difference: 3.34%
2:54:19.760036 INFO: Resetting torch num_threads to 80
2:54:19.768246 PROGRESS: === Extracted 278783 precursors and 2897123 fragments ===
2:54:19.768952 INFO: === FDR correction performed with classifier version 9 ===
2:54:19.780121 PROGRESS: ============================= Precursor FDR =============================
2:54:19.780416 PROGRESS: Total precursors accumulated: 50,015
2:54:19.780481 PROGRESS: Target precursors: 31,029 (62.04%)
2:54:19.780535 PROGRESS: Decoy precursors: 18,986 (37.96%)
2:54:19.780580 PROGRESS: 
2:54:19.780625 PROGRESS: Precursor Summary:
2:54:19.782108 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   360; 0.001 FDR:     0
2:54:19.782205 PROGRESS: 
2:54:19.782279 PROGRESS: Protein Summary:
2:54:19.783703 PROGRESS: Channel   0:	 0.050 FDR:   503; 0.010 FDR:   343; 0.001 FDR:     0
2:54:19.783796 PROGRESS: =========================================================================
2:54:19.825207 INFO: Target number of precursors reached.
2:54:20.021710 INFO: fragments_df: keeping 5000 of 2897123 [sum(precursor_idx_mask)=11472 sum(mass_error_mask)=2897121 stop_rank=5000
2:54:20.334378 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:54:20.466947 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:20.593093 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:54:20.712565 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:21.324381 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:21.324928 INFO: Using score_cutoff 46.350987248611446 (fac=0.99, q=1)
2:54:21.325289 INFO: Updating optimization_manager: fwhm_rt             : 3.004304885864258 -> 2.754077911376953
2:54:21.325368 INFO: Updating optimization_manager: fwhm_mobility       : 0.010516232810914516 -> 0.008786343969404697
2:54:21.325423 INFO: Updating optimization_manager: score_cutoff        : 53.98703915748597 -> 46.350987248611446
2:54:21.325482 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:54:21.339417 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:21.400393 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:54:21.416777 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:21.553082 INFO: === checking if optimization conditions were reached ===
2:54:21.555901 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
2:54:21.556016 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
2:54:21.556085 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2:54:21.557067 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2:54:21.557161 INFO: Updating optimization_manager: classifier_version  : 10 -> 10
2:54:21.557221 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2:54:21.557274 INFO: ==============================================
2:54:21.557346 PROGRESS: Optimization finished for ms2_error, ms1_error.
2:54:21.779902 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:54:21.794371 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:21.855978 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:54:21.872534 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:22.004275 INFO: Starting optimization step 0.
2:54:22.004588 PROGRESS: === Extracting elution groups 0 to 51000 ===
2:54:22.004678 INFO: Using classic extraction backend
2:54:22.004871 PROGRESS: Extracting batch of 100530 precursors
2:54:22.004952 INFO: === Search parameters used ===
2:54:22.005002 INFO: rt_error       : 2099.894844
2:54:22.005045 INFO: mobility_error : 0.1
2:54:22.005088 INFO: num_candidates : 3
2:54:22.005143 INFO: ms1_error      : 15.0
2:54:22.005184 INFO: ms2_error      : 15.0
2:54:22.005222 INFO: fwhm_rt        : 2.754077911376953
2:54:22.005259 INFO: quant_window   : 3
2:54:22.005296 INFO: ==============================================
2:54:22.037839 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:54:22.037996 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:54:22.038058 INFO: FWHM in RT is 2.75 seconds, sigma is 0.61
2:54:22.038084 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.08
2:54:22.046862 INFO: Starting candidate selection
3:03:42.775441 INFO: Starting candidate scoring
3:03:55.549607 INFO: Finished candidate processing
3:03:55.549787 INFO: Collecting candidate features
3:03:55.998683 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 279018)
3:03:56.012095 INFO: Collecting fragment features
3:03:56.190006 INFO: Finished candidate scoring
3:03:56.369907 INFO: performing precursor FDR with 47 features
3:03:56.370022 INFO: Decoy channel: -1
3:03:56.370052 INFO: Competetive: True
3:03:56.476492 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:56.537224 WARNING: dropped 2 target PSMs due to missing features
3:03:56.537399 WARNING: dropped 2 decoy PSMs due to missing features
3:03:56.614622 INFO: Using random state 935358 for train-test-split
3:04:01.602149 INFO: Test AUC: 0.574
3:04:01.602677 INFO: Train AUC: 0.592
3:04:01.602719 INFO: AUC difference: 3.05%
3:04:01.924471 INFO: Resetting torch num_threads to 80
3:04:01.930225 PROGRESS: === Extracted 279018 precursors and 2890175 fragments ===
3:04:01.930901 INFO: === FDR correction performed with classifier version 10 ===
3:04:01.939615 PROGRESS: ============================= Precursor FDR =============================
3:04:01.939886 PROGRESS: Total precursors accumulated: 50,065
3:04:01.939955 PROGRESS: Target precursors: 31,410 (62.74%)
3:04:01.940007 PROGRESS: Decoy precursors: 18,655 (37.26%)
3:04:01.940053 PROGRESS: 
3:04:01.940097 PROGRESS: Precursor Summary:
3:04:01.941480 PROGRESS: Channel   0:	 0.050 FDR:   603; 0.010 FDR:   422; 0.001 FDR:     0
3:04:01.941582 PROGRESS: 
3:04:01.941638 PROGRESS: Protein Summary:
3:04:01.943071 PROGRESS: Channel   0:	 0.050 FDR:   565; 0.010 FDR:   399; 0.001 FDR:     0
3:04:01.943167 PROGRESS: =========================================================================
3:04:01.945333 INFO: Target number of precursors reached.
3:04:02.139931 INFO: fragments_df: keeping 5000 of 2890175 [sum(precursor_idx_mask)=13386 sum(mass_error_mask)=2890174 stop_rank=5000
3:04:02.513801 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:04:02.645058 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:04:02.775309 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:04:02.904108 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:04:03.583230 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:04:03.583696 INFO: Using score_cutoff 40.28338297691345 (fac=0.99, q=1)
3:04:03.584032 INFO: Updating optimization_manager: fwhm_rt             : 2.754077911376953 -> 2.7726476192474365
3:04:03.584113 INFO: Updating optimization_manager: fwhm_mobility       : 0.008786343969404697 -> 0.008536355569958687
3:04:03.584168 INFO: Updating optimization_manager: score_cutoff        : 46.350987248611446 -> 40.28338297691345
3:04:03.584227 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:04:03.591583 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:04:03.621615 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:04:03.628697 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:04:03.690353 INFO: === checking if optimization conditions were reached ===
3:04:03.690699 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:04:03.693191 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 436.8637740717239
3:04:03.693312 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 436.8638.
3:04:03.693391 INFO: ==============================================
3:04:03.693475 INFO: Starting optimization step 1.
3:04:03.693541 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:04:03.693666 INFO: Using classic extraction backend
3:04:03.693914 PROGRESS: Extracting batch of 50061 precursors
3:04:03.694009 INFO: === Search parameters used ===
3:04:03.694088 INFO: rt_error       : 436.8637740717239
3:04:03.694144 INFO: mobility_error : 0.1
3:04:03.694195 INFO: num_candidates : 3
3:04:03.694245 INFO: ms1_error      : 15.0
3:04:03.694293 INFO: ms2_error      : 15.0
3:04:03.694344 INFO: fwhm_rt        : 2.7726476192474365
3:04:03.694392 INFO: quant_window   : 3
3:04:03.694440 INFO: ==============================================
3:04:03.713882 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:04:03.714038 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:04:03.714109 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
3:04:03.714138 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.96
3:04:03.723100 INFO: Starting candidate selection
3:05:07.458164 INFO: Starting candidate scoring
3:05:13.387722 INFO: Finished candidate processing
3:05:13.387906 INFO: Collecting candidate features
3:05:13.621695 WARNING: intensity_correlation has 35 NaNs ( 0.03 % out of 134424)
3:05:13.622064 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 134424)
3:05:13.630468 INFO: Collecting fragment features
3:05:13.731905 INFO: Finished candidate scoring
3:05:13.860082 INFO: performing precursor FDR with 47 features
3:05:13.860214 INFO: Decoy channel: -1
3:05:13.860247 INFO: Competetive: True
3:05:13.919000 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:13.950410 WARNING: dropped 22 target PSMs due to missing features
3:05:13.950553 WARNING: dropped 16 decoy PSMs due to missing features
3:05:13.985597 INFO: Using random state 935358 for train-test-split
3:05:16.623269 INFO: Test AUC: 0.558
3:05:16.623419 INFO: Train AUC: 0.581
3:05:16.623462 INFO: AUC difference: 3.83%
3:05:16.909916 INFO: Resetting torch num_threads to 80
3:05:16.914667 PROGRESS: === Extracted 134424 precursors and 1358773 fragments ===
3:05:16.915445 INFO: === FDR correction performed with classifier version 10 ===
3:05:16.920412 PROGRESS: ============================= Precursor FDR =============================
3:05:16.920567 PROGRESS: Total precursors accumulated: 24,481
3:05:16.920628 PROGRESS: Target precursors: 14,850 (60.66%)
3:05:16.920678 PROGRESS: Decoy precursors: 9,631 (39.34%)
3:05:16.920722 PROGRESS: 
3:05:16.920766 PROGRESS: Precursor Summary:
3:05:16.921983 PROGRESS: Channel   0:	 0.050 FDR:   329; 0.010 FDR:   252; 0.001 FDR:   203
3:05:16.922092 PROGRESS: 
3:05:16.922179 PROGRESS: Protein Summary:
3:05:16.923480 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   247; 0.001 FDR:   198
3:05:16.923574 PROGRESS: =========================================================================
3:05:16.960017 INFO: Target number of precursors reached.
3:05:17.051127 INFO: fragments_df: keeping 3704 of 1358773 [sum(precursor_idx_mask)=7983 sum(mass_error_mask)=1358771 stop_rank=3704
3:05:17.746984 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:05:17.903957 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:05:18.024294 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:05:18.141815 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:05:18.627184 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:05:18.627681 INFO: Using score_cutoff 41.344918203735354 (fac=0.99, q=1)
3:05:18.628093 INFO: Updating optimization_manager: fwhm_rt             : 2.7726476192474365 -> 2.7693843841552734
3:05:18.628175 INFO: Updating optimization_manager: fwhm_mobility       : 0.008536355569958687 -> 0.008448068052530289
3:05:18.628232 INFO: Updating optimization_manager: score_cutoff        : 40.28338297691345 -> 41.344918203735354
3:05:18.628304 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:05:18.636494 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:05:18.667176 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:05:18.675007 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:05:18.740183 INFO: === checking if optimization conditions were reached ===
3:05:18.740477 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:05:18.742793 INFO: Updating optimization_manager: rt_error            : 436.8637740717239 -> 412.39242703072097
3:05:18.742903 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 412.3924.
3:05:18.742975 INFO: ==============================================
3:05:18.743068 INFO: Starting optimization step 2.
3:05:18.743136 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:05:18.743225 INFO: Using classic extraction backend
3:05:18.743500 PROGRESS: Extracting batch of 50061 precursors
3:05:18.743585 INFO: === Search parameters used ===
3:05:18.743648 INFO: rt_error       : 412.39242703072097
3:05:18.743696 INFO: mobility_error : 0.1
3:05:18.743738 INFO: num_candidates : 3
3:05:18.743780 INFO: ms1_error      : 15.0
3:05:18.743820 INFO: ms2_error      : 15.0
3:05:18.743860 INFO: fwhm_rt        : 2.7693843841552734
3:05:18.743899 INFO: quant_window   : 3
3:05:18.743938 INFO: ==============================================
3:05:18.832956 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:05:18.833086 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:05:18.833167 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
3:05:18.833194 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.92
3:05:18.834181 INFO: Starting candidate selection
3:06:18.592081 INFO: Starting candidate scoring
3:06:24.812947 INFO: Finished candidate processing
3:06:24.813173 INFO: Collecting candidate features
3:06:25.050781 WARNING: intensity_correlation has 38 NaNs ( 0.03 % out of 134536)
3:06:25.051140 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 134536)
3:06:25.059206 INFO: Collecting fragment features
3:06:25.144875 INFO: Finished candidate scoring
3:06:25.218648 INFO: performing precursor FDR with 47 features
3:06:25.218785 INFO: Decoy channel: -1
3:06:25.218813 INFO: Competetive: True
3:06:25.265625 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:25.291508 WARNING: dropped 27 target PSMs due to missing features
3:06:25.291661 WARNING: dropped 13 decoy PSMs due to missing features
3:06:25.315091 INFO: Using random state 935358 for train-test-split
3:06:27.938702 INFO: Test AUC: 0.561
3:06:27.938833 INFO: Train AUC: 0.580
3:06:27.938866 INFO: AUC difference: 3.34%
3:06:28.213913 INFO: Resetting torch num_threads to 80
3:06:28.218062 PROGRESS: === Extracted 134536 precursors and 1357349 fragments ===
3:06:28.218645 INFO: === FDR correction performed with classifier version 10 ===
3:06:28.223465 PROGRESS: ============================= Precursor FDR =============================
3:06:28.223621 PROGRESS: Total precursors accumulated: 24,521
3:06:28.223686 PROGRESS: Target precursors: 15,009 (61.21%)
3:06:28.223735 PROGRESS: Decoy precursors: 9,512 (38.79%)
3:06:28.223789 PROGRESS: 
3:06:28.223835 PROGRESS: Precursor Summary:
3:06:28.225029 PROGRESS: Channel   0:	 0.050 FDR:   315; 0.010 FDR:   228; 0.001 FDR:   221
3:06:28.225130 PROGRESS: 
3:06:28.225192 PROGRESS: Protein Summary:
3:06:28.226469 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   223; 0.001 FDR:   216
3:06:28.226573 PROGRESS: =========================================================================
3:06:28.227744 INFO: Target number of precursors reached.
3:06:28.319421 INFO: fragments_df: keeping 3476 of 1357349 [sum(precursor_idx_mask)=7221 sum(mass_error_mask)=1357346 stop_rank=3476
3:06:28.732229 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:06:28.831445 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:06:28.927521 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:06:29.022343 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:06:29.411013 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:06:29.411512 INFO: Using score_cutoff 41.15193863639832 (fac=0.99, q=1)
3:06:29.411882 INFO: Updating optimization_manager: fwhm_rt             : 2.7693843841552734 -> 2.7099552154541016
3:06:29.411966 INFO: Updating optimization_manager: fwhm_mobility       : 0.008448068052530289 -> 0.008555054664611816
3:06:29.412032 INFO: Updating optimization_manager: score_cutoff        : 41.344918203735354 -> 41.15193863639832
3:06:29.412091 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:06:29.420459 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:06:29.450953 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:06:29.458993 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:06:29.522180 INFO: === checking if optimization conditions were reached ===
3:06:29.522481 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:06:29.524853 INFO: Updating optimization_manager: rt_error            : 412.39242703072097 -> 203.38081474167964
3:06:29.524969 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 203.3808.
3:06:29.525037 INFO: ==============================================
3:06:29.525120 INFO: Starting optimization step 3.
3:06:29.525185 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:06:29.525252 INFO: Using classic extraction backend
3:06:29.525422 PROGRESS: Extracting batch of 50061 precursors
3:06:29.525494 INFO: === Search parameters used ===
3:06:29.525542 INFO: rt_error       : 203.38081474167964
3:06:29.525583 INFO: mobility_error : 0.1
3:06:29.525623 INFO: num_candidates : 3
3:06:29.525662 INFO: ms1_error      : 15.0
3:06:29.525701 INFO: ms2_error      : 15.0
3:06:29.525747 INFO: fwhm_rt        : 2.7099552154541016
3:06:29.525788 INFO: quant_window   : 3
3:06:29.525826 INFO: ==============================================
3:06:29.542838 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:06:29.542969 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:06:29.543020 INFO: FWHM in RT is 2.71 seconds, sigma is 0.60
3:06:29.543043 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.97
3:06:29.551648 INFO: Starting candidate selection
3:07:02.388257 INFO: Starting candidate scoring
3:07:08.585614 INFO: Finished candidate processing
3:07:08.585835 INFO: Collecting candidate features
3:07:08.836370 WARNING: intensity_correlation has 55 NaNs ( 0.04 % out of 133614)
3:07:08.836762 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 133614)
3:07:08.844690 INFO: Collecting fragment features
3:07:08.941012 INFO: Finished candidate scoring
3:07:09.015801 INFO: performing precursor FDR with 47 features
3:07:09.015959 INFO: Decoy channel: -1
3:07:09.015986 INFO: Competetive: True
3:07:09.071280 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:09.101494 WARNING: dropped 40 target PSMs due to missing features
3:07:09.101671 WARNING: dropped 19 decoy PSMs due to missing features
3:07:09.128531 INFO: Using random state 935358 for train-test-split
3:07:11.724209 INFO: Test AUC: 0.556
3:07:11.724325 INFO: Train AUC: 0.580
3:07:11.724356 INFO: AUC difference: 4.17%
3:07:11.994654 INFO: Resetting torch num_threads to 80
3:07:11.997950 PROGRESS: === Extracted 133614 precursors and 1325499 fragments ===
3:07:11.998464 INFO: === FDR correction performed with classifier version 10 ===
3:07:12.002768 PROGRESS: ============================= Precursor FDR =============================
3:07:12.002898 PROGRESS: Total precursors accumulated: 24,428
3:07:12.002959 PROGRESS: Target precursors: 14,777 (60.49%)
3:07:12.003010 PROGRESS: Decoy precursors: 9,651 (39.51%)
3:07:12.003054 PROGRESS: 
3:07:12.003098 PROGRESS: Precursor Summary:
3:07:12.004247 PROGRESS: Channel   0:	 0.050 FDR:   391; 0.010 FDR:   264; 0.001 FDR:   239
3:07:12.004339 PROGRESS: 
3:07:12.004394 PROGRESS: Protein Summary:
3:07:12.005661 PROGRESS: Channel   0:	 0.050 FDR:   381; 0.010 FDR:   259; 0.001 FDR:   234
3:07:12.005765 PROGRESS: =========================================================================
3:07:12.006599 INFO: Target number of precursors reached.
3:07:12.097905 INFO: fragments_df: keeping 3789 of 1325499 [sum(precursor_idx_mask)=8292 sum(mass_error_mask)=1325494 stop_rank=3789
3:07:12.307482 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:07:12.423791 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:07:12.547982 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:07:12.665986 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:07:13.158250 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:07:13.158661 INFO: Using score_cutoff 40.58396057853699 (fac=0.99, q=1)
3:07:13.158987 INFO: Updating optimization_manager: fwhm_rt             : 2.7099552154541016 -> 2.789407253265381
3:07:13.159070 INFO: Updating optimization_manager: fwhm_mobility       : 0.008555054664611816 -> 0.008414494805037975
3:07:13.159136 INFO: Updating optimization_manager: score_cutoff        : 41.15193863639832 -> 40.58396057853699
3:07:13.159197 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:07:13.166664 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:07:13.196678 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:07:13.204246 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:07:13.263064 INFO: === checking if optimization conditions were reached ===
3:07:13.263355 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:07:13.265898 INFO: Updating optimization_manager: rt_error            : 203.38081474167964 -> 174.75663378054662
3:07:13.266018 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 174.7566.
3:07:13.266114 INFO: ==============================================
3:07:13.266207 INFO: Starting optimization step 4.
3:07:13.266277 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:07:13.266350 INFO: Using classic extraction backend
3:07:13.266546 PROGRESS: Extracting batch of 50061 precursors
3:07:13.266632 INFO: === Search parameters used ===
3:07:13.266692 INFO: rt_error       : 174.75663378054662
3:07:13.266747 INFO: mobility_error : 0.1
3:07:13.266799 INFO: num_candidates : 3
3:07:13.266852 INFO: ms1_error      : 15.0
3:07:13.266901 INFO: ms2_error      : 15.0
3:07:13.266951 INFO: fwhm_rt        : 2.789407253265381
3:07:13.267001 INFO: quant_window   : 3
3:07:13.267051 INFO: ==============================================
3:07:13.286968 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:07:13.287095 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:07:13.287154 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
3:07:13.287183 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
3:07:13.296125 INFO: Starting candidate selection
3:07:41.249855 INFO: Starting candidate scoring
3:07:47.450095 INFO: Finished candidate processing
3:07:47.450313 INFO: Collecting candidate features
3:07:47.720585 WARNING: intensity_correlation has 59 NaNs ( 0.04 % out of 133478)
3:07:47.720957 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 133478)
3:07:47.729064 INFO: Collecting fragment features
3:07:47.816366 INFO: Finished candidate scoring
3:07:47.918196 INFO: performing precursor FDR with 47 features
3:07:47.918355 INFO: Decoy channel: -1
3:07:47.918382 INFO: Competetive: True
3:07:47.973448 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:48.009296 WARNING: dropped 35 target PSMs due to missing features
3:07:48.009468 WARNING: dropped 27 decoy PSMs due to missing features
3:07:48.032379 INFO: Using random state 935358 for train-test-split
3:07:50.712366 INFO: Test AUC: 0.556
3:07:50.712577 INFO: Train AUC: 0.580
3:07:50.712611 INFO: AUC difference: 4.15%
3:07:50.983918 INFO: Resetting torch num_threads to 80
3:07:50.987343 PROGRESS: === Extracted 133478 precursors and 1316099 fragments ===
3:07:50.987896 INFO: === FDR correction performed with classifier version 10 ===
3:07:50.992099 PROGRESS: ============================= Precursor FDR =============================
3:07:50.992233 PROGRESS: Total precursors accumulated: 24,403
3:07:50.992297 PROGRESS: Target precursors: 14,845 (60.83%)
3:07:50.992348 PROGRESS: Decoy precursors: 9,558 (39.17%)
3:07:50.992393 PROGRESS: 
3:07:50.992438 PROGRESS: Precursor Summary:
3:07:50.993644 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   264; 0.001 FDR:   209
3:07:50.993748 PROGRESS: 
3:07:50.993807 PROGRESS: Protein Summary:
3:07:50.995108 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   259; 0.001 FDR:   204
3:07:50.995203 PROGRESS: =========================================================================
3:07:50.996155 INFO: Target number of precursors reached.
3:07:51.082984 INFO: fragments_df: keeping 3735 of 1316099 [sum(precursor_idx_mask)=8248 sum(mass_error_mask)=1316095 stop_rank=3735
3:07:51.310568 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:07:51.427037 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:07:51.549493 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:07:51.665389 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:07:52.123657 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:07:52.124224 INFO: Using score_cutoff 38.08483586196899 (fac=0.99, q=1)
3:07:52.124544 INFO: Updating optimization_manager: fwhm_rt             : 2.789407253265381 -> 2.7693843841552734
3:07:52.124625 INFO: Updating optimization_manager: fwhm_mobility       : 0.008414494805037975 -> 0.008394408039748669
3:07:52.124677 INFO: Updating optimization_manager: score_cutoff        : 40.58396057853699 -> 38.08483586196899
3:07:52.124733 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:07:52.132137 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:07:52.162031 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:07:52.168703 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:07:52.229847 INFO: === checking if optimization conditions were reached ===
3:07:52.230104 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:07:52.232243 INFO: Updating optimization_manager: rt_error            : 174.75663378054662 -> 142.70194023216018
3:07:52.232349 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 142.7019.
3:07:52.232415 INFO: ==============================================
3:07:52.232490 INFO: Starting optimization step 5.
3:07:52.232548 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:07:52.232623 INFO: Using classic extraction backend
3:07:52.232805 PROGRESS: Extracting batch of 50061 precursors
3:07:52.232883 INFO: === Search parameters used ===
3:07:52.232935 INFO: rt_error       : 142.70194023216018
3:07:52.232978 INFO: mobility_error : 0.1
3:07:52.233018 INFO: num_candidates : 3
3:07:52.233057 INFO: ms1_error      : 15.0
3:07:52.233094 INFO: ms2_error      : 15.0
3:07:52.233133 INFO: fwhm_rt        : 2.7693843841552734
3:07:52.233170 INFO: quant_window   : 3
3:07:52.233207 INFO: ==============================================
3:07:52.247318 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:07:52.247429 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:07:52.247479 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
3:07:52.247501 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.89
3:07:52.256220 INFO: Starting candidate selection
3:08:15.758454 INFO: Starting candidate scoring
3:08:22.344259 INFO: Finished candidate processing
3:08:22.344420 INFO: Collecting candidate features
3:08:22.550114 WARNING: intensity_correlation has 62 NaNs ( 0.05 % out of 133317)
3:08:22.550490 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 133317)
3:08:22.559415 INFO: Collecting fragment features
3:08:22.661572 INFO: Finished candidate scoring
3:08:22.720954 INFO: performing precursor FDR with 47 features
3:08:22.721065 INFO: Decoy channel: -1
3:08:22.721089 INFO: Competetive: True
3:08:22.767057 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:22.789836 WARNING: dropped 38 target PSMs due to missing features
3:08:22.789960 WARNING: dropped 27 decoy PSMs due to missing features
3:08:22.819613 INFO: Using random state 935358 for train-test-split
3:08:25.300921 INFO: Test AUC: 0.556
3:08:25.301033 INFO: Train AUC: 0.581
3:08:25.301066 INFO: AUC difference: 4.28%
3:08:25.568815 INFO: Resetting torch num_threads to 80
3:08:25.572047 PROGRESS: === Extracted 133317 precursors and 1311946 fragments ===
3:08:25.572794 INFO: === FDR correction performed with classifier version 10 ===
3:08:25.576931 PROGRESS: ============================= Precursor FDR =============================
3:08:25.577055 PROGRESS: Total precursors accumulated: 24,395
3:08:25.577127 PROGRESS: Target precursors: 14,827 (60.78%)
3:08:25.577178 PROGRESS: Decoy precursors: 9,568 (39.22%)
3:08:25.577230 PROGRESS: 
3:08:25.577275 PROGRESS: Precursor Summary:
3:08:25.578387 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   244; 0.001 FDR:     0
3:08:25.578479 PROGRESS: 
3:08:25.578535 PROGRESS: Protein Summary:
3:08:25.579738 PROGRESS: Channel   0:	 0.050 FDR:   344; 0.010 FDR:   239; 0.001 FDR:     0
3:08:25.579829 PROGRESS: =========================================================================
3:08:25.580614 INFO: Target number of precursors reached.
3:08:25.669207 INFO: fragments_df: keeping 3524 of 1311946 [sum(precursor_idx_mask)=7552 sum(mass_error_mask)=1311942 stop_rank=3524
3:08:25.875949 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:08:25.996552 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:08:26.122852 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:08:26.246004 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:08:26.640903 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:08:26.641344 INFO: Using score_cutoff 41.841914979171754 (fac=0.99, q=1)
3:08:26.641676 INFO: Updating optimization_manager: fwhm_rt             : 2.7693843841552734 -> 2.7693843841552734
3:08:26.641761 INFO: Updating optimization_manager: fwhm_mobility       : 0.008394408039748669 -> 0.008524795062839985
3:08:26.641822 INFO: Updating optimization_manager: score_cutoff        : 38.08483586196899 -> 41.841914979171754
3:08:26.641895 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:08:26.649428 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:08:26.679833 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:08:26.687676 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:08:26.787208 INFO: === checking if optimization conditions were reached ===
3:08:26.787490 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:08:26.790059 INFO: Updating optimization_manager: rt_error            : 142.70194023216018 -> 121.15322229225544
3:08:26.790188 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 121.1532.
3:08:26.790264 INFO: ==============================================
3:08:26.790348 INFO: Starting optimization step 6.
3:08:26.790413 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:08:26.790484 INFO: Using classic extraction backend
3:08:26.790658 PROGRESS: Extracting batch of 50061 precursors
3:08:26.790736 INFO: === Search parameters used ===
3:08:26.790793 INFO: rt_error       : 121.15322229225544
3:08:26.790845 INFO: mobility_error : 0.1
3:08:26.790897 INFO: num_candidates : 3
3:08:26.790945 INFO: ms1_error      : 15.0
3:08:26.790992 INFO: ms2_error      : 15.0
3:08:26.791038 INFO: fwhm_rt        : 2.7693843841552734
3:08:26.791098 INFO: quant_window   : 3
3:08:26.791145 INFO: ==============================================
3:08:26.810517 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:08:26.810637 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:08:26.810698 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
3:08:26.810725 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
3:08:26.818087 INFO: Starting candidate selection
3:08:46.514945 INFO: Starting candidate scoring
3:08:52.829547 INFO: Finished candidate processing
3:08:52.829799 INFO: Collecting candidate features
3:08:53.064878 WARNING: intensity_correlation has 59 NaNs ( 0.04 % out of 132946)
3:08:53.065254 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 132946)
3:08:53.073314 INFO: Collecting fragment features
3:08:53.165307 INFO: Finished candidate scoring
3:08:53.242085 INFO: performing precursor FDR with 47 features
3:08:53.242240 INFO: Decoy channel: -1
3:08:53.242268 INFO: Competetive: True
3:08:53.290801 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:53.320555 WARNING: dropped 34 target PSMs due to missing features
3:08:53.320713 WARNING: dropped 27 decoy PSMs due to missing features
3:08:53.344041 INFO: Using random state 935358 for train-test-split
3:08:55.787893 INFO: Test AUC: 0.556
3:08:55.788023 INFO: Train AUC: 0.579
3:08:55.788056 INFO: AUC difference: 4.00%
3:08:56.058529 INFO: Resetting torch num_threads to 80
3:08:56.064973 PROGRESS: === Extracted 132946 precursors and 1303855 fragments ===
3:08:56.065482 INFO: === FDR correction performed with classifier version 10 ===
3:08:56.070698 PROGRESS: ============================= Precursor FDR =============================
3:08:56.070840 PROGRESS: Total precursors accumulated: 24,335
3:08:56.070901 PROGRESS: Target precursors: 14,790 (60.78%)
3:08:56.070953 PROGRESS: Decoy precursors: 9,545 (39.22%)
3:08:56.071002 PROGRESS: 
3:08:56.071045 PROGRESS: Precursor Summary:
3:08:56.072227 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   265; 0.001 FDR:   218
3:08:56.072320 PROGRESS: 
3:08:56.072387 PROGRESS: Protein Summary:
3:08:56.073637 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   260; 0.001 FDR:   213
3:08:56.073731 PROGRESS: =========================================================================
3:08:56.074764 INFO: Target number of precursors reached.
3:08:56.168856 INFO: fragments_df: keeping 3686 of 1303855 [sum(precursor_idx_mask)=8208 sum(mass_error_mask)=1303850 stop_rank=3686
3:08:56.450804 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:08:56.549565 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:08:56.649533 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:08:56.747578 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:08:57.225571 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:08:57.226086 INFO: Using score_cutoff 41.598875953674316 (fac=0.99, q=1)
3:08:57.226417 INFO: Updating optimization_manager: fwhm_rt             : 2.7693843841552734 -> 2.791940927505493
3:08:57.226498 INFO: Updating optimization_manager: fwhm_mobility       : 0.008524795062839985 -> 0.008428771048784256
3:08:57.226553 INFO: Updating optimization_manager: score_cutoff        : 41.841914979171754 -> 41.598875953674316
3:08:57.226618 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:08:57.234859 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:08:57.265466 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:08:57.272830 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:08:57.331991 INFO: === checking if optimization conditions were reached ===
3:08:57.332237 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:08:57.334362 INFO: Updating optimization_manager: rt_error            : 121.15322229225544 -> 108.64565439226789
3:08:57.334474 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 108.6457.
3:08:57.334543 INFO: ==============================================
3:08:57.334621 INFO: Starting optimization step 7.
3:08:57.334686 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:08:57.334764 INFO: Using classic extraction backend
3:08:57.334964 PROGRESS: Extracting batch of 50061 precursors
3:08:57.335046 INFO: === Search parameters used ===
3:08:57.335095 INFO: rt_error       : 108.64565439226789
3:08:57.335137 INFO: mobility_error : 0.1
3:08:57.335178 INFO: num_candidates : 3
3:08:57.335215 INFO: ms1_error      : 15.0
3:08:57.335255 INFO: ms2_error      : 15.0
3:08:57.335293 INFO: fwhm_rt        : 2.791940927505493
3:08:57.335331 INFO: quant_window   : 3
3:08:57.335369 INFO: ==============================================
3:08:57.370597 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:08:57.370705 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:08:57.370756 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
3:08:57.370779 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.91
3:08:57.379678 INFO: Starting candidate selection
3:09:14.186006 INFO: Starting candidate scoring
3:09:20.477433 INFO: Finished candidate processing
3:09:20.477541 INFO: Collecting candidate features
3:09:20.683640 WARNING: intensity_correlation has 65 NaNs ( 0.05 % out of 132853)
3:09:20.684029 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 132853)
3:09:20.693689 INFO: Collecting fragment features
3:09:20.780482 INFO: Finished candidate scoring
3:09:20.847297 INFO: performing precursor FDR with 47 features
3:09:20.847408 INFO: Decoy channel: -1
3:09:20.847432 INFO: Competetive: True
3:09:20.897532 INFO: Setting torch num_threads to 2 for FDR classification task
3:09:20.924418 WARNING: dropped 38 target PSMs due to missing features
3:09:20.924539 WARNING: dropped 29 decoy PSMs due to missing features
3:09:20.956208 INFO: Using random state 935358 for train-test-split
3:09:23.343365 INFO: Test AUC: 0.557
3:09:23.343524 INFO: Train AUC: 0.579
3:09:23.343559 INFO: AUC difference: 3.88%
3:09:23.617873 INFO: Resetting torch num_threads to 80
3:09:23.622065 PROGRESS: === Extracted 132853 precursors and 1297481 fragments ===
3:09:23.622694 INFO: === FDR correction performed with classifier version 10 ===
3:09:23.627164 PROGRESS: ============================= Precursor FDR =============================
3:09:23.627308 PROGRESS: Total precursors accumulated: 24,325
3:09:23.627372 PROGRESS: Target precursors: 14,818 (60.92%)
3:09:23.627427 PROGRESS: Decoy precursors: 9,507 (39.08%)
3:09:23.627473 PROGRESS: 
3:09:23.627516 PROGRESS: Precursor Summary:
3:09:23.628763 PROGRESS: Channel   0:	 0.050 FDR:   372; 0.010 FDR:   251; 0.001 FDR:   238
3:09:23.628853 PROGRESS: 
3:09:23.628907 PROGRESS: Protein Summary:
3:09:23.630226 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   247; 0.001 FDR:   234
3:09:23.630327 PROGRESS: =========================================================================
3:09:23.631335 INFO: Target number of precursors reached.
3:09:23.719665 INFO: fragments_df: keeping 3514 of 1297481 [sum(precursor_idx_mask)=7786 sum(mass_error_mask)=1297476 stop_rank=3514
3:09:24.032510 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:09:24.149761 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:09:24.265881 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:09:24.384204 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:09:24.841269 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:09:24.841692 INFO: Using score_cutoff 43.65964427947998 (fac=0.99, q=1)
3:09:24.842022 INFO: Updating optimization_manager: fwhm_rt             : 2.791940927505493 -> 2.751204013824463
3:09:24.842111 INFO: Updating optimization_manager: fwhm_mobility       : 0.008428771048784256 -> 0.008428771048784256
3:09:24.842164 INFO: Updating optimization_manager: score_cutoff        : 41.598875953674316 -> 43.65964427947998
3:09:24.842222 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:09:24.849695 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:09:24.879918 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:09:24.887482 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:09:24.957944 INFO: === checking if optimization conditions were reached ===
3:09:24.970327 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
3:09:24.973234 INFO: Updating optimization_manager: rt_error            : 108.64565439226789 -> 98.24180571804278
3:09:24.976181 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 98.2418.
3:09:24.976503 INFO: ==============================================
3:09:24.976806 INFO: Starting optimization step 8.
3:09:24.977122 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:09:24.977426 INFO: Using classic extraction backend
3:09:24.977878 PROGRESS: Extracting batch of 50061 precursors
3:09:24.978353 INFO: === Search parameters used ===
3:09:24.978642 INFO: rt_error       : 98.24180571804278
3:09:24.978899 INFO: mobility_error : 0.1
3:09:24.979166 INFO: num_candidates : 3
3:09:24.979414 INFO: ms1_error      : 15.0
3:09:24.979659 INFO: ms2_error      : 15.0
3:09:24.979923 INFO: fwhm_rt        : 2.751204013824463
3:09:24.980171 INFO: quant_window   : 3
3:09:24.980416 INFO: ==============================================
3:09:25.021401 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:09:25.021512 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:09:25.021564 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
3:09:25.021587 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.91
3:09:25.026626 INFO: Starting candidate selection
3:09:42.152083 INFO: Starting candidate scoring
3:09:48.563172 INFO: Finished candidate processing
3:09:48.563374 INFO: Collecting candidate features
3:09:48.850037 WARNING: intensity_correlation has 68 NaNs ( 0.05 % out of 132775)
3:09:48.850426 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 132775)
3:09:48.858514 INFO: Collecting fragment features
3:09:48.966048 INFO: Finished candidate scoring
3:09:49.023419 INFO: performing precursor FDR with 47 features
3:09:49.023532 INFO: Decoy channel: -1
3:09:49.023557 INFO: Competetive: True
3:09:49.064725 INFO: Setting torch num_threads to 2 for FDR classification task
3:09:49.087669 WARNING: dropped 37 target PSMs due to missing features
3:09:49.087792 WARNING: dropped 34 decoy PSMs due to missing features
3:09:49.109313 INFO: Using random state 935358 for train-test-split
3:09:51.466440 INFO: Test AUC: 0.559
3:09:51.466597 INFO: Train AUC: 0.578
3:09:51.466631 INFO: AUC difference: 3.29%
3:09:53.034469 INFO: Resetting torch num_threads to 80
3:09:53.037902 PROGRESS: === Extracted 132775 precursors and 1292402 fragments ===
3:09:53.038384 INFO: === FDR correction performed with classifier version 10 ===
3:09:53.042684 PROGRESS: ============================= Precursor FDR =============================
3:09:53.042811 PROGRESS: Total precursors accumulated: 24,327
3:09:53.042872 PROGRESS: Target precursors: 14,799 (60.83%)
3:09:53.042934 PROGRESS: Decoy precursors: 9,528 (39.17%)
3:09:53.042979 PROGRESS: 
3:09:53.043022 PROGRESS: Precursor Summary:
3:09:53.044283 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   262; 0.001 FDR:   193
3:09:53.044381 PROGRESS: 
3:09:53.044436 PROGRESS: Protein Summary:
3:09:53.045707 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   257; 0.001 FDR:   189
3:09:53.045799 PROGRESS: =========================================================================
3:09:53.046780 INFO: Target number of precursors reached.
3:09:53.133007 INFO: fragments_df: keeping 3624 of 1292402 [sum(precursor_idx_mask)=7997 sum(mass_error_mask)=1292394 stop_rank=3624
3:09:53.384213 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:09:53.478488 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:09:53.580588 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:09:53.677025 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:09:54.082803 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:09:54.083226 INFO: Using score_cutoff 40.600475508499144 (fac=0.99, q=1)
3:09:54.083534 INFO: Updating optimization_manager: fwhm_rt             : 2.751204013824463 -> 2.791421413421631
3:09:54.083615 INFO: Updating optimization_manager: fwhm_mobility       : 0.008428771048784256 -> 0.008470434695482254
3:09:54.083672 INFO: Updating optimization_manager: score_cutoff        : 43.65964427947998 -> 40.600475508499144
3:09:54.083736 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:09:54.091146 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:09:54.121774 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:09:54.129390 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:09:54.192120 INFO: === checking if optimization conditions were reached ===
3:09:54.192395 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
3:09:54.194795 INFO: Updating optimization_manager: rt_error            : 98.24180571804278 -> 97.40100204251263
3:09:54.194915 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 97.4010.
3:09:54.195008 INFO: ==============================================
3:09:54.195086 INFO: Starting optimization step 9.
3:09:54.195152 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:09:54.195216 INFO: Using classic extraction backend
3:09:54.195350 PROGRESS: Extracting batch of 50061 precursors
3:09:54.195426 INFO: === Search parameters used ===
3:09:54.195482 INFO: rt_error       : 97.40100204251263
3:09:54.195536 INFO: mobility_error : 0.1
3:09:54.195586 INFO: num_candidates : 3
3:09:54.195635 INFO: ms1_error      : 15.0
3:09:54.195682 INFO: ms2_error      : 15.0
3:09:54.195730 INFO: fwhm_rt        : 2.791421413421631
3:09:54.195777 INFO: quant_window   : 3
3:09:54.195831 INFO: ==============================================
3:09:54.216687 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:09:54.216812 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:09:54.216862 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
3:09:54.216891 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
3:09:54.225660 INFO: Starting candidate selection
3:10:10.051876 INFO: Starting candidate scoring
3:10:16.333956 INFO: Finished candidate processing
3:10:16.334159 INFO: Collecting candidate features
3:10:16.549359 WARNING: intensity_correlation has 67 NaNs ( 0.05 % out of 132606)
3:10:16.549692 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 132606)
3:10:16.557665 INFO: Collecting fragment features
3:10:16.638522 INFO: Finished candidate scoring
3:10:16.725142 INFO: performing precursor FDR with 47 features
3:10:16.725255 INFO: Decoy channel: -1
3:10:16.725279 INFO: Competetive: True
3:10:16.764148 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:16.788597 WARNING: dropped 38 target PSMs due to missing features
3:10:16.788719 WARNING: dropped 32 decoy PSMs due to missing features
3:10:16.808570 INFO: Using random state 935358 for train-test-split
3:10:18.954441 INFO: Test AUC: 0.552
3:10:18.954550 INFO: Train AUC: 0.578
3:10:18.954581 INFO: AUC difference: 4.47%
3:10:19.215499 INFO: Resetting torch num_threads to 80
3:10:19.219056 PROGRESS: === Extracted 132606 precursors and 1292694 fragments ===
3:10:19.219519 INFO: === FDR correction performed with classifier version 10 ===
3:10:19.223808 PROGRESS: ============================= Precursor FDR =============================
3:10:19.223939 PROGRESS: Total precursors accumulated: 24,298
3:10:19.223999 PROGRESS: Target precursors: 14,655 (60.31%)
3:10:19.224047 PROGRESS: Decoy precursors: 9,643 (39.69%)
3:10:19.224091 PROGRESS: 
3:10:19.224133 PROGRESS: Precursor Summary:
3:10:19.225268 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   264; 0.001 FDR:     0
3:10:19.225367 PROGRESS: 
3:10:19.225423 PROGRESS: Protein Summary:
3:10:19.226633 PROGRESS: Channel   0:	 0.050 FDR:   330; 0.010 FDR:   259; 0.001 FDR:     0
3:10:19.226725 PROGRESS: =========================================================================
3:10:19.228402 INFO: Target number of precursors reached.
3:10:19.315243 INFO: fragments_df: keeping 3670 of 1292694 [sum(precursor_idx_mask)=8093 sum(mass_error_mask)=1292690 stop_rank=3670
3:10:19.528695 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:10:19.954182 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:10:20.086308 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:10:20.207308 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:10:20.687961 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:10:20.688377 INFO: Using score_cutoff 39.14827669830322 (fac=0.99, q=1)
3:10:20.688674 INFO: Updating optimization_manager: fwhm_rt             : 2.791421413421631 -> 2.766627311706543
3:10:20.688753 INFO: Updating optimization_manager: fwhm_mobility       : 0.008470434695482254 -> 0.008391964249312878
3:10:20.688807 INFO: Updating optimization_manager: score_cutoff        : 40.600475508499144 -> 39.14827669830322
3:10:20.688862 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:10:20.696563 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:10:20.726724 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:10:20.734339 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:10:20.814075 INFO: === checking if optimization conditions were reached ===
3:10:20.814343 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
3:10:20.815756 INFO: Updating optimization_manager: rt_error            : 97.40100204251263 -> 97.40100204251263
3:10:20.815923 INFO: Updating optimization_manager: classifier_version  : 10 -> 20
3:10:20.816039 INFO: Updating optimization_manager: score_cutoff        : 39.14827669830322 -> 39.14827669830322
3:10:20.816144 INFO: Updating optimization_manager: fwhm_rt             : 2.766627311706543 -> 2.766627311706543
3:10:20.816244 INFO: Updating optimization_manager: fwhm_mobility       : 0.008391964249312878 -> 0.008391964249312878
3:10:20.816346 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 97.4010 found after 10 searches.
3:10:20.816422 INFO: ==============================================
3:10:20.816516 PROGRESS: Optimization finished for rt_error.
3:10:20.983758 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:10:20.991786 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:10:21.023589 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:10:21.031425 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:10:21.143091 INFO: Starting optimization step 0.
3:10:21.143324 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:10:21.143406 INFO: Using classic extraction backend
3:10:21.143535 PROGRESS: Extracting batch of 50061 precursors
3:10:21.143617 INFO: === Search parameters used ===
3:10:21.143674 INFO: rt_error       : 97.40100204251263
3:10:21.143724 INFO: mobility_error : 0.1
3:10:21.143774 INFO: num_candidates : 3
3:10:21.143821 INFO: ms1_error      : 15.0
3:10:21.143872 INFO: ms2_error      : 15.0
3:10:21.143920 INFO: fwhm_rt        : 2.766627311706543
3:10:21.143970 INFO: quant_window   : 3
3:10:21.144019 INFO: ==============================================
3:10:21.165067 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:10:21.165188 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:10:21.165229 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
3:10:21.165251 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.89
3:10:21.165951 INFO: Starting candidate selection
3:10:38.352773 INFO: Starting candidate scoring
3:10:43.897508 INFO: Finished candidate processing
3:10:43.897701 INFO: Collecting candidate features
3:10:44.125180 WARNING: intensity_correlation has 74 NaNs ( 0.06 % out of 132785)
3:10:44.125524 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 132785)
3:10:44.133492 INFO: Collecting fragment features
3:10:44.213817 INFO: Finished candidate scoring
3:10:44.270940 INFO: performing precursor FDR with 47 features
3:10:44.271059 INFO: Decoy channel: -1
3:10:44.271083 INFO: Competetive: True
3:10:44.316508 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:44.342258 WARNING: dropped 45 target PSMs due to missing features
3:10:44.342387 WARNING: dropped 32 decoy PSMs due to missing features
3:10:44.361599 INFO: Using random state 762738 for train-test-split
3:10:46.536887 INFO: Test AUC: 0.558
3:10:46.537005 INFO: Train AUC: 0.591
3:10:46.537037 INFO: AUC difference: 5.55%
3:10:46.537059 WARNING: AUC difference > 5%. This may indicate overfitting.
3:10:46.808411 INFO: Resetting torch num_threads to 80
3:10:46.812479 PROGRESS: === Extracted 132785 precursors and 1292550 fragments ===
3:10:46.813039 INFO: === FDR correction performed with classifier version 20 ===
3:10:46.817507 PROGRESS: ============================= Precursor FDR =============================
3:10:46.817658 PROGRESS: Total precursors accumulated: 24,344
3:10:46.817722 PROGRESS: Target precursors: 15,026 (61.72%)
3:10:46.817778 PROGRESS: Decoy precursors: 9,318 (38.28%)
3:10:46.817829 PROGRESS: 
3:10:46.817872 PROGRESS: Precursor Summary:
3:10:46.819091 PROGRESS: Channel   0:	 0.050 FDR:   371; 0.010 FDR:   287; 0.001 FDR:   272
3:10:46.819185 PROGRESS: 
3:10:46.819239 PROGRESS: Protein Summary:
3:10:46.820529 PROGRESS: Channel   0:	 0.050 FDR:   364; 0.010 FDR:   282; 0.001 FDR:   267
3:10:46.820620 PROGRESS: =========================================================================
3:10:46.822003 INFO: Target number of precursors reached.
3:10:46.910271 INFO: fragments_df: keeping 3918 of 1292550 [sum(precursor_idx_mask)=8817 sum(mass_error_mask)=1292544 stop_rank=3918
3:10:47.123404 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:10:47.257895 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:10:47.383192 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:10:47.504452 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:10:48.020938 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:10:48.021410 INFO: Using score_cutoff 39.28013653793335 (fac=0.99, q=1)
3:10:48.021746 INFO: Updating optimization_manager: fwhm_rt             : 2.766627311706543 -> 2.798638343811035
3:10:48.021834 INFO: Updating optimization_manager: fwhm_mobility       : 0.008391964249312878 -> 0.008396580815315247
3:10:48.021893 INFO: Updating optimization_manager: score_cutoff        : 39.14827669830322 -> 39.28013653793335
3:10:48.021951 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:10:48.030242 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:10:48.060888 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:10:48.068352 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:10:48.130639 INFO: === checking if optimization conditions were reached ===
3:10:48.130951 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
3:10:48.133245 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07550776364896347
3:10:48.133362 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0755.
3:10:48.133438 INFO: ==============================================
3:10:48.133524 INFO: Starting optimization step 1.
3:10:48.133589 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:10:48.133662 INFO: Using classic extraction backend
3:10:48.133836 PROGRESS: Extracting batch of 50061 precursors
3:10:48.133914 INFO: === Search parameters used ===
3:10:48.133969 INFO: rt_error       : 97.40100204251263
3:10:48.134019 INFO: mobility_error : 0.07550776364896347
3:10:48.134084 INFO: num_candidates : 3
3:10:48.134135 INFO: ms1_error      : 15.0
3:10:48.134198 INFO: ms2_error      : 15.0
3:10:48.134246 INFO: fwhm_rt        : 2.798638343811035
3:10:48.134295 INFO: quant_window   : 3
3:10:48.134343 INFO: ==============================================
3:10:48.152623 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:10:48.152733 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:10:48.152784 INFO: FWHM in RT is 2.80 seconds, sigma is 0.62
3:10:48.152806 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.89
3:10:48.161410 INFO: Starting candidate selection
3:11:00.622868 INFO: Starting candidate scoring
3:11:06.902209 INFO: Finished candidate processing
3:11:06.902426 INFO: Collecting candidate features
3:11:07.126920 WARNING: intensity_correlation has 53 NaNs ( 0.04 % out of 130037)
3:11:07.127408 WARNING: height_correlation has 12 NaNs ( 0.01 % out of 130037)
3:11:07.139821 INFO: Collecting fragment features
3:11:07.231531 INFO: Finished candidate scoring
3:11:07.287588 INFO: performing precursor FDR with 47 features
3:11:07.287710 INFO: Decoy channel: -1
3:11:07.287736 INFO: Competetive: True
3:11:07.332050 INFO: Setting torch num_threads to 2 for FDR classification task
3:11:07.357023 WARNING: dropped 27 target PSMs due to missing features
3:11:07.357158 WARNING: dropped 35 decoy PSMs due to missing features
3:11:07.376036 INFO: Using random state 762738 for train-test-split
3:11:09.413056 INFO: Test AUC: 0.558
3:11:09.413178 INFO: Train AUC: 0.584
3:11:09.413213 INFO: AUC difference: 4.39%
3:11:09.679205 INFO: Resetting torch num_threads to 80
3:11:09.683056 PROGRESS: === Extracted 130037 precursors and 1259188 fragments ===
3:11:09.683607 INFO: === FDR correction performed with classifier version 20 ===
3:11:09.687699 PROGRESS: ============================= Precursor FDR =============================
3:11:09.687829 PROGRESS: Total precursors accumulated: 23,883
3:11:09.687891 PROGRESS: Target precursors: 14,431 (60.42%)
3:11:09.687943 PROGRESS: Decoy precursors: 9,452 (39.58%)
3:11:09.687990 PROGRESS: 
3:11:09.688035 PROGRESS: Precursor Summary:
3:11:09.689172 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   257; 0.001 FDR:   160
3:11:09.689263 PROGRESS: 
3:11:09.689320 PROGRESS: Protein Summary:
3:11:09.690567 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:   252; 0.001 FDR:   159
3:11:09.690661 PROGRESS: =========================================================================
3:11:09.692052 INFO: Target number of precursors reached.
3:11:09.776853 INFO: fragments_df: keeping 3568 of 1259188 [sum(precursor_idx_mask)=7909 sum(mass_error_mask)=1259182 stop_rank=3568
3:11:09.923564 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:11:10.021225 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:11:10.122959 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:11:10.225652 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:11:10.624134 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:11:10.624612 INFO: Using score_cutoff 39.636690092468264 (fac=0.99, q=1)
3:11:10.624954 INFO: Updating optimization_manager: fwhm_rt             : 2.798638343811035 -> 2.7868733406066895
3:11:10.625037 INFO: Updating optimization_manager: fwhm_mobility       : 0.008396580815315247 -> 0.008486448787152767
3:11:10.625091 INFO: Updating optimization_manager: score_cutoff        : 39.28013653793335 -> 39.636690092468264
3:11:10.625148 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:11:10.632773 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:11:10.663091 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:11:10.670707 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:11:10.731824 INFO: === checking if optimization conditions were reached ===
3:11:10.732092 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
3:11:10.734093 INFO: Updating optimization_manager: mobility_error      : 0.07550776364896347 -> 0.0655323773262731
3:11:10.734201 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0655.
3:11:10.734268 INFO: ==============================================
3:11:10.734344 INFO: Starting optimization step 2.
3:11:10.734406 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:11:10.734481 INFO: Using classic extraction backend
3:11:10.734643 PROGRESS: Extracting batch of 50061 precursors
3:11:10.734711 INFO: === Search parameters used ===
3:11:10.734758 INFO: rt_error       : 97.40100204251263
3:11:10.734799 INFO: mobility_error : 0.0655323773262731
3:11:10.734838 INFO: num_candidates : 3
3:11:10.734876 INFO: ms1_error      : 15.0
3:11:10.734915 INFO: ms2_error      : 15.0
3:11:10.734954 INFO: fwhm_rt        : 2.7868733406066895
3:11:10.734993 INFO: quant_window   : 3
3:11:10.735030 INFO: ==============================================
3:11:10.751011 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:11:10.751129 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:11:10.751180 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
3:11:10.751203 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.94
3:11:10.759970 INFO: Starting candidate selection
3:11:21.244721 INFO: Starting candidate scoring
3:11:27.611366 INFO: Finished candidate processing
3:11:27.612782 INFO: Collecting candidate features
3:11:27.791204 WARNING: intensity_correlation has 70 NaNs ( 0.05 % out of 128721)
3:11:27.791537 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 128721)
3:11:27.799239 INFO: Collecting fragment features
3:11:27.878069 INFO: Finished candidate scoring
3:11:27.938353 INFO: performing precursor FDR with 47 features
3:11:27.938468 INFO: Decoy channel: -1
3:11:27.938493 INFO: Competetive: True
3:11:27.981136 INFO: Setting torch num_threads to 2 for FDR classification task
3:11:28.005589 WARNING: dropped 40 target PSMs due to missing features
3:11:28.005718 WARNING: dropped 36 decoy PSMs due to missing features
3:11:28.023340 INFO: Using random state 762738 for train-test-split
3:11:30.120181 INFO: Test AUC: 0.560
3:11:30.120306 INFO: Train AUC: 0.584
3:11:30.120337 INFO: AUC difference: 4.12%
3:11:30.391733 INFO: Resetting torch num_threads to 80
3:11:30.407606 PROGRESS: === Extracted 128721 precursors and 1236792 fragments ===
3:11:30.408190 INFO: === FDR correction performed with classifier version 20 ===
3:11:30.412795 PROGRESS: ============================= Precursor FDR =============================
3:11:30.412924 PROGRESS: Total precursors accumulated: 23,659
3:11:30.412985 PROGRESS: Target precursors: 14,439 (61.03%)
3:11:30.413036 PROGRESS: Decoy precursors: 9,220 (38.97%)
3:11:30.413082 PROGRESS: 
3:11:30.413127 PROGRESS: Precursor Summary:
3:11:30.414293 PROGRESS: Channel   0:	 0.050 FDR:   349; 0.010 FDR:   260; 0.001 FDR:   187
3:11:30.414385 PROGRESS: 
3:11:30.414455 PROGRESS: Protein Summary:
3:11:30.415696 PROGRESS: Channel   0:	 0.050 FDR:   344; 0.010 FDR:   255; 0.001 FDR:   184
3:11:30.415789 PROGRESS: =========================================================================
3:11:30.417195 INFO: Target number of precursors reached.
3:11:30.500888 INFO: fragments_df: keeping 3627 of 1236792 [sum(precursor_idx_mask)=8038 sum(mass_error_mask)=1236789 stop_rank=3627
3:11:30.779478 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:11:30.876606 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:11:30.980915 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
3:11:31.084545 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:11:31.495395 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:11:31.495882 INFO: Using score_cutoff 38.10563003883362 (fac=0.99, q=1)
3:11:31.496191 INFO: Updating optimization_manager: fwhm_rt             : 2.7868733406066895 -> 2.791421413421631
3:11:31.496271 INFO: Updating optimization_manager: fwhm_mobility       : 0.008486448787152767 -> 0.008471187204122543
3:11:31.496325 INFO: Updating optimization_manager: score_cutoff        : 39.636690092468264 -> 38.10563003883362
3:11:31.496377 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:11:31.503846 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:11:31.534201 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:11:31.541877 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:11:31.603832 INFO: === checking if optimization conditions were reached ===
3:11:31.604140 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
3:11:31.605494 INFO: Updating optimization_manager: mobility_error      : 0.0655323773262731 -> 0.1
3:11:31.605637 INFO: Updating optimization_manager: classifier_version  : 20 -> 21
3:11:31.605745 INFO: Updating optimization_manager: score_cutoff        : 38.10563003883362 -> 39.28013653793335
3:11:31.605844 INFO: Updating optimization_manager: fwhm_rt             : 2.791421413421631 -> 2.798638343811035
3:11:31.605943 INFO: Updating optimization_manager: fwhm_mobility       : 0.008471187204122543 -> 0.008396580815315247
3:11:31.606060 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
3:11:31.606152 INFO: ==============================================
3:11:31.606235 PROGRESS: Optimization finished for mobility_error.
3:11:31.881384 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:11:31.889287 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:11:31.922094 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:11:31.929682 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:11:32.019246 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:11:32.019495 PROGRESS: ==============================================
3:11:32.019595 PROGRESS: ms2_error      : 15.0000
3:11:32.019716 PROGRESS: ms1_error      : 15.0000
3:11:32.019788 PROGRESS: rt_error       : 97.4010
3:11:32.019868 PROGRESS: mobility_error : 0.1000
3:11:32.019935 PROGRESS: ==============================================
3:11:32.029392 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:11:33.681720 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:11:41.250510 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
3:11:43.059690 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:11:59.812039 INFO: Using classic extraction backend
3:11:59.815487 PROGRESS: Extracting batch of 12073114 precursors
3:11:59.815764 INFO: === Search parameters used ===
3:11:59.815847 INFO: rt_error       : 97.40100204251263
3:11:59.815905 INFO: mobility_error : 0.1
3:11:59.815963 INFO: num_candidates : 3
3:11:59.816007 INFO: ms1_error      : 15.0
3:11:59.816048 INFO: ms2_error      : 15.0
3:11:59.816089 INFO: fwhm_rt        : 2.798638343811035
3:11:59.816129 INFO: quant_window   : 3
3:11:59.816169 INFO: ==============================================
3:12:03.009179 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:12:03.009325 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:12:03.009385 INFO: FWHM in RT is 2.80 seconds, sigma is 0.62
3:12:03.009408 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.89
3:12:03.014720 INFO: Starting candidate selection
4:09:34.556622 INFO: Removed 18024450 precursors with score below cutoff 39.28013653793335
4:09:37.373691 INFO: Starting candidate scoring
4:20:51.217758 INFO: Finished candidate processing
4:20:51.218748 INFO: Collecting candidate features
4:21:45.635081 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 15646774)
4:21:46.168166 INFO: Collecting fragment features
4:22:19.994268 INFO: Finished candidate scoring
4:22:38.843213 INFO: === Performing FDR correction with classifier version 21 ===
4:22:38.851193 INFO: performing precursor FDR with 47 features
4:22:38.851248 INFO: Decoy channel: -1
4:22:38.851273 INFO: Competetive: True
4:22:42.817860 INFO: Setting torch num_threads to 2 for FDR classification task
4:22:45.207748 WARNING: dropped 1 target PSMs due to missing features
4:22:45.207916 WARNING: dropped 4 decoy PSMs due to missing features
4:22:57.645544 INFO: Using random state 479071 for train-test-split
4:28:21.184648 INFO: Test AUC: 0.564
4:28:21.184795 INFO: Train AUC: 0.566
4:28:21.184832 INFO: AUC difference: 0.23%
4:28:24.988619 INFO: Resetting torch num_threads to 80
4:28:25.413113 INFO: Removing fragments below FDR threshold
4:28:26.923332 PROGRESS: ============================= Precursor FDR =============================
4:28:26.923584 PROGRESS: Total precursors accumulated: 69,642
4:28:26.923656 PROGRESS: Target precursors: 68,953 (99.01%)
4:28:26.923709 PROGRESS: Decoy precursors: 689 (0.99%)
4:28:26.923757 PROGRESS: 
4:28:26.923801 PROGRESS: Precursor Summary:
4:28:26.953797 PROGRESS: Channel   0:	 0.050 FDR: 68,953; 0.010 FDR: 68,953; 0.001 FDR: 47,803
4:28:26.954031 PROGRESS: 
4:28:26.954110 PROGRESS: Protein Summary:
4:28:26.984808 PROGRESS: Channel   0:	 0.050 FDR: 11,222; 0.010 FDR: 11,222; 0.001 FDR: 8,880
4:28:26.985018 PROGRESS: =========================================================================
4:28:27.193325 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/psm.parquet
4:28:27.559244 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/frag.parquet
4:28:27.837954 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
4:28:28.419348 PROGRESS: 
4:28:28.419497 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant
4:28:28.419576 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/figures
4:28:28.420618 INFO: Initializing TimingManager
4:28:28.421188 INFO: Initializing RawFileManager
4:28:28.421604 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:28.421666 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:28.421716 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:28.631679 INFO: Reading 39,128 frames with 2,897,842,446 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:37.792142 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
4:28:37.793972 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:37.795877 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:37.796099 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:37.796457 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:37.797815 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:37.812882 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:37.813088 INFO: Indexing quadrupole dimension
4:28:38.352531 INFO: Transposing detector events
4:28:47.982132 INFO: Finished transposing data
4:28:48.011799 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:28:48.012536 INFO: RT (min)            : 0.0 - 70.0
4:28:48.012626 INFO: RT duration (sec)   : 4199.8
4:28:48.012666 INFO: RT duration (min)   : 70.0
4:28:48.012701 INFO: Cycle len (scans)   : 9
4:28:48.012733 INFO: Cycle len (sec)     : 0.97
4:28:48.012763 INFO: Number of cycles    : 4347
4:28:48.012792 INFO: MS2 range (m/z)     : 400.0 - 1000.0
4:28:48.012872 INFO: Creating DIA data object took: 19.591577291488647
4:28:49.205101 INFO: Initializing CalibrationManager
4:28:49.205382 INFO: Setting up calibration estimators ..
4:28:49.205455 INFO: Found 1 estimator(s) in calibration group 'fragment'
4:28:49.205534 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'}' ..
4:28:49.205619 INFO: Found 3 estimator(s) in calibration group 'precursor'
4:28:49.205678 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'}' ..
4:28:49.205736 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}}' ..
4:28:49.205798 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}}' ..
4:28:49.205845 INFO: Done setting up calibration estimators.
4:28:49.205968 INFO: Initializing OptimizationManager
4:28:49.206079 INFO: initial parameter: ms1_error = 30
4:28:49.206140 INFO: initial parameter: ms2_error = 30
4:28:49.206186 INFO: initial parameter: rt_error = 2099.8992935
4:28:49.206228 INFO: initial parameter: mobility_error = 0.1
4:28:49.206269 INFO: initial parameter: num_candidates = 1
4:28:49.206309 INFO: initial parameter: fwhm_rt = 5
4:28:49.206349 INFO: initial parameter: fwhm_mobility = 0.01
4:28:49.206388 INFO: initial parameter: score_cutoff = 0
4:28:49.206427 INFO: initial parameter: classifier_version = -1
4:28:49.206496 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
4:28:49.206980 INFO: FDRManager: loading saved state not requested, will be initialized.
4:28:49.207028 INFO: Initializing FDRManager
4:28:49.207068 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
4:28:50.412900 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
4:28:51.200547 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
4:28:51.200948 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 2099.8992935
4:28:51.201056 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
4:28:51.201244 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
4:28:51.201352 PROGRESS: Starting initial search for precursors.
4:28:51.201441 INFO: Starting optimization step 0.
4:28:51.201503 PROGRESS: === Extracting elution groups 0 to 200 ===
4:28:51.201752 INFO: Using classic extraction backend
4:28:51.201952 PROGRESS: Extracting batch of 390 precursors
4:28:51.202029 INFO: === Search parameters used ===
4:28:51.202090 INFO: rt_error       : 2099.8992935
4:28:51.202134 INFO: mobility_error : 0.1
4:28:51.202175 INFO: num_candidates : 1
4:28:51.202216 INFO: ms1_error      : 30
4:28:51.202255 INFO: ms2_error      : 30
4:28:51.202292 INFO: fwhm_rt        : 5
4:28:51.202333 INFO: quant_window   : 3
4:28:51.202371 INFO: ==============================================
4:28:51.203197 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:28:51.203241 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:28:51.203278 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:28:51.203299 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:28:51.204211 INFO: Starting candidate selection
4:28:55.074978 INFO: Starting candidate scoring
4:28:55.143825 INFO: Finished candidate processing
4:28:55.143951 INFO: Collecting candidate features
4:28:55.154902 INFO: Collecting fragment features
4:28:55.157157 INFO: Finished candidate scoring
4:28:55.158203 INFO: performing precursor FDR with 47 features
4:28:55.158246 INFO: Decoy channel: -1
4:28:55.158270 INFO: Competetive: True
4:28:55.159586 INFO: Setting torch num_threads to 2 for FDR classification task
4:28:55.162826 INFO: Using random state 559780 for train-test-split
4:28:55.172044 INFO: Test AUC: 0.489
4:28:55.172108 INFO: Train AUC: 0.532
4:28:55.172138 INFO: AUC difference: 8.21%
4:28:55.172160 WARNING: AUC difference > 5%. This may indicate overfitting.
4:28:55.398287 INFO: Resetting torch num_threads to 80
4:28:55.398921 PROGRESS: === Extracted 363 precursors and 3936 fragments ===
4:28:55.399421 INFO: === FDR correction performed with classifier version -1 ===
4:28:55.399987 PROGRESS: ============================= Precursor FDR =============================
4:28:55.400075 PROGRESS: Total precursors accumulated: 188
4:28:55.400134 PROGRESS: Target precursors: 154 (81.91%)
4:28:55.400184 PROGRESS: Decoy precursors: 34 (18.09%)
4:28:55.400232 PROGRESS: 
4:28:55.400277 PROGRESS: Precursor Summary:
4:28:55.401201 PROGRESS: Channel   0:	 0.050 FDR:   140; 0.010 FDR:   140; 0.001 FDR:   140
4:28:55.401293 PROGRESS: 
4:28:55.401358 PROGRESS: Protein Summary:
4:28:55.402396 PROGRESS: Channel   0:	 0.050 FDR:   140; 0.010 FDR:   140; 0.001 FDR:   140
4:28:55.402486 PROGRESS: =========================================================================
4:28:55.402601 INFO: Target number of precursors not reached yet.
4:28:55.468514 INFO: Starting optimization step 1.
4:28:55.468786 PROGRESS: === Extracting elution groups 200 to 600 ===
4:28:55.468866 INFO: Using classic extraction backend
4:28:55.469000 PROGRESS: Extracting batch of 783 precursors
4:28:55.469071 INFO: === Search parameters used ===
4:28:55.469119 INFO: rt_error       : 2099.8992935
4:28:55.469161 INFO: mobility_error : 0.1
4:28:55.469203 INFO: num_candidates : 1
4:28:55.469244 INFO: ms1_error      : 30
4:28:55.469285 INFO: ms2_error      : 30
4:28:55.469325 INFO: fwhm_rt        : 5
4:28:55.469365 INFO: quant_window   : 3
4:28:55.469404 INFO: ==============================================
4:28:55.470143 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:28:55.470189 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:28:55.470219 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:28:55.470241 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:28:55.475013 INFO: Starting candidate selection
4:29:01.799080 INFO: Starting candidate scoring
4:29:01.934751 INFO: Finished candidate processing
4:29:01.934846 INFO: Collecting candidate features
4:29:01.944052 INFO: Collecting fragment features
4:29:01.946348 INFO: Finished candidate scoring
4:29:01.948268 INFO: performing precursor FDR with 47 features
4:29:01.948314 INFO: Decoy channel: -1
4:29:01.948338 INFO: Competetive: True
4:29:01.951136 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:01.952935 INFO: Using random state 458975 for train-test-split
4:29:01.960556 INFO: Test AUC: 0.502
4:29:01.960609 INFO: Train AUC: 0.508
4:29:01.960638 INFO: AUC difference: 1.25%
4:29:02.162419 INFO: Resetting torch num_threads to 80
4:29:02.163603 PROGRESS: === Extracted 1117 precursors and 12174 fragments ===
4:29:02.163977 INFO: === FDR correction performed with classifier version -1 ===
4:29:02.164543 PROGRESS: ============================= Precursor FDR =============================
4:29:02.164632 PROGRESS: Total precursors accumulated: 576
4:29:02.164691 PROGRESS: Target precursors: 460 (79.86%)
4:29:02.164745 PROGRESS: Decoy precursors: 116 (20.14%)
4:29:02.164793 PROGRESS: 
4:29:02.164834 PROGRESS: Precursor Summary:
4:29:02.165802 PROGRESS: Channel   0:	 0.050 FDR:   415; 0.010 FDR:   415; 0.001 FDR:   415
4:29:02.165891 PROGRESS: 
4:29:02.165948 PROGRESS: Protein Summary:
4:29:02.167099 PROGRESS: Channel   0:	 0.050 FDR:   408; 0.010 FDR:   408; 0.001 FDR:   408
4:29:02.167189 PROGRESS: =========================================================================
4:29:02.167323 INFO: Target number of precursors reached.
4:29:02.170219 INFO: fragments_df: keeping 878 of 12174 [sum(precursor_idx_mask)=4642 sum(mass_error_mask)=12174 stop_rank=878
4:29:02.269521 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:29:02.415931 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:29:02.549118 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:29:02.680396 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:29:02.839316 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
4:29:02.839850 INFO: Using score_cutoff 36.165623819732666 (fac=0.99, q=1)
4:29:02.840189 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.3044347763061523
4:29:02.840275 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007996694184839725
4:29:02.840329 INFO: Updating optimization_manager: score_cutoff        : 0 -> 36.165623819732666
4:29:02.840414 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:02.841646 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:02.842983 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:29:02.843762 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:02.845866 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
4:29:02.845963 PROGRESS: Required number of precursors found. Starting search parameter optimization.
4:29:02.846048 INFO: Starting optimization step 2.
4:29:02.846110 PROGRESS: === Extracting elution groups 0 to 600 ===
4:29:02.846176 INFO: Using classic extraction backend
4:29:02.846294 PROGRESS: Extracting batch of 1173 precursors
4:29:02.846356 INFO: === Search parameters used ===
4:29:02.846403 INFO: rt_error       : 2099.8992935
4:29:02.846442 INFO: mobility_error : 0.1
4:29:02.846486 INFO: num_candidates : 3
4:29:02.846527 INFO: ms1_error      : 30
4:29:02.846567 INFO: ms2_error      : 30
4:29:02.846604 INFO: fwhm_rt        : 3.3044347763061523
4:29:02.846642 INFO: quant_window   : 3
4:29:02.846679 INFO: ==============================================
4:29:02.847691 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:29:02.847735 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:29:02.847770 INFO: FWHM in RT is 3.30 seconds, sigma is 0.73
4:29:02.847791 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.71
4:29:02.848567 INFO: Starting candidate selection
4:29:12.788224 INFO: Starting candidate scoring
4:29:13.106912 INFO: Finished candidate processing
4:29:13.107041 INFO: Collecting candidate features
4:29:13.121684 INFO: Collecting fragment features
4:29:13.125418 INFO: Finished candidate scoring
4:29:13.127307 INFO: performing precursor FDR with 47 features
4:29:13.127352 INFO: Decoy channel: -1
4:29:13.127376 INFO: Competetive: True
4:29:13.130157 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:13.132159 INFO: Using random state 957507 for train-test-split
4:29:13.142233 INFO: Test AUC: 0.503
4:29:13.142292 INFO: Train AUC: 0.501
4:29:13.142319 INFO: AUC difference: 0.45%
4:29:13.361006 INFO: Resetting torch num_threads to 80
4:29:13.361564 PROGRESS: === Extracted 3219 precursors and 35228 fragments ===
4:29:13.361952 INFO: === FDR correction performed with classifier version 1 ===
4:29:13.363305 PROGRESS: ============================= Precursor FDR =============================
4:29:13.363398 PROGRESS: Total precursors accumulated: 587
4:29:13.363455 PROGRESS: Target precursors: 518 (88.25%)
4:29:13.363503 PROGRESS: Decoy precursors: 69 (11.75%)
4:29:13.363546 PROGRESS: 
4:29:13.363587 PROGRESS: Precursor Summary:
4:29:13.364579 PROGRESS: Channel   0:	 0.050 FDR:   507; 0.010 FDR:   507; 0.001 FDR:   507
4:29:13.364666 PROGRESS: 
4:29:13.364722 PROGRESS: Protein Summary:
4:29:13.365898 PROGRESS: Channel   0:	 0.050 FDR:   496; 0.010 FDR:   496; 0.001 FDR:   496
4:29:13.365985 PROGRESS: =========================================================================
4:29:13.366140 INFO: Target number of precursors reached.
4:29:13.372396 INFO: fragments_df: keeping 3076 of 35228 [sum(precursor_idx_mask)=15879 sum(mass_error_mask)=35228 stop_rank=3076
4:29:13.471027 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:29:13.602035 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:29:13.740714 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:29:13.878491 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:29:14.274386 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:29:14.274784 INFO: Using score_cutoff 37.11139104995728 (fac=0.99, q=1)
4:29:14.275080 INFO: Updating optimization_manager: fwhm_rt             : 3.3044347763061523 -> 3.3093373775482178
4:29:14.275168 INFO: Updating optimization_manager: fwhm_mobility       : 0.007996694184839725 -> 0.00797074381262064
4:29:14.275224 INFO: Updating optimization_manager: score_cutoff        : 36.165623819732666 -> 37.11139104995728
4:29:14.275276 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:14.276302 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:14.277604 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:29:14.278366 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:14.280459 INFO: === checking if optimization conditions were reached ===
4:29:14.281755 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.220022839617535
4:29:14.281853 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
4:29:14.281926 PROGRESS: ❌ ms2_error      : 17.2200 > 15.0000 or insufficient steps taken.
4:29:14.282865 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
4:29:14.282958 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
4:29:14.283017 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
4:29:14.283069 INFO: ==============================================
4:29:14.283130 INFO: Starting optimization step 3.
4:29:14.283182 PROGRESS: === Extracting elution groups 0 to 600 ===
4:29:14.283233 INFO: Using classic extraction backend
4:29:14.283332 PROGRESS: Extracting batch of 1173 precursors
4:29:14.283396 INFO: === Search parameters used ===
4:29:14.283717 INFO: rt_error       : 2099.8992935
4:29:14.283773 INFO: mobility_error : 0.1
4:29:14.283816 INFO: num_candidates : 3
4:29:14.283858 INFO: ms1_error      : 15.0
4:29:14.283898 INFO: ms2_error      : 17.220022839617535
4:29:14.283936 INFO: fwhm_rt        : 3.3093373775482178
4:29:14.283974 INFO: quant_window   : 3
4:29:14.284011 INFO: ==============================================
4:29:14.284855 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:29:14.284899 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:29:14.284932 INFO: FWHM in RT is 3.31 seconds, sigma is 0.73
4:29:14.284953 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.70
4:29:14.285689 INFO: Starting candidate selection
4:29:23.572058 INFO: Starting candidate scoring
4:29:23.809796 INFO: Finished candidate processing
4:29:23.809975 INFO: Collecting candidate features
4:29:23.824944 INFO: Collecting fragment features
4:29:23.828781 INFO: Finished candidate scoring
4:29:23.830623 INFO: performing precursor FDR with 47 features
4:29:23.830667 INFO: Decoy channel: -1
4:29:23.830694 INFO: Competetive: True
4:29:23.833433 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:23.835446 INFO: Using random state 360239 for train-test-split
4:29:23.846219 INFO: Test AUC: 0.509
4:29:23.846284 INFO: Train AUC: 0.512
4:29:23.846313 INFO: AUC difference: 0.49%
4:29:24.056645 INFO: Resetting torch num_threads to 80
4:29:24.057191 PROGRESS: === Extracted 3226 precursors and 34120 fragments ===
4:29:24.057570 INFO: === FDR correction performed with classifier version 2 ===
4:29:24.058193 PROGRESS: ============================= Precursor FDR =============================
4:29:24.058286 PROGRESS: Total precursors accumulated: 585
4:29:24.058343 PROGRESS: Target precursors: 477 (81.54%)
4:29:24.058393 PROGRESS: Decoy precursors: 108 (18.46%)
4:29:24.058438 PROGRESS: 
4:29:24.058479 PROGRESS: Precursor Summary:
4:29:24.059469 PROGRESS: Channel   0:	 0.050 FDR:   447; 0.010 FDR:   447; 0.001 FDR:   447
4:29:24.059559 PROGRESS: 
4:29:24.059615 PROGRESS: Protein Summary:
4:29:24.060770 PROGRESS: Channel   0:	 0.050 FDR:   439; 0.010 FDR:   439; 0.001 FDR:   439
4:29:24.060862 PROGRESS: =========================================================================
4:29:24.060993 INFO: Target number of precursors reached.
4:29:24.066833 INFO: fragments_df: keeping 2360 of 34120 [sum(precursor_idx_mask)=13724 sum(mass_error_mask)=34120 stop_rank=2360
4:29:24.166039 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:29:24.298934 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:29:24.428719 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:29:24.561739 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:29:24.872657 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:29:24.873043 INFO: Using score_cutoff 31.060587819671632 (fac=0.99, q=1)
4:29:24.873338 INFO: Updating optimization_manager: fwhm_rt             : 3.3093373775482178 -> 2.916696310043335
4:29:24.873417 INFO: Updating optimization_manager: fwhm_mobility       : 0.00797074381262064 -> 0.006039589177817106
4:29:24.873470 INFO: Updating optimization_manager: score_cutoff        : 37.11139104995728 -> 31.060587819671632
4:29:24.873521 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:24.874572 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:24.875880 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:29:24.876626 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:24.878729 INFO: === checking if optimization conditions were reached ===
4:29:24.879934 INFO: Updating optimization_manager: ms2_error           : 17.220022839617535 -> 15.0
4:29:24.880031 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
4:29:24.880092 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
4:29:24.881023 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
4:29:24.881115 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
4:29:24.881175 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
4:29:24.881225 INFO: ==============================================
4:29:24.881288 PROGRESS: Optimization finished for ms2_error, ms1_error.
4:29:24.979535 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:24.980654 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:24.981961 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:29:24.982726 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:24.984870 INFO: Starting optimization step 0.
4:29:24.984963 PROGRESS: === Extracting elution groups 0 to 600 ===
4:29:24.985031 INFO: Using classic extraction backend
4:29:24.985139 PROGRESS: Extracting batch of 1173 precursors
4:29:24.985210 INFO: === Search parameters used ===
4:29:24.985257 INFO: rt_error       : 2099.8992935
4:29:24.985299 INFO: mobility_error : 0.1
4:29:24.985338 INFO: num_candidates : 3
4:29:24.985378 INFO: ms1_error      : 15.0
4:29:24.985416 INFO: ms2_error      : 15.0
4:29:24.985454 INFO: fwhm_rt        : 2.916696310043335
4:29:24.985491 INFO: quant_window   : 3
4:29:24.985540 INFO: ==============================================
4:29:24.986262 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:29:24.986306 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:29:24.986340 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
4:29:24.986362 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.80
4:29:24.987018 INFO: Starting candidate selection
4:29:34.089262 INFO: Starting candidate scoring
4:29:34.320780 INFO: Finished candidate processing
4:29:34.320909 INFO: Collecting candidate features
4:29:34.334571 INFO: Collecting fragment features
4:29:34.338343 INFO: Finished candidate scoring
4:29:34.340262 INFO: performing precursor FDR with 47 features
4:29:34.340307 INFO: Decoy channel: -1
4:29:34.340331 INFO: Competetive: True
4:29:34.343133 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:34.345142 INFO: Using random state 478447 for train-test-split
4:29:34.355639 INFO: Test AUC: 0.491
4:29:34.355700 INFO: Train AUC: 0.519
4:29:34.355729 INFO: AUC difference: 5.36%
4:29:34.355751 WARNING: AUC difference > 5%. This may indicate overfitting.
4:29:35.576169 INFO: Resetting torch num_threads to 80
4:29:35.576735 PROGRESS: === Extracted 3223 precursors and 33414 fragments ===
4:29:35.577122 INFO: === FDR correction performed with classifier version 3 ===
4:29:35.577691 PROGRESS: ============================= Precursor FDR =============================
4:29:35.577777 PROGRESS: Total precursors accumulated: 585
4:29:35.577835 PROGRESS: Target precursors: 474 (81.03%)
4:29:35.577882 PROGRESS: Decoy precursors: 111 (18.97%)
4:29:35.577924 PROGRESS: 
4:29:35.577965 PROGRESS: Precursor Summary:
4:29:35.578959 PROGRESS: Channel   0:	 0.050 FDR:   439; 0.010 FDR:   439; 0.001 FDR:   439
4:29:35.579051 PROGRESS: 
4:29:35.579106 PROGRESS: Protein Summary:
4:29:35.580249 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   434; 0.001 FDR:   434
4:29:35.580338 PROGRESS: =========================================================================
4:29:35.580465 INFO: Target number of precursors reached.
4:29:35.586283 INFO: fragments_df: keeping 2337 of 33414 [sum(precursor_idx_mask)=13139 sum(mass_error_mask)=33414 stop_rank=2337
4:29:35.702622 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:29:35.834877 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:29:35.965477 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:29:36.098857 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:29:36.407828 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:29:36.408228 INFO: Using score_cutoff 30.695331204986573 (fac=0.99, q=1)
4:29:36.408523 INFO: Updating optimization_manager: fwhm_rt             : 2.916696310043335 -> 2.732630729675293
4:29:36.408603 INFO: Updating optimization_manager: fwhm_mobility       : 0.006039589177817106 -> 0.005579605232924223
4:29:36.408660 INFO: Updating optimization_manager: score_cutoff        : 31.060587819671632 -> 30.695331204986573
4:29:36.408716 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:36.409761 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:36.411139 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:29:36.411918 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:36.413987 INFO: === checking if optimization conditions were reached ===
4:29:36.414095 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
4:29:36.415623 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 1326.0576498160146
4:29:36.415728 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1326.0576.
4:29:36.415793 INFO: ==============================================
4:29:36.415859 INFO: Starting optimization step 1.
4:29:36.415916 PROGRESS: === Extracting elution groups 0 to 600 ===
4:29:36.415970 INFO: Using classic extraction backend
4:29:36.416074 PROGRESS: Extracting batch of 1173 precursors
4:29:36.416137 INFO: === Search parameters used ===
4:29:36.416503 INFO: rt_error       : 1326.0576498160146
4:29:36.416557 INFO: mobility_error : 0.1
4:29:36.416602 INFO: num_candidates : 3
4:29:36.416645 INFO: ms1_error      : 15.0
4:29:36.416687 INFO: ms2_error      : 15.0
4:29:36.416727 INFO: fwhm_rt        : 2.732630729675293
4:29:36.416767 INFO: quant_window   : 3
4:29:36.416807 INFO: ==============================================
4:29:36.417651 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:29:36.417695 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:29:36.417731 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
4:29:36.417754 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.59
4:29:36.418448 INFO: Starting candidate selection
4:29:42.618003 INFO: Starting candidate scoring
4:29:42.806962 INFO: Finished candidate processing
4:29:42.807143 INFO: Collecting candidate features
4:29:42.835520 INFO: Collecting fragment features
4:29:42.841712 INFO: Finished candidate scoring
4:29:42.844671 INFO: performing precursor FDR with 47 features
4:29:42.844719 INFO: Decoy channel: -1
4:29:42.844744 INFO: Competetive: True
4:29:42.848570 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:42.850660 INFO: Using random state 478447 for train-test-split
4:29:42.861637 INFO: Test AUC: 0.493
4:29:42.861691 INFO: Train AUC: 0.517
4:29:42.861720 INFO: AUC difference: 4.64%
4:29:43.075900 INFO: Resetting torch num_threads to 80
4:29:43.076483 PROGRESS: === Extracted 3198 precursors and 33110 fragments ===
4:29:43.076870 INFO: === FDR correction performed with classifier version 3 ===
4:29:43.077423 PROGRESS: ============================= Precursor FDR =============================
4:29:43.077510 PROGRESS: Total precursors accumulated: 586
4:29:43.077568 PROGRESS: Target precursors: 472 (80.55%)
4:29:43.077615 PROGRESS: Decoy precursors: 114 (19.45%)
4:29:43.077661 PROGRESS: 
4:29:43.077702 PROGRESS: Precursor Summary:
4:29:43.078700 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   432; 0.001 FDR:   432
4:29:43.078792 PROGRESS: 
4:29:43.078847 PROGRESS: Protein Summary:
4:29:43.080010 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   427; 0.001 FDR:   427
4:29:43.080108 PROGRESS: =========================================================================
4:29:43.080239 INFO: Target number of precursors reached.
4:29:43.085907 INFO: fragments_df: keeping 2299 of 33110 [sum(precursor_idx_mask)=12849 sum(mass_error_mask)=33110 stop_rank=2299
4:29:43.184490 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:29:43.317454 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:29:43.446022 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:29:43.559944 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:29:43.844657 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:29:43.845062 INFO: Using score_cutoff 30.91276769313812 (fac=0.99, q=1)
4:29:43.845356 INFO: Updating optimization_manager: fwhm_rt             : 2.732630729675293 -> 2.7561450004577637
4:29:43.845435 INFO: Updating optimization_manager: fwhm_mobility       : 0.005579605232924223 -> 0.005415637046098709
4:29:43.845490 INFO: Updating optimization_manager: score_cutoff        : 30.695331204986573 -> 30.91276769313812
4:29:43.845544 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:43.846610 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:43.847948 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:29:43.848717 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:43.850795 INFO: === checking if optimization conditions were reached ===
4:29:43.850893 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
4:29:43.852523 INFO: Updating optimization_manager: rt_error            : 1326.0576498160146 -> 880.2769843236346
4:29:43.852623 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 880.2770.
4:29:43.852698 INFO: ==============================================
4:29:43.852764 INFO: Starting optimization step 2.
4:29:43.852819 PROGRESS: === Extracting elution groups 0 to 600 ===
4:29:43.852873 INFO: Using classic extraction backend
4:29:43.852972 PROGRESS: Extracting batch of 1173 precursors
4:29:43.853034 INFO: === Search parameters used ===
4:29:43.853079 INFO: rt_error       : 880.2769843236346
4:29:43.853122 INFO: mobility_error : 0.1
4:29:43.853162 INFO: num_candidates : 3
4:29:43.853203 INFO: ms1_error      : 15.0
4:29:43.853242 INFO: ms2_error      : 15.0
4:29:43.853282 INFO: fwhm_rt        : 2.7561450004577637
4:29:43.853321 INFO: quant_window   : 3
4:29:43.853360 INFO: ==============================================
4:29:43.854225 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:29:43.854270 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:29:43.854303 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
4:29:43.854324 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.51
4:29:43.854979 INFO: Starting candidate selection
4:29:47.567699 INFO: Starting candidate scoring
4:29:47.791748 INFO: Finished candidate processing
4:29:47.791875 INFO: Collecting candidate features
4:29:47.814797 INFO: Collecting fragment features
4:29:47.820980 INFO: Finished candidate scoring
4:29:47.823915 INFO: performing precursor FDR with 47 features
4:29:47.823967 INFO: Decoy channel: -1
4:29:47.823993 INFO: Competetive: True
4:29:47.827096 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:47.829389 INFO: Using random state 478447 for train-test-split
4:29:47.840904 INFO: Test AUC: 0.525
4:29:47.840972 INFO: Train AUC: 0.513
4:29:47.841000 INFO: AUC difference: 2.28%
4:29:48.056805 INFO: Resetting torch num_threads to 80
4:29:48.057513 PROGRESS: === Extracted 3205 precursors and 33189 fragments ===
4:29:48.057916 INFO: === FDR correction performed with classifier version 3 ===
4:29:48.058501 PROGRESS: ============================= Precursor FDR =============================
4:29:48.058592 PROGRESS: Total precursors accumulated: 586
4:29:48.058651 PROGRESS: Target precursors: 474 (80.89%)
4:29:48.058709 PROGRESS: Decoy precursors: 112 (19.11%)
4:29:48.058754 PROGRESS: 
4:29:48.058805 PROGRESS: Precursor Summary:
4:29:48.059804 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   434; 0.001 FDR:   434
4:29:48.059895 PROGRESS: 
4:29:48.059950 PROGRESS: Protein Summary:
4:29:48.061110 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   428; 0.001 FDR:   428
4:29:48.061199 PROGRESS: =========================================================================
4:29:48.061458 INFO: Target number of precursors reached.
4:29:48.067147 INFO: fragments_df: keeping 2277 of 33189 [sum(precursor_idx_mask)=12938 sum(mass_error_mask)=33189 stop_rank=2277
4:29:48.166346 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:29:48.392415 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:29:48.539694 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:29:48.675878 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:29:48.981108 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:29:48.981523 INFO: Using score_cutoff 30.316460050964356 (fac=0.99, q=1)
4:29:48.981835 INFO: Updating optimization_manager: fwhm_rt             : 2.7561450004577637 -> 2.8010506629943848
4:29:48.981917 INFO: Updating optimization_manager: fwhm_mobility       : 0.005415637046098709 -> 0.005497446749359369
4:29:48.981972 INFO: Updating optimization_manager: score_cutoff        : 30.91276769313812 -> 30.316460050964356
4:29:48.982028 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:48.983121 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:48.984483 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:29:48.985256 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:48.987495 INFO: === checking if optimization conditions were reached ===
4:29:48.987595 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
4:29:48.989346 INFO: Updating optimization_manager: rt_error            : 880.2769843236346 -> 837.743783414305
4:29:48.989446 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 837.7438.
4:29:48.989510 INFO: ==============================================
4:29:48.989581 INFO: Starting optimization step 3.
4:29:48.989637 PROGRESS: === Extracting elution groups 0 to 600 ===
4:29:48.989689 INFO: Using classic extraction backend
4:29:48.989791 PROGRESS: Extracting batch of 1173 precursors
4:29:48.989854 INFO: === Search parameters used ===
4:29:48.989901 INFO: rt_error       : 837.743783414305
4:29:48.989943 INFO: mobility_error : 0.1
4:29:48.989984 INFO: num_candidates : 3
4:29:48.990023 INFO: ms1_error      : 15.0
4:29:48.990072 INFO: ms2_error      : 15.0
4:29:48.990115 INFO: fwhm_rt        : 2.8010506629943848
4:29:48.990155 INFO: quant_window   : 3
4:29:48.990192 INFO: ==============================================
4:29:48.992230 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:29:48.992276 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:29:48.992314 INFO: FWHM in RT is 2.80 seconds, sigma is 0.62
4:29:48.992337 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
4:29:48.993098 INFO: Starting candidate selection
4:29:53.494365 INFO: Starting candidate scoring
4:29:53.703992 INFO: Finished candidate processing
4:29:53.704122 INFO: Collecting candidate features
4:29:53.728421 INFO: Collecting fragment features
4:29:53.737459 INFO: Finished candidate scoring
4:29:53.741319 INFO: performing precursor FDR with 47 features
4:29:53.741423 INFO: Decoy channel: -1
4:29:53.741479 INFO: Competetive: True
4:29:53.749172 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:53.753859 INFO: Using random state 478447 for train-test-split
4:29:53.775913 INFO: Test AUC: 0.503
4:29:53.775995 INFO: Train AUC: 0.510
4:29:53.776036 INFO: AUC difference: 1.46%
4:29:54.015661 INFO: Resetting torch num_threads to 80
4:29:54.016384 PROGRESS: === Extracted 3219 precursors and 33389 fragments ===
4:29:54.017025 INFO: === FDR correction performed with classifier version 3 ===
4:29:54.017664 PROGRESS: ============================= Precursor FDR =============================
4:29:54.017755 PROGRESS: Total precursors accumulated: 586
4:29:54.017812 PROGRESS: Target precursors: 472 (80.55%)
4:29:54.017860 PROGRESS: Decoy precursors: 114 (19.45%)
4:29:54.017905 PROGRESS: 
4:29:54.017947 PROGRESS: Precursor Summary:
4:29:54.018997 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   427; 0.001 FDR:   427
4:29:54.019090 PROGRESS: 
4:29:54.019145 PROGRESS: Protein Summary:
4:29:54.020351 PROGRESS: Channel   0:	 0.050 FDR:   422; 0.010 FDR:   422; 0.001 FDR:   422
4:29:54.020439 PROGRESS: =========================================================================
4:29:54.020697 INFO: Target number of precursors reached.
4:29:54.026741 INFO: fragments_df: keeping 2205 of 33389 [sum(precursor_idx_mask)=12836 sum(mass_error_mask)=33389 stop_rank=2205
4:29:54.127234 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:29:54.242943 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:29:54.359447 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:29:54.475788 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:29:54.726287 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:29:54.726818 INFO: Using score_cutoff 32.03958854141236 (fac=0.99, q=1)
4:29:54.727218 INFO: Updating optimization_manager: fwhm_rt             : 2.8010506629943848 -> 2.7466018199920654
4:29:54.727300 INFO: Updating optimization_manager: fwhm_mobility       : 0.005497446749359369 -> 0.0054687317460775375
4:29:54.727355 INFO: Updating optimization_manager: score_cutoff        : 30.316460050964356 -> 32.03958854141236
4:29:54.727412 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:54.728663 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:54.730025 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:29:54.730815 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:54.732938 INFO: === checking if optimization conditions were reached ===
4:29:54.733039 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
4:29:54.734180 INFO: Updating optimization_manager: rt_error            : 837.743783414305 -> 837.743783414305
4:29:54.734303 INFO: Updating optimization_manager: classifier_version  : 3 -> 7
4:29:54.734396 INFO: Updating optimization_manager: score_cutoff        : 32.03958854141236 -> 32.03958854141236
4:29:54.734482 INFO: Updating optimization_manager: fwhm_rt             : 2.7466018199920654 -> 2.7466018199920654
4:29:54.734573 INFO: Updating optimization_manager: fwhm_mobility       : 0.0054687317460775375 -> 0.0054687317460775375
4:29:54.734660 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 837.7438 found after 4 searches.
4:29:54.734721 INFO: ==============================================
4:29:54.734788 PROGRESS: Optimization finished for rt_error.
4:29:54.834378 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:54.835688 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:54.837054 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:29:54.837820 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:54.867755 INFO: Starting optimization step 0.
4:29:54.867916 PROGRESS: === Extracting elution groups 0 to 600 ===
4:29:54.868002 INFO: Using classic extraction backend
4:29:54.868236 PROGRESS: Extracting batch of 1173 precursors
4:29:54.868322 INFO: === Search parameters used ===
4:29:54.868377 INFO: rt_error       : 837.743783414305
4:29:54.868423 INFO: mobility_error : 0.1
4:29:54.868467 INFO: num_candidates : 3
4:29:54.868510 INFO: ms1_error      : 15.0
4:29:54.868552 INFO: ms2_error      : 15.0
4:29:54.868592 INFO: fwhm_rt        : 2.7466018199920654
4:29:54.868630 INFO: quant_window   : 3
4:29:54.868682 INFO: ==============================================
4:29:54.869726 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:29:54.869771 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:29:54.869813 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
4:29:54.869835 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.54
4:29:54.870527 INFO: Starting candidate selection
4:29:59.388685 INFO: Starting candidate scoring
4:29:59.617111 INFO: Finished candidate processing
4:29:59.617298 INFO: Collecting candidate features
4:29:59.636391 INFO: Collecting fragment features
4:29:59.640364 INFO: Finished candidate scoring
4:29:59.642446 INFO: performing precursor FDR with 47 features
4:29:59.642491 INFO: Decoy channel: -1
4:29:59.642515 INFO: Competetive: True
4:29:59.645492 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:59.647595 INFO: Using random state 502504 for train-test-split
4:29:59.659270 INFO: Test AUC: 0.512
4:29:59.659331 INFO: Train AUC: 0.503
4:29:59.659359 INFO: AUC difference: 1.87%
4:29:59.871579 INFO: Resetting torch num_threads to 80
4:29:59.872122 PROGRESS: === Extracted 3221 precursors and 33438 fragments ===
4:29:59.872525 INFO: === FDR correction performed with classifier version 7 ===
4:29:59.873073 PROGRESS: ============================= Precursor FDR =============================
4:29:59.873162 PROGRESS: Total precursors accumulated: 587
4:29:59.873219 PROGRESS: Target precursors: 459 (78.19%)
4:29:59.873276 PROGRESS: Decoy precursors: 128 (21.81%)
4:29:59.873321 PROGRESS: 
4:29:59.873365 PROGRESS: Precursor Summary:
4:29:59.874361 PROGRESS: Channel   0:	 0.050 FDR:   417; 0.010 FDR:   417; 0.001 FDR:   417
4:29:59.874453 PROGRESS: 
4:29:59.874510 PROGRESS: Protein Summary:
4:29:59.875673 PROGRESS: Channel   0:	 0.050 FDR:   412; 0.010 FDR:   412; 0.001 FDR:   412
4:29:59.875762 PROGRESS: =========================================================================
4:29:59.875899 INFO: Target number of precursors reached.
4:29:59.881481 INFO: fragments_df: keeping 2135 of 33438 [sum(precursor_idx_mask)=12505 sum(mass_error_mask)=33438 stop_rank=2135
4:29:59.980163 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:30:00.097758 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:30:00.223916 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:30:00.341425 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:30:00.582193 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:30:00.582613 INFO: Using score_cutoff 31.111201599884033 (fac=0.99, q=1)
4:30:00.582922 INFO: Updating optimization_manager: fwhm_rt             : 2.7466018199920654 -> 2.7559306621551514
4:30:00.583003 INFO: Updating optimization_manager: fwhm_mobility       : 0.0054687317460775375 -> 0.005464643705636263
4:30:00.583061 INFO: Updating optimization_manager: score_cutoff        : 32.03958854141236 -> 31.111201599884033
4:30:00.583121 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:30:00.584167 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:30:00.585501 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:30:00.586304 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:30:00.588431 INFO: === checking if optimization conditions were reached ===
4:30:00.588539 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
4:30:00.589913 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.09925061851017485
4:30:00.590014 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0993.
4:30:00.590099 INFO: ==============================================
4:30:00.590175 INFO: Starting optimization step 1.
4:30:00.590233 PROGRESS: === Extracting elution groups 0 to 600 ===
4:30:00.590286 INFO: Using classic extraction backend
4:30:00.590387 PROGRESS: Extracting batch of 1173 precursors
4:30:00.590448 INFO: === Search parameters used ===
4:30:00.590505 INFO: rt_error       : 837.743783414305
4:30:00.590548 INFO: mobility_error : 0.09925061851017485
4:30:00.590587 INFO: num_candidates : 3
4:30:00.590626 INFO: ms1_error      : 15.0
4:30:00.590665 INFO: ms2_error      : 15.0
4:30:00.590704 INFO: fwhm_rt        : 2.7559306621551514
4:30:00.590748 INFO: quant_window   : 3
4:30:00.590794 INFO: ==============================================
4:30:00.591647 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:30:00.591691 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:30:00.591722 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
4:30:00.591744 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
4:30:00.592377 INFO: Starting candidate selection
4:30:05.221052 INFO: Starting candidate scoring
4:30:05.415707 INFO: Finished candidate processing
4:30:05.415871 INFO: Collecting candidate features
4:30:05.429155 INFO: Collecting fragment features
4:30:05.432847 INFO: Finished candidate scoring
4:30:05.434718 INFO: performing precursor FDR with 47 features
4:30:05.434761 INFO: Decoy channel: -1
4:30:05.434784 INFO: Competetive: True
4:30:05.437582 INFO: Setting torch num_threads to 2 for FDR classification task
4:30:05.439614 INFO: Using random state 502504 for train-test-split
4:30:05.450372 INFO: Test AUC: 0.497
4:30:05.450435 INFO: Train AUC: 0.514
4:30:05.450464 INFO: AUC difference: 3.39%
4:30:05.663323 INFO: Resetting torch num_threads to 80
4:30:05.663898 PROGRESS: === Extracted 3231 precursors and 33587 fragments ===
4:30:05.664296 INFO: === FDR correction performed with classifier version 7 ===
4:30:05.664853 PROGRESS: ============================= Precursor FDR =============================
4:30:05.664937 PROGRESS: Total precursors accumulated: 587
4:30:05.664993 PROGRESS: Target precursors: 471 (80.24%)
4:30:05.665043 PROGRESS: Decoy precursors: 116 (19.76%)
4:30:05.665086 PROGRESS: 
4:30:05.665128 PROGRESS: Precursor Summary:
4:30:05.666108 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   432; 0.001 FDR:   432
4:30:05.666196 PROGRESS: 
4:30:05.666250 PROGRESS: Protein Summary:
4:30:05.667397 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   428; 0.001 FDR:   428
4:30:05.667484 PROGRESS: =========================================================================
4:30:05.667616 INFO: Target number of precursors reached.
4:30:05.673328 INFO: fragments_df: keeping 2187 of 33587 [sum(precursor_idx_mask)=12947 sum(mass_error_mask)=33587 stop_rank=2187
4:30:05.772877 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:30:05.885025 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:30:05.997192 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:30:06.109781 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:30:06.357950 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:30:06.358372 INFO: Using score_cutoff 30.790015117836 (fac=0.99, q=1)
4:30:06.358673 INFO: Updating optimization_manager: fwhm_rt             : 2.7559306621551514 -> 2.80239200592041
4:30:06.358751 INFO: Updating optimization_manager: fwhm_mobility       : 0.005464643705636263 -> 0.005483257584273815
4:30:06.358803 INFO: Updating optimization_manager: score_cutoff        : 31.111201599884033 -> 30.790015117836
4:30:06.358855 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:30:06.359902 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:30:06.361212 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:30:06.361977 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:30:06.364122 INFO: === checking if optimization conditions were reached ===
4:30:06.364224 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
4:30:06.365628 INFO: Updating optimization_manager: mobility_error      : 0.09925061851017485 -> 0.1000518951425358
4:30:06.365731 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.1001.
4:30:06.365808 INFO: ==============================================
4:30:06.365873 INFO: Starting optimization step 2.
4:30:06.365929 PROGRESS: === Extracting elution groups 0 to 600 ===
4:30:06.365983 INFO: Using classic extraction backend
4:30:06.366097 PROGRESS: Extracting batch of 1173 precursors
4:30:06.366163 INFO: === Search parameters used ===
4:30:06.366215 INFO: rt_error       : 837.743783414305
4:30:06.366260 INFO: mobility_error : 0.1000518951425358
4:30:06.366306 INFO: num_candidates : 3
4:30:06.366346 INFO: ms1_error      : 15.0
4:30:06.366385 INFO: ms2_error      : 15.0
4:30:06.366423 INFO: fwhm_rt        : 2.80239200592041
4:30:06.366461 INFO: quant_window   : 3
4:30:06.366498 INFO: ==============================================
4:30:06.367331 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:30:06.367374 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:30:06.367410 INFO: FWHM in RT is 2.80 seconds, sigma is 0.62
4:30:06.367431 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.54
4:30:06.368081 INFO: Starting candidate selection
4:30:10.862302 INFO: Starting candidate scoring
4:30:11.057960 INFO: Finished candidate processing
4:30:11.058108 INFO: Collecting candidate features
4:30:11.071997 INFO: Collecting fragment features
4:30:11.075838 INFO: Finished candidate scoring
4:30:11.077685 INFO: performing precursor FDR with 47 features
4:30:11.077728 INFO: Decoy channel: -1
4:30:11.077751 INFO: Competetive: True
4:30:11.080713 INFO: Setting torch num_threads to 2 for FDR classification task
4:30:11.083048 INFO: Using random state 502504 for train-test-split
4:30:11.093880 INFO: Test AUC: 0.486
4:30:11.093931 INFO: Train AUC: 0.517
4:30:11.093960 INFO: AUC difference: 5.94%
4:30:11.093982 WARNING: AUC difference > 5%. This may indicate overfitting.
4:30:11.305766 INFO: Resetting torch num_threads to 80
4:30:11.306353 PROGRESS: === Extracted 3219 precursors and 33386 fragments ===
4:30:11.306743 INFO: === FDR correction performed with classifier version 7 ===
4:30:11.307330 PROGRESS: ============================= Precursor FDR =============================
4:30:11.307416 PROGRESS: Total precursors accumulated: 587
4:30:11.307473 PROGRESS: Target precursors: 474 (80.75%)
4:30:11.307523 PROGRESS: Decoy precursors: 113 (19.25%)
4:30:11.307566 PROGRESS: 
4:30:11.307607 PROGRESS: Precursor Summary:
4:30:11.308573 PROGRESS: Channel   0:	 0.050 FDR:   437; 0.010 FDR:   437; 0.001 FDR:   437
4:30:11.308660 PROGRESS: 
4:30:11.308715 PROGRESS: Protein Summary:
4:30:11.309851 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   432; 0.001 FDR:   432
4:30:11.309936 PROGRESS: =========================================================================
4:30:11.310099 INFO: Target number of precursors reached.
4:30:11.315769 INFO: fragments_df: keeping 2219 of 33386 [sum(precursor_idx_mask)=13063 sum(mass_error_mask)=33386 stop_rank=2219
4:30:11.414431 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:30:11.541031 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:30:11.668876 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:30:11.782213 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:30:12.027997 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:30:12.028406 INFO: Using score_cutoff 30.79293667602539 (fac=0.99, q=1)
4:30:12.028698 INFO: Updating optimization_manager: fwhm_rt             : 2.80239200592041 -> 2.802138090133667
4:30:12.028775 INFO: Updating optimization_manager: fwhm_mobility       : 0.005483257584273815 -> 0.005485893227159977
4:30:12.028827 INFO: Updating optimization_manager: score_cutoff        : 30.790015117836 -> 30.79293667602539
4:30:12.028877 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:30:12.029909 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:30:12.031282 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:30:12.032046 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:30:12.034135 INFO: === checking if optimization conditions were reached ===
4:30:12.034245 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
4:30:12.034897 INFO: Updating optimization_manager: mobility_error      : 0.1000518951425358 -> 0.1000518951425358
4:30:12.035022 INFO: Updating optimization_manager: classifier_version  : 7 -> 10
4:30:12.035113 INFO: Updating optimization_manager: score_cutoff        : 30.79293667602539 -> 30.79293667602539
4:30:12.035195 INFO: Updating optimization_manager: fwhm_rt             : 2.802138090133667 -> 2.802138090133667
4:30:12.035275 INFO: Updating optimization_manager: fwhm_mobility       : 0.005485893227159977 -> 0.005485893227159977
4:30:12.035354 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1001 found after 3 searches.
4:30:12.035412 INFO: ==============================================
4:30:12.035474 PROGRESS: Optimization finished for mobility_error.
4:30:12.134908 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:30:12.136037 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:30:12.137340 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:30:12.138117 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:30:12.164407 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
4:30:12.164544 PROGRESS: ==============================================
4:30:12.164610 PROGRESS: ms2_error      : 15.0000
4:30:12.164671 PROGRESS: ms1_error      : 15.0000
4:30:12.164722 PROGRESS: rt_error       : 837.7438
4:30:12.164768 PROGRESS: mobility_error : 0.1001
4:30:12.164810 PROGRESS: ==============================================
4:30:12.165354 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:30:13.678258 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:30:20.877650 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:30:22.412585 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:30:39.173103 INFO: Using classic extraction backend
4:30:39.173727 PROGRESS: Extracting batch of 12073114 precursors
4:30:39.173858 INFO: === Search parameters used ===
4:30:39.173918 INFO: rt_error       : 837.743783414305
4:30:39.173967 INFO: mobility_error : 0.1000518951425358
4:30:39.174014 INFO: num_candidates : 3
4:30:39.174070 INFO: ms1_error      : 15.0
4:30:39.174120 INFO: ms2_error      : 15.0
4:30:39.174165 INFO: fwhm_rt        : 2.802138090133667
4:30:39.174206 INFO: quant_window   : 3
4:30:39.174248 INFO: ==============================================
4:30:41.890536 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:30:41.890662 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:30:41.890715 INFO: FWHM in RT is 2.80 seconds, sigma is 0.62
4:30:41.890738 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.54
4:30:41.891879 INFO: Starting candidate selection
13:52:24.147600 INFO: Removed 1647684 precursors with score below cutoff 30.79293667602539
13:52:26.867744 INFO: Starting candidate scoring
14:12:16.024112 INFO: Finished candidate processing
14:12:16.024370 INFO: Collecting candidate features
14:14:54.441763 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 32190553)
14:14:55.958335 INFO: Collecting fragment features
14:15:49.928876 INFO: Finished candidate scoring
14:16:20.532373 INFO: === Performing FDR correction with classifier version 10 ===
14:16:20.538329 INFO: performing precursor FDR with 47 features
14:16:20.538381 INFO: Decoy channel: -1
14:16:20.538407 INFO: Competetive: True
14:16:28.119774 INFO: Setting torch num_threads to 2 for FDR classification task
14:16:32.772445 WARNING: dropped 3 target PSMs due to missing features
14:16:32.772573 WARNING: dropped 1 decoy PSMs due to missing features
14:16:47.230984 INFO: Using random state 811487 for train-test-split
14:28:44.911675 INFO: Test AUC: 0.577
14:28:44.912128 INFO: Train AUC: 0.577
14:28:44.912189 INFO: AUC difference: 0.08%
14:28:50.996196 INFO: Resetting torch num_threads to 80
14:28:51.413490 INFO: Removing fragments below FDR threshold
14:28:54.073355 PROGRESS: ============================= Precursor FDR =============================
14:28:54.073602 PROGRESS: Total precursors accumulated: 52,604
14:28:54.073669 PROGRESS: Target precursors: 52,084 (99.01%)
14:28:54.073722 PROGRESS: Decoy precursors: 520 (0.99%)
14:28:54.073783 PROGRESS: 
14:28:54.073830 PROGRESS: Precursor Summary:
14:28:54.090467 PROGRESS: Channel   0:	 0.050 FDR: 52,084; 0.010 FDR: 52,084; 0.001 FDR: 34,023
14:28:54.090705 PROGRESS: 
14:28:54.090765 PROGRESS: Protein Summary:
14:28:54.114008 PROGRESS: Channel   0:	 0.050 FDR: 9,273; 0.010 FDR: 9,273; 0.001 FDR: 7,169
14:28:54.114228 PROGRESS: =========================================================================
14:28:54.548004 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/psm.parquet
14:28:54.867495 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/frag.parquet
14:28:55.081581 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
14:28:55.580077 PROGRESS: 
14:28:55.580229 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant
14:28:55.580303 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/figures
14:28:55.580473 INFO: Initializing TimingManager
14:28:55.580921 INFO: Initializing RawFileManager
14:28:55.581030 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:28:55.581292 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:28:55.581340 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:28:55.902168 INFO: Reading 39,128 frames with 2,751,035,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:29:05.783886 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
14:29:05.792804 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:29:05.794932 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:29:05.795281 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:29:05.795614 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:29:05.796997 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:29:05.811754 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:29:05.812088 INFO: Indexing quadrupole dimension
14:29:06.283681 INFO: Transposing detector events
14:29:14.703069 INFO: Finished transposing data
14:29:14.739711 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
14:29:14.740406 INFO: RT (min)            : 0.0 - 70.0
14:29:14.740505 INFO: RT duration (sec)   : 4199.8
14:29:14.740562 INFO: RT duration (min)   : 70.0
14:29:14.740610 INFO: Cycle len (scans)   : 9
14:29:14.740656 INFO: Cycle len (sec)     : 0.97
14:29:14.740699 INFO: Number of cycles    : 4347
14:29:14.740744 INFO: MS2 range (m/z)     : 400.0 - 1000.0
14:29:14.740800 INFO: Creating DIA data object took: 19.159782886505127
14:29:15.907925 INFO: Initializing CalibrationManager
14:29:15.908214 INFO: Setting up calibration estimators ..
14:29:15.908274 INFO: Found 1 estimator(s) in calibration group 'fragment'
14:29:15.908351 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'}' ..
14:29:15.908430 INFO: Found 3 estimator(s) in calibration group 'precursor'
14:29:15.908497 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'}' ..
14:29:15.908552 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}}' ..
14:29:15.908610 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}}' ..
14:29:15.908656 INFO: Done setting up calibration estimators.
14:29:15.908765 INFO: Initializing OptimizationManager
14:29:15.908855 INFO: initial parameter: ms1_error = 30
14:29:15.908901 INFO: initial parameter: ms2_error = 30
14:29:15.908943 INFO: initial parameter: rt_error = 2099.891532
14:29:15.908985 INFO: initial parameter: mobility_error = 0.1
14:29:15.909027 INFO: initial parameter: num_candidates = 1
14:29:15.909065 INFO: initial parameter: fwhm_rt = 5
14:29:15.909106 INFO: initial parameter: fwhm_mobility = 0.01
14:29:15.909147 INFO: initial parameter: score_cutoff = 0
14:29:15.909184 INFO: initial parameter: classifier_version = -1
14:29:15.909249 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
14:29:15.909468 INFO: FDRManager: loading saved state not requested, will be initialized.
14:29:15.909499 INFO: Initializing FDRManager
14:29:15.909533 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
14:29:17.142608 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
14:29:17.931214 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
14:29:17.931623 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 2099.891532
14:29:17.931727 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
14:29:17.931901 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
14:29:17.931991 PROGRESS: Starting initial search for precursors.
14:29:17.932071 INFO: Starting optimization step 0.
14:29:17.932132 PROGRESS: === Extracting elution groups 0 to 200 ===
14:29:17.932207 INFO: Using classic extraction backend
14:29:17.932422 PROGRESS: Extracting batch of 390 precursors
14:29:17.932496 INFO: === Search parameters used ===
14:29:17.932547 INFO: rt_error       : 2099.891532
14:29:17.932589 INFO: mobility_error : 0.1
14:29:17.932631 INFO: num_candidates : 1
14:29:17.932670 INFO: ms1_error      : 30
14:29:17.932709 INFO: ms2_error      : 30
14:29:17.932747 INFO: fwhm_rt        : 5
14:29:17.932786 INFO: quant_window   : 3
14:29:17.932827 INFO: ==============================================
14:29:17.933536 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:29:17.933579 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:29:17.933618 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
14:29:17.933639 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
14:29:17.934885 INFO: Starting candidate selection
14:29:21.653547 INFO: Starting candidate scoring
14:29:21.723113 INFO: Finished candidate processing
14:29:21.723207 INFO: Collecting candidate features
14:29:21.732523 INFO: Collecting fragment features
14:29:21.734755 INFO: Finished candidate scoring
14:29:21.735430 INFO: performing precursor FDR with 47 features
14:29:21.735474 INFO: Decoy channel: -1
14:29:21.735498 INFO: Competetive: True
14:29:21.736703 INFO: Setting torch num_threads to 2 for FDR classification task
14:29:21.739319 INFO: Using random state 805290 for train-test-split
14:29:21.747111 INFO: Test AUC: 0.443
14:29:21.747167 INFO: Train AUC: 0.503
14:29:21.747196 INFO: AUC difference: 11.89%
14:29:21.747219 WARNING: AUC difference > 5%. This may indicate overfitting.
14:29:21.958674 INFO: Resetting torch num_threads to 80
14:29:21.959105 PROGRESS: === Extracted 364 precursors and 3956 fragments ===
14:29:21.959516 INFO: === FDR correction performed with classifier version -1 ===
14:29:21.960041 PROGRESS: ============================= Precursor FDR =============================
14:29:21.960127 PROGRESS: Total precursors accumulated: 187
14:29:21.960184 PROGRESS: Target precursors: 147 (78.61%)
14:29:21.960233 PROGRESS: Decoy precursors: 40 (21.39%)
14:29:21.960276 PROGRESS: 
14:29:21.960319 PROGRESS: Precursor Summary:
14:29:21.961147 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
14:29:21.961232 PROGRESS: 
14:29:21.961293 PROGRESS: Protein Summary:
14:29:21.962227 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
14:29:21.962315 PROGRESS: =========================================================================
14:29:21.962415 INFO: Target number of precursors not reached yet.
14:29:22.027494 INFO: Starting optimization step 1.
14:29:22.027681 PROGRESS: === Extracting elution groups 200 to 600 ===
14:29:22.027755 INFO: Using classic extraction backend
14:29:22.027872 PROGRESS: Extracting batch of 783 precursors
14:29:22.027942 INFO: === Search parameters used ===
14:29:22.027989 INFO: rt_error       : 2099.891532
14:29:22.028033 INFO: mobility_error : 0.1
14:29:22.028076 INFO: num_candidates : 1
14:29:22.028115 INFO: ms1_error      : 30
14:29:22.028155 INFO: ms2_error      : 30
14:29:22.028192 INFO: fwhm_rt        : 5
14:29:22.028230 INFO: quant_window   : 3
14:29:22.028269 INFO: ==============================================
14:29:22.028898 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:29:22.028943 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:29:22.028973 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
14:29:22.028994 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
14:29:22.031067 INFO: Starting candidate selection
14:29:28.784465 INFO: Starting candidate scoring
14:29:28.899602 INFO: Finished candidate processing
14:29:28.899696 INFO: Collecting candidate features
14:29:28.908757 INFO: Collecting fragment features
14:29:28.911042 INFO: Finished candidate scoring
14:29:28.912854 INFO: performing precursor FDR with 47 features
14:29:28.912900 INFO: Decoy channel: -1
14:29:28.912924 INFO: Competetive: True
14:29:28.915575 INFO: Setting torch num_threads to 2 for FDR classification task
14:29:28.917203 INFO: Using random state 979512 for train-test-split
14:29:28.924682 INFO: Test AUC: 0.537
14:29:28.924734 INFO: Train AUC: 0.484
14:29:28.924763 INFO: AUC difference: 11.06%
14:29:28.924785 WARNING: AUC difference > 5%. This may indicate overfitting.
14:29:29.127483 INFO: Resetting torch num_threads to 80
14:29:29.128697 PROGRESS: === Extracted 1117 precursors and 12152 fragments ===
14:29:29.129083 INFO: === FDR correction performed with classifier version -1 ===
14:29:29.129664 PROGRESS: ============================= Precursor FDR =============================
14:29:29.129752 PROGRESS: Total precursors accumulated: 575
14:29:29.129812 PROGRESS: Target precursors: 436 (75.83%)
14:29:29.129870 PROGRESS: Decoy precursors: 139 (24.17%)
14:29:29.129919 PROGRESS: 
14:29:29.129961 PROGRESS: Precursor Summary:
14:29:29.131271 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
14:29:29.131487 PROGRESS: 
14:29:29.131547 PROGRESS: Protein Summary:
14:29:29.132539 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
14:29:29.132628 PROGRESS: =========================================================================
14:29:29.132807 INFO: Target number of precursors not reached yet.
14:29:29.200295 INFO: Starting optimization step 2.
14:29:29.200490 PROGRESS: === Extracting elution groups 600 to 1400 ===
14:29:29.200567 INFO: Using classic extraction backend
14:29:29.200680 PROGRESS: Extracting batch of 1576 precursors
14:29:29.200749 INFO: === Search parameters used ===
14:29:29.200798 INFO: rt_error       : 2099.891532
14:29:29.200856 INFO: mobility_error : 0.1
14:29:29.200918 INFO: num_candidates : 1
14:29:29.200967 INFO: ms1_error      : 30
14:29:29.201025 INFO: ms2_error      : 30
14:29:29.201097 INFO: fwhm_rt        : 5
14:29:29.201156 INFO: quant_window   : 3
14:29:29.201213 INFO: ==============================================
14:29:29.201980 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:29:29.202028 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:29:29.202067 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
14:29:29.202090 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
14:29:29.207856 INFO: Starting candidate selection
14:29:41.534486 INFO: Starting candidate scoring
14:29:41.698677 INFO: Finished candidate processing
14:29:41.698773 INFO: Collecting candidate features
14:29:41.709190 INFO: Collecting fragment features
14:29:41.712449 INFO: Finished candidate scoring
14:29:41.715006 INFO: performing precursor FDR with 47 features
14:29:41.715053 INFO: Decoy channel: -1
14:29:41.715078 INFO: Competetive: True
14:29:41.718722 INFO: Setting torch num_threads to 2 for FDR classification task
14:29:41.720686 INFO: Using random state 712888 for train-test-split
14:29:41.731247 INFO: Test AUC: 0.541
14:29:41.731309 INFO: Train AUC: 0.484
14:29:41.731337 INFO: AUC difference: 11.76%
14:29:41.731358 WARNING: AUC difference > 5%. This may indicate overfitting.
14:29:41.940190 INFO: Resetting torch num_threads to 80
14:29:41.941818 PROGRESS: === Extracted 2639 precursors and 28566 fragments ===
14:29:41.942222 INFO: === FDR correction performed with classifier version -1 ===
14:29:41.942889 PROGRESS: ============================= Precursor FDR =============================
14:29:41.942978 PROGRESS: Total precursors accumulated: 1,354
14:29:41.943037 PROGRESS: Target precursors: 1,028 (75.92%)
14:29:41.943085 PROGRESS: Decoy precursors: 326 (24.08%)
14:29:41.943129 PROGRESS: 
14:29:41.943170 PROGRESS: Precursor Summary:
14:29:41.944026 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
14:29:41.944113 PROGRESS: 
14:29:41.944168 PROGRESS: Protein Summary:
14:29:41.945101 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
14:29:41.945189 PROGRESS: =========================================================================
14:29:41.945334 INFO: Target number of precursors not reached yet.
14:29:42.014975 INFO: Starting optimization step 3.
14:29:42.015176 PROGRESS: === Extracting elution groups 1400 to 3000 ===
14:29:42.015250 INFO: Using classic extraction backend
14:29:42.015363 PROGRESS: Extracting batch of 3162 precursors
14:29:42.015433 INFO: === Search parameters used ===
14:29:42.015480 INFO: rt_error       : 2099.891532
14:29:42.015522 INFO: mobility_error : 0.1
14:29:42.015577 INFO: num_candidates : 1
14:29:42.015621 INFO: ms1_error      : 30
14:29:42.015662 INFO: ms2_error      : 30
14:29:42.015702 INFO: fwhm_rt        : 5
14:29:42.015741 INFO: quant_window   : 3
14:29:42.015780 INFO: ==============================================
14:29:42.016738 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:29:42.016783 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:29:42.016811 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
14:29:42.016830 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
14:29:42.017637 INFO: Starting candidate selection
14:30:04.720011 INFO: Starting candidate scoring
14:30:05.015871 INFO: Finished candidate processing
14:30:05.015997 INFO: Collecting candidate features
14:30:05.028903 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3028)
14:30:05.032167 INFO: Collecting fragment features
14:30:05.037048 INFO: Finished candidate scoring
14:30:05.041800 INFO: performing precursor FDR with 47 features
14:30:05.041855 INFO: Decoy channel: -1
14:30:05.041879 INFO: Competetive: True
14:30:05.046510 INFO: Setting torch num_threads to 2 for FDR classification task
14:30:05.048244 WARNING: dropped 1 decoy PSMs due to missing features
14:30:05.049642 INFO: Using random state 335174 for train-test-split
14:30:05.069048 INFO: Test AUC: 0.472
14:30:05.069153 INFO: Train AUC: 0.504
14:30:05.069184 INFO: AUC difference: 6.37%
14:30:05.069207 WARNING: AUC difference > 5%. This may indicate overfitting.
14:30:05.277584 INFO: Resetting torch num_threads to 80
14:30:05.280310 PROGRESS: === Extracted 5667 precursors and 61145 fragments ===
14:30:05.280814 INFO: === FDR correction performed with classifier version -1 ===
14:30:05.281747 PROGRESS: ============================= Precursor FDR =============================
14:30:05.281847 PROGRESS: Total precursors accumulated: 2,900
14:30:05.281909 PROGRESS: Target precursors: 2,161 (74.52%)
14:30:05.281958 PROGRESS: Decoy precursors: 739 (25.48%)
14:30:05.282004 PROGRESS: 
14:30:05.282057 PROGRESS: Precursor Summary:
14:30:05.282937 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
14:30:05.283026 PROGRESS: 
14:30:05.283082 PROGRESS: Protein Summary:
14:30:05.284889 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
14:30:05.285043 PROGRESS: =========================================================================
14:30:05.285375 INFO: Target number of precursors not reached yet.
14:30:05.382123 INFO: Starting optimization step 4.
14:30:05.382343 PROGRESS: === Extracting elution groups 3000 to 6200 ===
14:30:05.382422 INFO: Using classic extraction backend
14:30:05.382541 PROGRESS: Extracting batch of 6312 precursors
14:30:05.382612 INFO: === Search parameters used ===
14:30:05.382660 INFO: rt_error       : 2099.891532
14:30:05.382705 INFO: mobility_error : 0.1
14:30:05.382749 INFO: num_candidates : 1
14:30:05.382790 INFO: ms1_error      : 30
14:30:05.382830 INFO: ms2_error      : 30
14:30:05.382870 INFO: fwhm_rt        : 5
14:30:05.382910 INFO: quant_window   : 3
14:30:05.382950 INFO: ==============================================
14:30:05.384367 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:30:05.384416 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:30:05.384444 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
14:30:05.384466 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
14:30:05.385238 INFO: Starting candidate selection
14:30:49.601263 INFO: Starting candidate scoring
14:30:50.126058 INFO: Finished candidate processing
14:30:50.126161 INFO: Collecting candidate features
14:30:50.145281 INFO: Collecting fragment features
14:30:50.151754 INFO: Finished candidate scoring
14:30:50.168460 INFO: performing precursor FDR with 47 features
14:30:50.168534 INFO: Decoy channel: -1
14:30:50.168559 INFO: Competetive: True
14:30:50.175393 INFO: Setting torch num_threads to 2 for FDR classification task
14:30:50.177979 WARNING: dropped 1 decoy PSMs due to missing features
14:30:50.180187 INFO: Using random state 50981 for train-test-split
14:30:50.218929 INFO: Test AUC: 0.488
14:30:50.219021 INFO: Train AUC: 0.495
14:30:50.219054 INFO: AUC difference: 1.27%
14:30:50.438124 INFO: Resetting torch num_threads to 80
14:30:50.441624 PROGRESS: === Extracted 11688 precursors and 125854 fragments ===
14:30:50.442134 INFO: === FDR correction performed with classifier version -1 ===
14:30:50.443324 PROGRESS: ============================= Precursor FDR =============================
14:30:50.443419 PROGRESS: Total precursors accumulated: 5,980
14:30:50.443478 PROGRESS: Target precursors: 4,423 (73.96%)
14:30:50.443529 PROGRESS: Decoy precursors: 1,557 (26.04%)
14:30:50.443572 PROGRESS: 
14:30:50.443615 PROGRESS: Precursor Summary:
14:30:50.444510 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
14:30:50.444597 PROGRESS: 
14:30:50.444660 PROGRESS: Protein Summary:
14:30:50.445601 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
14:30:50.445688 PROGRESS: =========================================================================
14:30:50.445986 INFO: Target number of precursors not reached yet.
14:30:50.573349 INFO: Starting optimization step 5.
14:30:50.573568 PROGRESS: === Extracting elution groups 6200 to 12600 ===
14:30:50.573677 INFO: Using classic extraction backend
14:30:50.573841 PROGRESS: Extracting batch of 12615 precursors
14:30:50.573917 INFO: === Search parameters used ===
14:30:50.573970 INFO: rt_error       : 2099.891532
14:30:50.574012 INFO: mobility_error : 0.1
14:30:50.574062 INFO: num_candidates : 1
14:30:50.574105 INFO: ms1_error      : 30
14:30:50.574143 INFO: ms2_error      : 30
14:30:50.574181 INFO: fwhm_rt        : 5
14:30:50.574219 INFO: quant_window   : 3
14:30:50.574255 INFO: ==============================================
14:30:50.576991 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:30:50.577040 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:30:50.577078 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
14:30:50.577100 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
14:30:50.577993 INFO: Starting candidate selection
14:32:13.804820 INFO: Starting candidate scoring
14:32:14.733213 INFO: Finished candidate processing
14:32:14.733382 INFO: Collecting candidate features
14:32:14.789131 WARNING: intensity_correlation has 2 NaNs ( 0.02 % out of 12022)
14:32:14.796785 INFO: Collecting fragment features
14:32:14.813356 INFO: Finished candidate scoring
14:32:14.846843 INFO: performing precursor FDR with 47 features
14:32:14.846961 INFO: Decoy channel: -1
14:32:14.846987 INFO: Competetive: True
14:32:14.859302 INFO: Setting torch num_threads to 2 for FDR classification task
14:32:14.864127 WARNING: dropped 1 target PSMs due to missing features
14:32:14.864217 WARNING: dropped 2 decoy PSMs due to missing features
14:32:14.867792 INFO: Using random state 839457 for train-test-split
14:32:15.142936 INFO: Test AUC: 0.526
14:32:15.143045 INFO: Train AUC: 0.522
14:32:15.143076 INFO: AUC difference: 0.89%
14:32:15.370727 INFO: Resetting torch num_threads to 80
14:32:15.376657 PROGRESS: === Extracted 23710 precursors and 255247 fragments ===
14:32:15.377306 INFO: === FDR correction performed with classifier version -1 ===
14:32:15.379556 PROGRESS: ============================= Precursor FDR =============================
14:32:15.379660 PROGRESS: Total precursors accumulated: 12,141
14:32:15.379732 PROGRESS: Target precursors: 6,498 (53.52%)
14:32:15.379783 PROGRESS: Decoy precursors: 5,643 (46.48%)
14:32:15.379827 PROGRESS: 
14:32:15.379871 PROGRESS: Precursor Summary:
14:32:15.380803 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
14:32:15.380890 PROGRESS: 
14:32:15.380944 PROGRESS: Protein Summary:
14:32:15.381897 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
14:32:15.381980 PROGRESS: =========================================================================
14:32:15.382422 INFO: Target number of precursors not reached yet.
14:32:15.579866 INFO: Starting optimization step 6.
14:32:15.580134 PROGRESS: === Extracting elution groups 12600 to 25400 ===
14:32:15.580233 INFO: Using classic extraction backend
14:32:15.580407 PROGRESS: Extracting batch of 25223 precursors
14:32:15.580485 INFO: === Search parameters used ===
14:32:15.580536 INFO: rt_error       : 2099.891532
14:32:15.580580 INFO: mobility_error : 0.1
14:32:15.580622 INFO: num_candidates : 1
14:32:15.580664 INFO: ms1_error      : 30
14:32:15.580708 INFO: ms2_error      : 30
14:32:15.580748 INFO: fwhm_rt        : 5
14:32:15.580790 INFO: quant_window   : 3
14:32:15.580841 INFO: ==============================================
14:32:15.591093 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:32:15.591166 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:32:15.591207 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
14:32:15.591231 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
14:32:15.594667 INFO: Starting candidate selection
14:35:06.362381 INFO: Starting candidate scoring
14:35:07.858179 INFO: Finished candidate processing
14:35:07.858367 INFO: Collecting candidate features
14:35:07.908472 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 24108)
14:35:07.912405 INFO: Collecting fragment features
14:35:07.930377 INFO: Finished candidate scoring
14:35:08.004565 INFO: performing precursor FDR with 47 features
14:35:08.004705 INFO: Decoy channel: -1
14:35:08.004730 INFO: Competetive: True
14:35:08.027638 INFO: Setting torch num_threads to 2 for FDR classification task
14:35:08.038491 WARNING: dropped 4 target PSMs due to missing features
14:35:08.038625 WARNING: dropped 4 decoy PSMs due to missing features
14:35:08.045716 INFO: Using random state 133356 for train-test-split
14:35:08.782621 INFO: Test AUC: 0.539
14:35:08.782749 INFO: Train AUC: 0.551
14:35:08.782789 INFO: AUC difference: 2.10%
14:35:10.118272 INFO: Resetting torch num_threads to 80
14:35:10.129035 PROGRESS: === Extracted 47818 precursors and 514275 fragments ===
14:35:10.129768 INFO: === FDR correction performed with classifier version -1 ===
14:35:10.135565 PROGRESS: ============================= Precursor FDR =============================
14:35:10.135699 PROGRESS: Total precursors accumulated: 24,492
14:35:10.135760 PROGRESS: Target precursors: 13,974 (57.06%)
14:35:10.135812 PROGRESS: Decoy precursors: 10,518 (42.94%)
14:35:10.135857 PROGRESS: 
14:35:10.135900 PROGRESS: Precursor Summary:
14:35:10.136999 PROGRESS: Channel   0:	 0.050 FDR:    45; 0.010 FDR:    29; 0.001 FDR:    29
14:35:10.137090 PROGRESS: 
14:35:10.137146 PROGRESS: Protein Summary:
14:35:10.138234 PROGRESS: Channel   0:	 0.050 FDR:    45; 0.010 FDR:    29; 0.001 FDR:    29
14:35:10.138324 PROGRESS: =========================================================================
14:35:10.138835 INFO: Target number of precursors not reached yet.
14:35:10.413328 INFO: Starting optimization step 7.
14:35:10.413611 PROGRESS: === Extracting elution groups 25400 to 51000 ===
14:35:10.413694 INFO: Using classic extraction backend
14:35:10.413842 PROGRESS: Extracting batch of 50469 precursors
14:35:10.413919 INFO: === Search parameters used ===
14:35:10.413967 INFO: rt_error       : 2099.891532
14:35:10.414023 INFO: mobility_error : 0.1
14:35:10.414076 INFO: num_candidates : 1
14:35:10.414118 INFO: ms1_error      : 30
14:35:10.414156 INFO: ms2_error      : 30
14:35:10.414194 INFO: fwhm_rt        : 5
14:35:10.414231 INFO: quant_window   : 3
14:35:10.414268 INFO: ==============================================
14:35:10.428996 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:35:10.429125 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:35:10.429162 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
14:35:10.429186 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
14:35:10.430076 INFO: Starting candidate selection
14:40:30.454465 INFO: Starting candidate scoring
14:40:34.140922 INFO: Finished candidate processing
14:40:34.141073 INFO: Collecting candidate features
14:40:34.237681 WARNING: intensity_correlation has 7 NaNs ( 0.01 % out of 48154)
14:40:34.244684 INFO: Collecting fragment features
14:40:34.281901 INFO: Finished candidate scoring
14:40:34.441436 INFO: performing precursor FDR with 47 features
14:40:34.441598 INFO: Decoy channel: -1
14:40:34.441625 INFO: Competetive: True
14:40:34.491765 INFO: Setting torch num_threads to 2 for FDR classification task
14:40:34.513828 WARNING: dropped 9 target PSMs due to missing features
14:40:34.513990 WARNING: dropped 6 decoy PSMs due to missing features
14:40:34.531312 INFO: Using random state 822932 for train-test-split
14:40:36.322748 INFO: Test AUC: 0.552
14:40:36.322860 INFO: Train AUC: 0.572
14:40:36.322894 INFO: AUC difference: 3.55%
14:40:36.578561 INFO: Resetting torch num_threads to 80
14:40:36.600869 PROGRESS: === Extracted 95972 precursors and 1031772 fragments ===
14:40:36.601649 INFO: === FDR correction performed with classifier version -1 ===
14:40:36.613384 PROGRESS: ============================= Precursor FDR =============================
14:40:36.613559 PROGRESS: Total precursors accumulated: 49,180
14:40:36.613624 PROGRESS: Target precursors: 29,253 (59.48%)
14:40:36.613674 PROGRESS: Decoy precursors: 19,927 (40.52%)
14:40:36.613719 PROGRESS: 
14:40:36.613761 PROGRESS: Precursor Summary:
14:40:36.615036 PROGRESS: Channel   0:	 0.050 FDR:   255; 0.010 FDR:     0; 0.001 FDR:     0
14:40:36.615146 PROGRESS: 
14:40:36.615202 PROGRESS: Protein Summary:
14:40:36.616440 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:     0; 0.001 FDR:     0
14:40:36.616536 PROGRESS: =========================================================================
14:40:36.617639 INFO: Target number of precursors not reached yet.
14:40:37.009835 INFO: Starting optimization step 8.
14:40:37.010114 PROGRESS: === Extracting elution groups 51000 to 102200 ===
14:40:37.010212 INFO: Using classic extraction backend
14:40:37.010382 PROGRESS: Extracting batch of 100931 precursors
14:40:37.010461 INFO: === Search parameters used ===
14:40:37.010513 INFO: rt_error       : 2099.891532
14:40:37.010557 INFO: mobility_error : 0.1
14:40:37.010599 INFO: num_candidates : 1
14:40:37.010642 INFO: ms1_error      : 30
14:40:37.010681 INFO: ms2_error      : 30
14:40:37.010722 INFO: fwhm_rt        : 5
14:40:37.010763 INFO: quant_window   : 3
14:40:37.010803 INFO: ==============================================
14:40:37.040221 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:40:37.040348 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:40:37.040389 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
14:40:37.040411 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
14:40:37.041217 INFO: Starting candidate selection
14:51:31.879136 INFO: Starting candidate scoring
14:51:38.694281 INFO: Finished candidate processing
14:51:38.694435 INFO: Collecting candidate features
14:51:38.885564 WARNING: intensity_correlation has 17 NaNs ( 0.02 % out of 96187)
14:51:38.885923 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 96187)
14:51:38.895320 INFO: Collecting fragment features
14:51:38.958590 INFO: Finished candidate scoring
14:51:39.150102 INFO: performing precursor FDR with 47 features
14:51:39.150228 INFO: Decoy channel: -1
14:51:39.150254 INFO: Competetive: True
14:51:39.232390 INFO: Setting torch num_threads to 2 for FDR classification task
14:51:39.268313 WARNING: dropped 22 target PSMs due to missing features
14:51:39.268437 WARNING: dropped 11 decoy PSMs due to missing features
14:51:39.311942 INFO: Using random state 379311 for train-test-split
14:51:42.490700 INFO: Test AUC: 0.556
14:51:42.490813 INFO: Train AUC: 0.578
14:51:42.490845 INFO: AUC difference: 3.82%
14:51:42.790979 INFO: Resetting torch num_threads to 80
14:51:42.833009 PROGRESS: === Extracted 192159 precursors and 2064637 fragments ===
14:51:42.833778 INFO: === FDR correction performed with classifier version -1 ===
14:51:42.852150 PROGRESS: ============================= Precursor FDR =============================
14:51:42.852399 PROGRESS: Total precursors accumulated: 98,427
14:51:42.852463 PROGRESS: Target precursors: 59,087 (60.03%)
14:51:42.852510 PROGRESS: Decoy precursors: 39,340 (39.97%)
14:51:42.852553 PROGRESS: 
14:51:42.852597 PROGRESS: Precursor Summary:
14:51:42.854381 PROGRESS: Channel   0:	 0.050 FDR:   689; 0.010 FDR:   459; 0.001 FDR:   342
14:51:42.854502 PROGRESS: 
14:51:42.854558 PROGRESS: Protein Summary:
14:51:42.856299 PROGRESS: Channel   0:	 0.050 FDR:   629; 0.010 FDR:   424; 0.001 FDR:   327
14:51:42.856394 PROGRESS: =========================================================================
14:51:42.858296 INFO: Target number of precursors reached.
14:51:43.007571 INFO: fragments_df: keeping 4315 of 2064637 [sum(precursor_idx_mask)=5234 sum(mass_error_mask)=2064636 stop_rank=4315
14:51:43.348636 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
14:51:43.483916 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
14:51:43.630377 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
14:51:43.771336 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
14:51:44.314997 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
14:51:44.315418 INFO: Using score_cutoff 56.5755958328247 (fac=0.99, q=1)
14:51:44.315769 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1207096576690674
14:51:44.315856 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.011226918548345566
14:51:44.315912 INFO: Updating optimization_manager: score_cutoff        : 0 -> 56.5755958328247
14:51:44.315969 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
14:51:44.329657 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
14:51:44.391420 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
14:51:44.407662 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
14:51:44.555674 INFO: Updating optimization_manager: classifier_version  : -1 -> 8
14:51:44.555932 PROGRESS: Required number of precursors found. Starting search parameter optimization.
14:51:44.556051 INFO: Starting optimization step 9.
14:51:44.556123 PROGRESS: === Extracting elution groups 0 to 51000 ===
14:51:44.556201 INFO: Using classic extraction backend
14:51:44.556388 PROGRESS: Extracting batch of 100530 precursors
14:51:44.556471 INFO: === Search parameters used ===
14:51:44.556528 INFO: rt_error       : 2099.891532
14:51:44.556579 INFO: mobility_error : 0.1
14:51:44.556629 INFO: num_candidates : 3
14:51:44.556678 INFO: ms1_error      : 30
14:51:44.556726 INFO: ms2_error      : 30
14:51:44.556773 INFO: fwhm_rt        : 3.1207096576690674
14:51:44.556819 INFO: quant_window   : 3
14:51:44.556869 INFO: ==============================================
14:51:44.597175 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:51:44.597309 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:51:44.597371 INFO: FWHM in RT is 3.12 seconds, sigma is 0.69
14:51:44.597399 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.21
14:51:44.646302 INFO: Starting candidate selection
15:02:35.824330 INFO: Starting candidate scoring
15:02:56.295321 INFO: Finished candidate processing
15:02:56.295763 INFO: Collecting candidate features
15:02:56.877940 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 279474)
15:02:56.891756 INFO: Collecting fragment features
15:02:57.068391 INFO: Finished candidate scoring
15:02:57.312107 INFO: performing precursor FDR with 47 features
15:02:57.312268 INFO: Decoy channel: -1
15:02:57.312294 INFO: Competetive: True
15:02:57.423513 INFO: Setting torch num_threads to 2 for FDR classification task
15:02:57.477358 WARNING: dropped 4 decoy PSMs due to missing features
15:02:57.554712 INFO: Using random state 889559 for train-test-split
15:03:02.681195 INFO: Test AUC: 0.573
15:03:02.681402 INFO: Train AUC: 0.591
15:03:02.681436 INFO: AUC difference: 3.02%
15:03:03.010406 INFO: Resetting torch num_threads to 80
15:03:03.016307 PROGRESS: === Extracted 279474 precursors and 3038762 fragments ===
15:03:03.016898 INFO: === FDR correction performed with classifier version 8 ===
15:03:03.025710 PROGRESS: ============================= Precursor FDR =============================
15:03:03.025956 PROGRESS: Total precursors accumulated: 50,115
15:03:03.026024 PROGRESS: Target precursors: 31,705 (63.26%)
15:03:03.026086 PROGRESS: Decoy precursors: 18,410 (36.74%)
15:03:03.026148 PROGRESS: 
15:03:03.026198 PROGRESS: Precursor Summary:
15:03:03.027589 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   227; 0.001 FDR:   211
15:03:03.027690 PROGRESS: 
15:03:03.027746 PROGRESS: Protein Summary:
15:03:03.029143 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   215; 0.001 FDR:   201
15:03:03.029236 PROGRESS: =========================================================================
15:03:03.071301 INFO: Target number of precursors reached.
15:03:03.272349 INFO: fragments_df: keeping 3575 of 3038762 [sum(precursor_idx_mask)=7546 sum(mass_error_mask)=3038758 stop_rank=3575
15:03:03.612663 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:03:03.733741 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:03:03.849146 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:03:03.968911 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:03:04.435297 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:03:04.435729 INFO: Using score_cutoff 60.49783501281738 (fac=0.99, q=1)
15:03:04.436045 INFO: Updating optimization_manager: fwhm_rt             : 3.1207096576690674 -> 3.0270280838012695
15:03:04.436130 INFO: Updating optimization_manager: fwhm_mobility       : 0.011226918548345566 -> 0.011041590943932533
15:03:04.436185 INFO: Updating optimization_manager: score_cutoff        : 56.5755958328247 -> 60.49783501281738
15:03:04.436244 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:03:04.450137 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:03:04.512022 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:03:04.528195 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:03:04.668465 INFO: === checking if optimization conditions were reached ===
15:03:04.670452 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
15:03:04.670558 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
15:03:04.670633 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
15:03:04.671581 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
15:03:04.671682 INFO: Updating optimization_manager: classifier_version  : 9 -> 9
15:03:04.671745 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
15:03:04.671800 INFO: ==============================================
15:03:04.671875 INFO: Starting optimization step 10.
15:03:04.671933 PROGRESS: === Extracting elution groups 0 to 51000 ===
15:03:04.672001 INFO: Using classic extraction backend
15:03:04.672174 PROGRESS: Extracting batch of 100530 precursors
15:03:04.672262 INFO: === Search parameters used ===
15:03:04.672316 INFO: rt_error       : 2099.891532
15:03:04.672359 INFO: mobility_error : 0.1
15:03:04.672401 INFO: num_candidates : 3
15:03:04.672442 INFO: ms1_error      : 15.0
15:03:04.672483 INFO: ms2_error      : 15.0
15:03:04.672534 INFO: fwhm_rt        : 3.0270280838012695
15:03:04.672576 INFO: quant_window   : 3
15:03:04.672616 INFO: ==============================================
15:03:04.699240 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:03:04.699359 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:03:04.699410 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
15:03:04.699434 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.12
15:03:04.708266 INFO: Starting candidate selection
15:12:42.916555 INFO: Starting candidate scoring
15:12:54.619766 INFO: Finished candidate processing
15:12:54.619925 INFO: Collecting candidate features
15:12:55.068940 WARNING: intensity_correlation has 11 NaNs ( 0.00 % out of 279559)
15:12:55.082029 INFO: Collecting fragment features
15:12:55.259081 INFO: Finished candidate scoring
15:12:55.400839 INFO: performing precursor FDR with 47 features
15:12:55.400956 INFO: Decoy channel: -1
15:12:55.400980 INFO: Competetive: True
15:12:55.485754 INFO: Setting torch num_threads to 2 for FDR classification task
15:12:55.531185 WARNING: dropped 6 target PSMs due to missing features
15:12:55.531316 WARNING: dropped 5 decoy PSMs due to missing features
15:12:55.604281 INFO: Using random state 961658 for train-test-split
15:13:00.274492 INFO: Test AUC: 0.567
15:13:00.274616 INFO: Train AUC: 0.584
15:13:00.274648 INFO: AUC difference: 2.89%
15:13:00.597192 INFO: Resetting torch num_threads to 80
15:13:00.614574 PROGRESS: === Extracted 279559 precursors and 2894067 fragments ===
15:13:00.615202 INFO: === FDR correction performed with classifier version 9 ===
15:13:00.624395 PROGRESS: ============================= Precursor FDR =============================
15:13:00.624625 PROGRESS: Total precursors accumulated: 50,069
15:13:00.624691 PROGRESS: Target precursors: 30,920 (61.75%)
15:13:00.624759 PROGRESS: Decoy precursors: 19,149 (38.25%)
15:13:00.624807 PROGRESS: 
15:13:00.624852 PROGRESS: Precursor Summary:
15:13:00.626285 PROGRESS: Channel   0:	 0.050 FDR:   534; 0.010 FDR:   440; 0.001 FDR:   218
15:13:00.626387 PROGRESS: 
15:13:00.626441 PROGRESS: Protein Summary:
15:13:00.627902 PROGRESS: Channel   0:	 0.050 FDR:   502; 0.010 FDR:   416; 0.001 FDR:   207
15:13:00.627999 PROGRESS: =========================================================================
15:13:00.629689 INFO: Target number of precursors reached.
15:13:00.825180 INFO: fragments_df: keeping 5000 of 2894067 [sum(precursor_idx_mask)=13935 sum(mass_error_mask)=2894065 stop_rank=5000
15:13:01.107184 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:13:01.244383 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:13:01.375628 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:13:01.516549 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:13:02.195133 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:13:02.195570 INFO: Using score_cutoff 41.19089968185425 (fac=0.99, q=1)
15:13:02.195896 INFO: Updating optimization_manager: fwhm_rt             : 3.0270280838012695 -> 2.782381772994995
15:13:02.195979 INFO: Updating optimization_manager: fwhm_mobility       : 0.011041590943932533 -> 0.008704202249646187
15:13:02.196036 INFO: Updating optimization_manager: score_cutoff        : 60.49783501281738 -> 41.19089968185425
15:13:02.196093 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:13:02.203427 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:13:02.233840 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:13:02.240871 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:13:02.306272 INFO: === checking if optimization conditions were reached ===
15:13:02.308827 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
15:13:02.308945 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
15:13:02.309022 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
15:13:02.310220 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
15:13:02.310328 INFO: Updating optimization_manager: classifier_version  : 10 -> 10
15:13:02.310399 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
15:13:02.310461 INFO: ==============================================
15:13:02.310560 PROGRESS: Optimization finished for ms2_error, ms1_error.
15:13:02.473847 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:13:02.481530 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:13:02.512073 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:13:02.519086 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:13:02.584803 INFO: Starting optimization step 0.
15:13:02.585122 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:13:02.585216 INFO: Using classic extraction backend
15:13:02.585414 PROGRESS: Extracting batch of 50061 precursors
15:13:02.585509 INFO: === Search parameters used ===
15:13:02.585569 INFO: rt_error       : 2099.891532
15:13:02.585623 INFO: mobility_error : 0.1
15:13:02.585676 INFO: num_candidates : 3
15:13:02.585726 INFO: ms1_error      : 15.0
15:13:02.585775 INFO: ms2_error      : 15.0
15:13:02.585823 INFO: fwhm_rt        : 2.782381772994995
15:13:02.585871 INFO: quant_window   : 3
15:13:02.585920 INFO: ==============================================
15:13:02.611331 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:13:02.611467 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:13:02.611527 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
15:13:02.611557 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
15:13:02.620421 INFO: Starting candidate selection
15:17:55.269566 INFO: Starting candidate scoring
15:18:01.329741 INFO: Finished candidate processing
15:18:01.329876 INFO: Collecting candidate features
15:18:01.565871 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 138873)
15:18:01.574457 INFO: Collecting fragment features
15:18:01.656310 INFO: Finished candidate scoring
15:18:01.730664 INFO: performing precursor FDR with 47 features
15:18:01.730791 INFO: Decoy channel: -1
15:18:01.730815 INFO: Competetive: True
15:18:01.771435 INFO: Setting torch num_threads to 2 for FDR classification task
15:18:01.794853 WARNING: dropped 1 target PSMs due to missing features
15:18:01.794984 WARNING: dropped 1 decoy PSMs due to missing features
15:18:01.819572 INFO: Using random state 873257 for train-test-split
15:18:04.075089 INFO: Test AUC: 0.572
15:18:04.075216 INFO: Train AUC: 0.611
15:18:04.075250 INFO: AUC difference: 6.37%
15:18:04.075273 WARNING: AUC difference > 5%. This may indicate overfitting.
15:18:04.346675 INFO: Resetting torch num_threads to 80
15:18:04.355136 PROGRESS: === Extracted 138873 precursors and 1431688 fragments ===
15:18:04.355647 INFO: === FDR correction performed with classifier version 10 ===
15:18:04.359623 PROGRESS: ============================= Precursor FDR =============================
15:18:04.359769 PROGRESS: Total precursors accumulated: 24,927
15:18:04.359838 PROGRESS: Target precursors: 15,953 (64.00%)
15:18:04.359889 PROGRESS: Decoy precursors: 8,974 (36.00%)
15:18:04.359935 PROGRESS: 
15:18:04.359977 PROGRESS: Precursor Summary:
15:18:04.361114 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   226; 0.001 FDR:   193
15:18:04.361208 PROGRESS: 
15:18:04.361265 PROGRESS: Protein Summary:
15:18:04.362521 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   221; 0.001 FDR:   188
15:18:04.362618 PROGRESS: =========================================================================
15:18:04.392508 INFO: Target number of precursors reached.
15:18:04.488222 INFO: fragments_df: keeping 3094 of 1431688 [sum(precursor_idx_mask)=7163 sum(mass_error_mask)=1431688 stop_rank=3094
15:18:04.726559 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:18:04.838275 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:18:04.929477 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:18:05.035387 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:18:05.440518 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:18:05.441006 INFO: Using score_cutoff 46.4452570438385 (fac=0.99, q=1)
15:18:05.441325 INFO: Updating optimization_manager: fwhm_rt             : 2.782381772994995 -> 2.671886920928955
15:18:05.441405 INFO: Updating optimization_manager: fwhm_mobility       : 0.008704202249646187 -> 0.008615652099251747
15:18:05.441471 INFO: Updating optimization_manager: score_cutoff        : 41.19089968185425 -> 46.4452570438385
15:18:05.441540 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:18:05.449994 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:18:05.480665 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:18:05.488579 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:18:05.552803 INFO: === checking if optimization conditions were reached ===
15:18:05.553073 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
15:18:05.555072 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 822.1300634301508
15:18:05.555183 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 822.1301.
15:18:05.555259 INFO: ==============================================
15:18:05.555344 INFO: Starting optimization step 1.
15:18:05.555416 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:18:05.555500 INFO: Using classic extraction backend
15:18:05.555706 PROGRESS: Extracting batch of 50061 precursors
15:18:05.555786 INFO: === Search parameters used ===
15:18:05.555841 INFO: rt_error       : 822.1300634301508
15:18:05.555893 INFO: mobility_error : 0.1
15:18:05.555939 INFO: num_candidates : 3
15:18:05.555984 INFO: ms1_error      : 15.0
15:18:05.556039 INFO: ms2_error      : 15.0
15:18:05.556087 INFO: fwhm_rt        : 2.671886920928955
15:18:05.556132 INFO: quant_window   : 3
15:18:05.556176 INFO: ==============================================
15:18:05.577899 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:18:05.578028 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:18:05.578125 INFO: FWHM in RT is 2.67 seconds, sigma is 0.59
15:18:05.578155 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.00
15:18:05.586862 INFO: Starting candidate selection
15:20:30.677588 INFO: Starting candidate scoring
15:20:36.641306 INFO: Finished candidate processing
15:20:36.641510 INFO: Collecting candidate features
15:20:36.886652 WARNING: intensity_correlation has 22 NaNs ( 0.02 % out of 136790)
15:20:36.887034 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 136790)
15:20:36.895503 INFO: Collecting fragment features
15:20:36.988019 INFO: Finished candidate scoring
15:20:37.075408 INFO: performing precursor FDR with 47 features
15:20:37.075562 INFO: Decoy channel: -1
15:20:37.075589 INFO: Competetive: True
15:20:37.129294 INFO: Setting torch num_threads to 2 for FDR classification task
15:20:37.158473 WARNING: dropped 12 target PSMs due to missing features
15:20:37.158632 WARNING: dropped 10 decoy PSMs due to missing features
15:20:37.188001 INFO: Using random state 873257 for train-test-split
15:20:39.933343 INFO: Test AUC: 0.572
15:20:39.933523 INFO: Train AUC: 0.603
15:20:39.933563 INFO: AUC difference: 5.10%
15:20:39.933587 WARNING: AUC difference > 5%. This may indicate overfitting.
15:20:40.227668 INFO: Resetting torch num_threads to 80
15:20:40.232301 PROGRESS: === Extracted 136790 precursors and 1394125 fragments ===
15:20:40.233001 INFO: === FDR correction performed with classifier version 10 ===
15:20:40.238289 PROGRESS: ============================= Precursor FDR =============================
15:20:40.238450 PROGRESS: Total precursors accumulated: 24,763
15:20:40.238521 PROGRESS: Target precursors: 15,587 (62.94%)
15:20:40.238576 PROGRESS: Decoy precursors: 9,176 (37.06%)
15:20:40.238629 PROGRESS: 
15:20:40.238677 PROGRESS: Precursor Summary:
15:20:40.239958 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   243; 0.001 FDR:   172
15:20:40.240059 PROGRESS: 
15:20:40.240122 PROGRESS: Protein Summary:
15:20:40.241410 PROGRESS: Channel   0:	 0.050 FDR:   317; 0.010 FDR:   238; 0.001 FDR:   168
15:20:40.241507 PROGRESS: =========================================================================
15:20:40.243137 INFO: Target number of precursors reached.
15:20:40.334748 INFO: fragments_df: keeping 3363 of 1394125 [sum(precursor_idx_mask)=7728 sum(mass_error_mask)=1394125 stop_rank=3363
15:20:41.104336 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:20:41.234813 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:20:41.362307 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:20:41.491355 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:20:41.957787 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:20:41.958385 INFO: Using score_cutoff 42.42359228439331 (fac=0.99, q=1)
15:20:41.958762 INFO: Updating optimization_manager: fwhm_rt             : 2.671886920928955 -> 2.6634764671325684
15:20:41.958843 INFO: Updating optimization_manager: fwhm_mobility       : 0.008615652099251747 -> 0.008542549796402454
15:20:41.958901 INFO: Updating optimization_manager: score_cutoff        : 46.4452570438385 -> 42.42359228439331
15:20:41.958968 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:20:41.967098 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:20:42.010756 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:20:42.020377 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:20:42.084501 INFO: === checking if optimization conditions were reached ===
15:20:42.084931 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
15:20:42.087701 INFO: Updating optimization_manager: rt_error            : 822.1300634301508 -> 588.7457184203265
15:20:42.087839 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 588.7457.
15:20:42.087920 INFO: ==============================================
15:20:42.088039 INFO: Starting optimization step 2.
15:20:42.088113 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:20:42.088202 INFO: Using classic extraction backend
15:20:42.088422 PROGRESS: Extracting batch of 50061 precursors
15:20:42.088506 INFO: === Search parameters used ===
15:20:42.088563 INFO: rt_error       : 588.7457184203265
15:20:42.088615 INFO: mobility_error : 0.1
15:20:42.088666 INFO: num_candidates : 3
15:20:42.088717 INFO: ms1_error      : 15.0
15:20:42.088767 INFO: ms2_error      : 15.0
15:20:42.088827 INFO: fwhm_rt        : 2.6634764671325684
15:20:42.088878 INFO: quant_window   : 3
15:20:42.088928 INFO: ==============================================
15:20:42.115347 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:20:42.115522 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:20:42.115604 INFO: FWHM in RT is 2.66 seconds, sigma is 0.59
15:20:42.115636 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.96
15:20:42.121962 INFO: Starting candidate selection
15:22:09.705373 INFO: Starting candidate scoring
15:22:15.089778 INFO: Finished candidate processing
15:22:15.089931 INFO: Collecting candidate features
15:22:15.295905 WARNING: intensity_correlation has 24 NaNs ( 0.02 % out of 134982)
15:22:15.296261 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 134982)
15:22:15.304348 INFO: Collecting fragment features
15:22:15.393834 INFO: Finished candidate scoring
15:22:15.501094 INFO: performing precursor FDR with 47 features
15:22:15.501210 INFO: Decoy channel: -1
15:22:15.501235 INFO: Competetive: True
15:22:15.546551 INFO: Setting torch num_threads to 2 for FDR classification task
15:22:15.571156 WARNING: dropped 17 target PSMs due to missing features
15:22:15.571292 WARNING: dropped 10 decoy PSMs due to missing features
15:22:15.591969 INFO: Using random state 873257 for train-test-split
15:22:18.124131 INFO: Test AUC: 0.559
15:22:18.124257 INFO: Train AUC: 0.600
15:22:18.124290 INFO: AUC difference: 6.73%
15:22:18.124312 WARNING: AUC difference > 5%. This may indicate overfitting.
15:22:18.397428 INFO: Resetting torch num_threads to 80
15:22:18.401198 PROGRESS: === Extracted 134982 precursors and 1365321 fragments ===
15:22:18.401720 INFO: === FDR correction performed with classifier version 10 ===
15:22:18.405917 PROGRESS: ============================= Precursor FDR =============================
15:22:18.406110 PROGRESS: Total precursors accumulated: 24,524
15:22:18.406177 PROGRESS: Target precursors: 15,293 (62.36%)
15:22:18.406225 PROGRESS: Decoy precursors: 9,231 (37.64%)
15:22:18.406272 PROGRESS: 
15:22:18.406316 PROGRESS: Precursor Summary:
15:22:18.407430 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   201; 0.001 FDR:   128
15:22:18.407526 PROGRESS: 
15:22:18.407583 PROGRESS: Protein Summary:
15:22:18.408788 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:   196; 0.001 FDR:   124
15:22:18.408889 PROGRESS: =========================================================================
15:22:18.409739 INFO: Target number of precursors reached.
15:22:18.502651 INFO: fragments_df: keeping 2831 of 1365321 [sum(precursor_idx_mask)=6360 sum(mass_error_mask)=1365321 stop_rank=2831
15:22:18.744365 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:22:18.862115 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:22:18.971692 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:22:19.072977 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:22:19.378479 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:22:19.378911 INFO: Using score_cutoff 48.113956947326656 (fac=0.99, q=1)
15:22:19.379235 INFO: Updating optimization_manager: fwhm_rt             : 2.6634764671325684 -> 2.758636236190796
15:22:19.379316 INFO: Updating optimization_manager: fwhm_mobility       : 0.008542549796402454 -> 0.009020067751407623
15:22:19.379369 INFO: Updating optimization_manager: score_cutoff        : 42.42359228439331 -> 48.113956947326656
15:22:19.379427 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:22:19.386924 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:22:19.417095 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:22:19.424883 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:22:19.485305 INFO: === checking if optimization conditions were reached ===
15:22:19.486241 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
15:22:19.488685 INFO: Updating optimization_manager: rt_error            : 588.7457184203265 -> 424.0472006320421
15:22:19.488808 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 424.0472.
15:22:19.488885 INFO: ==============================================
15:22:19.488972 INFO: Starting optimization step 3.
15:22:19.489039 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:22:19.489111 INFO: Using classic extraction backend
15:22:19.489290 PROGRESS: Extracting batch of 50061 precursors
15:22:19.489372 INFO: === Search parameters used ===
15:22:19.489454 INFO: rt_error       : 424.0472006320421
15:22:19.489511 INFO: mobility_error : 0.1
15:22:19.489564 INFO: num_candidates : 3
15:22:19.489614 INFO: ms1_error      : 15.0
15:22:19.489663 INFO: ms2_error      : 15.0
15:22:19.489711 INFO: fwhm_rt        : 2.758636236190796
15:22:19.489760 INFO: quant_window   : 3
15:22:19.489809 INFO: ==============================================
15:22:19.509938 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:22:19.510078 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:22:19.510141 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
15:22:19.510170 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.18
15:22:19.511028 INFO: Starting candidate selection
15:23:20.237906 INFO: Starting candidate scoring
15:23:26.332659 INFO: Finished candidate processing
15:23:26.332846 INFO: Collecting candidate features
15:23:26.584095 WARNING: intensity_correlation has 30 NaNs ( 0.02 % out of 134873)
15:23:26.584488 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 134873)
15:23:26.592547 INFO: Collecting fragment features
15:23:26.690703 INFO: Finished candidate scoring
15:23:26.765738 INFO: performing precursor FDR with 47 features
15:23:26.765889 INFO: Decoy channel: -1
15:23:26.765915 INFO: Competetive: True
15:23:26.819542 INFO: Setting torch num_threads to 2 for FDR classification task
15:23:26.847548 WARNING: dropped 22 target PSMs due to missing features
15:23:26.847702 WARNING: dropped 11 decoy PSMs due to missing features
15:23:26.876529 INFO: Using random state 873257 for train-test-split
15:23:29.501633 INFO: Test AUC: 0.553
15:23:29.501778 INFO: Train AUC: 0.585
15:23:29.501815 INFO: AUC difference: 5.45%
15:23:29.501838 WARNING: AUC difference > 5%. This may indicate overfitting.
15:23:29.771420 INFO: Resetting torch num_threads to 80
15:23:29.774854 PROGRESS: === Extracted 134873 precursors and 1352696 fragments ===
15:23:29.775400 INFO: === FDR correction performed with classifier version 10 ===
15:23:29.779619 PROGRESS: ============================= Precursor FDR =============================
15:23:29.779752 PROGRESS: Total precursors accumulated: 24,575
15:23:29.779822 PROGRESS: Target precursors: 14,923 (60.72%)
15:23:29.779875 PROGRESS: Decoy precursors: 9,652 (39.28%)
15:23:29.779919 PROGRESS: 
15:23:29.779964 PROGRESS: Precursor Summary:
15:23:29.781078 PROGRESS: Channel   0:	 0.050 FDR:   267; 0.010 FDR:   169; 0.001 FDR:   143
15:23:29.781170 PROGRESS: 
15:23:29.781226 PROGRESS: Protein Summary:
15:23:29.782447 PROGRESS: Channel   0:	 0.050 FDR:   262; 0.010 FDR:   165; 0.001 FDR:   139
15:23:29.782539 PROGRESS: =========================================================================
15:23:29.783795 INFO: Target number of precursors not reached yet.
15:23:30.562848 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:23:30.574200 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:23:30.605392 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:23:30.613478 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:23:30.682476 INFO: === skipping optimization until target number of precursors are found ===
15:23:30.682890 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
15:23:30.683018 INFO: Starting optimization step 4.
15:23:30.683096 PROGRESS: === Extracting elution groups 25400 to 51000 ===
15:23:30.683196 INFO: Using classic extraction backend
15:23:30.683514 PROGRESS: Extracting batch of 50469 precursors
15:23:30.683640 INFO: === Search parameters used ===
15:23:30.683703 INFO: rt_error       : 424.0472006320421
15:23:30.683756 INFO: mobility_error : 0.1
15:23:30.683805 INFO: num_candidates : 3
15:23:30.683857 INFO: ms1_error      : 15.0
15:23:30.683904 INFO: ms2_error      : 15.0
15:23:30.683950 INFO: fwhm_rt        : 2.758636236190796
15:23:30.683998 INFO: quant_window   : 3
15:23:30.684043 INFO: ==============================================
15:23:30.709514 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:23:30.709674 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:23:30.709750 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
15:23:30.709780 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.18
15:23:30.722354 INFO: Starting candidate selection
15:24:35.290884 INFO: Starting candidate scoring
15:24:41.067104 INFO: Finished candidate processing
15:24:41.067262 INFO: Collecting candidate features
15:24:41.311749 WARNING: intensity_correlation has 43 NaNs ( 0.03 % out of 135848)
15:24:41.312104 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 135848)
15:24:41.320034 INFO: Collecting fragment features
15:24:41.413432 INFO: Finished candidate scoring
15:24:41.586392 INFO: performing precursor FDR with 47 features
15:24:41.586524 INFO: Decoy channel: -1
15:24:41.586550 INFO: Competetive: True
15:24:41.690736 INFO: Setting torch num_threads to 2 for FDR classification task
15:24:41.735081 WARNING: dropped 51 target PSMs due to missing features
15:24:41.735212 WARNING: dropped 28 decoy PSMs due to missing features
15:24:41.807697 INFO: Using random state 873257 for train-test-split
15:24:46.589301 INFO: Test AUC: 0.557
15:24:46.589429 INFO: Train AUC: 0.577
15:24:46.589460 INFO: AUC difference: 3.55%
15:24:46.901733 INFO: Resetting torch num_threads to 80
15:24:46.950209 PROGRESS: === Extracted 270721 precursors and 2713859 fragments ===
15:24:46.950972 INFO: === FDR correction performed with classifier version 10 ===
15:24:46.960474 PROGRESS: ============================= Precursor FDR =============================
15:24:46.960665 PROGRESS: Total precursors accumulated: 49,349
15:24:46.960738 PROGRESS: Target precursors: 29,760 (60.31%)
15:24:46.960791 PROGRESS: Decoy precursors: 19,589 (39.69%)
15:24:46.960835 PROGRESS: 
15:24:46.960878 PROGRESS: Precursor Summary:
15:24:46.962244 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   349; 0.001 FDR:     7
15:24:46.962338 PROGRESS: 
15:24:46.962394 PROGRESS: Protein Summary:
15:24:46.963760 PROGRESS: Channel   0:	 0.050 FDR:   551; 0.010 FDR:   331; 0.001 FDR:     7
15:24:46.963854 PROGRESS: =========================================================================
15:24:46.964700 INFO: Target number of precursors reached.
15:24:47.158391 INFO: fragments_df: keeping 5000 of 2713859 [sum(precursor_idx_mask)=11153 sum(mass_error_mask)=2713853 stop_rank=5000
15:24:47.529676 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:24:47.641343 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:24:47.742950 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:24:47.854464 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:24:48.459877 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:24:48.460321 INFO: Using score_cutoff 44.981025389099116 (fac=0.99, q=1)
15:24:48.460658 INFO: Updating optimization_manager: fwhm_rt             : 2.758636236190796 -> 2.732163429260254
15:24:48.460739 INFO: Updating optimization_manager: fwhm_mobility       : 0.009020067751407623 -> 0.009064903482794762
15:24:48.460801 INFO: Updating optimization_manager: score_cutoff        : 48.113956947326656 -> 44.981025389099116
15:24:48.460857 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:24:48.474535 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:24:48.536363 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:24:48.553377 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:24:48.698606 INFO: === checking if optimization conditions were reached ===
15:24:48.698920 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
15:24:48.701664 INFO: Updating optimization_manager: rt_error            : 424.0472006320421 -> 150.85524481245713
15:24:48.701807 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 150.8552.
15:24:48.701891 INFO: ==============================================
15:24:48.701998 INFO: Starting optimization step 5.
15:24:48.702086 PROGRESS: === Extracting elution groups 0 to 51000 ===
15:24:48.702173 INFO: Using classic extraction backend
15:24:48.702368 PROGRESS: Extracting batch of 100530 precursors
15:24:48.702453 INFO: === Search parameters used ===
15:24:48.702511 INFO: rt_error       : 150.85524481245713
15:24:48.702565 INFO: mobility_error : 0.1
15:24:48.702617 INFO: num_candidates : 3
15:24:48.702668 INFO: ms1_error      : 15.0
15:24:48.702717 INFO: ms2_error      : 15.0
15:24:48.702767 INFO: fwhm_rt        : 2.732163429260254
15:24:48.702816 INFO: quant_window   : 3
15:24:48.702866 INFO: ==============================================
15:24:48.744091 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:24:48.744241 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:24:48.744323 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
15:24:48.744353 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.20
15:24:48.745933 INFO: Starting candidate selection
15:25:34.716215 INFO: Starting candidate scoring
15:25:45.775966 INFO: Finished candidate processing
15:25:45.776168 INFO: Collecting candidate features
15:25:46.295179 WARNING: intensity_correlation has 116 NaNs ( 0.04 % out of 266676)
15:25:46.295691 WARNING: height_correlation has 14 NaNs ( 0.01 % out of 266676)
15:25:46.308080 INFO: Collecting fragment features
15:25:46.487363 INFO: Finished candidate scoring
15:25:46.648853 INFO: performing precursor FDR with 47 features
15:25:46.649002 INFO: Decoy channel: -1
15:25:46.649029 INFO: Competetive: True
15:25:46.752858 INFO: Setting torch num_threads to 2 for FDR classification task
15:25:46.814532 WARNING: dropped 66 target PSMs due to missing features
15:25:46.814706 WARNING: dropped 59 decoy PSMs due to missing features
15:25:46.921595 INFO: Using random state 873257 for train-test-split
15:25:52.967625 INFO: Test AUC: 0.554
15:25:52.967857 INFO: Train AUC: 0.575
15:25:52.967891 INFO: AUC difference: 3.69%
15:25:53.280742 INFO: Resetting torch num_threads to 80
15:25:53.289380 PROGRESS: === Extracted 266676 precursors and 2609713 fragments ===
15:25:53.290014 INFO: === FDR correction performed with classifier version 10 ===
15:25:53.299953 PROGRESS: ============================= Precursor FDR =============================
15:25:53.300175 PROGRESS: Total precursors accumulated: 48,827
15:25:53.300247 PROGRESS: Target precursors: 29,272 (59.95%)
15:25:53.300299 PROGRESS: Decoy precursors: 19,555 (40.05%)
15:25:53.300355 PROGRESS: 
15:25:53.300400 PROGRESS: Precursor Summary:
15:25:53.301795 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   425; 0.001 FDR:   210
15:25:53.301887 PROGRESS: 
15:25:53.301944 PROGRESS: Protein Summary:
15:25:53.303420 PROGRESS: Channel   0:	 0.050 FDR:   551; 0.010 FDR:   406; 0.001 FDR:   200
15:25:53.303513 PROGRESS: =========================================================================
15:25:53.306284 INFO: Target number of precursors reached.
15:25:53.477518 INFO: fragments_df: keeping 5000 of 2609713 [sum(precursor_idx_mask)=13189 sum(mass_error_mask)=2609708 stop_rank=5000
15:25:53.763773 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:25:53.891926 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:25:54.018401 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:25:54.124308 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:25:54.728554 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:25:54.728960 INFO: Using score_cutoff 41.519620362854006 (fac=0.99, q=1)
15:25:54.729304 INFO: Updating optimization_manager: fwhm_rt             : 2.732163429260254 -> 2.781576156616211
15:25:54.729384 INFO: Updating optimization_manager: fwhm_mobility       : 0.009064903482794762 -> 0.008730575442314148
15:25:54.729437 INFO: Updating optimization_manager: score_cutoff        : 44.981025389099116 -> 41.519620362854006
15:25:54.729493 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:25:54.736885 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:25:54.767497 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:25:54.774193 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:25:54.837724 INFO: === checking if optimization conditions were reached ===
15:25:54.837991 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
15:25:54.840552 INFO: Updating optimization_manager: rt_error            : 150.85524481245713 -> 113.67569676809151
15:25:54.840669 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 113.6757.
15:25:54.840743 INFO: ==============================================
15:25:54.840827 INFO: Starting optimization step 6.
15:25:54.840890 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:25:54.840981 INFO: Using classic extraction backend
15:25:54.841305 PROGRESS: Extracting batch of 50061 precursors
15:25:54.841401 INFO: === Search parameters used ===
15:25:54.841459 INFO: rt_error       : 113.67569676809151
15:25:54.841510 INFO: mobility_error : 0.1
15:25:54.841559 INFO: num_candidates : 3
15:25:54.841607 INFO: ms1_error      : 15.0
15:25:54.841655 INFO: ms2_error      : 15.0
15:25:54.841703 INFO: fwhm_rt        : 2.781576156616211
15:25:54.841751 INFO: quant_window   : 3
15:25:54.841812 INFO: ==============================================
15:25:54.865776 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:25:54.865896 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:25:54.865965 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
15:25:54.865993 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.05
15:25:54.875033 INFO: Starting candidate selection
15:26:12.626568 INFO: Starting candidate scoring
15:26:18.108677 INFO: Finished candidate processing
15:26:18.108828 INFO: Collecting candidate features
15:26:18.337333 WARNING: intensity_correlation has 49 NaNs ( 0.04 % out of 132298)
15:26:18.337690 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 132298)
15:26:18.345567 INFO: Collecting fragment features
15:26:18.422512 INFO: Finished candidate scoring
15:26:18.483284 INFO: performing precursor FDR with 47 features
15:26:18.483382 INFO: Decoy channel: -1
15:26:18.483406 INFO: Competetive: True
15:26:18.531936 INFO: Setting torch num_threads to 2 for FDR classification task
15:26:18.558976 WARNING: dropped 28 target PSMs due to missing features
15:26:18.559092 WARNING: dropped 23 decoy PSMs due to missing features
15:26:18.584258 INFO: Using random state 873257 for train-test-split
15:26:20.804399 INFO: Test AUC: 0.551
15:26:20.804572 INFO: Train AUC: 0.585
15:26:20.804604 INFO: AUC difference: 5.70%
15:26:20.804628 WARNING: AUC difference > 5%. This may indicate overfitting.
15:26:21.072047 INFO: Resetting torch num_threads to 80
15:26:21.075181 PROGRESS: === Extracted 132298 precursors and 1292873 fragments ===
15:26:21.075742 INFO: === FDR correction performed with classifier version 10 ===
15:26:21.079588 PROGRESS: ============================= Precursor FDR =============================
15:26:21.079732 PROGRESS: Total precursors accumulated: 24,248
15:26:21.079798 PROGRESS: Target precursors: 14,556 (60.03%)
15:26:21.079849 PROGRESS: Decoy precursors: 9,692 (39.97%)
15:26:21.079893 PROGRESS: 
15:26:21.079938 PROGRESS: Precursor Summary:
15:26:21.081115 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   244; 0.001 FDR:   150
15:26:21.081207 PROGRESS: 
15:26:21.081267 PROGRESS: Protein Summary:
15:26:21.082490 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   240; 0.001 FDR:   147
15:26:21.082584 PROGRESS: =========================================================================
15:26:21.084406 INFO: Target number of precursors reached.
15:26:21.171067 INFO: fragments_df: keeping 3213 of 1292873 [sum(precursor_idx_mask)=7591 sum(mass_error_mask)=1292867 stop_rank=3213
15:26:21.335221 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:26:21.454476 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:26:21.576321 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:26:21.698078 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:26:22.123389 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:26:22.123932 INFO: Using score_cutoff 40.36979282684326 (fac=0.99, q=1)
15:26:22.124263 INFO: Updating optimization_manager: fwhm_rt             : 2.781576156616211 -> 2.7274222373962402
15:26:22.124343 INFO: Updating optimization_manager: fwhm_mobility       : 0.008730575442314148 -> 0.008521455340087414
15:26:22.124398 INFO: Updating optimization_manager: score_cutoff        : 41.519620362854006 -> 40.36979282684326
15:26:22.124453 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:26:22.132012 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:26:22.162302 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:26:22.169995 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:26:22.245955 INFO: === checking if optimization conditions were reached ===
15:26:22.246332 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
15:26:22.249269 INFO: Updating optimization_manager: rt_error            : 113.67569676809151 -> 98.95921573168566
15:26:22.249400 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 98.9592.
15:26:22.249483 INFO: ==============================================
15:26:22.249571 INFO: Starting optimization step 7.
15:26:22.249643 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:26:22.249722 INFO: Using classic extraction backend
15:26:22.249881 PROGRESS: Extracting batch of 50061 precursors
15:26:22.249966 INFO: === Search parameters used ===
15:26:22.250055 INFO: rt_error       : 98.95921573168566
15:26:22.250118 INFO: mobility_error : 0.1
15:26:22.250175 INFO: num_candidates : 3
15:26:22.250235 INFO: ms1_error      : 15.0
15:26:22.250288 INFO: ms2_error      : 15.0
15:26:22.250337 INFO: fwhm_rt        : 2.7274222373962402
15:26:22.250387 INFO: quant_window   : 3
15:26:22.250438 INFO: ==============================================
15:26:22.273507 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:26:22.273681 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:26:22.273743 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
15:26:22.273774 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
15:26:22.287165 INFO: Starting candidate selection
15:26:39.344966 INFO: Starting candidate scoring
15:26:45.235207 INFO: Finished candidate processing
15:26:45.235326 INFO: Collecting candidate features
15:26:45.467630 WARNING: intensity_correlation has 58 NaNs ( 0.04 % out of 132113)
15:26:45.467974 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 132113)
15:26:45.476034 INFO: Collecting fragment features
15:26:45.556424 INFO: Finished candidate scoring
15:26:45.624574 INFO: performing precursor FDR with 47 features
15:26:45.624685 INFO: Decoy channel: -1
15:26:45.624723 INFO: Competetive: True
15:26:45.678026 INFO: Setting torch num_threads to 2 for FDR classification task
15:26:45.709798 WARNING: dropped 26 target PSMs due to missing features
15:26:45.709920 WARNING: dropped 36 decoy PSMs due to missing features
15:26:45.742857 INFO: Using random state 873257 for train-test-split
15:26:48.173200 INFO: Test AUC: 0.556
15:26:48.173327 INFO: Train AUC: 0.579
15:26:48.173358 INFO: AUC difference: 3.97%
15:26:48.433840 INFO: Resetting torch num_threads to 80
15:26:48.438082 PROGRESS: === Extracted 132113 precursors and 1280128 fragments ===
15:26:48.438528 INFO: === FDR correction performed with classifier version 10 ===
15:26:48.442794 PROGRESS: ============================= Precursor FDR =============================
15:26:48.442922 PROGRESS: Total precursors accumulated: 24,202
15:26:48.442982 PROGRESS: Target precursors: 14,565 (60.18%)
15:26:48.443030 PROGRESS: Decoy precursors: 9,637 (39.82%)
15:26:48.443073 PROGRESS: 
15:26:48.443115 PROGRESS: Precursor Summary:
15:26:48.444242 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   163; 0.001 FDR:   159
15:26:48.444334 PROGRESS: 
15:26:48.444390 PROGRESS: Protein Summary:
15:26:48.445587 PROGRESS: Channel   0:	 0.050 FDR:   317; 0.010 FDR:   160; 0.001 FDR:   156
15:26:48.445677 PROGRESS: =========================================================================
15:26:48.446553 INFO: Target number of precursors not reached yet.
15:26:48.655621 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:26:48.663359 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:26:48.693997 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:26:48.701791 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:26:48.764966 INFO: === skipping optimization until target number of precursors are found ===
15:26:48.765254 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
15:26:48.765356 INFO: Starting optimization step 8.
15:26:48.765431 PROGRESS: === Extracting elution groups 25400 to 51000 ===
15:26:48.765501 INFO: Using classic extraction backend
15:26:48.765634 PROGRESS: Extracting batch of 50469 precursors
15:26:48.765720 INFO: === Search parameters used ===
15:26:48.765776 INFO: rt_error       : 98.95921573168566
15:26:48.765826 INFO: mobility_error : 0.1
15:26:48.765875 INFO: num_candidates : 3
15:26:48.765924 INFO: ms1_error      : 15.0
15:26:48.765973 INFO: ms2_error      : 15.0
15:26:48.766020 INFO: fwhm_rt        : 2.7274222373962402
15:26:48.766084 INFO: quant_window   : 3
15:26:48.766134 INFO: ==============================================
15:26:48.787717 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:26:48.787840 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:26:48.787889 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
15:26:48.787917 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
15:26:48.802792 INFO: Starting candidate selection
15:27:04.569775 INFO: Starting candidate scoring
15:27:10.615999 INFO: Finished candidate processing
15:27:10.616096 INFO: Collecting candidate features
15:27:10.808275 WARNING: intensity_correlation has 77 NaNs ( 0.06 % out of 132688)
15:27:10.808606 WARNING: height_correlation has 12 NaNs ( 0.01 % out of 132688)
15:27:10.816269 INFO: Collecting fragment features
15:27:10.895820 INFO: Finished candidate scoring
15:27:11.072509 INFO: performing precursor FDR with 47 features
15:27:11.072638 INFO: Decoy channel: -1
15:27:11.072663 INFO: Competetive: True
15:27:11.180566 INFO: Setting torch num_threads to 2 for FDR classification task
15:27:11.232992 WARNING: dropped 61 target PSMs due to missing features
15:27:11.233116 WARNING: dropped 85 decoy PSMs due to missing features
15:27:11.302923 INFO: Using random state 873257 for train-test-split
15:27:16.114958 INFO: Test AUC: 0.555
15:27:16.115077 INFO: Train AUC: 0.579
15:27:16.115108 INFO: AUC difference: 4.17%
15:27:16.420443 INFO: Resetting torch num_threads to 80
15:27:16.471927 PROGRESS: === Extracted 264801 precursors and 2561406 fragments ===
15:27:16.472681 INFO: === FDR correction performed with classifier version 10 ===
15:27:16.483665 PROGRESS: ============================= Precursor FDR =============================
15:27:16.483866 PROGRESS: Total precursors accumulated: 48,566
15:27:16.483930 PROGRESS: Target precursors: 29,163 (60.05%)
15:27:16.483978 PROGRESS: Decoy precursors: 19,403 (39.95%)
15:27:16.484022 PROGRESS: 
15:27:16.484065 PROGRESS: Precursor Summary:
15:27:16.485413 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   437; 0.001 FDR:   240
15:27:16.485504 PROGRESS: 
15:27:16.485559 PROGRESS: Protein Summary:
15:27:16.486993 PROGRESS: Channel   0:	 0.050 FDR:   563; 0.010 FDR:   416; 0.001 FDR:   231
15:27:16.487083 PROGRESS: =========================================================================
15:27:16.488076 INFO: Target number of precursors reached.
15:27:16.663774 INFO: fragments_df: keeping 5000 of 2561406 [sum(precursor_idx_mask)=13503 sum(mass_error_mask)=2561398 stop_rank=5000
15:27:16.892165 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:27:17.006264 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:27:17.119768 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:27:17.227170 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:27:17.833166 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:27:17.833583 INFO: Using score_cutoff 39.038045237731936 (fac=0.99, q=1)
15:27:17.833912 INFO: Updating optimization_manager: fwhm_rt             : 2.7274222373962402 -> 2.758366584777832
15:27:17.833994 INFO: Updating optimization_manager: fwhm_mobility       : 0.008521455340087414 -> 0.008543652482330799
15:27:17.834058 INFO: Updating optimization_manager: score_cutoff        : 40.36979282684326 -> 39.038045237731936
15:27:17.834116 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:27:17.841522 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:27:17.871909 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:27:17.879160 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:27:17.943186 INFO: === checking if optimization conditions were reached ===
15:27:17.943421 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
15:27:17.945599 INFO: Updating optimization_manager: rt_error            : 98.95921573168566 -> 96.3666147229007
15:27:17.945704 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 96.3666.
15:27:17.945770 INFO: ==============================================
15:27:17.945843 INFO: Starting optimization step 9.
15:27:17.945900 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:27:17.945963 INFO: Using classic extraction backend
15:27:17.946119 PROGRESS: Extracting batch of 50061 precursors
15:27:17.946192 INFO: === Search parameters used ===
15:27:17.946243 INFO: rt_error       : 96.3666147229007
15:27:17.946284 INFO: mobility_error : 0.1
15:27:17.946336 INFO: num_candidates : 3
15:27:17.946378 INFO: ms1_error      : 15.0
15:27:17.946421 INFO: ms2_error      : 15.0
15:27:17.946460 INFO: fwhm_rt        : 2.758366584777832
15:27:17.946497 INFO: quant_window   : 3
15:27:17.946534 INFO: ==============================================
15:27:17.962819 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:27:17.962932 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:27:17.962994 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
15:27:17.963030 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.96
15:27:17.966454 INFO: Starting candidate selection
15:27:35.048146 INFO: Starting candidate scoring
15:27:41.190530 INFO: Finished candidate processing
15:27:41.190712 INFO: Collecting candidate features
15:27:41.422489 WARNING: intensity_correlation has 58 NaNs ( 0.04 % out of 132107)
15:27:41.422874 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 132107)
15:27:41.431010 INFO: Collecting fragment features
15:27:41.513813 INFO: Finished candidate scoring
15:27:41.585852 INFO: performing precursor FDR with 47 features
15:27:41.586004 INFO: Decoy channel: -1
15:27:41.586029 INFO: Competetive: True
15:27:41.637639 INFO: Setting torch num_threads to 2 for FDR classification task
15:27:41.666216 WARNING: dropped 27 target PSMs due to missing features
15:27:41.666381 WARNING: dropped 35 decoy PSMs due to missing features
15:27:41.694586 INFO: Using random state 873257 for train-test-split
15:27:44.053404 INFO: Test AUC: 0.551
15:27:44.053518 INFO: Train AUC: 0.581
15:27:44.053551 INFO: AUC difference: 5.12%
15:27:44.053574 WARNING: AUC difference > 5%. This may indicate overfitting.
15:27:44.314307 INFO: Resetting torch num_threads to 80
15:27:44.317477 PROGRESS: === Extracted 132107 precursors and 1282093 fragments ===
15:27:44.317941 INFO: === FDR correction performed with classifier version 10 ===
15:27:44.321803 PROGRESS: ============================= Precursor FDR =============================
15:27:44.321915 PROGRESS: Total precursors accumulated: 24,205
15:27:44.321975 PROGRESS: Target precursors: 14,586 (60.26%)
15:27:44.322026 PROGRESS: Decoy precursors: 9,619 (39.74%)
15:27:44.322081 PROGRESS: 
15:27:44.322125 PROGRESS: Precursor Summary:
15:27:44.323237 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   170; 0.001 FDR:   149
15:27:44.323330 PROGRESS: 
15:27:44.323386 PROGRESS: Protein Summary:
15:27:44.324558 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   167; 0.001 FDR:   146
15:27:44.324648 PROGRESS: =========================================================================
15:27:44.387153 INFO: Target number of precursors not reached yet.
15:27:44.610276 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:27:44.617918 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:27:44.648464 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:27:44.655654 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:27:44.717413 INFO: === skipping optimization until target number of precursors are found ===
15:27:44.717721 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
15:27:44.717838 INFO: Starting optimization step 10.
15:27:44.717912 PROGRESS: === Extracting elution groups 25400 to 51000 ===
15:27:44.717991 INFO: Using classic extraction backend
15:27:44.718184 PROGRESS: Extracting batch of 50469 precursors
15:27:44.718280 INFO: === Search parameters used ===
15:27:44.718338 INFO: rt_error       : 96.3666147229007
15:27:44.718390 INFO: mobility_error : 0.1
15:27:44.718441 INFO: num_candidates : 3
15:27:44.718491 INFO: ms1_error      : 15.0
15:27:44.718541 INFO: ms2_error      : 15.0
15:27:44.718588 INFO: fwhm_rt        : 2.758366584777832
15:27:44.718635 INFO: quant_window   : 3
15:27:44.718682 INFO: ==============================================
15:27:44.739242 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:27:44.739369 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:27:44.739428 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
15:27:44.739455 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.96
15:27:44.786299 INFO: Starting candidate selection
15:28:01.865499 INFO: Starting candidate scoring
15:28:07.333621 INFO: Finished candidate processing
15:28:07.333817 INFO: Collecting candidate features
15:28:07.594976 WARNING: intensity_correlation has 77 NaNs ( 0.06 % out of 132659)
15:28:07.595308 WARNING: height_correlation has 10 NaNs ( 0.01 % out of 132659)
15:28:07.603282 INFO: Collecting fragment features
15:28:07.688164 INFO: Finished candidate scoring
15:28:07.883904 INFO: performing precursor FDR with 47 features
15:28:07.884022 INFO: Decoy channel: -1
15:28:07.884048 INFO: Competetive: True
15:28:07.987981 INFO: Setting torch num_threads to 2 for FDR classification task
15:28:08.037120 WARNING: dropped 64 target PSMs due to missing features
15:28:08.037243 WARNING: dropped 81 decoy PSMs due to missing features
15:28:08.120318 INFO: Using random state 873257 for train-test-split
15:28:12.443375 INFO: Test AUC: 0.555
15:28:12.443489 INFO: Train AUC: 0.579
15:28:12.443522 INFO: AUC difference: 4.04%
15:28:12.753435 INFO: Resetting torch num_threads to 80
15:28:12.796561 PROGRESS: === Extracted 264766 precursors and 2565364 fragments ===
15:28:12.797280 INFO: === FDR correction performed with classifier version 10 ===
15:28:12.806766 PROGRESS: ============================= Precursor FDR =============================
15:28:12.806971 PROGRESS: Total precursors accumulated: 48,560
15:28:12.807037 PROGRESS: Target precursors: 29,271 (60.28%)
15:28:12.807086 PROGRESS: Decoy precursors: 19,289 (39.72%)
15:28:12.807128 PROGRESS: 
15:28:12.807171 PROGRESS: Precursor Summary:
15:28:12.808524 PROGRESS: Channel   0:	 0.050 FDR:   626; 0.010 FDR:   405; 0.001 FDR:   157
15:28:12.808614 PROGRESS: 
15:28:12.808671 PROGRESS: Protein Summary:
15:28:12.810095 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   386; 0.001 FDR:   153
15:28:12.810193 PROGRESS: =========================================================================
15:28:12.811026 INFO: Target number of precursors reached.
15:28:12.985755 INFO: fragments_df: keeping 5000 of 2565364 [sum(precursor_idx_mask)=12488 sum(mass_error_mask)=2565348 stop_rank=5000
15:28:13.225939 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:28:13.351492 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:28:14.768574 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:28:14.879083 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:28:15.488162 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:28:15.488572 INFO: Using score_cutoff 40.870509919738765 (fac=0.99, q=1)
15:28:15.488906 INFO: Updating optimization_manager: fwhm_rt             : 2.758366584777832 -> 2.802720546722412
15:28:15.488987 INFO: Updating optimization_manager: fwhm_mobility       : 0.008543652482330799 -> 0.008932752534747124
15:28:15.489052 INFO: Updating optimization_manager: score_cutoff        : 39.038045237731936 -> 40.870509919738765
15:28:15.489112 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:28:15.496131 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:28:15.526119 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:28:15.533044 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:28:15.593671 INFO: === checking if optimization conditions were reached ===
15:28:15.593940 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
15:28:15.595223 INFO: Updating optimization_manager: rt_error            : 96.3666147229007 -> 113.67569676809151
15:28:15.595369 INFO: Updating optimization_manager: classifier_version  : 10 -> 17
15:28:15.595473 INFO: Updating optimization_manager: score_cutoff        : 40.870509919738765 -> 40.36979282684326
15:28:15.595569 INFO: Updating optimization_manager: fwhm_rt             : 2.802720546722412 -> 2.7274222373962402
15:28:15.595661 INFO: Updating optimization_manager: fwhm_mobility       : 0.008932752534747124 -> 0.008521455340087414
15:28:15.595754 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 113.6757 found after 8 searches.
15:28:15.595821 INFO: ==============================================
15:28:15.595894 PROGRESS: Optimization finished for rt_error.
15:28:15.744016 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:28:15.751311 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:28:15.781327 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:28:15.788343 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:28:15.880226 INFO: Starting optimization step 0.
15:28:15.880458 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:28:15.880537 INFO: Using classic extraction backend
15:28:15.880670 PROGRESS: Extracting batch of 50061 precursors
15:28:15.880748 INFO: === Search parameters used ===
15:28:15.880818 INFO: rt_error       : 113.67569676809151
15:28:15.880867 INFO: mobility_error : 0.1
15:28:15.880915 INFO: num_candidates : 3
15:28:15.880962 INFO: ms1_error      : 15.0
15:28:15.881009 INFO: ms2_error      : 15.0
15:28:15.881056 INFO: fwhm_rt        : 2.7274222373962402
15:28:15.881101 INFO: quant_window   : 3
15:28:15.881147 INFO: ==============================================
15:28:15.900685 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:28:15.900803 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:28:15.900852 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
15:28:15.900878 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
15:28:15.910159 INFO: Starting candidate selection
15:28:33.522781 INFO: Starting candidate scoring
15:28:39.382257 INFO: Finished candidate processing
15:28:39.382407 INFO: Collecting candidate features
15:28:39.560640 WARNING: intensity_correlation has 44 NaNs ( 0.03 % out of 132148)
15:28:39.560967 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 132148)
15:28:39.568544 INFO: Collecting fragment features
15:28:39.644795 INFO: Finished candidate scoring
15:28:39.701241 INFO: performing precursor FDR with 47 features
15:28:39.701350 INFO: Decoy channel: -1
15:28:39.701375 INFO: Competetive: True
15:28:39.739635 INFO: Setting torch num_threads to 2 for FDR classification task
15:28:39.761704 WARNING: dropped 23 target PSMs due to missing features
15:28:39.761825 WARNING: dropped 24 decoy PSMs due to missing features
15:28:39.780318 INFO: Using random state 44328 for train-test-split
15:28:41.890055 INFO: Test AUC: 0.570
15:28:41.890159 INFO: Train AUC: 0.594
15:28:41.890188 INFO: AUC difference: 4.07%
15:28:42.153182 INFO: Resetting torch num_threads to 80
15:28:42.156385 PROGRESS: === Extracted 132148 precursors and 1287517 fragments ===
15:28:42.156856 INFO: === FDR correction performed with classifier version 17 ===
15:28:42.160702 PROGRESS: ============================= Precursor FDR =============================
15:28:42.160830 PROGRESS: Total precursors accumulated: 24,218
15:28:42.160891 PROGRESS: Target precursors: 14,876 (61.43%)
15:28:42.160940 PROGRESS: Decoy precursors: 9,342 (38.57%)
15:28:42.160984 PROGRESS: 
15:28:42.161039 PROGRESS: Precursor Summary:
15:28:42.162163 PROGRESS: Channel   0:	 0.050 FDR:   301; 0.010 FDR:   151; 0.001 FDR:     0
15:28:42.162256 PROGRESS: 
15:28:42.162311 PROGRESS: Protein Summary:
15:28:42.163457 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   148; 0.001 FDR:     0
15:28:42.163547 PROGRESS: =========================================================================
15:28:42.165061 INFO: Target number of precursors not reached yet.
15:28:42.368952 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:28:42.376585 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:28:42.407203 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:28:42.414265 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:28:42.476687 INFO: === skipping optimization until target number of precursors are found ===
15:28:42.476962 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
15:28:42.477065 INFO: Starting optimization step 1.
15:28:42.477138 PROGRESS: === Extracting elution groups 25400 to 51000 ===
15:28:42.477206 INFO: Using classic extraction backend
15:28:42.477336 PROGRESS: Extracting batch of 50469 precursors
15:28:42.477420 INFO: === Search parameters used ===
15:28:42.477479 INFO: rt_error       : 113.67569676809151
15:28:42.477530 INFO: mobility_error : 0.1
15:28:42.477595 INFO: num_candidates : 3
15:28:42.477647 INFO: ms1_error      : 15.0
15:28:42.477698 INFO: ms2_error      : 15.0
15:28:42.477751 INFO: fwhm_rt        : 2.7274222373962402
15:28:42.477803 INFO: quant_window   : 3
15:28:42.477853 INFO: ==============================================
15:28:42.497375 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:28:42.497497 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:28:42.497559 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
15:28:42.497590 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
15:28:42.498486 INFO: Starting candidate selection
15:29:01.024466 INFO: Starting candidate scoring
15:29:07.301493 INFO: Finished candidate processing
15:29:07.301658 INFO: Collecting candidate features
15:29:07.517876 WARNING: intensity_correlation has 72 NaNs ( 0.05 % out of 132711)
15:29:07.518228 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 132711)
15:29:07.526261 INFO: Collecting fragment features
15:29:07.606121 INFO: Finished candidate scoring
15:29:07.772663 INFO: performing precursor FDR with 47 features
15:29:07.772799 INFO: Decoy channel: -1
15:29:07.772825 INFO: Competetive: True
15:29:07.868387 INFO: Setting torch num_threads to 2 for FDR classification task
15:29:07.914500 WARNING: dropped 58 target PSMs due to missing features
15:29:07.914633 WARNING: dropped 65 decoy PSMs due to missing features
15:29:07.983228 INFO: Using random state 44328 for train-test-split
15:29:12.327084 INFO: Test AUC: 0.558
15:29:12.327212 INFO: Train AUC: 0.581
15:29:12.327245 INFO: AUC difference: 3.87%
15:29:12.641106 INFO: Resetting torch num_threads to 80
15:29:12.688203 PROGRESS: === Extracted 264859 precursors and 2577060 fragments ===
15:29:12.689056 INFO: === FDR correction performed with classifier version 17 ===
15:29:12.699126 PROGRESS: ============================= Precursor FDR =============================
15:29:12.699339 PROGRESS: Total precursors accumulated: 48,587
15:29:12.699404 PROGRESS: Target precursors: 29,354 (60.42%)
15:29:12.699455 PROGRESS: Decoy precursors: 19,233 (39.58%)
15:29:12.699501 PROGRESS: 
15:29:12.699545 PROGRESS: Precursor Summary:
15:29:12.701020 PROGRESS: Channel   0:	 0.050 FDR:   606; 0.010 FDR:   352; 0.001 FDR:   185
15:29:12.701117 PROGRESS: 
15:29:12.701173 PROGRESS: Protein Summary:
15:29:12.703541 PROGRESS: Channel   0:	 0.050 FDR:   572; 0.010 FDR:   337; 0.001 FDR:   179
15:29:12.703635 PROGRESS: =========================================================================
15:29:12.704808 INFO: Target number of precursors reached.
15:29:12.890696 INFO: fragments_df: keeping 4906 of 2577060 [sum(precursor_idx_mask)=10832 sum(mass_error_mask)=2577053 stop_rank=4906
15:29:13.149527 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:29:13.273168 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:29:13.406333 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:29:13.537791 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:29:14.204433 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:29:14.204922 INFO: Using score_cutoff 40.97965195884704 (fac=0.99, q=1)
15:29:14.205259 INFO: Updating optimization_manager: fwhm_rt             : 2.7274222373962402 -> 2.8483786582946777
15:29:14.205338 INFO: Updating optimization_manager: fwhm_mobility       : 0.008521455340087414 -> 0.00929076224565506
15:29:14.205391 INFO: Updating optimization_manager: score_cutoff        : 40.36979282684326 -> 40.97965195884704
15:29:14.205448 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:29:14.218117 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:29:14.282945 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:29:14.300401 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:29:14.447651 INFO: === checking if optimization conditions were reached ===
15:29:14.447966 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
15:29:14.450222 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0706468173671826
15:29:14.450347 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0706.
15:29:14.450422 INFO: ==============================================
15:29:14.450520 INFO: Starting optimization step 2.
15:29:14.450589 PROGRESS: === Extracting elution groups 0 to 51000 ===
15:29:14.450668 INFO: Using classic extraction backend
15:29:14.450851 PROGRESS: Extracting batch of 100530 precursors
15:29:14.450930 INFO: === Search parameters used ===
15:29:14.450987 INFO: rt_error       : 113.67569676809151
15:29:14.451039 INFO: mobility_error : 0.0706468173671826
15:29:14.451086 INFO: num_candidates : 3
15:29:14.451135 INFO: ms1_error      : 15.0
15:29:14.451186 INFO: ms2_error      : 15.0
15:29:14.451236 INFO: fwhm_rt        : 2.8483786582946777
15:29:14.451286 INFO: quant_window   : 3
15:29:14.451334 INFO: ==============================================
15:29:14.493922 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:29:14.494080 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:29:14.494147 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
15:29:14.494175 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.31
15:29:14.497079 INFO: Starting candidate selection
15:29:39.351289 INFO: Starting candidate scoring
15:29:49.618781 INFO: Finished candidate processing
15:29:49.618965 INFO: Collecting candidate features
15:29:50.044352 WARNING: intensity_correlation has 139 NaNs ( 0.05 % out of 259243)
15:29:50.044815 WARNING: height_correlation has 16 NaNs ( 0.01 % out of 259243)
15:29:50.057885 INFO: Collecting fragment features
15:29:50.210441 INFO: Finished candidate scoring
15:29:50.367831 INFO: performing precursor FDR with 47 features
15:29:50.367951 INFO: Decoy channel: -1
15:29:50.367976 INFO: Competetive: True
15:29:50.442325 INFO: Setting torch num_threads to 2 for FDR classification task
15:29:50.485581 WARNING: dropped 71 target PSMs due to missing features
15:29:50.485713 WARNING: dropped 73 decoy PSMs due to missing features
15:29:50.550069 INFO: Using random state 44328 for train-test-split
15:29:54.715822 INFO: Test AUC: 0.553
15:29:54.715951 INFO: Train AUC: 0.580
15:29:54.715983 INFO: AUC difference: 4.63%
15:29:55.016334 INFO: Resetting torch num_threads to 80
15:29:55.022493 PROGRESS: === Extracted 259243 precursors and 2505755 fragments ===
15:29:55.023108 INFO: === FDR correction performed with classifier version 17 ===
15:29:55.031937 PROGRESS: ============================= Precursor FDR =============================
15:29:55.032162 PROGRESS: Total precursors accumulated: 47,615
15:29:55.032225 PROGRESS: Target precursors: 28,886 (60.67%)
15:29:55.032277 PROGRESS: Decoy precursors: 18,729 (39.33%)
15:29:55.032322 PROGRESS: 
15:29:55.032372 PROGRESS: Precursor Summary:
15:29:55.033816 PROGRESS: Channel   0:	 0.050 FDR:   609; 0.010 FDR:   471; 0.001 FDR:     1
15:29:55.033926 PROGRESS: 
15:29:55.033985 PROGRESS: Protein Summary:
15:29:55.035445 PROGRESS: Channel   0:	 0.050 FDR:   575; 0.010 FDR:   444; 0.001 FDR:     1
15:29:55.035542 PROGRESS: =========================================================================
15:29:55.037260 INFO: Target number of precursors reached.
15:29:55.205359 INFO: fragments_df: keeping 5000 of 2505755 [sum(precursor_idx_mask)=14665 sum(mass_error_mask)=2505748 stop_rank=5000
15:29:55.417769 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:29:55.528686 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:29:55.641662 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:29:55.756766 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:29:56.385327 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:29:56.385832 INFO: Using score_cutoff 40.63971979522705 (fac=0.99, q=1)
15:29:56.386189 INFO: Updating optimization_manager: fwhm_rt             : 2.8483786582946777 -> 2.822336196899414
15:29:56.386272 INFO: Updating optimization_manager: fwhm_mobility       : 0.00929076224565506 -> 0.00864972360432148
15:29:56.386325 INFO: Updating optimization_manager: score_cutoff        : 40.97965195884704 -> 40.63971979522705
15:29:56.386394 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:29:56.393577 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:29:56.423672 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:29:56.430772 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:29:56.495412 INFO: === checking if optimization conditions were reached ===
15:29:56.495682 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
15:29:56.497767 INFO: Updating optimization_manager: mobility_error      : 0.0706468173671826 -> 0.06253902021901318
15:29:56.497876 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0625.
15:29:56.497947 INFO: ==============================================
15:29:56.498025 INFO: Starting optimization step 3.
15:29:56.498101 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:29:56.498169 INFO: Using classic extraction backend
15:29:56.498335 PROGRESS: Extracting batch of 50061 precursors
15:29:56.498408 INFO: === Search parameters used ===
15:29:56.498457 INFO: rt_error       : 113.67569676809151
15:29:56.498501 INFO: mobility_error : 0.06253902021901318
15:29:56.498542 INFO: num_candidates : 3
15:29:56.498585 INFO: ms1_error      : 15.0
15:29:56.498627 INFO: ms2_error      : 15.0
15:29:56.498669 INFO: fwhm_rt        : 2.822336196899414
15:29:56.498712 INFO: quant_window   : 3
15:29:56.498754 INFO: ==============================================
15:29:56.516044 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:29:56.516168 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:29:56.516221 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
15:29:56.516244 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.01
15:29:56.525030 INFO: Starting candidate selection
15:30:07.912550 INFO: Starting candidate scoring
15:30:13.767141 INFO: Finished candidate processing
15:30:13.767327 INFO: Collecting candidate features
15:30:13.994028 WARNING: intensity_correlation has 69 NaNs ( 0.05 % out of 128176)
15:30:13.994464 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 128176)
15:30:14.004825 INFO: Collecting fragment features
15:30:14.093685 INFO: Finished candidate scoring
15:30:14.213738 INFO: performing precursor FDR with 47 features
15:30:14.213860 INFO: Decoy channel: -1
15:30:14.213885 INFO: Competetive: True
15:30:14.254274 INFO: Setting torch num_threads to 2 for FDR classification task
15:30:14.278786 WARNING: dropped 41 target PSMs due to missing features
15:30:14.278908 WARNING: dropped 31 decoy PSMs due to missing features
15:30:14.295331 INFO: Using random state 44328 for train-test-split
15:30:16.367367 INFO: Test AUC: 0.564
15:30:16.367476 INFO: Train AUC: 0.604
15:30:16.367508 INFO: AUC difference: 6.63%
15:30:16.367531 WARNING: AUC difference > 5%. This may indicate overfitting.
15:30:16.632129 INFO: Resetting torch num_threads to 80
15:30:16.635872 PROGRESS: === Extracted 128176 precursors and 1234143 fragments ===
15:30:16.636426 INFO: === FDR correction performed with classifier version 17 ===
15:30:16.640372 PROGRESS: ============================= Precursor FDR =============================
15:30:16.640492 PROGRESS: Total precursors accumulated: 23,526
15:30:16.640553 PROGRESS: Target precursors: 14,591 (62.02%)
15:30:16.640604 PROGRESS: Decoy precursors: 8,935 (37.98%)
15:30:16.640648 PROGRESS: 
15:30:16.640697 PROGRESS: Precursor Summary:
15:30:16.641849 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   211; 0.001 FDR:     0
15:30:16.641941 PROGRESS: 
15:30:16.642009 PROGRESS: Protein Summary:
15:30:16.643246 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   208; 0.001 FDR:     0
15:30:16.643337 PROGRESS: =========================================================================
15:30:16.688312 INFO: Target number of precursors reached.
15:30:16.770201 INFO: fragments_df: keeping 2845 of 1234143 [sum(precursor_idx_mask)=6597 sum(mass_error_mask)=1234141 stop_rank=2845
15:30:16.913062 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:30:17.023767 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:30:17.138422 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:30:17.256846 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:30:17.632591 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:30:17.633054 INFO: Using score_cutoff 44.95094274902344 (fac=0.99, q=1)
15:30:17.633389 INFO: Updating optimization_manager: fwhm_rt             : 2.822336196899414 -> 2.7886059284210205
15:30:17.633477 INFO: Updating optimization_manager: fwhm_mobility       : 0.00864972360432148 -> 0.008955848403275013
15:30:17.633533 INFO: Updating optimization_manager: score_cutoff        : 40.63971979522705 -> 44.95094274902344
15:30:17.633591 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:30:17.640897 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:30:17.677407 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:30:17.686745 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:30:17.753194 INFO: === checking if optimization conditions were reached ===
15:30:17.753502 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
15:30:17.755929 INFO: Updating optimization_manager: mobility_error      : 0.06253902021901318 -> 0.05892537779728436
15:30:17.756056 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0589.
15:30:17.756131 INFO: ==============================================
15:30:17.756217 INFO: Starting optimization step 4.
15:30:17.756283 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:30:17.756356 INFO: Using classic extraction backend
15:30:17.756540 PROGRESS: Extracting batch of 50061 precursors
15:30:17.756620 INFO: === Search parameters used ===
15:30:17.756680 INFO: rt_error       : 113.67569676809151
15:30:17.756732 INFO: mobility_error : 0.05892537779728436
15:30:17.756783 INFO: num_candidates : 3
15:30:17.756843 INFO: ms1_error      : 15.0
15:30:17.756896 INFO: ms2_error      : 15.0
15:30:17.756944 INFO: fwhm_rt        : 2.7886059284210205
15:30:17.756994 INFO: quant_window   : 3
15:30:17.757042 INFO: ==============================================
15:30:17.782358 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:30:17.782491 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:30:17.782553 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
15:30:17.782582 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.15
15:30:17.796071 INFO: Starting candidate selection
15:30:29.391910 INFO: Starting candidate scoring
15:30:35.264051 INFO: Finished candidate processing
15:30:35.264335 INFO: Collecting candidate features
15:30:35.563470 WARNING: intensity_correlation has 73 NaNs ( 0.06 % out of 128142)
15:30:35.563807 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 128142)
15:30:35.571763 INFO: Collecting fragment features
15:30:35.649428 INFO: Finished candidate scoring
15:30:35.758822 INFO: performing precursor FDR with 47 features
15:30:35.758934 INFO: Decoy channel: -1
15:30:35.758959 INFO: Competetive: True
15:30:35.802356 INFO: Setting torch num_threads to 2 for FDR classification task
15:30:35.827975 WARNING: dropped 41 target PSMs due to missing features
15:30:35.828101 WARNING: dropped 34 decoy PSMs due to missing features
15:30:35.852116 INFO: Using random state 44328 for train-test-split
15:30:37.956591 INFO: Test AUC: 0.562
15:30:37.956951 INFO: Train AUC: 0.586
15:30:37.956988 INFO: AUC difference: 4.05%
15:30:38.224398 INFO: Resetting torch num_threads to 80
15:30:38.228287 PROGRESS: === Extracted 128142 precursors and 1229067 fragments ===
15:30:38.228829 INFO: === FDR correction performed with classifier version 17 ===
15:30:38.232783 PROGRESS: ============================= Precursor FDR =============================
15:30:38.232906 PROGRESS: Total precursors accumulated: 23,516
15:30:38.232965 PROGRESS: Target precursors: 14,253 (60.61%)
15:30:38.233016 PROGRESS: Decoy precursors: 9,263 (39.39%)
15:30:38.233061 PROGRESS: 
15:30:38.233107 PROGRESS: Precursor Summary:
15:30:38.234255 PROGRESS: Channel   0:	 0.050 FDR:   309; 0.010 FDR:   240; 0.001 FDR:   179
15:30:38.234362 PROGRESS: 
15:30:38.234419 PROGRESS: Protein Summary:
15:30:38.235657 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   237; 0.001 FDR:   176
15:30:38.235746 PROGRESS: =========================================================================
15:30:38.236695 INFO: Target number of precursors reached.
15:30:38.319465 INFO: fragments_df: keeping 3139 of 1229067 [sum(precursor_idx_mask)=7467 sum(mass_error_mask)=1229064 stop_rank=3139
15:30:38.535050 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:30:38.656533 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:30:38.772679 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:30:38.883404 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:30:39.225692 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:30:39.226131 INFO: Using score_cutoff 40.95432546844482 (fac=0.99, q=1)
15:30:39.226458 INFO: Updating optimization_manager: fwhm_rt             : 2.7886059284210205 -> 2.842933177947998
15:30:39.226539 INFO: Updating optimization_manager: fwhm_mobility       : 0.008955848403275013 -> 0.008758852258324623
15:30:39.226592 INFO: Updating optimization_manager: score_cutoff        : 44.95094274902344 -> 40.95432546844482
15:30:39.226649 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:30:39.233929 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:30:39.264568 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:30:39.272361 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:30:39.336337 INFO: === checking if optimization conditions were reached ===
15:30:39.336632 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
15:30:39.338937 INFO: Updating optimization_manager: mobility_error      : 0.05892537779728436 -> 0.049737655389633297
15:30:39.339057 PROGRESS: ❌ mobility_error : optimization incomplete after 4 search(es). Will search with parameter 0.0497.
15:30:39.339136 INFO: ==============================================
15:30:39.339229 INFO: Starting optimization step 5.
15:30:39.339323 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:30:39.339416 INFO: Using classic extraction backend
15:30:39.339644 PROGRESS: Extracting batch of 50061 precursors
15:30:39.339731 INFO: === Search parameters used ===
15:30:39.339792 INFO: rt_error       : 113.67569676809151
15:30:39.339846 INFO: mobility_error : 0.049737655389633297
15:30:39.339898 INFO: num_candidates : 3
15:30:39.339952 INFO: ms1_error      : 15.0
15:30:39.340004 INFO: ms2_error      : 15.0
15:30:39.340053 INFO: fwhm_rt        : 2.842933177947998
15:30:39.340101 INFO: quant_window   : 3
15:30:39.340150 INFO: ==============================================
15:30:39.364580 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:30:39.364704 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:30:39.364764 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
15:30:39.364793 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.06
15:30:39.365749 INFO: Starting candidate selection
15:30:48.210602 INFO: Starting candidate scoring
15:30:54.062596 INFO: Finished candidate processing
15:30:54.062751 INFO: Collecting candidate features
15:30:54.266822 WARNING: intensity_correlation has 74 NaNs ( 0.06 % out of 125804)
15:30:54.267205 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 125804)
15:30:54.277170 INFO: Collecting fragment features
15:30:54.352774 INFO: Finished candidate scoring
15:30:54.411412 INFO: performing precursor FDR with 47 features
15:30:54.411524 INFO: Decoy channel: -1
15:30:54.411549 INFO: Competetive: True
15:30:54.450237 INFO: Setting torch num_threads to 2 for FDR classification task
15:30:54.475928 WARNING: dropped 35 target PSMs due to missing features
15:30:54.476053 WARNING: dropped 43 decoy PSMs due to missing features
15:30:54.495841 INFO: Using random state 44328 for train-test-split
15:30:56.544358 INFO: Test AUC: 0.564
15:30:56.544475 INFO: Train AUC: 0.595
15:30:56.544506 INFO: AUC difference: 5.22%
15:30:56.544528 WARNING: AUC difference > 5%. This may indicate overfitting.
15:30:56.803619 INFO: Resetting torch num_threads to 80
15:30:56.807420 PROGRESS: === Extracted 125804 precursors and 1193573 fragments ===
15:30:56.807884 INFO: === FDR correction performed with classifier version 17 ===
15:30:56.811701 PROGRESS: ============================= Precursor FDR =============================
15:30:56.811830 PROGRESS: Total precursors accumulated: 23,137
15:30:56.811890 PROGRESS: Target precursors: 14,162 (61.21%)
15:30:56.811940 PROGRESS: Decoy precursors: 8,975 (38.79%)
15:30:56.811985 PROGRESS: 
15:30:56.812029 PROGRESS: Precursor Summary:
15:30:56.813068 PROGRESS: Channel   0:	 0.050 FDR:   330; 0.010 FDR:     9; 0.001 FDR:     9
15:30:56.813169 PROGRESS: 
15:30:56.813225 PROGRESS: Protein Summary:
15:30:56.814356 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:     9; 0.001 FDR:     9
15:30:56.814451 PROGRESS: =========================================================================
15:30:56.815223 INFO: Target number of precursors not reached yet.
15:30:57.084248 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:30:57.091797 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:30:57.122757 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:30:57.130732 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:30:57.194499 INFO: === skipping optimization until target number of precursors are found ===
15:30:57.194767 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
15:30:57.194875 INFO: Starting optimization step 6.
15:30:57.194955 PROGRESS: === Extracting elution groups 25400 to 51000 ===
15:30:57.195032 INFO: Using classic extraction backend
15:30:57.195175 PROGRESS: Extracting batch of 50469 precursors
15:30:57.195271 INFO: === Search parameters used ===
15:30:57.195338 INFO: rt_error       : 113.67569676809151
15:30:57.195400 INFO: mobility_error : 0.049737655389633297
15:30:57.195461 INFO: num_candidates : 3
15:30:57.195521 INFO: ms1_error      : 15.0
15:30:57.195577 INFO: ms2_error      : 15.0
15:30:57.195652 INFO: fwhm_rt        : 2.842933177947998
15:30:57.195713 INFO: quant_window   : 3
15:30:57.195771 INFO: ==============================================
15:30:57.211882 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:30:57.211995 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:30:57.212047 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
15:30:57.212083 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.06
15:30:57.212911 INFO: Starting candidate selection
15:31:06.591522 INFO: Starting candidate scoring
15:31:12.543196 INFO: Finished candidate processing
15:31:12.544157 INFO: Collecting candidate features
15:31:12.757437 WARNING: intensity_correlation has 89 NaNs ( 0.07 % out of 126505)
15:31:12.757787 WARNING: height_correlation has 12 NaNs ( 0.01 % out of 126505)
15:31:12.766062 INFO: Collecting fragment features
15:31:12.852905 INFO: Finished candidate scoring
15:31:12.970166 INFO: performing precursor FDR with 47 features
15:31:12.970295 INFO: Decoy channel: -1
15:31:12.970321 INFO: Competetive: True
15:31:13.065386 INFO: Setting torch num_threads to 2 for FDR classification task
15:31:13.113400 WARNING: dropped 77 target PSMs due to missing features
15:31:13.113525 WARNING: dropped 94 decoy PSMs due to missing features
15:31:13.176116 INFO: Using random state 44328 for train-test-split
15:31:16.174328 INFO: Test AUC: 0.556
15:31:16.174445 INFO: Train AUC: 0.580
15:31:16.174477 INFO: AUC difference: 4.24%
15:31:16.469546 INFO: Resetting torch num_threads to 80
15:31:16.515510 PROGRESS: === Extracted 252309 precursors and 2389932 fragments ===
15:31:16.516204 INFO: === FDR correction performed with classifier version 17 ===
15:31:16.526694 PROGRESS: ============================= Precursor FDR =============================
15:31:16.526887 PROGRESS: Total precursors accumulated: 46,432
15:31:16.526948 PROGRESS: Target precursors: 28,031 (60.37%)
15:31:16.526995 PROGRESS: Decoy precursors: 18,401 (39.63%)
15:31:16.527038 PROGRESS: 
15:31:16.527081 PROGRESS: Precursor Summary:
15:31:16.528423 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:   303; 0.001 FDR:   142
15:31:16.528521 PROGRESS: 
15:31:16.528576 PROGRESS: Protein Summary:
15:31:16.529986 PROGRESS: Channel   0:	 0.050 FDR:   557; 0.010 FDR:   288; 0.001 FDR:   135
15:31:16.530086 PROGRESS: =========================================================================
15:31:16.530922 INFO: Target number of precursors reached.
15:31:16.702935 INFO: fragments_df: keeping 4165 of 2389932 [sum(precursor_idx_mask)=9431 sum(mass_error_mask)=2389923 stop_rank=4165
15:31:16.929620 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:31:17.056581 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:31:17.182009 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:31:17.299937 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:31:17.842403 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:31:17.842817 INFO: Using score_cutoff 45.64830632629395 (fac=0.99, q=1)
15:31:17.843119 INFO: Updating optimization_manager: fwhm_rt             : 2.842933177947998 -> 2.8947863578796387
15:31:17.843199 INFO: Updating optimization_manager: fwhm_mobility       : 0.008758852258324623 -> 0.009404970332980156
15:31:17.843252 INFO: Updating optimization_manager: score_cutoff        : 40.95432546844482 -> 45.64830632629395
15:31:17.843304 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:31:17.856234 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:31:17.923373 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:31:17.942004 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:31:18.080998 INFO: === checking if optimization conditions were reached ===
15:31:18.081273 PROGRESS: === Optimization of mobility_error has been performed 5 time(s); minimum number is 2 ===
15:31:18.082303 INFO: Updating optimization_manager: mobility_error      : 0.049737655389633297 -> 0.05892537779728436
15:31:18.082442 INFO: Updating optimization_manager: classifier_version  : 17 -> 26
15:31:18.082547 INFO: Updating optimization_manager: score_cutoff        : 45.64830632629395 -> 40.95432546844482
15:31:18.082645 INFO: Updating optimization_manager: fwhm_rt             : 2.8947863578796387 -> 2.842933177947998
15:31:18.082738 INFO: Updating optimization_manager: fwhm_mobility       : 0.009404970332980156 -> 0.008758852258324623
15:31:18.082851 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0589 found after 5 searches.
15:31:18.082927 INFO: ==============================================
15:31:18.083008 PROGRESS: Optimization finished for mobility_error.
15:31:18.278767 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:31:18.286086 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:31:18.316339 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:31:18.323580 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:31:18.424118 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
15:31:18.424354 PROGRESS: ==============================================
15:31:18.424431 PROGRESS: ms2_error      : 15.0000
15:31:18.424500 PROGRESS: ms1_error      : 15.0000
15:31:18.424563 PROGRESS: rt_error       : 113.6757
15:31:18.424618 PROGRESS: mobility_error : 0.0589
15:31:18.424671 PROGRESS: ==============================================
15:31:18.429908 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:31:20.064945 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:31:27.790632 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:31:29.482959 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:31:46.775354 INFO: Using classic extraction backend
15:31:46.776132 PROGRESS: Extracting batch of 12073114 precursors
15:31:46.776303 INFO: === Search parameters used ===
15:31:46.776364 INFO: rt_error       : 113.67569676809151
15:31:46.776416 INFO: mobility_error : 0.05892537779728436
15:31:46.776460 INFO: num_candidates : 3
15:31:46.776500 INFO: ms1_error      : 15.0
15:31:46.776545 INFO: ms2_error      : 15.0
15:31:46.776587 INFO: fwhm_rt        : 2.842933177947998
15:31:46.776627 INFO: quant_window   : 3
15:31:46.776669 INFO: ==============================================
15:31:49.413936 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:31:49.414066 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:31:49.414123 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
15:31:49.414148 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.06
15:31:49.415267 INFO: Starting candidate selection
16:09:42.807028 INFO: Removed 21091751 precursors with score below cutoff 40.95432546844482
16:09:45.550812 INFO: Starting candidate scoring
16:18:05.051220 INFO: Finished candidate processing
16:18:05.051723 INFO: Collecting candidate features
16:18:25.509965 INFO: Collecting fragment features
16:18:34.571083 INFO: Finished candidate scoring
16:18:48.840482 INFO: === Performing FDR correction with classifier version 26 ===
16:18:48.845257 INFO: performing precursor FDR with 47 features
16:18:48.845310 INFO: Decoy channel: -1
16:18:48.845337 INFO: Competetive: True
16:18:51.799971 INFO: Setting torch num_threads to 2 for FDR classification task
16:18:57.580643 INFO: Using random state 274847 for train-test-split
16:22:51.108714 INFO: Test AUC: 0.570
16:22:51.108852 INFO: Train AUC: 0.571
16:22:51.108887 INFO: AUC difference: 0.23%
16:22:54.154150 INFO: Resetting torch num_threads to 80
16:22:54.385349 INFO: Removing fragments below FDR threshold
16:22:55.556994 PROGRESS: ============================= Precursor FDR =============================
16:22:55.557238 PROGRESS: Total precursors accumulated: 69,716
16:22:55.557302 PROGRESS: Target precursors: 69,026 (99.01%)
16:22:55.557354 PROGRESS: Decoy precursors: 690 (0.99%)
16:22:55.557399 PROGRESS: 
16:22:55.557442 PROGRESS: Precursor Summary:
16:22:55.584634 PROGRESS: Channel   0:	 0.050 FDR: 69,026; 0.010 FDR: 69,026; 0.001 FDR: 49,860
16:22:55.584872 PROGRESS: 
16:22:55.584934 PROGRESS: Protein Summary:
16:22:55.616949 PROGRESS: Channel   0:	 0.050 FDR: 11,068; 0.010 FDR: 11,068; 0.001 FDR: 8,939
16:22:55.617158 PROGRESS: =========================================================================
16:22:55.771936 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/psm.parquet
16:22:56.138427 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/frag.parquet
16:22:56.405196 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
16:22:56.764454 PROGRESS: 
16:22:56.764596 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant
16:22:56.764664 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/figures
16:22:56.764828 INFO: Initializing TimingManager
16:22:56.765369 INFO: Initializing RawFileManager
16:22:56.765484 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:22:56.765539 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:22:56.765580 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:22:57.085806 INFO: Reading 39,128 frames with 2,766,418,119 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:23:04.550960 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
16:23:04.552362 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:23:04.556193 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:23:04.556585 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:23:04.557013 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:23:04.558739 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:23:04.572324 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:23:04.572583 INFO: Indexing quadrupole dimension
16:23:05.067914 INFO: Transposing detector events
16:23:13.912708 INFO: Finished transposing data
16:23:13.950521 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
16:23:13.951872 INFO: RT (min)            : 0.0 - 70.0
16:23:13.951966 INFO: RT duration (sec)   : 4199.9
16:23:13.952025 INFO: RT duration (min)   : 70.0
16:23:13.952073 INFO: Cycle len (scans)   : 9
16:23:13.952119 INFO: Cycle len (sec)     : 0.97
16:23:13.952162 INFO: Number of cycles    : 4347
16:23:13.952205 INFO: MS2 range (m/z)     : 400.0 - 1000.0
16:23:13.952328 INFO: Creating DIA data object took: 17.18683433532715
16:23:15.542573 INFO: Initializing CalibrationManager
16:23:15.542844 INFO: Setting up calibration estimators ..
16:23:15.542908 INFO: Found 1 estimator(s) in calibration group 'fragment'
16:23:15.542989 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'}' ..
16:23:15.543065 INFO: Found 3 estimator(s) in calibration group 'precursor'
16:23:15.543123 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'}' ..
16:23:15.543181 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}}' ..
16:23:15.543245 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}}' ..
16:23:15.543294 INFO: Done setting up calibration estimators.
16:23:15.543792 INFO: Initializing OptimizationManager
16:23:15.543894 INFO: initial parameter: ms1_error = 30
16:23:15.543943 INFO: initial parameter: ms2_error = 30
16:23:15.543987 INFO: initial parameter: rt_error = 2099.9331315
16:23:15.544030 INFO: initial parameter: mobility_error = 0.1
16:23:15.544070 INFO: initial parameter: num_candidates = 1
16:23:15.544109 INFO: initial parameter: fwhm_rt = 5
16:23:15.544151 INFO: initial parameter: fwhm_mobility = 0.01
16:23:15.544191 INFO: initial parameter: score_cutoff = 0
16:23:15.544229 INFO: initial parameter: classifier_version = -1
16:23:15.544303 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
16:23:15.544611 INFO: FDRManager: loading saved state not requested, will be initialized.
16:23:15.544646 INFO: Initializing FDRManager
16:23:15.544685 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
16:23:16.753793 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
16:23:17.505896 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
16:23:17.506298 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 2099.9331315
16:23:17.506408 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
16:23:17.506592 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
16:23:17.506679 PROGRESS: Starting initial search for precursors.
16:23:17.506768 INFO: Starting optimization step 0.
16:23:17.506829 PROGRESS: === Extracting elution groups 0 to 200 ===
16:23:17.506893 INFO: Using classic extraction backend
16:23:17.507062 PROGRESS: Extracting batch of 390 precursors
16:23:17.507129 INFO: === Search parameters used ===
16:23:17.507178 INFO: rt_error       : 2099.9331315
16:23:17.507220 INFO: mobility_error : 0.1
16:23:17.507261 INFO: num_candidates : 1
16:23:17.507302 INFO: ms1_error      : 30
16:23:17.507340 INFO: ms2_error      : 30
16:23:17.507379 INFO: fwhm_rt        : 5
16:23:17.507416 INFO: quant_window   : 3
16:23:17.507453 INFO: ==============================================
16:23:17.508222 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:23:17.508265 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:23:17.508303 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
16:23:17.508324 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
16:23:17.509249 INFO: Starting candidate selection
16:23:21.580607 INFO: Starting candidate scoring
16:23:21.653245 INFO: Finished candidate processing
16:23:21.653343 INFO: Collecting candidate features
16:23:21.662671 INFO: Collecting fragment features
16:23:21.664780 INFO: Finished candidate scoring
16:23:21.665620 INFO: performing precursor FDR with 47 features
16:23:21.665661 INFO: Decoy channel: -1
16:23:21.665684 INFO: Competetive: True
16:23:21.666945 INFO: Setting torch num_threads to 2 for FDR classification task
16:23:21.669425 INFO: Using random state 181464 for train-test-split
16:23:21.677520 INFO: Test AUC: 0.518
16:23:21.677588 INFO: Train AUC: 0.527
16:23:21.677618 INFO: AUC difference: 1.80%
16:23:21.895698 INFO: Resetting torch num_threads to 80
16:23:21.896134 PROGRESS: === Extracted 364 precursors and 3938 fragments ===
16:23:21.896530 INFO: === FDR correction performed with classifier version -1 ===
16:23:21.897046 PROGRESS: ============================= Precursor FDR =============================
16:23:21.897133 PROGRESS: Total precursors accumulated: 187
16:23:21.897192 PROGRESS: Target precursors: 132 (70.59%)
16:23:21.897243 PROGRESS: Decoy precursors: 55 (29.41%)
16:23:21.897289 PROGRESS: 
16:23:21.897334 PROGRESS: Precursor Summary:
16:23:21.898236 PROGRESS: Channel   0:	 0.050 FDR:   114; 0.010 FDR:   114; 0.001 FDR:   114
16:23:21.898328 PROGRESS: 
16:23:21.898392 PROGRESS: Protein Summary:
16:23:21.899378 PROGRESS: Channel   0:	 0.050 FDR:   114; 0.010 FDR:   114; 0.001 FDR:   114
16:23:21.899467 PROGRESS: =========================================================================
16:23:21.899572 INFO: Target number of precursors not reached yet.
16:23:21.964403 INFO: Starting optimization step 1.
16:23:21.964589 PROGRESS: === Extracting elution groups 200 to 600 ===
16:23:21.964665 INFO: Using classic extraction backend
16:23:21.964780 PROGRESS: Extracting batch of 783 precursors
16:23:21.964854 INFO: === Search parameters used ===
16:23:21.964911 INFO: rt_error       : 2099.9331315
16:23:21.964957 INFO: mobility_error : 0.1
16:23:21.965001 INFO: num_candidates : 1
16:23:21.965043 INFO: ms1_error      : 30
16:23:21.965083 INFO: ms2_error      : 30
16:23:21.965125 INFO: fwhm_rt        : 5
16:23:21.965166 INFO: quant_window   : 3
16:23:21.965206 INFO: ==============================================
16:23:21.965866 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:23:21.965910 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:23:21.965940 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
16:23:21.965963 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
16:23:21.966743 INFO: Starting candidate selection
16:23:28.316621 INFO: Starting candidate scoring
16:23:28.430412 INFO: Finished candidate processing
16:23:28.430509 INFO: Collecting candidate features
16:23:28.439954 INFO: Collecting fragment features
16:23:28.442293 INFO: Finished candidate scoring
16:23:28.444956 INFO: performing precursor FDR with 47 features
16:23:28.445013 INFO: Decoy channel: -1
16:23:28.445037 INFO: Competetive: True
16:23:28.447880 INFO: Setting torch num_threads to 2 for FDR classification task
16:23:28.449543 INFO: Using random state 815986 for train-test-split
16:23:28.458160 INFO: Test AUC: 0.502
16:23:28.458218 INFO: Train AUC: 0.500
16:23:28.458248 INFO: AUC difference: 0.37%
16:23:28.669790 INFO: Resetting torch num_threads to 80
16:23:28.671033 PROGRESS: === Extracted 1114 precursors and 12160 fragments ===
16:23:28.671419 INFO: === FDR correction performed with classifier version -1 ===
16:23:28.671976 PROGRESS: ============================= Precursor FDR =============================
16:23:28.672064 PROGRESS: Total precursors accumulated: 574
16:23:28.672123 PROGRESS: Target precursors: 409 (71.25%)
16:23:28.672179 PROGRESS: Decoy precursors: 165 (28.75%)
16:23:28.672227 PROGRESS: 
16:23:28.672276 PROGRESS: Precursor Summary:
16:23:28.673238 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   343; 0.001 FDR:   343
16:23:28.673327 PROGRESS: 
16:23:28.673382 PROGRESS: Protein Summary:
16:23:28.674520 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   339; 0.001 FDR:   339
16:23:28.674613 PROGRESS: =========================================================================
16:23:28.674756 INFO: Target number of precursors reached.
16:23:28.677541 INFO: fragments_df: keeping 694 of 12160 [sum(precursor_idx_mask)=3843 sum(mass_error_mask)=12160 stop_rank=694
16:23:28.776326 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:23:28.893050 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:23:29.026583 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:23:29.130652 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:23:29.262394 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
16:23:29.262783 INFO: Using score_cutoff 36.841109765625 (fac=0.99, q=1)
16:23:29.263093 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.290309429168701
16:23:29.263174 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008165770210325718
16:23:29.263231 INFO: Updating optimization_manager: score_cutoff        : 0 -> 36.841109765625
16:23:29.263294 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:23:29.264327 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:23:29.265647 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:23:29.266447 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:23:29.268601 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
16:23:29.268695 PROGRESS: Required number of precursors found. Starting search parameter optimization.
16:23:29.268776 INFO: Starting optimization step 2.
16:23:29.268836 PROGRESS: === Extracting elution groups 0 to 600 ===
16:23:29.268892 INFO: Using classic extraction backend
16:23:29.268993 PROGRESS: Extracting batch of 1173 precursors
16:23:29.269056 INFO: === Search parameters used ===
16:23:29.269103 INFO: rt_error       : 2099.9331315
16:23:29.269146 INFO: mobility_error : 0.1
16:23:29.269187 INFO: num_candidates : 3
16:23:29.269227 INFO: ms1_error      : 30
16:23:29.269267 INFO: ms2_error      : 30
16:23:29.269307 INFO: fwhm_rt        : 3.290309429168701
16:23:29.269347 INFO: quant_window   : 3
16:23:29.269386 INFO: ==============================================
16:23:29.270254 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:23:29.270301 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:23:29.270336 INFO: FWHM in RT is 3.29 seconds, sigma is 0.72
16:23:29.270357 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
16:23:29.271006 INFO: Starting candidate selection
16:23:38.685958 INFO: Starting candidate scoring
16:23:38.979876 INFO: Finished candidate processing
16:23:38.980010 INFO: Collecting candidate features
16:23:38.994777 INFO: Collecting fragment features
16:23:38.998732 INFO: Finished candidate scoring
16:23:39.000886 INFO: performing precursor FDR with 47 features
16:23:39.000943 INFO: Decoy channel: -1
16:23:39.000967 INFO: Competetive: True
16:23:39.004947 INFO: Setting torch num_threads to 2 for FDR classification task
16:23:39.007215 INFO: Using random state 277152 for train-test-split
16:23:39.018668 INFO: Test AUC: 0.497
16:23:39.018734 INFO: Train AUC: 0.504
16:23:39.018764 INFO: AUC difference: 1.30%
16:23:39.238988 INFO: Resetting torch num_threads to 80
16:23:39.239676 PROGRESS: === Extracted 3241 precursors and 35441 fragments ===
16:23:39.240185 INFO: === FDR correction performed with classifier version 1 ===
16:23:39.241197 PROGRESS: ============================= Precursor FDR =============================
16:23:39.241293 PROGRESS: Total precursors accumulated: 588
16:23:39.241353 PROGRESS: Target precursors: 491 (83.50%)
16:23:39.241402 PROGRESS: Decoy precursors: 97 (16.50%)
16:23:39.241447 PROGRESS: 
16:23:39.241489 PROGRESS: Precursor Summary:
16:23:39.242530 PROGRESS: Channel   0:	 0.050 FDR:   469; 0.010 FDR:   469; 0.001 FDR:   469
16:23:39.242624 PROGRESS: 
16:23:39.242680 PROGRESS: Protein Summary:
16:23:39.243895 PROGRESS: Channel   0:	 0.050 FDR:   462; 0.010 FDR:   462; 0.001 FDR:   462
16:23:39.243986 PROGRESS: =========================================================================
16:23:39.244184 INFO: Target number of precursors reached.
16:23:39.250773 INFO: fragments_df: keeping 2808 of 35441 [sum(precursor_idx_mask)=14802 sum(mass_error_mask)=35441 stop_rank=2808
16:23:39.352328 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:23:39.490693 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:23:39.628933 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:23:39.764208 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:23:40.140008 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:23:40.140568 INFO: Using score_cutoff 36.349938583374026 (fac=0.99, q=1)
16:23:40.140910 INFO: Updating optimization_manager: fwhm_rt             : 3.290309429168701 -> 3.107961893081665
16:23:40.140994 INFO: Updating optimization_manager: fwhm_mobility       : 0.008165770210325718 -> 0.007825210690498352
16:23:40.141050 INFO: Updating optimization_manager: score_cutoff        : 36.841109765625 -> 36.349938583374026
16:23:40.141104 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:23:40.142355 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:23:40.143684 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:23:40.144451 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:23:40.146622 INFO: === checking if optimization conditions were reached ===
16:23:40.147928 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.222457377501456
16:23:40.148023 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
16:23:40.148086 PROGRESS: ❌ ms2_error      : 17.2225 > 15.0000 or insufficient steps taken.
16:23:40.149031 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
16:23:40.149121 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
16:23:40.149181 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
16:23:40.149232 INFO: ==============================================
16:23:40.149293 INFO: Starting optimization step 3.
16:23:40.149351 PROGRESS: === Extracting elution groups 0 to 600 ===
16:23:40.149404 INFO: Using classic extraction backend
16:23:40.149522 PROGRESS: Extracting batch of 1173 precursors
16:23:40.149586 INFO: === Search parameters used ===
16:23:40.149638 INFO: rt_error       : 2099.9331315
16:23:40.149682 INFO: mobility_error : 0.1
16:23:40.149723 INFO: num_candidates : 3
16:23:40.149763 INFO: ms1_error      : 15.0
16:23:40.149802 INFO: ms2_error      : 17.222457377501456
16:23:40.149841 INFO: fwhm_rt        : 3.107961893081665
16:23:40.149879 INFO: quant_window   : 3
16:23:40.149918 INFO: ==============================================
16:23:40.150833 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:23:40.150894 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:23:40.150929 INFO: FWHM in RT is 3.11 seconds, sigma is 0.68
16:23:40.150951 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
16:23:40.151666 INFO: Starting candidate selection
16:23:48.883280 INFO: Starting candidate scoring
16:23:49.078214 INFO: Finished candidate processing
16:23:49.078399 INFO: Collecting candidate features
16:23:49.092971 INFO: Collecting fragment features
16:23:49.096752 INFO: Finished candidate scoring
16:23:49.098701 INFO: performing precursor FDR with 47 features
16:23:49.098745 INFO: Decoy channel: -1
16:23:49.098769 INFO: Competetive: True
16:23:49.101561 INFO: Setting torch num_threads to 2 for FDR classification task
16:23:49.103913 INFO: Using random state 489579 for train-test-split
16:23:49.114787 INFO: Test AUC: 0.523
16:23:49.114849 INFO: Train AUC: 0.531
16:23:49.114879 INFO: AUC difference: 1.50%
16:23:49.326342 INFO: Resetting torch num_threads to 80
16:23:49.326895 PROGRESS: === Extracted 3238 precursors and 34071 fragments ===
16:23:49.327304 INFO: === FDR correction performed with classifier version 2 ===
16:23:49.327865 PROGRESS: ============================= Precursor FDR =============================
16:23:49.327954 PROGRESS: Total precursors accumulated: 585
16:23:49.328011 PROGRESS: Target precursors: 449 (76.75%)
16:23:49.328060 PROGRESS: Decoy precursors: 136 (23.25%)
16:23:49.328105 PROGRESS: 
16:23:49.328149 PROGRESS: Precursor Summary:
16:23:49.329154 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   407; 0.001 FDR:   407
16:23:49.329243 PROGRESS: 
16:23:49.329298 PROGRESS: Protein Summary:
16:23:49.330450 PROGRESS: Channel   0:	 0.050 FDR:   399; 0.010 FDR:   399; 0.001 FDR:   399
16:23:49.330539 PROGRESS: =========================================================================
16:23:49.330683 INFO: Target number of precursors reached.
16:23:49.336366 INFO: fragments_df: keeping 2079 of 34071 [sum(precursor_idx_mask)=12305 sum(mass_error_mask)=34071 stop_rank=2079
16:23:49.435944 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:23:49.562101 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:23:49.685784 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:23:49.796832 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:23:50.027309 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:23:50.027710 INFO: Using score_cutoff 32.22899983520508 (fac=0.99, q=1)
16:23:50.028000 INFO: Updating optimization_manager: fwhm_rt             : 3.107961893081665 -> 2.860062837600708
16:23:50.028080 INFO: Updating optimization_manager: fwhm_mobility       : 0.007825210690498352 -> 0.006174369715154171
16:23:50.028138 INFO: Updating optimization_manager: score_cutoff        : 36.349938583374026 -> 32.22899983520508
16:23:50.028192 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:23:50.029197 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:23:50.030523 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:23:50.031281 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:23:50.033408 INFO: === checking if optimization conditions were reached ===
16:23:50.034600 INFO: Updating optimization_manager: ms2_error           : 17.222457377501456 -> 15.0
16:23:50.034700 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
16:23:50.034765 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
16:23:50.035702 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
16:23:50.035794 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
16:23:50.035856 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
16:23:50.035909 INFO: ==============================================
16:23:50.035972 PROGRESS: Optimization finished for ms2_error, ms1_error.
16:23:50.134578 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:23:50.135661 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:23:50.136984 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:23:50.137743 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:23:50.139919 INFO: Starting optimization step 0.
16:23:50.140017 PROGRESS: === Extracting elution groups 0 to 600 ===
16:23:50.140086 INFO: Using classic extraction backend
16:23:50.140198 PROGRESS: Extracting batch of 1173 precursors
16:23:50.140268 INFO: === Search parameters used ===
16:23:50.140317 INFO: rt_error       : 2099.9331315
16:23:50.140360 INFO: mobility_error : 0.1
16:23:50.140403 INFO: num_candidates : 3
16:23:50.140444 INFO: ms1_error      : 15.0
16:23:50.140483 INFO: ms2_error      : 15.0
16:23:50.140522 INFO: fwhm_rt        : 2.860062837600708
16:23:50.140566 INFO: quant_window   : 3
16:23:50.140612 INFO: ==============================================
16:23:50.141327 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:23:50.141371 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:23:50.141405 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
16:23:50.141426 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.86
16:23:50.142151 INFO: Starting candidate selection
16:23:59.442899 INFO: Starting candidate scoring
16:23:59.648613 INFO: Finished candidate processing
16:23:59.648762 INFO: Collecting candidate features
16:23:59.677118 INFO: Collecting fragment features
16:23:59.686763 INFO: Finished candidate scoring
16:23:59.689681 INFO: performing precursor FDR with 47 features
16:23:59.689771 INFO: Decoy channel: -1
16:23:59.689828 INFO: Competetive: True
16:23:59.695997 INFO: Setting torch num_threads to 2 for FDR classification task
16:23:59.699802 INFO: Using random state 503883 for train-test-split
16:23:59.715773 INFO: Test AUC: 0.520
16:23:59.715861 INFO: Train AUC: 0.514
16:23:59.715910 INFO: AUC difference: 1.27%
16:23:59.977229 INFO: Resetting torch num_threads to 80
16:23:59.977956 PROGRESS: === Extracted 3226 precursors and 33408 fragments ===
16:23:59.978748 INFO: === FDR correction performed with classifier version 3 ===
16:23:59.979695 PROGRESS: ============================= Precursor FDR =============================
16:23:59.980001 PROGRESS: Total precursors accumulated: 585
16:23:59.980267 PROGRESS: Target precursors: 437 (74.70%)
16:23:59.980532 PROGRESS: Decoy precursors: 148 (25.30%)
16:23:59.980786 PROGRESS: 
16:23:59.981036 PROGRESS: Precursor Summary:
16:23:59.982719 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   389; 0.001 FDR:   389
16:23:59.983293 PROGRESS: 
16:23:59.983660 PROGRESS: Protein Summary:
16:23:59.985497 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   383; 0.001 FDR:   383
16:23:59.986271 PROGRESS: =========================================================================
16:23:59.986657 INFO: Target number of precursors reached.
16:23:59.996123 INFO: fragments_df: keeping 2014 of 33408 [sum(precursor_idx_mask)=11605 sum(mass_error_mask)=33408 stop_rank=2014
16:24:00.140577 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:24:00.308670 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:24:00.437634 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:24:00.569752 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:24:00.834529 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:24:00.834932 INFO: Using score_cutoff 31.270629501342775 (fac=0.99, q=1)
16:24:00.835229 INFO: Updating optimization_manager: fwhm_rt             : 2.860062837600708 -> 2.717644214630127
16:24:00.835309 INFO: Updating optimization_manager: fwhm_mobility       : 0.006174369715154171 -> 0.005498193204402924
16:24:00.835364 INFO: Updating optimization_manager: score_cutoff        : 32.22899983520508 -> 31.270629501342775
16:24:00.835419 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:00.836436 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:00.837739 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:00.838525 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:00.840574 INFO: === checking if optimization conditions were reached ===
16:24:00.840674 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
16:24:00.842177 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 1336.830955718004
16:24:00.842278 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1336.8310.
16:24:00.842342 INFO: ==============================================
16:24:00.842405 INFO: Starting optimization step 1.
16:24:00.842460 PROGRESS: === Extracting elution groups 0 to 600 ===
16:24:00.842514 INFO: Using classic extraction backend
16:24:00.842616 PROGRESS: Extracting batch of 1173 precursors
16:24:00.842678 INFO: === Search parameters used ===
16:24:00.842730 INFO: rt_error       : 1336.830955718004
16:24:00.842775 INFO: mobility_error : 0.1
16:24:00.842816 INFO: num_candidates : 3
16:24:00.842856 INFO: ms1_error      : 15.0
16:24:00.842895 INFO: ms2_error      : 15.0
16:24:00.842934 INFO: fwhm_rt        : 2.717644214630127
16:24:00.842973 INFO: quant_window   : 3
16:24:00.843011 INFO: ==============================================
16:24:00.843829 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:24:00.843873 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:24:00.843906 INFO: FWHM in RT is 2.72 seconds, sigma is 0.60
16:24:00.843928 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
16:24:00.844858 INFO: Starting candidate selection
16:24:08.337487 INFO: Starting candidate scoring
16:24:08.546697 INFO: Finished candidate processing
16:24:08.546873 INFO: Collecting candidate features
16:24:08.561877 INFO: Collecting fragment features
16:24:08.565556 INFO: Finished candidate scoring
16:24:08.567493 INFO: performing precursor FDR with 47 features
16:24:08.567538 INFO: Decoy channel: -1
16:24:08.567562 INFO: Competetive: True
16:24:08.570657 INFO: Setting torch num_threads to 2 for FDR classification task
16:24:08.572665 INFO: Using random state 503883 for train-test-split
16:24:08.584333 INFO: Test AUC: 0.494
16:24:08.584392 INFO: Train AUC: 0.528
16:24:08.584420 INFO: AUC difference: 6.52%
16:24:08.584442 WARNING: AUC difference > 5%. This may indicate overfitting.
16:24:08.803397 INFO: Resetting torch num_threads to 80
16:24:08.803927 PROGRESS: === Extracted 3234 precursors and 33416 fragments ===
16:24:08.804330 INFO: === FDR correction performed with classifier version 3 ===
16:24:08.804891 PROGRESS: ============================= Precursor FDR =============================
16:24:08.804980 PROGRESS: Total precursors accumulated: 586
16:24:08.805039 PROGRESS: Target precursors: 438 (74.74%)
16:24:08.805090 PROGRESS: Decoy precursors: 148 (25.26%)
16:24:08.805135 PROGRESS: 
16:24:08.805177 PROGRESS: Precursor Summary:
16:24:08.806141 PROGRESS: Channel   0:	 0.050 FDR:   388; 0.010 FDR:   388; 0.001 FDR:   388
16:24:08.806237 PROGRESS: 
16:24:08.806294 PROGRESS: Protein Summary:
16:24:08.807435 PROGRESS: Channel   0:	 0.050 FDR:   381; 0.010 FDR:   381; 0.001 FDR:   381
16:24:08.807528 PROGRESS: =========================================================================
16:24:08.807761 INFO: Target number of precursors reached.
16:24:08.813169 INFO: fragments_df: keeping 2040 of 33416 [sum(precursor_idx_mask)=11622 sum(mass_error_mask)=33415 stop_rank=2040
16:24:08.912198 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:24:09.049894 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:24:09.173033 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:24:09.300393 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:24:09.571429 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:24:09.571841 INFO: Using score_cutoff 30.26385942764282 (fac=0.99, q=1)
16:24:09.572135 INFO: Updating optimization_manager: fwhm_rt             : 2.717644214630127 -> 2.7410945892333984
16:24:09.572216 INFO: Updating optimization_manager: fwhm_mobility       : 0.005498193204402924 -> 0.005625560879707336
16:24:09.572280 INFO: Updating optimization_manager: score_cutoff        : 31.270629501342775 -> 30.26385942764282
16:24:09.572336 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:09.573366 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:09.574723 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:09.575480 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:09.577566 INFO: === checking if optimization conditions were reached ===
16:24:09.577665 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
16:24:09.579264 INFO: Updating optimization_manager: rt_error            : 1336.830955718004 -> 911.6145081689975
16:24:09.579365 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 911.6145.
16:24:09.579437 INFO: ==============================================
16:24:09.579509 INFO: Starting optimization step 2.
16:24:09.579569 PROGRESS: === Extracting elution groups 0 to 600 ===
16:24:09.579623 INFO: Using classic extraction backend
16:24:09.579729 PROGRESS: Extracting batch of 1173 precursors
16:24:09.579792 INFO: === Search parameters used ===
16:24:09.579839 INFO: rt_error       : 911.6145081689975
16:24:09.579883 INFO: mobility_error : 0.1
16:24:09.579925 INFO: num_candidates : 3
16:24:09.579965 INFO: ms1_error      : 15.0
16:24:09.580004 INFO: ms2_error      : 15.0
16:24:09.580042 INFO: fwhm_rt        : 2.7410945892333984
16:24:09.580082 INFO: quant_window   : 3
16:24:09.580121 INFO: ==============================================
16:24:09.581652 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:24:09.581697 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:24:09.581730 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
16:24:09.581752 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.61
16:24:09.582572 INFO: Starting candidate selection
16:24:14.828420 INFO: Starting candidate scoring
16:24:15.046214 INFO: Finished candidate processing
16:24:15.046347 INFO: Collecting candidate features
16:24:15.060383 INFO: Collecting fragment features
16:24:15.065284 INFO: Finished candidate scoring
16:24:15.067211 INFO: performing precursor FDR with 47 features
16:24:15.067256 INFO: Decoy channel: -1
16:24:15.067281 INFO: Competetive: True
16:24:15.070861 INFO: Setting torch num_threads to 2 for FDR classification task
16:24:15.073193 INFO: Using random state 503883 for train-test-split
16:24:15.083762 INFO: Test AUC: 0.539
16:24:15.083826 INFO: Train AUC: 0.505
16:24:15.083857 INFO: AUC difference: 6.68%
16:24:15.083879 WARNING: AUC difference > 5%. This may indicate overfitting.
16:24:15.305040 INFO: Resetting torch num_threads to 80
16:24:15.305604 PROGRESS: === Extracted 3220 precursors and 33262 fragments ===
16:24:15.306052 INFO: === FDR correction performed with classifier version 3 ===
16:24:15.306621 PROGRESS: ============================= Precursor FDR =============================
16:24:15.306709 PROGRESS: Total precursors accumulated: 587
16:24:15.306768 PROGRESS: Target precursors: 439 (74.79%)
16:24:15.306817 PROGRESS: Decoy precursors: 148 (25.21%)
16:24:15.306860 PROGRESS: 
16:24:15.306910 PROGRESS: Precursor Summary:
16:24:15.307871 PROGRESS: Channel   0:	 0.050 FDR:   387; 0.010 FDR:   387; 0.001 FDR:   387
16:24:15.307958 PROGRESS: 
16:24:15.308013 PROGRESS: Protein Summary:
16:24:15.309156 PROGRESS: Channel   0:	 0.050 FDR:   380; 0.010 FDR:   380; 0.001 FDR:   380
16:24:15.309244 PROGRESS: =========================================================================
16:24:15.309389 INFO: Target number of precursors reached.
16:24:15.315012 INFO: fragments_df: keeping 2011 of 33262 [sum(precursor_idx_mask)=11516 sum(mass_error_mask)=33261 stop_rank=2011
16:24:15.413616 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:24:15.548960 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:24:15.678741 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:24:15.785912 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:24:16.011492 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:24:16.011899 INFO: Using score_cutoff 31.35433435935974 (fac=0.99, q=1)
16:24:16.012213 INFO: Updating optimization_manager: fwhm_rt             : 2.7410945892333984 -> 2.7331936359405518
16:24:16.012294 INFO: Updating optimization_manager: fwhm_mobility       : 0.005625560879707336 -> 0.005655203014612198
16:24:16.012349 INFO: Updating optimization_manager: score_cutoff        : 30.26385942764282 -> 31.35433435935974
16:24:16.012407 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:16.013432 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:16.014774 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:16.015547 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:16.017608 INFO: === checking if optimization conditions were reached ===
16:24:16.017712 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
16:24:16.019417 INFO: Updating optimization_manager: rt_error            : 911.6145081689975 -> 832.3091619734092
16:24:16.019526 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 832.3092.
16:24:16.019593 INFO: ==============================================
16:24:16.019665 INFO: Starting optimization step 3.
16:24:16.019727 PROGRESS: === Extracting elution groups 0 to 600 ===
16:24:16.019786 INFO: Using classic extraction backend
16:24:16.019924 PROGRESS: Extracting batch of 1173 precursors
16:24:16.019991 INFO: === Search parameters used ===
16:24:16.020041 INFO: rt_error       : 832.3091619734092
16:24:16.020084 INFO: mobility_error : 0.1
16:24:16.020129 INFO: num_candidates : 3
16:24:16.020170 INFO: ms1_error      : 15.0
16:24:16.020210 INFO: ms2_error      : 15.0
16:24:16.020251 INFO: fwhm_rt        : 2.7331936359405518
16:24:16.020290 INFO: quant_window   : 3
16:24:16.020329 INFO: ==============================================
16:24:17.468643 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:24:17.468751 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:24:17.468795 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
16:24:17.468818 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.62
16:24:17.469539 INFO: Starting candidate selection
16:24:21.542766 INFO: Starting candidate scoring
16:24:21.738519 INFO: Finished candidate processing
16:24:21.738649 INFO: Collecting candidate features
16:24:21.751077 INFO: Collecting fragment features
16:24:21.754742 INFO: Finished candidate scoring
16:24:21.757984 INFO: performing precursor FDR with 47 features
16:24:21.758028 INFO: Decoy channel: -1
16:24:21.758060 INFO: Competetive: True
16:24:21.760878 INFO: Setting torch num_threads to 2 for FDR classification task
16:24:21.762895 INFO: Using random state 503883 for train-test-split
16:24:21.773298 INFO: Test AUC: 0.535
16:24:21.773356 INFO: Train AUC: 0.516
16:24:21.773385 INFO: AUC difference: 3.74%
16:24:21.985801 INFO: Resetting torch num_threads to 80
16:24:21.986389 PROGRESS: === Extracted 3214 precursors and 33173 fragments ===
16:24:21.986784 INFO: === FDR correction performed with classifier version 3 ===
16:24:21.987351 PROGRESS: ============================= Precursor FDR =============================
16:24:21.987439 PROGRESS: Total precursors accumulated: 586
16:24:21.987495 PROGRESS: Target precursors: 450 (76.79%)
16:24:21.987544 PROGRESS: Decoy precursors: 136 (23.21%)
16:24:21.987588 PROGRESS: 
16:24:21.987632 PROGRESS: Precursor Summary:
16:24:21.988603 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   395; 0.001 FDR:   395
16:24:21.988690 PROGRESS: 
16:24:21.988744 PROGRESS: Protein Summary:
16:24:21.989887 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   389; 0.001 FDR:   389
16:24:21.989979 PROGRESS: =========================================================================
16:24:21.990120 INFO: Target number of precursors reached.
16:24:21.995648 INFO: fragments_df: keeping 2058 of 33173 [sum(precursor_idx_mask)=11698 sum(mass_error_mask)=33173 stop_rank=2058
16:24:22.094686 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:24:22.234260 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:24:22.364361 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:24:22.495141 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:24:22.764529 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:24:22.764942 INFO: Using score_cutoff 30.223680406951903 (fac=0.99, q=1)
16:24:22.765246 INFO: Updating optimization_manager: fwhm_rt             : 2.7331936359405518 -> 2.718893527984619
16:24:22.765328 INFO: Updating optimization_manager: fwhm_mobility       : 0.005655203014612198 -> 0.005581095814704895
16:24:22.765383 INFO: Updating optimization_manager: score_cutoff        : 31.35433435935974 -> 30.223680406951903
16:24:22.765436 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:22.766494 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:22.767845 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:22.768618 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:22.770684 INFO: === checking if optimization conditions were reached ===
16:24:22.770850 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
16:24:22.772548 INFO: Updating optimization_manager: rt_error            : 832.3091619734092 -> 770.1874368186747
16:24:22.772652 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 770.1874.
16:24:22.772719 INFO: ==============================================
16:24:22.772786 INFO: Starting optimization step 4.
16:24:22.772846 PROGRESS: === Extracting elution groups 0 to 600 ===
16:24:22.772901 INFO: Using classic extraction backend
16:24:22.773001 PROGRESS: Extracting batch of 1173 precursors
16:24:22.773063 INFO: === Search parameters used ===
16:24:22.773111 INFO: rt_error       : 770.1874368186747
16:24:22.773155 INFO: mobility_error : 0.1
16:24:22.773204 INFO: num_candidates : 3
16:24:22.773247 INFO: ms1_error      : 15.0
16:24:22.773288 INFO: ms2_error      : 15.0
16:24:22.773327 INFO: fwhm_rt        : 2.718893527984619
16:24:22.773366 INFO: quant_window   : 3
16:24:22.773405 INFO: ==============================================
16:24:22.774369 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:24:22.774417 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:24:22.774451 INFO: FWHM in RT is 2.72 seconds, sigma is 0.60
16:24:22.774474 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.59
16:24:22.775163 INFO: Starting candidate selection
16:24:27.143497 INFO: Starting candidate scoring
16:24:27.326851 INFO: Finished candidate processing
16:24:27.326982 INFO: Collecting candidate features
16:24:27.340045 INFO: Collecting fragment features
16:24:27.344431 INFO: Finished candidate scoring
16:24:27.347741 INFO: performing precursor FDR with 47 features
16:24:27.347795 INFO: Decoy channel: -1
16:24:27.347819 INFO: Competetive: True
16:24:27.351006 INFO: Setting torch num_threads to 2 for FDR classification task
16:24:27.353244 INFO: Using random state 503883 for train-test-split
16:24:27.364438 INFO: Test AUC: 0.511
16:24:27.364507 INFO: Train AUC: 0.522
16:24:27.364540 INFO: AUC difference: 2.18%
16:24:27.589891 INFO: Resetting torch num_threads to 80
16:24:27.590647 PROGRESS: === Extracted 3217 precursors and 33223 fragments ===
16:24:27.591160 INFO: === FDR correction performed with classifier version 3 ===
16:24:27.591855 PROGRESS: ============================= Precursor FDR =============================
16:24:27.591956 PROGRESS: Total precursors accumulated: 588
16:24:27.592022 PROGRESS: Target precursors: 445 (75.68%)
16:24:27.592079 PROGRESS: Decoy precursors: 143 (24.32%)
16:24:27.592139 PROGRESS: 
16:24:27.592190 PROGRESS: Precursor Summary:
16:24:27.593227 PROGRESS: Channel   0:	 0.050 FDR:   388; 0.010 FDR:   388; 0.001 FDR:   388
16:24:27.593323 PROGRESS: 
16:24:27.593384 PROGRESS: Protein Summary:
16:24:27.594598 PROGRESS: Channel   0:	 0.050 FDR:   381; 0.010 FDR:   381; 0.001 FDR:   381
16:24:27.594697 PROGRESS: =========================================================================
16:24:27.594872 INFO: Target number of precursors reached.
16:24:27.600660 INFO: fragments_df: keeping 2010 of 33223 [sum(precursor_idx_mask)=11598 sum(mass_error_mask)=33223 stop_rank=2010
16:24:27.700927 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:24:27.821014 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:24:27.933103 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:24:28.043989 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:24:28.276983 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:24:28.277530 INFO: Using score_cutoff 31.372308076286316 (fac=0.99, q=1)
16:24:28.277866 INFO: Updating optimization_manager: fwhm_rt             : 2.718893527984619 -> 2.7081215381622314
16:24:28.277948 INFO: Updating optimization_manager: fwhm_mobility       : 0.005581095814704895 -> 0.0054957009851932526
16:24:28.278003 INFO: Updating optimization_manager: score_cutoff        : 30.223680406951903 -> 31.372308076286316
16:24:28.278071 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:28.279408 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:28.280818 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:28.281603 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:28.283718 INFO: === checking if optimization conditions were reached ===
16:24:28.283820 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
16:24:28.285631 INFO: Updating optimization_manager: rt_error            : 770.1874368186747 -> 771.3709862298891
16:24:28.285741 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 771.3710.
16:24:28.285806 INFO: ==============================================
16:24:28.285880 INFO: Starting optimization step 5.
16:24:28.285941 PROGRESS: === Extracting elution groups 0 to 600 ===
16:24:28.285997 INFO: Using classic extraction backend
16:24:28.286129 PROGRESS: Extracting batch of 1173 precursors
16:24:28.286197 INFO: === Search parameters used ===
16:24:28.286243 INFO: rt_error       : 771.3709862298891
16:24:28.286287 INFO: mobility_error : 0.1
16:24:28.286326 INFO: num_candidates : 3
16:24:28.286366 INFO: ms1_error      : 15.0
16:24:28.286403 INFO: ms2_error      : 15.0
16:24:28.286442 INFO: fwhm_rt        : 2.7081215381622314
16:24:28.286481 INFO: quant_window   : 3
16:24:28.286517 INFO: ==============================================
16:24:28.287452 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:24:28.287496 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:24:28.287530 INFO: FWHM in RT is 2.71 seconds, sigma is 0.60
16:24:28.287550 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
16:24:28.288222 INFO: Starting candidate selection
16:24:31.316364 INFO: Starting candidate scoring
16:24:31.547199 INFO: Finished candidate processing
16:24:31.548458 INFO: Collecting candidate features
16:24:31.560171 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3229)
16:24:31.563567 INFO: Collecting fragment features
16:24:31.567152 INFO: Finished candidate scoring
16:24:31.569574 INFO: performing precursor FDR with 47 features
16:24:31.569617 INFO: Decoy channel: -1
16:24:31.569641 INFO: Competetive: True
16:24:31.572550 INFO: Setting torch num_threads to 2 for FDR classification task
16:24:31.573835 WARNING: dropped 1 decoy PSMs due to missing features
16:24:31.574819 INFO: Using random state 503883 for train-test-split
16:24:31.585872 INFO: Test AUC: 0.540
16:24:31.585935 INFO: Train AUC: 0.521
16:24:31.585974 INFO: AUC difference: 3.65%
16:24:31.805582 INFO: Resetting torch num_threads to 80
16:24:31.806159 PROGRESS: === Extracted 3229 precursors and 33268 fragments ===
16:24:31.806558 INFO: === FDR correction performed with classifier version 3 ===
16:24:31.807145 PROGRESS: ============================= Precursor FDR =============================
16:24:31.807239 PROGRESS: Total precursors accumulated: 589
16:24:31.807299 PROGRESS: Target precursors: 446 (75.72%)
16:24:31.807350 PROGRESS: Decoy precursors: 143 (24.28%)
16:24:31.807394 PROGRESS: 
16:24:31.807436 PROGRESS: Precursor Summary:
16:24:31.808417 PROGRESS: Channel   0:	 0.050 FDR:   387; 0.010 FDR:   387; 0.001 FDR:   387
16:24:31.808517 PROGRESS: 
16:24:31.808574 PROGRESS: Protein Summary:
16:24:31.809736 PROGRESS: Channel   0:	 0.050 FDR:   382; 0.010 FDR:   382; 0.001 FDR:   382
16:24:31.809827 PROGRESS: =========================================================================
16:24:31.809961 INFO: Target number of precursors reached.
16:24:31.815595 INFO: fragments_df: keeping 1982 of 33268 [sum(precursor_idx_mask)=11446 sum(mass_error_mask)=33268 stop_rank=1982
16:24:31.914308 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:24:32.048757 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:24:32.180013 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:24:32.310648 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:24:32.578286 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:24:32.578707 INFO: Using score_cutoff 30.665371227264405 (fac=0.99, q=1)
16:24:32.579005 INFO: Updating optimization_manager: fwhm_rt             : 2.7081215381622314 -> 2.745654582977295
16:24:32.579085 INFO: Updating optimization_manager: fwhm_mobility       : 0.0054957009851932526 -> 0.005513334646821022
16:24:32.579142 INFO: Updating optimization_manager: score_cutoff        : 31.372308076286316 -> 30.665371227264405
16:24:32.579195 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:32.580254 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:32.581605 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:32.582381 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:32.584515 INFO: === checking if optimization conditions were reached ===
16:24:32.584614 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
16:24:32.585526 INFO: Updating optimization_manager: rt_error            : 771.3709862298891 -> 770.1874368186747
16:24:32.585646 INFO: Updating optimization_manager: classifier_version  : 3 -> 8
16:24:32.585740 INFO: Updating optimization_manager: score_cutoff        : 30.665371227264405 -> 31.372308076286316
16:24:32.585825 INFO: Updating optimization_manager: fwhm_rt             : 2.745654582977295 -> 2.7081215381622314
16:24:32.585905 INFO: Updating optimization_manager: fwhm_mobility       : 0.005513334646821022 -> 0.0054957009851932526
16:24:32.585986 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 770.1874 found after 6 searches.
16:24:32.586059 INFO: ==============================================
16:24:32.586126 PROGRESS: Optimization finished for rt_error.
16:24:32.686131 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:32.687242 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:32.688586 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:32.689356 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:32.717233 INFO: Starting optimization step 0.
16:24:32.717386 PROGRESS: === Extracting elution groups 0 to 600 ===
16:24:32.717458 INFO: Using classic extraction backend
16:24:32.717569 PROGRESS: Extracting batch of 1173 precursors
16:24:32.717639 INFO: === Search parameters used ===
16:24:32.717701 INFO: rt_error       : 770.1874368186747
16:24:32.717747 INFO: mobility_error : 0.1
16:24:32.717792 INFO: num_candidates : 3
16:24:32.717841 INFO: ms1_error      : 15.0
16:24:32.717884 INFO: ms2_error      : 15.0
16:24:32.717924 INFO: fwhm_rt        : 2.7081215381622314
16:24:32.717964 INFO: quant_window   : 3
16:24:32.718005 INFO: ==============================================
16:24:32.718836 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:24:32.718882 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:24:32.718917 INFO: FWHM in RT is 2.71 seconds, sigma is 0.60
16:24:32.718939 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
16:24:32.719625 INFO: Starting candidate selection
16:24:36.013230 INFO: Starting candidate scoring
16:24:36.206267 INFO: Finished candidate processing
16:24:36.206363 INFO: Collecting candidate features
16:24:36.218939 INFO: Collecting fragment features
16:24:36.222766 INFO: Finished candidate scoring
16:24:36.225062 INFO: performing precursor FDR with 47 features
16:24:36.225108 INFO: Decoy channel: -1
16:24:36.225132 INFO: Competetive: True
16:24:36.227984 INFO: Setting torch num_threads to 2 for FDR classification task
16:24:36.230004 INFO: Using random state 579183 for train-test-split
16:24:36.241256 INFO: Test AUC: 0.494
16:24:36.241318 INFO: Train AUC: 0.528
16:24:36.241347 INFO: AUC difference: 6.35%
16:24:36.241369 WARNING: AUC difference > 5%. This may indicate overfitting.
16:24:36.455919 INFO: Resetting torch num_threads to 80
16:24:36.456489 PROGRESS: === Extracted 3240 precursors and 33404 fragments ===
16:24:36.456885 INFO: === FDR correction performed with classifier version 8 ===
16:24:36.457452 PROGRESS: ============================= Precursor FDR =============================
16:24:36.457541 PROGRESS: Total precursors accumulated: 589
16:24:36.457600 PROGRESS: Target precursors: 450 (76.40%)
16:24:36.457650 PROGRESS: Decoy precursors: 139 (23.60%)
16:24:36.457694 PROGRESS: 
16:24:36.457737 PROGRESS: Precursor Summary:
16:24:36.458762 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   395; 0.001 FDR:   395
16:24:36.458858 PROGRESS: 
16:24:36.458916 PROGRESS: Protein Summary:
16:24:36.460078 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   390; 0.001 FDR:   390
16:24:36.460171 PROGRESS: =========================================================================
16:24:36.460323 INFO: Target number of precursors reached.
16:24:36.465945 INFO: fragments_df: keeping 2054 of 33404 [sum(precursor_idx_mask)=11786 sum(mass_error_mask)=33404 stop_rank=2054
16:24:36.564753 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:24:36.693113 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:24:36.827360 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:24:36.939023 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:24:37.166815 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:24:37.167233 INFO: Using score_cutoff 30.37601133956909 (fac=0.99, q=1)
16:24:37.167534 INFO: Updating optimization_manager: fwhm_rt             : 2.7081215381622314 -> 2.736534357070923
16:24:37.167615 INFO: Updating optimization_manager: fwhm_mobility       : 0.0054957009851932526 -> 0.005547511391341686
16:24:37.167669 INFO: Updating optimization_manager: score_cutoff        : 31.372308076286316 -> 30.37601133956909
16:24:37.167720 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:37.168747 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:37.170115 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:37.170873 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:37.172996 INFO: === checking if optimization conditions were reached ===
16:24:37.173097 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
16:24:37.174392 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.09716659729026723
16:24:37.174492 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0972.
16:24:37.174564 INFO: ==============================================
16:24:37.174637 INFO: Starting optimization step 1.
16:24:37.174714 PROGRESS: === Extracting elution groups 0 to 600 ===
16:24:37.174767 INFO: Using classic extraction backend
16:24:37.174867 PROGRESS: Extracting batch of 1173 precursors
16:24:37.174931 INFO: === Search parameters used ===
16:24:37.174978 INFO: rt_error       : 770.1874368186747
16:24:37.175021 INFO: mobility_error : 0.09716659729026723
16:24:37.175060 INFO: num_candidates : 3
16:24:37.175098 INFO: ms1_error      : 15.0
16:24:37.175138 INFO: ms2_error      : 15.0
16:24:37.175176 INFO: fwhm_rt        : 2.736534357070923
16:24:37.175214 INFO: quant_window   : 3
16:24:37.175252 INFO: ==============================================
16:24:37.176152 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:24:37.176196 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:24:37.176229 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
16:24:37.176248 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.57
16:24:37.176910 INFO: Starting candidate selection
16:24:40.270514 INFO: Starting candidate scoring
16:24:40.475983 INFO: Finished candidate processing
16:24:40.476164 INFO: Collecting candidate features
16:24:40.505488 INFO: Collecting fragment features
16:24:40.514894 INFO: Finished candidate scoring
16:24:40.518749 INFO: performing precursor FDR with 47 features
16:24:40.518870 INFO: Decoy channel: -1
16:24:40.518936 INFO: Competetive: True
16:24:40.526362 INFO: Setting torch num_threads to 2 for FDR classification task
16:24:40.530115 INFO: Using random state 579183 for train-test-split
16:24:40.546942 INFO: Test AUC: 0.514
16:24:40.547045 INFO: Train AUC: 0.521
16:24:40.547092 INFO: AUC difference: 1.39%
16:24:40.776003 INFO: Resetting torch num_threads to 80
16:24:40.776734 PROGRESS: === Extracted 3242 precursors and 33415 fragments ===
16:24:40.777258 INFO: === FDR correction performed with classifier version 8 ===
16:24:40.777879 PROGRESS: ============================= Precursor FDR =============================
16:24:40.777971 PROGRESS: Total precursors accumulated: 591
16:24:40.778030 PROGRESS: Target precursors: 448 (75.80%)
16:24:40.778093 PROGRESS: Decoy precursors: 143 (24.20%)
16:24:40.778137 PROGRESS: 
16:24:40.778187 PROGRESS: Precursor Summary:
16:24:40.779196 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   390; 0.001 FDR:   390
16:24:40.779288 PROGRESS: 
16:24:40.779343 PROGRESS: Protein Summary:
16:24:40.780540 PROGRESS: Channel   0:	 0.050 FDR:   385; 0.010 FDR:   385; 0.001 FDR:   385
16:24:40.780633 PROGRESS: =========================================================================
16:24:40.780847 INFO: Target number of precursors reached.
16:24:40.786687 INFO: fragments_df: keeping 1977 of 33415 [sum(precursor_idx_mask)=11616 sum(mass_error_mask)=33414 stop_rank=1977
16:24:40.887187 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:24:40.995023 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:24:41.108046 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:24:41.221859 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:24:41.449712 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:24:41.450269 INFO: Using score_cutoff 31.397702960014346 (fac=0.99, q=1)
16:24:41.450604 INFO: Updating optimization_manager: fwhm_rt             : 2.736534357070923 -> 2.754395008087158
16:24:41.450684 INFO: Updating optimization_manager: fwhm_mobility       : 0.005547511391341686 -> 0.005597360897809267
16:24:41.450739 INFO: Updating optimization_manager: score_cutoff        : 30.37601133956909 -> 31.397702960014346
16:24:41.450793 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:41.452052 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:41.453428 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:41.454201 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:41.456326 INFO: === checking if optimization conditions were reached ===
16:24:41.456446 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
16:24:41.457952 INFO: Updating optimization_manager: mobility_error      : 0.09716659729026723 -> 0.09832350876180757
16:24:41.458082 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0983.
16:24:41.458154 INFO: ==============================================
16:24:41.458221 INFO: Starting optimization step 2.
16:24:41.458277 PROGRESS: === Extracting elution groups 0 to 600 ===
16:24:41.458337 INFO: Using classic extraction backend
16:24:41.458462 PROGRESS: Extracting batch of 1173 precursors
16:24:41.458529 INFO: === Search parameters used ===
16:24:41.458577 INFO: rt_error       : 770.1874368186747
16:24:41.458618 INFO: mobility_error : 0.09832350876180757
16:24:41.458659 INFO: num_candidates : 3
16:24:41.458700 INFO: ms1_error      : 15.0
16:24:41.458739 INFO: ms2_error      : 15.0
16:24:41.458779 INFO: fwhm_rt        : 2.754395008087158
16:24:41.458818 INFO: quant_window   : 3
16:24:41.458856 INFO: ==============================================
16:24:41.459789 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:24:41.459840 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:24:41.459875 INFO: FWHM in RT is 2.75 seconds, sigma is 0.61
16:24:41.459897 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.60
16:24:41.460585 INFO: Starting candidate selection
16:24:44.807937 INFO: Starting candidate scoring
16:24:45.021943 INFO: Finished candidate processing
16:24:45.022157 INFO: Collecting candidate features
16:24:45.050709 INFO: Collecting fragment features
16:24:45.059361 INFO: Finished candidate scoring
16:24:45.062678 INFO: performing precursor FDR with 47 features
16:24:45.062783 INFO: Decoy channel: -1
16:24:45.062849 INFO: Competetive: True
16:24:45.069410 INFO: Setting torch num_threads to 2 for FDR classification task
16:24:45.073204 INFO: Using random state 579183 for train-test-split
16:24:45.090229 INFO: Test AUC: 0.534
16:24:45.090325 INFO: Train AUC: 0.511
16:24:45.090374 INFO: AUC difference: 4.40%
16:24:45.320232 INFO: Resetting torch num_threads to 80
16:24:45.320935 PROGRESS: === Extracted 3248 precursors and 33463 fragments ===
16:24:45.321450 INFO: === FDR correction performed with classifier version 8 ===
16:24:45.322097 PROGRESS: ============================= Precursor FDR =============================
16:24:45.322187 PROGRESS: Total precursors accumulated: 590
16:24:45.322247 PROGRESS: Target precursors: 449 (76.10%)
16:24:45.322295 PROGRESS: Decoy precursors: 141 (23.90%)
16:24:45.322340 PROGRESS: 
16:24:45.322385 PROGRESS: Precursor Summary:
16:24:45.323384 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   390; 0.001 FDR:   390
16:24:45.323475 PROGRESS: 
16:24:45.323531 PROGRESS: Protein Summary:
16:24:45.324716 PROGRESS: Channel   0:	 0.050 FDR:   385; 0.010 FDR:   385; 0.001 FDR:   385
16:24:45.324807 PROGRESS: =========================================================================
16:24:45.324989 INFO: Target number of precursors reached.
16:24:45.330757 INFO: fragments_df: keeping 1960 of 33463 [sum(precursor_idx_mask)=11618 sum(mass_error_mask)=33462 stop_rank=1960
16:24:45.431039 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
16:24:45.544400 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
16:24:45.658015 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
16:24:45.770700 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
16:24:45.998098 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
16:24:45.998643 INFO: Using score_cutoff 30.458329127311707 (fac=0.99, q=1)
16:24:45.998978 INFO: Updating optimization_manager: fwhm_rt             : 2.754395008087158 -> 2.733203887939453
16:24:45.999059 INFO: Updating optimization_manager: fwhm_mobility       : 0.005597360897809267 -> 0.005596890114247799
16:24:45.999116 INFO: Updating optimization_manager: score_cutoff        : 31.397702960014346 -> 30.458329127311707
16:24:45.999181 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:46.000432 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:46.001791 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:46.002573 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:46.004704 INFO: === checking if optimization conditions were reached ===
16:24:46.004808 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
16:24:46.005566 INFO: Updating optimization_manager: mobility_error      : 0.09832350876180757 -> 0.1
16:24:46.005688 INFO: Updating optimization_manager: classifier_version  : 8 -> 10
16:24:46.005780 INFO: Updating optimization_manager: score_cutoff        : 30.458329127311707 -> 30.37601133956909
16:24:46.005868 INFO: Updating optimization_manager: fwhm_rt             : 2.733203887939453 -> 2.736534357070923
16:24:46.005952 INFO: Updating optimization_manager: fwhm_mobility       : 0.005596890114247799 -> 0.005547511391341686
16:24:46.006032 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
16:24:46.006106 INFO: ==============================================
16:24:46.006171 PROGRESS: Optimization finished for mobility_error.
16:24:46.104975 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:46.106084 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:46.107422 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:46.108180 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:24:46.133430 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
16:24:46.133571 PROGRESS: ==============================================
16:24:46.133646 PROGRESS: ms2_error      : 15.0000
16:24:46.133702 PROGRESS: ms1_error      : 15.0000
16:24:46.133752 PROGRESS: rt_error       : 770.1874
16:24:46.133799 PROGRESS: mobility_error : 0.1000
16:24:46.133841 PROGRESS: ==============================================
16:24:46.134354 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
16:24:47.721263 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
16:24:55.022884 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
16:24:56.486610 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
16:25:52.048174 INFO: Using classic extraction backend
16:25:52.048711 PROGRESS: Extracting batch of 12073114 precursors
16:25:52.048845 INFO: === Search parameters used ===
16:25:52.048903 INFO: rt_error       : 770.1874368186747
16:25:52.048955 INFO: mobility_error : 0.1
16:25:52.049012 INFO: num_candidates : 3
16:25:52.049058 INFO: ms1_error      : 15.0
16:25:52.049098 INFO: ms2_error      : 15.0
16:25:52.049146 INFO: fwhm_rt        : 2.736534357070923
16:25:52.049187 INFO: quant_window   : 3
16:25:52.049227 INFO: ==============================================
16:25:57.641794 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
16:25:57.642009 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
16:25:57.642084 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
16:25:57.642110 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.57
16:25:57.652318 INFO: Starting candidate selection
23:10:43.791311 INFO: Removed 1644677 precursors with score below cutoff 30.37601133956909
23:10:46.558667 INFO: Starting candidate scoring
23:30:29.019310 INFO: Finished candidate processing
23:30:29.020505 INFO: Collecting candidate features
23:33:44.519443 INFO: Collecting fragment features
23:34:50.067864 INFO: Finished candidate scoring
23:35:26.463196 INFO: === Performing FDR correction with classifier version 10 ===
23:35:26.466517 INFO: performing precursor FDR with 47 features
23:35:26.466571 INFO: Decoy channel: -1
23:35:26.466599 INFO: Competetive: True
23:35:34.686342 INFO: Setting torch num_threads to 2 for FDR classification task
23:35:51.442399 INFO: Using random state 166544 for train-test-split
23:47:57.839896 INFO: Test AUC: 0.576
23:47:57.840581 INFO: Train AUC: 0.576
23:47:57.840653 INFO: AUC difference: 0.07%
23:48:03.887167 INFO: Resetting torch num_threads to 80
23:48:04.257023 INFO: Removing fragments below FDR threshold
23:48:06.889940 PROGRESS: ============================= Precursor FDR =============================
23:48:06.890194 PROGRESS: Total precursors accumulated: 51,253
23:48:06.890259 PROGRESS: Target precursors: 50,746 (99.01%)
23:48:06.890316 PROGRESS: Decoy precursors: 507 (0.99%)
23:48:06.890364 PROGRESS: 
23:48:06.890410 PROGRESS: Precursor Summary:
23:48:06.906792 PROGRESS: Channel   0:	 0.050 FDR: 50,746; 0.010 FDR: 50,746; 0.001 FDR: 29,768
23:48:06.907039 PROGRESS: 
23:48:06.907100 PROGRESS: Protein Summary:
23:48:06.928615 PROGRESS: Channel   0:	 0.050 FDR: 9,010; 0.010 FDR: 9,010; 0.001 FDR: 6,652
23:48:06.928841 PROGRESS: =========================================================================
23:48:07.483450 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/psm.parquet
23:48:07.831979 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/frag.parquet
23:48:08.045183 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
23:48:08.560977 PROGRESS: 
23:48:08.561134 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant
23:48:08.561205 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/figures
23:48:08.561371 INFO: Initializing TimingManager
23:48:08.561831 INFO: Initializing RawFileManager
23:48:08.561940 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:08.561991 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:08.562032 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:08.770442 INFO: Reading 39,129 frames with 2,804,178,635 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:17.001383 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
23:48:17.020828 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:17.023269 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:17.023524 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:17.023932 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:17.025725 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:17.040525 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:17.040960 INFO: Indexing quadrupole dimension
23:48:17.555490 INFO: Transposing detector events
23:48:26.510572 INFO: Finished transposing data
23:48:26.548572 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
23:48:26.549344 INFO: RT (min)            : 0.0 - 70.0
23:48:26.549433 INFO: RT duration (sec)   : 4199.8
23:48:26.549487 INFO: RT duration (min)   : 70.0
23:48:26.549534 INFO: Cycle len (scans)   : 9
23:48:26.549582 INFO: Cycle len (sec)     : 0.97
23:48:26.549626 INFO: Number of cycles    : 4347
23:48:26.549668 INFO: MS2 range (m/z)     : 400.0 - 1000.0
23:48:26.549723 INFO: Creating DIA data object took: 17.987796545028687
23:48:27.707859 INFO: Initializing CalibrationManager
23:48:27.708131 INFO: Setting up calibration estimators ..
23:48:27.708189 INFO: Found 1 estimator(s) in calibration group 'fragment'
23:48:27.708256 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'}' ..
23:48:27.708342 INFO: Found 3 estimator(s) in calibration group 'precursor'
23:48:27.708395 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'}' ..
23:48:27.708448 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}}' ..
23:48:27.708505 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}}' ..
23:48:27.708549 INFO: Done setting up calibration estimators.
23:48:27.708658 INFO: Initializing OptimizationManager
23:48:27.708747 INFO: initial parameter: ms1_error = 30
23:48:27.708794 INFO: initial parameter: ms2_error = 30
23:48:27.708838 INFO: initial parameter: rt_error = 2099.9231665
23:48:27.708877 INFO: initial parameter: mobility_error = 0.1
23:48:27.708917 INFO: initial parameter: num_candidates = 1
23:48:27.708955 INFO: initial parameter: fwhm_rt = 5
23:48:27.708993 INFO: initial parameter: fwhm_mobility = 0.01
23:48:27.709031 INFO: initial parameter: score_cutoff = 0
23:48:27.709067 INFO: initial parameter: classifier_version = -1
23:48:27.709130 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
23:48:27.709334 INFO: FDRManager: loading saved state not requested, will be initialized.
23:48:27.709364 INFO: Initializing FDRManager
23:48:27.709395 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
23:48:28.915906 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
23:48:29.665911 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
23:48:29.666439 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 2099.9231665
23:48:29.666560 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
23:48:29.666760 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
23:48:29.666860 PROGRESS: Starting initial search for precursors.
23:48:29.666953 INFO: Starting optimization step 0.
23:48:29.667016 PROGRESS: === Extracting elution groups 0 to 200 ===
23:48:29.667092 INFO: Using classic extraction backend
23:48:29.667276 PROGRESS: Extracting batch of 390 precursors
23:48:29.667352 INFO: === Search parameters used ===
23:48:29.667403 INFO: rt_error       : 2099.9231665
23:48:29.667447 INFO: mobility_error : 0.1
23:48:29.667487 INFO: num_candidates : 1
23:48:29.667527 INFO: ms1_error      : 30
23:48:29.667567 INFO: ms2_error      : 30
23:48:29.667604 INFO: fwhm_rt        : 5
23:48:29.667644 INFO: quant_window   : 3
23:48:29.667681 INFO: ==============================================
23:48:29.668511 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
23:48:29.668556 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
23:48:29.668595 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
23:48:29.668616 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
23:48:29.670846 INFO: Starting candidate selection
23:48:33.432487 INFO: Starting candidate scoring
23:48:33.499611 INFO: Finished candidate processing
23:48:33.499722 INFO: Collecting candidate features
23:48:33.509556 INFO: Collecting fragment features
23:48:33.511735 INFO: Finished candidate scoring
23:48:33.512597 INFO: performing precursor FDR with 47 features
23:48:33.512637 INFO: Decoy channel: -1
23:48:33.512661 INFO: Competetive: True
23:48:33.514334 INFO: Setting torch num_threads to 2 for FDR classification task
23:48:33.517148 INFO: Using random state 385554 for train-test-split
23:48:33.524941 INFO: Test AUC: 0.463
23:48:33.524999 INFO: Train AUC: 0.492
23:48:33.525028 INFO: AUC difference: 5.92%
23:48:33.525049 WARNING: AUC difference > 5%. This may indicate overfitting.
23:48:33.743232 INFO: Resetting torch num_threads to 80
23:48:33.743744 PROGRESS: === Extracted 363 precursors and 3919 fragments ===
23:48:33.744213 INFO: === FDR correction performed with classifier version -1 ===
23:48:33.744741 PROGRESS: ============================= Precursor FDR =============================
23:48:33.744830 PROGRESS: Total precursors accumulated: 188
23:48:33.744886 PROGRESS: Target precursors: 164 (87.23%)
23:48:33.744934 PROGRESS: Decoy precursors: 24 (12.77%)
23:48:33.744977 PROGRESS: 
23:48:33.745019 PROGRESS: Precursor Summary:
23:48:33.745877 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
23:48:33.745966 PROGRESS: 
23:48:33.746027 PROGRESS: Protein Summary:
23:48:33.746971 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
23:48:33.747059 PROGRESS: =========================================================================
23:48:33.747178 INFO: Target number of precursors not reached yet.
23:48:33.813671 INFO: Starting optimization step 1.
23:48:33.813925 PROGRESS: === Extracting elution groups 200 to 600 ===
23:48:33.814005 INFO: Using classic extraction backend
23:48:33.814146 PROGRESS: Extracting batch of 783 precursors
23:48:33.814222 INFO: === Search parameters used ===
23:48:33.814270 INFO: rt_error       : 2099.9231665
23:48:33.814314 INFO: mobility_error : 0.1
23:48:33.814357 INFO: num_candidates : 1
23:48:33.814397 INFO: ms1_error      : 30
23:48:33.814436 INFO: ms2_error      : 30
23:48:33.814476 INFO: fwhm_rt        : 5
23:48:33.814515 INFO: quant_window   : 3
23:48:33.814554 INFO: ==============================================
23:48:33.815295 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
23:48:33.815341 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
23:48:33.815370 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
23:48:33.815393 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
23:48:33.816273 INFO: Starting candidate selection
23:48:39.940842 INFO: Starting candidate scoring
23:48:40.061565 INFO: Finished candidate processing
23:48:40.061740 INFO: Collecting candidate features
23:48:40.072033 INFO: Collecting fragment features
23:48:40.074798 INFO: Finished candidate scoring
23:48:40.076885 INFO: performing precursor FDR with 47 features
23:48:40.076929 INFO: Decoy channel: -1
23:48:40.076956 INFO: Competetive: True
23:48:40.079968 INFO: Setting torch num_threads to 2 for FDR classification task
23:48:40.081888 INFO: Using random state 368551 for train-test-split
23:48:40.090011 INFO: Test AUC: 0.494
23:48:40.090082 INFO: Train AUC: 0.494
23:48:40.090113 INFO: AUC difference: 0.04%
23:48:40.307427 INFO: Resetting torch num_threads to 80
23:48:40.308834 PROGRESS: === Extracted 1117 precursors and 12127 fragments ===
23:48:40.309275 INFO: === FDR correction performed with classifier version -1 ===
23:48:40.309881 PROGRESS: ============================= Precursor FDR =============================
23:48:40.309969 PROGRESS: Total precursors accumulated: 576
23:48:40.310028 PROGRESS: Target precursors: 514 (89.24%)
23:48:40.310206 PROGRESS: Decoy precursors: 62 (10.76%)
23:48:40.310259 PROGRESS: 
23:48:40.310303 PROGRESS: Precursor Summary:
23:48:40.311174 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
23:48:40.311263 PROGRESS: 
23:48:40.311318 PROGRESS: Protein Summary:
23:48:40.312255 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
23:48:40.312340 PROGRESS: =========================================================================
23:48:40.312514 INFO: Target number of precursors not reached yet.
23:48:40.381749 INFO: Starting optimization step 2.
23:48:40.382005 PROGRESS: === Extracting elution groups 600 to 1400 ===
23:48:40.382096 INFO: Using classic extraction backend
23:48:40.382228 PROGRESS: Extracting batch of 1576 precursors
23:48:40.382316 INFO: === Search parameters used ===
23:48:40.382363 INFO: rt_error       : 2099.9231665
23:48:40.382406 INFO: mobility_error : 0.1
23:48:40.382448 INFO: num_candidates : 1
23:48:40.382488 INFO: ms1_error      : 30
23:48:40.382529 INFO: ms2_error      : 30
23:48:40.382567 INFO: fwhm_rt        : 5
23:48:40.382605 INFO: quant_window   : 3
23:48:40.382642 INFO: ==============================================
23:48:40.383536 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
23:48:40.383582 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
23:48:40.383612 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
23:48:40.383635 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
23:48:40.384475 INFO: Starting candidate selection
23:49:21.901718 INFO: Starting candidate scoring
23:49:22.085445 INFO: Finished candidate processing
23:49:22.085561 INFO: Collecting candidate features
23:49:22.097806 INFO: Collecting fragment features
23:49:22.100887 INFO: Finished candidate scoring
23:49:22.103746 INFO: performing precursor FDR with 47 features
23:49:22.103793 INFO: Decoy channel: -1
23:49:22.103818 INFO: Competetive: True
23:49:22.108919 INFO: Setting torch num_threads to 2 for FDR classification task
23:49:22.112075 INFO: Using random state 261164 for train-test-split
23:49:22.128114 INFO: Test AUC: 0.489
23:49:22.128209 INFO: Train AUC: 0.499
23:49:22.128258 INFO: AUC difference: 2.11%
23:49:22.342497 INFO: Resetting torch num_threads to 80
23:49:22.344239 PROGRESS: === Extracted 2634 precursors and 28574 fragments ===
23:49:22.344671 INFO: === FDR correction performed with classifier version -1 ===
23:49:22.345399 PROGRESS: ============================= Precursor FDR =============================
23:49:22.345489 PROGRESS: Total precursors accumulated: 1,352
23:49:22.345547 PROGRESS: Target precursors: 1,208 (89.35%)
23:49:22.345596 PROGRESS: Decoy precursors: 144 (10.65%)
23:49:22.345640 PROGRESS: 
23:49:22.345684 PROGRESS: Precursor Summary:
23:49:22.346560 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
23:49:22.346651 PROGRESS: 
23:49:22.346706 PROGRESS: Protein Summary:
23:49:22.347640 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
23:49:22.347728 PROGRESS: =========================================================================
23:49:22.347888 INFO: Target number of precursors not reached yet.
23:49:22.436288 INFO: Starting optimization step 3.
23:49:22.436517 PROGRESS: === Extracting elution groups 1400 to 3000 ===
23:49:22.436595 INFO: Using classic extraction backend
23:49:22.436711 PROGRESS: Extracting batch of 3162 precursors
23:49:22.436783 INFO: === Search parameters used ===
23:49:22.436837 INFO: rt_error       : 2099.9231665
23:49:22.436883 INFO: mobility_error : 0.1
23:49:22.436937 INFO: num_candidates : 1
23:49:22.436980 INFO: ms1_error      : 30
23:49:22.437019 INFO: ms2_error      : 30
23:49:22.437058 INFO: fwhm_rt        : 5
23:49:22.437099 INFO: quant_window   : 3
23:49:22.437140 INFO: ==============================================
23:49:22.438111 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
23:49:22.438157 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
23:49:22.438186 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
23:49:22.438207 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
23:49:22.438954 INFO: Starting candidate selection
23:50:21.920426 INFO: Starting candidate scoring
23:50:22.214897 INFO: Finished candidate processing
23:50:22.215026 INFO: Collecting candidate features
23:50:22.230758 INFO: Collecting fragment features
23:50:22.235770 INFO: Finished candidate scoring
23:50:22.245591 INFO: performing precursor FDR with 47 features
23:50:22.245645 INFO: Decoy channel: -1
23:50:22.245669 INFO: Competetive: True
23:50:22.251463 INFO: Setting torch num_threads to 2 for FDR classification task
23:50:22.254271 INFO: Using random state 20706 for train-test-split
23:50:22.270450 INFO: Test AUC: 0.497
23:50:22.270517 INFO: Train AUC: 0.502
23:50:22.270558 INFO: AUC difference: 1.01%
23:50:22.481774 INFO: Resetting torch num_threads to 80
23:50:22.484145 PROGRESS: === Extracted 5660 precursors and 61120 fragments ===
23:50:22.484618 INFO: === FDR correction performed with classifier version -1 ===
23:50:22.485472 PROGRESS: ============================= Precursor FDR =============================
23:50:22.485564 PROGRESS: Total precursors accumulated: 2,900
23:50:22.485627 PROGRESS: Target precursors: 2,573 (88.72%)
23:50:22.485676 PROGRESS: Decoy precursors: 327 (11.28%)
23:50:22.485722 PROGRESS: 
23:50:22.485764 PROGRESS: Precursor Summary:
23:50:22.486615 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
23:50:22.486704 PROGRESS: 
23:50:22.486764 PROGRESS: Protein Summary:
23:50:22.487676 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
23:50:22.487764 PROGRESS: =========================================================================
23:50:22.487981 INFO: Target number of precursors not reached yet.
23:50:22.587431 INFO: Starting optimization step 4.
23:50:22.587661 PROGRESS: === Extracting elution groups 3000 to 6200 ===
23:50:22.587754 INFO: Using classic extraction backend
23:50:22.587909 PROGRESS: Extracting batch of 6312 precursors
23:50:22.587986 INFO: === Search parameters used ===
23:50:22.588036 INFO: rt_error       : 2099.9231665
23:50:22.588079 INFO: mobility_error : 0.1
23:50:22.588124 INFO: num_candidates : 1
23:50:22.588166 INFO: ms1_error      : 30
23:50:22.588209 INFO: ms2_error      : 30
23:50:22.588249 INFO: fwhm_rt        : 5
23:50:22.588287 INFO: quant_window   : 3
23:50:22.588326 INFO: ==============================================
23:50:22.590020 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
23:50:22.590075 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
23:50:22.590114 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
23:50:22.590136 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
23:50:22.590925 INFO: Starting candidate selection
23:51:21.925069 INFO: Starting candidate scoring
23:51:22.426276 INFO: Finished candidate processing
23:51:22.426409 INFO: Collecting candidate features
23:51:22.452060 WARNING: intensity_correlation has 1 NaNs ( 0.02 % out of 6005)
23:51:22.455410 INFO: Collecting fragment features
23:51:22.461734 INFO: Finished candidate scoring
23:51:22.478570 INFO: performing precursor FDR with 47 features
23:51:22.478649 INFO: Decoy channel: -1
23:51:22.478674 INFO: Competetive: True
23:51:22.485231 INFO: Setting torch num_threads to 2 for FDR classification task
23:51:22.488059 WARNING: dropped 1 target PSMs due to missing features
23:51:22.490237 INFO: Using random state 163035 for train-test-split
23:51:22.530779 INFO: Test AUC: 0.499
23:51:22.530885 INFO: Train AUC: 0.497
23:51:22.530916 INFO: AUC difference: 0.43%
23:51:22.758579 INFO: Resetting torch num_threads to 80
23:51:22.762110 PROGRESS: === Extracted 11665 precursors and 125805 fragments ===
23:51:22.762622 INFO: === FDR correction performed with classifier version -1 ===
23:51:22.763898 PROGRESS: ============================= Precursor FDR =============================
23:51:22.763992 PROGRESS: Total precursors accumulated: 5,975
23:51:22.764052 PROGRESS: Target precursors: 5,280 (88.37%)
23:51:22.764102 PROGRESS: Decoy precursors: 695 (11.63%)
23:51:22.764148 PROGRESS: 
23:51:22.764192 PROGRESS: Precursor Summary:
23:51:22.765080 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
23:51:22.765169 PROGRESS: 
23:51:22.765233 PROGRESS: Protein Summary:
23:51:22.766283 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
23:51:22.766372 PROGRESS: =========================================================================
23:51:22.766678 INFO: Target number of precursors not reached yet.
23:51:22.910724 INFO: Starting optimization step 5.
23:51:22.910956 PROGRESS: === Extracting elution groups 6200 to 12600 ===
23:51:22.911063 INFO: Using classic extraction backend
23:51:22.911226 PROGRESS: Extracting batch of 12615 precursors
23:51:22.911308 INFO: === Search parameters used ===
23:51:22.911357 INFO: rt_error       : 2099.9231665
23:51:22.911400 INFO: mobility_error : 0.1
23:51:22.911443 INFO: num_candidates : 1
23:51:22.911484 INFO: ms1_error      : 30
23:51:22.911522 INFO: ms2_error      : 30
23:51:22.911565 INFO: fwhm_rt        : 5
23:51:22.911605 INFO: quant_window   : 3
23:51:22.911642 INFO: ==============================================
23:51:22.914240 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
23:51:22.914293 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
23:51:22.914330 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
23:51:22.914350 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
23:51:22.915174 INFO: Starting candidate selection
23:52:44.882795 INFO: Starting candidate scoring
23:52:46.000801 INFO: Finished candidate processing
23:52:46.000897 INFO: Collecting candidate features
23:52:46.047802 WARNING: intensity_correlation has 3 NaNs ( 0.02 % out of 12017)
23:52:46.048151 WARNING: height_correlation has 1 NaNs ( 0.01 % out of 12017)
23:52:46.053810 INFO: Collecting fragment features
23:52:46.070306 INFO: Finished candidate scoring
23:52:46.101651 INFO: performing precursor FDR with 47 features
23:52:46.101756 INFO: Decoy channel: -1
23:52:46.101781 INFO: Competetive: True
23:52:46.113045 INFO: Setting torch num_threads to 2 for FDR classification task
23:52:46.117491 WARNING: dropped 3 target PSMs due to missing features
23:52:46.117577 WARNING: dropped 1 decoy PSMs due to missing features
23:52:46.121460 INFO: Using random state 895429 for train-test-split
23:52:46.374313 INFO: Test AUC: 0.502
23:52:46.374409 INFO: Train AUC: 0.522
23:52:46.374440 INFO: AUC difference: 3.69%
23:52:46.595239 INFO: Resetting torch num_threads to 80
23:52:46.600645 PROGRESS: === Extracted 23682 precursors and 255250 fragments ===
23:52:46.601236 INFO: === FDR correction performed with classifier version -1 ===
23:52:46.603398 PROGRESS: ============================= Precursor FDR =============================
23:52:46.603503 PROGRESS: Total precursors accumulated: 12,137
23:52:46.603575 PROGRESS: Target precursors: 6,467 (53.28%)
23:52:46.603627 PROGRESS: Decoy precursors: 5,670 (46.72%)
23:52:46.603671 PROGRESS: 
23:52:46.603716 PROGRESS: Precursor Summary:
23:52:46.604615 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
23:52:46.604705 PROGRESS: 
23:52:46.604758 PROGRESS: Protein Summary:
23:52:46.605702 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
23:52:46.605791 PROGRESS: =========================================================================
23:52:46.606212 INFO: Target number of precursors not reached yet.
23:52:46.817410 INFO: Starting optimization step 6.
23:52:46.817655 PROGRESS: === Extracting elution groups 12600 to 25400 ===
23:52:46.817754 INFO: Using classic extraction backend
23:52:46.817928 PROGRESS: Extracting batch of 25223 precursors
23:52:46.818013 INFO: === Search parameters used ===
23:52:46.818077 INFO: rt_error       : 2099.9231665
23:52:46.818131 INFO: mobility_error : 0.1
23:52:46.818179 INFO: num_candidates : 1
23:52:46.818228 INFO: ms1_error      : 30
23:52:46.818272 INFO: ms2_error      : 30
23:52:46.818319 INFO: fwhm_rt        : 5
23:52:46.818363 INFO: quant_window   : 3
23:52:46.818418 INFO: ==============================================
23:52:46.827377 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
23:52:46.827457 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
23:52:46.827499 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
23:52:46.827523 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
23:52:46.828455 INFO: Starting candidate selection
23:55:21.954798 INFO: Starting candidate scoring
23:55:23.806311 INFO: Finished candidate processing
23:55:23.806513 INFO: Collecting candidate features
23:55:23.896616 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 24071)
23:55:23.896968 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 24071)
23:55:23.903048 INFO: Collecting fragment features
23:55:23.921517 INFO: Finished candidate scoring
23:55:24.018829 INFO: performing precursor FDR with 47 features
23:55:24.018994 INFO: Decoy channel: -1
23:55:24.019019 INFO: Competetive: True
23:55:24.047543 INFO: Setting torch num_threads to 2 for FDR classification task
23:55:24.058989 WARNING: dropped 4 target PSMs due to missing features
23:55:24.059149 WARNING: dropped 1 decoy PSMs due to missing features
23:55:24.066678 INFO: Using random state 620552 for train-test-split
23:55:24.893598 INFO: Test AUC: 0.551
23:55:24.893748 INFO: Train AUC: 0.563
23:55:24.893789 INFO: AUC difference: 2.29%
23:55:25.145416 INFO: Resetting torch num_threads to 80
23:55:25.156800 PROGRESS: === Extracted 47753 precursors and 514564 fragments ===
23:55:25.157862 INFO: === FDR correction performed with classifier version -1 ===
23:55:25.163653 PROGRESS: ============================= Precursor FDR =============================
23:55:25.163780 PROGRESS: Total precursors accumulated: 24,478
23:55:25.163845 PROGRESS: Target precursors: 14,334 (58.56%)
23:55:25.163896 PROGRESS: Decoy precursors: 10,144 (41.44%)
23:55:25.163940 PROGRESS: 
23:55:25.163988 PROGRESS: Precursor Summary:
23:55:25.165047 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
23:55:25.165138 PROGRESS: 
23:55:25.165194 PROGRESS: Protein Summary:
23:55:25.166291 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
23:55:25.166383 PROGRESS: =========================================================================
23:55:25.167054 INFO: Target number of precursors not reached yet.
23:55:25.904385 INFO: Starting optimization step 7.
23:55:25.904742 PROGRESS: === Extracting elution groups 25400 to 51000 ===
23:55:25.904863 INFO: Using classic extraction backend
23:55:25.905151 PROGRESS: Extracting batch of 50469 precursors
23:55:25.905243 INFO: === Search parameters used ===
23:55:25.905298 INFO: rt_error       : 2099.9231665
23:55:25.905358 INFO: mobility_error : 0.1
23:55:25.905402 INFO: num_candidates : 1
23:55:25.905447 INFO: ms1_error      : 30
23:55:25.905488 INFO: ms2_error      : 30
23:55:25.905539 INFO: fwhm_rt        : 5
23:55:25.905581 INFO: quant_window   : 3
23:55:25.905622 INFO: ==============================================
23:55:25.920851 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
23:55:25.920997 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
23:55:25.921063 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
23:55:25.921087 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
23:55:25.922229 INFO: Starting candidate selection
1 day, 0:00:34.099594 INFO: Starting candidate scoring
1 day, 0:00:37.482094 INFO: Finished candidate processing
1 day, 0:00:37.482252 INFO: Collecting candidate features
1 day, 0:00:37.596937 WARNING: intensity_correlation has 11 NaNs ( 0.02 % out of 48075)
1 day, 0:00:37.604372 INFO: Collecting fragment features
1 day, 0:00:37.640764 INFO: Finished candidate scoring
1 day, 0:00:37.737158 INFO: performing precursor FDR with 47 features
1 day, 0:00:37.737283 INFO: Decoy channel: -1
1 day, 0:00:37.737309 INFO: Competetive: True
1 day, 0:00:37.782937 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:00:37.805930 WARNING: dropped 9 target PSMs due to missing features
1 day, 0:00:37.806058 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 0:00:37.821718 INFO: Using random state 365661 for train-test-split
1 day, 0:00:39.578638 INFO: Test AUC: 0.557
1 day, 0:00:39.578749 INFO: Train AUC: 0.575
1 day, 0:00:39.578782 INFO: AUC difference: 3.13%
1 day, 0:00:39.836905 INFO: Resetting torch num_threads to 80
1 day, 0:00:39.859242 PROGRESS: === Extracted 95828 precursors and 1032212 fragments ===
1 day, 0:00:39.859969 INFO: === FDR correction performed with classifier version -1 ===
1 day, 0:00:39.869879 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:00:39.870035 PROGRESS: Total precursors accumulated: 49,098
1 day, 0:00:39.870113 PROGRESS: Target precursors: 29,599 (60.29%)
1 day, 0:00:39.870177 PROGRESS: Decoy precursors: 19,499 (39.71%)
1 day, 0:00:39.870223 PROGRESS: 
1 day, 0:00:39.870265 PROGRESS: Precursor Summary:
1 day, 0:00:39.871531 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 0:00:39.871627 PROGRESS: 
1 day, 0:00:39.871682 PROGRESS: Protein Summary:
1 day, 0:00:39.872969 PROGRESS: Channel   0:	 0.050 FDR:   237; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 0:00:39.873060 PROGRESS: =========================================================================
1 day, 0:00:39.874272 INFO: Target number of precursors not reached yet.
1 day, 0:00:40.276834 INFO: Starting optimization step 8.
1 day, 0:00:40.277091 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1 day, 0:00:40.277188 INFO: Using classic extraction backend
1 day, 0:00:40.277367 PROGRESS: Extracting batch of 100931 precursors
1 day, 0:00:40.277441 INFO: === Search parameters used ===
1 day, 0:00:40.277492 INFO: rt_error       : 2099.9231665
1 day, 0:00:40.277535 INFO: mobility_error : 0.1
1 day, 0:00:40.277575 INFO: num_candidates : 1
1 day, 0:00:40.277615 INFO: ms1_error      : 30
1 day, 0:00:40.277653 INFO: ms2_error      : 30
1 day, 0:00:40.277690 INFO: fwhm_rt        : 5
1 day, 0:00:40.277727 INFO: quant_window   : 3
1 day, 0:00:40.277764 INFO: ==============================================
1 day, 0:00:40.304817 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:00:40.304938 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:00:40.304982 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 0:00:40.305004 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 0:00:40.305870 INFO: Starting candidate selection
1 day, 0:10:54.439516 INFO: Starting candidate scoring
1 day, 0:11:01.536110 INFO: Finished candidate processing
1 day, 0:11:01.536264 INFO: Collecting candidate features
1 day, 0:11:01.725929 WARNING: intensity_correlation has 19 NaNs ( 0.02 % out of 95991)
1 day, 0:11:01.732476 INFO: Collecting fragment features
1 day, 0:11:01.792622 INFO: Finished candidate scoring
1 day, 0:11:02.023588 INFO: performing precursor FDR with 47 features
1 day, 0:11:02.023714 INFO: Decoy channel: -1
1 day, 0:11:02.023741 INFO: Competetive: True
1 day, 0:11:02.106235 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:11:02.141224 WARNING: dropped 20 target PSMs due to missing features
1 day, 0:11:02.141349 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 0:11:02.180437 INFO: Using random state 500996 for train-test-split
1 day, 0:11:05.503784 INFO: Test AUC: 0.558
1 day, 0:11:05.503918 INFO: Train AUC: 0.582
1 day, 0:11:05.503964 INFO: AUC difference: 4.26%
1 day, 0:11:05.801727 INFO: Resetting torch num_threads to 80
1 day, 0:11:05.841130 PROGRESS: === Extracted 191819 precursors and 2065502 fragments ===
1 day, 0:11:05.841990 INFO: === FDR correction performed with classifier version -1 ===
1 day, 0:11:05.859502 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:11:05.859742 PROGRESS: Total precursors accumulated: 98,256
1 day, 0:11:05.859809 PROGRESS: Target precursors: 59,011 (60.06%)
1 day, 0:11:05.859861 PROGRESS: Decoy precursors: 39,245 (39.94%)
1 day, 0:11:05.859908 PROGRESS: 
1 day, 0:11:05.859951 PROGRESS: Precursor Summary:
1 day, 0:11:05.861670 PROGRESS: Channel   0:	 0.050 FDR:   659; 0.010 FDR:   405; 0.001 FDR:   257
1 day, 0:11:05.861778 PROGRESS: 
1 day, 0:11:05.861837 PROGRESS: Protein Summary:
1 day, 0:11:05.863591 PROGRESS: Channel   0:	 0.050 FDR:   608; 0.010 FDR:   379; 0.001 FDR:   245
1 day, 0:11:05.863690 PROGRESS: =========================================================================
1 day, 0:11:05.865466 INFO: Target number of precursors reached.
1 day, 0:11:06.012703 INFO: fragments_df: keeping 3857 of 2065502 [sum(precursor_idx_mask)=4613 sum(mass_error_mask)=2065498 stop_rank=3857
1 day, 0:11:06.649990 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:11:06.765695 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:11:06.879911 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:11:06.986776 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:11:07.422589 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 0:11:07.423016 INFO: Using score_cutoff 59.82521735687256 (fac=0.99, q=1)
1 day, 0:11:07.423326 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.231463670730591
1 day, 0:11:07.423407 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.011013076640665531
1 day, 0:11:07.423460 INFO: Updating optimization_manager: score_cutoff        : 0 -> 59.82521735687256
1 day, 0:11:07.423516 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:11:07.436765 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:11:07.499197 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:11:07.515566 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:11:07.667037 INFO: Updating optimization_manager: classifier_version  : -1 -> 8
1 day, 0:11:07.667320 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 0:11:07.667454 INFO: Starting optimization step 9.
1 day, 0:11:07.667529 PROGRESS: === Extracting elution groups 0 to 51000 ===
1 day, 0:11:07.667623 INFO: Using classic extraction backend
1 day, 0:11:07.667911 PROGRESS: Extracting batch of 100530 precursors
1 day, 0:11:07.668010 INFO: === Search parameters used ===
1 day, 0:11:07.668072 INFO: rt_error       : 2099.9231665
1 day, 0:11:07.668125 INFO: mobility_error : 0.1
1 day, 0:11:07.668179 INFO: num_candidates : 3
1 day, 0:11:07.668229 INFO: ms1_error      : 30
1 day, 0:11:07.668282 INFO: ms2_error      : 30
1 day, 0:11:07.668330 INFO: fwhm_rt        : 3.231463670730591
1 day, 0:11:07.668380 INFO: quant_window   : 3
1 day, 0:11:07.668429 INFO: ==============================================
1 day, 0:11:07.708413 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:11:07.708543 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:11:07.708626 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
1 day, 0:11:07.708651 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.11
1 day, 0:11:07.713892 INFO: Starting candidate selection
1 day, 0:21:22.096835 INFO: Starting candidate scoring
1 day, 0:22:21.556488 INFO: Finished candidate processing
1 day, 0:22:21.557153 INFO: Collecting candidate features
1 day, 0:22:22.316225 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 279274)
1 day, 0:22:22.332649 INFO: Collecting fragment features
1 day, 0:22:22.523115 INFO: Finished candidate scoring
1 day, 0:22:22.727556 INFO: performing precursor FDR with 47 features
1 day, 0:22:22.727671 INFO: Decoy channel: -1
1 day, 0:22:22.727697 INFO: Competetive: True
1 day, 0:22:22.828674 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:22:22.870737 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 0:22:22.942691 INFO: Using random state 906351 for train-test-split
1 day, 0:22:27.718976 INFO: Test AUC: 0.572
1 day, 0:22:27.719100 INFO: Train AUC: 0.591
1 day, 0:22:27.719132 INFO: AUC difference: 3.12%
1 day, 0:22:28.035659 INFO: Resetting torch num_threads to 80
1 day, 0:22:28.043265 PROGRESS: === Extracted 279274 precursors and 3041110 fragments ===
1 day, 0:22:28.043825 INFO: === FDR correction performed with classifier version 8 ===
1 day, 0:22:28.054110 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:22:28.054341 PROGRESS: Total precursors accumulated: 50,113
1 day, 0:22:28.054411 PROGRESS: Target precursors: 31,582 (63.02%)
1 day, 0:22:28.054464 PROGRESS: Decoy precursors: 18,531 (36.98%)
1 day, 0:22:28.054521 PROGRESS: 
1 day, 0:22:28.054568 PROGRESS: Precursor Summary:
1 day, 0:22:28.055903 PROGRESS: Channel   0:	 0.050 FDR:   282; 0.010 FDR:   205; 0.001 FDR:   121
1 day, 0:22:28.055995 PROGRESS: 
1 day, 0:22:28.056052 PROGRESS: Protein Summary:
1 day, 0:22:28.057363 PROGRESS: Channel   0:	 0.050 FDR:   271; 0.010 FDR:   198; 0.001 FDR:   117
1 day, 0:22:28.057460 PROGRESS: =========================================================================
1 day, 0:22:28.100039 INFO: Target number of precursors reached.
1 day, 0:22:28.302127 INFO: fragments_df: keeping 3390 of 3041110 [sum(precursor_idx_mask)=6731 sum(mass_error_mask)=3041110 stop_rank=3390
1 day, 0:22:28.613997 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:22:28.729162 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:22:28.846779 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:22:28.960037 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:22:29.332335 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:22:29.332759 INFO: Using score_cutoff 63.85647376098632 (fac=0.99, q=1)
1 day, 0:22:29.333071 INFO: Updating optimization_manager: fwhm_rt             : 3.231463670730591 -> 3.1314616203308105
1 day, 0:22:29.333153 INFO: Updating optimization_manager: fwhm_mobility       : 0.011013076640665531 -> 0.010928375646471977
1 day, 0:22:29.333207 INFO: Updating optimization_manager: score_cutoff        : 59.82521735687256 -> 63.85647376098632
1 day, 0:22:29.333264 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:22:29.346549 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:22:29.407910 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:22:29.423381 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:22:29.557152 INFO: === checking if optimization conditions were reached ===
1 day, 0:22:29.559098 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 0:22:29.559206 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1 day, 0:22:29.559273 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 0:22:29.560208 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 0:22:29.560308 INFO: Updating optimization_manager: classifier_version  : 9 -> 9
1 day, 0:22:29.560376 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 0:22:29.560433 INFO: ==============================================
1 day, 0:22:29.560506 INFO: Starting optimization step 10.
1 day, 0:22:29.560564 PROGRESS: === Extracting elution groups 0 to 51000 ===
1 day, 0:22:29.560630 INFO: Using classic extraction backend
1 day, 0:22:29.560793 PROGRESS: Extracting batch of 100530 precursors
1 day, 0:22:29.560860 INFO: === Search parameters used ===
1 day, 0:22:29.560907 INFO: rt_error       : 2099.9231665
1 day, 0:22:29.560949 INFO: mobility_error : 0.1
1 day, 0:22:29.560988 INFO: num_candidates : 3
1 day, 0:22:29.561027 INFO: ms1_error      : 15.0
1 day, 0:22:29.561077 INFO: ms2_error      : 15.0
1 day, 0:22:29.561118 INFO: fwhm_rt        : 3.1314616203308105
1 day, 0:22:29.561158 INFO: quant_window   : 3
1 day, 0:22:29.561198 INFO: ==============================================
1 day, 0:22:29.591584 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:22:29.591712 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:22:29.591765 INFO: FWHM in RT is 3.13 seconds, sigma is 0.69
1 day, 0:22:29.591787 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.07
1 day, 0:22:29.600703 INFO: Starting candidate selection
1 day, 0:31:49.941671 INFO: Starting candidate scoring
1 day, 0:32:01.561061 INFO: Finished candidate processing
1 day, 0:32:01.561260 INFO: Collecting candidate features
1 day, 0:32:02.047662 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 278902)
1 day, 0:32:02.061828 INFO: Collecting fragment features
1 day, 0:32:02.235631 INFO: Finished candidate scoring
1 day, 0:32:02.364995 INFO: performing precursor FDR with 47 features
1 day, 0:32:02.365116 INFO: Decoy channel: -1
1 day, 0:32:02.365147 INFO: Competetive: True
1 day, 0:32:02.456073 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:32:02.510174 WARNING: dropped 5 target PSMs due to missing features
1 day, 0:32:02.510298 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 0:32:02.586460 INFO: Using random state 12381 for train-test-split
1 day, 0:32:08.064058 INFO: Test AUC: 0.567
1 day, 0:32:08.064175 INFO: Train AUC: 0.590
1 day, 0:32:08.064209 INFO: AUC difference: 3.82%
1 day, 0:32:08.383860 INFO: Resetting torch num_threads to 80
1 day, 0:32:08.391321 PROGRESS: === Extracted 278902 precursors and 2889970 fragments ===
1 day, 0:32:08.391863 INFO: === FDR correction performed with classifier version 9 ===
1 day, 0:32:08.402070 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:32:08.402290 PROGRESS: Total precursors accumulated: 50,003
1 day, 0:32:08.402353 PROGRESS: Target precursors: 31,091 (62.18%)
1 day, 0:32:08.402402 PROGRESS: Decoy precursors: 18,912 (37.82%)
1 day, 0:32:08.402450 PROGRESS: 
1 day, 0:32:08.402493 PROGRESS: Precursor Summary:
1 day, 0:32:08.403857 PROGRESS: Channel   0:	 0.050 FDR:   486; 0.010 FDR:   375; 0.001 FDR:   231
1 day, 0:32:08.403950 PROGRESS: 
1 day, 0:32:08.404010 PROGRESS: Protein Summary:
1 day, 0:32:08.405423 PROGRESS: Channel   0:	 0.050 FDR:   457; 0.010 FDR:   358; 0.001 FDR:   222
1 day, 0:32:08.405517 PROGRESS: =========================================================================
1 day, 0:32:08.407208 INFO: Target number of precursors reached.
1 day, 0:32:08.596961 INFO: fragments_df: keeping 5000 of 2889970 [sum(precursor_idx_mask)=12083 sum(mass_error_mask)=2889970 stop_rank=5000
1 day, 0:32:08.894028 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:32:09.026718 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:32:09.146604 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:32:09.253150 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:32:09.859892 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:32:09.860314 INFO: Using score_cutoff 47.52912520294189 (fac=0.99, q=1)
1 day, 0:32:09.860656 INFO: Updating optimization_manager: fwhm_rt             : 3.1314616203308105 -> 2.892441987991333
1 day, 0:32:09.860742 INFO: Updating optimization_manager: fwhm_mobility       : 0.010928375646471977 -> 0.009091859683394432
1 day, 0:32:09.860799 INFO: Updating optimization_manager: score_cutoff        : 63.85647376098632 -> 47.52912520294189
1 day, 0:32:09.860855 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:32:09.874029 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:32:09.934587 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:32:09.950198 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:32:10.098140 INFO: === checking if optimization conditions were reached ===
1 day, 0:32:10.100568 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 0:32:10.100686 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1 day, 0:32:10.100766 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 0:32:10.101908 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 0:32:10.102014 INFO: Updating optimization_manager: classifier_version  : 10 -> 10
1 day, 0:32:10.102097 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 0:32:10.102161 INFO: ==============================================
1 day, 0:32:10.102262 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 0:32:10.323327 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:32:10.336801 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:32:10.397483 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:32:10.412423 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:32:10.558489 INFO: Starting optimization step 0.
1 day, 0:32:10.558762 PROGRESS: === Extracting elution groups 0 to 51000 ===
1 day, 0:32:10.558857 INFO: Using classic extraction backend
1 day, 0:32:10.559047 PROGRESS: Extracting batch of 100530 precursors
1 day, 0:32:10.559139 INFO: === Search parameters used ===
1 day, 0:32:10.559199 INFO: rt_error       : 2099.9231665
1 day, 0:32:10.559251 INFO: mobility_error : 0.1
1 day, 0:32:10.559303 INFO: num_candidates : 3
1 day, 0:32:10.559354 INFO: ms1_error      : 15.0
1 day, 0:32:10.559404 INFO: ms2_error      : 15.0
1 day, 0:32:10.559452 INFO: fwhm_rt        : 2.892441987991333
1 day, 0:32:10.559500 INFO: quant_window   : 3
1 day, 0:32:10.559549 INFO: ==============================================
1 day, 0:32:10.602732 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:32:10.602864 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:32:10.602923 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 0:32:10.602952 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.22
1 day, 0:32:10.606664 INFO: Starting candidate selection
1 day, 0:41:35.287471 INFO: Starting candidate scoring
1 day, 0:41:46.646240 INFO: Finished candidate processing
1 day, 0:41:46.646341 INFO: Collecting candidate features
1 day, 0:41:47.047487 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 277949)
1 day, 0:41:47.062202 INFO: Collecting fragment features
1 day, 0:41:47.226689 INFO: Finished candidate scoring
1 day, 0:41:47.436536 INFO: performing precursor FDR with 47 features
1 day, 0:41:47.436648 INFO: Decoy channel: -1
1 day, 0:41:47.436677 INFO: Competetive: True
1 day, 0:41:47.514970 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:41:47.558147 WARNING: dropped 2 target PSMs due to missing features
1 day, 0:41:47.558274 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 0:41:47.629718 INFO: Using random state 256294 for train-test-split
1 day, 0:41:52.504444 INFO: Test AUC: 0.576
1 day, 0:41:52.504562 INFO: Train AUC: 0.597
1 day, 0:41:52.504594 INFO: AUC difference: 3.40%
1 day, 0:41:52.812325 INFO: Resetting torch num_threads to 80
1 day, 0:41:52.818234 PROGRESS: === Extracted 277949 precursors and 2870612 fragments ===
1 day, 0:41:52.818776 INFO: === FDR correction performed with classifier version 10 ===
1 day, 0:41:52.828547 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:41:52.828798 PROGRESS: Total precursors accumulated: 49,927
1 day, 0:41:52.828863 PROGRESS: Target precursors: 31,403 (62.90%)
1 day, 0:41:52.828913 PROGRESS: Decoy precursors: 18,524 (37.10%)
1 day, 0:41:52.828959 PROGRESS: 
1 day, 0:41:52.829003 PROGRESS: Precursor Summary:
1 day, 0:41:52.830389 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   375; 0.001 FDR:   313
1 day, 0:41:52.830484 PROGRESS: 
1 day, 0:41:52.830540 PROGRESS: Protein Summary:
1 day, 0:41:52.831935 PROGRESS: Channel   0:	 0.050 FDR:   510; 0.010 FDR:   358; 0.001 FDR:   300
1 day, 0:41:52.832026 PROGRESS: =========================================================================
1 day, 0:41:52.833644 INFO: Target number of precursors reached.
1 day, 0:41:53.028450 INFO: fragments_df: keeping 5000 of 2870612 [sum(precursor_idx_mask)=12144 sum(mass_error_mask)=2870612 stop_rank=5000
1 day, 0:41:53.325028 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:41:53.454108 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:41:53.573822 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:41:53.695483 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:41:54.365572 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:41:54.365977 INFO: Using score_cutoff 45.8702694442749 (fac=0.99, q=1)
1 day, 0:41:54.366306 INFO: Updating optimization_manager: fwhm_rt             : 2.892441987991333 -> 2.9242753982543945
1 day, 0:41:54.366396 INFO: Updating optimization_manager: fwhm_mobility       : 0.009091859683394432 -> 0.009117077104747295
1 day, 0:41:54.366451 INFO: Updating optimization_manager: score_cutoff        : 47.52912520294189 -> 45.8702694442749
1 day, 0:41:54.366512 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:41:54.380054 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:41:54.441294 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:41:54.456626 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:41:54.602941 INFO: === checking if optimization conditions were reached ===
1 day, 0:41:54.603217 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 0:41:54.605478 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 493.21033509748673
1 day, 0:41:54.605597 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 493.2103.
1 day, 0:41:54.605675 INFO: ==============================================
1 day, 0:41:54.605775 INFO: Starting optimization step 1.
1 day, 0:41:54.605844 PROGRESS: === Extracting elution groups 0 to 51000 ===
1 day, 0:41:54.605917 INFO: Using classic extraction backend
1 day, 0:41:54.606106 PROGRESS: Extracting batch of 100530 precursors
1 day, 0:41:54.606197 INFO: === Search parameters used ===
1 day, 0:41:54.606255 INFO: rt_error       : 493.21033509748673
1 day, 0:41:54.606306 INFO: mobility_error : 0.1
1 day, 0:41:54.606356 INFO: num_candidates : 3
1 day, 0:41:54.606405 INFO: ms1_error      : 15.0
1 day, 0:41:54.606466 INFO: ms2_error      : 15.0
1 day, 0:41:54.606516 INFO: fwhm_rt        : 2.9242753982543945
1 day, 0:41:54.606566 INFO: quant_window   : 3
1 day, 0:41:54.606616 INFO: ==============================================
1 day, 0:41:54.643609 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:41:54.643745 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:41:54.643808 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
1 day, 0:41:54.643836 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.23
1 day, 0:41:54.650556 INFO: Starting candidate selection
1 day, 0:44:08.998661 INFO: Starting candidate scoring
1 day, 0:44:20.491457 INFO: Finished candidate processing
1 day, 0:44:20.491628 INFO: Collecting candidate features
1 day, 0:44:20.911607 WARNING: intensity_correlation has 53 NaNs ( 0.02 % out of 268577)
1 day, 0:44:20.912050 WARNING: height_correlation has 14 NaNs ( 0.01 % out of 268577)
1 day, 0:44:20.924014 INFO: Collecting fragment features
1 day, 0:44:21.082932 INFO: Finished candidate scoring
1 day, 0:44:21.210012 INFO: performing precursor FDR with 47 features
1 day, 0:44:21.210131 INFO: Decoy channel: -1
1 day, 0:44:21.210159 INFO: Competetive: True
1 day, 0:44:21.281863 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:44:21.323482 WARNING: dropped 32 target PSMs due to missing features
1 day, 0:44:21.323604 WARNING: dropped 29 decoy PSMs due to missing features
1 day, 0:44:21.391134 INFO: Using random state 256294 for train-test-split
1 day, 0:44:25.693007 INFO: Test AUC: 0.563
1 day, 0:44:25.693123 INFO: Train AUC: 0.578
1 day, 0:44:25.693155 INFO: AUC difference: 2.66%
1 day, 0:44:27.626726 INFO: Resetting torch num_threads to 80
1 day, 0:44:27.632511 PROGRESS: === Extracted 268577 precursors and 2720670 fragments ===
1 day, 0:44:27.633027 INFO: === FDR correction performed with classifier version 10 ===
1 day, 0:44:27.641830 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:44:27.642061 PROGRESS: Total precursors accumulated: 48,984
1 day, 0:44:27.642127 PROGRESS: Target precursors: 29,891 (61.02%)
1 day, 0:44:27.642178 PROGRESS: Decoy precursors: 19,093 (38.98%)
1 day, 0:44:27.642226 PROGRESS: 
1 day, 0:44:27.642270 PROGRESS: Precursor Summary:
1 day, 0:44:27.643706 PROGRESS: Channel   0:	 0.050 FDR:   621; 0.010 FDR:   465; 0.001 FDR:   347
1 day, 0:44:27.643808 PROGRESS: 
1 day, 0:44:27.643863 PROGRESS: Protein Summary:
1 day, 0:44:27.645315 PROGRESS: Channel   0:	 0.050 FDR:   580; 0.010 FDR:   440; 0.001 FDR:   335
1 day, 0:44:27.645425 PROGRESS: =========================================================================
1 day, 0:44:27.647169 INFO: Target number of precursors reached.
1 day, 0:44:27.817353 INFO: fragments_df: keeping 5000 of 2720670 [sum(precursor_idx_mask)=14885 sum(mass_error_mask)=2720659 stop_rank=5000
1 day, 0:44:28.031190 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:44:28.185503 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:44:28.319228 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:44:28.449305 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:44:29.124507 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:44:29.124919 INFO: Using score_cutoff 28.527981605529778 (fac=0.99, q=1)
1 day, 0:44:29.125214 INFO: Updating optimization_manager: fwhm_rt             : 2.9242753982543945 -> 2.8231961727142334
1 day, 0:44:29.125294 INFO: Updating optimization_manager: fwhm_mobility       : 0.009117077104747295 -> 0.008601783774793148
1 day, 0:44:29.125348 INFO: Updating optimization_manager: score_cutoff        : 45.8702694442749 -> 28.527981605529778
1 day, 0:44:29.125400 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:44:29.132872 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:44:29.162958 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:44:29.169787 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:44:29.232321 INFO: === checking if optimization conditions were reached ===
1 day, 0:44:29.232584 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 0:44:29.235035 INFO: Updating optimization_manager: rt_error            : 493.21033509748673 -> 461.4862207685295
1 day, 0:44:29.235160 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 461.4862.
1 day, 0:44:29.235237 INFO: ==============================================
1 day, 0:44:29.235316 INFO: Starting optimization step 2.
1 day, 0:44:29.235382 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 0:44:29.235462 INFO: Using classic extraction backend
1 day, 0:44:29.235598 PROGRESS: Extracting batch of 50061 precursors
1 day, 0:44:29.235676 INFO: === Search parameters used ===
1 day, 0:44:29.235735 INFO: rt_error       : 461.4862207685295
1 day, 0:44:29.235789 INFO: mobility_error : 0.1
1 day, 0:44:29.235839 INFO: num_candidates : 3
1 day, 0:44:29.235891 INFO: ms1_error      : 15.0
1 day, 0:44:29.235942 INFO: ms2_error      : 15.0
1 day, 0:44:29.235993 INFO: fwhm_rt        : 2.8231961727142334
1 day, 0:44:29.236043 INFO: quant_window   : 3
1 day, 0:44:29.236093 INFO: ==============================================
1 day, 0:44:29.255184 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:44:29.255301 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:44:29.255350 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 0:44:29.255378 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 0:44:29.264509 INFO: Starting candidate selection
1 day, 0:45:35.181283 INFO: Starting candidate scoring
1 day, 0:45:41.120447 INFO: Finished candidate processing
1 day, 0:45:41.120645 INFO: Collecting candidate features
1 day, 0:45:41.373241 WARNING: intensity_correlation has 32 NaNs ( 0.02 % out of 133792)
1 day, 0:45:41.373647 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 133792)
1 day, 0:45:41.382063 INFO: Collecting fragment features
1 day, 0:45:41.470444 INFO: Finished candidate scoring
1 day, 0:45:41.543261 INFO: performing precursor FDR with 47 features
1 day, 0:45:41.543420 INFO: Decoy channel: -1
1 day, 0:45:41.543468 INFO: Competetive: True
1 day, 0:45:41.594898 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:45:41.624917 WARNING: dropped 21 target PSMs due to missing features
1 day, 0:45:41.625096 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 0:45:41.654174 INFO: Using random state 256294 for train-test-split
1 day, 0:45:43.826437 INFO: Test AUC: 0.560
1 day, 0:45:43.826557 INFO: Train AUC: 0.590
1 day, 0:45:43.826590 INFO: AUC difference: 4.99%
1 day, 0:45:44.093467 INFO: Resetting torch num_threads to 80
1 day, 0:45:44.096764 PROGRESS: === Extracted 133792 precursors and 1351509 fragments ===
1 day, 0:45:44.097257 INFO: === FDR correction performed with classifier version 10 ===
1 day, 0:45:44.101068 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:45:44.101195 PROGRESS: Total precursors accumulated: 24,390
1 day, 0:45:44.101258 PROGRESS: Target precursors: 14,956 (61.32%)
1 day, 0:45:44.101311 PROGRESS: Decoy precursors: 9,434 (38.68%)
1 day, 0:45:44.101356 PROGRESS: 
1 day, 0:45:44.101403 PROGRESS: Precursor Summary:
1 day, 0:45:44.102587 PROGRESS: Channel   0:	 0.050 FDR:   297; 0.010 FDR:   232; 0.001 FDR:    75
1 day, 0:45:44.102682 PROGRESS: 
1 day, 0:45:44.102750 PROGRESS: Protein Summary:
1 day, 0:45:44.103963 PROGRESS: Channel   0:	 0.050 FDR:   293; 0.010 FDR:   228; 0.001 FDR:    74
1 day, 0:45:44.104055 PROGRESS: =========================================================================
1 day, 0:45:44.132872 INFO: Target number of precursors reached.
1 day, 0:45:44.223895 INFO: fragments_df: keeping 3390 of 1351509 [sum(precursor_idx_mask)=7399 sum(mass_error_mask)=1351505 stop_rank=3390
1 day, 0:45:44.432369 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:45:44.598533 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:45:44.717804 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:45:44.833611 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:45:45.281999 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:45:45.282425 INFO: Using score_cutoff 37.588827296447754 (fac=0.99, q=1)
1 day, 0:45:45.282744 INFO: Updating optimization_manager: fwhm_rt             : 2.8231961727142334 -> 2.8200416564941406
1 day, 0:45:45.282825 INFO: Updating optimization_manager: fwhm_mobility       : 0.008601783774793148 -> 0.008677328005433083
1 day, 0:45:45.282879 INFO: Updating optimization_manager: score_cutoff        : 28.527981605529778 -> 37.588827296447754
1 day, 0:45:45.282936 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:45:45.290498 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:45:45.320428 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:45:45.328242 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:45:45.399025 INFO: === checking if optimization conditions were reached ===
1 day, 0:45:45.399321 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 0:45:45.401709 INFO: Updating optimization_manager: rt_error            : 461.4862207685295 -> 391.81967968203116
1 day, 0:45:45.401825 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 391.8197.
1 day, 0:45:45.401901 INFO: ==============================================
1 day, 0:45:45.401985 INFO: Starting optimization step 3.
1 day, 0:45:45.402063 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 0:45:45.402137 INFO: Using classic extraction backend
1 day, 0:45:45.402314 PROGRESS: Extracting batch of 50061 precursors
1 day, 0:45:45.402393 INFO: === Search parameters used ===
1 day, 0:45:45.402451 INFO: rt_error       : 391.81967968203116
1 day, 0:45:45.402503 INFO: mobility_error : 0.1
1 day, 0:45:45.402555 INFO: num_candidates : 3
1 day, 0:45:45.402605 INFO: ms1_error      : 15.0
1 day, 0:45:45.402653 INFO: ms2_error      : 15.0
1 day, 0:45:45.402701 INFO: fwhm_rt        : 2.8200416564941406
1 day, 0:45:45.402748 INFO: quant_window   : 3
1 day, 0:45:45.402797 INFO: ==============================================
1 day, 0:45:45.422971 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:45:45.423113 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:45:45.423172 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 0:45:45.423200 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.02
1 day, 0:45:45.460413 INFO: Starting candidate selection
1 day, 0:46:42.928061 INFO: Starting candidate scoring
1 day, 0:46:48.905395 INFO: Finished candidate processing
1 day, 0:46:48.905556 INFO: Collecting candidate features
1 day, 0:46:49.141730 WARNING: intensity_correlation has 31 NaNs ( 0.02 % out of 133360)
1 day, 0:46:49.142119 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 133360)
1 day, 0:46:49.152206 INFO: Collecting fragment features
1 day, 0:46:49.235940 INFO: Finished candidate scoring
1 day, 0:46:49.292568 INFO: performing precursor FDR with 47 features
1 day, 0:46:49.292677 INFO: Decoy channel: -1
1 day, 0:46:49.292709 INFO: Competetive: True
1 day, 0:46:49.334236 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:46:49.357668 WARNING: dropped 18 target PSMs due to missing features
1 day, 0:46:49.357792 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 0:46:49.378625 INFO: Using random state 256294 for train-test-split
1 day, 0:46:51.581028 INFO: Test AUC: 0.557
1 day, 0:46:51.581140 INFO: Train AUC: 0.581
1 day, 0:46:51.581173 INFO: AUC difference: 4.23%
1 day, 0:46:51.864452 INFO: Resetting torch num_threads to 80
1 day, 0:46:51.868059 PROGRESS: === Extracted 133360 precursors and 1343408 fragments ===
1 day, 0:46:51.868592 INFO: === FDR correction performed with classifier version 10 ===
1 day, 0:46:51.873088 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:46:51.873236 PROGRESS: Total precursors accumulated: 24,325
1 day, 0:46:51.873306 PROGRESS: Target precursors: 14,769 (60.72%)
1 day, 0:46:51.873365 PROGRESS: Decoy precursors: 9,556 (39.28%)
1 day, 0:46:51.873419 PROGRESS: 
1 day, 0:46:51.873471 PROGRESS: Precursor Summary:
1 day, 0:46:51.874682 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   222; 0.001 FDR:   182
1 day, 0:46:51.874782 PROGRESS: 
1 day, 0:46:51.874844 PROGRESS: Protein Summary:
1 day, 0:46:51.876103 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   218; 0.001 FDR:   178
1 day, 0:46:51.876199 PROGRESS: =========================================================================
1 day, 0:46:51.877063 INFO: Target number of precursors reached.
1 day, 0:46:51.966905 INFO: fragments_df: keeping 3300 of 1343408 [sum(precursor_idx_mask)=7109 sum(mass_error_mask)=1343405 stop_rank=3300
1 day, 0:46:52.187529 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:46:52.308045 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:46:52.414409 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:46:52.512135 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:46:52.881449 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:46:52.881863 INFO: Using score_cutoff 48.168629612731934 (fac=0.99, q=1)
1 day, 0:46:52.882186 INFO: Updating optimization_manager: fwhm_rt             : 2.8200416564941406 -> 2.9087517261505127
1 day, 0:46:52.882270 INFO: Updating optimization_manager: fwhm_mobility       : 0.008677328005433083 -> 0.008924624882638454
1 day, 0:46:52.882334 INFO: Updating optimization_manager: score_cutoff        : 37.588827296447754 -> 48.168629612731934
1 day, 0:46:52.882394 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:46:52.889741 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:46:52.919763 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:46:52.927435 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:46:52.990284 INFO: === checking if optimization conditions were reached ===
1 day, 0:46:52.990508 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 0:46:52.992543 INFO: Updating optimization_manager: rt_error            : 391.81967968203116 -> 379.6684977461478
1 day, 0:46:52.992662 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 379.6685.
1 day, 0:46:52.992730 INFO: ==============================================
1 day, 0:46:52.992805 INFO: Starting optimization step 4.
1 day, 0:46:52.992866 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 0:46:52.992928 INFO: Using classic extraction backend
1 day, 0:46:52.993081 PROGRESS: Extracting batch of 50061 precursors
1 day, 0:46:52.993149 INFO: === Search parameters used ===
1 day, 0:46:52.993196 INFO: rt_error       : 379.6684977461478
1 day, 0:46:52.993237 INFO: mobility_error : 0.1
1 day, 0:46:52.993276 INFO: num_candidates : 3
1 day, 0:46:52.993319 INFO: ms1_error      : 15.0
1 day, 0:46:52.993359 INFO: ms2_error      : 15.0
1 day, 0:46:52.993406 INFO: fwhm_rt        : 2.9087517261505127
1 day, 0:46:52.993447 INFO: quant_window   : 3
1 day, 0:46:52.993484 INFO: ==============================================
1 day, 0:46:53.007190 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:46:53.007290 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:46:53.007342 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 0:46:53.007367 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
1 day, 0:46:53.016305 INFO: Starting candidate selection
1 day, 0:47:46.571682 INFO: Starting candidate scoring
1 day, 0:47:52.548220 INFO: Finished candidate processing
1 day, 0:47:52.548322 INFO: Collecting candidate features
1 day, 0:47:52.736758 WARNING: intensity_correlation has 31 NaNs ( 0.02 % out of 133387)
1 day, 0:47:52.737121 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 133387)
1 day, 0:47:52.745639 INFO: Collecting fragment features
1 day, 0:47:52.831474 INFO: Finished candidate scoring
1 day, 0:47:52.950017 INFO: performing precursor FDR with 47 features
1 day, 0:47:52.950141 INFO: Decoy channel: -1
1 day, 0:47:52.950166 INFO: Competetive: True
1 day, 0:47:52.990649 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:47:53.013382 WARNING: dropped 20 target PSMs due to missing features
1 day, 0:47:53.013509 WARNING: dropped 13 decoy PSMs due to missing features
1 day, 0:47:53.033188 INFO: Using random state 256294 for train-test-split
1 day, 0:47:55.319619 INFO: Test AUC: 0.549
1 day, 0:47:55.319737 INFO: Train AUC: 0.587
1 day, 0:47:55.319769 INFO: AUC difference: 6.34%
1 day, 0:47:55.319792 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 0:47:55.597126 INFO: Resetting torch num_threads to 80
1 day, 0:47:55.600382 PROGRESS: === Extracted 133387 precursors and 1343731 fragments ===
1 day, 0:47:55.600896 INFO: === FDR correction performed with classifier version 10 ===
1 day, 0:47:55.604988 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:47:55.605114 PROGRESS: Total precursors accumulated: 24,326
1 day, 0:47:55.605176 PROGRESS: Target precursors: 14,779 (60.75%)
1 day, 0:47:55.605227 PROGRESS: Decoy precursors: 9,547 (39.25%)
1 day, 0:47:55.605277 PROGRESS: 
1 day, 0:47:55.605324 PROGRESS: Precursor Summary:
1 day, 0:47:55.606536 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   241; 0.001 FDR:   226
1 day, 0:47:55.606632 PROGRESS: 
1 day, 0:47:55.606687 PROGRESS: Protein Summary:
1 day, 0:47:55.607938 PROGRESS: Channel   0:	 0.050 FDR:   340; 0.010 FDR:   237; 0.001 FDR:   222
1 day, 0:47:55.608029 PROGRESS: =========================================================================
1 day, 0:47:55.608850 INFO: Target number of precursors reached.
1 day, 0:47:55.697270 INFO: fragments_df: keeping 3536 of 1343731 [sum(precursor_idx_mask)=7716 sum(mass_error_mask)=1343729 stop_rank=3536
1 day, 0:47:55.906811 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:47:56.023972 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:47:56.146787 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:47:56.263734 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:47:56.673723 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:47:56.674151 INFO: Using score_cutoff 38.67282366943359 (fac=0.99, q=1)
1 day, 0:47:56.674464 INFO: Updating optimization_manager: fwhm_rt             : 2.9087517261505127 -> 2.7407875061035156
1 day, 0:47:56.674544 INFO: Updating optimization_manager: fwhm_mobility       : 0.008924624882638454 -> 0.008588041178882122
1 day, 0:47:56.674599 INFO: Updating optimization_manager: score_cutoff        : 48.168629612731934 -> 38.67282366943359
1 day, 0:47:56.674659 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:47:56.682293 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:47:56.712530 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:47:56.720331 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:47:56.781421 INFO: === checking if optimization conditions were reached ===
1 day, 0:47:56.781701 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 0:47:56.783149 INFO: Updating optimization_manager: rt_error            : 379.6684977461478 -> 379.6684977461478
1 day, 0:47:56.783300 INFO: Updating optimization_manager: classifier_version  : 10 -> 15
1 day, 0:47:56.783410 INFO: Updating optimization_manager: score_cutoff        : 38.67282366943359 -> 38.67282366943359
1 day, 0:47:56.783510 INFO: Updating optimization_manager: fwhm_rt             : 2.7407875061035156 -> 2.7407875061035156
1 day, 0:47:56.783609 INFO: Updating optimization_manager: fwhm_mobility       : 0.008588041178882122 -> 0.008588041178882122
1 day, 0:47:56.783723 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 379.6685 found after 5 searches.
1 day, 0:47:56.783800 INFO: ==============================================
1 day, 0:47:56.783885 PROGRESS: Optimization finished for rt_error.
1 day, 0:47:56.920242 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:47:56.928121 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:47:56.958619 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:47:56.966455 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:47:57.054271 INFO: Starting optimization step 0.
1 day, 0:47:57.054467 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 0:47:57.054544 INFO: Using classic extraction backend
1 day, 0:47:57.054692 PROGRESS: Extracting batch of 50061 precursors
1 day, 0:47:57.054767 INFO: === Search parameters used ===
1 day, 0:47:57.054820 INFO: rt_error       : 379.6684977461478
1 day, 0:47:57.054864 INFO: mobility_error : 0.1
1 day, 0:47:57.054906 INFO: num_candidates : 3
1 day, 0:47:57.054946 INFO: ms1_error      : 15.0
1 day, 0:47:57.054985 INFO: ms2_error      : 15.0
1 day, 0:47:57.055024 INFO: fwhm_rt        : 2.7407875061035156
1 day, 0:47:57.055062 INFO: quant_window   : 3
1 day, 0:47:57.055104 INFO: ==============================================
1 day, 0:47:57.069332 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:47:57.069444 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:47:57.069497 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
1 day, 0:47:57.069524 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
1 day, 0:47:57.078436 INFO: Starting candidate selection
1 day, 0:48:51.378149 INFO: Starting candidate scoring
1 day, 0:48:57.049608 INFO: Finished candidate processing
1 day, 0:48:57.049796 INFO: Collecting candidate features
1 day, 0:48:57.274624 WARNING: intensity_correlation has 31 NaNs ( 0.02 % out of 133304)
1 day, 0:48:57.275031 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 133304)
1 day, 0:48:57.286701 INFO: Collecting fragment features
1 day, 0:48:57.371544 INFO: Finished candidate scoring
1 day, 0:48:57.429438 INFO: performing precursor FDR with 47 features
1 day, 0:48:57.429545 INFO: Decoy channel: -1
1 day, 0:48:57.429579 INFO: Competetive: True
1 day, 0:48:57.468450 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:48:57.501165 WARNING: dropped 21 target PSMs due to missing features
1 day, 0:48:57.501296 WARNING: dropped 13 decoy PSMs due to missing features
1 day, 0:48:57.519750 INFO: Using random state 7577 for train-test-split
1 day, 0:48:59.610750 INFO: Test AUC: 0.570
1 day, 0:48:59.610867 INFO: Train AUC: 0.597
1 day, 0:48:59.610899 INFO: AUC difference: 4.43%
1 day, 0:48:59.878678 INFO: Resetting torch num_threads to 80
1 day, 0:48:59.881897 PROGRESS: === Extracted 133304 precursors and 1341741 fragments ===
1 day, 0:48:59.882690 INFO: === FDR correction performed with classifier version 15 ===
1 day, 0:48:59.886480 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:48:59.886601 PROGRESS: Total precursors accumulated: 24,319
1 day, 0:48:59.886663 PROGRESS: Target precursors: 15,055 (61.91%)
1 day, 0:48:59.886714 PROGRESS: Decoy precursors: 9,264 (38.09%)
1 day, 0:48:59.886759 PROGRESS: 
1 day, 0:48:59.886804 PROGRESS: Precursor Summary:
1 day, 0:48:59.887964 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   224; 0.001 FDR:   137
1 day, 0:48:59.888055 PROGRESS: 
1 day, 0:48:59.888112 PROGRESS: Protein Summary:
1 day, 0:48:59.889361 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   220; 0.001 FDR:   133
1 day, 0:48:59.889452 PROGRESS: =========================================================================
1 day, 0:48:59.890303 INFO: Target number of precursors reached.
1 day, 0:49:00.009655 INFO: fragments_df: keeping 3308 of 1341741 [sum(precursor_idx_mask)=7069 sum(mass_error_mask)=1341738 stop_rank=3308
1 day, 0:49:00.217451 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:49:00.342239 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:49:00.461648 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:49:00.576071 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:49:01.007935 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:49:01.008351 INFO: Using score_cutoff 42.112373308181766 (fac=0.99, q=1)
1 day, 0:49:01.008667 INFO: Updating optimization_manager: fwhm_rt             : 2.7407875061035156 -> 2.8176822662353516
1 day, 0:49:01.008745 INFO: Updating optimization_manager: fwhm_mobility       : 0.008588041178882122 -> 0.008851447142660618
1 day, 0:49:01.008798 INFO: Updating optimization_manager: score_cutoff        : 38.67282366943359 -> 42.112373308181766
1 day, 0:49:01.008853 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:49:01.016358 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:49:01.046477 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:49:01.054162 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:49:01.125842 INFO: === checking if optimization conditions were reached ===
1 day, 0:49:01.126147 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 0:49:01.128161 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0771147082297988
1 day, 0:49:01.128278 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0771.
1 day, 0:49:01.128358 INFO: ==============================================
1 day, 0:49:01.128446 INFO: Starting optimization step 1.
1 day, 0:49:01.128513 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 0:49:01.128586 INFO: Using classic extraction backend
1 day, 0:49:01.128759 PROGRESS: Extracting batch of 50061 precursors
1 day, 0:49:01.128843 INFO: === Search parameters used ===
1 day, 0:49:01.128903 INFO: rt_error       : 379.6684977461478
1 day, 0:49:01.128956 INFO: mobility_error : 0.0771147082297988
1 day, 0:49:01.129019 INFO: num_candidates : 3
1 day, 0:49:01.129073 INFO: ms1_error      : 15.0
1 day, 0:49:01.129124 INFO: ms2_error      : 15.0
1 day, 0:49:01.129182 INFO: fwhm_rt        : 2.8176822662353516
1 day, 0:49:01.129233 INFO: quant_window   : 3
1 day, 0:49:01.129283 INFO: ==============================================
1 day, 0:49:01.149109 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:49:01.149235 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:49:01.149299 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 0:49:01.149331 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.11
1 day, 0:49:01.160466 INFO: Starting candidate selection
1 day, 0:49:43.558317 INFO: Starting candidate scoring
1 day, 0:49:49.307385 INFO: Finished candidate processing
1 day, 0:49:49.307580 INFO: Collecting candidate features
1 day, 0:49:49.548018 WARNING: intensity_correlation has 40 NaNs ( 0.03 % out of 131262)
1 day, 0:49:49.548413 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 131262)
1 day, 0:49:49.556786 INFO: Collecting fragment features
1 day, 0:49:49.644778 INFO: Finished candidate scoring
1 day, 0:49:49.718616 INFO: performing precursor FDR with 47 features
1 day, 0:49:49.718771 INFO: Decoy channel: -1
1 day, 0:49:49.718797 INFO: Competetive: True
1 day, 0:49:49.774023 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:49:49.802372 WARNING: dropped 26 target PSMs due to missing features
1 day, 0:49:49.802541 WARNING: dropped 16 decoy PSMs due to missing features
1 day, 0:49:49.830927 INFO: Using random state 7577 for train-test-split
1 day, 0:49:52.359710 INFO: Test AUC: 0.569
1 day, 0:49:52.360258 INFO: Train AUC: 0.593
1 day, 0:49:52.360299 INFO: AUC difference: 4.00%
1 day, 0:49:52.655717 INFO: Resetting torch num_threads to 80
1 day, 0:49:52.660029 PROGRESS: === Extracted 131262 precursors and 1313321 fragments ===
1 day, 0:49:52.660750 INFO: === FDR correction performed with classifier version 15 ===
1 day, 0:49:52.665392 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:49:52.665528 PROGRESS: Total precursors accumulated: 24,007
1 day, 0:49:52.665591 PROGRESS: Target precursors: 14,835 (61.79%)
1 day, 0:49:52.665646 PROGRESS: Decoy precursors: 9,172 (38.21%)
1 day, 0:49:52.665693 PROGRESS: 
1 day, 0:49:52.665737 PROGRESS: Precursor Summary:
1 day, 0:49:52.666986 PROGRESS: Channel   0:	 0.050 FDR:   373; 0.010 FDR:   250; 0.001 FDR:   244
1 day, 0:49:52.667091 PROGRESS: 
1 day, 0:49:52.667147 PROGRESS: Protein Summary:
1 day, 0:49:52.668415 PROGRESS: Channel   0:	 0.050 FDR:   366; 0.010 FDR:   246; 0.001 FDR:   240
1 day, 0:49:52.668507 PROGRESS: =========================================================================
1 day, 0:49:52.669785 INFO: Target number of precursors reached.
1 day, 0:49:52.758608 INFO: fragments_df: keeping 3591 of 1313321 [sum(precursor_idx_mask)=7927 sum(mass_error_mask)=1313320 stop_rank=3591
1 day, 0:49:53.306886 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:49:53.412894 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:49:53.520120 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:49:53.630536 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:49:54.044114 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:49:54.044665 INFO: Using score_cutoff 41.35082537040711 (fac=0.99, q=1)
1 day, 0:49:54.045067 INFO: Updating optimization_manager: fwhm_rt             : 2.8176822662353516 -> 2.8728318214416504
1 day, 0:49:54.045153 INFO: Updating optimization_manager: fwhm_mobility       : 0.008851447142660618 -> 0.008783837780356407
1 day, 0:49:54.045227 INFO: Updating optimization_manager: score_cutoff        : 42.112373308181766 -> 41.35082537040711
1 day, 0:49:54.045298 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:49:54.053141 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:49:54.084205 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:49:54.092088 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:49:54.163233 INFO: === checking if optimization conditions were reached ===
1 day, 0:49:54.163658 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 0:49:54.166347 INFO: Updating optimization_manager: mobility_error      : 0.0771147082297988 -> 0.06414131798240581
1 day, 0:49:54.166482 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0641.
1 day, 0:49:54.166603 INFO: ==============================================
1 day, 0:49:54.166762 INFO: Starting optimization step 2.
1 day, 0:49:54.166856 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 0:49:54.166957 INFO: Using classic extraction backend
1 day, 0:49:54.167218 PROGRESS: Extracting batch of 50061 precursors
1 day, 0:49:54.167338 INFO: === Search parameters used ===
1 day, 0:49:54.167421 INFO: rt_error       : 379.6684977461478
1 day, 0:49:54.167503 INFO: mobility_error : 0.06414131798240581
1 day, 0:49:54.167577 INFO: num_candidates : 3
1 day, 0:49:54.167655 INFO: ms1_error      : 15.0
1 day, 0:49:54.167720 INFO: ms2_error      : 15.0
1 day, 0:49:54.167792 INFO: fwhm_rt        : 2.8728318214416504
1 day, 0:49:54.167859 INFO: quant_window   : 3
1 day, 0:49:54.167932 INFO: ==============================================
1 day, 0:49:54.194749 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:49:54.194953 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:49:54.195047 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 0:49:54.195099 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.07
1 day, 0:49:54.204472 INFO: Starting candidate selection
1 day, 0:50:28.162265 INFO: Starting candidate scoring
1 day, 0:50:34.007252 INFO: Finished candidate processing
1 day, 0:50:34.007351 INFO: Collecting candidate features
1 day, 0:50:34.184949 WARNING: intensity_correlation has 52 NaNs ( 0.04 % out of 129613)
1 day, 0:50:34.185390 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 129613)
1 day, 0:50:34.198704 INFO: Collecting fragment features
1 day, 0:50:34.275799 INFO: Finished candidate scoring
1 day, 0:50:34.332926 INFO: performing precursor FDR with 47 features
1 day, 0:50:34.333041 INFO: Decoy channel: -1
1 day, 0:50:34.333065 INFO: Competetive: True
1 day, 0:50:34.372893 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:50:34.395195 WARNING: dropped 38 target PSMs due to missing features
1 day, 0:50:34.395320 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 0:50:34.415239 INFO: Using random state 7577 for train-test-split
1 day, 0:50:36.455976 INFO: Test AUC: 0.565
1 day, 0:50:36.456094 INFO: Train AUC: 0.600
1 day, 0:50:36.456128 INFO: AUC difference: 5.82%
1 day, 0:50:36.456151 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 0:50:36.722538 INFO: Resetting torch num_threads to 80
1 day, 0:50:36.725725 PROGRESS: === Extracted 129613 precursors and 1287843 fragments ===
1 day, 0:50:36.726242 INFO: === FDR correction performed with classifier version 15 ===
1 day, 0:50:36.729965 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:50:36.730101 PROGRESS: Total precursors accumulated: 23,758
1 day, 0:50:36.730165 PROGRESS: Target precursors: 14,803 (62.31%)
1 day, 0:50:36.730216 PROGRESS: Decoy precursors: 8,955 (37.69%)
1 day, 0:50:36.730263 PROGRESS: 
1 day, 0:50:36.730308 PROGRESS: Precursor Summary:
1 day, 0:50:36.731455 PROGRESS: Channel   0:	 0.050 FDR:   373; 0.010 FDR:   227; 0.001 FDR:   206
1 day, 0:50:36.731546 PROGRESS: 
1 day, 0:50:36.731601 PROGRESS: Protein Summary:
1 day, 0:50:36.732826 PROGRESS: Channel   0:	 0.050 FDR:   364; 0.010 FDR:   223; 0.001 FDR:   202
1 day, 0:50:36.732921 PROGRESS: =========================================================================
1 day, 0:50:36.734171 INFO: Target number of precursors reached.
1 day, 0:50:36.818151 INFO: fragments_df: keeping 3359 of 1287843 [sum(precursor_idx_mask)=7291 sum(mass_error_mask)=1287843 stop_rank=3359
1 day, 0:50:37.016262 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:50:37.117891 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:50:37.217886 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:50:37.315166 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:50:37.689159 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:50:37.689573 INFO: Using score_cutoff 42.087887704467775 (fac=0.99, q=1)
1 day, 0:50:37.689883 INFO: Updating optimization_manager: fwhm_rt             : 2.8728318214416504 -> 2.908212900161743
1 day, 0:50:37.689963 INFO: Updating optimization_manager: fwhm_mobility       : 0.008783837780356407 -> 0.008958566002547741
1 day, 0:50:37.690018 INFO: Updating optimization_manager: score_cutoff        : 41.35082537040711 -> 42.087887704467775
1 day, 0:50:37.690089 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:50:37.697705 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:50:37.728234 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:50:37.735947 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:50:37.797915 INFO: === checking if optimization conditions were reached ===
1 day, 0:50:37.798195 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 0:50:37.799067 INFO: Updating optimization_manager: mobility_error      : 0.06414131798240581 -> 0.0771147082297988
1 day, 0:50:37.799198 INFO: Updating optimization_manager: classifier_version  : 15 -> 17
1 day, 0:50:37.799301 INFO: Updating optimization_manager: score_cutoff        : 42.087887704467775 -> 41.35082537040711
1 day, 0:50:37.799396 INFO: Updating optimization_manager: fwhm_rt             : 2.908212900161743 -> 2.8728318214416504
1 day, 0:50:37.799488 INFO: Updating optimization_manager: fwhm_mobility       : 0.008958566002547741 -> 0.008783837780356407
1 day, 0:50:37.799582 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0771 found after 3 searches.
1 day, 0:50:37.799654 INFO: ==============================================
1 day, 0:50:37.799731 PROGRESS: Optimization finished for mobility_error.
1 day, 0:50:37.944245 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:50:37.952158 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:50:37.982598 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:50:37.990345 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:50:38.077618 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 0:50:38.077821 PROGRESS: ==============================================
1 day, 0:50:38.077896 PROGRESS: ms2_error      : 15.0000
1 day, 0:50:38.077962 PROGRESS: ms1_error      : 15.0000
1 day, 0:50:38.078039 PROGRESS: rt_error       : 379.6685
1 day, 0:50:38.078115 PROGRESS: mobility_error : 0.0771
1 day, 0:50:38.078167 PROGRESS: ==============================================
1 day, 0:50:38.080382 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:50:39.780875 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:50:47.466974 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:50:49.345556 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:51:06.658907 INFO: Using classic extraction backend
1 day, 0:51:06.661870 PROGRESS: Extracting batch of 12073114 precursors
1 day, 0:51:06.662017 INFO: === Search parameters used ===
1 day, 0:51:06.662087 INFO: rt_error       : 379.6684977461478
1 day, 0:51:06.662141 INFO: mobility_error : 0.0771147082297988
1 day, 0:51:06.662184 INFO: num_candidates : 3
1 day, 0:51:06.662228 INFO: ms1_error      : 15.0
1 day, 0:51:06.662268 INFO: ms2_error      : 15.0
1 day, 0:51:06.662308 INFO: fwhm_rt        : 2.8728318214416504
1 day, 0:51:06.662350 INFO: quant_window   : 3
1 day, 0:51:06.662402 INFO: ==============================================
1 day, 0:51:09.436775 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:51:09.436905 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:51:09.436960 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 0:51:09.436985 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.07
1 day, 0:51:09.437783 INFO: Starting candidate selection
1 day, 3:27:36.484607 INFO: Removed 16557667 precursors with score below cutoff 41.35082537040711
1 day, 3:27:39.330062 INFO: Starting candidate scoring
1 day, 3:38:42.390787 INFO: Finished candidate processing
1 day, 3:38:42.391240 INFO: Collecting candidate features
1 day, 3:39:22.013947 INFO: Collecting fragment features
1 day, 3:39:44.920123 INFO: Finished candidate scoring
1 day, 3:40:09.450733 INFO: === Performing FDR correction with classifier version 17 ===
1 day, 3:40:09.461250 INFO: performing precursor FDR with 47 features
1 day, 3:40:09.461375 INFO: Decoy channel: -1
1 day, 3:40:09.461402 INFO: Competetive: True
1 day, 3:40:41.431849 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:40:49.968929 INFO: Using random state 22334 for train-test-split
1 day, 3:46:30.355630 INFO: Test AUC: 0.568
1 day, 3:46:30.355860 INFO: Train AUC: 0.569
1 day, 3:46:30.355900 INFO: AUC difference: 0.25%
1 day, 3:46:34.345275 INFO: Resetting torch num_threads to 80
1 day, 3:46:34.612089 INFO: Removing fragments below FDR threshold
1 day, 3:46:36.230418 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:46:36.230700 PROGRESS: Total precursors accumulated: 70,125
1 day, 3:46:36.230783 PROGRESS: Target precursors: 69,431 (99.01%)
1 day, 3:46:36.230848 PROGRESS: Decoy precursors: 694 (0.99%)
1 day, 3:46:36.230906 PROGRESS: 
1 day, 3:46:36.230960 PROGRESS: Precursor Summary:
1 day, 3:46:36.255402 PROGRESS: Channel   0:	 0.050 FDR: 69,431; 0.010 FDR: 69,431; 0.001 FDR: 49,094
1 day, 3:46:36.255669 PROGRESS: 
1 day, 3:46:36.255751 PROGRESS: Protein Summary:
1 day, 3:46:36.287370 PROGRESS: Channel   0:	 0.050 FDR: 10,909; 0.010 FDR: 10,909; 0.001 FDR: 8,827
1 day, 3:46:36.287628 PROGRESS: =========================================================================
1 day, 3:46:36.479718 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/psm.parquet
1 day, 3:46:36.823458 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/frag.parquet
1 day, 3:46:37.082224 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 3:47:04.721693 PROGRESS: Processing search outputs
1 day, 3:47:04.721804 PROGRESS: Performing protein grouping and FDR
1 day, 3:47:04.721841 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 3:47:04.828231 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 3:47:04.925888 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 3:47:05.001022 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 3:47:05.104847 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 3:47:05.144083 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 3:47:05.192755 INFO: Building combined output
1 day, 3:47:05.226071 INFO: Performing protein inference
1 day, 3:47:05.659112 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1 day, 3:47:30.113011 INFO: Performing protein FDR
1 day, 3:47:34.765266 INFO: Normalizing q-values using 14,167 targets and 2,791 decoys
1 day, 3:47:34.768278 INFO: Test AUC: 0.886
1 day, 3:47:34.768330 INFO: Train AUC: 0.883
1 day, 3:47:34.768362 INFO: AUC difference: 0.29%
1 day, 3:47:35.321114 PROGRESS: ================ Protein FDR =================
1 day, 3:47:35.321252 PROGRESS: Unique protein groups in output
1 day, 3:47:35.321680 PROGRESS:   1% protein FDR: 8,880
1 day, 3:47:35.321707 PROGRESS: 
1 day, 3:47:35.321725 PROGRESS: Unique precursor in output
1 day, 3:47:35.321744 PROGRESS:   1% protein FDR: 90,710
1 day, 3:47:35.321762 PROGRESS: ================================================
1 day, 3:47:35.377185 PROGRESS: Building search statistics
1 day, 3:47:35.473633 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
1 day, 3:47:35.473994 INFO: Initializing OptimizationManager
1 day, 3:47:35.474274 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
1 day, 3:47:35.474352 INFO: Initializing CalibrationManager
1 day, 3:47:35.474579 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
1 day, 3:47:35.474654 INFO: Initializing RawFileManager
1 day, 3:47:35.502345 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
1 day, 3:47:35.502658 INFO: Initializing OptimizationManager
1 day, 3:47:35.503013 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
1 day, 3:47:35.503099 INFO: Initializing CalibrationManager
1 day, 3:47:35.503481 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
1 day, 3:47:35.503564 INFO: Initializing RawFileManager
1 day, 3:47:35.528445 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
1 day, 3:47:35.528765 INFO: Initializing OptimizationManager
1 day, 3:47:35.529112 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
1 day, 3:47:35.529192 INFO: Initializing CalibrationManager
1 day, 3:47:35.529558 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
1 day, 3:47:35.529638 INFO: Initializing RawFileManager
1 day, 3:47:35.563297 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
1 day, 3:47:35.563596 INFO: Initializing OptimizationManager
1 day, 3:47:35.563924 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
1 day, 3:47:35.564004 INFO: Initializing CalibrationManager
1 day, 3:47:35.564352 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
1 day, 3:47:35.564438 INFO: Initializing RawFileManager
1 day, 3:47:35.589495 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
1 day, 3:47:35.589681 INFO: Initializing OptimizationManager
1 day, 3:47:35.590020 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
1 day, 3:47:35.590108 INFO: Initializing CalibrationManager
1 day, 3:47:35.590481 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
1 day, 3:47:35.590563 INFO: Initializing RawFileManager
1 day, 3:47:35.617958 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
1 day, 3:47:35.618175 INFO: Initializing OptimizationManager
1 day, 3:47:35.618386 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
1 day, 3:47:35.618463 INFO: Initializing CalibrationManager
1 day, 3:47:35.618644 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
1 day, 3:47:35.618712 INFO: Initializing RawFileManager
1 day, 3:47:35.620990 INFO: Writing stat output to disk
1 day, 3:47:35.621058 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/library/stat.tsv to disk
1 day, 3:47:35.629060 PROGRESS: Building internal statistics
1 day, 3:47:35.629532 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
1 day, 3:47:35.629587 INFO: Initializing TimingManager
1 day, 3:47:35.630058 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
1 day, 3:47:35.630108 INFO: Initializing TimingManager
1 day, 3:47:35.630460 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
1 day, 3:47:35.630507 INFO: Initializing TimingManager
1 day, 3:47:35.630826 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
1 day, 3:47:35.630870 INFO: Initializing TimingManager
1 day, 3:47:35.631058 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
1 day, 3:47:35.631098 INFO: Initializing TimingManager
1 day, 3:47:35.631277 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
1 day, 3:47:35.631314 INFO: Initializing TimingManager
1 day, 3:47:35.631734 INFO: Writing internal output to disk
1 day, 3:47:35.631779 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/library/internal.tsv to disk
1 day, 3:47:35.632290 PROGRESS: Performing label free quantification
1 day, 3:47:35.703645 INFO: Accumulating fragment data
1 day, 3:47:35.703813 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 3:47:35.941538 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 3:47:37.109489 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 3:47:38.118262 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 3:47:39.280810 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 3:47:40.358073 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 3:47:41.760300 PROGRESS: Performing label free quantification on the precursor level
1 day, 3:47:41.760437 INFO: Filtering fragments by quality
1 day, 3:47:42.030071 INFO: Performing label-free quantification using directLFQ
1 day, 3:47:43.455874 INFO: 90710 lfq-groups total
1 day, 3:49:16.082381 INFO: using 80 processes
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1 day, 3:50:17.951628 INFO: lfq-object 89700
1 day, 3:50:17.982961 INFO: lfq-object 90100
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1 day, 3:50:25.845925 INFO: Writing precursor output to disk
1 day, 3:50:25.846076 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/library/precursor.matrix.tsv to disk
1 day, 3:50:26.266424 PROGRESS: Performing label free quantification on the pg level
1 day, 3:50:26.266533 INFO: Filtering fragments by quality
1 day, 3:50:26.544084 INFO: Performing label-free quantification using directLFQ
1 day, 3:50:26.896020 INFO: 8880 lfq-groups total
1 day, 3:51:47.865163 INFO: using 80 processes
1 day, 3:51:48.074818 INFO: lfq-object 0
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1 day, 3:51:51.703388 INFO: lfq-object 7600
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1 day, 3:51:51.843505 INFO: lfq-object 8000
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1 day, 3:51:52.172214 INFO: lfq-object 8800
1 day, 3:51:52.337566 INFO: lfq-object 8700
1 day, 3:51:56.490702 INFO: Writing pg output to disk
1 day, 3:51:56.490872 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/library/pg.matrix.tsv to disk
1 day, 3:51:56.680704 INFO: Writing psm output to disk
1 day, 3:51:56.680837 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/library/precursors.tsv to disk
1 day, 3:52:17.463930 PROGRESS: Building MBR spectral library
1 day, 3:52:17.552926 INFO: Running MbrLibraryBuilder
1 day, 3:52:19.260315 INFO: MBR spectral library contains 90,710 precursors, 8,880 proteins
1 day, 3:52:19.260445 INFO: Writing MBR spectral library to disk
1 day, 3:52:20.521131 PROGRESS: =================== Search Finished ===================
1 day, 3:52:22.333298 INFO: Running step 'mbr'
1 day, 3:52:22.337180 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 15.0, 'target_ms2_tolerance': 15.0}})
1 day, 3:52:22.337336 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
1 day, 3:52:22.350038 INFO: loading additional config provided via CLI
1 day, 3:52:22.350113 INFO: loading additional config provided via CLI parameters
1 day, 3:52:22.350686 INFO: Updating config with 'user defined'
1 day, 3:52:22.350856 INFO: Updating config with 'user defined (cli)'
1 day, 3:52:22.351029 INFO: updating config with user defined values: [{'version': 1, 'workflow_name': None, 'output_directory': None, 'library_path': None, 'raw_paths': ['./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.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': False, 'save_figures': True, 'save_library': True, 'save_flat_library': False, 'input_library_type': 'base', 'save_mbr_library': True, 'random_state': None}, 'library_loading': {'rt_heuristic': 180}, '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': 'classic', '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': {'initial_num_candidates': 1, 'initial_ms1_tolerance': 30, 'initial_ms2_tolerance': 30, 'initial_mobility_tolerance': 0.1, 'initial_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, 'competetive_scoring': True}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins', 'inference_strategy': 'heuristic', 'competetive_scoring': True, 'keep_decoys': False, 'channel_wise_fdr': False, 'enable_two_step_classifier': False, 'two_step_classifier_max_iterations': 5, 'enable_nn_hyperparameter_tuning': False}, 'search_output': {'file_format': 'tsv', 'peptide_level_lfq': False, 'precursor_level_lfq': True, 'save_fragment_quant_matrix': False, 'min_k_fragments': 12, 'min_correlation': 0.9, 'num_samples_quadratic': 50, 'min_nonnan': 3, 'normalize_lfq': True}, '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': 'timsTOF'}}, {'raw_paths': ['./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d'], 'library_path': '/home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/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, 'general': {'reuse_quant': False}, 'library_prediction': {'enabled': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_path': 'run_output/alphadia_1.12.1_rs_benchmark_MBR/library/speclib.mbr.hdf', 'output_directory': 'run_output/alphadia_1.12.1_rs_benchmark_MBR'}]
1 day, 3:52:22.351298 INFO: Updating config with 'user defined'
1 day, 3:52:22.351417 INFO: Updating config with 'user defined (cli)'
1 day, 3:52:22.351447 INFO: Updating config with 'multistep search'
1 day, 3:52:22.351499 INFO: ├──version: 1
1 day, 3:52:22.351525 INFO: ├──workflow_name: None
1 day, 3:52:22.351552 INFO: [32;20m├──output_directory: run_output/alphadia_1.12.1_rs_benchmark_MBR [multistep search, default: None][0m
1 day, 3:52:22.351573 INFO: [32;20m├──library_path: run_output/alphadia_1.12.1_rs_benchmark_MBR/library/speclib.mbr.hdf [multistep search, default: None][0m
1 day, 3:52:22.351593 INFO: ├──raw_paths:
1 day, 3:52:22.351613 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
1 day, 3:52:22.351633 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
1 day, 3:52:22.351651 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
1 day, 3:52:22.351671 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
1 day, 3:52:22.351689 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
1 day, 3:52:22.351707 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
1 day, 3:52:22.351727 INFO: ├──fasta_paths:
1 day, 3:52:22.351745 INFO: ├──quant_directory: None
1 day, 3:52:22.351763 INFO: ├──general
1 day, 3:52:22.351785 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
1 day, 3:52:22.351805 INFO: │   ├──transfer_step_enabled: False
1 day, 3:52:22.351826 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
1 day, 3:52:22.351846 INFO: │   ├──reuse_calibration: False
1 day, 3:52:22.351865 INFO: │   ├──reuse_quant: False
1 day, 3:52:22.351883 INFO: │   ├──astral_ms1: False
1 day, 3:52:22.351902 INFO: │   ├──log_level: INFO
1 day, 3:52:22.351920 INFO: │   ├──mmap_detector_events: False
1 day, 3:52:22.351939 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
1 day, 3:52:22.351958 INFO: │   ├──save_figures: True
1 day, 3:52:22.351977 INFO: │   ├──save_library: True
1 day, 3:52:22.351994 INFO: │   ├──save_flat_library: False
1 day, 3:52:22.352013 INFO: │   ├──input_library_type: base
1 day, 3:52:22.352031 INFO: │   ├──save_mbr_library: True
1 day, 3:52:22.352050 INFO: │   └──random_state: None
1 day, 3:52:22.352070 INFO: ├──library_loading
1 day, 3:52:22.352089 INFO: │   └──rt_heuristic: 180
1 day, 3:52:22.352107 INFO: ├──library_prediction
1 day, 3:52:22.352127 INFO: │   ├──enabled: False
1 day, 3:52:22.352145 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
1 day, 3:52:22.352165 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
1 day, 3:52:22.352187 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
1 day, 3:52:22.352207 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
1 day, 3:52:22.352225 INFO: │   ├──missed_cleavages: 1
1 day, 3:52:22.352245 INFO: │   ├──precursor_len:
1 day, 3:52:22.352263 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
1 day, 3:52:22.352283 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
1 day, 3:52:22.352303 INFO: │   ├──precursor_charge:
1 day, 3:52:22.352321 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
1 day, 3:52:22.352340 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
1 day, 3:52:22.352360 INFO: │   ├──precursor_mz:
1 day, 3:52:22.352378 INFO: │   │   - 400
1 day, 3:52:22.352396 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
1 day, 3:52:22.352415 INFO: │   ├──fragment_mz:
1 day, 3:52:22.352434 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
1 day, 3:52:22.352458 INFO: │   │   - 2000
1 day, 3:52:22.352480 INFO: │   ├──nce: 25.0
1 day, 3:52:22.352499 INFO: │   ├──fragment_types:
1 day, 3:52:22.352518 INFO: │   │   - b
1 day, 3:52:22.352536 INFO: │   │   - y
1 day, 3:52:22.352555 INFO: │   ├──max_fragment_charge: 2
1 day, 3:52:22.352575 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
1 day, 3:52:22.352594 INFO: │   ├──peptdeep_model_path: None
1 day, 3:52:22.352613 INFO: │   └──peptdeep_model_type: generic
1 day, 3:52:22.352633 INFO: ├──custom_modifications:
1 day, 3:52:22.352652 INFO: │   ├──name: Dimethyl:d12@K
1 day, 3:52:22.352670 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 3:52:22.352689 INFO: │   ├──name: Dimethyl:d12@Any_N-term
1 day, 3:52:22.352707 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 3:52:22.352726 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
1 day, 3:52:22.352745 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 3:52:22.352763 INFO: │   ├──name: mTRAQ:d12@K
1 day, 3:52:22.352781 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
1 day, 3:52:22.352801 INFO: │   ├──name: mTRAQ:d12@Any_N-term
1 day, 3:52:22.352819 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1 day, 3:52:22.352837 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
1 day, 3:52:22.352857 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1 day, 3:52:22.352876 INFO: │   ├──name: Label:13C(12)@K
1 day, 3:52:22.352894 INFO: │   └──composition: C(12)
1 day, 3:52:22.352913 INFO: ├──search
1 day, 3:52:22.352933 INFO: │   ├──extraction_backend: classic
1 day, 3:52:22.352953 INFO: │   [32;20m├──target_ms1_tolerance: 15.0 [multistep search, default: 5][0m
1 day, 3:52:22.352973 INFO: │   [32;20m├──target_ms2_tolerance: 15.0 [multistep search, default: 10][0m
1 day, 3:52:22.352994 INFO: │   ├──target_rt_tolerance: 0.0
1 day, 3:52:22.353012 INFO: │   ├──target_mobility_tolerance: 0.0
1 day, 3:52:22.353030 INFO: │   ├──quant_window: 3
1 day, 3:52:22.353048 INFO: │   ├──target_num_candidates: 3
1 day, 3:52:22.353067 INFO: │   ├──channel_filter: 
1 day, 3:52:22.353085 INFO: │   ├──exclude_shared_ions: True
1 day, 3:52:22.353103 INFO: │   ├──compete_for_fragments: True
1 day, 3:52:22.353122 INFO: │   ├──quant_all: True
1 day, 3:52:22.353140 INFO: │   ├──top_k_fragments_selection: 12
1 day, 3:52:22.353158 INFO: │   ├──top_k_fragments_scoring: 12
1 day, 3:52:22.353177 INFO: │   ├──min_fragment_intensity: 0.01
1 day, 3:52:22.353195 INFO: │   ├──experimental_xic: True
1 day, 3:52:22.353213 INFO: │   └──optimized_peak_group_score: False
1 day, 3:52:22.353232 INFO: ├──calibration
1 day, 3:52:22.353252 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
1 day, 3:52:22.353270 INFO: │   ├──optimization_lock_target: 200
1 day, 3:52:22.353290 INFO: │   ├──max_steps: 20
1 day, 3:52:22.353308 INFO: │   ├──min_steps: 2
1 day, 3:52:22.353326 INFO: │   ├──max_skips: 1
1 day, 3:52:22.353345 INFO: │   ├──max_fragments: 5000
1 day, 3:52:22.353363 INFO: │   └──min_correlation: 0.7
1 day, 3:52:22.353380 INFO: ├──search_initial
1 day, 3:52:22.353400 INFO: │   ├──initial_num_candidates: 1
1 day, 3:52:22.353418 INFO: │   ├──initial_ms1_tolerance: 30
1 day, 3:52:22.353436 INFO: │   ├──initial_ms2_tolerance: 30
1 day, 3:52:22.353456 INFO: │   ├──initial_mobility_tolerance: 0.1
1 day, 3:52:22.353476 INFO: │   └──initial_rt_tolerance: 0.5
1 day, 3:52:22.353494 INFO: ├──selection_config
1 day, 3:52:22.353514 INFO: │   ├──peak_len_rt: 10.0
1 day, 3:52:22.353533 INFO: │   ├──sigma_scale_rt: 0.5
1 day, 3:52:22.353552 INFO: │   ├──peak_len_mobility: 0.01
1 day, 3:52:22.353576 INFO: │   ├──sigma_scale_mobility: 1.0
1 day, 3:52:22.353594 INFO: │   ├──top_k_precursors: 3
1 day, 3:52:22.353613 INFO: │   ├──kernel_size: 30
1 day, 3:52:22.353633 INFO: │   ├──f_mobility: 1.0
1 day, 3:52:22.353652 INFO: │   ├──f_rt: 0.99
1 day, 3:52:22.353671 INFO: │   ├──center_fraction: 0.5
1 day, 3:52:22.353690 INFO: │   ├──min_size_mobility: 8
1 day, 3:52:22.353709 INFO: │   ├──min_size_rt: 3
1 day, 3:52:22.353727 INFO: │   ├──max_size_mobility: 20
1 day, 3:52:22.353746 INFO: │   ├──max_size_rt: 15
1 day, 3:52:22.353765 INFO: │   ├──group_channels: False
1 day, 3:52:22.353785 INFO: │   ├──use_weighted_score: True
1 day, 3:52:22.353805 INFO: │   ├──join_close_candidates: False
1 day, 3:52:22.353823 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
1 day, 3:52:22.353841 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
1 day, 3:52:22.353860 INFO: ├──scoring_config
1 day, 3:52:22.353879 INFO: │   ├──score_grouped: False
1 day, 3:52:22.353897 INFO: │   ├──top_k_isotopes: 3
1 day, 3:52:22.353916 INFO: │   ├──reference_channel: -1
1 day, 3:52:22.353935 INFO: │   ├──precursor_mz_tolerance: 10
1 day, 3:52:22.353952 INFO: │   └──fragment_mz_tolerance: 15
1 day, 3:52:22.353971 INFO: ├──library_multiplexing
1 day, 3:52:22.353988 INFO: │   ├──enabled: False
1 day, 3:52:22.354006 INFO: │   ├──input_channel: 0
1 day, 3:52:22.354026 INFO: │   └──multiplex_mapping:
1 day, 3:52:22.354048 INFO: ├──multiplexing
1 day, 3:52:22.354067 INFO: │   ├──enabled: False
1 day, 3:52:22.354084 INFO: │   ├──target_channels: 4,8
1 day, 3:52:22.354105 INFO: │   ├──decoy_channel: 12
1 day, 3:52:22.354122 INFO: │   ├──reference_channel: 0
1 day, 3:52:22.354140 INFO: │   └──competetive_scoring: True
1 day, 3:52:22.354159 INFO: ├──fdr
1 day, 3:52:22.354178 INFO: │   ├──fdr: 0.01
1 day, 3:52:22.354196 INFO: │   ├──group_level: proteins
1 day, 3:52:22.354216 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
1 day, 3:52:22.354234 INFO: │   ├──competetive_scoring: True
1 day, 3:52:22.354252 INFO: │   ├──keep_decoys: False
1 day, 3:52:22.354271 INFO: │   ├──channel_wise_fdr: False
1 day, 3:52:22.354290 INFO: │   ├──enable_two_step_classifier: False
1 day, 3:52:22.354308 INFO: │   ├──two_step_classifier_max_iterations: 5
1 day, 3:52:22.354328 INFO: │   └──enable_nn_hyperparameter_tuning: False
1 day, 3:52:22.354345 INFO: ├──search_output
1 day, 3:52:22.354363 INFO: │   ├──file_format: tsv
1 day, 3:52:22.354383 INFO: │   ├──peptide_level_lfq: False
1 day, 3:52:22.354401 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
1 day, 3:52:22.354419 INFO: │   ├──save_fragment_quant_matrix: False
1 day, 3:52:22.354439 INFO: │   ├──min_k_fragments: 12
1 day, 3:52:22.354458 INFO: │   ├──min_correlation: 0.9
1 day, 3:52:22.354476 INFO: │   ├──num_samples_quadratic: 50
1 day, 3:52:22.354495 INFO: │   ├──min_nonnan: 3
1 day, 3:52:22.354513 INFO: │   └──normalize_lfq: True
1 day, 3:52:22.354530 INFO: ├──optimization
1 day, 3:52:22.354550 INFO: │   ├──order_of_optimization: None
1 day, 3:52:22.354568 INFO: │   ├──ms2_error
1 day, 3:52:22.354586 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 3:52:22.354606 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 3:52:22.354625 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 3:52:22.354643 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 3:52:22.354662 INFO: │   │   ├──try_narrower_values: True
1 day, 3:52:22.354681 INFO: │   │   ├──maximal_decrease: 0.5
1 day, 3:52:22.354699 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 3:52:22.354724 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 3:52:22.354743 INFO: │   ├──ms1_error
1 day, 3:52:22.354762 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 3:52:22.354783 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 3:52:22.354802 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 3:52:22.354820 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 3:52:22.354840 INFO: │   │   ├──try_narrower_values: False
1 day, 3:52:22.354859 INFO: │   │   ├──maximal_decrease: 0.2
1 day, 3:52:22.354877 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 3:52:22.354897 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 3:52:22.354915 INFO: │   ├──mobility_error
1 day, 3:52:22.354934 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 3:52:22.354954 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 3:52:22.354973 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 3:52:22.354991 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 3:52:22.355011 INFO: │   │   ├──try_narrower_values: False
1 day, 3:52:22.355029 INFO: │   │   ├──maximal_decrease: 0.2
1 day, 3:52:22.355047 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 3:52:22.355067 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 3:52:22.355086 INFO: │   └──rt_error
1 day, 3:52:22.355104 INFO: │       ├──targeted_update_percentile_range: 0.95
1 day, 3:52:22.355123 INFO: │       ├──targeted_update_factor: 1.0
1 day, 3:52:22.355141 INFO: │       ├──automatic_update_percentile_range: 0.99
1 day, 3:52:22.355159 INFO: │       ├──automatic_update_factor: 1.1
1 day, 3:52:22.355178 INFO: │       ├──try_narrower_values: True
1 day, 3:52:22.355196 INFO: │       ├──maximal_decrease: 0.2
1 day, 3:52:22.355213 INFO: │       ├──favour_narrower_optimum: True
1 day, 3:52:22.355232 INFO: │       └──maximum_decrease_from_maximum: 0.1
1 day, 3:52:22.355250 INFO: ├──optimization_manager
1 day, 3:52:22.355269 INFO: │   ├──fwhm_rt: 5
1 day, 3:52:22.355289 INFO: │   ├──fwhm_mobility: 0.01
1 day, 3:52:22.355307 INFO: │   └──score_cutoff: 0
1 day, 3:52:22.355325 INFO: ├──transfer_library
1 day, 3:52:22.355344 INFO: │   ├──enabled: False
1 day, 3:52:22.355362 INFO: │   ├──fragment_types:
1 day, 3:52:22.355380 INFO: │   │   - b
1 day, 3:52:22.355400 INFO: │   │   - y
1 day, 3:52:22.355418 INFO: │   ├──max_charge: 2
1 day, 3:52:22.355436 INFO: │   ├──top_k_samples: 3
1 day, 3:52:22.355456 INFO: │   ├──norm_delta_max: True
1 day, 3:52:22.355474 INFO: │   ├──precursor_correlation_cutoff: 0.5
1 day, 3:52:22.355493 INFO: │   └──fragment_correlation_ratio: 0.75
1 day, 3:52:22.355512 INFO: └──transfer_learning
1 day, 3:52:22.355530 INFO:     ├──enabled: False
1 day, 3:52:22.355548 INFO:     ├──batch_size: 2000
1 day, 3:52:22.355568 INFO:     ├──max_lr: 0.0001
1 day, 3:52:22.355586 INFO:     ├──train_fraction: 0.7
1 day, 3:52:22.355605 INFO:     ├──validation_fraction: 0.2
1 day, 3:52:22.355624 INFO:     ├──test_fraction: 0.1
1 day, 3:52:22.355643 INFO:     ├──test_interval: 1
1 day, 3:52:22.355661 INFO:     ├──lr_patience: 3
1 day, 3:52:22.355680 INFO:     ├──epochs: 51
1 day, 3:52:22.355699 INFO:     ├──warmup_epochs: 5
1 day, 3:52:22.355716 INFO:     ├──nce: 25
1 day, 3:52:22.355737 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
1 day, 3:52:22.360923 INFO: Moved existing config file run_output/alphadia_1.12.1_rs_benchmark_MBR/frozen_config.yaml to run_output/alphadia_1.12.1_rs_benchmark_MBR/frozen_config.yaml
1 day, 3:52:22.362311 INFO: Registering 7 custom modifications
1 day, 3:52:22.381993 INFO: Searching 6 files:
1 day, 3:52:22.382065 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:22.382096 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 3:52:22.382115 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:52:22.382134 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 3:52:22.382151 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:52:22.382167 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 3:52:22.382185 INFO: Using 0 fasta files:
1 day, 3:52:22.382205 INFO: Using library: run_output/alphadia_1.12.1_rs_benchmark_MBR/library/speclib.mbr.hdf
1 day, 3:52:22.382223 INFO: Saving output to: run_output/alphadia_1.12.1_rs_benchmark_MBR
1 day, 3:52:22.382254 PROGRESS: Loading spectral library
1 day, 3:52:22.382291 PROGRESS: Loading library (type: base) from disk..
1 day, 3:52:22.382411 INFO: Running DynamicLoader
1 day, 3:52:22.382487 INFO: Loading .hdf library from run_output/alphadia_1.12.1_rs_benchmark_MBR/library/speclib.mbr.hdf
1 day, 3:52:22.790312 INFO: Running PrecursorInitializer
1 day, 3:52:22.790478 INFO: Running AnnotateFasta
1 day, 3:52:22.790782 INFO: Dropping decoys from input library before annotation
1 day, 3:52:22.803387 INFO: Running IsotopeGenerator
1 day, 3:52:22.803632 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
1 day, 3:52:22.803678 INFO: Running RTNormalization
1 day, 3:52:22.806616 INFO: Saving library to run_output/alphadia_1.12.1_rs_benchmark_MBR/speclib.hdf
1 day, 3:52:23.444087 INFO: Running DecoyGenerator
1 day, 3:52:29.421702 INFO: Running FlattenLibrary
1 day, 3:52:30.786237 INFO: Running InitFlatColumns
1 day, 3:52:30.790713 INFO: Running LogFlatLibraryStats
1 day, 3:52:30.790828 INFO: ============ Library Stats ============
1 day, 3:52:30.790859 INFO: Number of precursors: 181,406
1 day, 3:52:30.817004 INFO: 	thereof targets:90,710
1 day, 3:52:30.817128 INFO: 	thereof decoys: 90,696
1 day, 3:52:30.818701 INFO: Number of elution groups: 90,710
1 day, 3:52:30.818768 INFO: 	average size: 2.00
1 day, 3:52:30.824129 INFO: Number of proteins: 8,880
1 day, 3:52:30.824863 INFO: Number of channels: 1 ([0])
1 day, 3:52:30.824952 INFO: Isotopes Distribution for 4 isotopes
1 day, 3:52:30.824980 INFO: =======================================
1 day, 3:52:30.825962 PROGRESS: Starting Search Workflows
1 day, 3:52:30.826035 PROGRESS: 
1 day, 3:52:30.826118 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/quant
1 day, 3:52:30.826178 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/figures
1 day, 3:52:30.826385 INFO: Initializing TimingManager
1 day, 3:52:30.826838 INFO: Initializing RawFileManager
1 day, 3:52:30.826977 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:30.827033 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:30.827077 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:31.130197 INFO: Reading 39,128 frames with 2,835,410,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:36.769367 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
1 day, 3:52:36.770570 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:36.772760 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:36.772983 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:36.773357 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:36.775016 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:36.784082 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:36.784637 INFO: Indexing quadrupole dimension
1 day, 3:52:37.252407 INFO: Transposing detector events
1 day, 3:52:45.772372 INFO: Finished transposing data
1 day, 3:52:45.816321 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 3:52:45.817351 INFO: RT (min)            : 0.0 - 70.0
1 day, 3:52:45.817447 INFO: RT duration (sec)   : 4199.9
1 day, 3:52:45.817506 INFO: RT duration (min)   : 70.0
1 day, 3:52:45.817558 INFO: Cycle len (scans)   : 9
1 day, 3:52:45.817603 INFO: Cycle len (sec)     : 0.97
1 day, 3:52:45.817647 INFO: Number of cycles    : 4347
1 day, 3:52:45.817691 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 3:52:45.817747 INFO: Creating DIA data object took: 14.990801572799683
1 day, 3:52:45.835422 INFO: Initializing CalibrationManager
1 day, 3:52:45.835759 INFO: Setting up calibration estimators ..
1 day, 3:52:45.835859 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 3:52:45.836003 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, 3:52:45.836138 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 3:52:45.836234 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, 3:52:45.836324 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, 3:52:45.836423 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, 3:52:45.836504 INFO: Done setting up calibration estimators.
1 day, 3:52:45.836665 INFO: Initializing OptimizationManager
1 day, 3:52:45.836808 INFO: initial parameter: ms1_error = 30
1 day, 3:52:45.836885 INFO: initial parameter: ms2_error = 30
1 day, 3:52:45.836959 INFO: initial parameter: rt_error = 2099.928159
1 day, 3:52:45.837028 INFO: initial parameter: mobility_error = 0.1
1 day, 3:52:45.837095 INFO: initial parameter: num_candidates = 1
1 day, 3:52:45.837159 INFO: initial parameter: fwhm_rt = 5
1 day, 3:52:45.837232 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 3:52:45.837299 INFO: initial parameter: score_cutoff = 0
1 day, 3:52:45.837369 INFO: initial parameter: classifier_version = -1
1 day, 3:52:45.837478 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 3:52:45.837904 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 3:52:45.837965 INFO: Initializing FDRManager
1 day, 3:52:45.838037 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 3:52:45.864548 PROGRESS: Initializing spectral library: 90,710 target precursors potentially observable (0 removed)
1 day, 3:52:45.879234 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 3:52:45.879606 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 2099.928159
1 day, 3:52:45.879709 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 3:52:45.879874 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 3:52:45.879961 PROGRESS: Starting initial search for precursors.
1 day, 3:52:45.880057 INFO: Starting optimization step 0.
1 day, 3:52:45.880122 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 3:52:45.880194 INFO: Using classic extraction backend
1 day, 3:52:45.880407 PROGRESS: Extracting batch of 398 precursors
1 day, 3:52:45.880477 INFO: === Search parameters used ===
1 day, 3:52:45.880525 INFO: rt_error       : 2099.928159
1 day, 3:52:45.880568 INFO: mobility_error : 0.1
1 day, 3:52:45.880608 INFO: num_candidates : 1
1 day, 3:52:45.880647 INFO: ms1_error      : 30
1 day, 3:52:45.880685 INFO: ms2_error      : 30
1 day, 3:52:45.880724 INFO: fwhm_rt        : 5
1 day, 3:52:45.880762 INFO: quant_window   : 3
1 day, 3:52:45.880799 INFO: ==============================================
1 day, 3:52:45.881549 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:52:45.881596 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:52:45.881634 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 3:52:45.881655 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 3:52:45.884665 INFO: Starting candidate selection
1 day, 3:52:50.623310 INFO: Starting candidate scoring
1 day, 3:52:50.715317 INFO: Finished candidate processing
1 day, 3:52:50.715417 INFO: Collecting candidate features
1 day, 3:52:50.724547 INFO: Collecting fragment features
1 day, 3:52:50.726841 INFO: Finished candidate scoring
1 day, 3:52:50.727889 INFO: performing precursor FDR with 47 features
1 day, 3:52:50.727931 INFO: Decoy channel: -1
1 day, 3:52:50.727955 INFO: Competetive: True
1 day, 3:52:50.729098 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:52:50.731725 INFO: Using random state 132215 for train-test-split
1 day, 3:52:50.745594 INFO: Test AUC: 0.469
1 day, 3:52:50.745688 INFO: Train AUC: 0.507
1 day, 3:52:50.745743 INFO: AUC difference: 7.66%
1 day, 3:52:50.745784 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:52:50.994955 INFO: Resetting torch num_threads to 80
1 day, 3:52:50.995392 PROGRESS: === Extracted 398 precursors and 4563 fragments ===
1 day, 3:52:50.995785 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:52:50.996359 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:52:50.996446 PROGRESS: Total precursors accumulated: 200
1 day, 3:52:50.996504 PROGRESS: Target precursors: 181 (90.50%)
1 day, 3:52:50.996554 PROGRESS: Decoy precursors: 19 (9.50%)
1 day, 3:52:50.996600 PROGRESS: 
1 day, 3:52:50.996642 PROGRESS: Precursor Summary:
1 day, 3:52:50.997555 PROGRESS: Channel   0:	 0.050 FDR:   181; 0.010 FDR:   181; 0.001 FDR:   181
1 day, 3:52:50.997647 PROGRESS: 
1 day, 3:52:50.997707 PROGRESS: Protein Summary:
1 day, 3:52:50.998785 PROGRESS: Channel   0:	 0.050 FDR:   171; 0.010 FDR:   171; 0.001 FDR:   171
1 day, 3:52:50.998873 PROGRESS: =========================================================================
1 day, 3:52:50.998972 INFO: Target number of precursors not reached yet.
1 day, 3:52:51.002445 INFO: Starting optimization step 1.
1 day, 3:52:51.002548 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 3:52:51.002620 INFO: Using classic extraction backend
1 day, 3:52:51.002727 PROGRESS: Extracting batch of 796 precursors
1 day, 3:52:51.002793 INFO: === Search parameters used ===
1 day, 3:52:51.002838 INFO: rt_error       : 2099.928159
1 day, 3:52:51.002880 INFO: mobility_error : 0.1
1 day, 3:52:51.002921 INFO: num_candidates : 1
1 day, 3:52:51.002960 INFO: ms1_error      : 30
1 day, 3:52:51.002999 INFO: ms2_error      : 30
1 day, 3:52:51.003038 INFO: fwhm_rt        : 5
1 day, 3:52:51.003081 INFO: quant_window   : 3
1 day, 3:52:51.003119 INFO: ==============================================
1 day, 3:52:51.003724 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:52:51.003771 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:52:51.003800 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 3:52:51.003822 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 3:52:51.008053 INFO: Starting candidate selection
1 day, 3:52:57.471505 INFO: Starting candidate scoring
1 day, 3:52:57.595942 INFO: Finished candidate processing
1 day, 3:52:57.596092 INFO: Collecting candidate features
1 day, 3:52:57.606202 INFO: Collecting fragment features
1 day, 3:52:57.608792 INFO: Finished candidate scoring
1 day, 3:52:57.611063 INFO: performing precursor FDR with 47 features
1 day, 3:52:57.611112 INFO: Decoy channel: -1
1 day, 3:52:57.611137 INFO: Competetive: True
1 day, 3:52:57.614356 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:52:57.616067 INFO: Using random state 267855 for train-test-split
1 day, 3:52:57.626772 INFO: Test AUC: 0.496
1 day, 3:52:57.626832 INFO: Train AUC: 0.500
1 day, 3:52:57.626861 INFO: AUC difference: 0.63%
1 day, 3:52:57.838803 INFO: Resetting torch num_threads to 80
1 day, 3:52:57.840035 PROGRESS: === Extracted 1194 precursors and 13608 fragments ===
1 day, 3:52:57.840422 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:52:57.841071 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:52:57.841161 PROGRESS: Total precursors accumulated: 600
1 day, 3:52:57.841219 PROGRESS: Target precursors: 554 (92.33%)
1 day, 3:52:57.841272 PROGRESS: Decoy precursors: 46 (7.67%)
1 day, 3:52:57.841318 PROGRESS: 
1 day, 3:52:57.841359 PROGRESS: Precursor Summary:
1 day, 3:52:57.842435 PROGRESS: Channel   0:	 0.050 FDR:   544; 0.010 FDR:   544; 0.001 FDR:   544
1 day, 3:52:57.842528 PROGRESS: 
1 day, 3:52:57.842584 PROGRESS: Protein Summary:
1 day, 3:52:57.843833 PROGRESS: Channel   0:	 0.050 FDR:   508; 0.010 FDR:   508; 0.001 FDR:   508
1 day, 3:52:57.843924 PROGRESS: =========================================================================
1 day, 3:52:57.844059 INFO: Target number of precursors reached.
1 day, 3:52:57.847629 INFO: fragments_df: keeping 3206 of 13608 [sum(precursor_idx_mask)=6179 sum(mass_error_mask)=13608 stop_rank=3206
1 day, 3:52:57.852219 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:52:58.005595 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:52:58.156188 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:52:58.300031 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:52:58.727234 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 3:52:58.727658 INFO: Using score_cutoff 49.20765014190673 (fac=0.99, q=1)
1 day, 3:52:58.727999 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.486407518386841
1 day, 3:52:58.728080 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010340431705117226
1 day, 3:52:58.728134 INFO: Updating optimization_manager: score_cutoff        : 0 -> 49.20765014190673
1 day, 3:52:58.728199 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:52:58.729255 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:52:58.730592 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:52:58.731366 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:52:58.733642 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
1 day, 3:52:58.733735 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 3:52:58.733811 INFO: Starting optimization step 2.
1 day, 3:52:58.733871 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:52:58.733925 INFO: Using classic extraction backend
1 day, 3:52:58.734031 PROGRESS: Extracting batch of 1194 precursors
1 day, 3:52:58.734105 INFO: === Search parameters used ===
1 day, 3:52:58.734150 INFO: rt_error       : 2099.928159
1 day, 3:52:58.734195 INFO: mobility_error : 0.1
1 day, 3:52:58.734237 INFO: num_candidates : 3
1 day, 3:52:58.734278 INFO: ms1_error      : 30
1 day, 3:52:58.734317 INFO: ms2_error      : 30
1 day, 3:52:58.734356 INFO: fwhm_rt        : 3.486407518386841
1 day, 3:52:58.734396 INFO: quant_window   : 3
1 day, 3:52:58.734433 INFO: ==============================================
1 day, 3:52:58.735244 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:52:58.735298 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:52:58.735334 INFO: FWHM in RT is 3.49 seconds, sigma is 0.77
1 day, 3:52:58.735355 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.80
1 day, 3:52:58.738442 INFO: Starting candidate selection
1 day, 3:53:07.993524 INFO: Starting candidate scoring
1 day, 3:53:08.343197 INFO: Finished candidate processing
1 day, 3:53:08.343332 INFO: Collecting candidate features
1 day, 3:53:08.356508 INFO: Collecting fragment features
1 day, 3:53:08.360850 INFO: Finished candidate scoring
1 day, 3:53:08.362995 INFO: performing precursor FDR with 47 features
1 day, 3:53:08.363045 INFO: Decoy channel: -1
1 day, 3:53:08.363071 INFO: Competetive: True
1 day, 3:53:08.367111 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:53:08.369204 INFO: Using random state 331205 for train-test-split
1 day, 3:53:08.379374 INFO: Test AUC: 0.507
1 day, 3:53:08.379437 INFO: Train AUC: 0.506
1 day, 3:53:08.379466 INFO: AUC difference: 0.09%
1 day, 3:53:08.597379 INFO: Resetting torch num_threads to 80
1 day, 3:53:08.597913 PROGRESS: === Extracted 3394 precursors and 38627 fragments ===
1 day, 3:53:08.598310 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:53:08.598897 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:53:08.598983 PROGRESS: Total precursors accumulated: 600
1 day, 3:53:08.599039 PROGRESS: Target precursors: 586 (97.67%)
1 day, 3:53:08.599088 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 3:53:08.599133 PROGRESS: 
1 day, 3:53:08.599177 PROGRESS: Precursor Summary:
1 day, 3:53:08.600219 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   586; 0.001 FDR:   586
1 day, 3:53:08.600307 PROGRESS: 
1 day, 3:53:08.600362 PROGRESS: Protein Summary:
1 day, 3:53:08.601640 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   540; 0.001 FDR:   540
1 day, 3:53:08.601730 PROGRESS: =========================================================================
1 day, 3:53:08.601885 INFO: Target number of precursors reached.
1 day, 3:53:08.609356 INFO: fragments_df: keeping 5000 of 38627 [sum(precursor_idx_mask)=19056 sum(mass_error_mask)=38627 stop_rank=5000
1 day, 3:53:08.618458 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:08.769485 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:08.914561 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:09.061456 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:09.749016 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:53:09.749441 INFO: Using score_cutoff 47.01656545257568 (fac=0.99, q=1)
1 day, 3:53:09.749746 INFO: Updating optimization_manager: fwhm_rt             : 3.486407518386841 -> 3.421574831008911
1 day, 3:53:09.749829 INFO: Updating optimization_manager: fwhm_mobility       : 0.010340431705117226 -> 0.010076383128762245
1 day, 3:53:09.749884 INFO: Updating optimization_manager: score_cutoff        : 49.20765014190673 -> 47.01656545257568
1 day, 3:53:09.749938 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:09.751034 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:09.752324 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:09.753088 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:09.755284 INFO: === checking if optimization conditions were reached ===
1 day, 3:53:09.756912 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 3:53:09.757010 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 3:53:09.757073 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 3:53:09.758075 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 3:53:09.758170 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 3:53:09.758230 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 3:53:09.758292 INFO: ==============================================
1 day, 3:53:09.758353 INFO: Starting optimization step 3.
1 day, 3:53:09.758405 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:53:09.758456 INFO: Using classic extraction backend
1 day, 3:53:09.758598 PROGRESS: Extracting batch of 1194 precursors
1 day, 3:53:09.758673 INFO: === Search parameters used ===
1 day, 3:53:09.758727 INFO: rt_error       : 2099.928159
1 day, 3:53:09.758769 INFO: mobility_error : 0.1
1 day, 3:53:09.758809 INFO: num_candidates : 3
1 day, 3:53:09.758847 INFO: ms1_error      : 15.0
1 day, 3:53:09.758884 INFO: ms2_error      : 15.0
1 day, 3:53:09.758922 INFO: fwhm_rt        : 3.421574831008911
1 day, 3:53:09.758960 INFO: quant_window   : 3
1 day, 3:53:09.758998 INFO: ==============================================
1 day, 3:53:09.759856 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:53:09.759901 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:53:09.759936 INFO: FWHM in RT is 3.42 seconds, sigma is 0.75
1 day, 3:53:09.759957 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.67
1 day, 3:53:09.760610 INFO: Starting candidate selection
1 day, 3:53:18.980260 INFO: Starting candidate scoring
1 day, 3:53:19.229481 INFO: Finished candidate processing
1 day, 3:53:19.229702 INFO: Collecting candidate features
1 day, 3:53:19.265227 INFO: Collecting fragment features
1 day, 3:53:19.276161 INFO: Finished candidate scoring
1 day, 3:53:19.279517 INFO: performing precursor FDR with 47 features
1 day, 3:53:19.279597 INFO: Decoy channel: -1
1 day, 3:53:19.279638 INFO: Competetive: True
1 day, 3:53:19.286275 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:53:19.290616 INFO: Using random state 16001 for train-test-split
1 day, 3:53:19.310320 INFO: Test AUC: 0.524
1 day, 3:53:19.310409 INFO: Train AUC: 0.495
1 day, 3:53:19.310444 INFO: AUC difference: 5.91%
1 day, 3:53:19.310472 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:53:19.548592 INFO: Resetting torch num_threads to 80
1 day, 3:53:19.549364 PROGRESS: === Extracted 3406 precursors and 37794 fragments ===
1 day, 3:53:19.550001 INFO: === FDR correction performed with classifier version 2 ===
1 day, 3:53:19.550658 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:53:19.550751 PROGRESS: Total precursors accumulated: 600
1 day, 3:53:19.550815 PROGRESS: Target precursors: 560 (93.33%)
1 day, 3:53:19.550870 PROGRESS: Decoy precursors: 40 (6.67%)
1 day, 3:53:19.550922 PROGRESS: 
1 day, 3:53:19.550970 PROGRESS: Precursor Summary:
1 day, 3:53:19.552070 PROGRESS: Channel   0:	 0.050 FDR:   552; 0.010 FDR:   552; 0.001 FDR:   552
1 day, 3:53:19.552164 PROGRESS: 
1 day, 3:53:19.552223 PROGRESS: Protein Summary:
1 day, 3:53:19.553572 PROGRESS: Channel   0:	 0.050 FDR:   514; 0.010 FDR:   514; 0.001 FDR:   514
1 day, 3:53:19.553671 PROGRESS: =========================================================================
1 day, 3:53:19.554074 INFO: Target number of precursors reached.
1 day, 3:53:19.562112 INFO: fragments_df: keeping 5000 of 37794 [sum(precursor_idx_mask)=17411 sum(mass_error_mask)=37794 stop_rank=5000
1 day, 3:53:19.569139 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:19.695455 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:19.823629 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:19.948745 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:20.570523 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:53:20.571082 INFO: Using score_cutoff 40.267119187545774 (fac=0.99, q=1)
1 day, 3:53:20.571466 INFO: Updating optimization_manager: fwhm_rt             : 3.421574831008911 -> 3.1158814430236816
1 day, 3:53:20.571548 INFO: Updating optimization_manager: fwhm_mobility       : 0.010076383128762245 -> 0.008490917272865772
1 day, 3:53:20.571608 INFO: Updating optimization_manager: score_cutoff        : 47.01656545257568 -> 40.267119187545774
1 day, 3:53:20.571680 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:20.572970 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:20.574302 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:20.575089 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:20.577321 INFO: === checking if optimization conditions were reached ===
1 day, 3:53:20.579057 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 3:53:20.579164 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
1 day, 3:53:20.579234 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 3:53:20.580262 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 3:53:20.580356 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
1 day, 3:53:20.580422 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 3:53:20.580479 INFO: ==============================================
1 day, 3:53:20.580552 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 3:53:20.585656 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:20.586521 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:20.587819 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:20.588608 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:20.590802 INFO: Starting optimization step 0.
1 day, 3:53:20.590904 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:53:20.590984 INFO: Using classic extraction backend
1 day, 3:53:20.591155 PROGRESS: Extracting batch of 1194 precursors
1 day, 3:53:20.591232 INFO: === Search parameters used ===
1 day, 3:53:20.591285 INFO: rt_error       : 2099.928159
1 day, 3:53:20.591333 INFO: mobility_error : 0.1
1 day, 3:53:20.591379 INFO: num_candidates : 3
1 day, 3:53:20.591423 INFO: ms1_error      : 15.0
1 day, 3:53:20.591467 INFO: ms2_error      : 15.0
1 day, 3:53:20.591509 INFO: fwhm_rt        : 3.1158814430236816
1 day, 3:53:20.591551 INFO: quant_window   : 3
1 day, 3:53:20.591595 INFO: ==============================================
1 day, 3:53:20.592666 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:53:20.592716 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:53:20.592770 INFO: FWHM in RT is 3.12 seconds, sigma is 0.68
1 day, 3:53:20.592797 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.94
1 day, 3:53:20.593603 INFO: Starting candidate selection
1 day, 3:53:30.194130 INFO: Starting candidate scoring
1 day, 3:53:30.409655 INFO: Finished candidate processing
1 day, 3:53:30.409757 INFO: Collecting candidate features
1 day, 3:53:30.423149 INFO: Collecting fragment features
1 day, 3:53:30.426927 INFO: Finished candidate scoring
1 day, 3:53:30.428951 INFO: performing precursor FDR with 47 features
1 day, 3:53:30.428999 INFO: Decoy channel: -1
1 day, 3:53:30.429023 INFO: Competetive: True
1 day, 3:53:30.432101 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:53:30.434200 INFO: Using random state 411560 for train-test-split
1 day, 3:53:30.444395 INFO: Test AUC: 0.508
1 day, 3:53:30.444456 INFO: Train AUC: 0.495
1 day, 3:53:30.444484 INFO: AUC difference: 2.58%
1 day, 3:53:30.660969 INFO: Resetting torch num_threads to 80
1 day, 3:53:30.661527 PROGRESS: === Extracted 3401 precursors and 37709 fragments ===
1 day, 3:53:30.661929 INFO: === FDR correction performed with classifier version 3 ===
1 day, 3:53:30.662501 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:53:30.662589 PROGRESS: Total precursors accumulated: 600
1 day, 3:53:30.662650 PROGRESS: Target precursors: 555 (92.50%)
1 day, 3:53:30.662701 PROGRESS: Decoy precursors: 45 (7.50%)
1 day, 3:53:30.662745 PROGRESS: 
1 day, 3:53:30.662788 PROGRESS: Precursor Summary:
1 day, 3:53:30.664008 PROGRESS: Channel   0:	 0.050 FDR:   547; 0.010 FDR:   547; 0.001 FDR:   547
1 day, 3:53:30.664104 PROGRESS: 
1 day, 3:53:30.664160 PROGRESS: Protein Summary:
1 day, 3:53:30.665399 PROGRESS: Channel   0:	 0.050 FDR:   509; 0.010 FDR:   509; 0.001 FDR:   509
1 day, 3:53:30.665488 PROGRESS: =========================================================================
1 day, 3:53:30.665628 INFO: Target number of precursors reached.
1 day, 3:53:30.672534 INFO: fragments_df: keeping 5000 of 37709 [sum(precursor_idx_mask)=17313 sum(mass_error_mask)=37709 stop_rank=5000
1 day, 3:53:30.677108 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:30.818685 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:32.563198 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:32.705171 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:33.384261 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:53:33.384701 INFO: Using score_cutoff 40.6420716796875 (fac=0.99, q=1)
1 day, 3:53:33.385004 INFO: Updating optimization_manager: fwhm_rt             : 3.1158814430236816 -> 3.085857629776001
1 day, 3:53:33.385081 INFO: Updating optimization_manager: fwhm_mobility       : 0.008490917272865772 -> 0.008430319838225842
1 day, 3:53:33.385133 INFO: Updating optimization_manager: score_cutoff        : 40.267119187545774 -> 40.6420716796875
1 day, 3:53:33.385184 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:33.386243 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:33.387526 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:33.388286 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:33.390499 INFO: === checking if optimization conditions were reached ===
1 day, 3:53:33.390612 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:53:33.392220 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 1143.404837970801
1 day, 3:53:33.392315 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1143.4048.
1 day, 3:53:33.392378 INFO: ==============================================
1 day, 3:53:33.392440 INFO: Starting optimization step 1.
1 day, 3:53:33.392495 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:53:33.392548 INFO: Using classic extraction backend
1 day, 3:53:33.392653 PROGRESS: Extracting batch of 1194 precursors
1 day, 3:53:33.392714 INFO: === Search parameters used ===
1 day, 3:53:33.393058 INFO: rt_error       : 1143.404837970801
1 day, 3:53:33.393111 INFO: mobility_error : 0.1
1 day, 3:53:33.393151 INFO: num_candidates : 3
1 day, 3:53:33.393192 INFO: ms1_error      : 15.0
1 day, 3:53:33.393232 INFO: ms2_error      : 15.0
1 day, 3:53:33.393269 INFO: fwhm_rt        : 3.085857629776001
1 day, 3:53:33.393307 INFO: quant_window   : 3
1 day, 3:53:33.393345 INFO: ==============================================
1 day, 3:53:33.394169 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:53:33.394215 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:53:33.394248 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
1 day, 3:53:33.394272 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.91
1 day, 3:53:33.394892 INFO: Starting candidate selection
1 day, 3:53:38.905418 INFO: Starting candidate scoring
1 day, 3:53:39.138682 INFO: Finished candidate processing
1 day, 3:53:39.138811 INFO: Collecting candidate features
1 day, 3:53:39.159855 INFO: Collecting fragment features
1 day, 3:53:39.165988 INFO: Finished candidate scoring
1 day, 3:53:39.169168 INFO: performing precursor FDR with 47 features
1 day, 3:53:39.169250 INFO: Decoy channel: -1
1 day, 3:53:39.169297 INFO: Competetive: True
1 day, 3:53:39.172629 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:53:39.174748 INFO: Using random state 411560 for train-test-split
1 day, 3:53:39.185672 INFO: Test AUC: 0.472
1 day, 3:53:39.185741 INFO: Train AUC: 0.506
1 day, 3:53:39.185771 INFO: AUC difference: 6.73%
1 day, 3:53:39.185793 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:53:39.409929 INFO: Resetting torch num_threads to 80
1 day, 3:53:39.410487 PROGRESS: === Extracted 3402 precursors and 37705 fragments ===
1 day, 3:53:39.410887 INFO: === FDR correction performed with classifier version 3 ===
1 day, 3:53:39.411494 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:53:39.411581 PROGRESS: Total precursors accumulated: 600
1 day, 3:53:39.411639 PROGRESS: Target precursors: 557 (92.83%)
1 day, 3:53:39.411689 PROGRESS: Decoy precursors: 43 (7.17%)
1 day, 3:53:39.411734 PROGRESS: 
1 day, 3:53:39.411776 PROGRESS: Precursor Summary:
1 day, 3:53:39.412813 PROGRESS: Channel   0:	 0.050 FDR:   546; 0.010 FDR:   546; 0.001 FDR:   546
1 day, 3:53:39.412902 PROGRESS: 
1 day, 3:53:39.412959 PROGRESS: Protein Summary:
1 day, 3:53:39.414202 PROGRESS: Channel   0:	 0.050 FDR:   507; 0.010 FDR:   507; 0.001 FDR:   507
1 day, 3:53:39.414292 PROGRESS: =========================================================================
1 day, 3:53:39.414431 INFO: Target number of precursors reached.
1 day, 3:53:39.421374 INFO: fragments_df: keeping 5000 of 37705 [sum(precursor_idx_mask)=17236 sum(mass_error_mask)=37705 stop_rank=5000
1 day, 3:53:39.425997 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:39.619542 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:39.802543 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:39.943206 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:40.619188 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:53:40.619597 INFO: Using score_cutoff 40.11451400184632 (fac=0.99, q=1)
1 day, 3:53:40.619900 INFO: Updating optimization_manager: fwhm_rt             : 3.085857629776001 -> 3.0928831100463867
1 day, 3:53:40.619977 INFO: Updating optimization_manager: fwhm_mobility       : 0.008430319838225842 -> 0.008464284241199493
1 day, 3:53:40.620032 INFO: Updating optimization_manager: score_cutoff        : 40.6420716796875 -> 40.11451400184632
1 day, 3:53:40.620084 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:40.621109 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:40.622401 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:40.623163 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:40.625400 INFO: === checking if optimization conditions were reached ===
1 day, 3:53:40.625496 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:53:40.627198 INFO: Updating optimization_manager: rt_error            : 1143.404837970801 -> 995.5293653048154
1 day, 3:53:40.627298 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 995.5294.
1 day, 3:53:40.627370 INFO: ==============================================
1 day, 3:53:40.627440 INFO: Starting optimization step 2.
1 day, 3:53:40.627496 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:53:40.627552 INFO: Using classic extraction backend
1 day, 3:53:40.627660 PROGRESS: Extracting batch of 1194 precursors
1 day, 3:53:40.627722 INFO: === Search parameters used ===
1 day, 3:53:40.627770 INFO: rt_error       : 995.5293653048154
1 day, 3:53:40.627813 INFO: mobility_error : 0.1
1 day, 3:53:40.627854 INFO: num_candidates : 3
1 day, 3:53:40.627896 INFO: ms1_error      : 15.0
1 day, 3:53:40.627936 INFO: ms2_error      : 15.0
1 day, 3:53:40.627975 INFO: fwhm_rt        : 3.0928831100463867
1 day, 3:53:40.628016 INFO: quant_window   : 3
1 day, 3:53:40.628054 INFO: ==============================================
1 day, 3:53:40.628932 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:53:40.628978 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:53:40.629019 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
1 day, 3:53:40.629043 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 3:53:40.634257 INFO: Starting candidate selection
1 day, 3:53:45.233258 INFO: Starting candidate scoring
1 day, 3:53:45.452322 INFO: Finished candidate processing
1 day, 3:53:45.452422 INFO: Collecting candidate features
1 day, 3:53:45.464790 INFO: Collecting fragment features
1 day, 3:53:45.468545 INFO: Finished candidate scoring
1 day, 3:53:45.470684 INFO: performing precursor FDR with 47 features
1 day, 3:53:45.470731 INFO: Decoy channel: -1
1 day, 3:53:45.470754 INFO: Competetive: True
1 day, 3:53:45.473584 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:53:45.475705 INFO: Using random state 411560 for train-test-split
1 day, 3:53:45.485839 INFO: Test AUC: 0.485
1 day, 3:53:45.485900 INFO: Train AUC: 0.499
1 day, 3:53:45.485930 INFO: AUC difference: 2.86%
1 day, 3:53:45.700373 INFO: Resetting torch num_threads to 80
1 day, 3:53:45.700917 PROGRESS: === Extracted 3401 precursors and 37677 fragments ===
1 day, 3:53:45.701315 INFO: === FDR correction performed with classifier version 3 ===
1 day, 3:53:45.701881 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:53:45.701967 PROGRESS: Total precursors accumulated: 600
1 day, 3:53:45.702026 PROGRESS: Target precursors: 554 (92.33%)
1 day, 3:53:45.702085 PROGRESS: Decoy precursors: 46 (7.67%)
1 day, 3:53:45.702132 PROGRESS: 
1 day, 3:53:45.702174 PROGRESS: Precursor Summary:
1 day, 3:53:45.703230 PROGRESS: Channel   0:	 0.050 FDR:   545; 0.010 FDR:   545; 0.001 FDR:   545
1 day, 3:53:45.703318 PROGRESS: 
1 day, 3:53:45.703375 PROGRESS: Protein Summary:
1 day, 3:53:45.704629 PROGRESS: Channel   0:	 0.050 FDR:   507; 0.010 FDR:   507; 0.001 FDR:   507
1 day, 3:53:45.704717 PROGRESS: =========================================================================
1 day, 3:53:45.704859 INFO: Target number of precursors reached.
1 day, 3:53:45.711670 INFO: fragments_df: keeping 5000 of 37677 [sum(precursor_idx_mask)=17199 sum(mass_error_mask)=37677 stop_rank=5000
1 day, 3:53:45.716233 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:45.860861 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:46.006588 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:46.146954 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:46.821936 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:53:46.822640 INFO: Using score_cutoff 39.93977381286621 (fac=0.99, q=1)
1 day, 3:53:46.822948 INFO: Updating optimization_manager: fwhm_rt             : 3.0928831100463867 -> 3.085857629776001
1 day, 3:53:46.823026 INFO: Updating optimization_manager: fwhm_mobility       : 0.008464284241199493 -> 0.008407051675021648
1 day, 3:53:46.823079 INFO: Updating optimization_manager: score_cutoff        : 40.11451400184632 -> 39.93977381286621
1 day, 3:53:46.823130 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:46.824170 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:46.825450 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:46.826238 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:46.828381 INFO: === checking if optimization conditions were reached ===
1 day, 3:53:46.828475 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:53:46.830282 INFO: Updating optimization_manager: rt_error            : 995.5293653048154 -> 999.3726088885339
1 day, 3:53:46.830379 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 999.3726.
1 day, 3:53:46.830444 INFO: ==============================================
1 day, 3:53:46.830508 INFO: Starting optimization step 3.
1 day, 3:53:46.830564 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:53:46.830625 INFO: Using classic extraction backend
1 day, 3:53:46.830730 PROGRESS: Extracting batch of 1194 precursors
1 day, 3:53:46.830793 INFO: === Search parameters used ===
1 day, 3:53:46.830839 INFO: rt_error       : 999.3726088885339
1 day, 3:53:46.830881 INFO: mobility_error : 0.1
1 day, 3:53:46.830920 INFO: num_candidates : 3
1 day, 3:53:46.830961 INFO: ms1_error      : 15.0
1 day, 3:53:46.830999 INFO: ms2_error      : 15.0
1 day, 3:53:46.831037 INFO: fwhm_rt        : 3.085857629776001
1 day, 3:53:46.831075 INFO: quant_window   : 3
1 day, 3:53:46.831112 INFO: ==============================================
1 day, 3:53:46.831990 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:53:46.832035 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:53:46.832069 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
1 day, 3:53:46.832092 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 3:53:46.832743 INFO: Starting candidate selection
1 day, 3:53:51.625508 INFO: Starting candidate scoring
1 day, 3:53:51.860727 INFO: Finished candidate processing
1 day, 3:53:51.860862 INFO: Collecting candidate features
1 day, 3:53:51.874590 INFO: Collecting fragment features
1 day, 3:53:51.878305 INFO: Finished candidate scoring
1 day, 3:53:51.880177 INFO: performing precursor FDR with 47 features
1 day, 3:53:51.880222 INFO: Decoy channel: -1
1 day, 3:53:51.880246 INFO: Competetive: True
1 day, 3:53:51.883265 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:53:51.885305 INFO: Using random state 411560 for train-test-split
1 day, 3:53:51.895716 INFO: Test AUC: 0.472
1 day, 3:53:51.895774 INFO: Train AUC: 0.503
1 day, 3:53:51.895803 INFO: AUC difference: 6.11%
1 day, 3:53:51.895825 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:53:52.110738 INFO: Resetting torch num_threads to 80
1 day, 3:53:52.111287 PROGRESS: === Extracted 3403 precursors and 37790 fragments ===
1 day, 3:53:52.111682 INFO: === FDR correction performed with classifier version 3 ===
1 day, 3:53:52.112242 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:53:52.112326 PROGRESS: Total precursors accumulated: 600
1 day, 3:53:52.112384 PROGRESS: Target precursors: 557 (92.83%)
1 day, 3:53:52.112435 PROGRESS: Decoy precursors: 43 (7.17%)
1 day, 3:53:52.112479 PROGRESS: 
1 day, 3:53:52.112520 PROGRESS: Precursor Summary:
1 day, 3:53:52.113559 PROGRESS: Channel   0:	 0.050 FDR:   549; 0.010 FDR:   549; 0.001 FDR:   549
1 day, 3:53:52.113647 PROGRESS: 
1 day, 3:53:52.113702 PROGRESS: Protein Summary:
1 day, 3:53:52.114971 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   511; 0.001 FDR:   511
1 day, 3:53:52.115060 PROGRESS: =========================================================================
1 day, 3:53:52.115188 INFO: Target number of precursors reached.
1 day, 3:53:52.122119 INFO: fragments_df: keeping 5000 of 37790 [sum(precursor_idx_mask)=17439 sum(mass_error_mask)=37790 stop_rank=5000
1 day, 3:53:52.126702 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:52.322511 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:52.477054 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:52.615254 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:53.294764 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:53:53.295189 INFO: Using score_cutoff 39.98551055603027 (fac=0.99, q=1)
1 day, 3:53:53.295499 INFO: Updating optimization_manager: fwhm_rt             : 3.085857629776001 -> 3.085857629776001
1 day, 3:53:53.295576 INFO: Updating optimization_manager: fwhm_mobility       : 0.008407051675021648 -> 0.00847393088042736
1 day, 3:53:53.295629 INFO: Updating optimization_manager: score_cutoff        : 39.93977381286621 -> 39.98551055603027
1 day, 3:53:53.295680 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:53.296720 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:53.298014 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:53.298781 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:53.300947 INFO: === checking if optimization conditions were reached ===
1 day, 3:53:53.301041 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 3:53:53.302023 INFO: Updating optimization_manager: rt_error            : 999.3726088885339 -> 995.5293653048154
1 day, 3:53:53.302153 INFO: Updating optimization_manager: classifier_version  : 3 -> 6
1 day, 3:53:53.302248 INFO: Updating optimization_manager: score_cutoff        : 39.98551055603027 -> 39.93977381286621
1 day, 3:53:53.302328 INFO: Updating optimization_manager: fwhm_rt             : 3.085857629776001 -> 3.085857629776001
1 day, 3:53:53.302406 INFO: Updating optimization_manager: fwhm_mobility       : 0.00847393088042736 -> 0.008407051675021648
1 day, 3:53:53.302484 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 995.5294 found after 4 searches.
1 day, 3:53:53.302540 INFO: ==============================================
1 day, 3:53:53.302602 PROGRESS: Optimization finished for rt_error.
1 day, 3:53:53.306767 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:53.307577 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:53.308829 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:53:53.309582 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:53:53.335499 INFO: Starting optimization step 0.
1 day, 3:53:53.335636 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:53:53.335706 INFO: Using classic extraction backend
1 day, 3:53:53.335819 PROGRESS: Extracting batch of 1194 precursors
1 day, 3:53:53.335887 INFO: === Search parameters used ===
1 day, 3:53:53.335935 INFO: rt_error       : 995.5293653048154
1 day, 3:53:53.335977 INFO: mobility_error : 0.1
1 day, 3:53:53.336019 INFO: num_candidates : 3
1 day, 3:53:53.336060 INFO: ms1_error      : 15.0
1 day, 3:53:53.336099 INFO: ms2_error      : 15.0
1 day, 3:53:53.336138 INFO: fwhm_rt        : 3.085857629776001
1 day, 3:53:53.336176 INFO: quant_window   : 3
1 day, 3:53:53.336215 INFO: ==============================================
1 day, 3:53:53.336935 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:53:53.336979 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:53:53.337015 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
1 day, 3:53:53.337039 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 3:53:53.345559 INFO: Starting candidate selection
1 day, 3:53:59.125415 INFO: Starting candidate scoring
1 day, 3:53:59.340789 INFO: Finished candidate processing
1 day, 3:53:59.341658 INFO: Collecting candidate features
1 day, 3:53:59.354676 INFO: Collecting fragment features
1 day, 3:53:59.358542 INFO: Finished candidate scoring
1 day, 3:53:59.360442 INFO: performing precursor FDR with 47 features
1 day, 3:53:59.360486 INFO: Decoy channel: -1
1 day, 3:53:59.360509 INFO: Competetive: True
1 day, 3:53:59.363384 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:53:59.365436 INFO: Using random state 859197 for train-test-split
1 day, 3:53:59.376459 INFO: Test AUC: 0.506
1 day, 3:53:59.376522 INFO: Train AUC: 0.494
1 day, 3:53:59.376552 INFO: AUC difference: 2.59%
1 day, 3:53:59.592064 INFO: Resetting torch num_threads to 80
1 day, 3:53:59.592591 PROGRESS: === Extracted 3398 precursors and 37731 fragments ===
1 day, 3:53:59.592994 INFO: === FDR correction performed with classifier version 6 ===
1 day, 3:53:59.593548 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:53:59.593633 PROGRESS: Total precursors accumulated: 600
1 day, 3:53:59.593692 PROGRESS: Target precursors: 554 (92.33%)
1 day, 3:53:59.593748 PROGRESS: Decoy precursors: 46 (7.67%)
1 day, 3:53:59.593794 PROGRESS: 
1 day, 3:53:59.593837 PROGRESS: Precursor Summary:
1 day, 3:53:59.594868 PROGRESS: Channel   0:	 0.050 FDR:   547; 0.010 FDR:   547; 0.001 FDR:   547
1 day, 3:53:59.594955 PROGRESS: 
1 day, 3:53:59.595009 PROGRESS: Protein Summary:
1 day, 3:53:59.596229 PROGRESS: Channel   0:	 0.050 FDR:   509; 0.010 FDR:   509; 0.001 FDR:   509
1 day, 3:53:59.596316 PROGRESS: =========================================================================
1 day, 3:53:59.596450 INFO: Target number of precursors reached.
1 day, 3:53:59.603380 INFO: fragments_df: keeping 5000 of 37731 [sum(precursor_idx_mask)=17357 sum(mass_error_mask)=37731 stop_rank=5000
1 day, 3:53:59.607898 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:53:59.743821 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:53:59.885060 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:54:00.025010 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:54:00.700153 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:54:00.700570 INFO: Using score_cutoff 39.585005131530764 (fac=0.99, q=1)
1 day, 3:54:00.700872 INFO: Updating optimization_manager: fwhm_rt             : 3.085857629776001 -> 3.085857629776001
1 day, 3:54:00.700950 INFO: Updating optimization_manager: fwhm_mobility       : 0.008407051675021648 -> 0.008430319838225842
1 day, 3:54:00.701005 INFO: Updating optimization_manager: score_cutoff        : 39.93977381286621 -> 39.585005131530764
1 day, 3:54:00.701060 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:54:00.702736 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:54:00.704029 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:54:00.704782 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:54:00.706895 INFO: === checking if optimization conditions were reached ===
1 day, 3:54:00.706995 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:54:00.708324 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.08358902606492252
1 day, 3:54:00.708420 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0836.
1 day, 3:54:00.708484 INFO: ==============================================
1 day, 3:54:00.708549 INFO: Starting optimization step 1.
1 day, 3:54:00.708604 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:54:00.708658 INFO: Using classic extraction backend
1 day, 3:54:00.708765 PROGRESS: Extracting batch of 1194 precursors
1 day, 3:54:00.708827 INFO: === Search parameters used ===
1 day, 3:54:00.708873 INFO: rt_error       : 995.5293653048154
1 day, 3:54:00.708915 INFO: mobility_error : 0.08358902606492252
1 day, 3:54:00.708957 INFO: num_candidates : 3
1 day, 3:54:00.708997 INFO: ms1_error      : 15.0
1 day, 3:54:00.709037 INFO: ms2_error      : 15.0
1 day, 3:54:00.709077 INFO: fwhm_rt        : 3.085857629776001
1 day, 3:54:00.709120 INFO: quant_window   : 3
1 day, 3:54:00.709167 INFO: ==============================================
1 day, 3:54:00.709926 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:54:00.709972 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:54:00.710007 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
1 day, 3:54:00.710031 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.91
1 day, 3:54:00.710647 INFO: Starting candidate selection
1 day, 3:54:06.065193 INFO: Starting candidate scoring
1 day, 3:54:06.291859 INFO: Finished candidate processing
1 day, 3:54:06.292002 INFO: Collecting candidate features
1 day, 3:54:06.305847 INFO: Collecting fragment features
1 day, 3:54:06.309520 INFO: Finished candidate scoring
1 day, 3:54:06.311353 INFO: performing precursor FDR with 47 features
1 day, 3:54:06.311398 INFO: Decoy channel: -1
1 day, 3:54:06.311424 INFO: Competetive: True
1 day, 3:54:06.314381 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:54:06.316459 INFO: Using random state 859197 for train-test-split
1 day, 3:54:06.326536 INFO: Test AUC: 0.493
1 day, 3:54:06.326595 INFO: Train AUC: 0.495
1 day, 3:54:06.326624 INFO: AUC difference: 0.37%
1 day, 3:54:06.542681 INFO: Resetting torch num_threads to 80
1 day, 3:54:06.543185 PROGRESS: === Extracted 3393 precursors and 37611 fragments ===
1 day, 3:54:06.543581 INFO: === FDR correction performed with classifier version 6 ===
1 day, 3:54:06.544127 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:54:06.544213 PROGRESS: Total precursors accumulated: 600
1 day, 3:54:06.544270 PROGRESS: Target precursors: 552 (92.00%)
1 day, 3:54:06.544318 PROGRESS: Decoy precursors: 48 (8.00%)
1 day, 3:54:06.544362 PROGRESS: 
1 day, 3:54:06.544403 PROGRESS: Precursor Summary:
1 day, 3:54:06.545416 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   540; 0.001 FDR:   540
1 day, 3:54:06.545503 PROGRESS: 
1 day, 3:54:06.545557 PROGRESS: Protein Summary:
1 day, 3:54:06.546813 PROGRESS: Channel   0:	 0.050 FDR:   502; 0.010 FDR:   502; 0.001 FDR:   502
1 day, 3:54:06.546902 PROGRESS: =========================================================================
1 day, 3:54:06.547042 INFO: Target number of precursors reached.
1 day, 3:54:06.553768 INFO: fragments_df: keeping 5000 of 37611 [sum(precursor_idx_mask)=17133 sum(mass_error_mask)=37611 stop_rank=5000
1 day, 3:54:06.558290 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:54:06.696960 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:54:06.840652 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:54:06.981415 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:54:07.658314 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:54:07.658727 INFO: Using score_cutoff 39.87079897384644 (fac=0.99, q=1)
1 day, 3:54:07.659029 INFO: Updating optimization_manager: fwhm_rt             : 3.085857629776001 -> 3.1007518768310547
1 day, 3:54:07.659104 INFO: Updating optimization_manager: fwhm_mobility       : 0.008430319838225842 -> 0.008492212742567062
1 day, 3:54:07.659157 INFO: Updating optimization_manager: score_cutoff        : 39.585005131530764 -> 39.87079897384644
1 day, 3:54:07.659208 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:54:07.660233 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:54:07.661506 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:54:07.662276 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:54:07.664459 INFO: === checking if optimization conditions were reached ===
1 day, 3:54:07.664553 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:54:07.665982 INFO: Updating optimization_manager: mobility_error      : 0.08358902606492252 -> 0.07389843741501793
1 day, 3:54:07.666085 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0739.
1 day, 3:54:07.666151 INFO: ==============================================
1 day, 3:54:07.666214 INFO: Starting optimization step 2.
1 day, 3:54:07.666271 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:54:07.666324 INFO: Using classic extraction backend
1 day, 3:54:07.666431 PROGRESS: Extracting batch of 1194 precursors
1 day, 3:54:07.666493 INFO: === Search parameters used ===
1 day, 3:54:07.666548 INFO: rt_error       : 995.5293653048154
1 day, 3:54:07.666593 INFO: mobility_error : 0.07389843741501793
1 day, 3:54:07.666634 INFO: num_candidates : 3
1 day, 3:54:07.666675 INFO: ms1_error      : 15.0
1 day, 3:54:07.666715 INFO: ms2_error      : 15.0
1 day, 3:54:07.666753 INFO: fwhm_rt        : 3.1007518768310547
1 day, 3:54:07.666792 INFO: quant_window   : 3
1 day, 3:54:07.666831 INFO: ==============================================
1 day, 3:54:07.667583 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:54:07.667626 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:54:07.667668 INFO: FWHM in RT is 3.10 seconds, sigma is 0.68
1 day, 3:54:07.667691 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.94
1 day, 3:54:07.668308 INFO: Starting candidate selection
1 day, 3:54:12.051204 INFO: Starting candidate scoring
1 day, 3:54:12.266618 INFO: Finished candidate processing
1 day, 3:54:12.266752 INFO: Collecting candidate features
1 day, 3:54:12.281928 INFO: Collecting fragment features
1 day, 3:54:12.287089 INFO: Finished candidate scoring
1 day, 3:54:12.289407 INFO: performing precursor FDR with 47 features
1 day, 3:54:12.289461 INFO: Decoy channel: -1
1 day, 3:54:12.289485 INFO: Competetive: True
1 day, 3:54:12.293362 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:54:12.295693 INFO: Using random state 859197 for train-test-split
1 day, 3:54:12.307633 INFO: Test AUC: 0.500
1 day, 3:54:12.307699 INFO: Train AUC: 0.494
1 day, 3:54:12.307729 INFO: AUC difference: 1.10%
1 day, 3:54:12.526562 INFO: Resetting torch num_threads to 80
1 day, 3:54:12.527083 PROGRESS: === Extracted 3402 precursors and 37671 fragments ===
1 day, 3:54:12.527486 INFO: === FDR correction performed with classifier version 6 ===
1 day, 3:54:12.528035 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:54:12.528120 PROGRESS: Total precursors accumulated: 600
1 day, 3:54:12.528177 PROGRESS: Target precursors: 548 (91.33%)
1 day, 3:54:12.528227 PROGRESS: Decoy precursors: 52 (8.67%)
1 day, 3:54:12.528273 PROGRESS: 
1 day, 3:54:12.528318 PROGRESS: Precursor Summary:
1 day, 3:54:12.529344 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   537; 0.001 FDR:   537
1 day, 3:54:12.529430 PROGRESS: 
1 day, 3:54:12.529486 PROGRESS: Protein Summary:
1 day, 3:54:12.530722 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   500; 0.001 FDR:   500
1 day, 3:54:12.530811 PROGRESS: =========================================================================
1 day, 3:54:12.530999 INFO: Target number of precursors reached.
1 day, 3:54:12.537896 INFO: fragments_df: keeping 5000 of 37671 [sum(precursor_idx_mask)=17019 sum(mass_error_mask)=37671 stop_rank=5000
1 day, 3:54:12.544527 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:54:12.680124 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:54:12.820776 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:54:12.962783 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:54:13.647679 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:54:13.648091 INFO: Using score_cutoff 39.18196201629639 (fac=0.99, q=1)
1 day, 3:54:13.648391 INFO: Updating optimization_manager: fwhm_rt             : 3.1007518768310547 -> 3.0975852012634277
1 day, 3:54:13.648468 INFO: Updating optimization_manager: fwhm_mobility       : 0.008492212742567062 -> 0.008480086922645569
1 day, 3:54:13.648521 INFO: Updating optimization_manager: score_cutoff        : 39.87079897384644 -> 39.18196201629639
1 day, 3:54:13.648574 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:54:13.649602 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:54:13.650890 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:54:13.651651 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:54:13.653745 INFO: === checking if optimization conditions were reached ===
1 day, 3:54:13.653839 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:54:13.654529 INFO: Updating optimization_manager: mobility_error      : 0.07389843741501793 -> 0.1
1 day, 3:54:13.654652 INFO: Updating optimization_manager: classifier_version  : 6 -> 8
1 day, 3:54:13.654751 INFO: Updating optimization_manager: score_cutoff        : 39.18196201629639 -> 39.585005131530764
1 day, 3:54:13.654835 INFO: Updating optimization_manager: fwhm_rt             : 3.0975852012634277 -> 3.085857629776001
1 day, 3:54:13.654924 INFO: Updating optimization_manager: fwhm_mobility       : 0.008480086922645569 -> 0.008430319838225842
1 day, 3:54:13.655005 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 3:54:13.655062 INFO: ==============================================
1 day, 3:54:13.655125 PROGRESS: Optimization finished for mobility_error.
1 day, 3:54:13.659286 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:54:13.660086 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:54:13.661330 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:54:13.662092 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:54:13.686110 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 3:54:13.686243 PROGRESS: ==============================================
1 day, 3:54:13.686309 PROGRESS: ms2_error      : 15.0000
1 day, 3:54:13.686363 PROGRESS: ms1_error      : 15.0000
1 day, 3:54:13.686412 PROGRESS: rt_error       : 995.5294
1 day, 3:54:13.686456 PROGRESS: mobility_error : 0.1000
1 day, 3:54:13.686498 PROGRESS: ==============================================
1 day, 3:54:13.687005 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:54:13.710791 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:54:13.809873 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:54:13.834771 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:54:14.106608 INFO: Using classic extraction backend
1 day, 3:54:14.106991 PROGRESS: Extracting batch of 180112 precursors
1 day, 3:54:14.107094 INFO: === Search parameters used ===
1 day, 3:54:14.107158 INFO: rt_error       : 995.5293653048154
1 day, 3:54:14.107214 INFO: mobility_error : 0.1
1 day, 3:54:14.107271 INFO: num_candidates : 3
1 day, 3:54:14.107336 INFO: ms1_error      : 15.0
1 day, 3:54:14.107391 INFO: ms2_error      : 15.0
1 day, 3:54:14.107444 INFO: fwhm_rt        : 3.085857629776001
1 day, 3:54:14.107496 INFO: quant_window   : 3
1 day, 3:54:14.107548 INFO: ==============================================
1 day, 3:54:14.149185 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:54:14.149314 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:54:14.149357 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
1 day, 3:54:14.149379 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.91
1 day, 3:54:14.151357 INFO: Starting candidate selection
1 day, 4:03:33.774693 INFO: Removed 23488 precursors with score below cutoff 39.585005131530764
1 day, 4:03:34.132425 INFO: Starting candidate scoring
1 day, 4:03:54.793219 INFO: Finished candidate processing
1 day, 4:03:54.793628 INFO: Collecting candidate features
1 day, 4:03:55.469686 INFO: Collecting fragment features
1 day, 4:03:55.793835 INFO: Finished candidate scoring
1 day, 4:03:56.165866 INFO: === Performing FDR correction with classifier version 8 ===
1 day, 4:03:56.166896 INFO: performing precursor FDR with 47 features
1 day, 4:03:56.166949 INFO: Decoy channel: -1
1 day, 4:03:56.166972 INFO: Competetive: True
1 day, 4:03:56.286367 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:03:56.486242 INFO: Using random state 696158 for train-test-split
1 day, 4:04:04.436405 INFO: Test AUC: 0.743
1 day, 4:04:04.436529 INFO: Train AUC: 0.749
1 day, 4:04:04.436562 INFO: AUC difference: 0.72%
1 day, 4:04:04.865359 INFO: Resetting torch num_threads to 80
1 day, 4:04:04.886237 INFO: Removing fragments below FDR threshold
1 day, 4:04:05.002142 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:04:05.002412 PROGRESS: Total precursors accumulated: 76,451
1 day, 4:04:05.002494 PROGRESS: Target precursors: 75,695 (99.01%)
1 day, 4:04:05.002567 PROGRESS: Decoy precursors: 756 (0.99%)
1 day, 4:04:05.002634 PROGRESS: 
1 day, 4:04:05.002711 PROGRESS: Precursor Summary:
1 day, 4:04:05.040939 PROGRESS: Channel   0:	 0.050 FDR: 75,695; 0.010 FDR: 75,695; 0.001 FDR: 67,114
1 day, 4:04:05.041252 PROGRESS: 
1 day, 4:04:05.041341 PROGRESS: Protein Summary:
1 day, 4:04:05.094701 PROGRESS: Channel   0:	 0.050 FDR: 8,648; 0.010 FDR: 8,648; 0.001 FDR: 8,448
1 day, 4:04:05.094959 PROGRESS: =========================================================================
1 day, 4:04:05.096757 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/psm.parquet
1 day, 4:04:05.471902 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/frag.parquet
1 day, 4:04:05.850479 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 4:04:05.900001 PROGRESS: 
1 day, 4:04:05.900190 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/quant
1 day, 4:04:05.900278 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/figures
1 day, 4:04:05.900465 INFO: Initializing TimingManager
1 day, 4:04:05.901028 INFO: Initializing RawFileManager
1 day, 4:04:05.901160 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:05.901222 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:05.901280 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:06.170717 INFO: Reading 39,128 frames with 2,860,596,893 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:11.945506 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
1 day, 4:04:11.947977 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:11.952068 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:11.952376 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:11.952942 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:11.954896 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:11.975597 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:11.975978 INFO: Indexing quadrupole dimension
1 day, 4:04:12.469180 INFO: Transposing detector events
1 day, 4:04:21.269687 INFO: Finished transposing data
1 day, 4:04:21.312055 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 4:04:21.313705 INFO: RT (min)            : 0.0 - 70.0
1 day, 4:04:21.313837 INFO: RT duration (sec)   : 4199.8
1 day, 4:04:21.313894 INFO: RT duration (min)   : 70.0
1 day, 4:04:21.313943 INFO: Cycle len (scans)   : 9
1 day, 4:04:21.313988 INFO: Cycle len (sec)     : 0.97
1 day, 4:04:21.314031 INFO: Number of cycles    : 4347
1 day, 4:04:21.314100 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 4:04:21.314333 INFO: Creating DIA data object took: 15.413141012191772
1 day, 4:04:21.368862 INFO: Initializing CalibrationManager
1 day, 4:04:21.369138 INFO: Setting up calibration estimators ..
1 day, 4:04:21.369200 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 4:04:21.369300 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, 4:04:21.369398 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 4:04:21.369460 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, 4:04:21.369532 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, 4:04:21.369597 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, 4:04:21.369648 INFO: Done setting up calibration estimators.
1 day, 4:04:21.369782 INFO: Initializing OptimizationManager
1 day, 4:04:21.369882 INFO: initial parameter: ms1_error = 30
1 day, 4:04:21.369930 INFO: initial parameter: ms2_error = 30
1 day, 4:04:21.369977 INFO: initial parameter: rt_error = 2099.894844
1 day, 4:04:21.370018 INFO: initial parameter: mobility_error = 0.1
1 day, 4:04:21.370077 INFO: initial parameter: num_candidates = 1
1 day, 4:04:21.370123 INFO: initial parameter: fwhm_rt = 5
1 day, 4:04:21.370172 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 4:04:21.370214 INFO: initial parameter: score_cutoff = 0
1 day, 4:04:21.370255 INFO: initial parameter: classifier_version = -1
1 day, 4:04:21.370341 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 4:04:21.370656 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 4:04:21.370693 INFO: Initializing FDRManager
1 day, 4:04:21.370737 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 4:04:21.394242 PROGRESS: Initializing spectral library: 90,710 target precursors potentially observable (0 removed)
1 day, 4:04:21.409985 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 4:04:21.410367 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 2099.894844
1 day, 4:04:21.410486 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 4:04:21.410669 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 4:04:21.410762 PROGRESS: Starting initial search for precursors.
1 day, 4:04:21.410853 INFO: Starting optimization step 0.
1 day, 4:04:21.410916 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:04:21.410994 INFO: Using classic extraction backend
1 day, 4:04:21.411252 PROGRESS: Extracting batch of 398 precursors
1 day, 4:04:21.411332 INFO: === Search parameters used ===
1 day, 4:04:21.411384 INFO: rt_error       : 2099.894844
1 day, 4:04:21.411429 INFO: mobility_error : 0.1
1 day, 4:04:21.411471 INFO: num_candidates : 1
1 day, 4:04:21.411512 INFO: ms1_error      : 30
1 day, 4:04:21.411552 INFO: ms2_error      : 30
1 day, 4:04:21.411595 INFO: fwhm_rt        : 5
1 day, 4:04:21.411639 INFO: quant_window   : 3
1 day, 4:04:21.411680 INFO: ==============================================
1 day, 4:04:21.412563 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:04:21.412608 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:04:21.412647 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:04:21.412668 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:04:21.416840 INFO: Starting candidate selection
1 day, 4:04:25.710601 INFO: Starting candidate scoring
1 day, 4:04:25.793901 INFO: Finished candidate processing
1 day, 4:04:25.794056 INFO: Collecting candidate features
1 day, 4:04:25.806008 INFO: Collecting fragment features
1 day, 4:04:25.808862 INFO: Finished candidate scoring
1 day, 4:04:25.809793 INFO: performing precursor FDR with 47 features
1 day, 4:04:25.809835 INFO: Decoy channel: -1
1 day, 4:04:25.809861 INFO: Competetive: True
1 day, 4:04:25.811098 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:04:25.813805 INFO: Using random state 845015 for train-test-split
1 day, 4:04:25.824041 INFO: Test AUC: 0.517
1 day, 4:04:25.824270 INFO: Train AUC: 0.496
1 day, 4:04:25.824349 INFO: AUC difference: 4.37%
1 day, 4:04:26.057730 INFO: Resetting torch num_threads to 80
1 day, 4:04:26.058177 PROGRESS: === Extracted 398 precursors and 4574 fragments ===
1 day, 4:04:26.058575 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:04:26.059104 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:04:26.059190 PROGRESS: Total precursors accumulated: 200
1 day, 4:04:26.059254 PROGRESS: Target precursors: 142 (71.00%)
1 day, 4:04:26.059308 PROGRESS: Decoy precursors: 58 (29.00%)
1 day, 4:04:26.059356 PROGRESS: 
1 day, 4:04:26.059407 PROGRESS: Precursor Summary:
1 day, 4:04:26.060234 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:04:26.060323 PROGRESS: 
1 day, 4:04:26.060385 PROGRESS: Protein Summary:
1 day, 4:04:26.061273 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:04:26.061360 PROGRESS: =========================================================================
1 day, 4:04:26.061464 INFO: Target number of precursors not reached yet.
1 day, 4:04:26.064983 INFO: Starting optimization step 1.
1 day, 4:04:26.065092 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 4:04:26.065166 INFO: Using classic extraction backend
1 day, 4:04:26.065273 PROGRESS: Extracting batch of 796 precursors
1 day, 4:04:26.065341 INFO: === Search parameters used ===
1 day, 4:04:26.065392 INFO: rt_error       : 2099.894844
1 day, 4:04:26.065437 INFO: mobility_error : 0.1
1 day, 4:04:26.065479 INFO: num_candidates : 1
1 day, 4:04:26.065523 INFO: ms1_error      : 30
1 day, 4:04:26.065567 INFO: ms2_error      : 30
1 day, 4:04:26.065609 INFO: fwhm_rt        : 5
1 day, 4:04:26.065649 INFO: quant_window   : 3
1 day, 4:04:26.065688 INFO: ==============================================
1 day, 4:04:26.066298 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:04:26.066345 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:04:26.066374 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:04:26.066395 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:04:26.067065 INFO: Starting candidate selection
1 day, 4:04:33.484571 INFO: Starting candidate scoring
1 day, 4:04:33.599201 INFO: Finished candidate processing
1 day, 4:04:33.599303 INFO: Collecting candidate features
1 day, 4:04:33.608864 INFO: Collecting fragment features
1 day, 4:04:33.611223 INFO: Finished candidate scoring
1 day, 4:04:33.613221 INFO: performing precursor FDR with 47 features
1 day, 4:04:33.613267 INFO: Decoy channel: -1
1 day, 4:04:33.613292 INFO: Competetive: True
1 day, 4:04:33.616123 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:04:33.617819 INFO: Using random state 590180 for train-test-split
1 day, 4:04:33.625919 INFO: Test AUC: 0.490
1 day, 4:04:33.625976 INFO: Train AUC: 0.517
1 day, 4:04:33.626006 INFO: AUC difference: 5.26%
1 day, 4:04:33.626028 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:04:33.838173 INFO: Resetting torch num_threads to 80
1 day, 4:04:33.839378 PROGRESS: === Extracted 1194 precursors and 13593 fragments ===
1 day, 4:04:33.839763 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:04:33.840342 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:04:33.840431 PROGRESS: Total precursors accumulated: 600
1 day, 4:04:33.840491 PROGRESS: Target precursors: 449 (74.83%)
1 day, 4:04:33.840547 PROGRESS: Decoy precursors: 151 (25.17%)
1 day, 4:04:33.840595 PROGRESS: 
1 day, 4:04:33.840638 PROGRESS: Precursor Summary:
1 day, 4:04:33.841495 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 4:04:33.841583 PROGRESS: 
1 day, 4:04:33.841638 PROGRESS: Protein Summary:
1 day, 4:04:33.842602 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 4:04:33.842690 PROGRESS: =========================================================================
1 day, 4:04:33.842837 INFO: Target number of precursors not reached yet.
1 day, 4:04:33.847274 INFO: Starting optimization step 2.
1 day, 4:04:33.847376 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 4:04:33.847447 INFO: Using classic extraction backend
1 day, 4:04:33.847558 PROGRESS: Extracting batch of 1593 precursors
1 day, 4:04:33.847624 INFO: === Search parameters used ===
1 day, 4:04:33.847672 INFO: rt_error       : 2099.894844
1 day, 4:04:33.847714 INFO: mobility_error : 0.1
1 day, 4:04:33.847757 INFO: num_candidates : 1
1 day, 4:04:33.847797 INFO: ms1_error      : 30
1 day, 4:04:33.847836 INFO: ms2_error      : 30
1 day, 4:04:33.847875 INFO: fwhm_rt        : 5
1 day, 4:04:33.847914 INFO: quant_window   : 3
1 day, 4:04:33.847953 INFO: ==============================================
1 day, 4:04:33.848648 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:04:33.848693 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:04:33.848722 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:04:33.848744 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:04:33.849399 INFO: Starting candidate selection
1 day, 4:04:47.179420 INFO: Starting candidate scoring
1 day, 4:04:47.403398 INFO: Finished candidate processing
1 day, 4:04:47.403556 INFO: Collecting candidate features
1 day, 4:04:47.417538 INFO: Collecting fragment features
1 day, 4:04:47.422329 INFO: Finished candidate scoring
1 day, 4:04:47.426147 INFO: performing precursor FDR with 47 features
1 day, 4:04:47.426199 INFO: Decoy channel: -1
1 day, 4:04:47.426225 INFO: Competetive: True
1 day, 4:04:47.434640 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:04:47.436860 INFO: Using random state 191326 for train-test-split
1 day, 4:04:47.451424 INFO: Test AUC: 0.463
1 day, 4:04:47.451490 INFO: Train AUC: 0.496
1 day, 4:04:47.451521 INFO: AUC difference: 6.52%
1 day, 4:04:47.451544 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:04:47.676937 INFO: Resetting torch num_threads to 80
1 day, 4:04:47.678910 PROGRESS: === Extracted 2785 precursors and 31687 fragments ===
1 day, 4:04:47.679430 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:04:47.680226 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:04:47.680320 PROGRESS: Total precursors accumulated: 1,400
1 day, 4:04:47.680379 PROGRESS: Target precursors: 1,020 (72.86%)
1 day, 4:04:47.680427 PROGRESS: Decoy precursors: 380 (27.14%)
1 day, 4:04:47.680473 PROGRESS: 
1 day, 4:04:47.680516 PROGRESS: Precursor Summary:
1 day, 4:04:47.681469 PROGRESS: Channel   0:	 0.050 FDR:   539; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 4:04:47.681563 PROGRESS: 
1 day, 4:04:47.681619 PROGRESS: Protein Summary:
1 day, 4:04:47.682718 PROGRESS: Channel   0:	 0.050 FDR:   507; 0.010 FDR:     5; 0.001 FDR:     5
1 day, 4:04:47.682812 PROGRESS: =========================================================================
1 day, 4:04:47.683040 INFO: Target number of precursors not reached yet.
1 day, 4:04:47.694597 INFO: Starting optimization step 3.
1 day, 4:04:47.694752 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 4:04:47.694828 INFO: Using classic extraction backend
1 day, 4:04:47.695017 PROGRESS: Extracting batch of 3169 precursors
1 day, 4:04:47.695091 INFO: === Search parameters used ===
1 day, 4:04:47.695138 INFO: rt_error       : 2099.894844
1 day, 4:04:47.695182 INFO: mobility_error : 0.1
1 day, 4:04:47.695230 INFO: num_candidates : 1
1 day, 4:04:47.695273 INFO: ms1_error      : 30
1 day, 4:04:47.695314 INFO: ms2_error      : 30
1 day, 4:04:47.695351 INFO: fwhm_rt        : 5
1 day, 4:04:47.695392 INFO: quant_window   : 3
1 day, 4:04:47.695431 INFO: ==============================================
1 day, 4:04:47.696518 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:04:47.696563 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:04:47.696592 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:04:47.696620 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:04:47.697369 INFO: Starting candidate selection
1 day, 4:05:09.225034 INFO: Starting candidate scoring
1 day, 4:05:09.563843 INFO: Finished candidate processing
1 day, 4:05:09.563953 INFO: Collecting candidate features
1 day, 4:05:09.578584 INFO: Collecting fragment features
1 day, 4:05:09.583014 INFO: Finished candidate scoring
1 day, 4:05:09.590180 INFO: performing precursor FDR with 47 features
1 day, 4:05:09.590233 INFO: Decoy channel: -1
1 day, 4:05:09.590259 INFO: Competetive: True
1 day, 4:05:09.595123 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:05:09.598149 INFO: Using random state 153446 for train-test-split
1 day, 4:05:09.615554 INFO: Test AUC: 0.485
1 day, 4:05:09.615649 INFO: Train AUC: 0.490
1 day, 4:05:09.615681 INFO: AUC difference: 1.16%
1 day, 4:05:09.837584 INFO: Resetting torch num_threads to 80
1 day, 4:05:09.839802 PROGRESS: === Extracted 5953 precursors and 67653 fragments ===
1 day, 4:05:09.840268 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:05:09.841252 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:05:09.841345 PROGRESS: Total precursors accumulated: 3,000
1 day, 4:05:09.841411 PROGRESS: Target precursors: 2,184 (72.80%)
1 day, 4:05:09.841463 PROGRESS: Decoy precursors: 816 (27.20%)
1 day, 4:05:09.841509 PROGRESS: 
1 day, 4:05:09.841552 PROGRESS: Precursor Summary:
1 day, 4:05:09.842567 PROGRESS: Channel   0:	 0.050 FDR: 1,163; 0.010 FDR:    13; 0.001 FDR:    13
1 day, 4:05:09.842659 PROGRESS: 
1 day, 4:05:09.842716 PROGRESS: Protein Summary:
1 day, 4:05:09.843897 PROGRESS: Channel   0:	 0.050 FDR: 1,018; 0.010 FDR:    13; 0.001 FDR:    13
1 day, 4:05:09.843987 PROGRESS: =========================================================================
1 day, 4:05:09.844209 INFO: Target number of precursors not reached yet.
1 day, 4:05:09.857302 INFO: Starting optimization step 4.
1 day, 4:05:09.857435 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 4:05:09.857535 INFO: Using classic extraction backend
1 day, 4:05:09.857680 PROGRESS: Extracting batch of 6346 precursors
1 day, 4:05:09.857755 INFO: === Search parameters used ===
1 day, 4:05:09.857806 INFO: rt_error       : 2099.894844
1 day, 4:05:09.857853 INFO: mobility_error : 0.1
1 day, 4:05:09.857897 INFO: num_candidates : 1
1 day, 4:05:09.857939 INFO: ms1_error      : 30
1 day, 4:05:09.857980 INFO: ms2_error      : 30
1 day, 4:05:09.858019 INFO: fwhm_rt        : 5
1 day, 4:05:09.858104 INFO: quant_window   : 3
1 day, 4:05:09.858148 INFO: ==============================================
1 day, 4:05:09.859689 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:05:09.859736 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:05:09.859779 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:05:09.859802 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:05:09.860665 INFO: Starting candidate selection
1 day, 4:05:50.251846 INFO: Starting candidate scoring
1 day, 4:05:50.919517 INFO: Finished candidate processing
1 day, 4:05:50.919650 INFO: Collecting candidate features
1 day, 4:05:50.942081 INFO: Collecting fragment features
1 day, 4:05:50.951400 INFO: Finished candidate scoring
1 day, 4:05:50.966888 INFO: performing precursor FDR with 47 features
1 day, 4:05:50.966993 INFO: Decoy channel: -1
1 day, 4:05:50.967020 INFO: Competetive: True
1 day, 4:05:50.978173 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:05:50.983875 INFO: Using random state 663503 for train-test-split
1 day, 4:05:51.029782 INFO: Test AUC: 0.487
1 day, 4:05:51.029918 INFO: Train AUC: 0.492
1 day, 4:05:51.029955 INFO: AUC difference: 0.85%
1 day, 4:05:51.267399 INFO: Resetting torch num_threads to 80
1 day, 4:05:51.271053 PROGRESS: === Extracted 12285 precursors and 139683 fragments ===
1 day, 4:05:51.271698 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:05:51.273008 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:05:51.273115 PROGRESS: Total precursors accumulated: 6,194
1 day, 4:05:51.273191 PROGRESS: Target precursors: 4,525 (73.05%)
1 day, 4:05:51.273246 PROGRESS: Decoy precursors: 1,669 (26.95%)
1 day, 4:05:51.273291 PROGRESS: 
1 day, 4:05:51.273337 PROGRESS: Precursor Summary:
1 day, 4:05:51.274642 PROGRESS: Channel   0:	 0.050 FDR: 2,406; 0.010 FDR:    26; 0.001 FDR:    26
1 day, 4:05:51.274745 PROGRESS: 
1 day, 4:05:51.274812 PROGRESS: Protein Summary:
1 day, 4:05:51.276268 PROGRESS: Channel   0:	 0.050 FDR: 1,867; 0.010 FDR:    26; 0.001 FDR:    26
1 day, 4:05:51.276363 PROGRESS: =========================================================================
1 day, 4:05:51.276850 INFO: Target number of precursors not reached yet.
1 day, 4:05:51.305927 INFO: Starting optimization step 5.
1 day, 4:05:51.306227 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1 day, 4:05:51.306350 INFO: Using classic extraction backend
1 day, 4:05:51.306716 PROGRESS: Extracting batch of 12719 precursors
1 day, 4:05:51.306802 INFO: === Search parameters used ===
1 day, 4:05:51.306855 INFO: rt_error       : 2099.894844
1 day, 4:05:51.306902 INFO: mobility_error : 0.1
1 day, 4:05:51.306945 INFO: num_candidates : 1
1 day, 4:05:51.306989 INFO: ms1_error      : 30
1 day, 4:05:51.307030 INFO: ms2_error      : 30
1 day, 4:05:51.307070 INFO: fwhm_rt        : 5
1 day, 4:05:51.307117 INFO: quant_window   : 3
1 day, 4:05:51.307159 INFO: ==============================================
1 day, 4:05:51.310816 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:05:51.310877 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:05:51.310932 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:05:51.310956 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:05:51.311799 INFO: Starting candidate selection
1 day, 4:07:13.968945 INFO: Starting candidate scoring
1 day, 4:07:15.192401 INFO: Finished candidate processing
1 day, 4:07:15.192583 INFO: Collecting candidate features
1 day, 4:07:15.236073 INFO: Collecting fragment features
1 day, 4:07:15.249774 INFO: Finished candidate scoring
1 day, 4:07:15.273605 INFO: performing precursor FDR with 47 features
1 day, 4:07:15.273752 INFO: Decoy channel: -1
1 day, 4:07:15.273779 INFO: Competetive: True
1 day, 4:07:15.287604 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:07:15.295458 INFO: Using random state 373051 for train-test-split
1 day, 4:07:15.594312 INFO: Test AUC: 0.812
1 day, 4:07:15.594451 INFO: Train AUC: 0.814
1 day, 4:07:15.594483 INFO: AUC difference: 0.28%
1 day, 4:07:15.840875 INFO: Resetting torch num_threads to 80
1 day, 4:07:15.846461 PROGRESS: === Extracted 24994 precursors and 284319 fragments ===
1 day, 4:07:15.847076 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:07:15.849338 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:07:15.849436 PROGRESS: Total precursors accumulated: 12,592
1 day, 4:07:15.849507 PROGRESS: Target precursors: 10,350 (82.20%)
1 day, 4:07:15.849561 PROGRESS: Decoy precursors: 2,242 (17.80%)
1 day, 4:07:15.849609 PROGRESS: 
1 day, 4:07:15.849651 PROGRESS: Precursor Summary:
1 day, 4:07:15.852153 PROGRESS: Channel   0:	 0.050 FDR: 7,712; 0.010 FDR: 4,611; 0.001 FDR:   215
1 day, 4:07:15.852251 PROGRESS: 
1 day, 4:07:15.852309 PROGRESS: Protein Summary:
1 day, 4:07:15.855448 PROGRESS: Channel   0:	 0.050 FDR: 3,854; 0.010 FDR: 2,645; 0.001 FDR:   198
1 day, 4:07:15.855549 PROGRESS: =========================================================================
1 day, 4:07:15.855930 INFO: Target number of precursors reached.
1 day, 4:07:15.893436 INFO: fragments_df: keeping 5000 of 284319 [sum(precursor_idx_mask)=52021 sum(mass_error_mask)=284319 stop_rank=5000
1 day, 4:07:15.905993 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:07:16.526308 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:07:17.152890 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:07:17.772698 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:07:18.452402 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 4:07:18.452906 INFO: Using score_cutoff 51.76955075454712 (fac=0.99, q=1)
1 day, 4:07:18.453366 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0377986431121826
1 day, 4:07:18.453447 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010767740197479725
1 day, 4:07:18.453501 INFO: Updating optimization_manager: score_cutoff        : 0 -> 51.76955075454712
1 day, 4:07:18.453569 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:07:18.454782 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:07:18.456044 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:07:18.456800 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:07:18.458987 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
1 day, 4:07:18.459084 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 4:07:18.459179 INFO: Starting optimization step 6.
1 day, 4:07:18.459242 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:07:18.459306 INFO: Using classic extraction backend
1 day, 4:07:18.459490 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:07:18.459556 INFO: === Search parameters used ===
1 day, 4:07:18.459601 INFO: rt_error       : 2099.894844
1 day, 4:07:18.459642 INFO: mobility_error : 0.1
1 day, 4:07:18.459682 INFO: num_candidates : 3
1 day, 4:07:18.459723 INFO: ms1_error      : 30
1 day, 4:07:18.459762 INFO: ms2_error      : 30
1 day, 4:07:18.459800 INFO: fwhm_rt        : 3.0377986431121826
1 day, 4:07:18.459839 INFO: quant_window   : 3
1 day, 4:07:18.459876 INFO: ==============================================
1 day, 4:07:18.460881 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:07:18.460927 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:07:18.460974 INFO: FWHM in RT is 3.04 seconds, sigma is 0.67
1 day, 4:07:18.460995 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.99
1 day, 4:07:18.462023 INFO: Starting candidate selection
1 day, 4:07:28.517272 INFO: Starting candidate scoring
1 day, 4:07:28.882735 INFO: Finished candidate processing
1 day, 4:07:28.882858 INFO: Collecting candidate features
1 day, 4:07:28.896517 INFO: Collecting fragment features
1 day, 4:07:28.901819 INFO: Finished candidate scoring
1 day, 4:07:28.903880 INFO: performing precursor FDR with 47 features
1 day, 4:07:28.903928 INFO: Decoy channel: -1
1 day, 4:07:28.903953 INFO: Competetive: True
1 day, 4:07:28.907770 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:07:28.910024 INFO: Using random state 397438 for train-test-split
1 day, 4:07:28.922607 INFO: Test AUC: 0.658
1 day, 4:07:28.922667 INFO: Train AUC: 0.662
1 day, 4:07:28.922696 INFO: AUC difference: 0.59%
1 day, 4:07:29.144738 INFO: Resetting torch num_threads to 80
1 day, 4:07:29.145343 PROGRESS: === Extracted 3394 precursors and 38595 fragments ===
1 day, 4:07:29.145821 INFO: === FDR correction performed with classifier version 5 ===
1 day, 4:07:29.146481 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:07:29.146575 PROGRESS: Total precursors accumulated: 600
1 day, 4:07:29.146635 PROGRESS: Target precursors: 507 (84.50%)
1 day, 4:07:29.146687 PROGRESS: Decoy precursors: 93 (15.50%)
1 day, 4:07:29.146732 PROGRESS: 
1 day, 4:07:29.146774 PROGRESS: Precursor Summary:
1 day, 4:07:29.147691 PROGRESS: Channel   0:	 0.050 FDR:   396; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:07:29.147781 PROGRESS: 
1 day, 4:07:29.147836 PROGRESS: Protein Summary:
1 day, 4:07:29.148851 PROGRESS: Channel   0:	 0.050 FDR:   372; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:07:29.148940 PROGRESS: =========================================================================
1 day, 4:07:29.149828 INFO: Target number of precursors not reached yet.
1 day, 4:07:29.158323 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:07:29.159438 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:07:29.160919 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:07:29.161753 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:07:29.168804 INFO: === skipping optimization until target number of precursors are found ===
1 day, 4:07:29.169075 INFO: Starting optimization step 7.
1 day, 4:07:29.169149 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 4:07:29.169220 INFO: Using classic extraction backend
1 day, 4:07:29.169397 PROGRESS: Extracting batch of 1593 precursors
1 day, 4:07:29.169483 INFO: === Search parameters used ===
1 day, 4:07:29.169533 INFO: rt_error       : 2099.894844
1 day, 4:07:29.169578 INFO: mobility_error : 0.1
1 day, 4:07:29.169621 INFO: num_candidates : 3
1 day, 4:07:29.169665 INFO: ms1_error      : 30
1 day, 4:07:29.169706 INFO: ms2_error      : 30
1 day, 4:07:29.169744 INFO: fwhm_rt        : 3.0377986431121826
1 day, 4:07:29.169786 INFO: quant_window   : 3
1 day, 4:07:29.169826 INFO: ==============================================
1 day, 4:07:29.170974 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:07:29.171022 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:07:29.171061 INFO: FWHM in RT is 3.04 seconds, sigma is 0.67
1 day, 4:07:29.171082 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.99
1 day, 4:07:29.182478 INFO: Starting candidate selection
1 day, 4:07:42.843644 INFO: Starting candidate scoring
1 day, 4:07:43.328717 INFO: Finished candidate processing
1 day, 4:07:43.328852 INFO: Collecting candidate features
1 day, 4:07:43.352186 INFO: Collecting fragment features
1 day, 4:07:43.359307 INFO: Finished candidate scoring
1 day, 4:07:43.369822 INFO: performing precursor FDR with 47 features
1 day, 4:07:43.370290 INFO: Decoy channel: -1
1 day, 4:07:43.370446 INFO: Competetive: True
1 day, 4:07:43.376940 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:07:43.381646 INFO: Using random state 397438 for train-test-split
1 day, 4:07:43.410398 INFO: Test AUC: 0.660
1 day, 4:07:43.410519 INFO: Train AUC: 0.656
1 day, 4:07:43.410558 INFO: AUC difference: 0.61%
1 day, 4:07:43.668472 INFO: Resetting torch num_threads to 80
1 day, 4:07:43.671114 PROGRESS: === Extracted 7912 precursors and 89955 fragments ===
1 day, 4:07:43.673539 INFO: === FDR correction performed with classifier version 5 ===
1 day, 4:07:43.674506 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:07:43.675323 PROGRESS: Total precursors accumulated: 1,400
1 day, 4:07:43.675443 PROGRESS: Target precursors: 1,180 (84.29%)
1 day, 4:07:43.675527 PROGRESS: Decoy precursors: 220 (15.71%)
1 day, 4:07:43.675594 PROGRESS: 
1 day, 4:07:43.675655 PROGRESS: Precursor Summary:
1 day, 4:07:43.676887 PROGRESS: Channel   0:	 0.050 FDR:   919; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 4:07:43.676996 PROGRESS: 
1 day, 4:07:43.677068 PROGRESS: Protein Summary:
1 day, 4:07:43.678441 PROGRESS: Channel   0:	 0.050 FDR:   802; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 4:07:43.678562 PROGRESS: =========================================================================
1 day, 4:07:43.678861 INFO: Target number of precursors not reached yet.
1 day, 4:07:43.704124 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:07:43.706121 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:07:43.708519 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:07:43.709538 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:07:43.716072 INFO: === skipping optimization until target number of precursors are found ===
1 day, 4:07:43.716258 INFO: Starting optimization step 8.
1 day, 4:07:43.716345 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 4:07:43.716528 INFO: Using classic extraction backend
1 day, 4:07:43.716840 PROGRESS: Extracting batch of 3169 precursors
1 day, 4:07:43.716950 INFO: === Search parameters used ===
1 day, 4:07:43.717008 INFO: rt_error       : 2099.894844
1 day, 4:07:43.717056 INFO: mobility_error : 0.1
1 day, 4:07:43.717098 INFO: num_candidates : 3
1 day, 4:07:43.717139 INFO: ms1_error      : 30
1 day, 4:07:43.717179 INFO: ms2_error      : 30
1 day, 4:07:43.717218 INFO: fwhm_rt        : 3.0377986431121826
1 day, 4:07:43.717260 INFO: quant_window   : 3
1 day, 4:07:43.717299 INFO: ==============================================
1 day, 4:07:43.719636 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:07:43.719707 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:07:43.719805 INFO: FWHM in RT is 3.04 seconds, sigma is 0.67
1 day, 4:07:43.719848 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.99
1 day, 4:07:43.728679 INFO: Starting candidate selection
1 day, 4:08:08.708054 INFO: Starting candidate scoring
1 day, 4:08:09.600368 INFO: Finished candidate processing
1 day, 4:08:09.600473 INFO: Collecting candidate features
1 day, 4:08:09.653139 INFO: Collecting fragment features
1 day, 4:08:09.668453 INFO: Finished candidate scoring
1 day, 4:08:09.684539 INFO: performing precursor FDR with 47 features
1 day, 4:08:09.684651 INFO: Decoy channel: -1
1 day, 4:08:09.684678 INFO: Competetive: True
1 day, 4:08:09.692492 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:08:09.697335 INFO: Using random state 397438 for train-test-split
1 day, 4:08:09.838840 INFO: Test AUC: 0.679
1 day, 4:08:09.838952 INFO: Train AUC: 0.679
1 day, 4:08:09.838983 INFO: AUC difference: 0.06%
1 day, 4:08:10.066019 INFO: Resetting torch num_threads to 80
1 day, 4:08:10.069353 PROGRESS: === Extracted 16923 precursors and 192072 fragments ===
1 day, 4:08:10.069893 INFO: === FDR correction performed with classifier version 5 ===
1 day, 4:08:10.070769 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:08:10.070862 PROGRESS: Total precursors accumulated: 3,000
1 day, 4:08:10.070921 PROGRESS: Target precursors: 2,583 (86.10%)
1 day, 4:08:10.070970 PROGRESS: Decoy precursors: 417 (13.90%)
1 day, 4:08:10.071019 PROGRESS: 
1 day, 4:08:10.071063 PROGRESS: Precursor Summary:
1 day, 4:08:10.072387 PROGRESS: Channel   0:	 0.050 FDR: 2,095; 0.010 FDR:   869; 0.001 FDR:   431
1 day, 4:08:10.072481 PROGRESS: 
1 day, 4:08:10.072536 PROGRESS: Protein Summary:
1 day, 4:08:10.074154 PROGRESS: Channel   0:	 0.050 FDR: 1,604; 0.010 FDR:   729; 0.001 FDR:   383
1 day, 4:08:10.074251 PROGRESS: =========================================================================
1 day, 4:08:10.074469 INFO: Target number of precursors reached.
1 day, 4:08:10.094890 INFO: fragments_df: keeping 5000 of 192072 [sum(precursor_idx_mask)=28273 sum(mass_error_mask)=192072 stop_rank=5000
1 day, 4:08:10.110193 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:10.439270 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:10.736419 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:10.911194 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:11.602320 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:08:11.602793 INFO: Using score_cutoff 53.109115727233885 (fac=0.99, q=1)
1 day, 4:08:11.603149 INFO: Updating optimization_manager: fwhm_rt             : 3.0377986431121826 -> 3.0693764686584473
1 day, 4:08:11.603236 INFO: Updating optimization_manager: fwhm_mobility       : 0.010767740197479725 -> 0.0107954116538167
1 day, 4:08:11.603295 INFO: Updating optimization_manager: score_cutoff        : 51.76955075454712 -> 53.109115727233885
1 day, 4:08:11.603352 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:11.604701 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:11.606788 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:11.607965 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:11.613626 INFO: === checking if optimization conditions were reached ===
1 day, 4:08:11.615270 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 4:08:11.615378 INFO: Updating optimization_manager: classifier_version  : 5 -> 8
1 day, 4:08:11.615446 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:08:11.616478 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 4:08:11.616575 INFO: Updating optimization_manager: classifier_version  : 8 -> 8
1 day, 4:08:11.616641 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:08:11.616701 INFO: ==============================================
1 day, 4:08:11.616771 INFO: Starting optimization step 9.
1 day, 4:08:11.616833 PROGRESS: === Extracting elution groups 0 to 1400 ===
1 day, 4:08:11.616893 INFO: Using classic extraction backend
1 day, 4:08:11.617126 PROGRESS: Extracting batch of 2787 precursors
1 day, 4:08:11.617203 INFO: === Search parameters used ===
1 day, 4:08:11.617254 INFO: rt_error       : 2099.894844
1 day, 4:08:11.617300 INFO: mobility_error : 0.1
1 day, 4:08:11.617345 INFO: num_candidates : 3
1 day, 4:08:11.617389 INFO: ms1_error      : 15.0
1 day, 4:08:11.617432 INFO: ms2_error      : 15.0
1 day, 4:08:11.617475 INFO: fwhm_rt        : 3.0693764686584473
1 day, 4:08:11.617518 INFO: quant_window   : 3
1 day, 4:08:11.617559 INFO: ==============================================
1 day, 4:08:11.620386 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:08:11.620438 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:08:11.620477 INFO: FWHM in RT is 3.07 seconds, sigma is 0.67
1 day, 4:08:11.620501 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.01
1 day, 4:08:11.632989 INFO: Starting candidate selection
1 day, 4:08:33.722038 INFO: Starting candidate scoring
1 day, 4:08:34.187884 INFO: Finished candidate processing
1 day, 4:08:34.188081 INFO: Collecting candidate features
1 day, 4:08:34.240105 INFO: Collecting fragment features
1 day, 4:08:34.253879 INFO: Finished candidate scoring
1 day, 4:08:34.259795 INFO: performing precursor FDR with 47 features
1 day, 4:08:34.259893 INFO: Decoy channel: -1
1 day, 4:08:34.259932 INFO: Competetive: True
1 day, 4:08:34.267462 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:08:34.271253 INFO: Using random state 84622 for train-test-split
1 day, 4:08:34.292867 INFO: Test AUC: 0.693
1 day, 4:08:34.292984 INFO: Train AUC: 0.712
1 day, 4:08:34.293015 INFO: AUC difference: 2.68%
1 day, 4:08:34.527714 INFO: Resetting torch num_threads to 80
1 day, 4:08:34.528605 PROGRESS: === Extracted 7929 precursors and 87960 fragments ===
1 day, 4:08:34.529271 INFO: === FDR correction performed with classifier version 8 ===
1 day, 4:08:34.529998 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:08:34.530101 PROGRESS: Total precursors accumulated: 1,400
1 day, 4:08:34.530173 PROGRESS: Target precursors: 1,272 (90.86%)
1 day, 4:08:34.530228 PROGRESS: Decoy precursors: 128 (9.14%)
1 day, 4:08:34.530283 PROGRESS: 
1 day, 4:08:34.530328 PROGRESS: Precursor Summary:
1 day, 4:08:34.531546 PROGRESS: Channel   0:	 0.050 FDR: 1,195; 0.010 FDR:   776; 0.001 FDR:    67
1 day, 4:08:34.531645 PROGRESS: 
1 day, 4:08:34.531704 PROGRESS: Protein Summary:
1 day, 4:08:34.533133 PROGRESS: Channel   0:	 0.050 FDR: 1,020; 0.010 FDR:   685; 0.001 FDR:    65
1 day, 4:08:34.533236 PROGRESS: =========================================================================
1 day, 4:08:34.535048 INFO: Target number of precursors reached.
1 day, 4:08:34.548199 INFO: fragments_df: keeping 5000 of 87960 [sum(precursor_idx_mask)=24521 sum(mass_error_mask)=87960 stop_rank=5000
1 day, 4:08:34.558779 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:34.698341 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:34.843286 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:34.975874 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:35.595703 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:08:35.596249 INFO: Using score_cutoff 46.0266585445404 (fac=0.99, q=1)
1 day, 4:08:35.596660 INFO: Updating optimization_manager: fwhm_rt             : 3.0693764686584473 -> 2.900667190551758
1 day, 4:08:35.596745 INFO: Updating optimization_manager: fwhm_mobility       : 0.0107954116538167 -> 0.009192167781293392
1 day, 4:08:35.596807 INFO: Updating optimization_manager: score_cutoff        : 53.109115727233885 -> 46.0266585445404
1 day, 4:08:35.596880 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:35.598112 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:35.599439 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:35.600231 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:35.602414 INFO: === checking if optimization conditions were reached ===
1 day, 4:08:35.604066 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 4:08:35.604178 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1 day, 4:08:35.604244 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 4:08:35.605249 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 4:08:35.605348 INFO: Updating optimization_manager: classifier_version  : 9 -> 9
1 day, 4:08:35.605410 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 4:08:35.605465 INFO: ==============================================
1 day, 4:08:35.605542 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 4:08:35.610402 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:35.611238 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:35.612491 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:35.613252 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:35.615386 INFO: Starting optimization step 0.
1 day, 4:08:35.615487 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:08:35.615565 INFO: Using classic extraction backend
1 day, 4:08:35.615749 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:08:35.615827 INFO: === Search parameters used ===
1 day, 4:08:35.615879 INFO: rt_error       : 2099.894844
1 day, 4:08:35.615923 INFO: mobility_error : 0.1
1 day, 4:08:35.615967 INFO: num_candidates : 3
1 day, 4:08:35.616008 INFO: ms1_error      : 15.0
1 day, 4:08:35.616048 INFO: ms2_error      : 15.0
1 day, 4:08:35.616092 INFO: fwhm_rt        : 2.900667190551758
1 day, 4:08:35.616133 INFO: quant_window   : 3
1 day, 4:08:35.616174 INFO: ==============================================
1 day, 4:08:35.617244 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:08:35.617290 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:08:35.617345 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 4:08:35.617368 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.26
1 day, 4:08:35.618135 INFO: Starting candidate selection
1 day, 4:08:46.114918 INFO: Starting candidate scoring
1 day, 4:08:46.387236 INFO: Finished candidate processing
1 day, 4:08:46.387417 INFO: Collecting candidate features
1 day, 4:08:46.401446 INFO: Collecting fragment features
1 day, 4:08:46.405874 INFO: Finished candidate scoring
1 day, 4:08:46.407711 INFO: performing precursor FDR with 47 features
1 day, 4:08:46.407754 INFO: Decoy channel: -1
1 day, 4:08:46.407778 INFO: Competetive: True
1 day, 4:08:46.411035 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:08:46.413982 INFO: Using random state 186908 for train-test-split
1 day, 4:08:46.424780 INFO: Test AUC: 0.712
1 day, 4:08:46.424839 INFO: Train AUC: 0.708
1 day, 4:08:46.424868 INFO: AUC difference: 0.53%
1 day, 4:08:46.641868 INFO: Resetting torch num_threads to 80
1 day, 4:08:46.642409 PROGRESS: === Extracted 3373 precursors and 37434 fragments ===
1 day, 4:08:46.642823 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:08:46.643394 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:08:46.643480 PROGRESS: Total precursors accumulated: 600
1 day, 4:08:46.643537 PROGRESS: Target precursors: 547 (91.17%)
1 day, 4:08:46.643586 PROGRESS: Decoy precursors: 53 (8.83%)
1 day, 4:08:46.643629 PROGRESS: 
1 day, 4:08:46.643672 PROGRESS: Precursor Summary:
1 day, 4:08:46.644650 PROGRESS: Channel   0:	 0.050 FDR:   513; 0.010 FDR:   410; 0.001 FDR:    47
1 day, 4:08:46.644737 PROGRESS: 
1 day, 4:08:46.644791 PROGRESS: Protein Summary:
1 day, 4:08:46.645909 PROGRESS: Channel   0:	 0.050 FDR:   472; 0.010 FDR:   385; 0.001 FDR:    46
1 day, 4:08:46.645998 PROGRESS: =========================================================================
1 day, 4:08:46.646225 INFO: Target number of precursors reached.
1 day, 4:08:46.652310 INFO: fragments_df: keeping 5000 of 37434 [sum(precursor_idx_mask)=13009 sum(mass_error_mask)=37434 stop_rank=5000
1 day, 4:08:46.657566 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:46.773264 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:46.877427 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:46.989713 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:47.634825 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:08:47.635257 INFO: Using score_cutoff 44.135918481445316 (fac=0.99, q=1)
1 day, 4:08:47.635566 INFO: Updating optimization_manager: fwhm_rt             : 2.900667190551758 -> 2.9002342224121094
1 day, 4:08:47.635646 INFO: Updating optimization_manager: fwhm_mobility       : 0.009192167781293392 -> 0.00888922531157732
1 day, 4:08:47.635700 INFO: Updating optimization_manager: score_cutoff        : 46.0266585445404 -> 44.135918481445316
1 day, 4:08:47.635751 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:47.636833 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:47.638111 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:47.638878 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:47.641026 INFO: === checking if optimization conditions were reached ===
1 day, 4:08:47.641137 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:08:47.642715 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 17.258319797101567
1 day, 4:08:47.642823 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 17.2583.
1 day, 4:08:47.642888 INFO: ==============================================
1 day, 4:08:47.642954 INFO: Starting optimization step 1.
1 day, 4:08:47.643014 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:08:47.643069 INFO: Using classic extraction backend
1 day, 4:08:47.643191 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:08:47.643256 INFO: === Search parameters used ===
1 day, 4:08:47.643307 INFO: rt_error       : 17.258319797101567
1 day, 4:08:47.643350 INFO: mobility_error : 0.1
1 day, 4:08:47.643390 INFO: num_candidates : 3
1 day, 4:08:47.643429 INFO: ms1_error      : 15.0
1 day, 4:08:47.643467 INFO: ms2_error      : 15.0
1 day, 4:08:47.643506 INFO: fwhm_rt        : 2.9002342224121094
1 day, 4:08:47.643545 INFO: quant_window   : 3
1 day, 4:08:47.643583 INFO: ==============================================
1 day, 4:08:47.644767 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:08:47.644811 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:08:47.644845 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 4:08:47.644867 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 4:08:47.645559 INFO: Starting candidate selection
1 day, 4:08:48.169084 INFO: Starting candidate scoring
1 day, 4:08:48.375522 INFO: Finished candidate processing
1 day, 4:08:48.375678 INFO: Collecting candidate features
1 day, 4:08:48.414531 INFO: Collecting fragment features
1 day, 4:08:48.426897 INFO: Finished candidate scoring
1 day, 4:08:48.429409 INFO: performing precursor FDR with 47 features
1 day, 4:08:48.429478 INFO: Decoy channel: -1
1 day, 4:08:48.429518 INFO: Competetive: True
1 day, 4:08:48.435108 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:08:48.438423 INFO: Using random state 186908 for train-test-split
1 day, 4:08:48.455407 INFO: Test AUC: 0.751
1 day, 4:08:48.455469 INFO: Train AUC: 0.777
1 day, 4:08:48.455497 INFO: AUC difference: 3.29%
1 day, 4:08:48.673826 INFO: Resetting torch num_threads to 80
1 day, 4:08:48.674349 PROGRESS: === Extracted 3386 precursors and 35975 fragments ===
1 day, 4:08:48.674771 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:08:48.675340 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:08:48.675428 PROGRESS: Total precursors accumulated: 600
1 day, 4:08:48.675487 PROGRESS: Target precursors: 588 (98.00%)
1 day, 4:08:48.675537 PROGRESS: Decoy precursors: 12 (2.00%)
1 day, 4:08:48.675583 PROGRESS: 
1 day, 4:08:48.675627 PROGRESS: Precursor Summary:
1 day, 4:08:48.676647 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   545; 0.001 FDR:   289
1 day, 4:08:48.676739 PROGRESS: 
1 day, 4:08:48.676798 PROGRESS: Protein Summary:
1 day, 4:08:48.678011 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   502; 0.001 FDR:   277
1 day, 4:08:48.678117 PROGRESS: =========================================================================
1 day, 4:08:48.678264 INFO: Target number of precursors reached.
1 day, 4:08:48.685341 INFO: fragments_df: keeping 5000 of 35975 [sum(precursor_idx_mask)=16806 sum(mass_error_mask)=35975 stop_rank=5000
1 day, 4:08:48.692420 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:48.836179 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:48.976006 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:49.136487 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:49.844115 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:08:49.844546 INFO: Using score_cutoff 37.60764207000733 (fac=0.99, q=1)
1 day, 4:08:49.844858 INFO: Updating optimization_manager: fwhm_rt             : 2.9002342224121094 -> 2.871316909790039
1 day, 4:08:49.844940 INFO: Updating optimization_manager: fwhm_mobility       : 0.00888922531157732 -> 0.008248520083725452
1 day, 4:08:49.844993 INFO: Updating optimization_manager: score_cutoff        : 44.135918481445316 -> 37.60764207000733
1 day, 4:08:49.845047 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:49.846168 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:49.847444 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:49.848204 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:49.853988 INFO: === checking if optimization conditions were reached ===
1 day, 4:08:49.854104 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:08:49.855821 INFO: Updating optimization_manager: rt_error            : 17.258319797101567 -> 13.474611461823915
1 day, 4:08:49.855922 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 13.4746.
1 day, 4:08:49.855989 INFO: ==============================================
1 day, 4:08:49.856059 INFO: Starting optimization step 2.
1 day, 4:08:49.856116 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:08:49.856172 INFO: Using classic extraction backend
1 day, 4:08:49.856323 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:08:49.856391 INFO: === Search parameters used ===
1 day, 4:08:49.856439 INFO: rt_error       : 13.474611461823915
1 day, 4:08:49.856639 INFO: mobility_error : 0.1
1 day, 4:08:49.856688 INFO: num_candidates : 3
1 day, 4:08:49.856730 INFO: ms1_error      : 15.0
1 day, 4:08:49.856771 INFO: ms2_error      : 15.0
1 day, 4:08:49.856810 INFO: fwhm_rt        : 2.871316909790039
1 day, 4:08:49.856850 INFO: quant_window   : 3
1 day, 4:08:49.856889 INFO: ==============================================
1 day, 4:08:49.857914 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:08:49.857959 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:08:49.857993 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 4:08:49.858014 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
1 day, 4:08:49.858770 INFO: Starting candidate selection
1 day, 4:08:50.384247 INFO: Starting candidate scoring
1 day, 4:08:50.594102 INFO: Finished candidate processing
1 day, 4:08:50.594238 INFO: Collecting candidate features
1 day, 4:08:50.609366 INFO: Collecting fragment features
1 day, 4:08:50.614246 INFO: Finished candidate scoring
1 day, 4:08:50.616224 INFO: performing precursor FDR with 47 features
1 day, 4:08:50.616274 INFO: Decoy channel: -1
1 day, 4:08:50.616298 INFO: Competetive: True
1 day, 4:08:50.619784 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:08:50.621993 INFO: Using random state 186908 for train-test-split
1 day, 4:08:50.635006 INFO: Test AUC: 0.777
1 day, 4:08:50.635088 INFO: Train AUC: 0.787
1 day, 4:08:50.635119 INFO: AUC difference: 1.24%
1 day, 4:08:50.853225 INFO: Resetting torch num_threads to 80
1 day, 4:08:50.853781 PROGRESS: === Extracted 3383 precursors and 35690 fragments ===
1 day, 4:08:50.854195 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:08:50.854810 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:08:50.854897 PROGRESS: Total precursors accumulated: 600
1 day, 4:08:50.854955 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:08:50.855011 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:08:50.855057 PROGRESS: 
1 day, 4:08:50.855098 PROGRESS: Precursor Summary:
1 day, 4:08:50.856128 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   561; 0.001 FDR:   290
1 day, 4:08:50.856215 PROGRESS: 
1 day, 4:08:50.856268 PROGRESS: Protein Summary:
1 day, 4:08:50.857492 PROGRESS: Channel   0:	 0.050 FDR:   539; 0.010 FDR:   516; 0.001 FDR:   278
1 day, 4:08:50.857581 PROGRESS: =========================================================================
1 day, 4:08:50.857714 INFO: Target number of precursors reached.
1 day, 4:08:50.864797 INFO: fragments_df: keeping 5000 of 35690 [sum(precursor_idx_mask)=17213 sum(mass_error_mask)=35690 stop_rank=5000
1 day, 4:08:50.870116 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:51.008090 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:51.150013 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:51.293815 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:52.005570 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:08:52.006033 INFO: Using score_cutoff 37.23848231506347 (fac=0.99, q=1)
1 day, 4:08:52.006365 INFO: Updating optimization_manager: fwhm_rt             : 2.871316909790039 -> 2.8616557121276855
1 day, 4:08:52.006457 INFO: Updating optimization_manager: fwhm_mobility       : 0.008248520083725452 -> 0.00817367434501648
1 day, 4:08:52.006512 INFO: Updating optimization_manager: score_cutoff        : 37.60764207000733 -> 37.23848231506347
1 day, 4:08:52.006574 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:52.007715 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:52.009010 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:52.009781 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:52.012710 INFO: === checking if optimization conditions were reached ===
1 day, 4:08:52.012815 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:08:52.014706 INFO: Updating optimization_manager: rt_error            : 13.474611461823915 -> 12.329490998542347
1 day, 4:08:52.014807 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 12.3295.
1 day, 4:08:52.014871 INFO: ==============================================
1 day, 4:08:52.014939 INFO: Starting optimization step 3.
1 day, 4:08:52.015007 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:08:52.015073 INFO: Using classic extraction backend
1 day, 4:08:52.015195 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:08:52.015262 INFO: === Search parameters used ===
1 day, 4:08:52.015309 INFO: rt_error       : 12.329490998542347
1 day, 4:08:52.015350 INFO: mobility_error : 0.1
1 day, 4:08:52.015390 INFO: num_candidates : 3
1 day, 4:08:52.015431 INFO: ms1_error      : 15.0
1 day, 4:08:52.015471 INFO: ms2_error      : 15.0
1 day, 4:08:52.015509 INFO: fwhm_rt        : 2.8616557121276855
1 day, 4:08:52.015553 INFO: quant_window   : 3
1 day, 4:08:52.015594 INFO: ==============================================
1 day, 4:08:52.017346 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:08:52.017392 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:08:52.017426 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 4:08:52.017447 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:08:52.018191 INFO: Starting candidate selection
1 day, 4:08:52.558578 INFO: Starting candidate scoring
1 day, 4:08:52.776328 INFO: Finished candidate processing
1 day, 4:08:52.776442 INFO: Collecting candidate features
1 day, 4:08:52.791514 INFO: Collecting fragment features
1 day, 4:08:52.796551 INFO: Finished candidate scoring
1 day, 4:08:52.799800 INFO: performing precursor FDR with 47 features
1 day, 4:08:52.799846 INFO: Decoy channel: -1
1 day, 4:08:52.799869 INFO: Competetive: True
1 day, 4:08:52.803244 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:08:52.805424 INFO: Using random state 186908 for train-test-split
1 day, 4:08:52.817108 INFO: Test AUC: 0.753
1 day, 4:08:52.817168 INFO: Train AUC: 0.789
1 day, 4:08:52.817196 INFO: AUC difference: 4.55%
1 day, 4:08:53.040803 INFO: Resetting torch num_threads to 80
1 day, 4:08:53.041909 PROGRESS: === Extracted 3373 precursors and 35546 fragments ===
1 day, 4:08:53.042770 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:08:53.043498 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:08:53.043593 PROGRESS: Total precursors accumulated: 600
1 day, 4:08:53.043655 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:08:53.043706 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:08:53.043750 PROGRESS: 
1 day, 4:08:53.043792 PROGRESS: Precursor Summary:
1 day, 4:08:53.044874 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   561; 0.001 FDR:   289
1 day, 4:08:53.044960 PROGRESS: 
1 day, 4:08:53.045016 PROGRESS: Protein Summary:
1 day, 4:08:53.046335 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   518; 0.001 FDR:   277
1 day, 4:08:53.046430 PROGRESS: =========================================================================
1 day, 4:08:53.046663 INFO: Target number of precursors reached.
1 day, 4:08:53.054195 INFO: fragments_df: keeping 5000 of 35546 [sum(precursor_idx_mask)=17204 sum(mass_error_mask)=35546 stop_rank=5000
1 day, 4:08:53.060094 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:53.184357 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:53.305677 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:53.429698 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:54.064144 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:08:54.064699 INFO: Using score_cutoff 37.08649353790283 (fac=0.99, q=1)
1 day, 4:08:54.065130 INFO: Updating optimization_manager: fwhm_rt             : 2.8616557121276855 -> 2.8513996601104736
1 day, 4:08:54.065224 INFO: Updating optimization_manager: fwhm_mobility       : 0.00817367434501648 -> 0.008155543357133865
1 day, 4:08:54.065282 INFO: Updating optimization_manager: score_cutoff        : 37.23848231506347 -> 37.08649353790283
1 day, 4:08:54.065356 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:54.066679 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:54.067982 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:54.068757 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:54.071050 INFO: === checking if optimization conditions were reached ===
1 day, 4:08:54.071177 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 4:08:54.073257 INFO: Updating optimization_manager: rt_error            : 12.329490998542347 -> 13.826540692800135
1 day, 4:08:54.073367 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 13.8265.
1 day, 4:08:54.073436 INFO: ==============================================
1 day, 4:08:54.073530 INFO: Starting optimization step 4.
1 day, 4:08:54.073598 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:08:54.073689 INFO: Using classic extraction backend
1 day, 4:08:54.073920 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:08:54.074012 INFO: === Search parameters used ===
1 day, 4:08:54.074082 INFO: rt_error       : 13.826540692800135
1 day, 4:08:54.074130 INFO: mobility_error : 0.1
1 day, 4:08:54.074174 INFO: num_candidates : 3
1 day, 4:08:54.074216 INFO: ms1_error      : 15.0
1 day, 4:08:54.074256 INFO: ms2_error      : 15.0
1 day, 4:08:54.074298 INFO: fwhm_rt        : 2.8513996601104736
1 day, 4:08:54.074341 INFO: quant_window   : 3
1 day, 4:08:54.074383 INFO: ==============================================
1 day, 4:08:54.075748 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:08:54.075794 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:08:54.075857 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:08:54.075881 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.78
1 day, 4:08:54.076714 INFO: Starting candidate selection
1 day, 4:08:54.596190 INFO: Starting candidate scoring
1 day, 4:08:54.811222 INFO: Finished candidate processing
1 day, 4:08:54.811319 INFO: Collecting candidate features
1 day, 4:08:54.825981 INFO: Collecting fragment features
1 day, 4:08:54.832767 INFO: Finished candidate scoring
1 day, 4:08:54.835040 INFO: performing precursor FDR with 47 features
1 day, 4:08:54.835089 INFO: Decoy channel: -1
1 day, 4:08:54.835114 INFO: Competetive: True
1 day, 4:08:54.839397 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:08:54.841852 INFO: Using random state 186908 for train-test-split
1 day, 4:08:54.854386 INFO: Test AUC: 0.770
1 day, 4:08:54.854455 INFO: Train AUC: 0.788
1 day, 4:08:54.854485 INFO: AUC difference: 2.36%
1 day, 4:08:55.072572 INFO: Resetting torch num_threads to 80
1 day, 4:08:55.073260 PROGRESS: === Extracted 3383 precursors and 35669 fragments ===
1 day, 4:08:55.073764 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:08:55.074451 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:08:55.074546 PROGRESS: Total precursors accumulated: 600
1 day, 4:08:55.074606 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:08:55.074658 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:08:55.074704 PROGRESS: 
1 day, 4:08:55.074749 PROGRESS: Precursor Summary:
1 day, 4:08:55.075822 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   562; 0.001 FDR:   284
1 day, 4:08:55.075916 PROGRESS: 
1 day, 4:08:55.075991 PROGRESS: Protein Summary:
1 day, 4:08:55.077237 PROGRESS: Channel   0:	 0.050 FDR:   539; 0.010 FDR:   518; 0.001 FDR:   273
1 day, 4:08:55.077347 PROGRESS: =========================================================================
1 day, 4:08:55.077516 INFO: Target number of precursors reached.
1 day, 4:08:55.084379 INFO: fragments_df: keeping 5000 of 35669 [sum(precursor_idx_mask)=17248 sum(mass_error_mask)=35669 stop_rank=5000
1 day, 4:08:55.089600 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:58.208960 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:58.328430 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:58.453280 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:59.078221 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:08:59.078758 INFO: Using score_cutoff 36.83313939399719 (fac=0.99, q=1)
1 day, 4:08:59.079093 INFO: Updating optimization_manager: fwhm_rt             : 2.8513996601104736 -> 2.844001293182373
1 day, 4:08:59.079176 INFO: Updating optimization_manager: fwhm_mobility       : 0.008155543357133865 -> 0.008178280666470528
1 day, 4:08:59.079231 INFO: Updating optimization_manager: score_cutoff        : 37.08649353790283 -> 36.83313939399719
1 day, 4:08:59.079285 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:08:59.080533 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:08:59.081899 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:08:59.082707 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:08:59.084940 INFO: === checking if optimization conditions were reached ===
1 day, 4:08:59.085040 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 4:08:59.086967 INFO: Updating optimization_manager: rt_error            : 13.826540692800135 -> 12.333565442136829
1 day, 4:08:59.087134 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 12.3336.
1 day, 4:08:59.087212 INFO: ==============================================
1 day, 4:08:59.087281 INFO: Starting optimization step 5.
1 day, 4:08:59.087342 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:08:59.087397 INFO: Using classic extraction backend
1 day, 4:08:59.087519 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:08:59.087583 INFO: === Search parameters used ===
1 day, 4:08:59.087632 INFO: rt_error       : 12.333565442136829
1 day, 4:08:59.087675 INFO: mobility_error : 0.1
1 day, 4:08:59.087718 INFO: num_candidates : 3
1 day, 4:08:59.087759 INFO: ms1_error      : 15.0
1 day, 4:08:59.087801 INFO: ms2_error      : 15.0
1 day, 4:08:59.087841 INFO: fwhm_rt        : 2.844001293182373
1 day, 4:08:59.087883 INFO: quant_window   : 3
1 day, 4:08:59.087921 INFO: ==============================================
1 day, 4:08:59.088850 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:08:59.088898 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:08:59.088934 INFO: FWHM in RT is 2.84 seconds, sigma is 0.63
1 day, 4:08:59.088960 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:08:59.089668 INFO: Starting candidate selection
1 day, 4:08:59.615089 INFO: Starting candidate scoring
1 day, 4:08:59.830370 INFO: Finished candidate processing
1 day, 4:08:59.830471 INFO: Collecting candidate features
1 day, 4:08:59.845111 INFO: Collecting fragment features
1 day, 4:08:59.849607 INFO: Finished candidate scoring
1 day, 4:08:59.853281 INFO: performing precursor FDR with 47 features
1 day, 4:08:59.853332 INFO: Decoy channel: -1
1 day, 4:08:59.853356 INFO: Competetive: True
1 day, 4:08:59.857006 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:08:59.859416 INFO: Using random state 186908 for train-test-split
1 day, 4:08:59.873027 INFO: Test AUC: 0.777
1 day, 4:08:59.873095 INFO: Train AUC: 0.786
1 day, 4:08:59.873125 INFO: AUC difference: 1.09%
1 day, 4:09:00.093144 INFO: Resetting torch num_threads to 80
1 day, 4:09:00.093879 PROGRESS: === Extracted 3378 precursors and 35614 fragments ===
1 day, 4:09:00.094406 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:00.095207 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:00.095300 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:00.095362 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:09:00.095414 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:00.095468 PROGRESS: 
1 day, 4:09:00.095515 PROGRESS: Precursor Summary:
1 day, 4:09:00.096606 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   560; 0.001 FDR:   283
1 day, 4:09:00.096712 PROGRESS: 
1 day, 4:09:00.096771 PROGRESS: Protein Summary:
1 day, 4:09:00.098096 PROGRESS: Channel   0:	 0.050 FDR:   542; 0.010 FDR:   518; 0.001 FDR:   271
1 day, 4:09:00.098192 PROGRESS: =========================================================================
1 day, 4:09:00.098353 INFO: Target number of precursors reached.
1 day, 4:09:00.105595 INFO: fragments_df: keeping 5000 of 35614 [sum(precursor_idx_mask)=17182 sum(mass_error_mask)=35614 stop_rank=5000
1 day, 4:09:00.111069 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:00.230140 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:00.354665 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:00.477653 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:01.099418 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:01.099953 INFO: Using score_cutoff 36.50350286178589 (fac=0.99, q=1)
1 day, 4:09:01.100293 INFO: Updating optimization_manager: fwhm_rt             : 2.844001293182373 -> 2.844365119934082
1 day, 4:09:01.100375 INFO: Updating optimization_manager: fwhm_mobility       : 0.008178280666470528 -> 0.008155358955264091
1 day, 4:09:01.100429 INFO: Updating optimization_manager: score_cutoff        : 36.83313939399719 -> 36.50350286178589
1 day, 4:09:01.100486 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:01.101730 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:01.103150 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:01.103959 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:01.106112 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:01.106215 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 4:09:01.108105 INFO: Updating optimization_manager: rt_error            : 12.333565442136829 -> 13.81002614047565
1 day, 4:09:01.108210 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 13.8100.
1 day, 4:09:01.108278 INFO: ==============================================
1 day, 4:09:01.108344 INFO: Starting optimization step 6.
1 day, 4:09:01.108406 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:01.108464 INFO: Using classic extraction backend
1 day, 4:09:01.108588 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:01.108653 INFO: === Search parameters used ===
1 day, 4:09:01.108702 INFO: rt_error       : 13.81002614047565
1 day, 4:09:01.108747 INFO: mobility_error : 0.1
1 day, 4:09:01.108789 INFO: num_candidates : 3
1 day, 4:09:01.108830 INFO: ms1_error      : 15.0
1 day, 4:09:01.108871 INFO: ms2_error      : 15.0
1 day, 4:09:01.108912 INFO: fwhm_rt        : 2.844365119934082
1 day, 4:09:01.108953 INFO: quant_window   : 3
1 day, 4:09:01.108991 INFO: ==============================================
1 day, 4:09:01.109908 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:01.109956 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:01.109991 INFO: FWHM in RT is 2.84 seconds, sigma is 0.63
1 day, 4:09:01.110014 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.78
1 day, 4:09:01.110691 INFO: Starting candidate selection
1 day, 4:09:01.642554 INFO: Starting candidate scoring
1 day, 4:09:01.847260 INFO: Finished candidate processing
1 day, 4:09:01.847360 INFO: Collecting candidate features
1 day, 4:09:01.862326 INFO: Collecting fragment features
1 day, 4:09:01.866382 INFO: Finished candidate scoring
1 day, 4:09:01.869627 INFO: performing precursor FDR with 47 features
1 day, 4:09:01.869672 INFO: Decoy channel: -1
1 day, 4:09:01.869696 INFO: Competetive: True
1 day, 4:09:01.873278 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:01.875599 INFO: Using random state 186908 for train-test-split
1 day, 4:09:01.887774 INFO: Test AUC: 0.772
1 day, 4:09:01.887841 INFO: Train AUC: 0.785
1 day, 4:09:01.887871 INFO: AUC difference: 1.66%
1 day, 4:09:02.106585 INFO: Resetting torch num_threads to 80
1 day, 4:09:02.107684 PROGRESS: === Extracted 3380 precursors and 35651 fragments ===
1 day, 4:09:02.108188 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:02.108962 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:02.109055 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:02.109118 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:09:02.109169 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:09:02.109213 PROGRESS: 
1 day, 4:09:02.109257 PROGRESS: Precursor Summary:
1 day, 4:09:02.110360 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   560; 0.001 FDR:   281
1 day, 4:09:02.110471 PROGRESS: 
1 day, 4:09:02.110528 PROGRESS: Protein Summary:
1 day, 4:09:02.111800 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   517; 0.001 FDR:   270
1 day, 4:09:02.111896 PROGRESS: =========================================================================
1 day, 4:09:02.112059 INFO: Target number of precursors reached.
1 day, 4:09:02.119267 INFO: fragments_df: keeping 5000 of 35651 [sum(precursor_idx_mask)=17188 sum(mass_error_mask)=35651 stop_rank=5000
1 day, 4:09:02.124660 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:02.245425 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:02.363483 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:02.490486 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:03.113019 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:03.113584 INFO: Using score_cutoff 36.465225447463986 (fac=0.99, q=1)
1 day, 4:09:03.113941 INFO: Updating optimization_manager: fwhm_rt             : 2.844365119934082 -> 2.851511001586914
1 day, 4:09:03.114024 INFO: Updating optimization_manager: fwhm_mobility       : 0.008155358955264091 -> 0.008168540894985199
1 day, 4:09:03.114097 INFO: Updating optimization_manager: score_cutoff        : 36.50350286178589 -> 36.465225447463986
1 day, 4:09:03.114153 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:03.115413 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:03.116767 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:03.117569 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:03.119951 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:03.120059 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 4:09:03.121992 INFO: Updating optimization_manager: rt_error            : 13.81002614047565 -> 12.279386746341178
1 day, 4:09:03.122108 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 12.2794.
1 day, 4:09:03.122178 INFO: ==============================================
1 day, 4:09:03.122245 INFO: Starting optimization step 7.
1 day, 4:09:03.122305 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:03.122362 INFO: Using classic extraction backend
1 day, 4:09:03.122485 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:03.122551 INFO: === Search parameters used ===
1 day, 4:09:03.122601 INFO: rt_error       : 12.279386746341178
1 day, 4:09:03.122655 INFO: mobility_error : 0.1
1 day, 4:09:03.122701 INFO: num_candidates : 3
1 day, 4:09:03.122742 INFO: ms1_error      : 15.0
1 day, 4:09:03.122782 INFO: ms2_error      : 15.0
1 day, 4:09:03.122828 INFO: fwhm_rt        : 2.851511001586914
1 day, 4:09:03.122868 INFO: quant_window   : 3
1 day, 4:09:03.122908 INFO: ==============================================
1 day, 4:09:03.123873 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:03.123920 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:03.123954 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:03.123977 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:09:03.124824 INFO: Starting candidate selection
1 day, 4:09:03.657221 INFO: Starting candidate scoring
1 day, 4:09:03.917235 INFO: Finished candidate processing
1 day, 4:09:03.917395 INFO: Collecting candidate features
1 day, 4:09:03.932204 INFO: Collecting fragment features
1 day, 4:09:03.936363 INFO: Finished candidate scoring
1 day, 4:09:03.939258 INFO: performing precursor FDR with 47 features
1 day, 4:09:03.939309 INFO: Decoy channel: -1
1 day, 4:09:03.939334 INFO: Competetive: True
1 day, 4:09:03.943048 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:03.945469 INFO: Using random state 186908 for train-test-split
1 day, 4:09:03.959452 INFO: Test AUC: 0.796
1 day, 4:09:03.959527 INFO: Train AUC: 0.781
1 day, 4:09:03.959557 INFO: AUC difference: 1.87%
1 day, 4:09:04.185485 INFO: Resetting torch num_threads to 80
1 day, 4:09:04.186228 PROGRESS: === Extracted 3374 precursors and 35566 fragments ===
1 day, 4:09:04.186744 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:04.187397 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:04.187485 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:04.187550 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:09:04.187605 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:04.187655 PROGRESS: 
1 day, 4:09:04.187711 PROGRESS: Precursor Summary:
1 day, 4:09:04.188823 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   561; 0.001 FDR:   281
1 day, 4:09:04.188913 PROGRESS: 
1 day, 4:09:04.188983 PROGRESS: Protein Summary:
1 day, 4:09:04.190319 PROGRESS: Channel   0:	 0.050 FDR:   542; 0.010 FDR:   519; 0.001 FDR:   270
1 day, 4:09:04.190417 PROGRESS: =========================================================================
1 day, 4:09:04.190606 INFO: Target number of precursors reached.
1 day, 4:09:04.197798 INFO: fragments_df: keeping 5000 of 35566 [sum(precursor_idx_mask)=17202 sum(mass_error_mask)=35566 stop_rank=5000
1 day, 4:09:04.203238 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:04.323562 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:04.448353 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:04.572142 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:05.196205 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:05.196746 INFO: Using score_cutoff 36.50858541870117 (fac=0.99, q=1)
1 day, 4:09:05.197077 INFO: Updating optimization_manager: fwhm_rt             : 2.851511001586914 -> 2.8496592044830322
1 day, 4:09:05.197159 INFO: Updating optimization_manager: fwhm_mobility       : 0.008168540894985199 -> 0.008155543357133865
1 day, 4:09:05.197214 INFO: Updating optimization_manager: score_cutoff        : 36.465225447463986 -> 36.50858541870117
1 day, 4:09:05.197271 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:05.198526 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:05.199865 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:05.200643 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:05.202874 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:05.202979 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 4:09:05.204866 INFO: Updating optimization_manager: rt_error            : 12.279386746341178 -> 13.81609484166705
1 day, 4:09:05.204976 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 13.8161.
1 day, 4:09:05.205052 INFO: ==============================================
1 day, 4:09:05.205120 INFO: Starting optimization step 8.
1 day, 4:09:05.205180 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:05.205234 INFO: Using classic extraction backend
1 day, 4:09:05.205356 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:05.205418 INFO: === Search parameters used ===
1 day, 4:09:05.205465 INFO: rt_error       : 13.81609484166705
1 day, 4:09:05.205508 INFO: mobility_error : 0.1
1 day, 4:09:05.205550 INFO: num_candidates : 3
1 day, 4:09:05.205592 INFO: ms1_error      : 15.0
1 day, 4:09:05.205635 INFO: ms2_error      : 15.0
1 day, 4:09:05.205678 INFO: fwhm_rt        : 2.8496592044830322
1 day, 4:09:05.205721 INFO: quant_window   : 3
1 day, 4:09:05.205760 INFO: ==============================================
1 day, 4:09:05.206884 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:05.206935 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:05.206969 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:05.206993 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.78
1 day, 4:09:05.207725 INFO: Starting candidate selection
1 day, 4:09:05.712056 INFO: Starting candidate scoring
1 day, 4:09:05.931101 INFO: Finished candidate processing
1 day, 4:09:05.931234 INFO: Collecting candidate features
1 day, 4:09:05.944630 INFO: Collecting fragment features
1 day, 4:09:05.948836 INFO: Finished candidate scoring
1 day, 4:09:05.951363 INFO: performing precursor FDR with 47 features
1 day, 4:09:05.951414 INFO: Decoy channel: -1
1 day, 4:09:05.951440 INFO: Competetive: True
1 day, 4:09:05.955538 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:05.957829 INFO: Using random state 186908 for train-test-split
1 day, 4:09:05.970006 INFO: Test AUC: 0.790
1 day, 4:09:05.970091 INFO: Train AUC: 0.782
1 day, 4:09:05.970121 INFO: AUC difference: 1.10%
1 day, 4:09:06.190417 INFO: Resetting torch num_threads to 80
1 day, 4:09:06.191111 PROGRESS: === Extracted 3380 precursors and 35660 fragments ===
1 day, 4:09:06.191606 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:06.192261 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:06.192353 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:06.192413 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:09:06.192464 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:09:06.192510 PROGRESS: 
1 day, 4:09:06.192557 PROGRESS: Precursor Summary:
1 day, 4:09:06.193648 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   560; 0.001 FDR:   281
1 day, 4:09:06.193744 PROGRESS: 
1 day, 4:09:06.193809 PROGRESS: Protein Summary:
1 day, 4:09:06.195071 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   517; 0.001 FDR:   270
1 day, 4:09:06.195171 PROGRESS: =========================================================================
1 day, 4:09:06.195347 INFO: Target number of precursors reached.
1 day, 4:09:06.202537 INFO: fragments_df: keeping 5000 of 35660 [sum(precursor_idx_mask)=17188 sum(mass_error_mask)=35660 stop_rank=5000
1 day, 4:09:06.207818 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:06.333696 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:06.452799 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:06.576753 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:07.196845 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:07.197373 INFO: Using score_cutoff 36.46228109779358 (fac=0.99, q=1)
1 day, 4:09:07.197708 INFO: Updating optimization_manager: fwhm_rt             : 2.8496592044830322 -> 2.8505756855010986
1 day, 4:09:07.197792 INFO: Updating optimization_manager: fwhm_mobility       : 0.008155543357133865 -> 0.008178280666470528
1 day, 4:09:07.197848 INFO: Updating optimization_manager: score_cutoff        : 36.50858541870117 -> 36.46228109779358
1 day, 4:09:07.197913 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:07.199151 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:07.200467 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:07.201262 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:07.203410 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:07.203519 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1 day, 4:09:07.205378 INFO: Updating optimization_manager: rt_error            : 13.81609484166705 -> 12.2837728039008
1 day, 4:09:07.205482 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 12.2838.
1 day, 4:09:07.205553 INFO: ==============================================
1 day, 4:09:07.205620 INFO: Starting optimization step 9.
1 day, 4:09:07.205680 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:07.205738 INFO: Using classic extraction backend
1 day, 4:09:07.205858 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:07.205921 INFO: === Search parameters used ===
1 day, 4:09:07.205968 INFO: rt_error       : 12.2837728039008
1 day, 4:09:07.206009 INFO: mobility_error : 0.1
1 day, 4:09:07.206062 INFO: num_candidates : 3
1 day, 4:09:07.206106 INFO: ms1_error      : 15.0
1 day, 4:09:07.206146 INFO: ms2_error      : 15.0
1 day, 4:09:07.206187 INFO: fwhm_rt        : 2.8505756855010986
1 day, 4:09:07.206226 INFO: quant_window   : 3
1 day, 4:09:07.206266 INFO: ==============================================
1 day, 4:09:07.207144 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:07.207192 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:07.207227 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:07.207252 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:09:07.207967 INFO: Starting candidate selection
1 day, 4:09:07.722197 INFO: Starting candidate scoring
1 day, 4:09:07.925873 INFO: Finished candidate processing
1 day, 4:09:07.926006 INFO: Collecting candidate features
1 day, 4:09:07.939675 INFO: Collecting fragment features
1 day, 4:09:07.943530 INFO: Finished candidate scoring
1 day, 4:09:07.945901 INFO: performing precursor FDR with 47 features
1 day, 4:09:07.945949 INFO: Decoy channel: -1
1 day, 4:09:07.945973 INFO: Competetive: True
1 day, 4:09:07.949049 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:07.951272 INFO: Using random state 186908 for train-test-split
1 day, 4:09:07.962478 INFO: Test AUC: 0.773
1 day, 4:09:07.962550 INFO: Train AUC: 0.785
1 day, 4:09:07.962580 INFO: AUC difference: 1.45%
1 day, 4:09:08.201203 INFO: Resetting torch num_threads to 80
1 day, 4:09:08.201974 PROGRESS: === Extracted 3374 precursors and 35577 fragments ===
1 day, 4:09:08.202545 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:08.203283 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:08.203377 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:08.203437 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:09:08.203488 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:08.203533 PROGRESS: 
1 day, 4:09:08.203580 PROGRESS: Precursor Summary:
1 day, 4:09:08.204783 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   561; 0.001 FDR:   283
1 day, 4:09:08.204893 PROGRESS: 
1 day, 4:09:08.204962 PROGRESS: Protein Summary:
1 day, 4:09:08.206560 PROGRESS: Channel   0:	 0.050 FDR:   542; 0.010 FDR:   519; 0.001 FDR:   272
1 day, 4:09:08.206665 PROGRESS: =========================================================================
1 day, 4:09:08.206857 INFO: Target number of precursors reached.
1 day, 4:09:08.214299 INFO: fragments_df: keeping 5000 of 35577 [sum(precursor_idx_mask)=17210 sum(mass_error_mask)=35577 stop_rank=5000
1 day, 4:09:08.219764 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:08.349546 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:08.471908 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:08.595443 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:09.215683 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:09.216219 INFO: Using score_cutoff 36.51013229370117 (fac=0.99, q=1)
1 day, 4:09:09.216568 INFO: Updating optimization_manager: fwhm_rt             : 2.8505756855010986 -> 2.8496592044830322
1 day, 4:09:09.216650 INFO: Updating optimization_manager: fwhm_mobility       : 0.008178280666470528 -> 0.008155543357133865
1 day, 4:09:09.216705 INFO: Updating optimization_manager: score_cutoff        : 36.46228109779358 -> 36.51013229370117
1 day, 4:09:09.216760 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:09.217995 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:09.219373 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:09.220160 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:09.222380 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:09.222483 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
1 day, 4:09:09.224347 INFO: Updating optimization_manager: rt_error            : 12.2837728039008 -> 13.820385008632204
1 day, 4:09:09.224451 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 13.8204.
1 day, 4:09:09.224522 INFO: ==============================================
1 day, 4:09:09.224588 INFO: Starting optimization step 10.
1 day, 4:09:09.224650 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:09.224706 INFO: Using classic extraction backend
1 day, 4:09:09.224825 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:09.224890 INFO: === Search parameters used ===
1 day, 4:09:09.224936 INFO: rt_error       : 13.820385008632204
1 day, 4:09:09.224979 INFO: mobility_error : 0.1
1 day, 4:09:09.225029 INFO: num_candidates : 3
1 day, 4:09:09.225072 INFO: ms1_error      : 15.0
1 day, 4:09:09.225113 INFO: ms2_error      : 15.0
1 day, 4:09:09.225151 INFO: fwhm_rt        : 2.8496592044830322
1 day, 4:09:09.225192 INFO: quant_window   : 3
1 day, 4:09:09.225232 INFO: ==============================================
1 day, 4:09:09.226229 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:09.226279 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:09.226314 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:09.226337 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.78
1 day, 4:09:09.227074 INFO: Starting candidate selection
1 day, 4:09:09.739890 INFO: Starting candidate scoring
1 day, 4:09:09.949499 INFO: Finished candidate processing
1 day, 4:09:09.949656 INFO: Collecting candidate features
1 day, 4:09:09.964062 INFO: Collecting fragment features
1 day, 4:09:09.968096 INFO: Finished candidate scoring
1 day, 4:09:09.970301 INFO: performing precursor FDR with 47 features
1 day, 4:09:09.970356 INFO: Decoy channel: -1
1 day, 4:09:09.970382 INFO: Competetive: True
1 day, 4:09:09.973734 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:09.975967 INFO: Using random state 186908 for train-test-split
1 day, 4:09:09.989252 INFO: Test AUC: 0.771
1 day, 4:09:09.989324 INFO: Train AUC: 0.785
1 day, 4:09:09.989360 INFO: AUC difference: 1.73%
1 day, 4:09:10.209786 INFO: Resetting torch num_threads to 80
1 day, 4:09:10.210515 PROGRESS: === Extracted 3383 precursors and 35683 fragments ===
1 day, 4:09:10.211011 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:10.211646 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:10.211736 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:10.211795 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:09:10.211854 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:10.211901 PROGRESS: 
1 day, 4:09:10.211943 PROGRESS: Precursor Summary:
1 day, 4:09:10.213067 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   563; 0.001 FDR:   283
1 day, 4:09:10.213161 PROGRESS: 
1 day, 4:09:10.213221 PROGRESS: Protein Summary:
1 day, 4:09:10.214496 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   519; 0.001 FDR:   272
1 day, 4:09:10.214595 PROGRESS: =========================================================================
1 day, 4:09:10.214779 INFO: Target number of precursors reached.
1 day, 4:09:10.221966 INFO: fragments_df: keeping 5000 of 35683 [sum(precursor_idx_mask)=17283 sum(mass_error_mask)=35683 stop_rank=5000
1 day, 4:09:10.227298 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:10.347024 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:10.467059 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:10.589678 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:11.209116 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:11.209661 INFO: Using score_cutoff 36.30706046218872 (fac=0.99, q=1)
1 day, 4:09:11.210000 INFO: Updating optimization_manager: fwhm_rt             : 2.8496592044830322 -> 2.844266176223755
1 day, 4:09:11.210092 INFO: Updating optimization_manager: fwhm_mobility       : 0.008155543357133865 -> 0.008182886987924576
1 day, 4:09:11.210148 INFO: Updating optimization_manager: score_cutoff        : 36.51013229370117 -> 36.30706046218872
1 day, 4:09:11.210203 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:11.211425 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:11.212741 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:11.213508 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:11.215732 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:11.215844 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
1 day, 4:09:11.217721 INFO: Updating optimization_manager: rt_error            : 13.820385008632204 -> 12.271783489341585
1 day, 4:09:11.217826 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 12.2718.
1 day, 4:09:11.217891 INFO: ==============================================
1 day, 4:09:11.217959 INFO: Starting optimization step 11.
1 day, 4:09:11.218027 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:11.218095 INFO: Using classic extraction backend
1 day, 4:09:11.218220 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:11.218285 INFO: === Search parameters used ===
1 day, 4:09:11.218332 INFO: rt_error       : 12.271783489341585
1 day, 4:09:11.218375 INFO: mobility_error : 0.1
1 day, 4:09:11.218417 INFO: num_candidates : 3
1 day, 4:09:11.218459 INFO: ms1_error      : 15.0
1 day, 4:09:11.218499 INFO: ms2_error      : 15.0
1 day, 4:09:11.218538 INFO: fwhm_rt        : 2.844266176223755
1 day, 4:09:11.218578 INFO: quant_window   : 3
1 day, 4:09:11.218618 INFO: ==============================================
1 day, 4:09:11.219482 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:11.219527 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:11.219560 INFO: FWHM in RT is 2.84 seconds, sigma is 0.63
1 day, 4:09:11.219583 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:11.220292 INFO: Starting candidate selection
1 day, 4:09:11.748342 INFO: Starting candidate scoring
1 day, 4:09:11.969105 INFO: Finished candidate processing
1 day, 4:09:11.969250 INFO: Collecting candidate features
1 day, 4:09:11.984145 INFO: Collecting fragment features
1 day, 4:09:11.988019 INFO: Finished candidate scoring
1 day, 4:09:11.990112 INFO: performing precursor FDR with 47 features
1 day, 4:09:11.990165 INFO: Decoy channel: -1
1 day, 4:09:11.990190 INFO: Competetive: True
1 day, 4:09:11.993347 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:11.995509 INFO: Using random state 186908 for train-test-split
1 day, 4:09:12.005952 INFO: Test AUC: 0.762
1 day, 4:09:12.006017 INFO: Train AUC: 0.787
1 day, 4:09:12.006054 INFO: AUC difference: 3.24%
1 day, 4:09:12.223673 INFO: Resetting torch num_threads to 80
1 day, 4:09:12.224261 PROGRESS: === Extracted 3373 precursors and 35560 fragments ===
1 day, 4:09:12.224662 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:12.225220 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:12.225308 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:12.225369 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:09:12.225421 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:09:12.225466 PROGRESS: 
1 day, 4:09:12.225509 PROGRESS: Precursor Summary:
1 day, 4:09:12.226572 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   560; 0.001 FDR:   283
1 day, 4:09:12.226669 PROGRESS: 
1 day, 4:09:12.226728 PROGRESS: Protein Summary:
1 day, 4:09:12.227966 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   518; 0.001 FDR:   272
1 day, 4:09:12.228060 PROGRESS: =========================================================================
1 day, 4:09:12.228214 INFO: Target number of precursors reached.
1 day, 4:09:12.234990 INFO: fragments_df: keeping 5000 of 35560 [sum(precursor_idx_mask)=17169 sum(mass_error_mask)=35560 stop_rank=5000
1 day, 4:09:12.239803 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:12.378469 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:12.521540 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:12.664180 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:13.341108 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:13.341536 INFO: Using score_cutoff 36.83627857589722 (fac=0.99, q=1)
1 day, 4:09:13.341846 INFO: Updating optimization_manager: fwhm_rt             : 2.844266176223755 -> 2.8469626903533936
1 day, 4:09:13.341923 INFO: Updating optimization_manager: fwhm_mobility       : 0.008182886987924576 -> 0.008178280666470528
1 day, 4:09:13.341977 INFO: Updating optimization_manager: score_cutoff        : 36.30706046218872 -> 36.83627857589722
1 day, 4:09:13.342029 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:13.343109 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:13.344399 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:13.345172 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:13.347380 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:13.347479 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
1 day, 4:09:13.349259 INFO: Updating optimization_manager: rt_error            : 12.271783489341585 -> 13.968599141547413
1 day, 4:09:13.349357 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 13.9686.
1 day, 4:09:13.349423 INFO: ==============================================
1 day, 4:09:13.349489 INFO: Starting optimization step 12.
1 day, 4:09:13.349545 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:13.349597 INFO: Using classic extraction backend
1 day, 4:09:13.349706 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:13.349767 INFO: === Search parameters used ===
1 day, 4:09:13.349814 INFO: rt_error       : 13.968599141547413
1 day, 4:09:13.349854 INFO: mobility_error : 0.1
1 day, 4:09:13.349894 INFO: num_candidates : 3
1 day, 4:09:13.349934 INFO: ms1_error      : 15.0
1 day, 4:09:13.349972 INFO: ms2_error      : 15.0
1 day, 4:09:13.350010 INFO: fwhm_rt        : 2.8469626903533936
1 day, 4:09:13.350057 INFO: quant_window   : 3
1 day, 4:09:13.350099 INFO: ==============================================
1 day, 4:09:13.350989 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:13.351036 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:13.351070 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:13.351092 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:09:13.351756 INFO: Starting candidate selection
1 day, 4:09:13.884033 INFO: Starting candidate scoring
1 day, 4:09:14.100080 INFO: Finished candidate processing
1 day, 4:09:14.100179 INFO: Collecting candidate features
1 day, 4:09:14.113058 INFO: Collecting fragment features
1 day, 4:09:14.117149 INFO: Finished candidate scoring
1 day, 4:09:14.119213 INFO: performing precursor FDR with 47 features
1 day, 4:09:14.119263 INFO: Decoy channel: -1
1 day, 4:09:14.119287 INFO: Competetive: True
1 day, 4:09:14.122435 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:14.124687 INFO: Using random state 186908 for train-test-split
1 day, 4:09:14.135922 INFO: Test AUC: 0.805
1 day, 4:09:14.136000 INFO: Train AUC: 0.776
1 day, 4:09:14.136030 INFO: AUC difference: 3.71%
1 day, 4:09:14.427862 INFO: Resetting torch num_threads to 80
1 day, 4:09:14.428446 PROGRESS: === Extracted 3385 precursors and 35747 fragments ===
1 day, 4:09:14.428858 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:14.429428 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:14.429524 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:14.429585 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:09:14.429638 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:14.429685 PROGRESS: 
1 day, 4:09:14.429730 PROGRESS: Precursor Summary:
1 day, 4:09:14.430828 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   563; 0.001 FDR:   284
1 day, 4:09:14.430922 PROGRESS: 
1 day, 4:09:14.430980 PROGRESS: Protein Summary:
1 day, 4:09:14.432212 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   519; 0.001 FDR:   272
1 day, 4:09:14.432301 PROGRESS: =========================================================================
1 day, 4:09:14.432461 INFO: Target number of precursors reached.
1 day, 4:09:14.440161 INFO: fragments_df: keeping 5000 of 35747 [sum(precursor_idx_mask)=17293 sum(mass_error_mask)=35747 stop_rank=5000
1 day, 4:09:14.444951 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:14.698271 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:14.888934 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:15.030225 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:15.892251 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:15.892682 INFO: Using score_cutoff 36.837152394104 (fac=0.99, q=1)
1 day, 4:09:15.892993 INFO: Updating optimization_manager: fwhm_rt             : 2.8469626903533936 -> 2.8496592044830322
1 day, 4:09:15.893076 INFO: Updating optimization_manager: fwhm_mobility       : 0.008178280666470528 -> 0.008182886987924576
1 day, 4:09:15.893986 INFO: Updating optimization_manager: score_cutoff        : 36.83627857589722 -> 36.837152394104
1 day, 4:09:15.894059 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:15.895138 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:15.896415 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:15.897177 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:15.899364 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:15.899461 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 2 ===
1 day, 4:09:15.901243 INFO: Updating optimization_manager: rt_error            : 13.968599141547413 -> 12.274857235514746
1 day, 4:09:15.901344 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 12.2749.
1 day, 4:09:15.901409 INFO: ==============================================
1 day, 4:09:15.901482 INFO: Starting optimization step 13.
1 day, 4:09:15.901541 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:15.901604 INFO: Using classic extraction backend
1 day, 4:09:15.901721 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:15.901788 INFO: === Search parameters used ===
1 day, 4:09:15.901837 INFO: rt_error       : 12.274857235514746
1 day, 4:09:15.901878 INFO: mobility_error : 0.1
1 day, 4:09:15.901919 INFO: num_candidates : 3
1 day, 4:09:15.901959 INFO: ms1_error      : 15.0
1 day, 4:09:15.902004 INFO: ms2_error      : 15.0
1 day, 4:09:15.902052 INFO: fwhm_rt        : 2.8496592044830322
1 day, 4:09:15.902096 INFO: quant_window   : 3
1 day, 4:09:15.902135 INFO: ==============================================
1 day, 4:09:15.902996 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:15.903043 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:15.903079 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:15.903101 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:15.904541 INFO: Starting candidate selection
1 day, 4:09:16.430480 INFO: Starting candidate scoring
1 day, 4:09:16.682817 INFO: Finished candidate processing
1 day, 4:09:16.682923 INFO: Collecting candidate features
1 day, 4:09:16.696787 INFO: Collecting fragment features
1 day, 4:09:16.701178 INFO: Finished candidate scoring
1 day, 4:09:16.703250 INFO: performing precursor FDR with 47 features
1 day, 4:09:16.703298 INFO: Decoy channel: -1
1 day, 4:09:16.703321 INFO: Competetive: True
1 day, 4:09:16.706871 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:16.709050 INFO: Using random state 186908 for train-test-split
1 day, 4:09:16.719343 INFO: Test AUC: 0.757
1 day, 4:09:16.719400 INFO: Train AUC: 0.787
1 day, 4:09:16.719429 INFO: AUC difference: 3.90%
1 day, 4:09:16.933951 INFO: Resetting torch num_threads to 80
1 day, 4:09:16.934536 PROGRESS: === Extracted 3376 precursors and 35590 fragments ===
1 day, 4:09:16.934951 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:16.935529 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:16.935616 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:16.935673 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:09:16.935720 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:09:16.935764 PROGRESS: 
1 day, 4:09:16.935804 PROGRESS: Precursor Summary:
1 day, 4:09:16.936822 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   560; 0.001 FDR:   283
1 day, 4:09:16.936909 PROGRESS: 
1 day, 4:09:16.936965 PROGRESS: Protein Summary:
1 day, 4:09:16.938185 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   518; 0.001 FDR:   272
1 day, 4:09:16.938276 PROGRESS: =========================================================================
1 day, 4:09:16.938448 INFO: Target number of precursors reached.
1 day, 4:09:16.945297 INFO: fragments_df: keeping 5000 of 35590 [sum(precursor_idx_mask)=17192 sum(mass_error_mask)=35590 stop_rank=5000
1 day, 4:09:16.951267 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:17.202970 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:17.343590 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:17.485070 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:18.107718 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:18.108284 INFO: Using score_cutoff 36.308636907577515 (fac=0.99, q=1)
1 day, 4:09:18.108638 INFO: Updating optimization_manager: fwhm_rt             : 2.8496592044830322 -> 2.8416686058044434
1 day, 4:09:18.108722 INFO: Updating optimization_manager: fwhm_mobility       : 0.008182886987924576 -> 0.008178280666470528
1 day, 4:09:18.108778 INFO: Updating optimization_manager: score_cutoff        : 36.837152394104 -> 36.308636907577515
1 day, 4:09:18.108833 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:18.110075 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:18.111386 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:18.112162 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:18.114391 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:18.114497 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 2 ===
1 day, 4:09:18.116408 INFO: Updating optimization_manager: rt_error            : 12.274857235514746 -> 13.965464315837856
1 day, 4:09:18.116514 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 13.9655.
1 day, 4:09:18.116581 INFO: ==============================================
1 day, 4:09:18.116647 INFO: Starting optimization step 14.
1 day, 4:09:18.116703 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:18.116765 INFO: Using classic extraction backend
1 day, 4:09:18.116929 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:18.116997 INFO: === Search parameters used ===
1 day, 4:09:18.117044 INFO: rt_error       : 13.965464315837856
1 day, 4:09:18.117086 INFO: mobility_error : 0.1
1 day, 4:09:18.117126 INFO: num_candidates : 3
1 day, 4:09:18.117166 INFO: ms1_error      : 15.0
1 day, 4:09:18.117207 INFO: ms2_error      : 15.0
1 day, 4:09:18.117248 INFO: fwhm_rt        : 2.8416686058044434
1 day, 4:09:18.117286 INFO: quant_window   : 3
1 day, 4:09:18.117326 INFO: ==============================================
1 day, 4:09:18.118205 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:18.118252 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:18.118286 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
1 day, 4:09:18.118309 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:09:18.119436 INFO: Starting candidate selection
1 day, 4:09:18.634655 INFO: Starting candidate scoring
1 day, 4:09:18.829242 INFO: Finished candidate processing
1 day, 4:09:18.829351 INFO: Collecting candidate features
1 day, 4:09:18.842589 INFO: Collecting fragment features
1 day, 4:09:18.848208 INFO: Finished candidate scoring
1 day, 4:09:18.850215 INFO: performing precursor FDR with 47 features
1 day, 4:09:18.850260 INFO: Decoy channel: -1
1 day, 4:09:18.850284 INFO: Competetive: True
1 day, 4:09:18.853191 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:18.855333 INFO: Using random state 186908 for train-test-split
1 day, 4:09:18.866002 INFO: Test AUC: 0.787
1 day, 4:09:18.867029 INFO: Train AUC: 0.780
1 day, 4:09:18.867065 INFO: AUC difference: 1.00%
1 day, 4:09:19.083970 INFO: Resetting torch num_threads to 80
1 day, 4:09:19.084539 PROGRESS: === Extracted 3385 precursors and 35695 fragments ===
1 day, 4:09:19.084945 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:19.085508 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:19.085599 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:19.085658 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:09:19.085706 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:19.085753 PROGRESS: 
1 day, 4:09:19.085795 PROGRESS: Precursor Summary:
1 day, 4:09:19.086812 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   563; 0.001 FDR:   284
1 day, 4:09:19.086904 PROGRESS: 
1 day, 4:09:19.086961 PROGRESS: Protein Summary:
1 day, 4:09:19.088181 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   519; 0.001 FDR:   272
1 day, 4:09:19.088277 PROGRESS: =========================================================================
1 day, 4:09:19.088451 INFO: Target number of precursors reached.
1 day, 4:09:19.095234 INFO: fragments_df: keeping 5000 of 35695 [sum(precursor_idx_mask)=17277 sum(mass_error_mask)=35695 stop_rank=5000
1 day, 4:09:19.100123 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:19.238529 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:19.375874 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:19.518487 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:20.198003 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:20.198459 INFO: Using score_cutoff 36.83786306533814 (fac=0.99, q=1)
1 day, 4:09:20.198792 INFO: Updating optimization_manager: fwhm_rt             : 2.8416686058044434 -> 2.8496592044830322
1 day, 4:09:20.198872 INFO: Updating optimization_manager: fwhm_mobility       : 0.008178280666470528 -> 0.00819235760718584
1 day, 4:09:20.198925 INFO: Updating optimization_manager: score_cutoff        : 36.308636907577515 -> 36.83786306533814
1 day, 4:09:20.198982 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:20.200091 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:20.201378 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:20.202150 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:20.204482 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:20.204598 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 2 ===
1 day, 4:09:20.208459 INFO: Updating optimization_manager: rt_error            : 13.965464315837856 -> 12.26042718313065
1 day, 4:09:20.208571 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 12.2604.
1 day, 4:09:20.208637 INFO: ==============================================
1 day, 4:09:20.208704 INFO: Starting optimization step 15.
1 day, 4:09:20.208775 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:20.208838 INFO: Using classic extraction backend
1 day, 4:09:20.208967 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:20.209036 INFO: === Search parameters used ===
1 day, 4:09:20.209083 INFO: rt_error       : 12.26042718313065
1 day, 4:09:20.209124 INFO: mobility_error : 0.1
1 day, 4:09:20.209165 INFO: num_candidates : 3
1 day, 4:09:20.209203 INFO: ms1_error      : 15.0
1 day, 4:09:20.209242 INFO: ms2_error      : 15.0
1 day, 4:09:20.209283 INFO: fwhm_rt        : 2.8496592044830322
1 day, 4:09:20.209321 INFO: quant_window   : 3
1 day, 4:09:20.209358 INFO: ==============================================
1 day, 4:09:20.211241 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:20.211289 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:20.211325 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:20.211347 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:20.212471 INFO: Starting candidate selection
1 day, 4:09:20.728784 INFO: Starting candidate scoring
1 day, 4:09:20.919342 INFO: Finished candidate processing
1 day, 4:09:20.919496 INFO: Collecting candidate features
1 day, 4:09:20.952517 INFO: Collecting fragment features
1 day, 4:09:20.961959 INFO: Finished candidate scoring
1 day, 4:09:20.966076 INFO: performing precursor FDR with 47 features
1 day, 4:09:20.966177 INFO: Decoy channel: -1
1 day, 4:09:20.966234 INFO: Competetive: True
1 day, 4:09:20.972455 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:20.976031 INFO: Using random state 186908 for train-test-split
1 day, 4:09:21.000356 INFO: Test AUC: 0.796
1 day, 4:09:21.000443 INFO: Train AUC: 0.778
1 day, 4:09:21.000480 INFO: AUC difference: 2.28%
1 day, 4:09:21.224309 INFO: Resetting torch num_threads to 80
1 day, 4:09:21.225342 PROGRESS: === Extracted 3375 precursors and 35569 fragments ===
1 day, 4:09:21.226157 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:21.226851 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:21.226940 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:21.227006 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:09:21.227057 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:09:21.227103 PROGRESS: 
1 day, 4:09:21.227146 PROGRESS: Precursor Summary:
1 day, 4:09:21.228206 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   560; 0.001 FDR:   283
1 day, 4:09:21.228301 PROGRESS: 
1 day, 4:09:21.228358 PROGRESS: Protein Summary:
1 day, 4:09:21.229628 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   518; 0.001 FDR:   272
1 day, 4:09:21.229721 PROGRESS: =========================================================================
1 day, 4:09:21.229961 INFO: Target number of precursors reached.
1 day, 4:09:21.236874 INFO: fragments_df: keeping 5000 of 35569 [sum(precursor_idx_mask)=17197 sum(mass_error_mask)=35569 stop_rank=5000
1 day, 4:09:21.245260 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:21.373245 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:21.495832 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:21.622164 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:22.278020 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:22.278598 INFO: Using score_cutoff 36.30991379699707 (fac=0.99, q=1)
1 day, 4:09:22.279039 INFO: Updating optimization_manager: fwhm_rt             : 2.8496592044830322 -> 2.8416686058044434
1 day, 4:09:22.279124 INFO: Updating optimization_manager: fwhm_mobility       : 0.00819235760718584 -> 0.008187524043023586
1 day, 4:09:22.279180 INFO: Updating optimization_manager: score_cutoff        : 36.83786306533814 -> 36.30991379699707
1 day, 4:09:22.279260 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:22.280621 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:22.281946 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:22.282732 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:22.286377 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:22.286505 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 2 ===
1 day, 4:09:22.288932 INFO: Updating optimization_manager: rt_error            : 12.26042718313065 -> 13.965146785182338
1 day, 4:09:22.289055 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 13.9651.
1 day, 4:09:22.289129 INFO: ==============================================
1 day, 4:09:22.289212 INFO: Starting optimization step 16.
1 day, 4:09:22.289284 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:22.289400 INFO: Using classic extraction backend
1 day, 4:09:22.289679 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:22.289757 INFO: === Search parameters used ===
1 day, 4:09:22.289809 INFO: rt_error       : 13.965146785182338
1 day, 4:09:22.289854 INFO: mobility_error : 0.1
1 day, 4:09:22.289898 INFO: num_candidates : 3
1 day, 4:09:22.289941 INFO: ms1_error      : 15.0
1 day, 4:09:22.289980 INFO: ms2_error      : 15.0
1 day, 4:09:22.290020 INFO: fwhm_rt        : 2.8416686058044434
1 day, 4:09:22.290079 INFO: quant_window   : 3
1 day, 4:09:22.290138 INFO: ==============================================
1 day, 4:09:22.291532 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:22.291579 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:22.291621 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
1 day, 4:09:22.291646 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:22.292428 INFO: Starting candidate selection
1 day, 4:09:22.799425 INFO: Starting candidate scoring
1 day, 4:09:23.016625 INFO: Finished candidate processing
1 day, 4:09:23.016783 INFO: Collecting candidate features
1 day, 4:09:23.031773 INFO: Collecting fragment features
1 day, 4:09:23.037899 INFO: Finished candidate scoring
1 day, 4:09:23.039971 INFO: performing precursor FDR with 47 features
1 day, 4:09:23.040023 INFO: Decoy channel: -1
1 day, 4:09:23.040048 INFO: Competetive: True
1 day, 4:09:23.043967 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:23.046386 INFO: Using random state 186908 for train-test-split
1 day, 4:09:23.059290 INFO: Test AUC: 0.806
1 day, 4:09:23.059366 INFO: Train AUC: 0.775
1 day, 4:09:23.059396 INFO: AUC difference: 3.99%
1 day, 4:09:23.284928 INFO: Resetting torch num_threads to 80
1 day, 4:09:23.285612 PROGRESS: === Extracted 3384 precursors and 35679 fragments ===
1 day, 4:09:23.286126 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:23.286810 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:23.286903 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:23.286970 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:09:23.287020 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:23.287070 PROGRESS: 
1 day, 4:09:23.287114 PROGRESS: Precursor Summary:
1 day, 4:09:23.288258 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   563; 0.001 FDR:   284
1 day, 4:09:23.288368 PROGRESS: 
1 day, 4:09:23.288425 PROGRESS: Protein Summary:
1 day, 4:09:23.289712 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   519; 0.001 FDR:   272
1 day, 4:09:23.289806 PROGRESS: =========================================================================
1 day, 4:09:23.289954 INFO: Target number of precursors reached.
1 day, 4:09:23.296921 INFO: fragments_df: keeping 5000 of 35679 [sum(precursor_idx_mask)=17277 sum(mass_error_mask)=35679 stop_rank=5000
1 day, 4:09:23.302223 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:23.425147 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:23.544829 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:23.668955 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:24.315372 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:24.315889 INFO: Using score_cutoff 36.83898976135254 (fac=0.99, q=1)
1 day, 4:09:24.316223 INFO: Updating optimization_manager: fwhm_rt             : 2.8416686058044434 -> 2.8496592044830322
1 day, 4:09:24.316305 INFO: Updating optimization_manager: fwhm_mobility       : 0.008187524043023586 -> 0.008192161098122597
1 day, 4:09:24.316360 INFO: Updating optimization_manager: score_cutoff        : 36.30991379699707 -> 36.83898976135254
1 day, 4:09:24.316414 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:24.317624 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:24.318925 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:24.319692 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:24.321881 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:24.321980 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 2 ===
1 day, 4:09:24.323824 INFO: Updating optimization_manager: rt_error            : 13.965146785182338 -> 12.260427184611178
1 day, 4:09:24.323931 PROGRESS: ❌ rt_error       : optimization incomplete after 17 search(es). Will search with parameter 12.2604.
1 day, 4:09:24.323997 INFO: ==============================================
1 day, 4:09:24.324063 INFO: Starting optimization step 17.
1 day, 4:09:24.324122 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:24.324177 INFO: Using classic extraction backend
1 day, 4:09:24.324291 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:24.324363 INFO: === Search parameters used ===
1 day, 4:09:24.324420 INFO: rt_error       : 12.260427184611178
1 day, 4:09:24.324463 INFO: mobility_error : 0.1
1 day, 4:09:24.324505 INFO: num_candidates : 3
1 day, 4:09:24.324545 INFO: ms1_error      : 15.0
1 day, 4:09:24.324585 INFO: ms2_error      : 15.0
1 day, 4:09:24.324623 INFO: fwhm_rt        : 2.8496592044830322
1 day, 4:09:24.324661 INFO: quant_window   : 3
1 day, 4:09:24.324698 INFO: ==============================================
1 day, 4:09:24.325792 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:24.325839 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:24.325873 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:24.325902 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:24.326615 INFO: Starting candidate selection
1 day, 4:09:24.832266 INFO: Starting candidate scoring
1 day, 4:09:25.026671 INFO: Finished candidate processing
1 day, 4:09:25.026775 INFO: Collecting candidate features
1 day, 4:09:25.041134 INFO: Collecting fragment features
1 day, 4:09:25.045591 INFO: Finished candidate scoring
1 day, 4:09:25.047581 INFO: performing precursor FDR with 47 features
1 day, 4:09:25.047630 INFO: Decoy channel: -1
1 day, 4:09:25.047661 INFO: Competetive: True
1 day, 4:09:25.051981 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:25.055259 INFO: Using random state 186908 for train-test-split
1 day, 4:09:25.071408 INFO: Test AUC: 0.781
1 day, 4:09:25.071509 INFO: Train AUC: 0.782
1 day, 4:09:25.071571 INFO: AUC difference: 0.03%
1 day, 4:09:25.286597 INFO: Resetting torch num_threads to 80
1 day, 4:09:25.287220 PROGRESS: === Extracted 3376 precursors and 35583 fragments ===
1 day, 4:09:25.287657 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:25.288249 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:25.288345 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:25.288416 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:09:25.288480 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:09:25.288536 PROGRESS: 
1 day, 4:09:25.288591 PROGRESS: Precursor Summary:
1 day, 4:09:25.289687 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   560; 0.001 FDR:   283
1 day, 4:09:25.289788 PROGRESS: 
1 day, 4:09:25.289855 PROGRESS: Protein Summary:
1 day, 4:09:25.291132 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   518; 0.001 FDR:   272
1 day, 4:09:25.291241 PROGRESS: =========================================================================
1 day, 4:09:25.291428 INFO: Target number of precursors reached.
1 day, 4:09:25.298130 INFO: fragments_df: keeping 5000 of 35583 [sum(precursor_idx_mask)=17199 sum(mass_error_mask)=35583 stop_rank=5000
1 day, 4:09:25.302743 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:25.444673 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:25.585119 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:25.727904 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:26.430053 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:26.430507 INFO: Using score_cutoff 36.30988872070312 (fac=0.99, q=1)
1 day, 4:09:26.430847 INFO: Updating optimization_manager: fwhm_rt             : 2.8496592044830322 -> 2.8505756855010986
1 day, 4:09:26.430944 INFO: Updating optimization_manager: fwhm_mobility       : 0.008192161098122597 -> 0.008187524043023586
1 day, 4:09:26.431011 INFO: Updating optimization_manager: score_cutoff        : 36.83898976135254 -> 36.30988872070312
1 day, 4:09:26.431078 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:26.432193 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:26.433495 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:26.434304 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:26.436418 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:26.436522 PROGRESS: === Optimization of rt_error has been performed 18 time(s); minimum number is 2 ===
1 day, 4:09:26.438357 INFO: Updating optimization_manager: rt_error            : 12.260427184611178 -> 13.96514681505001
1 day, 4:09:26.438485 PROGRESS: ❌ rt_error       : optimization incomplete after 18 search(es). Will search with parameter 13.9651.
1 day, 4:09:26.438570 INFO: ==============================================
1 day, 4:09:26.438655 INFO: Starting optimization step 18.
1 day, 4:09:26.438723 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:26.438793 INFO: Using classic extraction backend
1 day, 4:09:26.438937 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:26.439016 INFO: === Search parameters used ===
1 day, 4:09:26.439074 INFO: rt_error       : 13.96514681505001
1 day, 4:09:26.439129 INFO: mobility_error : 0.1
1 day, 4:09:26.439181 INFO: num_candidates : 3
1 day, 4:09:26.439233 INFO: ms1_error      : 15.0
1 day, 4:09:26.439283 INFO: ms2_error      : 15.0
1 day, 4:09:26.439333 INFO: fwhm_rt        : 2.8505756855010986
1 day, 4:09:26.439389 INFO: quant_window   : 3
1 day, 4:09:26.439438 INFO: ==============================================
1 day, 4:09:26.440444 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:26.440490 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:26.440536 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:26.440564 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:26.441249 INFO: Starting candidate selection
1 day, 4:09:26.992949 INFO: Starting candidate scoring
1 day, 4:09:27.187852 INFO: Finished candidate processing
1 day, 4:09:27.187984 INFO: Collecting candidate features
1 day, 4:09:27.202629 INFO: Collecting fragment features
1 day, 4:09:27.207357 INFO: Finished candidate scoring
1 day, 4:09:27.209189 INFO: performing precursor FDR with 47 features
1 day, 4:09:27.209232 INFO: Decoy channel: -1
1 day, 4:09:27.209256 INFO: Competetive: True
1 day, 4:09:27.212169 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:27.214249 INFO: Using random state 186908 for train-test-split
1 day, 4:09:27.226487 INFO: Test AUC: 0.781
1 day, 4:09:27.226548 INFO: Train AUC: 0.781
1 day, 4:09:27.226580 INFO: AUC difference: 0.02%
1 day, 4:09:27.438497 INFO: Resetting torch num_threads to 80
1 day, 4:09:27.439034 PROGRESS: === Extracted 3383 precursors and 35669 fragments ===
1 day, 4:09:27.439438 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:27.440043 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:27.440135 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:27.440194 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:09:27.440250 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:27.440298 PROGRESS: 
1 day, 4:09:27.440341 PROGRESS: Precursor Summary:
1 day, 4:09:27.441350 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   563; 0.001 FDR:   284
1 day, 4:09:27.441439 PROGRESS: 
1 day, 4:09:27.441495 PROGRESS: Protein Summary:
1 day, 4:09:27.442713 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   519; 0.001 FDR:   272
1 day, 4:09:27.442806 PROGRESS: =========================================================================
1 day, 4:09:27.442950 INFO: Target number of precursors reached.
1 day, 4:09:27.449582 INFO: fragments_df: keeping 5000 of 35669 [sum(precursor_idx_mask)=17266 sum(mass_error_mask)=35669 stop_rank=5000
1 day, 4:09:27.454112 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:27.598162 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:27.717704 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:27.842031 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:28.518001 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:28.518532 INFO: Using score_cutoff 36.837783757781985 (fac=0.99, q=1)
1 day, 4:09:28.518869 INFO: Updating optimization_manager: fwhm_rt             : 2.8505756855010986 -> 2.851492166519165
1 day, 4:09:28.518951 INFO: Updating optimization_manager: fwhm_mobility       : 0.008187524043023586 -> 0.008192161098122597
1 day, 4:09:28.519005 INFO: Updating optimization_manager: score_cutoff        : 36.30988872070312 -> 36.837783757781985
1 day, 4:09:28.519057 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:28.520269 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:28.521680 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:28.522464 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:28.526157 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:28.526262 PROGRESS: === Optimization of rt_error has been performed 19 time(s); minimum number is 2 ===
1 day, 4:09:28.528152 INFO: Updating optimization_manager: rt_error            : 13.96514681505001 -> 12.260168837689184
1 day, 4:09:28.528255 PROGRESS: ❌ rt_error       : optimization incomplete after 19 search(es). Will search with parameter 12.2602.
1 day, 4:09:28.528321 INFO: ==============================================
1 day, 4:09:28.528387 INFO: Starting optimization step 19.
1 day, 4:09:28.528444 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:28.528497 INFO: Using classic extraction backend
1 day, 4:09:28.528615 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:28.528677 INFO: === Search parameters used ===
1 day, 4:09:28.528722 INFO: rt_error       : 12.260168837689184
1 day, 4:09:28.528763 INFO: mobility_error : 0.1
1 day, 4:09:28.528802 INFO: num_candidates : 3
1 day, 4:09:28.528854 INFO: ms1_error      : 15.0
1 day, 4:09:28.528896 INFO: ms2_error      : 15.0
1 day, 4:09:28.528936 INFO: fwhm_rt        : 2.851492166519165
1 day, 4:09:28.528973 INFO: quant_window   : 3
1 day, 4:09:28.529017 INFO: ==============================================
1 day, 4:09:28.530236 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:28.530285 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:28.530316 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:28.530337 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:28.531024 INFO: Starting candidate selection
1 day, 4:09:29.047145 INFO: Starting candidate scoring
1 day, 4:09:29.264076 INFO: Finished candidate processing
1 day, 4:09:29.264179 INFO: Collecting candidate features
1 day, 4:09:29.279504 INFO: Collecting fragment features
1 day, 4:09:29.284487 INFO: Finished candidate scoring
1 day, 4:09:29.286480 INFO: performing precursor FDR with 47 features
1 day, 4:09:29.286529 INFO: Decoy channel: -1
1 day, 4:09:29.286553 INFO: Competetive: True
1 day, 4:09:29.289621 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:29.291858 INFO: Using random state 186908 for train-test-split
1 day, 4:09:29.305345 INFO: Test AUC: 0.780
1 day, 4:09:29.305406 INFO: Train AUC: 0.782
1 day, 4:09:29.305434 INFO: AUC difference: 0.34%
1 day, 4:09:29.524628 INFO: Resetting torch num_threads to 80
1 day, 4:09:29.525266 PROGRESS: === Extracted 3377 precursors and 35590 fragments ===
1 day, 4:09:29.525757 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:29.526366 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:29.526460 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:29.526521 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:09:29.526571 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:09:29.526618 PROGRESS: 
1 day, 4:09:29.526662 PROGRESS: Precursor Summary:
1 day, 4:09:29.527698 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   560; 0.001 FDR:   283
1 day, 4:09:29.527790 PROGRESS: 
1 day, 4:09:29.527846 PROGRESS: Protein Summary:
1 day, 4:09:29.529081 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   518; 0.001 FDR:   272
1 day, 4:09:29.529174 PROGRESS: =========================================================================
1 day, 4:09:29.529329 INFO: Target number of precursors reached.
1 day, 4:09:29.536189 INFO: fragments_df: keeping 5000 of 35590 [sum(precursor_idx_mask)=17199 sum(mass_error_mask)=35590 stop_rank=5000
1 day, 4:09:29.541478 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:29.664686 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:29.786830 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:29.914717 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:30.568305 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:30.568845 INFO: Using score_cutoff 36.30932416419983 (fac=0.99, q=1)
1 day, 4:09:30.569176 INFO: Updating optimization_manager: fwhm_rt             : 2.851492166519165 -> 2.8505756855010986
1 day, 4:09:30.569257 INFO: Updating optimization_manager: fwhm_mobility       : 0.008192161098122597 -> 0.008178280666470528
1 day, 4:09:30.569313 INFO: Updating optimization_manager: score_cutoff        : 36.837783757781985 -> 36.30932416419983
1 day, 4:09:30.569369 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:30.570599 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:30.571889 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:30.572658 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:30.576327 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:30.576433 PROGRESS: === Optimization of rt_error has been performed 20 time(s); minimum number is 2 ===
1 day, 4:09:30.578355 INFO: Updating optimization_manager: rt_error            : 12.260168837689184 -> 13.96514680988507
1 day, 4:09:30.578462 PROGRESS: ❌ rt_error       : optimization incomplete after 20 search(es). Will search with parameter 13.9651.
1 day, 4:09:30.578532 INFO: ==============================================
1 day, 4:09:30.578604 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
1 day, 4:09:30.578705 INFO: Starting optimization step 0.
1 day, 4:09:30.578769 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:30.578825 INFO: Using classic extraction backend
1 day, 4:09:30.578938 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:30.579011 INFO: === Search parameters used ===
1 day, 4:09:30.579061 INFO: rt_error       : 13.96514680988507
1 day, 4:09:30.579103 INFO: mobility_error : 0.1
1 day, 4:09:30.579144 INFO: num_candidates : 3
1 day, 4:09:30.579186 INFO: ms1_error      : 15.0
1 day, 4:09:30.579225 INFO: ms2_error      : 15.0
1 day, 4:09:30.579265 INFO: fwhm_rt        : 2.8505756855010986
1 day, 4:09:30.579304 INFO: quant_window   : 3
1 day, 4:09:30.579344 INFO: ==============================================
1 day, 4:09:30.580344 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:30.580391 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:30.580426 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:30.580449 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:09:30.581136 INFO: Starting candidate selection
1 day, 4:09:31.102093 INFO: Starting candidate scoring
1 day, 4:09:31.311897 INFO: Finished candidate processing
1 day, 4:09:31.312002 INFO: Collecting candidate features
1 day, 4:09:31.327049 INFO: Collecting fragment features
1 day, 4:09:31.333194 INFO: Finished candidate scoring
1 day, 4:09:31.335137 INFO: performing precursor FDR with 47 features
1 day, 4:09:31.335184 INFO: Decoy channel: -1
1 day, 4:09:31.335208 INFO: Competetive: True
1 day, 4:09:31.338197 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:31.340380 INFO: Using random state 186908 for train-test-split
1 day, 4:09:31.353183 INFO: Test AUC: 0.752
1 day, 4:09:31.353256 INFO: Train AUC: 0.788
1 day, 4:09:31.353286 INFO: AUC difference: 4.57%
1 day, 4:09:31.571094 INFO: Resetting torch num_threads to 80
1 day, 4:09:31.571729 PROGRESS: === Extracted 3383 precursors and 35671 fragments ===
1 day, 4:09:31.572224 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:31.572980 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:31.573070 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:31.573131 PROGRESS: Target precursors: 587 (97.83%)
1 day, 4:09:31.573180 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:31.573228 PROGRESS: 
1 day, 4:09:31.573272 PROGRESS: Precursor Summary:
1 day, 4:09:31.574319 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   563; 0.001 FDR:   284
1 day, 4:09:31.574422 PROGRESS: 
1 day, 4:09:31.574478 PROGRESS: Protein Summary:
1 day, 4:09:31.575728 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   519; 0.001 FDR:   272
1 day, 4:09:31.575829 PROGRESS: =========================================================================
1 day, 4:09:31.575962 INFO: Target number of precursors reached.
1 day, 4:09:31.582741 INFO: fragments_df: keeping 5000 of 35671 [sum(precursor_idx_mask)=17268 sum(mass_error_mask)=35671 stop_rank=5000
1 day, 4:09:31.587980 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:31.708962 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:31.840908 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:31.965999 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:32.626673 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:32.627211 INFO: Using score_cutoff 36.836657061767575 (fac=0.99, q=1)
1 day, 4:09:32.627546 INFO: Updating optimization_manager: fwhm_rt             : 2.8505756855010986 -> 2.8496592044830322
1 day, 4:09:32.627628 INFO: Updating optimization_manager: fwhm_mobility       : 0.008178280666470528 -> 0.008192161098122597
1 day, 4:09:32.627682 INFO: Updating optimization_manager: score_cutoff        : 36.30932416419983 -> 36.836657061767575
1 day, 4:09:32.627736 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:32.628946 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:32.630249 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:32.631035 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:32.633136 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:32.633239 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:09:32.634697 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06670245043552735
1 day, 4:09:32.635011 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0667.
1 day, 4:09:32.635082 INFO: ==============================================
1 day, 4:09:32.635147 INFO: Starting optimization step 1.
1 day, 4:09:32.635205 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:32.635258 INFO: Using classic extraction backend
1 day, 4:09:32.635370 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:32.635432 INFO: === Search parameters used ===
1 day, 4:09:32.635478 INFO: rt_error       : 13.96514680988507
1 day, 4:09:32.635522 INFO: mobility_error : 0.06670245043552735
1 day, 4:09:32.635562 INFO: num_candidates : 3
1 day, 4:09:32.635602 INFO: ms1_error      : 15.0
1 day, 4:09:32.635640 INFO: ms2_error      : 15.0
1 day, 4:09:32.635678 INFO: fwhm_rt        : 2.8496592044830322
1 day, 4:09:32.635716 INFO: quant_window   : 3
1 day, 4:09:32.635753 INFO: ==============================================
1 day, 4:09:32.636780 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:32.636825 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:32.636859 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:32.636879 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:32.637565 INFO: Starting candidate selection
1 day, 4:09:33.120572 INFO: Starting candidate scoring
1 day, 4:09:33.332511 INFO: Finished candidate processing
1 day, 4:09:33.332642 INFO: Collecting candidate features
1 day, 4:09:33.348388 INFO: Collecting fragment features
1 day, 4:09:33.354470 INFO: Finished candidate scoring
1 day, 4:09:33.356366 INFO: performing precursor FDR with 47 features
1 day, 4:09:33.356412 INFO: Decoy channel: -1
1 day, 4:09:33.356436 INFO: Competetive: True
1 day, 4:09:33.360211 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:33.362413 INFO: Using random state 186908 for train-test-split
1 day, 4:09:33.373600 INFO: Test AUC: 0.795
1 day, 4:09:33.373672 INFO: Train AUC: 0.769
1 day, 4:09:33.373714 INFO: AUC difference: 3.30%
1 day, 4:09:33.592789 INFO: Resetting torch num_threads to 80
1 day, 4:09:33.593425 PROGRESS: === Extracted 3380 precursors and 35420 fragments ===
1 day, 4:09:33.593916 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:33.594569 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:33.594662 PROGRESS: Total precursors accumulated: 600
1 day, 4:09:33.594722 PROGRESS: Target precursors: 589 (98.17%)
1 day, 4:09:33.594779 PROGRESS: Decoy precursors: 11 (1.83%)
1 day, 4:09:33.594829 PROGRESS: 
1 day, 4:09:33.594872 PROGRESS: Precursor Summary:
1 day, 4:09:33.595907 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   563; 0.001 FDR:   280
1 day, 4:09:33.595998 PROGRESS: 
1 day, 4:09:33.596068 PROGRESS: Protein Summary:
1 day, 4:09:33.597363 PROGRESS: Channel   0:	 0.050 FDR:   542; 0.010 FDR:   520; 0.001 FDR:   269
1 day, 4:09:33.597459 PROGRESS: =========================================================================
1 day, 4:09:33.597597 INFO: Target number of precursors reached.
1 day, 4:09:33.604378 INFO: fragments_df: keeping 5000 of 35420 [sum(precursor_idx_mask)=17232 sum(mass_error_mask)=35420 stop_rank=5000
1 day, 4:09:33.609622 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:33.732080 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:33.850366 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:33.972615 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:34.621981 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:34.622524 INFO: Using score_cutoff 36.31625349197388 (fac=0.99, q=1)
1 day, 4:09:34.622857 INFO: Updating optimization_manager: fwhm_rt             : 2.8496592044830322 -> 2.8515625
1 day, 4:09:34.622941 INFO: Updating optimization_manager: fwhm_mobility       : 0.008192161098122597 -> 0.008182886987924576
1 day, 4:09:34.622997 INFO: Updating optimization_manager: score_cutoff        : 36.836657061767575 -> 36.31625349197388
1 day, 4:09:34.623051 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:34.624278 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:34.625586 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:34.626381 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:34.629308 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:34.629416 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:09:34.630944 INFO: Updating optimization_manager: mobility_error      : 0.06670245043552735 -> 0.062384384984851014
1 day, 4:09:34.631047 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0624.
1 day, 4:09:34.631114 INFO: ==============================================
1 day, 4:09:34.631178 INFO: Starting optimization step 2.
1 day, 4:09:34.631238 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:09:34.631293 INFO: Using classic extraction backend
1 day, 4:09:34.631410 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:09:34.631481 INFO: === Search parameters used ===
1 day, 4:09:34.631548 INFO: rt_error       : 13.96514680988507
1 day, 4:09:34.631594 INFO: mobility_error : 0.062384384984851014
1 day, 4:09:34.631636 INFO: num_candidates : 3
1 day, 4:09:34.631678 INFO: ms1_error      : 15.0
1 day, 4:09:34.631719 INFO: ms2_error      : 15.0
1 day, 4:09:34.631759 INFO: fwhm_rt        : 2.8515625
1 day, 4:09:34.631799 INFO: quant_window   : 3
1 day, 4:09:34.631845 INFO: ==============================================
1 day, 4:09:34.632763 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:34.632810 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:34.632843 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:34.632865 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:34.633618 INFO: Starting candidate selection
1 day, 4:09:35.105606 INFO: Starting candidate scoring
1 day, 4:09:35.357364 INFO: Finished candidate processing
1 day, 4:09:35.357469 INFO: Collecting candidate features
1 day, 4:09:35.370577 INFO: Collecting fragment features
1 day, 4:09:35.374696 INFO: Finished candidate scoring
1 day, 4:09:35.376612 INFO: performing precursor FDR with 47 features
1 day, 4:09:35.376657 INFO: Decoy channel: -1
1 day, 4:09:35.376681 INFO: Competetive: True
1 day, 4:09:35.379938 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:09:35.382051 INFO: Using random state 186908 for train-test-split
1 day, 4:09:35.392605 INFO: Test AUC: 0.785
1 day, 4:09:35.392669 INFO: Train AUC: 0.773
1 day, 4:09:35.392697 INFO: AUC difference: 1.53%
1 day, 4:09:35.608785 INFO: Resetting torch num_threads to 80
1 day, 4:09:35.609348 PROGRESS: === Extracted 3366 precursors and 35208 fragments ===
1 day, 4:09:35.609765 INFO: === FDR correction performed with classifier version 9 ===
1 day, 4:09:35.610393 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:09:35.610486 PROGRESS: Total precursors accumulated: 599
1 day, 4:09:35.610545 PROGRESS: Target precursors: 586 (97.83%)
1 day, 4:09:35.610594 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 4:09:35.610640 PROGRESS: 
1 day, 4:09:35.610681 PROGRESS: Precursor Summary:
1 day, 4:09:35.611717 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   557; 0.001 FDR:   278
1 day, 4:09:35.611807 PROGRESS: 
1 day, 4:09:35.611863 PROGRESS: Protein Summary:
1 day, 4:09:35.613116 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   516; 0.001 FDR:   267
1 day, 4:09:35.613207 PROGRESS: =========================================================================
1 day, 4:09:35.613363 INFO: Target number of precursors reached.
1 day, 4:09:35.620262 INFO: fragments_df: keeping 5000 of 35208 [sum(precursor_idx_mask)=16998 sum(mass_error_mask)=35208 stop_rank=5000
1 day, 4:09:35.624894 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:35.767194 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:35.904419 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:36.043050 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:36.737515 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:09:36.737956 INFO: Using score_cutoff 36.83641324768067 (fac=0.99, q=1)
1 day, 4:09:36.738280 INFO: Updating optimization_manager: fwhm_rt             : 2.8515625 -> 2.8515625
1 day, 4:09:36.738363 INFO: Updating optimization_manager: fwhm_mobility       : 0.008182886987924576 -> 0.008182886987924576
1 day, 4:09:36.738417 INFO: Updating optimization_manager: score_cutoff        : 36.31625349197388 -> 36.83641324768067
1 day, 4:09:36.738470 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:36.739543 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:36.740822 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:36.741586 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:36.744290 INFO: === checking if optimization conditions were reached ===
1 day, 4:09:36.744394 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:09:36.745096 INFO: Updating optimization_manager: mobility_error      : 0.062384384984851014 -> 0.1
1 day, 4:09:36.745214 INFO: Updating optimization_manager: classifier_version  : 9 -> 30
1 day, 4:09:36.745304 INFO: Updating optimization_manager: score_cutoff        : 36.83641324768067 -> 36.836657061767575
1 day, 4:09:36.745388 INFO: Updating optimization_manager: fwhm_rt             : 2.8515625 -> 2.8496592044830322
1 day, 4:09:36.745470 INFO: Updating optimization_manager: fwhm_mobility       : 0.008182886987924576 -> 0.008192161098122597
1 day, 4:09:36.745559 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 4:09:36.745630 INFO: ==============================================
1 day, 4:09:36.745703 PROGRESS: Optimization finished for mobility_error.
1 day, 4:09:36.750304 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:36.751137 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:36.752396 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:36.753153 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:36.780425 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 4:09:36.780558 PROGRESS: ==============================================
1 day, 4:09:36.780631 PROGRESS: ms2_error      : 15.0000
1 day, 4:09:36.780691 PROGRESS: ms1_error      : 15.0000
1 day, 4:09:36.780740 PROGRESS: rt_error       : 13.9651
1 day, 4:09:36.780786 PROGRESS: mobility_error : 0.1000
1 day, 4:09:36.780828 PROGRESS: ==============================================
1 day, 4:09:36.781607 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:09:36.815327 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:09:36.911026 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:09:36.933789 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:09:37.198247 INFO: Using classic extraction backend
1 day, 4:09:37.198679 PROGRESS: Extracting batch of 180112 precursors
1 day, 4:09:37.198769 INFO: === Search parameters used ===
1 day, 4:09:37.198823 INFO: rt_error       : 13.96514680988507
1 day, 4:09:37.198882 INFO: mobility_error : 0.1
1 day, 4:09:37.198927 INFO: num_candidates : 3
1 day, 4:09:37.198970 INFO: ms1_error      : 15.0
1 day, 4:09:37.199010 INFO: ms2_error      : 15.0
1 day, 4:09:37.199051 INFO: fwhm_rt        : 2.8496592044830322
1 day, 4:09:37.199091 INFO: quant_window   : 3
1 day, 4:09:37.199130 INFO: ==============================================
1 day, 4:09:37.249928 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:09:37.250107 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:09:37.250154 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 4:09:37.250177 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 4:09:37.251178 INFO: Starting candidate selection
1 day, 4:09:52.671530 INFO: Removed 139786 precursors with score below cutoff 36.836657061767575
1 day, 4:09:53.023745 INFO: Starting candidate scoring
1 day, 4:10:08.975219 INFO: Finished candidate processing
1 day, 4:10:08.975616 INFO: Collecting candidate features
1 day, 4:10:09.496802 INFO: Collecting fragment features
1 day, 4:10:09.737439 INFO: Finished candidate scoring
1 day, 4:10:10.102841 INFO: === Performing FDR correction with classifier version 30 ===
1 day, 4:10:10.103918 INFO: performing precursor FDR with 47 features
1 day, 4:10:10.103976 INFO: Decoy channel: -1
1 day, 4:10:10.104001 INFO: Competetive: True
1 day, 4:10:10.202810 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:10:10.245063 WARNING: FDR calculation for 215081 target and 151830 decoy PSMs
1 day, 4:10:10.245195 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 4:10:10.353857 INFO: Using random state 392974 for train-test-split
1 day, 4:10:17.785692 INFO: Test AUC: 0.863
1 day, 4:10:17.785871 INFO: Train AUC: 0.868
1 day, 4:10:17.785906 INFO: AUC difference: 0.54%
1 day, 4:10:18.140282 INFO: Resetting torch num_threads to 80
1 day, 4:10:18.167043 INFO: Removing fragments below FDR threshold
1 day, 4:10:18.272595 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:10:18.272911 PROGRESS: Total precursors accumulated: 88,337
1 day, 4:10:18.272984 PROGRESS: Target precursors: 87,463 (99.01%)
1 day, 4:10:18.273036 PROGRESS: Decoy precursors: 874 (0.99%)
1 day, 4:10:18.273084 PROGRESS: 
1 day, 4:10:18.273156 PROGRESS: Precursor Summary:
1 day, 4:10:18.321817 PROGRESS: Channel   0:	 0.050 FDR: 87,463; 0.010 FDR: 87,463; 0.001 FDR: 84,186
1 day, 4:10:18.322155 PROGRESS: 
1 day, 4:10:18.322223 PROGRESS: Protein Summary:
1 day, 4:10:18.379144 PROGRESS: Channel   0:	 0.050 FDR: 8,861; 0.010 FDR: 8,861; 0.001 FDR: 8,811
1 day, 4:10:18.379448 PROGRESS: =========================================================================
1 day, 4:10:18.388540 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/psm.parquet
1 day, 4:10:18.752780 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/frag.parquet
1 day, 4:10:19.072047 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 4:10:19.138570 PROGRESS: 
1 day, 4:10:19.138876 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/quant
1 day, 4:10:19.138980 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/figures
1 day, 4:10:19.139244 INFO: Initializing TimingManager
1 day, 4:10:19.139985 INFO: Initializing RawFileManager
1 day, 4:10:19.140128 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:19.140202 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:19.140278 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:19.351225 INFO: Reading 39,128 frames with 2,897,842,446 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:26.127676 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
1 day, 4:10:26.129364 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:26.137327 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:26.137620 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:26.138093 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:26.139678 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:26.153190 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:26.153542 INFO: Indexing quadrupole dimension
1 day, 4:10:26.703061 INFO: Transposing detector events
1 day, 4:10:43.494724 INFO: Finished transposing data
1 day, 4:10:43.547404 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 4:10:43.552349 INFO: RT (min)            : 0.0 - 70.0
1 day, 4:10:43.552437 INFO: RT duration (sec)   : 4199.8
1 day, 4:10:43.552478 INFO: RT duration (min)   : 70.0
1 day, 4:10:43.552515 INFO: Cycle len (scans)   : 9
1 day, 4:10:43.552547 INFO: Cycle len (sec)     : 0.97
1 day, 4:10:43.552577 INFO: Number of cycles    : 4347
1 day, 4:10:43.552617 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 4:10:43.552751 INFO: Creating DIA data object took: 24.412603616714478
1 day, 4:10:43.641097 INFO: Initializing CalibrationManager
1 day, 4:10:43.641508 INFO: Setting up calibration estimators ..
1 day, 4:10:43.641575 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 4:10:43.641719 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, 4:10:43.641838 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 4:10:43.641903 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, 4:10:43.641986 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, 4:10:43.642078 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, 4:10:43.642134 INFO: Done setting up calibration estimators.
1 day, 4:10:43.642294 INFO: Initializing OptimizationManager
1 day, 4:10:43.642396 INFO: initial parameter: ms1_error = 30
1 day, 4:10:43.642445 INFO: initial parameter: ms2_error = 30
1 day, 4:10:43.642491 INFO: initial parameter: rt_error = 2099.8992935
1 day, 4:10:43.642533 INFO: initial parameter: mobility_error = 0.1
1 day, 4:10:43.642574 INFO: initial parameter: num_candidates = 1
1 day, 4:10:43.642615 INFO: initial parameter: fwhm_rt = 5
1 day, 4:10:43.642655 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 4:10:43.642696 INFO: initial parameter: score_cutoff = 0
1 day, 4:10:43.642735 INFO: initial parameter: classifier_version = -1
1 day, 4:10:43.642834 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 4:10:43.643322 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 4:10:43.643364 INFO: Initializing FDRManager
1 day, 4:10:43.643419 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 4:10:43.676300 PROGRESS: Initializing spectral library: 90,710 target precursors potentially observable (0 removed)
1 day, 4:10:43.695042 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 4:10:43.695517 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 2099.8992935
1 day, 4:10:43.695632 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 4:10:43.695812 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 4:10:43.695931 PROGRESS: Starting initial search for precursors.
1 day, 4:10:43.696015 INFO: Starting optimization step 0.
1 day, 4:10:43.696084 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:10:43.696161 INFO: Using classic extraction backend
1 day, 4:10:43.696540 PROGRESS: Extracting batch of 398 precursors
1 day, 4:10:43.696621 INFO: === Search parameters used ===
1 day, 4:10:43.696682 INFO: rt_error       : 2099.8992935
1 day, 4:10:43.696727 INFO: mobility_error : 0.1
1 day, 4:10:43.696768 INFO: num_candidates : 1
1 day, 4:10:43.696808 INFO: ms1_error      : 30
1 day, 4:10:43.696847 INFO: ms2_error      : 30
1 day, 4:10:43.696887 INFO: fwhm_rt        : 5
1 day, 4:10:43.696927 INFO: quant_window   : 3
1 day, 4:10:43.696966 INFO: ==============================================
1 day, 4:10:43.697965 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:10:43.698010 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:10:43.698057 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:10:43.698080 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:10:43.699214 INFO: Starting candidate selection
1 day, 4:10:48.260481 INFO: Starting candidate scoring
1 day, 4:10:48.373547 INFO: Finished candidate processing
1 day, 4:10:48.373704 INFO: Collecting candidate features
1 day, 4:10:48.383716 INFO: Collecting fragment features
1 day, 4:10:48.385902 INFO: Finished candidate scoring
1 day, 4:10:48.386829 INFO: performing precursor FDR with 47 features
1 day, 4:10:48.386873 INFO: Decoy channel: -1
1 day, 4:10:48.386896 INFO: Competetive: True
1 day, 4:10:48.388210 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:10:48.391186 INFO: Using random state 720225 for train-test-split
1 day, 4:10:48.403966 INFO: Test AUC: 0.512
1 day, 4:10:48.404061 INFO: Train AUC: 0.503
1 day, 4:10:48.404113 INFO: AUC difference: 1.73%
1 day, 4:10:48.646965 INFO: Resetting torch num_threads to 80
1 day, 4:10:48.647464 PROGRESS: === Extracted 398 precursors and 4587 fragments ===
1 day, 4:10:48.647928 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:10:48.648505 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:10:48.648596 PROGRESS: Total precursors accumulated: 200
1 day, 4:10:48.648658 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:10:48.648710 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:10:48.648757 PROGRESS: 
1 day, 4:10:48.648801 PROGRESS: Precursor Summary:
1 day, 4:10:48.649781 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:10:48.649871 PROGRESS: 
1 day, 4:10:48.649928 PROGRESS: Protein Summary:
1 day, 4:10:48.651079 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:10:48.651175 PROGRESS: =========================================================================
1 day, 4:10:48.651284 INFO: Target number of precursors reached.
1 day, 4:10:48.653268 INFO: fragments_df: keeping 1120 of 4587 [sum(precursor_idx_mask)=2299 sum(mass_error_mask)=4587 stop_rank=1120
1 day, 4:10:48.656439 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:10:48.755002 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:10:48.857435 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:10:48.962066 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:10:49.132706 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 4:10:49.133181 INFO: Using score_cutoff 50.45436492462158 (fac=0.99, q=1)
1 day, 4:10:49.133513 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.4368574619293213
1 day, 4:10:49.133596 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.01006571389734745
1 day, 4:10:49.133650 INFO: Updating optimization_manager: score_cutoff        : 0 -> 50.45436492462158
1 day, 4:10:49.133704 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:10:49.134754 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:10:49.135668 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:10:49.136365 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:10:49.137855 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 4:10:49.137950 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 4:10:49.138028 INFO: Starting optimization step 1.
1 day, 4:10:49.138099 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:10:49.138153 INFO: Using classic extraction backend
1 day, 4:10:49.138261 PROGRESS: Extracting batch of 398 precursors
1 day, 4:10:49.138322 INFO: === Search parameters used ===
1 day, 4:10:49.138366 INFO: rt_error       : 2099.8992935
1 day, 4:10:49.138407 INFO: mobility_error : 0.1
1 day, 4:10:49.138447 INFO: num_candidates : 3
1 day, 4:10:49.138488 INFO: ms1_error      : 30
1 day, 4:10:49.138528 INFO: ms2_error      : 30
1 day, 4:10:49.138570 INFO: fwhm_rt        : 3.4368574619293213
1 day, 4:10:49.138628 INFO: quant_window   : 3
1 day, 4:10:49.138670 INFO: ==============================================
1 day, 4:10:51.592935 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:10:51.593076 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:10:51.593120 INFO: FWHM in RT is 3.44 seconds, sigma is 0.76
1 day, 4:10:51.593142 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.67
1 day, 4:10:51.593963 INFO: Starting candidate selection
1 day, 4:10:55.747337 INFO: Starting candidate scoring
1 day, 4:10:55.930806 INFO: Finished candidate processing
1 day, 4:10:55.930919 INFO: Collecting candidate features
1 day, 4:10:55.941498 INFO: Collecting fragment features
1 day, 4:10:55.947280 INFO: Finished candidate scoring
1 day, 4:10:55.950262 INFO: performing precursor FDR with 47 features
1 day, 4:10:55.950370 INFO: Decoy channel: -1
1 day, 4:10:55.950438 INFO: Competetive: True
1 day, 4:10:55.956253 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:10:55.960236 INFO: Using random state 512978 for train-test-split
1 day, 4:10:55.972813 INFO: Test AUC: 0.500
1 day, 4:10:55.972912 INFO: Train AUC: 0.505
1 day, 4:10:55.972969 INFO: AUC difference: 1.05%
1 day, 4:10:56.197132 INFO: Resetting torch num_threads to 80
1 day, 4:10:56.197659 PROGRESS: === Extracted 1128 precursors and 12971 fragments ===
1 day, 4:10:56.198102 INFO: === FDR correction performed with classifier version 0 ===
1 day, 4:10:56.198679 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:10:56.198781 PROGRESS: Total precursors accumulated: 200
1 day, 4:10:56.198846 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:10:56.198902 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:10:56.198954 PROGRESS: 
1 day, 4:10:56.199003 PROGRESS: Precursor Summary:
1 day, 4:10:56.200009 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:10:56.200107 PROGRESS: 
1 day, 4:10:56.200168 PROGRESS: Protein Summary:
1 day, 4:10:56.201330 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:10:56.201422 PROGRESS: =========================================================================
1 day, 4:10:56.201548 INFO: Target number of precursors reached.
1 day, 4:10:56.204861 INFO: fragments_df: keeping 2236 of 12971 [sum(precursor_idx_mask)=6492 sum(mass_error_mask)=12971 stop_rank=2236
1 day, 4:10:56.208129 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:10:56.323608 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:10:56.443642 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:10:56.536471 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:10:56.784386 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:10:56.784893 INFO: Using score_cutoff 52.91207093009949 (fac=0.99, q=1)
1 day, 4:10:56.785220 INFO: Updating optimization_manager: fwhm_rt             : 3.4368574619293213 -> 3.3089354038238525
1 day, 4:10:56.785309 INFO: Updating optimization_manager: fwhm_mobility       : 0.01006571389734745 -> 0.009871488437056541
1 day, 4:10:56.785375 INFO: Updating optimization_manager: score_cutoff        : 50.45436492462158 -> 52.91207093009949
1 day, 4:10:56.785439 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:10:56.786549 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:10:56.787530 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:10:56.788264 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:10:56.789553 INFO: === checking if optimization conditions were reached ===
1 day, 4:10:56.790853 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 4:10:56.790967 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
1 day, 4:10:56.791044 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:10:56.792011 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 4:10:56.792115 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
1 day, 4:10:56.792188 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:10:56.792253 INFO: ==============================================
1 day, 4:10:56.792326 INFO: Starting optimization step 2.
1 day, 4:10:56.792395 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:10:56.792460 INFO: Using classic extraction backend
1 day, 4:10:56.792589 PROGRESS: Extracting batch of 398 precursors
1 day, 4:10:56.792664 INFO: === Search parameters used ===
1 day, 4:10:56.792722 INFO: rt_error       : 2099.8992935
1 day, 4:10:56.793054 INFO: mobility_error : 0.1
1 day, 4:10:56.793115 INFO: num_candidates : 3
1 day, 4:10:56.793167 INFO: ms1_error      : 15.0
1 day, 4:10:56.793219 INFO: ms2_error      : 15.0
1 day, 4:10:56.793271 INFO: fwhm_rt        : 3.3089354038238525
1 day, 4:10:56.793330 INFO: quant_window   : 3
1 day, 4:10:56.793383 INFO: ==============================================
1 day, 4:10:56.794248 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:10:56.794297 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:10:56.794341 INFO: FWHM in RT is 3.31 seconds, sigma is 0.73
1 day, 4:10:56.794368 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.58
1 day, 4:10:56.795018 INFO: Starting candidate selection
1 day, 4:11:00.376079 INFO: Starting candidate scoring
1 day, 4:11:00.483835 INFO: Finished candidate processing
1 day, 4:11:00.483945 INFO: Collecting candidate features
1 day, 4:11:00.494694 INFO: Collecting fragment features
1 day, 4:11:00.497489 INFO: Finished candidate scoring
1 day, 4:11:00.499363 INFO: performing precursor FDR with 47 features
1 day, 4:11:00.499411 INFO: Decoy channel: -1
1 day, 4:11:00.499435 INFO: Competetive: True
1 day, 4:11:00.502168 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:11:00.503983 INFO: Using random state 985094 for train-test-split
1 day, 4:11:00.511427 INFO: Test AUC: 0.494
1 day, 4:11:00.511486 INFO: Train AUC: 0.512
1 day, 4:11:00.511516 INFO: AUC difference: 3.47%
1 day, 4:11:00.727535 INFO: Resetting torch num_threads to 80
1 day, 4:11:00.728084 PROGRESS: === Extracted 1141 precursors and 12803 fragments ===
1 day, 4:11:00.728525 INFO: === FDR correction performed with classifier version 1 ===
1 day, 4:11:00.729125 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:11:00.729224 PROGRESS: Total precursors accumulated: 200
1 day, 4:11:00.729285 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:11:00.729335 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:11:00.729380 PROGRESS: 
1 day, 4:11:00.729425 PROGRESS: Precursor Summary:
1 day, 4:11:00.730422 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:11:00.730520 PROGRESS: 
1 day, 4:11:00.730577 PROGRESS: Protein Summary:
1 day, 4:11:00.731698 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:11:00.731788 PROGRESS: =========================================================================
1 day, 4:11:00.731908 INFO: Target number of precursors reached.
1 day, 4:11:00.735169 INFO: fragments_df: keeping 2199 of 12803 [sum(precursor_idx_mask)=6398 sum(mass_error_mask)=12803 stop_rank=2199
1 day, 4:11:00.738443 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:00.837839 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:00.935771 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:01.029219 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:01.271556 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:11:01.272073 INFO: Using score_cutoff 44.90810987091064 (fac=0.99, q=1)
1 day, 4:11:01.272395 INFO: Updating optimization_manager: fwhm_rt             : 3.3089354038238525 -> 2.833536148071289
1 day, 4:11:01.272487 INFO: Updating optimization_manager: fwhm_mobility       : 0.009871488437056541 -> 0.007889742963016033
1 day, 4:11:01.272557 INFO: Updating optimization_manager: score_cutoff        : 52.91207093009949 -> 44.90810987091064
1 day, 4:11:01.272627 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:01.273686 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:01.274659 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:01.275387 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:01.276617 INFO: === checking if optimization conditions were reached ===
1 day, 4:11:01.277920 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 4:11:01.278038 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 4:11:01.278128 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 4:11:01.279078 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 4:11:01.279184 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 4:11:01.279260 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 4:11:01.279330 INFO: ==============================================
1 day, 4:11:01.279411 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 4:11:01.282514 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:01.283281 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:01.284189 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:01.284898 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:01.286076 INFO: Starting optimization step 0.
1 day, 4:11:01.286184 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:11:01.286268 INFO: Using classic extraction backend
1 day, 4:11:01.286398 PROGRESS: Extracting batch of 398 precursors
1 day, 4:11:01.286481 INFO: === Search parameters used ===
1 day, 4:11:01.286548 INFO: rt_error       : 2099.8992935
1 day, 4:11:01.286612 INFO: mobility_error : 0.1
1 day, 4:11:01.286672 INFO: num_candidates : 3
1 day, 4:11:01.286730 INFO: ms1_error      : 15.0
1 day, 4:11:01.286788 INFO: ms2_error      : 15.0
1 day, 4:11:01.286844 INFO: fwhm_rt        : 2.833536148071289
1 day, 4:11:01.286901 INFO: quant_window   : 3
1 day, 4:11:01.286957 INFO: ==============================================
1 day, 4:11:01.287586 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:11:01.287638 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:11:01.287691 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1 day, 4:11:01.287729 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
1 day, 4:11:01.288404 INFO: Starting candidate selection
1 day, 4:11:05.533789 INFO: Starting candidate scoring
1 day, 4:11:05.639492 INFO: Finished candidate processing
1 day, 4:11:05.639617 INFO: Collecting candidate features
1 day, 4:11:05.649857 INFO: Collecting fragment features
1 day, 4:11:05.652835 INFO: Finished candidate scoring
1 day, 4:11:05.654370 INFO: performing precursor FDR with 47 features
1 day, 4:11:05.654417 INFO: Decoy channel: -1
1 day, 4:11:05.654442 INFO: Competetive: True
1 day, 4:11:05.657272 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:11:05.659093 INFO: Using random state 504846 for train-test-split
1 day, 4:11:05.666969 INFO: Test AUC: 0.521
1 day, 4:11:05.667029 INFO: Train AUC: 0.494
1 day, 4:11:05.667057 INFO: AUC difference: 5.66%
1 day, 4:11:05.667079 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:11:05.883341 INFO: Resetting torch num_threads to 80
1 day, 4:11:05.883889 PROGRESS: === Extracted 1144 precursors and 12810 fragments ===
1 day, 4:11:05.884325 INFO: === FDR correction performed with classifier version 2 ===
1 day, 4:11:05.884911 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:11:05.885010 PROGRESS: Total precursors accumulated: 200
1 day, 4:11:05.885070 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:11:05.885126 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:11:05.885176 PROGRESS: 
1 day, 4:11:05.885221 PROGRESS: Precursor Summary:
1 day, 4:11:05.886206 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:11:05.886299 PROGRESS: 
1 day, 4:11:05.886356 PROGRESS: Protein Summary:
1 day, 4:11:05.887456 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:11:05.887548 PROGRESS: =========================================================================
1 day, 4:11:05.887681 INFO: Target number of precursors reached.
1 day, 4:11:05.891110 INFO: fragments_df: keeping 2321 of 12810 [sum(precursor_idx_mask)=6410 sum(mass_error_mask)=12810 stop_rank=2321
1 day, 4:11:05.895174 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:05.992121 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:06.092118 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:06.189192 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:06.446204 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:11:06.446692 INFO: Using score_cutoff 44.435430151748655 (fac=0.99, q=1)
1 day, 4:11:06.446994 INFO: Updating optimization_manager: fwhm_rt             : 2.833536148071289 -> 2.809497594833374
1 day, 4:11:06.447073 INFO: Updating optimization_manager: fwhm_mobility       : 0.007889742963016033 -> 0.007788928225636482
1 day, 4:11:06.447127 INFO: Updating optimization_manager: score_cutoff        : 44.90810987091064 -> 44.435430151748655
1 day, 4:11:06.447185 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:06.448236 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:06.449153 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:06.449881 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:06.451144 INFO: === checking if optimization conditions were reached ===
1 day, 4:11:06.451244 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:11:06.452631 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 799.0596807438725
1 day, 4:11:06.452729 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 799.0597.
1 day, 4:11:06.452792 INFO: ==============================================
1 day, 4:11:06.452857 INFO: Starting optimization step 1.
1 day, 4:11:06.452912 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:11:06.452966 INFO: Using classic extraction backend
1 day, 4:11:06.453100 PROGRESS: Extracting batch of 398 precursors
1 day, 4:11:06.453175 INFO: === Search parameters used ===
1 day, 4:11:06.453223 INFO: rt_error       : 799.0596807438725
1 day, 4:11:06.453263 INFO: mobility_error : 0.1
1 day, 4:11:06.453303 INFO: num_candidates : 3
1 day, 4:11:06.453342 INFO: ms1_error      : 15.0
1 day, 4:11:06.453385 INFO: ms2_error      : 15.0
1 day, 4:11:06.453426 INFO: fwhm_rt        : 2.809497594833374
1 day, 4:11:06.453470 INFO: quant_window   : 3
1 day, 4:11:06.453511 INFO: ==============================================
1 day, 4:11:06.454224 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:11:06.454269 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:11:06.454302 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 4:11:06.454323 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 4:11:06.455213 INFO: Starting candidate selection
1 day, 4:11:08.120394 INFO: Starting candidate scoring
1 day, 4:11:08.231977 INFO: Finished candidate processing
1 day, 4:11:08.232086 INFO: Collecting candidate features
1 day, 4:11:08.242779 INFO: Collecting fragment features
1 day, 4:11:08.245782 INFO: Finished candidate scoring
1 day, 4:11:08.247469 INFO: performing precursor FDR with 47 features
1 day, 4:11:08.247516 INFO: Decoy channel: -1
1 day, 4:11:08.247541 INFO: Competetive: True
1 day, 4:11:08.250297 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:11:08.252117 INFO: Using random state 504846 for train-test-split
1 day, 4:11:08.259647 INFO: Test AUC: 0.507
1 day, 4:11:08.259705 INFO: Train AUC: 0.501
1 day, 4:11:08.259734 INFO: AUC difference: 1.26%
1 day, 4:11:08.479595 INFO: Resetting torch num_threads to 80
1 day, 4:11:08.480216 PROGRESS: === Extracted 1142 precursors and 12780 fragments ===
1 day, 4:11:08.480682 INFO: === FDR correction performed with classifier version 2 ===
1 day, 4:11:08.481289 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:11:08.481390 PROGRESS: Total precursors accumulated: 200
1 day, 4:11:08.481457 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:11:08.481508 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:11:08.481558 PROGRESS: 
1 day, 4:11:08.481602 PROGRESS: Precursor Summary:
1 day, 4:11:08.482597 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:11:08.482693 PROGRESS: 
1 day, 4:11:08.482749 PROGRESS: Protein Summary:
1 day, 4:11:08.483861 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:11:08.483952 PROGRESS: =========================================================================
1 day, 4:11:08.484105 INFO: Target number of precursors reached.
1 day, 4:11:08.487466 INFO: fragments_df: keeping 2331 of 12780 [sum(precursor_idx_mask)=6437 sum(mass_error_mask)=12780 stop_rank=2331
1 day, 4:11:08.491222 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:08.613829 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:08.732841 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:08.851878 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:09.172856 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:11:09.173351 INFO: Using score_cutoff 44.40342026252746 (fac=0.99, q=1)
1 day, 4:11:09.173667 INFO: Updating optimization_manager: fwhm_rt             : 2.809497594833374 -> 2.786423683166504
1 day, 4:11:09.173748 INFO: Updating optimization_manager: fwhm_mobility       : 0.007788928225636482 -> 0.00786142610013485
1 day, 4:11:09.173802 INFO: Updating optimization_manager: score_cutoff        : 44.435430151748655 -> 44.40342026252746
1 day, 4:11:09.173856 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:09.174958 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:09.175892 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:09.176590 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:09.177906 INFO: === checking if optimization conditions were reached ===
1 day, 4:11:09.178007 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:11:09.179588 INFO: Updating optimization_manager: rt_error            : 799.0596807438725 -> 750.6913338608053
1 day, 4:11:09.179724 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 750.6913.
1 day, 4:11:09.179789 INFO: ==============================================
1 day, 4:11:09.179853 INFO: Starting optimization step 2.
1 day, 4:11:09.179912 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:11:09.179971 INFO: Using classic extraction backend
1 day, 4:11:09.180093 PROGRESS: Extracting batch of 398 precursors
1 day, 4:11:09.180165 INFO: === Search parameters used ===
1 day, 4:11:09.180212 INFO: rt_error       : 750.6913338608053
1 day, 4:11:09.180258 INFO: mobility_error : 0.1
1 day, 4:11:09.180298 INFO: num_candidates : 3
1 day, 4:11:09.180337 INFO: ms1_error      : 15.0
1 day, 4:11:09.180375 INFO: ms2_error      : 15.0
1 day, 4:11:09.180412 INFO: fwhm_rt        : 2.786423683166504
1 day, 4:11:09.180451 INFO: quant_window   : 3
1 day, 4:11:09.180493 INFO: ==============================================
1 day, 4:11:09.181254 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:11:09.181299 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:11:09.181334 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 4:11:09.181356 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.65
1 day, 4:11:09.182072 INFO: Starting candidate selection
1 day, 4:11:10.560458 INFO: Starting candidate scoring
1 day, 4:11:10.680901 INFO: Finished candidate processing
1 day, 4:11:10.681016 INFO: Collecting candidate features
1 day, 4:11:10.691663 INFO: Collecting fragment features
1 day, 4:11:10.694379 INFO: Finished candidate scoring
1 day, 4:11:10.696013 INFO: performing precursor FDR with 47 features
1 day, 4:11:10.696056 INFO: Decoy channel: -1
1 day, 4:11:10.696090 INFO: Competetive: True
1 day, 4:11:10.698799 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:11:10.700624 INFO: Using random state 504846 for train-test-split
1 day, 4:11:10.708452 INFO: Test AUC: 0.504
1 day, 4:11:10.708510 INFO: Train AUC: 0.499
1 day, 4:11:10.708542 INFO: AUC difference: 0.86%
1 day, 4:11:10.935493 INFO: Resetting torch num_threads to 80
1 day, 4:11:10.936164 PROGRESS: === Extracted 1139 precursors and 12753 fragments ===
1 day, 4:11:10.936643 INFO: === FDR correction performed with classifier version 2 ===
1 day, 4:11:10.937259 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:11:10.937359 PROGRESS: Total precursors accumulated: 200
1 day, 4:11:10.937418 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:11:10.937467 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:11:10.937515 PROGRESS: 
1 day, 4:11:10.937558 PROGRESS: Precursor Summary:
1 day, 4:11:10.938576 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:11:10.938671 PROGRESS: 
1 day, 4:11:10.938729 PROGRESS: Protein Summary:
1 day, 4:11:10.939871 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:11:10.939964 PROGRESS: =========================================================================
1 day, 4:11:10.940183 INFO: Target number of precursors reached.
1 day, 4:11:10.943588 INFO: fragments_df: keeping 2296 of 12753 [sum(precursor_idx_mask)=6415 sum(mass_error_mask)=12753 stop_rank=2296
1 day, 4:11:10.948136 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:11.065269 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:11.185270 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:11.304770 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:11.615269 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:11:11.615751 INFO: Using score_cutoff 44.415078284454346 (fac=0.99, q=1)
1 day, 4:11:11.616070 INFO: Updating optimization_manager: fwhm_rt             : 2.786423683166504 -> 2.8052573204040527
1 day, 4:11:11.616151 INFO: Updating optimization_manager: fwhm_mobility       : 0.00786142610013485 -> 0.007859650999307632
1 day, 4:11:11.616204 INFO: Updating optimization_manager: score_cutoff        : 44.40342026252746 -> 44.415078284454346
1 day, 4:11:11.616259 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:11.617345 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:11.618267 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:11.618956 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:11.620238 INFO: === checking if optimization conditions were reached ===
1 day, 4:11:11.620338 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:11:11.621993 INFO: Updating optimization_manager: rt_error            : 750.6913338608053 -> 750.760711941798
1 day, 4:11:11.622112 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 750.7607.
1 day, 4:11:11.622179 INFO: ==============================================
1 day, 4:11:11.622245 INFO: Starting optimization step 3.
1 day, 4:11:11.622301 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:11:11.622356 INFO: Using classic extraction backend
1 day, 4:11:11.622479 PROGRESS: Extracting batch of 398 precursors
1 day, 4:11:11.622542 INFO: === Search parameters used ===
1 day, 4:11:11.622589 INFO: rt_error       : 750.760711941798
1 day, 4:11:11.622631 INFO: mobility_error : 0.1
1 day, 4:11:11.622673 INFO: num_candidates : 3
1 day, 4:11:11.622712 INFO: ms1_error      : 15.0
1 day, 4:11:11.622753 INFO: ms2_error      : 15.0
1 day, 4:11:11.622792 INFO: fwhm_rt        : 2.8052573204040527
1 day, 4:11:11.622830 INFO: quant_window   : 3
1 day, 4:11:11.622867 INFO: ==============================================
1 day, 4:11:11.623637 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:11:11.623682 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:11:11.623718 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 4:11:11.623744 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.65
1 day, 4:11:11.626485 INFO: Starting candidate selection
1 day, 4:11:12.999217 INFO: Starting candidate scoring
1 day, 4:11:13.119182 INFO: Finished candidate processing
1 day, 4:11:13.119291 INFO: Collecting candidate features
1 day, 4:11:13.129731 INFO: Collecting fragment features
1 day, 4:11:13.132411 INFO: Finished candidate scoring
1 day, 4:11:13.133903 INFO: performing precursor FDR with 47 features
1 day, 4:11:13.133945 INFO: Decoy channel: -1
1 day, 4:11:13.133969 INFO: Competetive: True
1 day, 4:11:13.136594 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:11:13.138417 INFO: Using random state 504846 for train-test-split
1 day, 4:11:13.145803 INFO: Test AUC: 0.493
1 day, 4:11:13.145859 INFO: Train AUC: 0.504
1 day, 4:11:13.145888 INFO: AUC difference: 2.27%
1 day, 4:11:13.371107 INFO: Resetting torch num_threads to 80
1 day, 4:11:13.371731 PROGRESS: === Extracted 1142 precursors and 12783 fragments ===
1 day, 4:11:13.372185 INFO: === FDR correction performed with classifier version 2 ===
1 day, 4:11:13.372777 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:11:13.372866 PROGRESS: Total precursors accumulated: 200
1 day, 4:11:13.372926 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:11:13.372974 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:11:13.375151 PROGRESS: 
1 day, 4:11:13.375212 PROGRESS: Precursor Summary:
1 day, 4:11:13.376238 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:11:13.376325 PROGRESS: 
1 day, 4:11:13.376381 PROGRESS: Protein Summary:
1 day, 4:11:13.377485 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:11:13.377570 PROGRESS: =========================================================================
1 day, 4:11:13.377717 INFO: Target number of precursors reached.
1 day, 4:11:13.381079 INFO: fragments_df: keeping 2307 of 12783 [sum(precursor_idx_mask)=6426 sum(mass_error_mask)=12783 stop_rank=2307
1 day, 4:11:13.386830 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:13.487623 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:13.591873 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:13.720027 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:14.036863 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:11:14.037343 INFO: Using score_cutoff 44.42089251022339 (fac=0.99, q=1)
1 day, 4:11:14.037689 INFO: Updating optimization_manager: fwhm_rt             : 2.8052573204040527 -> 2.7902536392211914
1 day, 4:11:14.037772 INFO: Updating optimization_manager: fwhm_mobility       : 0.007859650999307632 -> 0.007859650999307632
1 day, 4:11:14.037826 INFO: Updating optimization_manager: score_cutoff        : 44.415078284454346 -> 44.42089251022339
1 day, 4:11:14.037892 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:14.039067 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:14.040017 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:14.040704 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:14.042018 INFO: === checking if optimization conditions were reached ===
1 day, 4:11:14.042148 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 4:11:14.043231 INFO: Updating optimization_manager: rt_error            : 750.760711941798 -> 750.6913338608053
1 day, 4:11:14.043353 INFO: Updating optimization_manager: classifier_version  : 2 -> 5
1 day, 4:11:14.043444 INFO: Updating optimization_manager: score_cutoff        : 44.42089251022339 -> 44.415078284454346
1 day, 4:11:14.043538 INFO: Updating optimization_manager: fwhm_rt             : 2.7902536392211914 -> 2.8052573204040527
1 day, 4:11:14.043620 INFO: Updating optimization_manager: fwhm_mobility       : 0.007859650999307632 -> 0.007859650999307632
1 day, 4:11:14.043698 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 750.6913 found after 4 searches.
1 day, 4:11:14.043758 INFO: ==============================================
1 day, 4:11:14.043832 PROGRESS: Optimization finished for rt_error.
1 day, 4:11:14.047053 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:14.047773 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:14.048629 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:14.049303 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:14.075299 INFO: Starting optimization step 0.
1 day, 4:11:14.075430 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:11:14.075512 INFO: Using classic extraction backend
1 day, 4:11:14.075680 PROGRESS: Extracting batch of 398 precursors
1 day, 4:11:14.075754 INFO: === Search parameters used ===
1 day, 4:11:14.075803 INFO: rt_error       : 750.6913338608053
1 day, 4:11:14.075847 INFO: mobility_error : 0.1
1 day, 4:11:14.075889 INFO: num_candidates : 3
1 day, 4:11:14.075930 INFO: ms1_error      : 15.0
1 day, 4:11:14.075971 INFO: ms2_error      : 15.0
1 day, 4:11:14.076016 INFO: fwhm_rt        : 2.8052573204040527
1 day, 4:11:14.076060 INFO: quant_window   : 3
1 day, 4:11:14.076101 INFO: ==============================================
1 day, 4:11:14.076851 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:11:14.076896 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:11:14.076931 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 4:11:14.076953 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.65
1 day, 4:11:14.077690 INFO: Starting candidate selection
1 day, 4:11:15.629068 INFO: Starting candidate scoring
1 day, 4:11:15.746169 INFO: Finished candidate processing
1 day, 4:11:15.746289 INFO: Collecting candidate features
1 day, 4:11:15.757514 INFO: Collecting fragment features
1 day, 4:11:15.760396 INFO: Finished candidate scoring
1 day, 4:11:15.761725 INFO: performing precursor FDR with 47 features
1 day, 4:11:15.761769 INFO: Decoy channel: -1
1 day, 4:11:15.761794 INFO: Competetive: True
1 day, 4:11:15.766085 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:11:15.769073 INFO: Using random state 56303 for train-test-split
1 day, 4:11:15.778193 INFO: Test AUC: 0.504
1 day, 4:11:15.778250 INFO: Train AUC: 0.503
1 day, 4:11:15.778281 INFO: AUC difference: 0.11%
1 day, 4:11:16.001849 INFO: Resetting torch num_threads to 80
1 day, 4:11:16.002394 PROGRESS: === Extracted 1144 precursors and 12798 fragments ===
1 day, 4:11:16.002841 INFO: === FDR correction performed with classifier version 5 ===
1 day, 4:11:16.003397 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:11:16.003492 PROGRESS: Total precursors accumulated: 200
1 day, 4:11:16.003552 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:11:16.003603 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:11:16.003654 PROGRESS: 
1 day, 4:11:16.003699 PROGRESS: Precursor Summary:
1 day, 4:11:16.004671 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:11:16.004759 PROGRESS: 
1 day, 4:11:16.004815 PROGRESS: Protein Summary:
1 day, 4:11:16.005951 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:11:16.006051 PROGRESS: =========================================================================
1 day, 4:11:16.006434 INFO: Target number of precursors reached.
1 day, 4:11:16.010279 INFO: fragments_df: keeping 2283 of 12798 [sum(precursor_idx_mask)=6425 sum(mass_error_mask)=12798 stop_rank=2283
1 day, 4:11:16.015103 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:16.116606 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:16.217700 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:16.315785 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:16.571800 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:11:16.572230 INFO: Using score_cutoff 44.42489973220825 (fac=0.99, q=1)
1 day, 4:11:16.572593 INFO: Updating optimization_manager: fwhm_rt             : 2.8052573204040527 -> 2.780242919921875
1 day, 4:11:16.572672 INFO: Updating optimization_manager: fwhm_mobility       : 0.007859650999307632 -> 0.007887656800448895
1 day, 4:11:16.572725 INFO: Updating optimization_manager: score_cutoff        : 44.415078284454346 -> 44.42489973220825
1 day, 4:11:16.572780 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:16.573787 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:16.574678 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:16.575364 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:16.576555 INFO: === checking if optimization conditions were reached ===
1 day, 4:11:16.576671 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:11:16.577997 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0887655619146256
1 day, 4:11:16.578112 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0888.
1 day, 4:11:16.578176 INFO: ==============================================
1 day, 4:11:16.578245 INFO: Starting optimization step 1.
1 day, 4:11:16.578304 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:11:16.578366 INFO: Using classic extraction backend
1 day, 4:11:16.578516 PROGRESS: Extracting batch of 398 precursors
1 day, 4:11:16.578585 INFO: === Search parameters used ===
1 day, 4:11:16.578631 INFO: rt_error       : 750.6913338608053
1 day, 4:11:16.578673 INFO: mobility_error : 0.0887655619146256
1 day, 4:11:16.578713 INFO: num_candidates : 3
1 day, 4:11:16.578753 INFO: ms1_error      : 15.0
1 day, 4:11:16.578792 INFO: ms2_error      : 15.0
1 day, 4:11:16.578832 INFO: fwhm_rt        : 2.780242919921875
1 day, 4:11:16.578870 INFO: quant_window   : 3
1 day, 4:11:16.578907 INFO: ==============================================
1 day, 4:11:16.579719 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:11:16.579765 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:11:16.579809 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1 day, 4:11:16.579831 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
1 day, 4:11:16.580509 INFO: Starting candidate selection
1 day, 4:11:18.084981 INFO: Starting candidate scoring
1 day, 4:11:18.207689 INFO: Finished candidate processing
1 day, 4:11:18.207811 INFO: Collecting candidate features
1 day, 4:11:18.218472 INFO: Collecting fragment features
1 day, 4:11:18.221151 INFO: Finished candidate scoring
1 day, 4:11:18.222395 INFO: performing precursor FDR with 47 features
1 day, 4:11:18.222442 INFO: Decoy channel: -1
1 day, 4:11:18.222466 INFO: Competetive: True
1 day, 4:11:18.225226 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:11:18.227158 INFO: Using random state 56303 for train-test-split
1 day, 4:11:18.235246 INFO: Test AUC: 0.502
1 day, 4:11:18.235312 INFO: Train AUC: 0.502
1 day, 4:11:18.235343 INFO: AUC difference: 0.07%
1 day, 4:11:18.458359 INFO: Resetting torch num_threads to 80
1 day, 4:11:18.458971 PROGRESS: === Extracted 1143 precursors and 12772 fragments ===
1 day, 4:11:18.459452 INFO: === FDR correction performed with classifier version 5 ===
1 day, 4:11:18.460070 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:11:18.460166 PROGRESS: Total precursors accumulated: 200
1 day, 4:11:18.460233 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:11:18.460285 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:11:18.460339 PROGRESS: 
1 day, 4:11:18.460383 PROGRESS: Precursor Summary:
1 day, 4:11:18.461548 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:11:18.461638 PROGRESS: 
1 day, 4:11:18.461698 PROGRESS: Protein Summary:
1 day, 4:11:18.462882 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:11:18.462982 PROGRESS: =========================================================================
1 day, 4:11:18.463143 INFO: Target number of precursors reached.
1 day, 4:11:18.466559 INFO: fragments_df: keeping 2293 of 12772 [sum(precursor_idx_mask)=6407 sum(mass_error_mask)=12772 stop_rank=2293
1 day, 4:11:18.470113 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:18.594969 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:18.717896 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:18.841746 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:19.110650 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:11:19.111126 INFO: Using score_cutoff 43.92501280059814 (fac=0.99, q=1)
1 day, 4:11:19.111443 INFO: Updating optimization_manager: fwhm_rt             : 2.780242919921875 -> 2.8331241607666016
1 day, 4:11:19.111524 INFO: Updating optimization_manager: fwhm_mobility       : 0.007887656800448895 -> 0.007887656800448895
1 day, 4:11:19.111580 INFO: Updating optimization_manager: score_cutoff        : 44.42489973220825 -> 43.92501280059814
1 day, 4:11:19.111643 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:19.112759 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:19.113652 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:19.114346 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:19.115610 INFO: === checking if optimization conditions were reached ===
1 day, 4:11:19.115728 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:11:19.117271 INFO: Updating optimization_manager: mobility_error      : 0.0887655619146256 -> 0.07823671426547797
1 day, 4:11:19.117371 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0782.
1 day, 4:11:19.117436 INFO: ==============================================
1 day, 4:11:19.117503 INFO: Starting optimization step 2.
1 day, 4:11:19.117562 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:11:19.117618 INFO: Using classic extraction backend
1 day, 4:11:19.117744 PROGRESS: Extracting batch of 398 precursors
1 day, 4:11:19.117812 INFO: === Search parameters used ===
1 day, 4:11:19.117863 INFO: rt_error       : 750.6913338608053
1 day, 4:11:19.117906 INFO: mobility_error : 0.07823671426547797
1 day, 4:11:19.117947 INFO: num_candidates : 3
1 day, 4:11:19.117988 INFO: ms1_error      : 15.0
1 day, 4:11:19.118026 INFO: ms2_error      : 15.0
1 day, 4:11:19.118077 INFO: fwhm_rt        : 2.8331241607666016
1 day, 4:11:19.118128 INFO: quant_window   : 3
1 day, 4:11:19.118169 INFO: ==============================================
1 day, 4:11:19.118889 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:11:19.118934 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:11:19.118969 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1 day, 4:11:19.118994 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
1 day, 4:11:19.120585 INFO: Starting candidate selection
1 day, 4:11:20.888519 INFO: Starting candidate scoring
1 day, 4:11:21.011869 INFO: Finished candidate processing
1 day, 4:11:21.012965 INFO: Collecting candidate features
1 day, 4:11:21.023061 INFO: Collecting fragment features
1 day, 4:11:21.025553 INFO: Finished candidate scoring
1 day, 4:11:21.026532 INFO: performing precursor FDR with 47 features
1 day, 4:11:21.026578 INFO: Decoy channel: -1
1 day, 4:11:21.026603 INFO: Competetive: True
1 day, 4:11:21.029145 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:11:21.030878 INFO: Using random state 56303 for train-test-split
1 day, 4:11:21.038003 INFO: Test AUC: 0.476
1 day, 4:11:21.038067 INFO: Train AUC: 0.508
1 day, 4:11:21.038098 INFO: AUC difference: 6.48%
1 day, 4:11:21.038120 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:11:21.259829 INFO: Resetting torch num_threads to 80
1 day, 4:11:21.260307 PROGRESS: === Extracted 1141 precursors and 12729 fragments ===
1 day, 4:11:21.260723 INFO: === FDR correction performed with classifier version 5 ===
1 day, 4:11:21.261273 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:11:21.261364 PROGRESS: Total precursors accumulated: 200
1 day, 4:11:21.261427 PROGRESS: Target precursors: 200 (100.00%)
1 day, 4:11:21.261478 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:11:21.261525 PROGRESS: 
1 day, 4:11:21.261570 PROGRESS: Precursor Summary:
1 day, 4:11:21.262548 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 4:11:21.262641 PROGRESS: 
1 day, 4:11:21.262699 PROGRESS: Protein Summary:
1 day, 4:11:21.263797 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
1 day, 4:11:21.263887 PROGRESS: =========================================================================
1 day, 4:11:21.264013 INFO: Target number of precursors reached.
1 day, 4:11:21.267130 INFO: fragments_df: keeping 2285 of 12729 [sum(precursor_idx_mask)=6413 sum(mass_error_mask)=12729 stop_rank=2285
1 day, 4:11:21.270234 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:21.391711 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:21.491367 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:21.628414 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:21.935673 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:11:21.936152 INFO: Using score_cutoff 43.8791254863739 (fac=0.99, q=1)
1 day, 4:11:21.936465 INFO: Updating optimization_manager: fwhm_rt             : 2.8331241607666016 -> 2.813236951828003
1 day, 4:11:21.936546 INFO: Updating optimization_manager: fwhm_mobility       : 0.007887656800448895 -> 0.007911350578069687
1 day, 4:11:21.936601 INFO: Updating optimization_manager: score_cutoff        : 43.92501280059814 -> 43.8791254863739
1 day, 4:11:21.936655 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:21.937695 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:21.938592 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:21.939275 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:21.940549 INFO: === checking if optimization conditions were reached ===
1 day, 4:11:21.940662 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:11:21.941440 INFO: Updating optimization_manager: mobility_error      : 0.07823671426547797 -> 0.1
1 day, 4:11:21.941562 INFO: Updating optimization_manager: classifier_version  : 5 -> 7
1 day, 4:11:21.941656 INFO: Updating optimization_manager: score_cutoff        : 43.8791254863739 -> 44.42489973220825
1 day, 4:11:21.941749 INFO: Updating optimization_manager: fwhm_rt             : 2.813236951828003 -> 2.780242919921875
1 day, 4:11:21.941860 INFO: Updating optimization_manager: fwhm_mobility       : 0.007911350578069687 -> 0.007887656800448895
1 day, 4:11:21.941968 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 4:11:21.943410 INFO: ==============================================
1 day, 4:11:21.943493 PROGRESS: Optimization finished for mobility_error.
1 day, 4:11:21.946425 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:21.947163 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:21.948028 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:21.948715 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:21.974588 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 4:11:21.974721 PROGRESS: ==============================================
1 day, 4:11:21.974796 PROGRESS: ms2_error      : 15.0000
1 day, 4:11:21.974867 PROGRESS: ms1_error      : 15.0000
1 day, 4:11:21.974922 PROGRESS: rt_error       : 750.6913
1 day, 4:11:21.974972 PROGRESS: mobility_error : 0.1000
1 day, 4:11:21.975017 PROGRESS: ==============================================
1 day, 4:11:21.975557 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:11:22.001973 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:11:22.108435 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:11:22.136808 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:11:22.413511 INFO: Using classic extraction backend
1 day, 4:11:22.413900 PROGRESS: Extracting batch of 180112 precursors
1 day, 4:11:22.414016 INFO: === Search parameters used ===
1 day, 4:11:22.414125 INFO: rt_error       : 750.6913338608053
1 day, 4:11:22.414202 INFO: mobility_error : 0.1
1 day, 4:11:22.414272 INFO: num_candidates : 3
1 day, 4:11:22.414343 INFO: ms1_error      : 15.0
1 day, 4:11:22.414425 INFO: ms2_error      : 15.0
1 day, 4:11:22.414506 INFO: fwhm_rt        : 2.780242919921875
1 day, 4:11:22.414577 INFO: quant_window   : 3
1 day, 4:11:22.414645 INFO: ==============================================
1 day, 4:11:22.461219 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:11:22.461375 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:11:22.461425 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1 day, 4:11:22.461451 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
1 day, 4:11:22.478419 INFO: Starting candidate selection
1 day, 4:18:15.078508 INFO: Removed 72008 precursors with score below cutoff 44.42489973220825
1 day, 4:18:15.437477 INFO: Starting candidate scoring
1 day, 4:18:35.634433 INFO: Finished candidate processing
1 day, 4:18:35.634845 INFO: Collecting candidate features
1 day, 4:18:36.275275 INFO: Collecting fragment features
1 day, 4:18:36.616566 INFO: Finished candidate scoring
1 day, 4:18:36.964353 INFO: === Performing FDR correction with classifier version 7 ===
1 day, 4:18:36.965765 INFO: performing precursor FDR with 47 features
1 day, 4:18:36.965801 INFO: Decoy channel: -1
1 day, 4:18:36.965825 INFO: Competetive: True
1 day, 4:18:37.087547 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:18:37.135330 WARNING: FDR calculation for 233749 target and 204784 decoy PSMs
1 day, 4:18:37.135490 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 4:18:37.267234 INFO: Using random state 564430 for train-test-split
1 day, 4:18:44.694230 INFO: Test AUC: 0.756
1 day, 4:18:44.694379 INFO: Train AUC: 0.756
1 day, 4:18:44.694412 INFO: AUC difference: 0.02%
1 day, 4:18:45.101511 INFO: Resetting torch num_threads to 80
1 day, 4:18:45.119082 INFO: Removing fragments below FDR threshold
1 day, 4:18:45.205939 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:18:45.206260 PROGRESS: Total precursors accumulated: 76,591
1 day, 4:18:45.206327 PROGRESS: Target precursors: 75,833 (99.01%)
1 day, 4:18:45.206379 PROGRESS: Decoy precursors: 758 (0.99%)
1 day, 4:18:45.206425 PROGRESS: 
1 day, 4:18:45.206468 PROGRESS: Precursor Summary:
1 day, 4:18:45.238311 PROGRESS: Channel   0:	 0.050 FDR: 75,833; 0.010 FDR: 75,833; 0.001 FDR: 70,655
1 day, 4:18:45.238627 PROGRESS: 
1 day, 4:18:45.238689 PROGRESS: Protein Summary:
1 day, 4:18:45.282207 PROGRESS: Channel   0:	 0.050 FDR: 8,644; 0.010 FDR: 8,644; 0.001 FDR: 8,516
1 day, 4:18:45.282518 PROGRESS: =========================================================================
1 day, 4:18:45.287138 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/psm.parquet
1 day, 4:18:45.598257 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/frag.parquet
1 day, 4:18:45.883379 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 4:18:47.120115 PROGRESS: 
1 day, 4:18:47.120291 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/quant
1 day, 4:18:47.120380 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/figures
1 day, 4:18:47.120573 INFO: Initializing TimingManager
1 day, 4:18:47.121120 INFO: Initializing RawFileManager
1 day, 4:18:47.121228 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:47.121282 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:47.121324 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:47.462935 INFO: Reading 39,128 frames with 2,751,035,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:53.792394 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
1 day, 4:18:53.794419 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:53.799756 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:53.800292 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:53.800883 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:53.802835 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:53.817690 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:18:53.818175 INFO: Indexing quadrupole dimension
1 day, 4:18:54.417156 INFO: Transposing detector events
1 day, 4:19:07.769346 INFO: Finished transposing data
1 day, 4:19:07.813164 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:19:07.815529 INFO: RT (min)            : 0.0 - 70.0
1 day, 4:19:07.815629 INFO: RT duration (sec)   : 4199.8
1 day, 4:19:07.815687 INFO: RT duration (min)   : 70.0
1 day, 4:19:07.815738 INFO: Cycle len (scans)   : 9
1 day, 4:19:07.815784 INFO: Cycle len (sec)     : 0.97
1 day, 4:19:07.815829 INFO: Number of cycles    : 4347
1 day, 4:19:07.815877 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 4:19:07.815983 INFO: Creating DIA data object took: 20.69473910331726
1 day, 4:19:07.872895 INFO: Initializing CalibrationManager
1 day, 4:19:07.873239 INFO: Setting up calibration estimators ..
1 day, 4:19:07.873303 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 4:19:07.873387 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, 4:19:07.873474 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 4:19:07.873531 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, 4:19:07.873589 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, 4:19:07.873667 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, 4:19:07.873735 INFO: Done setting up calibration estimators.
1 day, 4:19:07.873857 INFO: Initializing OptimizationManager
1 day, 4:19:07.873948 INFO: initial parameter: ms1_error = 30
1 day, 4:19:07.873992 INFO: initial parameter: ms2_error = 30
1 day, 4:19:07.874036 INFO: initial parameter: rt_error = 2099.891532
1 day, 4:19:07.874089 INFO: initial parameter: mobility_error = 0.1
1 day, 4:19:07.874130 INFO: initial parameter: num_candidates = 1
1 day, 4:19:07.874168 INFO: initial parameter: fwhm_rt = 5
1 day, 4:19:07.874211 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 4:19:07.874250 INFO: initial parameter: score_cutoff = 0
1 day, 4:19:07.874289 INFO: initial parameter: classifier_version = -1
1 day, 4:19:07.874365 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 4:19:07.874663 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 4:19:07.874698 INFO: Initializing FDRManager
1 day, 4:19:07.874738 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 4:19:07.898532 PROGRESS: Initializing spectral library: 90,710 target precursors potentially observable (0 removed)
1 day, 4:19:07.913687 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 4:19:07.914127 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 2099.891532
1 day, 4:19:07.914246 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 4:19:07.914419 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 4:19:07.914507 PROGRESS: Starting initial search for precursors.
1 day, 4:19:07.914584 INFO: Starting optimization step 0.
1 day, 4:19:07.914643 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:19:07.914715 INFO: Using classic extraction backend
1 day, 4:19:07.914941 PROGRESS: Extracting batch of 398 precursors
1 day, 4:19:07.915022 INFO: === Search parameters used ===
1 day, 4:19:07.915077 INFO: rt_error       : 2099.891532
1 day, 4:19:07.915122 INFO: mobility_error : 0.1
1 day, 4:19:07.915163 INFO: num_candidates : 1
1 day, 4:19:07.915203 INFO: ms1_error      : 30
1 day, 4:19:07.915241 INFO: ms2_error      : 30
1 day, 4:19:07.915281 INFO: fwhm_rt        : 5
1 day, 4:19:07.915321 INFO: quant_window   : 3
1 day, 4:19:07.915361 INFO: ==============================================
1 day, 4:19:07.916171 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:19:07.916216 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:19:07.916252 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:19:07.916274 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:19:07.919978 INFO: Starting candidate selection
1 day, 4:19:12.063372 INFO: Starting candidate scoring
1 day, 4:19:12.141527 INFO: Finished candidate processing
1 day, 4:19:12.141704 INFO: Collecting candidate features
1 day, 4:19:12.152575 INFO: Collecting fragment features
1 day, 4:19:12.155058 INFO: Finished candidate scoring
1 day, 4:19:12.156014 INFO: performing precursor FDR with 47 features
1 day, 4:19:12.156056 INFO: Decoy channel: -1
1 day, 4:19:12.156080 INFO: Competetive: True
1 day, 4:19:12.157796 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:19:12.160757 INFO: Using random state 268383 for train-test-split
1 day, 4:19:12.172032 INFO: Test AUC: 0.497
1 day, 4:19:12.172151 INFO: Train AUC: 0.501
1 day, 4:19:12.172184 INFO: AUC difference: 0.71%
1 day, 4:19:12.394570 INFO: Resetting torch num_threads to 80
1 day, 4:19:12.395051 PROGRESS: === Extracted 398 precursors and 4584 fragments ===
1 day, 4:19:12.395490 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:19:12.396052 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:19:12.396149 PROGRESS: Total precursors accumulated: 200
1 day, 4:19:12.396209 PROGRESS: Target precursors: 172 (86.00%)
1 day, 4:19:12.396265 PROGRESS: Decoy precursors: 28 (14.00%)
1 day, 4:19:12.396311 PROGRESS: 
1 day, 4:19:12.396356 PROGRESS: Precursor Summary:
1 day, 4:19:12.397184 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:19:12.397277 PROGRESS: 
1 day, 4:19:12.397336 PROGRESS: Protein Summary:
1 day, 4:19:12.398253 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:19:12.398343 PROGRESS: =========================================================================
1 day, 4:19:12.398448 INFO: Target number of precursors not reached yet.
1 day, 4:19:12.401942 INFO: Starting optimization step 1.
1 day, 4:19:12.402057 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 4:19:12.402134 INFO: Using classic extraction backend
1 day, 4:19:12.402246 PROGRESS: Extracting batch of 796 precursors
1 day, 4:19:12.402316 INFO: === Search parameters used ===
1 day, 4:19:12.402367 INFO: rt_error       : 2099.891532
1 day, 4:19:12.402410 INFO: mobility_error : 0.1
1 day, 4:19:12.402452 INFO: num_candidates : 1
1 day, 4:19:12.402493 INFO: ms1_error      : 30
1 day, 4:19:12.402534 INFO: ms2_error      : 30
1 day, 4:19:12.402575 INFO: fwhm_rt        : 5
1 day, 4:19:12.402615 INFO: quant_window   : 3
1 day, 4:19:12.402657 INFO: ==============================================
1 day, 4:19:12.403272 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:19:12.403319 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:19:12.403347 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:19:12.403368 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:19:12.404078 INFO: Starting candidate selection
1 day, 4:19:19.033517 INFO: Starting candidate scoring
1 day, 4:19:19.163826 INFO: Finished candidate processing
1 day, 4:19:19.163969 INFO: Collecting candidate features
1 day, 4:19:19.179705 INFO: Collecting fragment features
1 day, 4:19:19.183701 INFO: Finished candidate scoring
1 day, 4:19:19.186925 INFO: performing precursor FDR with 47 features
1 day, 4:19:19.187004 INFO: Decoy channel: -1
1 day, 4:19:19.187046 INFO: Competetive: True
1 day, 4:19:19.191763 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:19:19.194682 INFO: Using random state 329297 for train-test-split
1 day, 4:19:19.207491 INFO: Test AUC: 0.483
1 day, 4:19:19.207588 INFO: Train AUC: 0.501
1 day, 4:19:19.207638 INFO: AUC difference: 3.54%
1 day, 4:19:19.425104 INFO: Resetting torch num_threads to 80
1 day, 4:19:19.426402 PROGRESS: === Extracted 1194 precursors and 13599 fragments ===
1 day, 4:19:19.426818 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:19:19.427409 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:19:19.427495 PROGRESS: Total precursors accumulated: 600
1 day, 4:19:19.427554 PROGRESS: Target precursors: 520 (86.67%)
1 day, 4:19:19.427610 PROGRESS: Decoy precursors: 80 (13.33%)
1 day, 4:19:19.427661 PROGRESS: 
1 day, 4:19:19.427705 PROGRESS: Precursor Summary:
1 day, 4:19:19.428533 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:19:19.428618 PROGRESS: 
1 day, 4:19:19.428673 PROGRESS: Protein Summary:
1 day, 4:19:19.429572 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:19:19.429657 PROGRESS: =========================================================================
1 day, 4:19:19.429806 INFO: Target number of precursors not reached yet.
1 day, 4:19:19.434220 INFO: Starting optimization step 2.
1 day, 4:19:19.434323 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 4:19:19.434394 INFO: Using classic extraction backend
1 day, 4:19:19.434503 PROGRESS: Extracting batch of 1593 precursors
1 day, 4:19:19.434572 INFO: === Search parameters used ===
1 day, 4:19:19.434619 INFO: rt_error       : 2099.891532
1 day, 4:19:19.434663 INFO: mobility_error : 0.1
1 day, 4:19:19.434717 INFO: num_candidates : 1
1 day, 4:19:19.434763 INFO: ms1_error      : 30
1 day, 4:19:19.434804 INFO: ms2_error      : 30
1 day, 4:19:19.434843 INFO: fwhm_rt        : 5
1 day, 4:19:19.434882 INFO: quant_window   : 3
1 day, 4:19:19.434921 INFO: ==============================================
1 day, 4:19:19.435689 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:19:19.435734 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:19:19.435762 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:19:19.435784 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:19:19.436478 INFO: Starting candidate selection
1 day, 4:19:31.119351 INFO: Starting candidate scoring
1 day, 4:19:31.309511 INFO: Finished candidate processing
1 day, 4:19:31.309628 INFO: Collecting candidate features
1 day, 4:19:31.320797 INFO: Collecting fragment features
1 day, 4:19:31.324088 INFO: Finished candidate scoring
1 day, 4:19:31.327193 INFO: performing precursor FDR with 47 features
1 day, 4:19:31.327244 INFO: Decoy channel: -1
1 day, 4:19:31.327270 INFO: Competetive: True
1 day, 4:19:31.331125 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:19:31.333358 INFO: Using random state 123023 for train-test-split
1 day, 4:19:31.344854 INFO: Test AUC: 0.501
1 day, 4:19:31.344910 INFO: Train AUC: 0.497
1 day, 4:19:31.344940 INFO: AUC difference: 0.85%
1 day, 4:19:31.560053 INFO: Resetting torch num_threads to 80
1 day, 4:19:31.561639 PROGRESS: === Extracted 2785 precursors and 31667 fragments ===
1 day, 4:19:31.562077 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:19:31.562780 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:19:31.562878 PROGRESS: Total precursors accumulated: 1,400
1 day, 4:19:31.562938 PROGRESS: Target precursors: 1,209 (86.36%)
1 day, 4:19:31.562988 PROGRESS: Decoy precursors: 191 (13.64%)
1 day, 4:19:31.563036 PROGRESS: 
1 day, 4:19:31.563080 PROGRESS: Precursor Summary:
1 day, 4:19:31.563914 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:19:31.564004 PROGRESS: 
1 day, 4:19:31.564059 PROGRESS: Protein Summary:
1 day, 4:19:31.564963 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 4:19:31.565051 PROGRESS: =========================================================================
1 day, 4:19:31.565223 INFO: Target number of precursors not reached yet.
1 day, 4:19:31.571287 INFO: Starting optimization step 3.
1 day, 4:19:31.571396 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 4:19:31.571465 INFO: Using classic extraction backend
1 day, 4:19:31.571578 PROGRESS: Extracting batch of 3169 precursors
1 day, 4:19:31.571643 INFO: === Search parameters used ===
1 day, 4:19:31.571693 INFO: rt_error       : 2099.891532
1 day, 4:19:31.571738 INFO: mobility_error : 0.1
1 day, 4:19:31.571789 INFO: num_candidates : 1
1 day, 4:19:31.571833 INFO: ms1_error      : 30
1 day, 4:19:31.571874 INFO: ms2_error      : 30
1 day, 4:19:31.571913 INFO: fwhm_rt        : 5
1 day, 4:19:31.571953 INFO: quant_window   : 3
1 day, 4:19:31.571992 INFO: ==============================================
1 day, 4:19:31.572933 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:19:31.572978 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:19:31.573005 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:19:31.573026 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:19:31.573669 INFO: Starting candidate selection
1 day, 4:19:53.429078 INFO: Starting candidate scoring
1 day, 4:19:53.818818 INFO: Finished candidate processing
1 day, 4:19:53.819006 INFO: Collecting candidate features
1 day, 4:19:53.850025 INFO: Collecting fragment features
1 day, 4:19:53.861011 INFO: Finished candidate scoring
1 day, 4:19:53.873499 INFO: performing precursor FDR with 47 features
1 day, 4:19:53.873596 INFO: Decoy channel: -1
1 day, 4:19:53.873640 INFO: Competetive: True
1 day, 4:19:53.881186 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:19:53.886346 INFO: Using random state 474987 for train-test-split
1 day, 4:19:53.911177 INFO: Test AUC: 0.500
1 day, 4:19:53.911280 INFO: Train AUC: 0.503
1 day, 4:19:53.911314 INFO: AUC difference: 0.67%
1 day, 4:19:54.128485 INFO: Resetting torch num_threads to 80
1 day, 4:19:54.130784 PROGRESS: === Extracted 5953 precursors and 67522 fragments ===
1 day, 4:19:54.131423 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:19:54.132276 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:19:54.132368 PROGRESS: Total precursors accumulated: 3,000
1 day, 4:19:54.132435 PROGRESS: Target precursors: 2,616 (87.20%)
1 day, 4:19:54.132490 PROGRESS: Decoy precursors: 384 (12.80%)
1 day, 4:19:54.132539 PROGRESS: 
1 day, 4:19:54.132583 PROGRESS: Precursor Summary:
1 day, 4:19:54.133464 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 4:19:54.133551 PROGRESS: 
1 day, 4:19:54.133610 PROGRESS: Protein Summary:
1 day, 4:19:54.134589 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 4:19:54.134679 PROGRESS: =========================================================================
1 day, 4:19:54.134913 INFO: Target number of precursors not reached yet.
1 day, 4:19:54.147226 INFO: Starting optimization step 4.
1 day, 4:19:54.147367 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 4:19:54.147455 INFO: Using classic extraction backend
1 day, 4:19:54.147635 PROGRESS: Extracting batch of 6346 precursors
1 day, 4:19:54.147707 INFO: === Search parameters used ===
1 day, 4:19:54.147756 INFO: rt_error       : 2099.891532
1 day, 4:19:54.147799 INFO: mobility_error : 0.1
1 day, 4:19:54.147840 INFO: num_candidates : 1
1 day, 4:19:54.147880 INFO: ms1_error      : 30
1 day, 4:19:54.147920 INFO: ms2_error      : 30
1 day, 4:19:54.147959 INFO: fwhm_rt        : 5
1 day, 4:19:54.148000 INFO: quant_window   : 3
1 day, 4:19:54.148039 INFO: ==============================================
1 day, 4:19:54.150181 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:19:54.150232 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:19:54.150269 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:19:54.150291 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:19:54.151071 INFO: Starting candidate selection
1 day, 4:20:36.098029 INFO: Starting candidate scoring
1 day, 4:20:36.745851 INFO: Finished candidate processing
1 day, 4:20:36.745979 INFO: Collecting candidate features
1 day, 4:20:36.768467 INFO: Collecting fragment features
1 day, 4:20:36.778776 INFO: Finished candidate scoring
1 day, 4:20:36.794224 INFO: performing precursor FDR with 47 features
1 day, 4:20:36.794325 INFO: Decoy channel: -1
1 day, 4:20:36.794350 INFO: Competetive: True
1 day, 4:20:36.802796 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:20:36.809750 INFO: Using random state 997524 for train-test-split
1 day, 4:20:36.845945 INFO: Test AUC: 0.505
1 day, 4:20:36.846071 INFO: Train AUC: 0.508
1 day, 4:20:36.846106 INFO: AUC difference: 0.69%
1 day, 4:20:37.077114 INFO: Resetting torch num_threads to 80
1 day, 4:20:37.081525 PROGRESS: === Extracted 12284 precursors and 139495 fragments ===
1 day, 4:20:37.082158 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:20:37.083721 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:20:37.083822 PROGRESS: Total precursors accumulated: 6,194
1 day, 4:20:37.083885 PROGRESS: Target precursors: 5,444 (87.89%)
1 day, 4:20:37.083939 PROGRESS: Decoy precursors: 750 (12.11%)
1 day, 4:20:37.083986 PROGRESS: 
1 day, 4:20:37.084029 PROGRESS: Precursor Summary:
1 day, 4:20:37.084951 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 4:20:37.085041 PROGRESS: 
1 day, 4:20:37.085104 PROGRESS: Protein Summary:
1 day, 4:20:37.086093 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 4:20:37.086189 PROGRESS: =========================================================================
1 day, 4:20:37.086714 INFO: Target number of precursors not reached yet.
1 day, 4:20:37.110270 INFO: Starting optimization step 5.
1 day, 4:20:37.110551 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1 day, 4:20:37.110662 INFO: Using classic extraction backend
1 day, 4:20:37.111040 PROGRESS: Extracting batch of 12719 precursors
1 day, 4:20:37.111132 INFO: === Search parameters used ===
1 day, 4:20:37.111186 INFO: rt_error       : 2099.891532
1 day, 4:20:37.111238 INFO: mobility_error : 0.1
1 day, 4:20:37.111283 INFO: num_candidates : 1
1 day, 4:20:37.111326 INFO: ms1_error      : 30
1 day, 4:20:37.111368 INFO: ms2_error      : 30
1 day, 4:20:37.111408 INFO: fwhm_rt        : 5
1 day, 4:20:37.111450 INFO: quant_window   : 3
1 day, 4:20:37.111492 INFO: ==============================================
1 day, 4:20:37.115319 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:20:37.115374 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:20:37.115419 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:20:37.115442 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:20:37.116637 INFO: Starting candidate selection
1 day, 4:21:58.385767 INFO: Starting candidate scoring
1 day, 4:21:59.591127 INFO: Finished candidate processing
1 day, 4:21:59.591275 INFO: Collecting candidate features
1 day, 4:21:59.622088 INFO: Collecting fragment features
1 day, 4:21:59.632569 INFO: Finished candidate scoring
1 day, 4:21:59.649538 INFO: performing precursor FDR with 47 features
1 day, 4:21:59.649688 INFO: Decoy channel: -1
1 day, 4:21:59.649713 INFO: Competetive: True
1 day, 4:21:59.660729 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:21:59.667372 INFO: Using random state 873517 for train-test-split
1 day, 4:21:59.850667 INFO: Test AUC: 0.801
1 day, 4:21:59.850800 INFO: Train AUC: 0.806
1 day, 4:21:59.850832 INFO: AUC difference: 0.56%
1 day, 4:22:00.091087 INFO: Resetting torch num_threads to 80
1 day, 4:22:00.096059 PROGRESS: === Extracted 24992 precursors and 283932 fragments ===
1 day, 4:22:00.096661 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:22:00.098761 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:00.098871 PROGRESS: Total precursors accumulated: 12,591
1 day, 4:22:00.098946 PROGRESS: Target precursors: 10,162 (80.71%)
1 day, 4:22:00.099000 PROGRESS: Decoy precursors: 2,429 (19.29%)
1 day, 4:22:00.099048 PROGRESS: 
1 day, 4:22:00.099096 PROGRESS: Precursor Summary:
1 day, 4:22:00.101848 PROGRESS: Channel   0:	 0.050 FDR: 7,582; 0.010 FDR: 5,447; 0.001 FDR: 1,441
1 day, 4:22:00.101945 PROGRESS: 
1 day, 4:22:00.102005 PROGRESS: Protein Summary:
1 day, 4:22:00.105348 PROGRESS: Channel   0:	 0.050 FDR: 3,837; 0.010 FDR: 3,036; 0.001 FDR: 1,101
1 day, 4:22:00.105465 PROGRESS: =========================================================================
1 day, 4:22:00.105924 INFO: Target number of precursors reached.
1 day, 4:22:00.145663 INFO: fragments_df: keeping 5000 of 283932 [sum(precursor_idx_mask)=61734 sum(mass_error_mask)=283932 stop_rank=5000
1 day, 4:22:00.156254 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:00.844620 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:01.548820 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:02.252594 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:02.923843 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 4:22:02.924393 INFO: Using score_cutoff 50.310144209289554 (fac=0.99, q=1)
1 day, 4:22:02.924862 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0960206985473633
1 day, 4:22:02.924944 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010541314259171486
1 day, 4:22:02.924999 INFO: Updating optimization_manager: score_cutoff        : 0 -> 50.310144209289554
1 day, 4:22:02.925068 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:02.926208 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:02.927614 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:02.928583 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:02.931011 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
1 day, 4:22:02.931322 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 4:22:02.931556 INFO: Starting optimization step 6.
1 day, 4:22:02.931651 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:02.931739 INFO: Using classic extraction backend
1 day, 4:22:02.931962 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:02.932052 INFO: === Search parameters used ===
1 day, 4:22:02.932118 INFO: rt_error       : 2099.891532
1 day, 4:22:02.932178 INFO: mobility_error : 0.1
1 day, 4:22:02.932235 INFO: num_candidates : 3
1 day, 4:22:02.932298 INFO: ms1_error      : 30
1 day, 4:22:02.932355 INFO: ms2_error      : 30
1 day, 4:22:02.932410 INFO: fwhm_rt        : 3.0960206985473633
1 day, 4:22:02.932466 INFO: quant_window   : 3
1 day, 4:22:02.932521 INFO: ==============================================
1 day, 4:22:02.933858 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:02.933908 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:02.933968 INFO: FWHM in RT is 3.10 seconds, sigma is 0.68
1 day, 4:22:02.934001 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.89
1 day, 4:22:02.934865 INFO: Starting candidate selection
1 day, 4:22:12.966339 INFO: Starting candidate scoring
1 day, 4:22:13.317498 INFO: Finished candidate processing
1 day, 4:22:13.317619 INFO: Collecting candidate features
1 day, 4:22:13.331155 INFO: Collecting fragment features
1 day, 4:22:13.335583 INFO: Finished candidate scoring
1 day, 4:22:13.337577 INFO: performing precursor FDR with 47 features
1 day, 4:22:13.337620 INFO: Decoy channel: -1
1 day, 4:22:13.337645 INFO: Competetive: True
1 day, 4:22:13.340997 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:13.343129 INFO: Using random state 386454 for train-test-split
1 day, 4:22:13.355577 INFO: Test AUC: 0.679
1 day, 4:22:13.355652 INFO: Train AUC: 0.673
1 day, 4:22:13.355683 INFO: AUC difference: 0.93%
1 day, 4:22:13.579258 INFO: Resetting torch num_threads to 80
1 day, 4:22:13.579834 PROGRESS: === Extracted 3387 precursors and 38530 fragments ===
1 day, 4:22:13.580293 INFO: === FDR correction performed with classifier version 5 ===
1 day, 4:22:13.580891 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:13.580979 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:13.581039 PROGRESS: Target precursors: 520 (86.67%)
1 day, 4:22:13.581086 PROGRESS: Decoy precursors: 80 (13.33%)
1 day, 4:22:13.581132 PROGRESS: 
1 day, 4:22:13.581175 PROGRESS: Precursor Summary:
1 day, 4:22:13.582227 PROGRESS: Channel   0:	 0.050 FDR:   423; 0.010 FDR:   257; 0.001 FDR:   141
1 day, 4:22:13.582324 PROGRESS: 
1 day, 4:22:13.582380 PROGRESS: Protein Summary:
1 day, 4:22:13.583521 PROGRESS: Channel   0:	 0.050 FDR:   397; 0.010 FDR:   249; 0.001 FDR:   137
1 day, 4:22:13.583611 PROGRESS: =========================================================================
1 day, 4:22:13.584266 INFO: Target number of precursors reached.
1 day, 4:22:13.589628 INFO: fragments_df: keeping 3809 of 38530 [sum(precursor_idx_mask)=8268 sum(mass_error_mask)=38530 stop_rank=3809
1 day, 4:22:13.598246 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:13.696219 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:13.793986 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:13.899707 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:14.336304 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:14.336795 INFO: Using score_cutoff 50.89031085662842 (fac=0.99, q=1)
1 day, 4:22:14.337113 INFO: Updating optimization_manager: fwhm_rt             : 3.0960206985473633 -> 3.0514206886291504
1 day, 4:22:14.337200 INFO: Updating optimization_manager: fwhm_mobility       : 0.010541314259171486 -> 0.010369054041802883
1 day, 4:22:14.337256 INFO: Updating optimization_manager: score_cutoff        : 50.310144209289554 -> 50.89031085662842
1 day, 4:22:14.337308 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:14.338465 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:14.339767 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:14.340535 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:14.342661 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:14.344102 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 4:22:14.344199 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
1 day, 4:22:14.344267 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:22:14.345183 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 4:22:14.345274 INFO: Updating optimization_manager: classifier_version  : 6 -> 6
1 day, 4:22:14.345335 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:22:14.345388 INFO: ==============================================
1 day, 4:22:14.345449 INFO: Starting optimization step 7.
1 day, 4:22:14.345503 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:14.345558 INFO: Using classic extraction backend
1 day, 4:22:14.345792 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:14.345860 INFO: === Search parameters used ===
1 day, 4:22:14.345913 INFO: rt_error       : 2099.891532
1 day, 4:22:14.345956 INFO: mobility_error : 0.1
1 day, 4:22:14.345996 INFO: num_candidates : 3
1 day, 4:22:14.346036 INFO: ms1_error      : 15.0
1 day, 4:22:14.346084 INFO: ms2_error      : 15.0
1 day, 4:22:14.346123 INFO: fwhm_rt        : 3.0514206886291504
1 day, 4:22:14.346163 INFO: quant_window   : 3
1 day, 4:22:14.346202 INFO: ==============================================
1 day, 4:22:14.347026 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:14.347071 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:14.347105 INFO: FWHM in RT is 3.05 seconds, sigma is 0.67
1 day, 4:22:14.347126 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.81
1 day, 4:22:14.347794 INFO: Starting candidate selection
1 day, 4:22:23.940167 INFO: Starting candidate scoring
1 day, 4:22:24.173410 INFO: Finished candidate processing
1 day, 4:22:24.173539 INFO: Collecting candidate features
1 day, 4:22:24.190186 INFO: Collecting fragment features
1 day, 4:22:24.198745 INFO: Finished candidate scoring
1 day, 4:22:24.202218 INFO: performing precursor FDR with 47 features
1 day, 4:22:24.202352 INFO: Decoy channel: -1
1 day, 4:22:24.202429 INFO: Competetive: True
1 day, 4:22:24.214590 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:24.219046 INFO: Using random state 423746 for train-test-split
1 day, 4:22:24.241106 INFO: Test AUC: 0.701
1 day, 4:22:24.241422 INFO: Train AUC: 0.705
1 day, 4:22:24.241514 INFO: AUC difference: 0.59%
1 day, 4:22:24.481673 INFO: Resetting torch num_threads to 80
1 day, 4:22:24.482296 PROGRESS: === Extracted 3394 precursors and 37662 fragments ===
1 day, 4:22:24.482846 INFO: === FDR correction performed with classifier version 6 ===
1 day, 4:22:24.483451 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:24.483543 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:24.483607 PROGRESS: Target precursors: 544 (90.67%)
1 day, 4:22:24.483659 PROGRESS: Decoy precursors: 56 (9.33%)
1 day, 4:22:24.483703 PROGRESS: 
1 day, 4:22:24.483749 PROGRESS: Precursor Summary:
1 day, 4:22:24.484812 PROGRESS: Channel   0:	 0.050 FDR:   503; 0.010 FDR:   409; 0.001 FDR:   299
1 day, 4:22:24.484907 PROGRESS: 
1 day, 4:22:24.484966 PROGRESS: Protein Summary:
1 day, 4:22:24.486191 PROGRESS: Channel   0:	 0.050 FDR:   466; 0.010 FDR:   384; 0.001 FDR:   287
1 day, 4:22:24.486289 PROGRESS: =========================================================================
1 day, 4:22:24.486522 INFO: Target number of precursors reached.
1 day, 4:22:24.492828 INFO: fragments_df: keeping 5000 of 37662 [sum(precursor_idx_mask)=12928 sum(mass_error_mask)=37662 stop_rank=5000
1 day, 4:22:24.499103 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:24.616261 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:24.729070 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:24.882350 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:25.599005 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:25.599495 INFO: Using score_cutoff 44.387074031066895 (fac=0.99, q=1)
1 day, 4:22:25.599841 INFO: Updating optimization_manager: fwhm_rt             : 3.0514206886291504 -> 2.8829538822174072
1 day, 4:22:25.599921 INFO: Updating optimization_manager: fwhm_mobility       : 0.010369054041802883 -> 0.00878858007490635
1 day, 4:22:25.599975 INFO: Updating optimization_manager: score_cutoff        : 50.89031085662842 -> 44.387074031066895
1 day, 4:22:25.600032 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:25.601168 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:25.602481 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:25.603261 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:25.605719 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:25.607363 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 4:22:25.607465 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1 day, 4:22:25.607528 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 4:22:25.608490 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 4:22:25.608583 INFO: Updating optimization_manager: classifier_version  : 7 -> 7
1 day, 4:22:25.608646 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 4:22:25.608699 INFO: ==============================================
1 day, 4:22:25.608778 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 4:22:25.613065 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:25.613891 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:25.615180 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:25.615949 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:25.618153 INFO: Starting optimization step 0.
1 day, 4:22:25.618252 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:25.618325 INFO: Using classic extraction backend
1 day, 4:22:25.618478 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:25.618551 INFO: === Search parameters used ===
1 day, 4:22:25.618601 INFO: rt_error       : 2099.891532
1 day, 4:22:25.618644 INFO: mobility_error : 0.1
1 day, 4:22:25.618686 INFO: num_candidates : 3
1 day, 4:22:25.618730 INFO: ms1_error      : 15.0
1 day, 4:22:25.618775 INFO: ms2_error      : 15.0
1 day, 4:22:25.618817 INFO: fwhm_rt        : 2.8829538822174072
1 day, 4:22:25.618857 INFO: quant_window   : 3
1 day, 4:22:25.618904 INFO: ==============================================
1 day, 4:22:25.619790 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:25.619837 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:25.619885 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1 day, 4:22:25.619908 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.08
1 day, 4:22:25.620662 INFO: Starting candidate selection
1 day, 4:22:36.154167 INFO: Starting candidate scoring
1 day, 4:22:36.452892 INFO: Finished candidate processing
1 day, 4:22:36.453064 INFO: Collecting candidate features
1 day, 4:22:36.483319 INFO: Collecting fragment features
1 day, 4:22:36.492472 INFO: Finished candidate scoring
1 day, 4:22:36.495624 INFO: performing precursor FDR with 47 features
1 day, 4:22:36.495728 INFO: Decoy channel: -1
1 day, 4:22:36.495789 INFO: Competetive: True
1 day, 4:22:36.503697 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:36.507040 INFO: Using random state 316627 for train-test-split
1 day, 4:22:36.524401 INFO: Test AUC: 0.705
1 day, 4:22:36.524511 INFO: Train AUC: 0.715
1 day, 4:22:36.524560 INFO: AUC difference: 1.32%
1 day, 4:22:36.768220 INFO: Resetting torch num_threads to 80
1 day, 4:22:36.769133 PROGRESS: === Extracted 3392 precursors and 37652 fragments ===
1 day, 4:22:36.769631 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:36.770297 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:36.770392 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:36.770454 PROGRESS: Target precursors: 545 (90.83%)
1 day, 4:22:36.770504 PROGRESS: Decoy precursors: 55 (9.17%)
1 day, 4:22:36.770554 PROGRESS: 
1 day, 4:22:36.770600 PROGRESS: Precursor Summary:
1 day, 4:22:36.771647 PROGRESS: Channel   0:	 0.050 FDR:   506; 0.010 FDR:   406; 0.001 FDR:   299
1 day, 4:22:36.771746 PROGRESS: 
1 day, 4:22:36.771804 PROGRESS: Protein Summary:
1 day, 4:22:36.773029 PROGRESS: Channel   0:	 0.050 FDR:   468; 0.010 FDR:   383; 0.001 FDR:   288
1 day, 4:22:36.773124 PROGRESS: =========================================================================
1 day, 4:22:36.773299 INFO: Target number of precursors reached.
1 day, 4:22:36.779499 INFO: fragments_df: keeping 5000 of 37652 [sum(precursor_idx_mask)=12846 sum(mass_error_mask)=37652 stop_rank=5000
1 day, 4:22:36.785163 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:36.929250 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:37.043876 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:37.168922 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:37.846598 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:37.847070 INFO: Using score_cutoff 44.774835788726804 (fac=0.99, q=1)
1 day, 4:22:37.847384 INFO: Updating optimization_manager: fwhm_rt             : 2.8829538822174072 -> 2.820862293243408
1 day, 4:22:37.847470 INFO: Updating optimization_manager: fwhm_mobility       : 0.00878858007490635 -> 0.008733654394745827
1 day, 4:22:37.847525 INFO: Updating optimization_manager: score_cutoff        : 44.387074031066895 -> 44.774835788726804
1 day, 4:22:37.847576 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:37.848694 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:37.849981 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:37.850766 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:37.852866 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:37.852994 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:22:37.854602 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 216.96888207445284
1 day, 4:22:37.854711 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 216.9689.
1 day, 4:22:37.854775 INFO: ==============================================
1 day, 4:22:37.854840 INFO: Starting optimization step 1.
1 day, 4:22:37.854897 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:37.854952 INFO: Using classic extraction backend
1 day, 4:22:37.855060 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:37.855129 INFO: === Search parameters used ===
1 day, 4:22:37.855176 INFO: rt_error       : 216.96888207445284
1 day, 4:22:37.855224 INFO: mobility_error : 0.1
1 day, 4:22:37.855265 INFO: num_candidates : 3
1 day, 4:22:37.855305 INFO: ms1_error      : 15.0
1 day, 4:22:37.855344 INFO: ms2_error      : 15.0
1 day, 4:22:37.855382 INFO: fwhm_rt        : 2.820862293243408
1 day, 4:22:37.855423 INFO: quant_window   : 3
1 day, 4:22:37.855466 INFO: ==============================================
1 day, 4:22:37.856231 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:37.856276 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:37.856309 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 4:22:37.856331 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.05
1 day, 4:22:37.857066 INFO: Starting candidate selection
1 day, 4:22:39.870438 INFO: Starting candidate scoring
1 day, 4:22:40.087898 INFO: Finished candidate processing
1 day, 4:22:40.088013 INFO: Collecting candidate features
1 day, 4:22:40.105364 INFO: Collecting fragment features
1 day, 4:22:40.110031 INFO: Finished candidate scoring
1 day, 4:22:40.112113 INFO: performing precursor FDR with 47 features
1 day, 4:22:40.112164 INFO: Decoy channel: -1
1 day, 4:22:40.112187 INFO: Competetive: True
1 day, 4:22:40.115443 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:40.117573 INFO: Using random state 316627 for train-test-split
1 day, 4:22:40.129003 INFO: Test AUC: 0.713
1 day, 4:22:40.129082 INFO: Train AUC: 0.737
1 day, 4:22:40.129111 INFO: AUC difference: 3.20%
1 day, 4:22:40.347186 INFO: Resetting torch num_threads to 80
1 day, 4:22:40.347786 PROGRESS: === Extracted 3384 precursors and 36866 fragments ===
1 day, 4:22:40.348238 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:40.348842 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:40.348930 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:40.348989 PROGRESS: Target precursors: 567 (94.50%)
1 day, 4:22:40.349040 PROGRESS: Decoy precursors: 33 (5.50%)
1 day, 4:22:40.349083 PROGRESS: 
1 day, 4:22:40.349125 PROGRESS: Precursor Summary:
1 day, 4:22:40.350488 PROGRESS: Channel   0:	 0.050 FDR:   562; 0.010 FDR:   453; 0.001 FDR:   414
1 day, 4:22:40.350580 PROGRESS: 
1 day, 4:22:40.350637 PROGRESS: Protein Summary:
1 day, 4:22:40.351917 PROGRESS: Channel   0:	 0.050 FDR:   518; 0.010 FDR:   425; 0.001 FDR:   392
1 day, 4:22:40.352007 PROGRESS: =========================================================================
1 day, 4:22:40.352159 INFO: Target number of precursors reached.
1 day, 4:22:40.358344 INFO: fragments_df: keeping 5000 of 36866 [sum(precursor_idx_mask)=14184 sum(mass_error_mask)=36866 stop_rank=5000
1 day, 4:22:40.362997 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:40.476268 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:40.588263 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:40.703663 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:41.346199 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:41.346673 INFO: Using score_cutoff 40.28322825164795 (fac=0.99, q=1)
1 day, 4:22:41.346999 INFO: Updating optimization_manager: fwhm_rt             : 2.820862293243408 -> 2.7913706302642822
1 day, 4:22:41.347081 INFO: Updating optimization_manager: fwhm_mobility       : 0.008733654394745827 -> 0.008506592363119125
1 day, 4:22:41.347134 INFO: Updating optimization_manager: score_cutoff        : 44.774835788726804 -> 40.28322825164795
1 day, 4:22:41.347185 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:41.348334 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:41.349646 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:41.350437 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:41.352534 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:41.352628 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:22:41.354313 INFO: Updating optimization_manager: rt_error            : 216.96888207445284 -> 16.336444158475427
1 day, 4:22:41.354417 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 16.3364.
1 day, 4:22:41.354485 INFO: ==============================================
1 day, 4:22:41.354551 INFO: Starting optimization step 2.
1 day, 4:22:41.354606 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:41.354659 INFO: Using classic extraction backend
1 day, 4:22:41.354765 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:41.354825 INFO: === Search parameters used ===
1 day, 4:22:41.354870 INFO: rt_error       : 16.336444158475427
1 day, 4:22:41.354911 INFO: mobility_error : 0.1
1 day, 4:22:41.354950 INFO: num_candidates : 3
1 day, 4:22:41.354988 INFO: ms1_error      : 15.0
1 day, 4:22:41.355026 INFO: ms2_error      : 15.0
1 day, 4:22:41.355063 INFO: fwhm_rt        : 2.7913706302642822
1 day, 4:22:41.355101 INFO: quant_window   : 3
1 day, 4:22:41.355139 INFO: ==============================================
1 day, 4:22:41.355968 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:41.356012 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:41.356047 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 4:22:41.356071 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
1 day, 4:22:41.356725 INFO: Starting candidate selection
1 day, 4:22:41.905428 INFO: Starting candidate scoring
1 day, 4:22:42.106636 INFO: Finished candidate processing
1 day, 4:22:42.106753 INFO: Collecting candidate features
1 day, 4:22:42.117167 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3366)
1 day, 4:22:42.120379 INFO: Collecting fragment features
1 day, 4:22:42.125854 INFO: Finished candidate scoring
1 day, 4:22:42.127831 INFO: performing precursor FDR with 47 features
1 day, 4:22:42.127878 INFO: Decoy channel: -1
1 day, 4:22:42.127903 INFO: Competetive: True
1 day, 4:22:42.131290 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:42.132642 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 4:22:42.133805 INFO: Using random state 316627 for train-test-split
1 day, 4:22:42.146232 INFO: Test AUC: 0.795
1 day, 4:22:42.146305 INFO: Train AUC: 0.771
1 day, 4:22:42.146336 INFO: AUC difference: 3.14%
1 day, 4:22:42.364761 INFO: Resetting torch num_threads to 80
1 day, 4:22:42.365395 PROGRESS: === Extracted 3366 precursors and 35667 fragments ===
1 day, 4:22:42.365849 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:42.366522 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:42.366613 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:42.366673 PROGRESS: Target precursors: 585 (97.50%)
1 day, 4:22:42.366722 PROGRESS: Decoy precursors: 15 (2.50%)
1 day, 4:22:42.366776 PROGRESS: 
1 day, 4:22:42.366822 PROGRESS: Precursor Summary:
1 day, 4:22:42.367967 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   561; 0.001 FDR:   379
1 day, 4:22:42.368060 PROGRESS: 
1 day, 4:22:42.368116 PROGRESS: Protein Summary:
1 day, 4:22:42.369371 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   519; 0.001 FDR:   362
1 day, 4:22:42.369461 PROGRESS: =========================================================================
1 day, 4:22:42.369622 INFO: Target number of precursors reached.
1 day, 4:22:42.376592 INFO: fragments_df: keeping 5000 of 35667 [sum(precursor_idx_mask)=17283 sum(mass_error_mask)=35667 stop_rank=5000
1 day, 4:22:42.381370 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:42.510366 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:42.627641 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:42.755373 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:43.378731 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:43.379216 INFO: Using score_cutoff 34.35981289672852 (fac=0.99, q=1)
1 day, 4:22:43.379542 INFO: Updating optimization_manager: fwhm_rt             : 2.7913706302642822 -> 2.7463817596435547
1 day, 4:22:43.379625 INFO: Updating optimization_manager: fwhm_mobility       : 0.008506592363119125 -> 0.008155995048582554
1 day, 4:22:43.379681 INFO: Updating optimization_manager: score_cutoff        : 40.28322825164795 -> 34.35981289672852
1 day, 4:22:43.379734 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:43.380872 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:43.382178 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:43.382945 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:43.385034 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:43.385142 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:22:43.386957 INFO: Updating optimization_manager: rt_error            : 16.336444158475427 -> 20.366666078630157
1 day, 4:22:43.387061 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 20.3667.
1 day, 4:22:43.387128 INFO: ==============================================
1 day, 4:22:43.387194 INFO: Starting optimization step 3.
1 day, 4:22:43.387252 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:43.387308 INFO: Using classic extraction backend
1 day, 4:22:43.387417 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:43.387480 INFO: === Search parameters used ===
1 day, 4:22:43.387528 INFO: rt_error       : 20.366666078630157
1 day, 4:22:43.387573 INFO: mobility_error : 0.1
1 day, 4:22:43.387614 INFO: num_candidates : 3
1 day, 4:22:43.387655 INFO: ms1_error      : 15.0
1 day, 4:22:43.387694 INFO: ms2_error      : 15.0
1 day, 4:22:43.387733 INFO: fwhm_rt        : 2.7463817596435547
1 day, 4:22:43.387771 INFO: quant_window   : 3
1 day, 4:22:43.387809 INFO: ==============================================
1 day, 4:22:43.388646 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:43.388692 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:43.388728 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 4:22:43.388753 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.78
1 day, 4:22:43.389413 INFO: Starting candidate selection
1 day, 4:22:43.936915 INFO: Starting candidate scoring
1 day, 4:22:44.128746 INFO: Finished candidate processing
1 day, 4:22:44.128864 INFO: Collecting candidate features
1 day, 4:22:44.143666 INFO: Collecting fragment features
1 day, 4:22:44.148538 INFO: Finished candidate scoring
1 day, 4:22:44.150594 INFO: performing precursor FDR with 47 features
1 day, 4:22:44.150642 INFO: Decoy channel: -1
1 day, 4:22:44.150666 INFO: Competetive: True
1 day, 4:22:44.153843 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:44.156050 INFO: Using random state 316627 for train-test-split
1 day, 4:22:44.167097 INFO: Test AUC: 0.793
1 day, 4:22:44.167161 INFO: Train AUC: 0.773
1 day, 4:22:44.167191 INFO: AUC difference: 2.64%
1 day, 4:22:44.456416 INFO: Resetting torch num_threads to 80
1 day, 4:22:44.457164 PROGRESS: === Extracted 3376 precursors and 35742 fragments ===
1 day, 4:22:44.457684 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:44.458398 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:44.458500 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:44.458565 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:22:44.458618 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:22:44.458665 PROGRESS: 
1 day, 4:22:44.458711 PROGRESS: Precursor Summary:
1 day, 4:22:44.459911 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   560; 0.001 FDR:   376
1 day, 4:22:44.460008 PROGRESS: 
1 day, 4:22:44.460066 PROGRESS: Protein Summary:
1 day, 4:22:44.461572 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   520; 0.001 FDR:   358
1 day, 4:22:44.465022 PROGRESS: =========================================================================
1 day, 4:22:44.465238 INFO: Target number of precursors reached.
1 day, 4:22:44.474317 INFO: fragments_df: keeping 5000 of 35742 [sum(precursor_idx_mask)=17246 sum(mass_error_mask)=35742 stop_rank=5000
1 day, 4:22:44.479870 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:44.692139 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:44.831402 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:44.981926 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:45.677976 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:45.678509 INFO: Using score_cutoff 34.27506759910583 (fac=0.99, q=1)
1 day, 4:22:45.678853 INFO: Updating optimization_manager: fwhm_rt             : 2.7463817596435547 -> 2.7466678619384766
1 day, 4:22:45.678942 INFO: Updating optimization_manager: fwhm_mobility       : 0.008155995048582554 -> 0.0081082284450531
1 day, 4:22:45.679011 INFO: Updating optimization_manager: score_cutoff        : 34.35981289672852 -> 34.27506759910583
1 day, 4:22:45.679078 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:45.680246 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:45.681555 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:45.682362 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:45.684482 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:45.684600 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 4:22:45.686448 INFO: Updating optimization_manager: rt_error            : 20.366666078630157 -> 16.07929782312467
1 day, 4:22:45.686561 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.0793.
1 day, 4:22:45.686641 INFO: ==============================================
1 day, 4:22:45.686722 INFO: Starting optimization step 4.
1 day, 4:22:45.686792 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:45.686859 INFO: Using classic extraction backend
1 day, 4:22:45.686993 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:45.687074 INFO: === Search parameters used ===
1 day, 4:22:45.687133 INFO: rt_error       : 16.07929782312467
1 day, 4:22:45.687197 INFO: mobility_error : 0.1
1 day, 4:22:45.687253 INFO: num_candidates : 3
1 day, 4:22:45.687306 INFO: ms1_error      : 15.0
1 day, 4:22:45.687358 INFO: ms2_error      : 15.0
1 day, 4:22:45.687410 INFO: fwhm_rt        : 2.7466678619384766
1 day, 4:22:45.687463 INFO: quant_window   : 3
1 day, 4:22:45.687514 INFO: ==============================================
1 day, 4:22:45.688550 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:45.688598 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:45.688641 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 4:22:45.688669 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
1 day, 4:22:45.689366 INFO: Starting candidate selection
1 day, 4:22:46.222217 INFO: Starting candidate scoring
1 day, 4:22:46.419946 INFO: Finished candidate processing
1 day, 4:22:46.420064 INFO: Collecting candidate features
1 day, 4:22:46.433306 INFO: Collecting fragment features
1 day, 4:22:46.437004 INFO: Finished candidate scoring
1 day, 4:22:46.439070 INFO: performing precursor FDR with 47 features
1 day, 4:22:46.439121 INFO: Decoy channel: -1
1 day, 4:22:46.439145 INFO: Competetive: True
1 day, 4:22:46.442520 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:46.444627 INFO: Using random state 316627 for train-test-split
1 day, 4:22:46.456043 INFO: Test AUC: 0.806
1 day, 4:22:46.456109 INFO: Train AUC: 0.773
1 day, 4:22:46.456138 INFO: AUC difference: 4.28%
1 day, 4:22:46.673289 INFO: Resetting torch num_threads to 80
1 day, 4:22:46.673906 PROGRESS: === Extracted 3370 precursors and 35692 fragments ===
1 day, 4:22:46.674357 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:46.674961 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:46.675049 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:46.675111 PROGRESS: Target precursors: 584 (97.33%)
1 day, 4:22:46.675163 PROGRESS: Decoy precursors: 16 (2.67%)
1 day, 4:22:46.675207 PROGRESS: 
1 day, 4:22:46.675249 PROGRESS: Precursor Summary:
1 day, 4:22:46.676288 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   556; 0.001 FDR:   418
1 day, 4:22:46.676378 PROGRESS: 
1 day, 4:22:46.676434 PROGRESS: Protein Summary:
1 day, 4:22:46.677673 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   514; 0.001 FDR:   397
1 day, 4:22:46.677763 PROGRESS: =========================================================================
1 day, 4:22:46.677912 INFO: Target number of precursors reached.
1 day, 4:22:46.684613 INFO: fragments_df: keeping 5000 of 35692 [sum(precursor_idx_mask)=17083 sum(mass_error_mask)=35692 stop_rank=5000
1 day, 4:22:46.689277 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:46.810745 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:46.929530 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:47.056308 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:47.714509 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:47.714997 INFO: Using score_cutoff 36.03828915596008 (fac=0.99, q=1)
1 day, 4:22:47.715328 INFO: Updating optimization_manager: fwhm_rt             : 2.7466678619384766 -> 2.7572884559631348
1 day, 4:22:47.715412 INFO: Updating optimization_manager: fwhm_mobility       : 0.0081082284450531 -> 0.008119720034301281
1 day, 4:22:47.715468 INFO: Updating optimization_manager: score_cutoff        : 34.27506759910583 -> 36.03828915596008
1 day, 4:22:47.715522 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:47.716680 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:47.717978 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:47.720483 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:47.722653 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:47.722753 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 4:22:47.724600 INFO: Updating optimization_manager: rt_error            : 16.07929782312467 -> 19.455795592457736
1 day, 4:22:47.724703 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 19.4558.
1 day, 4:22:47.724782 INFO: ==============================================
1 day, 4:22:47.724852 INFO: Starting optimization step 5.
1 day, 4:22:47.724910 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:47.724964 INFO: Using classic extraction backend
1 day, 4:22:47.725073 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:47.725144 INFO: === Search parameters used ===
1 day, 4:22:47.725194 INFO: rt_error       : 19.455795592457736
1 day, 4:22:47.725236 INFO: mobility_error : 0.1
1 day, 4:22:47.725277 INFO: num_candidates : 3
1 day, 4:22:47.725317 INFO: ms1_error      : 15.0
1 day, 4:22:47.725355 INFO: ms2_error      : 15.0
1 day, 4:22:47.725393 INFO: fwhm_rt        : 2.7572884559631348
1 day, 4:22:47.725430 INFO: quant_window   : 3
1 day, 4:22:47.725468 INFO: ==============================================
1 day, 4:22:47.726491 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:47.726537 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:47.726571 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 4:22:47.726598 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.77
1 day, 4:22:47.727666 INFO: Starting candidate selection
1 day, 4:22:48.254329 INFO: Starting candidate scoring
1 day, 4:22:48.454962 INFO: Finished candidate processing
1 day, 4:22:48.455076 INFO: Collecting candidate features
1 day, 4:22:48.469617 INFO: Collecting fragment features
1 day, 4:22:48.474911 INFO: Finished candidate scoring
1 day, 4:22:48.477813 INFO: performing precursor FDR with 47 features
1 day, 4:22:48.477919 INFO: Decoy channel: -1
1 day, 4:22:48.477978 INFO: Competetive: True
1 day, 4:22:48.484094 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:48.487710 INFO: Using random state 316627 for train-test-split
1 day, 4:22:48.506776 INFO: Test AUC: 0.766
1 day, 4:22:48.506855 INFO: Train AUC: 0.785
1 day, 4:22:48.506884 INFO: AUC difference: 2.34%
1 day, 4:22:48.726036 INFO: Resetting torch num_threads to 80
1 day, 4:22:48.726650 PROGRESS: === Extracted 3365 precursors and 35666 fragments ===
1 day, 4:22:48.727109 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:48.727700 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:48.727794 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:48.727856 PROGRESS: Target precursors: 586 (97.67%)
1 day, 4:22:48.727906 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 4:22:48.727950 PROGRESS: 
1 day, 4:22:48.727992 PROGRESS: Precursor Summary:
1 day, 4:22:48.729065 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   558; 0.001 FDR:   366
1 day, 4:22:48.729159 PROGRESS: 
1 day, 4:22:48.729217 PROGRESS: Protein Summary:
1 day, 4:22:48.730518 PROGRESS: Channel   0:	 0.050 FDR:   539; 0.010 FDR:   517; 0.001 FDR:   350
1 day, 4:22:48.730614 PROGRESS: =========================================================================
1 day, 4:22:48.730837 INFO: Target number of precursors reached.
1 day, 4:22:48.737552 INFO: fragments_df: keeping 5000 of 35666 [sum(precursor_idx_mask)=17120 sum(mass_error_mask)=35666 stop_rank=5000
1 day, 4:22:48.745983 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:48.868122 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:48.984500 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:49.112221 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:49.735144 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:49.735640 INFO: Using score_cutoff 35.96105828704834 (fac=0.99, q=1)
1 day, 4:22:49.735989 INFO: Updating optimization_manager: fwhm_rt             : 2.7572884559631348 -> 2.7572884559631348
1 day, 4:22:49.736068 INFO: Updating optimization_manager: fwhm_mobility       : 0.008119720034301281 -> 0.008092820644378662
1 day, 4:22:49.736121 INFO: Updating optimization_manager: score_cutoff        : 36.03828915596008 -> 35.96105828704834
1 day, 4:22:49.736173 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:49.737311 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:49.738617 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:49.739384 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:49.742007 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:49.742110 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 4:22:49.743932 INFO: Updating optimization_manager: rt_error            : 19.455795592457736 -> 15.710196632255087
1 day, 4:22:49.744029 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 15.7102.
1 day, 4:22:49.744092 INFO: ==============================================
1 day, 4:22:49.744158 INFO: Starting optimization step 6.
1 day, 4:22:49.744215 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:49.744270 INFO: Using classic extraction backend
1 day, 4:22:49.744380 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:49.744440 INFO: === Search parameters used ===
1 day, 4:22:49.744485 INFO: rt_error       : 15.710196632255087
1 day, 4:22:49.744525 INFO: mobility_error : 0.1
1 day, 4:22:49.744572 INFO: num_candidates : 3
1 day, 4:22:49.744613 INFO: ms1_error      : 15.0
1 day, 4:22:49.744651 INFO: ms2_error      : 15.0
1 day, 4:22:49.744689 INFO: fwhm_rt        : 2.7572884559631348
1 day, 4:22:49.744728 INFO: quant_window   : 3
1 day, 4:22:49.744765 INFO: ==============================================
1 day, 4:22:49.745683 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:49.745725 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:49.745758 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 4:22:49.745779 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 4:22:49.748995 INFO: Starting candidate selection
1 day, 4:22:50.277592 INFO: Starting candidate scoring
1 day, 4:22:50.472344 INFO: Finished candidate processing
1 day, 4:22:50.472459 INFO: Collecting candidate features
1 day, 4:22:50.486884 INFO: Collecting fragment features
1 day, 4:22:50.491932 INFO: Finished candidate scoring
1 day, 4:22:50.493983 INFO: performing precursor FDR with 47 features
1 day, 4:22:50.494034 INFO: Decoy channel: -1
1 day, 4:22:50.494076 INFO: Competetive: True
1 day, 4:22:50.497102 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:50.499262 INFO: Using random state 316627 for train-test-split
1 day, 4:22:50.510458 INFO: Test AUC: 0.784
1 day, 4:22:50.510525 INFO: Train AUC: 0.793
1 day, 4:22:50.510563 INFO: AUC difference: 1.12%
1 day, 4:22:50.733227 INFO: Resetting torch num_threads to 80
1 day, 4:22:50.733853 PROGRESS: === Extracted 3368 precursors and 35531 fragments ===
1 day, 4:22:50.734350 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:50.734995 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:50.735096 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:50.735172 PROGRESS: Target precursors: 584 (97.33%)
1 day, 4:22:50.735235 PROGRESS: Decoy precursors: 16 (2.67%)
1 day, 4:22:50.735294 PROGRESS: 
1 day, 4:22:50.735351 PROGRESS: Precursor Summary:
1 day, 4:22:50.736500 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   562; 0.001 FDR:   450
1 day, 4:22:50.736600 PROGRESS: 
1 day, 4:22:50.736671 PROGRESS: Protein Summary:
1 day, 4:22:50.737997 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   520; 0.001 FDR:   424
1 day, 4:22:50.738113 PROGRESS: =========================================================================
1 day, 4:22:50.738304 INFO: Target number of precursors reached.
1 day, 4:22:50.745265 INFO: fragments_df: keeping 5000 of 35531 [sum(precursor_idx_mask)=17240 sum(mass_error_mask)=35531 stop_rank=5000
1 day, 4:22:50.750273 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:50.874076 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:50.991766 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:51.181951 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:51.818753 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:51.819224 INFO: Using score_cutoff 34.81359981880188 (fac=0.99, q=1)
1 day, 4:22:51.819558 INFO: Updating optimization_manager: fwhm_rt             : 2.7572884559631348 -> 2.7466678619384766
1 day, 4:22:51.819639 INFO: Updating optimization_manager: fwhm_mobility       : 0.008092820644378662 -> 0.008077099919319153
1 day, 4:22:51.819695 INFO: Updating optimization_manager: score_cutoff        : 35.96105828704834 -> 34.81359981880188
1 day, 4:22:51.819749 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:51.820921 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:51.822231 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:51.823007 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:51.825217 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:51.825319 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 4:22:51.827205 INFO: Updating optimization_manager: rt_error            : 15.710196632255087 -> 19.932922247530502
1 day, 4:22:51.827308 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 19.9329.
1 day, 4:22:51.827374 INFO: ==============================================
1 day, 4:22:51.827441 INFO: Starting optimization step 7.
1 day, 4:22:51.827497 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:51.827571 INFO: Using classic extraction backend
1 day, 4:22:51.827727 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:51.827797 INFO: === Search parameters used ===
1 day, 4:22:51.827845 INFO: rt_error       : 19.932922247530502
1 day, 4:22:51.827888 INFO: mobility_error : 0.1
1 day, 4:22:51.827934 INFO: num_candidates : 3
1 day, 4:22:51.827980 INFO: ms1_error      : 15.0
1 day, 4:22:51.828020 INFO: ms2_error      : 15.0
1 day, 4:22:51.828059 INFO: fwhm_rt        : 2.7466678619384766
1 day, 4:22:51.828098 INFO: quant_window   : 3
1 day, 4:22:51.828137 INFO: ==============================================
1 day, 4:22:51.829554 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:51.829601 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:51.829634 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 4:22:51.829659 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 4:22:51.830381 INFO: Starting candidate selection
1 day, 4:22:52.381400 INFO: Starting candidate scoring
1 day, 4:22:52.635502 INFO: Finished candidate processing
1 day, 4:22:52.635646 INFO: Collecting candidate features
1 day, 4:22:52.650625 INFO: Collecting fragment features
1 day, 4:22:52.656440 INFO: Finished candidate scoring
1 day, 4:22:52.658879 INFO: performing precursor FDR with 47 features
1 day, 4:22:52.658926 INFO: Decoy channel: -1
1 day, 4:22:52.658950 INFO: Competetive: True
1 day, 4:22:52.662514 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:52.664772 INFO: Using random state 316627 for train-test-split
1 day, 4:22:52.676543 INFO: Test AUC: 0.765
1 day, 4:22:52.676602 INFO: Train AUC: 0.786
1 day, 4:22:52.676633 INFO: AUC difference: 2.63%
1 day, 4:22:55.304017 INFO: Resetting torch num_threads to 80
1 day, 4:22:55.304722 PROGRESS: === Extracted 3370 precursors and 35667 fragments ===
1 day, 4:22:55.305165 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:55.305800 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:55.305894 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:55.305953 PROGRESS: Target precursors: 584 (97.33%)
1 day, 4:22:55.306002 PROGRESS: Decoy precursors: 16 (2.67%)
1 day, 4:22:55.306056 PROGRESS: 
1 day, 4:22:55.306102 PROGRESS: Precursor Summary:
1 day, 4:22:55.307192 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   556; 0.001 FDR:   383
1 day, 4:22:55.307284 PROGRESS: 
1 day, 4:22:55.307340 PROGRESS: Protein Summary:
1 day, 4:22:55.308602 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   515; 0.001 FDR:   365
1 day, 4:22:55.308700 PROGRESS: =========================================================================
1 day, 4:22:55.308843 INFO: Target number of precursors reached.
1 day, 4:22:55.315800 INFO: fragments_df: keeping 5000 of 35667 [sum(precursor_idx_mask)=17006 sum(mass_error_mask)=35667 stop_rank=5000
1 day, 4:22:55.320853 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:55.446206 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:55.565800 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:55.716976 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:56.361590 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:56.362088 INFO: Using score_cutoff 35.92153748130798 (fac=0.99, q=1)
1 day, 4:22:56.362412 INFO: Updating optimization_manager: fwhm_rt             : 2.7466678619384766 -> 2.762636661529541
1 day, 4:22:56.362502 INFO: Updating optimization_manager: fwhm_mobility       : 0.008077099919319153 -> 0.008094865828752518
1 day, 4:22:56.362556 INFO: Updating optimization_manager: score_cutoff        : 34.81359981880188 -> 35.92153748130798
1 day, 4:22:56.362609 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:56.363725 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:56.365057 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:56.365842 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:56.368115 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:56.368217 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 4:22:56.370063 INFO: Updating optimization_manager: rt_error            : 19.932922247530502 -> 15.69604738275666
1 day, 4:22:56.370168 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 15.6960.
1 day, 4:22:56.370236 INFO: ==============================================
1 day, 4:22:56.370311 INFO: Starting optimization step 8.
1 day, 4:22:56.370370 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:56.370425 INFO: Using classic extraction backend
1 day, 4:22:56.370533 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:56.370597 INFO: === Search parameters used ===
1 day, 4:22:56.370645 INFO: rt_error       : 15.69604738275666
1 day, 4:22:56.370687 INFO: mobility_error : 0.1
1 day, 4:22:56.370728 INFO: num_candidates : 3
1 day, 4:22:56.370768 INFO: ms1_error      : 15.0
1 day, 4:22:56.370807 INFO: ms2_error      : 15.0
1 day, 4:22:56.370846 INFO: fwhm_rt        : 2.762636661529541
1 day, 4:22:56.370884 INFO: quant_window   : 3
1 day, 4:22:56.370924 INFO: ==============================================
1 day, 4:22:56.371800 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:56.371844 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:56.371878 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 4:22:56.371901 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 4:22:56.372571 INFO: Starting candidate selection
1 day, 4:22:56.919027 INFO: Starting candidate scoring
1 day, 4:22:57.107311 INFO: Finished candidate processing
1 day, 4:22:57.107425 INFO: Collecting candidate features
1 day, 4:22:57.122782 INFO: Collecting fragment features
1 day, 4:22:57.127081 INFO: Finished candidate scoring
1 day, 4:22:57.130590 INFO: performing precursor FDR with 47 features
1 day, 4:22:57.130641 INFO: Decoy channel: -1
1 day, 4:22:57.130674 INFO: Competetive: True
1 day, 4:22:57.134537 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:57.136831 INFO: Using random state 316627 for train-test-split
1 day, 4:22:57.149376 INFO: Test AUC: 0.760
1 day, 4:22:57.149465 INFO: Train AUC: 0.797
1 day, 4:22:57.149503 INFO: AUC difference: 4.70%
1 day, 4:22:57.366980 INFO: Resetting torch num_threads to 80
1 day, 4:22:57.367657 PROGRESS: === Extracted 3367 precursors and 35524 fragments ===
1 day, 4:22:57.368123 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:57.368756 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:57.368856 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:57.368932 PROGRESS: Target precursors: 584 (97.33%)
1 day, 4:22:57.368994 PROGRESS: Decoy precursors: 16 (2.67%)
1 day, 4:22:57.369051 PROGRESS: 
1 day, 4:22:57.369107 PROGRESS: Precursor Summary:
1 day, 4:22:57.370314 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   555; 0.001 FDR:   434
1 day, 4:22:57.370433 PROGRESS: 
1 day, 4:22:57.370510 PROGRESS: Protein Summary:
1 day, 4:22:57.371868 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   513; 0.001 FDR:   409
1 day, 4:22:57.371974 PROGRESS: =========================================================================
1 day, 4:22:57.372143 INFO: Target number of precursors reached.
1 day, 4:22:57.378986 INFO: fragments_df: keeping 5000 of 35524 [sum(precursor_idx_mask)=17005 sum(mass_error_mask)=35524 stop_rank=5000
1 day, 4:22:57.383657 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:57.526734 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:57.666128 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:57.815817 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:58.500251 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:22:58.500762 INFO: Using score_cutoff 35.36486917190552 (fac=0.99, q=1)
1 day, 4:22:58.501108 INFO: Updating optimization_manager: fwhm_rt             : 2.762636661529541 -> 2.750089168548584
1 day, 4:22:58.501199 INFO: Updating optimization_manager: fwhm_mobility       : 0.008094865828752518 -> 0.0080790426582098
1 day, 4:22:58.501268 INFO: Updating optimization_manager: score_cutoff        : 35.92153748130798 -> 35.36486917190552
1 day, 4:22:58.501337 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:58.502507 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:58.503850 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:58.504671 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:22:58.506808 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:58.506918 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1 day, 4:22:58.508784 INFO: Updating optimization_manager: rt_error            : 15.69604738275666 -> 17.670927927192746
1 day, 4:22:58.508896 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 17.6709.
1 day, 4:22:58.508976 INFO: ==============================================
1 day, 4:22:58.509057 INFO: Starting optimization step 9.
1 day, 4:22:58.509125 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:22:58.509192 INFO: Using classic extraction backend
1 day, 4:22:58.509326 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:22:58.509403 INFO: === Search parameters used ===
1 day, 4:22:58.509466 INFO: rt_error       : 17.670927927192746
1 day, 4:22:58.509521 INFO: mobility_error : 0.1
1 day, 4:22:58.509573 INFO: num_candidates : 3
1 day, 4:22:58.509626 INFO: ms1_error      : 15.0
1 day, 4:22:58.509677 INFO: ms2_error      : 15.0
1 day, 4:22:58.509727 INFO: fwhm_rt        : 2.750089168548584
1 day, 4:22:58.509777 INFO: quant_window   : 3
1 day, 4:22:58.509827 INFO: ==============================================
1 day, 4:22:58.510814 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:58.510863 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:58.510906 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 4:22:58.510936 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 4:22:58.532438 INFO: Starting candidate selection
1 day, 4:22:59.072100 INFO: Starting candidate scoring
1 day, 4:22:59.286217 INFO: Finished candidate processing
1 day, 4:22:59.286329 INFO: Collecting candidate features
1 day, 4:22:59.298983 INFO: Collecting fragment features
1 day, 4:22:59.303010 INFO: Finished candidate scoring
1 day, 4:22:59.305963 INFO: performing precursor FDR with 47 features
1 day, 4:22:59.306005 INFO: Decoy channel: -1
1 day, 4:22:59.306029 INFO: Competetive: True
1 day, 4:22:59.309073 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:59.311190 INFO: Using random state 316627 for train-test-split
1 day, 4:22:59.322481 INFO: Test AUC: 0.790
1 day, 4:22:59.322547 INFO: Train AUC: 0.782
1 day, 4:22:59.322576 INFO: AUC difference: 0.97%
1 day, 4:22:59.537720 INFO: Resetting torch num_threads to 80
1 day, 4:22:59.538337 PROGRESS: === Extracted 3372 precursors and 35729 fragments ===
1 day, 4:22:59.538788 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:22:59.539411 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:59.539506 PROGRESS: Total precursors accumulated: 600
1 day, 4:22:59.539567 PROGRESS: Target precursors: 583 (97.17%)
1 day, 4:22:59.539618 PROGRESS: Decoy precursors: 17 (2.83%)
1 day, 4:22:59.539668 PROGRESS: 
1 day, 4:22:59.539711 PROGRESS: Precursor Summary:
1 day, 4:22:59.540805 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   476; 0.001 FDR:   386
1 day, 4:22:59.540898 PROGRESS: 
1 day, 4:22:59.540955 PROGRESS: Protein Summary:
1 day, 4:22:59.542254 PROGRESS: Channel   0:	 0.050 FDR:   536; 0.010 FDR:   447; 0.001 FDR:   368
1 day, 4:22:59.542352 PROGRESS: =========================================================================
1 day, 4:22:59.542490 INFO: Target number of precursors reached.
1 day, 4:22:59.549265 INFO: fragments_df: keeping 5000 of 35729 [sum(precursor_idx_mask)=14646 sum(mass_error_mask)=35729 stop_rank=5000
1 day, 4:22:59.553936 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:22:59.672024 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:22:59.790754 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:22:59.934317 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:00.620562 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:23:00.621041 INFO: Using score_cutoff 40.347091341018675 (fac=0.99, q=1)
1 day, 4:23:00.621358 INFO: Updating optimization_manager: fwhm_rt             : 2.750089168548584 -> 2.762636661529541
1 day, 4:23:00.621448 INFO: Updating optimization_manager: fwhm_mobility       : 0.0080790426582098 -> 0.008428830653429031
1 day, 4:23:00.621505 INFO: Updating optimization_manager: score_cutoff        : 35.36486917190552 -> 40.347091341018675
1 day, 4:23:00.621558 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:00.622691 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:00.624006 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:00.624794 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:00.626965 INFO: === checking if optimization conditions were reached ===
1 day, 4:23:00.627069 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
1 day, 4:23:00.628855 INFO: Updating optimization_manager: rt_error            : 17.670927927192746 -> 13.194385237883024
1 day, 4:23:00.628957 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 13.1944.
1 day, 4:23:00.629024 INFO: ==============================================
1 day, 4:23:00.629089 INFO: Starting optimization step 10.
1 day, 4:23:00.629147 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:23:00.629200 INFO: Using classic extraction backend
1 day, 4:23:00.629306 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:23:00.629368 INFO: === Search parameters used ===
1 day, 4:23:00.629415 INFO: rt_error       : 13.194385237883024
1 day, 4:23:00.629460 INFO: mobility_error : 0.1
1 day, 4:23:00.629502 INFO: num_candidates : 3
1 day, 4:23:00.629548 INFO: ms1_error      : 15.0
1 day, 4:23:00.629593 INFO: ms2_error      : 15.0
1 day, 4:23:00.629633 INFO: fwhm_rt        : 2.762636661529541
1 day, 4:23:00.629673 INFO: quant_window   : 3
1 day, 4:23:00.629712 INFO: ==============================================
1 day, 4:23:00.630548 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:23:00.630594 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:23:00.630627 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 4:23:00.630649 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.91
1 day, 4:23:00.631331 INFO: Starting candidate selection
1 day, 4:23:01.161260 INFO: Starting candidate scoring
1 day, 4:23:01.350573 INFO: Finished candidate processing
1 day, 4:23:01.350688 INFO: Collecting candidate features
1 day, 4:23:01.363304 INFO: Collecting fragment features
1 day, 4:23:01.367112 INFO: Finished candidate scoring
1 day, 4:23:01.369839 INFO: performing precursor FDR with 47 features
1 day, 4:23:01.369886 INFO: Decoy channel: -1
1 day, 4:23:01.369910 INFO: Competetive: True
1 day, 4:23:01.373060 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:23:01.375184 INFO: Using random state 316627 for train-test-split
1 day, 4:23:01.386020 INFO: Test AUC: 0.787
1 day, 4:23:01.386094 INFO: Train AUC: 0.782
1 day, 4:23:01.386125 INFO: AUC difference: 0.65%
1 day, 4:23:01.603601 INFO: Resetting torch num_threads to 80
1 day, 4:23:01.604216 PROGRESS: === Extracted 3355 precursors and 35276 fragments ===
1 day, 4:23:01.604670 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:23:01.605299 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:23:01.605390 PROGRESS: Total precursors accumulated: 600
1 day, 4:23:01.605451 PROGRESS: Target precursors: 582 (97.00%)
1 day, 4:23:01.605501 PROGRESS: Decoy precursors: 18 (3.00%)
1 day, 4:23:01.605546 PROGRESS: 
1 day, 4:23:01.605590 PROGRESS: Precursor Summary:
1 day, 4:23:01.606677 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   550; 0.001 FDR:   433
1 day, 4:23:01.606777 PROGRESS: 
1 day, 4:23:01.606836 PROGRESS: Protein Summary:
1 day, 4:23:01.608103 PROGRESS: Channel   0:	 0.050 FDR:   536; 0.010 FDR:   510; 0.001 FDR:   410
1 day, 4:23:01.608198 PROGRESS: =========================================================================
1 day, 4:23:01.608335 INFO: Target number of precursors reached.
1 day, 4:23:01.615090 INFO: fragments_df: keeping 5000 of 35276 [sum(precursor_idx_mask)=16757 sum(mass_error_mask)=35276 stop_rank=5000
1 day, 4:23:01.619762 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:01.739751 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:01.857998 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:01.985324 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:02.602700 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:23:02.603176 INFO: Using score_cutoff 34.09618400573731 (fac=0.99, q=1)
1 day, 4:23:02.603497 INFO: Updating optimization_manager: fwhm_rt             : 2.762636661529541 -> 2.7688422203063965
1 day, 4:23:02.603582 INFO: Updating optimization_manager: fwhm_mobility       : 0.008428830653429031 -> 0.008174974471330643
1 day, 4:23:02.603637 INFO: Updating optimization_manager: score_cutoff        : 40.347091341018675 -> 34.09618400573731
1 day, 4:23:02.603694 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:02.604818 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:02.606138 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:02.606933 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:02.609061 INFO: === checking if optimization conditions were reached ===
1 day, 4:23:02.609170 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
1 day, 4:23:02.610998 INFO: Updating optimization_manager: rt_error            : 13.194385237883024 -> 12.941376634672888
1 day, 4:23:02.611106 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 12.9414.
1 day, 4:23:02.611175 INFO: ==============================================
1 day, 4:23:02.611242 INFO: Starting optimization step 11.
1 day, 4:23:02.611313 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:23:02.611371 INFO: Using classic extraction backend
1 day, 4:23:02.611480 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:23:02.611545 INFO: === Search parameters used ===
1 day, 4:23:02.611594 INFO: rt_error       : 12.941376634672888
1 day, 4:23:02.611638 INFO: mobility_error : 0.1
1 day, 4:23:02.611682 INFO: num_candidates : 3
1 day, 4:23:02.611726 INFO: ms1_error      : 15.0
1 day, 4:23:02.611767 INFO: ms2_error      : 15.0
1 day, 4:23:02.611808 INFO: fwhm_rt        : 2.7688422203063965
1 day, 4:23:02.611856 INFO: quant_window   : 3
1 day, 4:23:02.611898 INFO: ==============================================
1 day, 4:23:02.612720 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:23:02.612767 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:23:02.612801 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 4:23:02.612825 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:23:02.613519 INFO: Starting candidate selection
1 day, 4:23:03.160436 INFO: Starting candidate scoring
1 day, 4:23:03.339957 INFO: Finished candidate processing
1 day, 4:23:03.340073 INFO: Collecting candidate features
1 day, 4:23:03.354330 INFO: Collecting fragment features
1 day, 4:23:03.358271 INFO: Finished candidate scoring
1 day, 4:23:03.361299 INFO: performing precursor FDR with 47 features
1 day, 4:23:03.361347 INFO: Decoy channel: -1
1 day, 4:23:03.361372 INFO: Competetive: True
1 day, 4:23:03.365472 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:23:03.369354 INFO: Using random state 316627 for train-test-split
1 day, 4:23:03.382244 INFO: Test AUC: 0.806
1 day, 4:23:03.382314 INFO: Train AUC: 0.780
1 day, 4:23:03.382343 INFO: AUC difference: 3.28%
1 day, 4:23:03.600746 INFO: Resetting torch num_threads to 80
1 day, 4:23:03.601364 PROGRESS: === Extracted 3352 precursors and 35213 fragments ===
1 day, 4:23:03.601803 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:23:03.602438 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:23:03.602529 PROGRESS: Total precursors accumulated: 600
1 day, 4:23:03.602588 PROGRESS: Target precursors: 581 (96.83%)
1 day, 4:23:03.602638 PROGRESS: Decoy precursors: 19 (3.17%)
1 day, 4:23:03.602684 PROGRESS: 
1 day, 4:23:03.602727 PROGRESS: Precursor Summary:
1 day, 4:23:03.603792 PROGRESS: Channel   0:	 0.050 FDR:   581; 0.010 FDR:   550; 0.001 FDR:   434
1 day, 4:23:03.603886 PROGRESS: 
1 day, 4:23:03.603951 PROGRESS: Protein Summary:
1 day, 4:23:03.605249 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:   510; 0.001 FDR:   411
1 day, 4:23:03.605339 PROGRESS: =========================================================================
1 day, 4:23:03.605486 INFO: Target number of precursors reached.
1 day, 4:23:03.612206 INFO: fragments_df: keeping 5000 of 35213 [sum(precursor_idx_mask)=16780 sum(mass_error_mask)=35213 stop_rank=5000
1 day, 4:23:03.616904 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:03.760974 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:03.894698 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:04.023335 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:04.662971 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:23:04.663455 INFO: Using score_cutoff 32.99618140411376 (fac=0.99, q=1)
1 day, 4:23:04.663776 INFO: Updating optimization_manager: fwhm_rt             : 2.7688422203063965 -> 2.749415397644043
1 day, 4:23:04.663854 INFO: Updating optimization_manager: fwhm_mobility       : 0.008174974471330643 -> 0.008078240789473057
1 day, 4:23:04.663907 INFO: Updating optimization_manager: score_cutoff        : 34.09618400573731 -> 32.99618140411376
1 day, 4:23:04.663961 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:04.665089 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:04.666414 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:04.667206 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:04.669278 INFO: === checking if optimization conditions were reached ===
1 day, 4:23:04.669384 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
1 day, 4:23:04.670380 INFO: Updating optimization_manager: rt_error            : 12.941376634672888 -> 12.941376634672888
1 day, 4:23:04.670505 INFO: Updating optimization_manager: classifier_version  : 7 -> 19
1 day, 4:23:04.670803 INFO: Updating optimization_manager: score_cutoff        : 32.99618140411376 -> 32.99618140411376
1 day, 4:23:04.670890 INFO: Updating optimization_manager: fwhm_rt             : 2.749415397644043 -> 2.749415397644043
1 day, 4:23:04.670971 INFO: Updating optimization_manager: fwhm_mobility       : 0.008078240789473057 -> 0.008078240789473057
1 day, 4:23:04.671053 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 12.9414 found after 12 searches.
1 day, 4:23:04.671112 INFO: ==============================================
1 day, 4:23:04.671176 PROGRESS: Optimization finished for rt_error.
1 day, 4:23:04.675456 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:04.676285 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:04.677555 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:04.678339 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:04.704006 INFO: Starting optimization step 0.
1 day, 4:23:04.704180 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:23:04.704251 INFO: Using classic extraction backend
1 day, 4:23:04.704364 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:23:04.704431 INFO: === Search parameters used ===
1 day, 4:23:04.704478 INFO: rt_error       : 12.941376634672888
1 day, 4:23:04.704534 INFO: mobility_error : 0.1
1 day, 4:23:04.704578 INFO: num_candidates : 3
1 day, 4:23:04.704619 INFO: ms1_error      : 15.0
1 day, 4:23:04.704659 INFO: ms2_error      : 15.0
1 day, 4:23:04.704699 INFO: fwhm_rt        : 2.749415397644043
1 day, 4:23:04.704738 INFO: quant_window   : 3
1 day, 4:23:04.704776 INFO: ==============================================
1 day, 4:23:04.705558 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:23:04.705607 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:23:04.705641 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 4:23:04.705662 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 4:23:04.709008 INFO: Starting candidate selection
1 day, 4:23:05.219570 INFO: Starting candidate scoring
1 day, 4:23:05.415611 INFO: Finished candidate processing
1 day, 4:23:05.415725 INFO: Collecting candidate features
1 day, 4:23:05.428313 INFO: Collecting fragment features
1 day, 4:23:05.431966 INFO: Finished candidate scoring
1 day, 4:23:05.434326 INFO: performing precursor FDR with 47 features
1 day, 4:23:05.434372 INFO: Decoy channel: -1
1 day, 4:23:05.434397 INFO: Competetive: True
1 day, 4:23:05.437589 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:23:05.439728 INFO: Using random state 553620 for train-test-split
1 day, 4:23:05.450320 INFO: Test AUC: 0.769
1 day, 4:23:05.450390 INFO: Train AUC: 0.791
1 day, 4:23:05.450419 INFO: AUC difference: 2.67%
1 day, 4:23:05.670409 INFO: Resetting torch num_threads to 80
1 day, 4:23:05.671026 PROGRESS: === Extracted 3356 precursors and 35258 fragments ===
1 day, 4:23:05.671478 INFO: === FDR correction performed with classifier version 19 ===
1 day, 4:23:05.672081 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:23:05.672171 PROGRESS: Total precursors accumulated: 600
1 day, 4:23:05.672232 PROGRESS: Target precursors: 581 (96.83%)
1 day, 4:23:05.672280 PROGRESS: Decoy precursors: 19 (3.17%)
1 day, 4:23:05.672326 PROGRESS: 
1 day, 4:23:05.672370 PROGRESS: Precursor Summary:
1 day, 4:23:05.673439 PROGRESS: Channel   0:	 0.050 FDR:   581; 0.010 FDR:   550; 0.001 FDR:   433
1 day, 4:23:05.673536 PROGRESS: 
1 day, 4:23:05.673593 PROGRESS: Protein Summary:
1 day, 4:23:05.674865 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:   510; 0.001 FDR:   410
1 day, 4:23:05.674964 PROGRESS: =========================================================================
1 day, 4:23:05.675098 INFO: Target number of precursors reached.
1 day, 4:23:05.681748 INFO: fragments_df: keeping 5000 of 35258 [sum(precursor_idx_mask)=16756 sum(mass_error_mask)=35258 stop_rank=5000
1 day, 4:23:05.686428 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:05.806836 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:05.926358 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:06.054102 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:06.673209 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:23:06.673692 INFO: Using score_cutoff 33.00603381958008 (fac=0.99, q=1)
1 day, 4:23:06.674016 INFO: Updating optimization_manager: fwhm_rt             : 2.749415397644043 -> 2.750880718231201
1 day, 4:23:06.674118 INFO: Updating optimization_manager: fwhm_mobility       : 0.008078240789473057 -> 0.008164186030626297
1 day, 4:23:06.674175 INFO: Updating optimization_manager: score_cutoff        : 32.99618140411376 -> 33.00603381958008
1 day, 4:23:06.674231 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:06.675340 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:06.676651 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:06.677435 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:06.679530 INFO: === checking if optimization conditions were reached ===
1 day, 4:23:06.679635 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:23:06.680990 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06517172205257662
1 day, 4:23:06.681093 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0652.
1 day, 4:23:06.681165 INFO: ==============================================
1 day, 4:23:06.681233 INFO: Starting optimization step 1.
1 day, 4:23:06.681291 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:23:06.681347 INFO: Using classic extraction backend
1 day, 4:23:06.681457 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:23:06.681518 INFO: === Search parameters used ===
1 day, 4:23:06.681565 INFO: rt_error       : 12.941376634672888
1 day, 4:23:06.681608 INFO: mobility_error : 0.06517172205257662
1 day, 4:23:06.681651 INFO: num_candidates : 3
1 day, 4:23:06.681691 INFO: ms1_error      : 15.0
1 day, 4:23:06.681732 INFO: ms2_error      : 15.0
1 day, 4:23:06.681771 INFO: fwhm_rt        : 2.750880718231201
1 day, 4:23:06.681811 INFO: quant_window   : 3
1 day, 4:23:06.681850 INFO: ==============================================
1 day, 4:23:06.682663 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:23:06.682709 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:23:06.682744 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 4:23:06.682765 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:23:06.683422 INFO: Starting candidate selection
1 day, 4:23:07.157549 INFO: Starting candidate scoring
1 day, 4:23:07.343181 INFO: Finished candidate processing
1 day, 4:23:07.343301 INFO: Collecting candidate features
1 day, 4:23:07.353298 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3344)
1 day, 4:23:07.356658 INFO: Collecting fragment features
1 day, 4:23:07.361316 INFO: Finished candidate scoring
1 day, 4:23:07.363734 INFO: performing precursor FDR with 47 features
1 day, 4:23:07.363779 INFO: Decoy channel: -1
1 day, 4:23:07.363802 INFO: Competetive: True
1 day, 4:23:07.368314 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:23:07.369675 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 4:23:07.370679 INFO: Using random state 553620 for train-test-split
1 day, 4:23:07.381497 INFO: Test AUC: 0.778
1 day, 4:23:07.381569 INFO: Train AUC: 0.790
1 day, 4:23:07.381599 INFO: AUC difference: 1.51%
1 day, 4:23:07.599258 INFO: Resetting torch num_threads to 80
1 day, 4:23:07.599864 PROGRESS: === Extracted 3344 precursors and 34804 fragments ===
1 day, 4:23:07.600303 INFO: === FDR correction performed with classifier version 19 ===
1 day, 4:23:07.600908 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:23:07.600998 PROGRESS: Total precursors accumulated: 600
1 day, 4:23:07.601058 PROGRESS: Target precursors: 580 (96.67%)
1 day, 4:23:07.601108 PROGRESS: Decoy precursors: 20 (3.33%)
1 day, 4:23:07.601153 PROGRESS: 
1 day, 4:23:07.601202 PROGRESS: Precursor Summary:
1 day, 4:23:07.602316 PROGRESS: Channel   0:	 0.050 FDR:   580; 0.010 FDR:   548; 0.001 FDR:   429
1 day, 4:23:07.602415 PROGRESS: 
1 day, 4:23:07.602474 PROGRESS: Protein Summary:
1 day, 4:23:07.603770 PROGRESS: Channel   0:	 0.050 FDR:   534; 0.010 FDR:   510; 0.001 FDR:   406
1 day, 4:23:07.603863 PROGRESS: =========================================================================
1 day, 4:23:07.604004 INFO: Target number of precursors reached.
1 day, 4:23:07.610658 INFO: fragments_df: keeping 5000 of 34804 [sum(precursor_idx_mask)=16592 sum(mass_error_mask)=34804 stop_rank=5000
1 day, 4:23:07.615322 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:07.746867 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:07.864344 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:07.988492 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:08.609988 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:23:08.610498 INFO: Using score_cutoff 33.406790611267084 (fac=0.99, q=1)
1 day, 4:23:08.610828 INFO: Updating optimization_manager: fwhm_rt             : 2.750880718231201 -> 2.7568130493164062
1 day, 4:23:08.610910 INFO: Updating optimization_manager: fwhm_mobility       : 0.008164186030626297 -> 0.008164186030626297
1 day, 4:23:08.610965 INFO: Updating optimization_manager: score_cutoff        : 33.00603381958008 -> 33.406790611267084
1 day, 4:23:08.611019 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:08.612136 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:08.613459 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:08.614245 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:08.616336 INFO: === checking if optimization conditions were reached ===
1 day, 4:23:08.616437 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:23:08.617920 INFO: Updating optimization_manager: mobility_error      : 0.06517172205257662 -> 0.05623151979328048
1 day, 4:23:08.618018 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0562.
1 day, 4:23:08.618094 INFO: ==============================================
1 day, 4:23:08.618160 INFO: Starting optimization step 2.
1 day, 4:23:08.618216 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:23:08.618271 INFO: Using classic extraction backend
1 day, 4:23:08.618382 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:23:08.618445 INFO: === Search parameters used ===
1 day, 4:23:08.618491 INFO: rt_error       : 12.941376634672888
1 day, 4:23:08.618535 INFO: mobility_error : 0.05623151979328048
1 day, 4:23:08.618574 INFO: num_candidates : 3
1 day, 4:23:08.618615 INFO: ms1_error      : 15.0
1 day, 4:23:08.618654 INFO: ms2_error      : 15.0
1 day, 4:23:08.618694 INFO: fwhm_rt        : 2.7568130493164062
1 day, 4:23:08.618734 INFO: quant_window   : 3
1 day, 4:23:08.618772 INFO: ==============================================
1 day, 4:23:08.619576 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:23:08.619620 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:23:08.619653 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 4:23:08.619676 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:23:08.620404 INFO: Starting candidate selection
1 day, 4:23:09.114712 INFO: Starting candidate scoring
1 day, 4:23:09.326769 INFO: Finished candidate processing
1 day, 4:23:09.326886 INFO: Collecting candidate features
1 day, 4:23:09.338471 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3346)
1 day, 4:23:09.341927 INFO: Collecting fragment features
1 day, 4:23:09.345633 INFO: Finished candidate scoring
1 day, 4:23:09.347852 INFO: performing precursor FDR with 47 features
1 day, 4:23:09.347901 INFO: Decoy channel: -1
1 day, 4:23:09.347934 INFO: Competetive: True
1 day, 4:23:09.351686 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:23:09.353072 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 4:23:09.354134 INFO: Using random state 553620 for train-test-split
1 day, 4:23:09.365821 INFO: Test AUC: 0.788
1 day, 4:23:09.365882 INFO: Train AUC: 0.784
1 day, 4:23:09.365921 INFO: AUC difference: 0.60%
1 day, 4:23:09.585168 INFO: Resetting torch num_threads to 80
1 day, 4:23:09.585795 PROGRESS: === Extracted 3346 precursors and 34663 fragments ===
1 day, 4:23:09.586274 INFO: === FDR correction performed with classifier version 19 ===
1 day, 4:23:09.586902 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:23:09.587000 PROGRESS: Total precursors accumulated: 599
1 day, 4:23:09.587074 PROGRESS: Target precursors: 579 (96.66%)
1 day, 4:23:09.587137 PROGRESS: Decoy precursors: 20 (3.34%)
1 day, 4:23:09.587194 PROGRESS: 
1 day, 4:23:09.587250 PROGRESS: Precursor Summary:
1 day, 4:23:09.588391 PROGRESS: Channel   0:	 0.050 FDR:   579; 0.010 FDR:   544; 0.001 FDR:   425
1 day, 4:23:09.588497 PROGRESS: 
1 day, 4:23:09.588571 PROGRESS: Protein Summary:
1 day, 4:23:09.589902 PROGRESS: Channel   0:	 0.050 FDR:   536; 0.010 FDR:   507; 0.001 FDR:   402
1 day, 4:23:09.590004 PROGRESS: =========================================================================
1 day, 4:23:09.590188 INFO: Target number of precursors reached.
1 day, 4:23:09.596853 INFO: fragments_df: keeping 5000 of 34663 [sum(precursor_idx_mask)=16440 sum(mass_error_mask)=34663 stop_rank=5000
1 day, 4:23:09.601555 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:09.722112 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:09.839039 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:09.953872 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:10.570884 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:23:10.571399 INFO: Using score_cutoff 35.637405321121214 (fac=0.99, q=1)
1 day, 4:23:10.571751 INFO: Updating optimization_manager: fwhm_rt             : 2.7568130493164062 -> 2.759922981262207
1 day, 4:23:10.571844 INFO: Updating optimization_manager: fwhm_mobility       : 0.008164186030626297 -> 0.00822931807488203
1 day, 4:23:10.571914 INFO: Updating optimization_manager: score_cutoff        : 33.406790611267084 -> 35.637405321121214
1 day, 4:23:10.571981 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:10.573117 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:10.574460 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:10.575264 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:10.577363 INFO: === checking if optimization conditions were reached ===
1 day, 4:23:10.577484 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:23:10.578218 INFO: Updating optimization_manager: mobility_error      : 0.05623151979328048 -> 0.1
1 day, 4:23:10.578360 INFO: Updating optimization_manager: classifier_version  : 19 -> 20
1 day, 4:23:10.578483 INFO: Updating optimization_manager: score_cutoff        : 35.637405321121214 -> 33.00603381958008
1 day, 4:23:10.578598 INFO: Updating optimization_manager: fwhm_rt             : 2.759922981262207 -> 2.750880718231201
1 day, 4:23:10.578704 INFO: Updating optimization_manager: fwhm_mobility       : 0.00822931807488203 -> 0.008164186030626297
1 day, 4:23:10.578807 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 4:23:10.578899 INFO: ==============================================
1 day, 4:23:10.578984 PROGRESS: Optimization finished for mobility_error.
1 day, 4:23:10.583283 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:10.584142 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:10.585441 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:10.586246 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:10.611788 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 4:23:10.611958 PROGRESS: ==============================================
1 day, 4:23:10.612045 PROGRESS: ms2_error      : 15.0000
1 day, 4:23:10.612116 PROGRESS: ms1_error      : 15.0000
1 day, 4:23:10.612179 PROGRESS: rt_error       : 12.9414
1 day, 4:23:10.612237 PROGRESS: mobility_error : 0.1000
1 day, 4:23:10.612292 PROGRESS: ==============================================
1 day, 4:23:10.612927 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:23:10.637997 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:23:10.741897 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:23:10.768935 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:23:11.038736 INFO: Using classic extraction backend
1 day, 4:23:11.039905 PROGRESS: Extracting batch of 180112 precursors
1 day, 4:23:11.040001 INFO: === Search parameters used ===
1 day, 4:23:11.040055 INFO: rt_error       : 12.941376634672888
1 day, 4:23:11.040103 INFO: mobility_error : 0.1
1 day, 4:23:11.040146 INFO: num_candidates : 3
1 day, 4:23:11.040203 INFO: ms1_error      : 15.0
1 day, 4:23:11.040245 INFO: ms2_error      : 15.0
1 day, 4:23:11.040286 INFO: fwhm_rt        : 2.750880718231201
1 day, 4:23:11.040326 INFO: quant_window   : 3
1 day, 4:23:11.040366 INFO: ==============================================
1 day, 4:23:11.074554 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:23:11.074701 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:23:11.074744 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 4:23:11.074767 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:23:11.075638 INFO: Starting candidate selection
1 day, 4:23:26.527141 INFO: Removed 94249 precursors with score below cutoff 33.00603381958008
1 day, 4:23:26.881742 INFO: Starting candidate scoring
1 day, 4:23:43.541095 INFO: Finished candidate processing
1 day, 4:23:43.541400 INFO: Collecting candidate features
1 day, 4:23:44.086315 INFO: Collecting fragment features
1 day, 4:23:44.354793 INFO: Finished candidate scoring
1 day, 4:23:44.633164 INFO: === Performing FDR correction with classifier version 20 ===
1 day, 4:23:44.634923 INFO: performing precursor FDR with 47 features
1 day, 4:23:44.634982 INFO: Decoy channel: -1
1 day, 4:23:44.635008 INFO: Competetive: True
1 day, 4:23:44.745237 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:23:44.791478 WARNING: FDR calculation for 230986 target and 181385 decoy PSMs
1 day, 4:23:44.791646 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 4:23:44.916301 INFO: Using random state 237511 for train-test-split
1 day, 4:23:52.305161 INFO: Test AUC: 0.849
1 day, 4:23:52.305305 INFO: Train AUC: 0.851
1 day, 4:23:52.305342 INFO: AUC difference: 0.25%
1 day, 4:23:52.677528 INFO: Resetting torch num_threads to 80
1 day, 4:23:52.696496 INFO: Removing fragments below FDR threshold
1 day, 4:23:52.781726 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:23:52.782023 PROGRESS: Total precursors accumulated: 89,437
1 day, 4:23:52.782104 PROGRESS: Target precursors: 88,552 (99.01%)
1 day, 4:23:52.782158 PROGRESS: Decoy precursors: 885 (0.99%)
1 day, 4:23:52.782205 PROGRESS: 
1 day, 4:23:52.782249 PROGRESS: Precursor Summary:
1 day, 4:23:52.821010 PROGRESS: Channel   0:	 0.050 FDR: 88,552; 0.010 FDR: 88,552; 0.001 FDR: 83,585
1 day, 4:23:52.821330 PROGRESS: 
1 day, 4:23:52.821399 PROGRESS: Protein Summary:
1 day, 4:23:52.871673 PROGRESS: Channel   0:	 0.050 FDR: 8,875; 0.010 FDR: 8,875; 0.001 FDR: 8,857
1 day, 4:23:52.871966 PROGRESS: =========================================================================
1 day, 4:23:52.876736 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/psm.parquet
1 day, 4:23:53.253563 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/frag.parquet
1 day, 4:23:53.568803 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 4:23:54.576349 PROGRESS: 
1 day, 4:23:54.576528 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/quant
1 day, 4:23:54.576612 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/figures
1 day, 4:23:54.576804 INFO: Initializing TimingManager
1 day, 4:23:54.577491 INFO: Initializing RawFileManager
1 day, 4:23:54.577607 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:23:54.577663 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:23:54.577704 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:23:54.898925 INFO: Reading 39,128 frames with 2,766,418,119 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:24:01.318456 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
1 day, 4:24:01.320454 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:24:01.322529 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:24:01.322962 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:24:01.323408 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:24:01.324864 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:24:01.345673 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:24:01.345857 INFO: Indexing quadrupole dimension
1 day, 4:24:01.888604 INFO: Transposing detector events
1 day, 4:24:17.681929 INFO: Finished transposing data
1 day, 4:24:17.734707 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 4:24:17.735607 INFO: RT (min)            : 0.0 - 70.0
1 day, 4:24:17.735698 INFO: RT duration (sec)   : 4199.9
1 day, 4:24:17.735756 INFO: RT duration (min)   : 70.0
1 day, 4:24:17.735807 INFO: Cycle len (scans)   : 9
1 day, 4:24:17.735851 INFO: Cycle len (sec)     : 0.97
1 day, 4:24:17.735895 INFO: Number of cycles    : 4347
1 day, 4:24:17.735943 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 4:24:17.735998 INFO: Creating DIA data object took: 23.158400535583496
1 day, 4:24:17.764843 INFO: Initializing CalibrationManager
1 day, 4:24:17.765261 INFO: Setting up calibration estimators ..
1 day, 4:24:17.765364 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 4:24:17.765476 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, 4:24:17.765590 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 4:24:17.765676 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, 4:24:17.765797 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, 4:24:17.765891 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, 4:24:17.765973 INFO: Done setting up calibration estimators.
1 day, 4:24:17.766169 INFO: Initializing OptimizationManager
1 day, 4:24:17.766321 INFO: initial parameter: ms1_error = 30
1 day, 4:24:17.766398 INFO: initial parameter: ms2_error = 30
1 day, 4:24:17.766448 INFO: initial parameter: rt_error = 2099.9331315
1 day, 4:24:17.766490 INFO: initial parameter: mobility_error = 0.1
1 day, 4:24:17.766530 INFO: initial parameter: num_candidates = 1
1 day, 4:24:17.766567 INFO: initial parameter: fwhm_rt = 5
1 day, 4:24:17.766608 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 4:24:17.766650 INFO: initial parameter: score_cutoff = 0
1 day, 4:24:17.766692 INFO: initial parameter: classifier_version = -1
1 day, 4:24:17.766757 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 4:24:17.766944 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 4:24:17.766977 INFO: Initializing FDRManager
1 day, 4:24:17.767010 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 4:24:17.787822 PROGRESS: Initializing spectral library: 90,710 target precursors potentially observable (0 removed)
1 day, 4:24:17.803938 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 4:24:17.804361 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 2099.9331315
1 day, 4:24:17.804463 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 4:24:17.804630 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 4:24:17.804717 PROGRESS: Starting initial search for precursors.
1 day, 4:24:17.804796 INFO: Starting optimization step 0.
1 day, 4:24:17.804858 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:24:17.804928 INFO: Using classic extraction backend
1 day, 4:24:17.805101 PROGRESS: Extracting batch of 398 precursors
1 day, 4:24:17.805169 INFO: === Search parameters used ===
1 day, 4:24:17.805217 INFO: rt_error       : 2099.9331315
1 day, 4:24:17.805261 INFO: mobility_error : 0.1
1 day, 4:24:17.805302 INFO: num_candidates : 1
1 day, 4:24:17.805343 INFO: ms1_error      : 30
1 day, 4:24:17.805384 INFO: ms2_error      : 30
1 day, 4:24:17.805423 INFO: fwhm_rt        : 5
1 day, 4:24:17.805461 INFO: quant_window   : 3
1 day, 4:24:17.805500 INFO: ==============================================
1 day, 4:24:17.806231 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:24:17.806277 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:24:17.806314 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:24:17.806335 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:24:17.832372 INFO: Starting candidate selection
1 day, 4:24:22.171169 INFO: Starting candidate scoring
1 day, 4:24:22.258720 INFO: Finished candidate processing
1 day, 4:24:22.258861 INFO: Collecting candidate features
1 day, 4:24:22.271590 INFO: Collecting fragment features
1 day, 4:24:22.274516 INFO: Finished candidate scoring
1 day, 4:24:22.275847 INFO: performing precursor FDR with 47 features
1 day, 4:24:22.275898 INFO: Decoy channel: -1
1 day, 4:24:22.275928 INFO: Competetive: True
1 day, 4:24:22.277656 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:24:22.280685 INFO: Using random state 149869 for train-test-split
1 day, 4:24:22.288839 INFO: Test AUC: 0.531
1 day, 4:24:22.288909 INFO: Train AUC: 0.491
1 day, 4:24:22.288950 INFO: AUC difference: 8.10%
1 day, 4:24:22.288973 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:24:22.518067 INFO: Resetting torch num_threads to 80
1 day, 4:24:22.518562 PROGRESS: === Extracted 398 precursors and 4582 fragments ===
1 day, 4:24:22.519003 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:24:22.519564 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:24:22.519654 PROGRESS: Total precursors accumulated: 200
1 day, 4:24:22.519713 PROGRESS: Target precursors: 179 (89.50%)
1 day, 4:24:22.519765 PROGRESS: Decoy precursors: 21 (10.50%)
1 day, 4:24:22.519811 PROGRESS: 
1 day, 4:24:22.519854 PROGRESS: Precursor Summary:
1 day, 4:24:22.520797 PROGRESS: Channel   0:	 0.050 FDR:   175; 0.010 FDR:   175; 0.001 FDR:   175
1 day, 4:24:22.520885 PROGRESS: 
1 day, 4:24:22.520947 PROGRESS: Protein Summary:
1 day, 4:24:22.522007 PROGRESS: Channel   0:	 0.050 FDR:   165; 0.010 FDR:   165; 0.001 FDR:   165
1 day, 4:24:22.522105 PROGRESS: =========================================================================
1 day, 4:24:22.522213 INFO: Target number of precursors not reached yet.
1 day, 4:24:22.525956 INFO: Starting optimization step 1.
1 day, 4:24:22.526073 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 4:24:22.526148 INFO: Using classic extraction backend
1 day, 4:24:22.526258 PROGRESS: Extracting batch of 796 precursors
1 day, 4:24:22.526325 INFO: === Search parameters used ===
1 day, 4:24:22.526374 INFO: rt_error       : 2099.9331315
1 day, 4:24:22.526418 INFO: mobility_error : 0.1
1 day, 4:24:22.526459 INFO: num_candidates : 1
1 day, 4:24:22.526499 INFO: ms1_error      : 30
1 day, 4:24:22.526541 INFO: ms2_error      : 30
1 day, 4:24:22.526584 INFO: fwhm_rt        : 5
1 day, 4:24:22.526625 INFO: quant_window   : 3
1 day, 4:24:22.526664 INFO: ==============================================
1 day, 4:24:22.527269 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:24:22.527313 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:24:22.527341 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:24:22.527363 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:24:22.528155 INFO: Starting candidate selection
1 day, 4:24:28.580074 INFO: Starting candidate scoring
1 day, 4:24:28.712589 INFO: Finished candidate processing
1 day, 4:24:28.712704 INFO: Collecting candidate features
1 day, 4:24:28.723252 INFO: Collecting fragment features
1 day, 4:24:28.726560 INFO: Finished candidate scoring
1 day, 4:24:28.728822 INFO: performing precursor FDR with 47 features
1 day, 4:24:28.728870 INFO: Decoy channel: -1
1 day, 4:24:28.728896 INFO: Competetive: True
1 day, 4:24:28.732744 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:24:28.734638 INFO: Using random state 389379 for train-test-split
1 day, 4:24:28.743062 INFO: Test AUC: 0.504
1 day, 4:24:28.743121 INFO: Train AUC: 0.494
1 day, 4:24:28.743150 INFO: AUC difference: 1.98%
1 day, 4:24:28.961938 INFO: Resetting torch num_threads to 80
1 day, 4:24:28.963439 PROGRESS: === Extracted 1194 precursors and 13584 fragments ===
1 day, 4:24:28.963903 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:24:28.964575 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:24:28.964667 PROGRESS: Total precursors accumulated: 600
1 day, 4:24:28.964728 PROGRESS: Target precursors: 534 (89.00%)
1 day, 4:24:28.964783 PROGRESS: Decoy precursors: 66 (11.00%)
1 day, 4:24:28.964833 PROGRESS: 
1 day, 4:24:28.964876 PROGRESS: Precursor Summary:
1 day, 4:24:28.965924 PROGRESS: Channel   0:	 0.050 FDR:   517; 0.010 FDR:   517; 0.001 FDR:   517
1 day, 4:24:28.966018 PROGRESS: 
1 day, 4:24:28.966082 PROGRESS: Protein Summary:
1 day, 4:24:28.967330 PROGRESS: Channel   0:	 0.050 FDR:   480; 0.010 FDR:   480; 0.001 FDR:   480
1 day, 4:24:28.967424 PROGRESS: =========================================================================
1 day, 4:24:28.967607 INFO: Target number of precursors reached.
1 day, 4:24:28.971133 INFO: fragments_df: keeping 2991 of 13584 [sum(precursor_idx_mask)=5871 sum(mass_error_mask)=13584 stop_rank=2991
1 day, 4:24:28.976434 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:24:29.113414 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:24:29.240257 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:24:29.364462 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:24:29.692477 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 4:24:29.692989 INFO: Using score_cutoff 48.424271855163575 (fac=0.99, q=1)
1 day, 4:24:29.693348 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.4356837272644043
1 day, 4:24:29.693434 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010250127874314785
1 day, 4:24:29.693491 INFO: Updating optimization_manager: score_cutoff        : 0 -> 48.424271855163575
1 day, 4:24:29.693557 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:24:29.694803 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:24:29.696149 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:24:29.696928 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:24:29.699308 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
1 day, 4:24:29.699405 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 4:24:29.699488 INFO: Starting optimization step 2.
1 day, 4:24:29.699548 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:24:29.699608 INFO: Using classic extraction backend
1 day, 4:24:29.699736 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:24:29.699800 INFO: === Search parameters used ===
1 day, 4:24:29.699847 INFO: rt_error       : 2099.9331315
1 day, 4:24:29.699888 INFO: mobility_error : 0.1
1 day, 4:24:29.699927 INFO: num_candidates : 3
1 day, 4:24:29.699969 INFO: ms1_error      : 30
1 day, 4:24:29.700007 INFO: ms2_error      : 30
1 day, 4:24:29.700045 INFO: fwhm_rt        : 3.4356837272644043
1 day, 4:24:29.700085 INFO: quant_window   : 3
1 day, 4:24:29.700123 INFO: ==============================================
1 day, 4:24:29.701048 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:24:29.701093 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:24:29.701129 INFO: FWHM in RT is 3.44 seconds, sigma is 0.76
1 day, 4:24:29.701152 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.75
1 day, 4:24:29.701845 INFO: Starting candidate selection
1 day, 4:24:40.124139 INFO: Starting candidate scoring
1 day, 4:24:40.463519 INFO: Finished candidate processing
1 day, 4:24:40.463641 INFO: Collecting candidate features
1 day, 4:24:40.477785 INFO: Collecting fragment features
1 day, 4:24:40.481898 INFO: Finished candidate scoring
1 day, 4:24:40.484070 INFO: performing precursor FDR with 47 features
1 day, 4:24:40.484117 INFO: Decoy channel: -1
1 day, 4:24:40.484143 INFO: Competetive: True
1 day, 4:24:40.487396 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:24:40.489631 INFO: Using random state 759711 for train-test-split
1 day, 4:24:40.499700 INFO: Test AUC: 0.493
1 day, 4:24:40.499765 INFO: Train AUC: 0.501
1 day, 4:24:40.499795 INFO: AUC difference: 1.57%
1 day, 4:24:40.719914 INFO: Resetting torch num_threads to 80
1 day, 4:24:40.720482 PROGRESS: === Extracted 3388 precursors and 38537 fragments ===
1 day, 4:24:40.720930 INFO: === FDR correction performed with classifier version 1 ===
1 day, 4:24:40.721512 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:24:40.721604 PROGRESS: Total precursors accumulated: 600
1 day, 4:24:40.721662 PROGRESS: Target precursors: 584 (97.33%)
1 day, 4:24:40.721717 PROGRESS: Decoy precursors: 16 (2.67%)
1 day, 4:24:40.721763 PROGRESS: 
1 day, 4:24:40.721807 PROGRESS: Precursor Summary:
1 day, 4:24:40.722879 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   578; 0.001 FDR:   578
1 day, 4:24:40.722973 PROGRESS: 
1 day, 4:24:40.723030 PROGRESS: Protein Summary:
1 day, 4:24:40.724323 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   535; 0.001 FDR:   535
1 day, 4:24:40.724414 PROGRESS: =========================================================================
1 day, 4:24:40.724595 INFO: Target number of precursors reached.
1 day, 4:24:40.732187 INFO: fragments_df: keeping 5000 of 38537 [sum(precursor_idx_mask)=18659 sum(mass_error_mask)=38537 stop_rank=5000
1 day, 4:24:40.737311 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:24:40.875136 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:24:41.017897 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:24:41.157983 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:24:41.837968 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:24:41.838458 INFO: Using score_cutoff 45.85247313079834 (fac=0.99, q=1)
1 day, 4:24:41.838774 INFO: Updating optimization_manager: fwhm_rt             : 3.4356837272644043 -> 3.440070152282715
1 day, 4:24:41.838861 INFO: Updating optimization_manager: fwhm_mobility       : 0.010250127874314785 -> 0.009815804660320282
1 day, 4:24:41.838917 INFO: Updating optimization_manager: score_cutoff        : 48.424271855163575 -> 45.85247313079834
1 day, 4:24:41.838970 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:24:41.840064 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:24:41.841366 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:24:41.842146 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:24:41.844332 INFO: === checking if optimization conditions were reached ===
1 day, 4:24:41.845895 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 4:24:41.845998 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 4:24:41.846072 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:24:41.847038 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 4:24:41.847131 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 4:24:41.847193 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:24:41.847246 INFO: ==============================================
1 day, 4:24:41.847307 INFO: Starting optimization step 3.
1 day, 4:24:41.847360 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:24:41.847410 INFO: Using classic extraction backend
1 day, 4:24:41.847518 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:24:41.847579 INFO: === Search parameters used ===
1 day, 4:24:41.847625 INFO: rt_error       : 2099.9331315
1 day, 4:24:41.847679 INFO: mobility_error : 0.1
1 day, 4:24:41.847723 INFO: num_candidates : 3
1 day, 4:24:41.847767 INFO: ms1_error      : 15.0
1 day, 4:24:41.847807 INFO: ms2_error      : 15.0
1 day, 4:24:41.847848 INFO: fwhm_rt        : 3.440070152282715
1 day, 4:24:41.847888 INFO: quant_window   : 3
1 day, 4:24:41.847926 INFO: ==============================================
1 day, 4:24:41.848729 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:24:41.848773 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:24:41.848807 INFO: FWHM in RT is 3.44 seconds, sigma is 0.76
1 day, 4:24:41.848830 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.55
1 day, 4:24:41.849650 INFO: Starting candidate selection
1 day, 4:24:51.222896 INFO: Starting candidate scoring
1 day, 4:24:51.439401 INFO: Finished candidate processing
1 day, 4:24:51.439521 INFO: Collecting candidate features
1 day, 4:24:51.453460 INFO: Collecting fragment features
1 day, 4:24:51.457754 INFO: Finished candidate scoring
1 day, 4:24:51.459774 INFO: performing precursor FDR with 47 features
1 day, 4:24:51.459821 INFO: Decoy channel: -1
1 day, 4:24:51.459861 INFO: Competetive: True
1 day, 4:24:51.463206 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:24:51.465407 INFO: Using random state 578378 for train-test-split
1 day, 4:24:51.475845 INFO: Test AUC: 0.479
1 day, 4:24:51.475905 INFO: Train AUC: 0.493
1 day, 4:24:51.475935 INFO: AUC difference: 2.92%
1 day, 4:24:51.692137 INFO: Resetting torch num_threads to 80
1 day, 4:24:51.692701 PROGRESS: === Extracted 3394 precursors and 37616 fragments ===
1 day, 4:24:51.693137 INFO: === FDR correction performed with classifier version 2 ===
1 day, 4:24:51.693761 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:24:51.693852 PROGRESS: Total precursors accumulated: 600
1 day, 4:24:51.693914 PROGRESS: Target precursors: 537 (89.50%)
1 day, 4:24:51.693964 PROGRESS: Decoy precursors: 63 (10.50%)
1 day, 4:24:51.694011 PROGRESS: 
1 day, 4:24:51.694069 PROGRESS: Precursor Summary:
1 day, 4:24:51.695127 PROGRESS: Channel   0:	 0.050 FDR:   518; 0.010 FDR:   518; 0.001 FDR:   518
1 day, 4:24:51.695219 PROGRESS: 
1 day, 4:24:51.695275 PROGRESS: Protein Summary:
1 day, 4:24:51.696511 PROGRESS: Channel   0:	 0.050 FDR:   487; 0.010 FDR:   487; 0.001 FDR:   487
1 day, 4:24:51.696602 PROGRESS: =========================================================================
1 day, 4:24:51.696758 INFO: Target number of precursors reached.
1 day, 4:24:51.703801 INFO: fragments_df: keeping 5000 of 37616 [sum(precursor_idx_mask)=16493 sum(mass_error_mask)=37616 stop_rank=5000
1 day, 4:24:51.709235 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:24:51.833402 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:24:51.947100 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:24:52.064045 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:24:52.669711 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:24:52.670200 INFO: Using score_cutoff 39.774167021942134 (fac=0.99, q=1)
1 day, 4:24:52.670512 INFO: Updating optimization_manager: fwhm_rt             : 3.440070152282715 -> 3.00846529006958
1 day, 4:24:52.670592 INFO: Updating optimization_manager: fwhm_mobility       : 0.009815804660320282 -> 0.008430088870227337
1 day, 4:24:52.670647 INFO: Updating optimization_manager: score_cutoff        : 45.85247313079834 -> 39.774167021942134
1 day, 4:24:52.670702 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:24:52.671793 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:24:52.673079 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:24:52.673850 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:24:52.676020 INFO: === checking if optimization conditions were reached ===
1 day, 4:24:52.677596 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 4:24:52.677697 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
1 day, 4:24:52.677760 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 4:24:52.678728 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 4:24:52.679015 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
1 day, 4:24:52.679080 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 4:24:52.679136 INFO: ==============================================
1 day, 4:24:52.679201 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 4:24:52.683879 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:24:52.684692 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:24:52.685950 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:24:52.686723 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:24:52.688822 INFO: Starting optimization step 0.
1 day, 4:24:52.688916 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:24:52.688982 INFO: Using classic extraction backend
1 day, 4:24:52.689100 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:24:52.689168 INFO: === Search parameters used ===
1 day, 4:24:52.689218 INFO: rt_error       : 2099.9331315
1 day, 4:24:52.689263 INFO: mobility_error : 0.1
1 day, 4:24:52.689305 INFO: num_candidates : 3
1 day, 4:24:52.689347 INFO: ms1_error      : 15.0
1 day, 4:24:52.689387 INFO: ms2_error      : 15.0
1 day, 4:24:52.689428 INFO: fwhm_rt        : 3.00846529006958
1 day, 4:24:52.689467 INFO: quant_window   : 3
1 day, 4:24:52.689508 INFO: ==============================================
1 day, 4:24:52.690219 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:24:52.690269 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:24:52.690304 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 4:24:52.690325 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.91
1 day, 4:24:52.691008 INFO: Starting candidate selection
1 day, 4:25:01.806178 INFO: Starting candidate scoring
1 day, 4:25:02.066433 INFO: Finished candidate processing
1 day, 4:25:02.066567 INFO: Collecting candidate features
1 day, 4:25:02.080716 INFO: Collecting fragment features
1 day, 4:25:02.085779 INFO: Finished candidate scoring
1 day, 4:25:02.088036 INFO: performing precursor FDR with 47 features
1 day, 4:25:02.088083 INFO: Decoy channel: -1
1 day, 4:25:02.088107 INFO: Competetive: True
1 day, 4:25:02.091877 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:25:02.094243 INFO: Using random state 402443 for train-test-split
1 day, 4:25:02.105090 INFO: Test AUC: 0.503
1 day, 4:25:02.105150 INFO: Train AUC: 0.478
1 day, 4:25:02.105181 INFO: AUC difference: 5.21%
1 day, 4:25:02.105204 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:25:02.330118 INFO: Resetting torch num_threads to 80
1 day, 4:25:02.330823 PROGRESS: === Extracted 3371 precursors and 37283 fragments ===
1 day, 4:25:02.331340 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:25:02.331958 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:25:02.332048 PROGRESS: Total precursors accumulated: 600
1 day, 4:25:02.332113 PROGRESS: Target precursors: 522 (87.00%)
1 day, 4:25:02.332165 PROGRESS: Decoy precursors: 78 (13.00%)
1 day, 4:25:02.332211 PROGRESS: 
1 day, 4:25:02.332256 PROGRESS: Precursor Summary:
1 day, 4:25:02.333311 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   500; 0.001 FDR:   500
1 day, 4:25:02.333405 PROGRESS: 
1 day, 4:25:02.333461 PROGRESS: Protein Summary:
1 day, 4:25:02.334725 PROGRESS: Channel   0:	 0.050 FDR:   469; 0.010 FDR:   469; 0.001 FDR:   469
1 day, 4:25:02.334821 PROGRESS: =========================================================================
1 day, 4:25:02.335091 INFO: Target number of precursors reached.
1 day, 4:25:02.341654 INFO: fragments_df: keeping 5000 of 37283 [sum(precursor_idx_mask)=15695 sum(mass_error_mask)=37283 stop_rank=5000
1 day, 4:25:02.347945 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:02.487541 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:02.627794 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:02.763506 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:03.437537 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:25:03.438392 INFO: Using score_cutoff 40.25085494499207 (fac=0.99, q=1)
1 day, 4:25:03.438751 INFO: Updating optimization_manager: fwhm_rt             : 3.00846529006958 -> 3.031679153442383
1 day, 4:25:03.438832 INFO: Updating optimization_manager: fwhm_mobility       : 0.008430088870227337 -> 0.008402020670473576
1 day, 4:25:03.438888 INFO: Updating optimization_manager: score_cutoff        : 39.774167021942134 -> 40.25085494499207
1 day, 4:25:03.438946 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:03.440049 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:03.441324 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:03.442111 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:03.444321 INFO: === checking if optimization conditions were reached ===
1 day, 4:25:03.444432 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:25:03.446100 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 1060.5057404059514
1 day, 4:25:03.446207 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1060.5057.
1 day, 4:25:03.446272 INFO: ==============================================
1 day, 4:25:03.446343 INFO: Starting optimization step 1.
1 day, 4:25:03.446399 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:25:03.446458 INFO: Using classic extraction backend
1 day, 4:25:03.446627 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:25:03.446692 INFO: === Search parameters used ===
1 day, 4:25:03.446739 INFO: rt_error       : 1060.5057404059514
1 day, 4:25:03.446787 INFO: mobility_error : 0.1
1 day, 4:25:03.446831 INFO: num_candidates : 3
1 day, 4:25:03.446871 INFO: ms1_error      : 15.0
1 day, 4:25:03.446909 INFO: ms2_error      : 15.0
1 day, 4:25:03.446949 INFO: fwhm_rt        : 3.031679153442383
1 day, 4:25:03.446988 INFO: quant_window   : 3
1 day, 4:25:03.447027 INFO: ==============================================
1 day, 4:25:03.448021 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:25:03.448068 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:25:03.448113 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 4:25:03.448137 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 4:25:03.448848 INFO: Starting candidate selection
1 day, 4:25:09.534066 INFO: Starting candidate scoring
1 day, 4:25:09.776512 INFO: Finished candidate processing
1 day, 4:25:09.776693 INFO: Collecting candidate features
1 day, 4:25:09.818826 INFO: Collecting fragment features
1 day, 4:25:09.829924 INFO: Finished candidate scoring
1 day, 4:25:09.832493 INFO: performing precursor FDR with 47 features
1 day, 4:25:09.832564 INFO: Decoy channel: -1
1 day, 4:25:09.832602 INFO: Competetive: True
1 day, 4:25:09.838014 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:25:09.841409 INFO: Using random state 402443 for train-test-split
1 day, 4:25:09.856864 INFO: Test AUC: 0.513
1 day, 4:25:09.856936 INFO: Train AUC: 0.482
1 day, 4:25:09.856965 INFO: AUC difference: 6.52%
1 day, 4:25:09.856988 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:25:10.072518 INFO: Resetting torch num_threads to 80
1 day, 4:25:10.073112 PROGRESS: === Extracted 3380 precursors and 37357 fragments ===
1 day, 4:25:10.073560 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:25:10.074184 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:25:10.074274 PROGRESS: Total precursors accumulated: 600
1 day, 4:25:10.074334 PROGRESS: Target precursors: 528 (88.00%)
1 day, 4:25:10.074384 PROGRESS: Decoy precursors: 72 (12.00%)
1 day, 4:25:10.074428 PROGRESS: 
1 day, 4:25:10.074471 PROGRESS: Precursor Summary:
1 day, 4:25:10.075494 PROGRESS: Channel   0:	 0.050 FDR:   504; 0.010 FDR:   504; 0.001 FDR:   504
1 day, 4:25:10.075582 PROGRESS: 
1 day, 4:25:10.075640 PROGRESS: Protein Summary:
1 day, 4:25:10.076870 PROGRESS: Channel   0:	 0.050 FDR:   473; 0.010 FDR:   473; 0.001 FDR:   473
1 day, 4:25:10.076959 PROGRESS: =========================================================================
1 day, 4:25:10.077100 INFO: Target number of precursors reached.
1 day, 4:25:10.083842 INFO: fragments_df: keeping 5000 of 37357 [sum(precursor_idx_mask)=15854 sum(mass_error_mask)=37357 stop_rank=5000
1 day, 4:25:10.088703 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:10.235563 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:10.376338 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:10.511912 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:11.186023 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:25:11.186509 INFO: Using score_cutoff 40.2604975730896 (fac=0.99, q=1)
1 day, 4:25:11.186826 INFO: Updating optimization_manager: fwhm_rt             : 3.031679153442383 -> 3.004176378250122
1 day, 4:25:11.186907 INFO: Updating optimization_manager: fwhm_mobility       : 0.008402020670473576 -> 0.008334742859005928
1 day, 4:25:11.186961 INFO: Updating optimization_manager: score_cutoff        : 40.25085494499207 -> 40.2604975730896
1 day, 4:25:11.187016 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:11.188103 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:11.189390 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:11.190162 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:11.192352 INFO: === checking if optimization conditions were reached ===
1 day, 4:25:11.192455 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:25:11.194131 INFO: Updating optimization_manager: rt_error            : 1060.5057404059514 -> 979.7477956587438
1 day, 4:25:11.194236 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 979.7478.
1 day, 4:25:11.194310 INFO: ==============================================
1 day, 4:25:11.194383 INFO: Starting optimization step 2.
1 day, 4:25:11.194442 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:25:11.194495 INFO: Using classic extraction backend
1 day, 4:25:11.194613 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:25:11.194676 INFO: === Search parameters used ===
1 day, 4:25:11.194721 INFO: rt_error       : 979.7477956587438
1 day, 4:25:11.194762 INFO: mobility_error : 0.1
1 day, 4:25:11.194802 INFO: num_candidates : 3
1 day, 4:25:11.194841 INFO: ms1_error      : 15.0
1 day, 4:25:11.194880 INFO: ms2_error      : 15.0
1 day, 4:25:11.194917 INFO: fwhm_rt        : 3.004176378250122
1 day, 4:25:11.194955 INFO: quant_window   : 3
1 day, 4:25:11.194993 INFO: ==============================================
1 day, 4:25:11.195803 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:25:11.195848 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:25:11.195881 INFO: FWHM in RT is 3.00 seconds, sigma is 0.66
1 day, 4:25:11.195903 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
1 day, 4:25:11.196615 INFO: Starting candidate selection
1 day, 4:25:17.025824 INFO: Starting candidate scoring
1 day, 4:25:17.287029 INFO: Finished candidate processing
1 day, 4:25:17.287151 INFO: Collecting candidate features
1 day, 4:25:17.301043 INFO: Collecting fragment features
1 day, 4:25:17.304747 INFO: Finished candidate scoring
1 day, 4:25:17.306783 INFO: performing precursor FDR with 47 features
1 day, 4:25:17.306829 INFO: Decoy channel: -1
1 day, 4:25:17.306854 INFO: Competetive: True
1 day, 4:25:17.309820 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:25:17.311891 INFO: Using random state 402443 for train-test-split
1 day, 4:25:17.323473 INFO: Test AUC: 0.478
1 day, 4:25:17.323539 INFO: Train AUC: 0.497
1 day, 4:25:17.323569 INFO: AUC difference: 3.75%
1 day, 4:25:17.540611 INFO: Resetting torch num_threads to 80
1 day, 4:25:17.541147 PROGRESS: === Extracted 3381 precursors and 37373 fragments ===
1 day, 4:25:17.541574 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:25:17.542194 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:25:17.542289 PROGRESS: Total precursors accumulated: 600
1 day, 4:25:17.542350 PROGRESS: Target precursors: 531 (88.50%)
1 day, 4:25:17.542400 PROGRESS: Decoy precursors: 69 (11.50%)
1 day, 4:25:17.542445 PROGRESS: 
1 day, 4:25:17.542488 PROGRESS: Precursor Summary:
1 day, 4:25:17.543521 PROGRESS: Channel   0:	 0.050 FDR:   505; 0.010 FDR:   505; 0.001 FDR:   505
1 day, 4:25:17.543620 PROGRESS: 
1 day, 4:25:17.543679 PROGRESS: Protein Summary:
1 day, 4:25:17.544901 PROGRESS: Channel   0:	 0.050 FDR:   473; 0.010 FDR:   473; 0.001 FDR:   473
1 day, 4:25:17.544993 PROGRESS: =========================================================================
1 day, 4:25:17.545130 INFO: Target number of precursors reached.
1 day, 4:25:17.551919 INFO: fragments_df: keeping 5000 of 37373 [sum(precursor_idx_mask)=15854 sum(mass_error_mask)=37373 stop_rank=5000
1 day, 4:25:17.556646 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:17.672154 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:17.788933 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:17.926962 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:18.632881 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:25:18.633364 INFO: Using score_cutoff 40.27540867767334 (fac=0.99, q=1)
1 day, 4:25:18.633680 INFO: Updating optimization_manager: fwhm_rt             : 3.004176378250122 -> 2.9992337226867676
1 day, 4:25:18.633761 INFO: Updating optimization_manager: fwhm_mobility       : 0.008334742859005928 -> 0.008298013359308243
1 day, 4:25:18.633820 INFO: Updating optimization_manager: score_cutoff        : 40.2604975730896 -> 40.27540867767334
1 day, 4:25:18.633874 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:18.634987 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:18.636288 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:18.637064 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:18.640221 INFO: === checking if optimization conditions were reached ===
1 day, 4:25:18.640325 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:25:18.642118 INFO: Updating optimization_manager: rt_error            : 979.7477956587438 -> 957.9723608412336
1 day, 4:25:18.642221 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 957.9724.
1 day, 4:25:18.642286 INFO: ==============================================
1 day, 4:25:18.642351 INFO: Starting optimization step 3.
1 day, 4:25:18.642409 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:25:18.642462 INFO: Using classic extraction backend
1 day, 4:25:18.642574 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:25:18.642636 INFO: === Search parameters used ===
1 day, 4:25:18.642682 INFO: rt_error       : 957.9723608412336
1 day, 4:25:18.642724 INFO: mobility_error : 0.1
1 day, 4:25:18.642764 INFO: num_candidates : 3
1 day, 4:25:18.642804 INFO: ms1_error      : 15.0
1 day, 4:25:18.642846 INFO: ms2_error      : 15.0
1 day, 4:25:18.642886 INFO: fwhm_rt        : 2.9992337226867676
1 day, 4:25:18.642925 INFO: quant_window   : 3
1 day, 4:25:18.642964 INFO: ==============================================
1 day, 4:25:18.644026 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:25:18.644071 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:25:18.644105 INFO: FWHM in RT is 3.00 seconds, sigma is 0.66
1 day, 4:25:18.644127 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.85
1 day, 4:25:18.645906 INFO: Starting candidate selection
1 day, 4:25:23.729575 INFO: Starting candidate scoring
1 day, 4:25:23.933283 INFO: Finished candidate processing
1 day, 4:25:23.933401 INFO: Collecting candidate features
1 day, 4:25:23.964586 INFO: Collecting fragment features
1 day, 4:25:23.973446 INFO: Finished candidate scoring
1 day, 4:25:23.976430 INFO: performing precursor FDR with 47 features
1 day, 4:25:23.976540 INFO: Decoy channel: -1
1 day, 4:25:23.976605 INFO: Competetive: True
1 day, 4:25:23.981601 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:25:23.984872 INFO: Using random state 402443 for train-test-split
1 day, 4:25:24.001170 INFO: Test AUC: 0.492
1 day, 4:25:24.001287 INFO: Train AUC: 0.496
1 day, 4:25:24.001344 INFO: AUC difference: 0.80%
1 day, 4:25:24.219498 INFO: Resetting torch num_threads to 80
1 day, 4:25:24.220053 PROGRESS: === Extracted 3383 precursors and 37411 fragments ===
1 day, 4:25:24.220492 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:25:24.221113 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:25:24.221207 PROGRESS: Total precursors accumulated: 600
1 day, 4:25:24.221272 PROGRESS: Target precursors: 529 (88.17%)
1 day, 4:25:24.221330 PROGRESS: Decoy precursors: 71 (11.83%)
1 day, 4:25:24.221383 PROGRESS: 
1 day, 4:25:24.221432 PROGRESS: Precursor Summary:
1 day, 4:25:24.222470 PROGRESS: Channel   0:	 0.050 FDR:   503; 0.010 FDR:   503; 0.001 FDR:   503
1 day, 4:25:24.222562 PROGRESS: 
1 day, 4:25:24.222621 PROGRESS: Protein Summary:
1 day, 4:25:24.223881 PROGRESS: Channel   0:	 0.050 FDR:   471; 0.010 FDR:   471; 0.001 FDR:   471
1 day, 4:25:24.223972 PROGRESS: =========================================================================
1 day, 4:25:24.224111 INFO: Target number of precursors reached.
1 day, 4:25:24.230667 INFO: fragments_df: keeping 5000 of 37411 [sum(precursor_idx_mask)=15804 sum(mass_error_mask)=37411 stop_rank=5000
1 day, 4:25:24.239294 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:24.377260 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:24.514943 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:24.651942 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:25.356181 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:25:25.356666 INFO: Using score_cutoff 40.6194743888855 (fac=0.99, q=1)
1 day, 4:25:25.357007 INFO: Updating optimization_manager: fwhm_rt             : 2.9992337226867676 -> 3.017404556274414
1 day, 4:25:25.357087 INFO: Updating optimization_manager: fwhm_mobility       : 0.008298013359308243 -> 0.00823031086474657
1 day, 4:25:25.357141 INFO: Updating optimization_manager: score_cutoff        : 40.27540867767334 -> 40.6194743888855
1 day, 4:25:25.357194 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:25.358291 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:25.359584 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:25.360356 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:25.363690 INFO: === checking if optimization conditions were reached ===
1 day, 4:25:25.363797 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 4:25:25.364775 INFO: Updating optimization_manager: rt_error            : 957.9723608412336 -> 957.9723608412336
1 day, 4:25:25.364898 INFO: Updating optimization_manager: classifier_version  : 3 -> 7
1 day, 4:25:25.364990 INFO: Updating optimization_manager: score_cutoff        : 40.6194743888855 -> 40.6194743888855
1 day, 4:25:25.365073 INFO: Updating optimization_manager: fwhm_rt             : 3.017404556274414 -> 3.017404556274414
1 day, 4:25:25.365154 INFO: Updating optimization_manager: fwhm_mobility       : 0.00823031086474657 -> 0.00823031086474657
1 day, 4:25:25.365236 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 957.9724 found after 4 searches.
1 day, 4:25:25.365299 INFO: ==============================================
1 day, 4:25:25.365363 PROGRESS: Optimization finished for rt_error.
1 day, 4:25:25.370589 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:25.371691 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:25.372957 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:25.373728 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:25.400648 INFO: Starting optimization step 0.
1 day, 4:25:25.400811 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:25:25.400892 INFO: Using classic extraction backend
1 day, 4:25:25.401011 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:25:25.401086 INFO: === Search parameters used ===
1 day, 4:25:25.401134 INFO: rt_error       : 957.9723608412336
1 day, 4:25:25.401178 INFO: mobility_error : 0.1
1 day, 4:25:25.401219 INFO: num_candidates : 3
1 day, 4:25:25.401259 INFO: ms1_error      : 15.0
1 day, 4:25:25.401299 INFO: ms2_error      : 15.0
1 day, 4:25:25.401338 INFO: fwhm_rt        : 3.017404556274414
1 day, 4:25:25.401379 INFO: quant_window   : 3
1 day, 4:25:25.401418 INFO: ==============================================
1 day, 4:25:25.402727 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:25:25.402774 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:25:25.402809 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
1 day, 4:25:25.402833 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 4:25:25.403456 INFO: Starting candidate selection
1 day, 4:25:30.636040 INFO: Starting candidate scoring
1 day, 4:25:30.890895 INFO: Finished candidate processing
1 day, 4:25:30.891064 INFO: Collecting candidate features
1 day, 4:25:30.905929 INFO: Collecting fragment features
1 day, 4:25:30.911037 INFO: Finished candidate scoring
1 day, 4:25:30.912990 INFO: performing precursor FDR with 47 features
1 day, 4:25:30.913036 INFO: Decoy channel: -1
1 day, 4:25:30.913060 INFO: Competetive: True
1 day, 4:25:30.916219 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:25:30.918267 INFO: Using random state 698873 for train-test-split
1 day, 4:25:30.928597 INFO: Test AUC: 0.488
1 day, 4:25:30.928669 INFO: Train AUC: 0.495
1 day, 4:25:30.928699 INFO: AUC difference: 1.34%
1 day, 4:25:31.148199 INFO: Resetting torch num_threads to 80
1 day, 4:25:31.148766 PROGRESS: === Extracted 3391 precursors and 37508 fragments ===
1 day, 4:25:31.149212 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:25:31.149798 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:25:31.149887 PROGRESS: Total precursors accumulated: 600
1 day, 4:25:31.149947 PROGRESS: Target precursors: 529 (88.17%)
1 day, 4:25:31.150005 PROGRESS: Decoy precursors: 71 (11.83%)
1 day, 4:25:31.150062 PROGRESS: 
1 day, 4:25:31.150110 PROGRESS: Precursor Summary:
1 day, 4:25:31.151118 PROGRESS: Channel   0:	 0.050 FDR:   504; 0.010 FDR:   504; 0.001 FDR:   504
1 day, 4:25:31.151208 PROGRESS: 
1 day, 4:25:31.151263 PROGRESS: Protein Summary:
1 day, 4:25:31.152485 PROGRESS: Channel   0:	 0.050 FDR:   472; 0.010 FDR:   472; 0.001 FDR:   472
1 day, 4:25:31.152577 PROGRESS: =========================================================================
1 day, 4:25:31.152759 INFO: Target number of precursors reached.
1 day, 4:25:31.159367 INFO: fragments_df: keeping 5000 of 37508 [sum(precursor_idx_mask)=15870 sum(mass_error_mask)=37508 stop_rank=5000
1 day, 4:25:31.164273 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:31.300653 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:31.440347 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:31.575727 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:32.298256 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:25:32.298732 INFO: Using score_cutoff 40.26197114524841 (fac=0.99, q=1)
1 day, 4:25:32.299041 INFO: Updating optimization_manager: fwhm_rt             : 3.017404556274414 -> 3.0104098320007324
1 day, 4:25:32.299120 INFO: Updating optimization_manager: fwhm_mobility       : 0.00823031086474657 -> 0.008222141303122044
1 day, 4:25:32.299172 INFO: Updating optimization_manager: score_cutoff        : 40.6194743888855 -> 40.26197114524841
1 day, 4:25:32.299223 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:32.300318 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:32.301603 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:32.302640 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:32.305781 INFO: === checking if optimization conditions were reached ===
1 day, 4:25:32.305887 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:25:32.307278 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07585459223986309
1 day, 4:25:32.307381 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0759.
1 day, 4:25:32.307445 INFO: ==============================================
1 day, 4:25:32.307508 INFO: Starting optimization step 1.
1 day, 4:25:32.307563 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:25:32.307616 INFO: Using classic extraction backend
1 day, 4:25:32.307727 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:25:32.307788 INFO: === Search parameters used ===
1 day, 4:25:32.307834 INFO: rt_error       : 957.9723608412336
1 day, 4:25:32.307876 INFO: mobility_error : 0.07585459223986309
1 day, 4:25:32.307917 INFO: num_candidates : 3
1 day, 4:25:32.307956 INFO: ms1_error      : 15.0
1 day, 4:25:32.307997 INFO: ms2_error      : 15.0
1 day, 4:25:32.308035 INFO: fwhm_rt        : 3.0104098320007324
1 day, 4:25:32.308072 INFO: quant_window   : 3
1 day, 4:25:32.308118 INFO: ==============================================
1 day, 4:25:32.309229 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:25:32.309274 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:25:32.309308 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 4:25:32.309330 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 4:25:32.317845 INFO: Starting candidate selection
1 day, 4:25:37.232644 INFO: Starting candidate scoring
1 day, 4:25:37.468318 INFO: Finished candidate processing
1 day, 4:25:37.468481 INFO: Collecting candidate features
1 day, 4:25:37.483135 INFO: Collecting fragment features
1 day, 4:25:37.487626 INFO: Finished candidate scoring
1 day, 4:25:37.492145 INFO: performing precursor FDR with 47 features
1 day, 4:25:37.492330 INFO: Decoy channel: -1
1 day, 4:25:37.492375 INFO: Competetive: True
1 day, 4:25:37.497792 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:25:37.501378 INFO: Using random state 698873 for train-test-split
1 day, 4:25:37.515787 INFO: Test AUC: 0.493
1 day, 4:25:37.515848 INFO: Train AUC: 0.493
1 day, 4:25:37.515878 INFO: AUC difference: 0.06%
1 day, 4:25:37.735507 INFO: Resetting torch num_threads to 80
1 day, 4:25:37.736058 PROGRESS: === Extracted 3384 precursors and 37356 fragments ===
1 day, 4:25:37.736498 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:25:37.737079 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:25:37.737170 PROGRESS: Total precursors accumulated: 600
1 day, 4:25:37.737231 PROGRESS: Target precursors: 528 (88.00%)
1 day, 4:25:37.737282 PROGRESS: Decoy precursors: 72 (12.00%)
1 day, 4:25:37.737330 PROGRESS: 
1 day, 4:25:37.737376 PROGRESS: Precursor Summary:
1 day, 4:25:37.738393 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   501; 0.001 FDR:   501
1 day, 4:25:37.738492 PROGRESS: 
1 day, 4:25:37.738549 PROGRESS: Protein Summary:
1 day, 4:25:37.739774 PROGRESS: Channel   0:	 0.050 FDR:   469; 0.010 FDR:   469; 0.001 FDR:   469
1 day, 4:25:37.739871 PROGRESS: =========================================================================
1 day, 4:25:37.740022 INFO: Target number of precursors reached.
1 day, 4:25:37.746687 INFO: fragments_df: keeping 5000 of 37356 [sum(precursor_idx_mask)=15736 sum(mass_error_mask)=37356 stop_rank=5000
1 day, 4:25:37.751481 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:37.889152 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:38.026837 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:38.167419 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:38.881098 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:25:38.881580 INFO: Using score_cutoff 40.25921573638916 (fac=0.99, q=1)
1 day, 4:25:38.881897 INFO: Updating optimization_manager: fwhm_rt             : 3.0104098320007324 -> 3.0001397132873535
1 day, 4:25:38.881976 INFO: Updating optimization_manager: fwhm_mobility       : 0.008222141303122044 -> 0.008274669758975506
1 day, 4:25:38.882031 INFO: Updating optimization_manager: score_cutoff        : 40.26197114524841 -> 40.25921573638916
1 day, 4:25:38.882098 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:38.883200 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:38.884482 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:38.885266 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:38.888396 INFO: === checking if optimization conditions were reached ===
1 day, 4:25:38.888510 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:25:38.890000 INFO: Updating optimization_manager: mobility_error      : 0.07585459223986309 -> 0.06691708496288325
1 day, 4:25:38.890116 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0669.
1 day, 4:25:38.890184 INFO: ==============================================
1 day, 4:25:38.890254 INFO: Starting optimization step 2.
1 day, 4:25:38.890311 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:25:38.890366 INFO: Using classic extraction backend
1 day, 4:25:38.890480 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:25:38.890545 INFO: === Search parameters used ===
1 day, 4:25:38.890603 INFO: rt_error       : 957.9723608412336
1 day, 4:25:38.890648 INFO: mobility_error : 0.06691708496288325
1 day, 4:25:38.890692 INFO: num_candidates : 3
1 day, 4:25:38.890732 INFO: ms1_error      : 15.0
1 day, 4:25:38.890772 INFO: ms2_error      : 15.0
1 day, 4:25:38.890811 INFO: fwhm_rt        : 3.0001397132873535
1 day, 4:25:38.890850 INFO: quant_window   : 3
1 day, 4:25:38.890888 INFO: ==============================================
1 day, 4:25:38.891946 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:25:38.891992 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:25:38.892027 INFO: FWHM in RT is 3.00 seconds, sigma is 0.66
1 day, 4:25:38.892050 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 4:25:38.892768 INFO: Starting candidate selection
1 day, 4:25:42.656346 INFO: Starting candidate scoring
1 day, 4:25:42.883503 INFO: Finished candidate processing
1 day, 4:25:42.883669 INFO: Collecting candidate features
1 day, 4:25:42.915050 INFO: Collecting fragment features
1 day, 4:25:42.923987 INFO: Finished candidate scoring
1 day, 4:25:42.927362 INFO: performing precursor FDR with 47 features
1 day, 4:25:42.927471 INFO: Decoy channel: -1
1 day, 4:25:42.927530 INFO: Competetive: True
1 day, 4:25:42.934299 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:25:42.937823 INFO: Using random state 698873 for train-test-split
1 day, 4:25:42.954620 INFO: Test AUC: 0.497
1 day, 4:25:42.954719 INFO: Train AUC: 0.498
1 day, 4:25:42.954765 INFO: AUC difference: 0.21%
1 day, 4:25:43.173738 INFO: Resetting torch num_threads to 80
1 day, 4:25:43.174575 PROGRESS: === Extracted 3389 precursors and 37351 fragments ===
1 day, 4:25:43.175203 INFO: === FDR correction performed with classifier version 7 ===
1 day, 4:25:43.175823 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:25:43.175913 PROGRESS: Total precursors accumulated: 600
1 day, 4:25:43.175970 PROGRESS: Target precursors: 527 (87.83%)
1 day, 4:25:43.176019 PROGRESS: Decoy precursors: 73 (12.17%)
1 day, 4:25:43.176065 PROGRESS: 
1 day, 4:25:43.176111 PROGRESS: Precursor Summary:
1 day, 4:25:43.177138 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   500; 0.001 FDR:   500
1 day, 4:25:43.177230 PROGRESS: 
1 day, 4:25:43.177294 PROGRESS: Protein Summary:
1 day, 4:25:43.178524 PROGRESS: Channel   0:	 0.050 FDR:   467; 0.010 FDR:   467; 0.001 FDR:   467
1 day, 4:25:43.178618 PROGRESS: =========================================================================
1 day, 4:25:43.178757 INFO: Target number of precursors reached.
1 day, 4:25:43.185705 INFO: fragments_df: keeping 5000 of 37351 [sum(precursor_idx_mask)=15735 sum(mass_error_mask)=37351 stop_rank=5000
1 day, 4:25:43.191028 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:43.328411 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:43.467683 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:43.612565 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:44.325070 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:25:44.325538 INFO: Using score_cutoff 40.11887429351807 (fac=0.99, q=1)
1 day, 4:25:44.325847 INFO: Updating optimization_manager: fwhm_rt             : 3.0001397132873535 -> 3.0035977363586426
1 day, 4:25:44.325928 INFO: Updating optimization_manager: fwhm_mobility       : 0.008274669758975506 -> 0.008334592916071415
1 day, 4:25:44.325982 INFO: Updating optimization_manager: score_cutoff        : 40.25921573638916 -> 40.11887429351807
1 day, 4:25:44.326046 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:44.327164 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:44.328455 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:44.329218 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:44.332350 INFO: === checking if optimization conditions were reached ===
1 day, 4:25:44.332464 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:25:44.333161 INFO: Updating optimization_manager: mobility_error      : 0.06691708496288325 -> 0.1
1 day, 4:25:44.333280 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1 day, 4:25:44.333383 INFO: Updating optimization_manager: score_cutoff        : 40.11887429351807 -> 40.26197114524841
1 day, 4:25:44.333469 INFO: Updating optimization_manager: fwhm_rt             : 3.0035977363586426 -> 3.0104098320007324
1 day, 4:25:44.333548 INFO: Updating optimization_manager: fwhm_mobility       : 0.008334592916071415 -> 0.008222141303122044
1 day, 4:25:44.333628 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 4:25:44.333688 INFO: ==============================================
1 day, 4:25:44.333752 PROGRESS: Optimization finished for mobility_error.
1 day, 4:25:44.338759 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:44.339650 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:44.340913 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:44.341674 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:44.366465 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 4:25:44.366619 PROGRESS: ==============================================
1 day, 4:25:44.366690 PROGRESS: ms2_error      : 15.0000
1 day, 4:25:44.366751 PROGRESS: ms1_error      : 15.0000
1 day, 4:25:44.366801 PROGRESS: rt_error       : 957.9724
1 day, 4:25:44.366848 PROGRESS: mobility_error : 0.1000
1 day, 4:25:44.366893 PROGRESS: ==============================================
1 day, 4:25:44.367454 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:25:44.392643 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:25:44.487704 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:25:44.513874 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:25:44.794576 INFO: Using classic extraction backend
1 day, 4:25:44.794984 PROGRESS: Extracting batch of 180112 precursors
1 day, 4:25:44.795092 INFO: === Search parameters used ===
1 day, 4:25:44.795148 INFO: rt_error       : 957.9723608412336
1 day, 4:25:44.795195 INFO: mobility_error : 0.1
1 day, 4:25:44.795240 INFO: num_candidates : 3
1 day, 4:25:44.795285 INFO: ms1_error      : 15.0
1 day, 4:25:44.795328 INFO: ms2_error      : 15.0
1 day, 4:25:44.795367 INFO: fwhm_rt        : 3.0104098320007324
1 day, 4:25:44.795408 INFO: quant_window   : 3
1 day, 4:25:44.795448 INFO: ==============================================
1 day, 4:25:44.833544 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:25:44.833701 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:25:44.833746 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 4:25:44.833770 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 4:25:44.835071 INFO: Starting candidate selection
1 day, 4:34:25.649742 INFO: Removed 29262 precursors with score below cutoff 40.26197114524841
1 day, 4:34:25.998437 INFO: Starting candidate scoring
1 day, 4:34:46.431224 INFO: Finished candidate processing
1 day, 4:34:46.432010 INFO: Collecting candidate features
1 day, 4:34:47.135798 INFO: Collecting fragment features
1 day, 4:34:47.442403 INFO: Finished candidate scoring
1 day, 4:34:48.247878 INFO: === Performing FDR correction with classifier version 8 ===
1 day, 4:34:48.249625 INFO: performing precursor FDR with 47 features
1 day, 4:34:48.249688 INFO: Decoy channel: -1
1 day, 4:34:48.249713 INFO: Competetive: True
1 day, 4:34:48.373827 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:34:48.579353 INFO: Using random state 306864 for train-test-split
1 day, 4:34:57.636875 INFO: Test AUC: 0.730
1 day, 4:34:57.637004 INFO: Train AUC: 0.731
1 day, 4:34:57.637038 INFO: AUC difference: 0.03%
1 day, 4:34:58.080103 INFO: Resetting torch num_threads to 80
1 day, 4:34:58.101443 INFO: Removing fragments below FDR threshold
1 day, 4:34:58.225123 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:34:58.225376 PROGRESS: Total precursors accumulated: 77,068
1 day, 4:34:58.225449 PROGRESS: Target precursors: 76,305 (99.01%)
1 day, 4:34:58.225501 PROGRESS: Decoy precursors: 763 (0.99%)
1 day, 4:34:58.225545 PROGRESS: 
1 day, 4:34:58.225613 PROGRESS: Precursor Summary:
1 day, 4:34:58.266656 PROGRESS: Channel   0:	 0.050 FDR: 76,305; 0.010 FDR: 76,305; 0.001 FDR: 68,761
1 day, 4:34:58.266905 PROGRESS: 
1 day, 4:34:58.266968 PROGRESS: Protein Summary:
1 day, 4:34:58.321197 PROGRESS: Channel   0:	 0.050 FDR: 8,615; 0.010 FDR: 8,615; 0.001 FDR: 8,415
1 day, 4:34:58.321435 PROGRESS: =========================================================================
1 day, 4:34:58.323076 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/psm.parquet
1 day, 4:34:58.649592 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/frag.parquet
1 day, 4:34:58.944118 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 4:35:00.379669 PROGRESS: 
1 day, 4:35:00.379831 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR/quant
1 day, 4:35:00.379912 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/figures
1 day, 4:35:00.380098 INFO: Initializing TimingManager
1 day, 4:35:00.380731 INFO: Initializing RawFileManager
1 day, 4:35:00.380850 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:00.380916 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:00.380963 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:00.585037 INFO: Reading 39,129 frames with 2,804,178,635 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:07.638680 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
1 day, 4:35:07.641282 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:07.644593 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:07.644886 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:07.645376 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:07.647020 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:07.671138 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:07.671599 INFO: Indexing quadrupole dimension
1 day, 4:35:08.301356 INFO: Transposing detector events
1 day, 4:35:22.818667 INFO: Finished transposing data
1 day, 4:35:22.861702 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:35:22.862742 INFO: RT (min)            : 0.0 - 70.0
1 day, 4:35:22.862847 INFO: RT duration (sec)   : 4199.8
1 day, 4:35:22.862909 INFO: RT duration (min)   : 70.0
1 day, 4:35:22.862966 INFO: Cycle len (scans)   : 9
1 day, 4:35:22.863018 INFO: Cycle len (sec)     : 0.97
1 day, 4:35:22.863069 INFO: Number of cycles    : 4347
1 day, 4:35:22.863126 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 4:35:22.863230 INFO: Creating DIA data object took: 22.4823796749115
1 day, 4:35:22.908319 INFO: Initializing CalibrationManager
1 day, 4:35:22.908698 INFO: Setting up calibration estimators ..
1 day, 4:35:22.908768 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 4:35:22.908864 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, 4:35:22.908967 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 4:35:22.909036 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, 4:35:22.909104 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, 4:35:22.909177 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, 4:35:22.909233 INFO: Done setting up calibration estimators.
1 day, 4:35:22.909383 INFO: Initializing OptimizationManager
1 day, 4:35:22.909489 INFO: initial parameter: ms1_error = 30
1 day, 4:35:22.909546 INFO: initial parameter: ms2_error = 30
1 day, 4:35:22.909599 INFO: initial parameter: rt_error = 2099.9231665
1 day, 4:35:22.909648 INFO: initial parameter: mobility_error = 0.1
1 day, 4:35:22.909695 INFO: initial parameter: num_candidates = 1
1 day, 4:35:22.909742 INFO: initial parameter: fwhm_rt = 5
1 day, 4:35:22.909787 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 4:35:22.909832 INFO: initial parameter: score_cutoff = 0
1 day, 4:35:22.909876 INFO: initial parameter: classifier_version = -1
1 day, 4:35:22.909968 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 4:35:22.910296 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 4:35:22.910338 INFO: Initializing FDRManager
1 day, 4:35:22.910380 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 4:35:22.932781 PROGRESS: Initializing spectral library: 90,710 target precursors potentially observable (0 removed)
1 day, 4:35:22.949605 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 4:35:22.950054 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 2099.9231665
1 day, 4:35:22.950168 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 4:35:22.950349 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 4:35:22.950459 PROGRESS: Starting initial search for precursors.
1 day, 4:35:22.950548 INFO: Starting optimization step 0.
1 day, 4:35:22.950619 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:35:22.950706 INFO: Using classic extraction backend
1 day, 4:35:22.950984 PROGRESS: Extracting batch of 398 precursors
1 day, 4:35:22.951070 INFO: === Search parameters used ===
1 day, 4:35:22.951127 INFO: rt_error       : 2099.9231665
1 day, 4:35:22.951174 INFO: mobility_error : 0.1
1 day, 4:35:22.951219 INFO: num_candidates : 1
1 day, 4:35:22.951262 INFO: ms1_error      : 30
1 day, 4:35:22.951307 INFO: ms2_error      : 30
1 day, 4:35:22.951354 INFO: fwhm_rt        : 5
1 day, 4:35:22.951398 INFO: quant_window   : 3
1 day, 4:35:22.951441 INFO: ==============================================
1 day, 4:35:22.952341 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:35:22.952390 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:35:22.952428 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:35:22.952452 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:35:22.953465 INFO: Starting candidate selection
1 day, 4:35:26.675869 INFO: Starting candidate scoring
1 day, 4:35:26.746684 INFO: Finished candidate processing
1 day, 4:35:26.746812 INFO: Collecting candidate features
1 day, 4:35:26.756708 INFO: Collecting fragment features
1 day, 4:35:26.759254 INFO: Finished candidate scoring
1 day, 4:35:26.760023 INFO: performing precursor FDR with 47 features
1 day, 4:35:26.760067 INFO: Decoy channel: -1
1 day, 4:35:26.760091 INFO: Competetive: True
1 day, 4:35:26.761312 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:35:26.763893 INFO: Using random state 13017 for train-test-split
1 day, 4:35:26.772437 INFO: Test AUC: 0.407
1 day, 4:35:26.772493 INFO: Train AUC: 0.543
1 day, 4:35:26.772522 INFO: AUC difference: 25.03%
1 day, 4:35:26.772544 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:35:27.015144 INFO: Resetting torch num_threads to 80
1 day, 4:35:27.015692 PROGRESS: === Extracted 398 precursors and 4566 fragments ===
1 day, 4:35:27.016196 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:35:27.016759 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:35:27.016851 PROGRESS: Total precursors accumulated: 200
1 day, 4:35:27.016912 PROGRESS: Target precursors: 160 (80.00%)
1 day, 4:35:27.016964 PROGRESS: Decoy precursors: 40 (20.00%)
1 day, 4:35:27.017016 PROGRESS: 
1 day, 4:35:27.017062 PROGRESS: Precursor Summary:
1 day, 4:35:27.017995 PROGRESS: Channel   0:	 0.050 FDR:   149; 0.010 FDR:   149; 0.001 FDR:   149
1 day, 4:35:27.018097 PROGRESS: 
1 day, 4:35:27.018162 PROGRESS: Protein Summary:
1 day, 4:35:27.019214 PROGRESS: Channel   0:	 0.050 FDR:   145; 0.010 FDR:   145; 0.001 FDR:   145
1 day, 4:35:27.019308 PROGRESS: =========================================================================
1 day, 4:35:27.019422 INFO: Target number of precursors not reached yet.
1 day, 4:35:27.024028 INFO: Starting optimization step 1.
1 day, 4:35:27.024137 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 4:35:27.024210 INFO: Using classic extraction backend
1 day, 4:35:27.024329 PROGRESS: Extracting batch of 796 precursors
1 day, 4:35:27.024398 INFO: === Search parameters used ===
1 day, 4:35:27.024449 INFO: rt_error       : 2099.9231665
1 day, 4:35:27.024493 INFO: mobility_error : 0.1
1 day, 4:35:27.024537 INFO: num_candidates : 1
1 day, 4:35:27.024581 INFO: ms1_error      : 30
1 day, 4:35:27.024632 INFO: ms2_error      : 30
1 day, 4:35:27.024672 INFO: fwhm_rt        : 5
1 day, 4:35:27.024713 INFO: quant_window   : 3
1 day, 4:35:27.024752 INFO: ==============================================
1 day, 4:35:27.025415 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:35:27.025460 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:35:27.025488 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:35:27.025511 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:35:27.026397 INFO: Starting candidate selection
1 day, 4:35:34.767344 INFO: Starting candidate scoring
1 day, 4:35:34.874889 INFO: Finished candidate processing
1 day, 4:35:34.875019 INFO: Collecting candidate features
1 day, 4:35:34.886923 INFO: Collecting fragment features
1 day, 4:35:34.889897 INFO: Finished candidate scoring
1 day, 4:35:34.892775 INFO: performing precursor FDR with 47 features
1 day, 4:35:34.892826 INFO: Decoy channel: -1
1 day, 4:35:34.892852 INFO: Competetive: True
1 day, 4:35:34.896022 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:35:34.897969 INFO: Using random state 553844 for train-test-split
1 day, 4:35:34.907529 INFO: Test AUC: 0.518
1 day, 4:35:34.907585 INFO: Train AUC: 0.537
1 day, 4:35:34.907614 INFO: AUC difference: 3.40%
1 day, 4:35:35.120060 INFO: Resetting torch num_threads to 80
1 day, 4:35:35.121371 PROGRESS: === Extracted 1194 precursors and 13573 fragments ===
1 day, 4:35:35.121801 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:35:35.122412 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:35:35.122513 PROGRESS: Total precursors accumulated: 600
1 day, 4:35:35.122573 PROGRESS: Target precursors: 498 (83.00%)
1 day, 4:35:35.122629 PROGRESS: Decoy precursors: 102 (17.00%)
1 day, 4:35:35.122678 PROGRESS: 
1 day, 4:35:35.122721 PROGRESS: Precursor Summary:
1 day, 4:35:35.123759 PROGRESS: Channel   0:	 0.050 FDR:   459; 0.010 FDR:   459; 0.001 FDR:   459
1 day, 4:35:35.123852 PROGRESS: 
1 day, 4:35:35.123909 PROGRESS: Protein Summary:
1 day, 4:35:35.125113 PROGRESS: Channel   0:	 0.050 FDR:   435; 0.010 FDR:   435; 0.001 FDR:   435
1 day, 4:35:35.125205 PROGRESS: =========================================================================
1 day, 4:35:35.125365 INFO: Target number of precursors reached.
1 day, 4:35:35.128604 INFO: fragments_df: keeping 2739 of 13573 [sum(precursor_idx_mask)=5186 sum(mass_error_mask)=13573 stop_rank=2739
1 day, 4:35:35.133863 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:35:35.257406 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:35:35.377071 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:35:35.495351 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:35:35.805151 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 4:35:35.805591 INFO: Using score_cutoff 51.892642501831055 (fac=0.99, q=1)
1 day, 4:35:35.805974 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.5166733264923096
1 day, 4:35:35.806066 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010439947247505188
1 day, 4:35:35.806123 INFO: Updating optimization_manager: score_cutoff        : 0 -> 51.892642501831055
1 day, 4:35:35.806205 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:35:35.807334 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:35:35.808639 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:35:35.809406 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:35:35.812591 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
1 day, 4:35:35.812696 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 4:35:35.812776 INFO: Starting optimization step 2.
1 day, 4:35:35.812836 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:35:35.813074 INFO: Using classic extraction backend
1 day, 4:35:35.813208 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:35:35.813275 INFO: === Search parameters used ===
1 day, 4:35:35.813321 INFO: rt_error       : 2099.9231665
1 day, 4:35:35.813363 INFO: mobility_error : 0.1
1 day, 4:35:35.813405 INFO: num_candidates : 3
1 day, 4:35:35.813445 INFO: ms1_error      : 30
1 day, 4:35:35.813484 INFO: ms2_error      : 30
1 day, 4:35:35.813523 INFO: fwhm_rt        : 3.5166733264923096
1 day, 4:35:35.813564 INFO: quant_window   : 3
1 day, 4:35:35.813603 INFO: ==============================================
1 day, 4:35:35.814682 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:35:35.814729 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:35:35.814766 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
1 day, 4:35:35.814797 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.84
1 day, 4:35:35.815452 INFO: Starting candidate selection
1 day, 4:35:45.757017 INFO: Starting candidate scoring
1 day, 4:35:46.197649 INFO: Finished candidate processing
1 day, 4:35:46.200136 INFO: Collecting candidate features
1 day, 4:35:46.215578 INFO: Collecting fragment features
1 day, 4:35:46.219726 INFO: Finished candidate scoring
1 day, 4:35:46.221869 INFO: performing precursor FDR with 47 features
1 day, 4:35:46.221915 INFO: Decoy channel: -1
1 day, 4:35:46.221939 INFO: Competetive: True
1 day, 4:35:46.225271 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:35:46.227407 INFO: Using random state 990527 for train-test-split
1 day, 4:35:46.238670 INFO: Test AUC: 0.529
1 day, 4:35:46.238729 INFO: Train AUC: 0.511
1 day, 4:35:46.238759 INFO: AUC difference: 3.43%
1 day, 4:35:46.454763 INFO: Resetting torch num_threads to 80
1 day, 4:35:46.455320 PROGRESS: === Extracted 3421 precursors and 38902 fragments ===
1 day, 4:35:46.455761 INFO: === FDR correction performed with classifier version 1 ===
1 day, 4:35:46.456350 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:35:46.456439 PROGRESS: Total precursors accumulated: 600
1 day, 4:35:46.456499 PROGRESS: Target precursors: 560 (93.33%)
1 day, 4:35:46.456550 PROGRESS: Decoy precursors: 40 (6.67%)
1 day, 4:35:46.456595 PROGRESS: 
1 day, 4:35:46.456637 PROGRESS: Precursor Summary:
1 day, 4:35:46.457659 PROGRESS: Channel   0:	 0.050 FDR:   544; 0.010 FDR:   544; 0.001 FDR:   544
1 day, 4:35:46.457747 PROGRESS: 
1 day, 4:35:46.457803 PROGRESS: Protein Summary:
1 day, 4:35:46.459043 PROGRESS: Channel   0:	 0.050 FDR:   506; 0.010 FDR:   506; 0.001 FDR:   506
1 day, 4:35:46.459137 PROGRESS: =========================================================================
1 day, 4:35:46.459311 INFO: Target number of precursors reached.
1 day, 4:35:46.466461 INFO: fragments_df: keeping 5000 of 38902 [sum(precursor_idx_mask)=17855 sum(mass_error_mask)=38902 stop_rank=5000
1 day, 4:35:46.471357 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:35:46.613628 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:35:46.755871 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:35:46.893211 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:35:47.579271 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:35:47.579792 INFO: Using score_cutoff 49.05886742935181 (fac=0.99, q=1)
1 day, 4:35:47.580128 INFO: Updating optimization_manager: fwhm_rt             : 3.5166733264923096 -> 3.397160053253174
1 day, 4:35:47.580217 INFO: Updating optimization_manager: fwhm_mobility       : 0.010439947247505188 -> 0.010180555284023285
1 day, 4:35:47.580273 INFO: Updating optimization_manager: score_cutoff        : 51.892642501831055 -> 49.05886742935181
1 day, 4:35:47.580325 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:35:47.581524 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:35:47.582838 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:35:47.583619 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:35:47.585757 INFO: === checking if optimization conditions were reached ===
1 day, 4:35:47.587562 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 4:35:47.587662 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 4:35:47.587726 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:35:47.588681 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 4:35:47.588771 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 4:35:47.588832 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:35:47.588890 INFO: ==============================================
1 day, 4:35:47.588952 INFO: Starting optimization step 3.
1 day, 4:35:47.589008 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:35:47.589059 INFO: Using classic extraction backend
1 day, 4:35:47.589169 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:35:47.589230 INFO: === Search parameters used ===
1 day, 4:35:47.589277 INFO: rt_error       : 2099.9231665
1 day, 4:35:47.589325 INFO: mobility_error : 0.1
1 day, 4:35:47.589368 INFO: num_candidates : 3
1 day, 4:35:47.589411 INFO: ms1_error      : 15.0
1 day, 4:35:47.589450 INFO: ms2_error      : 15.0
1 day, 4:35:47.589489 INFO: fwhm_rt        : 3.397160053253174
1 day, 4:35:47.589528 INFO: quant_window   : 3
1 day, 4:35:47.589568 INFO: ==============================================
1 day, 4:35:47.590483 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:35:47.590531 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:35:47.590566 INFO: FWHM in RT is 3.40 seconds, sigma is 0.75
1 day, 4:35:47.590589 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.72
1 day, 4:35:47.591389 INFO: Starting candidate selection
1 day, 4:35:57.693629 INFO: Starting candidate scoring
1 day, 4:35:57.900409 INFO: Finished candidate processing
1 day, 4:35:57.900533 INFO: Collecting candidate features
1 day, 4:35:57.915198 INFO: Collecting fragment features
1 day, 4:35:57.920305 INFO: Finished candidate scoring
1 day, 4:35:57.922462 INFO: performing precursor FDR with 47 features
1 day, 4:35:57.922511 INFO: Decoy channel: -1
1 day, 4:35:57.922535 INFO: Competetive: True
1 day, 4:35:57.925576 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:35:57.927673 INFO: Using random state 530434 for train-test-split
1 day, 4:35:57.938493 INFO: Test AUC: 0.519
1 day, 4:35:57.938571 INFO: Train AUC: 0.532
1 day, 4:35:57.938600 INFO: AUC difference: 2.50%
1 day, 4:35:58.159958 INFO: Resetting torch num_threads to 80
1 day, 4:35:58.160579 PROGRESS: === Extracted 3416 precursors and 37891 fragments ===
1 day, 4:35:58.161066 INFO: === FDR correction performed with classifier version 2 ===
1 day, 4:35:58.161695 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:35:58.161787 PROGRESS: Total precursors accumulated: 600
1 day, 4:35:58.161848 PROGRESS: Target precursors: 530 (88.33%)
1 day, 4:35:58.161897 PROGRESS: Decoy precursors: 70 (11.67%)
1 day, 4:35:58.161942 PROGRESS: 
1 day, 4:35:58.161986 PROGRESS: Precursor Summary:
1 day, 4:35:58.163027 PROGRESS: Channel   0:	 0.050 FDR:   498; 0.010 FDR:   498; 0.001 FDR:   498
1 day, 4:35:58.163121 PROGRESS: 
1 day, 4:35:58.163179 PROGRESS: Protein Summary:
1 day, 4:35:58.164395 PROGRESS: Channel   0:	 0.050 FDR:   465; 0.010 FDR:   465; 0.001 FDR:   465
1 day, 4:35:58.164491 PROGRESS: =========================================================================
1 day, 4:35:58.164651 INFO: Target number of precursors reached.
1 day, 4:35:58.171489 INFO: fragments_df: keeping 5000 of 37891 [sum(precursor_idx_mask)=15804 sum(mass_error_mask)=37891 stop_rank=5000
1 day, 4:35:58.176395 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:35:58.291622 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:35:58.411696 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:35:58.526781 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:35:59.155868 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:35:59.156398 INFO: Using score_cutoff 42.110920204925534 (fac=0.99, q=1)
1 day, 4:35:59.156728 INFO: Updating optimization_manager: fwhm_rt             : 3.397160053253174 -> 3.0323476791381836
1 day, 4:35:59.156809 INFO: Updating optimization_manager: fwhm_mobility       : 0.010180555284023285 -> 0.00841155182570219
1 day, 4:35:59.156864 INFO: Updating optimization_manager: score_cutoff        : 49.05886742935181 -> 42.110920204925534
1 day, 4:35:59.156918 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:35:59.158125 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:35:59.159431 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:35:59.160202 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:35:59.162385 INFO: === checking if optimization conditions were reached ===
1 day, 4:35:59.163979 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 4:35:59.164079 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
1 day, 4:35:59.164144 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 4:35:59.165102 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 4:35:59.165204 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
1 day, 4:35:59.165266 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 4:35:59.165322 INFO: ==============================================
1 day, 4:35:59.165388 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 4:35:59.169920 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:35:59.170762 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:35:59.172032 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:35:59.172804 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:35:59.174987 INFO: Starting optimization step 0.
1 day, 4:35:59.175084 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:35:59.175151 INFO: Using classic extraction backend
1 day, 4:35:59.175267 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:35:59.175335 INFO: === Search parameters used ===
1 day, 4:35:59.175383 INFO: rt_error       : 2099.9231665
1 day, 4:35:59.175426 INFO: mobility_error : 0.1
1 day, 4:35:59.175468 INFO: num_candidates : 3
1 day, 4:35:59.175510 INFO: ms1_error      : 15.0
1 day, 4:35:59.175551 INFO: ms2_error      : 15.0
1 day, 4:35:59.175594 INFO: fwhm_rt        : 3.0323476791381836
1 day, 4:35:59.175635 INFO: quant_window   : 3
1 day, 4:35:59.175674 INFO: ==============================================
1 day, 4:35:59.176426 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:35:59.176473 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:35:59.176507 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 4:35:59.176530 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 4:35:59.177240 INFO: Starting candidate selection
1 day, 4:36:09.052654 INFO: Starting candidate scoring
1 day, 4:36:09.302809 INFO: Finished candidate processing
1 day, 4:36:09.307000 INFO: Collecting candidate features
1 day, 4:36:09.322164 INFO: Collecting fragment features
1 day, 4:36:09.326772 INFO: Finished candidate scoring
1 day, 4:36:09.329031 INFO: performing precursor FDR with 47 features
1 day, 4:36:09.329080 INFO: Decoy channel: -1
1 day, 4:36:09.329107 INFO: Competetive: True
1 day, 4:36:09.332099 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:09.334263 INFO: Using random state 656817 for train-test-split
1 day, 4:36:09.346213 INFO: Test AUC: 0.554
1 day, 4:36:09.346354 INFO: Train AUC: 0.524
1 day, 4:36:09.346386 INFO: AUC difference: 5.80%
1 day, 4:36:09.346409 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:36:09.565511 INFO: Resetting torch num_threads to 80
1 day, 4:36:09.566182 PROGRESS: === Extracted 3401 precursors and 37643 fragments ===
1 day, 4:36:09.566676 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:36:09.567311 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:09.567402 PROGRESS: Total precursors accumulated: 600
1 day, 4:36:09.567461 PROGRESS: Target precursors: 525 (87.50%)
1 day, 4:36:09.567510 PROGRESS: Decoy precursors: 75 (12.50%)
1 day, 4:36:09.567556 PROGRESS: 
1 day, 4:36:09.567598 PROGRESS: Precursor Summary:
1 day, 4:36:09.568647 PROGRESS: Channel   0:	 0.050 FDR:   491; 0.010 FDR:   491; 0.001 FDR:   491
1 day, 4:36:09.568738 PROGRESS: 
1 day, 4:36:09.568793 PROGRESS: Protein Summary:
1 day, 4:36:09.570012 PROGRESS: Channel   0:	 0.050 FDR:   459; 0.010 FDR:   459; 0.001 FDR:   459
1 day, 4:36:09.570113 PROGRESS: =========================================================================
1 day, 4:36:09.570271 INFO: Target number of precursors reached.
1 day, 4:36:09.577203 INFO: fragments_df: keeping 5000 of 37643 [sum(precursor_idx_mask)=15518 sum(mass_error_mask)=37643 stop_rank=5000
1 day, 4:36:09.582230 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:09.739388 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:09.883531 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:10.027845 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:10.727058 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:36:10.727634 INFO: Using score_cutoff 41.42117868804932 (fac=0.99, q=1)
1 day, 4:36:10.727988 INFO: Updating optimization_manager: fwhm_rt             : 3.0323476791381836 -> 3.0388379096984863
1 day, 4:36:10.728078 INFO: Updating optimization_manager: fwhm_mobility       : 0.00841155182570219 -> 0.008303740993142128
1 day, 4:36:10.728147 INFO: Updating optimization_manager: score_cutoff        : 42.110920204925534 -> 41.42117868804932
1 day, 4:36:10.728214 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:10.729457 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:10.730800 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:10.731622 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:10.733914 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:10.734031 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:36:10.735724 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 1076.828222073201
1 day, 4:36:10.735840 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1076.8282.
1 day, 4:36:10.735919 INFO: ==============================================
1 day, 4:36:10.735999 INFO: Starting optimization step 1.
1 day, 4:36:10.736068 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:36:10.736134 INFO: Using classic extraction backend
1 day, 4:36:10.736269 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:36:10.736345 INFO: === Search parameters used ===
1 day, 4:36:10.736403 INFO: rt_error       : 1076.828222073201
1 day, 4:36:10.736465 INFO: mobility_error : 0.1
1 day, 4:36:10.736518 INFO: num_candidates : 3
1 day, 4:36:10.736572 INFO: ms1_error      : 15.0
1 day, 4:36:10.736624 INFO: ms2_error      : 15.0
1 day, 4:36:10.736675 INFO: fwhm_rt        : 3.0388379096984863
1 day, 4:36:10.736727 INFO: quant_window   : 3
1 day, 4:36:10.736778 INFO: ==============================================
1 day, 4:36:10.737924 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:10.737975 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:10.738022 INFO: FWHM in RT is 3.04 seconds, sigma is 0.67
1 day, 4:36:10.738061 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.85
1 day, 4:36:10.738920 INFO: Starting candidate selection
1 day, 4:36:17.107064 INFO: Starting candidate scoring
1 day, 4:36:17.321458 INFO: Finished candidate processing
1 day, 4:36:17.321590 INFO: Collecting candidate features
1 day, 4:36:17.335678 INFO: Collecting fragment features
1 day, 4:36:17.340748 INFO: Finished candidate scoring
1 day, 4:36:17.343337 INFO: performing precursor FDR with 47 features
1 day, 4:36:17.343398 INFO: Decoy channel: -1
1 day, 4:36:17.343422 INFO: Competetive: True
1 day, 4:36:17.346349 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:17.348434 INFO: Using random state 656817 for train-test-split
1 day, 4:36:17.359493 INFO: Test AUC: 0.545
1 day, 4:36:17.359555 INFO: Train AUC: 0.542
1 day, 4:36:17.359585 INFO: AUC difference: 0.54%
1 day, 4:36:20.271617 INFO: Resetting torch num_threads to 80
1 day, 4:36:20.272334 PROGRESS: === Extracted 3393 precursors and 37549 fragments ===
1 day, 4:36:20.272822 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:36:20.273540 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:20.273642 PROGRESS: Total precursors accumulated: 600
1 day, 4:36:20.273700 PROGRESS: Target precursors: 541 (90.17%)
1 day, 4:36:20.273748 PROGRESS: Decoy precursors: 59 (9.83%)
1 day, 4:36:20.273793 PROGRESS: 
1 day, 4:36:20.273835 PROGRESS: Precursor Summary:
1 day, 4:36:20.274942 PROGRESS: Channel   0:	 0.050 FDR:   503; 0.010 FDR:   503; 0.001 FDR:   503
1 day, 4:36:20.275036 PROGRESS: 
1 day, 4:36:20.275092 PROGRESS: Protein Summary:
1 day, 4:36:20.276364 PROGRESS: Channel   0:	 0.050 FDR:   470; 0.010 FDR:   470; 0.001 FDR:   470
1 day, 4:36:20.276457 PROGRESS: =========================================================================
1 day, 4:36:20.276602 INFO: Target number of precursors reached.
1 day, 4:36:20.283824 INFO: fragments_df: keeping 5000 of 37549 [sum(precursor_idx_mask)=15780 sum(mass_error_mask)=37549 stop_rank=5000
1 day, 4:36:20.288969 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:20.407279 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:20.523141 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:20.640544 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:21.259645 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:36:21.260188 INFO: Using score_cutoff 41.59397912750244 (fac=0.99, q=1)
1 day, 4:36:21.260520 INFO: Updating optimization_manager: fwhm_rt             : 3.0388379096984863 -> 3.026151418685913
1 day, 4:36:21.260600 INFO: Updating optimization_manager: fwhm_mobility       : 0.008303740993142128 -> 0.008241826668381691
1 day, 4:36:21.260655 INFO: Updating optimization_manager: score_cutoff        : 41.42117868804932 -> 41.59397912750244
1 day, 4:36:21.260709 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:21.261947 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:21.263342 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:21.264144 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:21.266365 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:21.266466 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:36:21.268256 INFO: Updating optimization_manager: rt_error            : 1076.828222073201 -> 991.0551434396905
1 day, 4:36:21.268361 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 991.0551.
1 day, 4:36:21.268436 INFO: ==============================================
1 day, 4:36:21.268505 INFO: Starting optimization step 2.
1 day, 4:36:21.268567 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:36:21.268620 INFO: Using classic extraction backend
1 day, 4:36:21.268735 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:36:21.268799 INFO: === Search parameters used ===
1 day, 4:36:21.268853 INFO: rt_error       : 991.0551434396905
1 day, 4:36:21.268896 INFO: mobility_error : 0.1
1 day, 4:36:21.268936 INFO: num_candidates : 3
1 day, 4:36:21.268977 INFO: ms1_error      : 15.0
1 day, 4:36:21.269017 INFO: ms2_error      : 15.0
1 day, 4:36:21.269055 INFO: fwhm_rt        : 3.026151418685913
1 day, 4:36:21.269093 INFO: quant_window   : 3
1 day, 4:36:21.269132 INFO: ==============================================
1 day, 4:36:21.270073 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:21.270120 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:21.270154 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 4:36:21.270178 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 4:36:21.270864 INFO: Starting candidate selection
1 day, 4:36:27.284691 INFO: Starting candidate scoring
1 day, 4:36:27.502441 INFO: Finished candidate processing
1 day, 4:36:27.502546 INFO: Collecting candidate features
1 day, 4:36:27.515529 INFO: Collecting fragment features
1 day, 4:36:27.520377 INFO: Finished candidate scoring
1 day, 4:36:27.525288 INFO: performing precursor FDR with 47 features
1 day, 4:36:27.525338 INFO: Decoy channel: -1
1 day, 4:36:27.525362 INFO: Competetive: True
1 day, 4:36:27.528647 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:27.531359 INFO: Using random state 656817 for train-test-split
1 day, 4:36:27.544855 INFO: Test AUC: 0.566
1 day, 4:36:27.544924 INFO: Train AUC: 0.535
1 day, 4:36:27.544953 INFO: AUC difference: 5.77%
1 day, 4:36:27.544975 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:36:27.772009 INFO: Resetting torch num_threads to 80
1 day, 4:36:27.772676 PROGRESS: === Extracted 3389 precursors and 37484 fragments ===
1 day, 4:36:27.773132 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:36:27.773777 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:27.773870 PROGRESS: Total precursors accumulated: 600
1 day, 4:36:27.773932 PROGRESS: Target precursors: 536 (89.33%)
1 day, 4:36:27.773982 PROGRESS: Decoy precursors: 64 (10.67%)
1 day, 4:36:27.774027 PROGRESS: 
1 day, 4:36:27.774094 PROGRESS: Precursor Summary:
1 day, 4:36:27.775172 PROGRESS: Channel   0:	 0.050 FDR:   495; 0.010 FDR:   495; 0.001 FDR:   495
1 day, 4:36:27.775265 PROGRESS: 
1 day, 4:36:27.775323 PROGRESS: Protein Summary:
1 day, 4:36:27.776557 PROGRESS: Channel   0:	 0.050 FDR:   464; 0.010 FDR:   464; 0.001 FDR:   464
1 day, 4:36:27.776651 PROGRESS: =========================================================================
1 day, 4:36:27.776806 INFO: Target number of precursors reached.
1 day, 4:36:27.787378 INFO: fragments_df: keeping 5000 of 37484 [sum(precursor_idx_mask)=15484 sum(mass_error_mask)=37484 stop_rank=5000
1 day, 4:36:27.794035 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:27.912850 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:28.033072 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:28.151830 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:28.771714 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:36:28.772162 INFO: Using score_cutoff 40.637136559295655 (fac=0.99, q=1)
1 day, 4:36:28.772489 INFO: Updating optimization_manager: fwhm_rt             : 3.026151418685913 -> 3.0388379096984863
1 day, 4:36:28.772569 INFO: Updating optimization_manager: fwhm_mobility       : 0.008241826668381691 -> 0.008302769623696804
1 day, 4:36:28.772622 INFO: Updating optimization_manager: score_cutoff        : 41.59397912750244 -> 40.637136559295655
1 day, 4:36:28.772676 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:28.773814 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:28.775148 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:28.775945 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:28.778204 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:28.778308 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:36:28.780120 INFO: Updating optimization_manager: rt_error            : 991.0551434396905 -> 904.7505944862925
1 day, 4:36:28.780224 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 904.7506.
1 day, 4:36:28.780289 INFO: ==============================================
1 day, 4:36:28.780354 INFO: Starting optimization step 3.
1 day, 4:36:28.780412 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:36:28.780471 INFO: Using classic extraction backend
1 day, 4:36:28.780646 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:36:28.780719 INFO: === Search parameters used ===
1 day, 4:36:28.780768 INFO: rt_error       : 904.7505944862925
1 day, 4:36:28.780812 INFO: mobility_error : 0.1
1 day, 4:36:28.780854 INFO: num_candidates : 3
1 day, 4:36:28.780895 INFO: ms1_error      : 15.0
1 day, 4:36:28.780937 INFO: ms2_error      : 15.0
1 day, 4:36:28.780976 INFO: fwhm_rt        : 3.0388379096984863
1 day, 4:36:28.781016 INFO: quant_window   : 3
1 day, 4:36:28.781055 INFO: ==============================================
1 day, 4:36:28.781952 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:28.781996 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:28.782032 INFO: FWHM in RT is 3.04 seconds, sigma is 0.67
1 day, 4:36:28.782063 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.85
1 day, 4:36:28.782738 INFO: Starting candidate selection
1 day, 4:36:33.328371 INFO: Starting candidate scoring
1 day, 4:36:33.535431 INFO: Finished candidate processing
1 day, 4:36:33.535537 INFO: Collecting candidate features
1 day, 4:36:33.550113 INFO: Collecting fragment features
1 day, 4:36:33.554623 INFO: Finished candidate scoring
1 day, 4:36:33.558467 INFO: performing precursor FDR with 47 features
1 day, 4:36:33.558519 INFO: Decoy channel: -1
1 day, 4:36:33.558544 INFO: Competetive: True
1 day, 4:36:33.561897 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:33.564118 INFO: Using random state 656817 for train-test-split
1 day, 4:36:33.575521 INFO: Test AUC: 0.523
1 day, 4:36:33.575593 INFO: Train AUC: 0.544
1 day, 4:36:33.575624 INFO: AUC difference: 3.80%
1 day, 4:36:33.793856 INFO: Resetting torch num_threads to 80
1 day, 4:36:33.794548 PROGRESS: === Extracted 3388 precursors and 37479 fragments ===
1 day, 4:36:33.795041 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:36:33.795700 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:33.795791 PROGRESS: Total precursors accumulated: 600
1 day, 4:36:33.795850 PROGRESS: Target precursors: 535 (89.17%)
1 day, 4:36:33.795899 PROGRESS: Decoy precursors: 65 (10.83%)
1 day, 4:36:33.795945 PROGRESS: 
1 day, 4:36:33.795988 PROGRESS: Precursor Summary:
1 day, 4:36:33.797050 PROGRESS: Channel   0:	 0.050 FDR:   495; 0.010 FDR:   495; 0.001 FDR:   495
1 day, 4:36:33.797146 PROGRESS: 
1 day, 4:36:33.797201 PROGRESS: Protein Summary:
1 day, 4:36:33.798496 PROGRESS: Channel   0:	 0.050 FDR:   469; 0.010 FDR:   469; 0.001 FDR:   469
1 day, 4:36:33.798590 PROGRESS: =========================================================================
1 day, 4:36:33.798744 INFO: Target number of precursors reached.
1 day, 4:36:33.805538 INFO: fragments_df: keeping 5000 of 37479 [sum(precursor_idx_mask)=15495 sum(mass_error_mask)=37479 stop_rank=5000
1 day, 4:36:33.810672 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:33.950011 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:34.093303 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:34.241820 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:34.920647 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:36:34.921297 INFO: Using score_cutoff 40.63398623657226 (fac=0.99, q=1)
1 day, 4:36:34.921641 INFO: Updating optimization_manager: fwhm_rt             : 3.0388379096984863 -> 3.032304525375366
1 day, 4:36:34.921722 INFO: Updating optimization_manager: fwhm_mobility       : 0.008302769623696804 -> 0.008262165822088718
1 day, 4:36:34.921774 INFO: Updating optimization_manager: score_cutoff        : 40.637136559295655 -> 40.63398623657226
1 day, 4:36:34.921828 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:34.923067 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:34.924401 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:34.925195 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:34.927490 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:34.927601 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 4:36:34.929446 INFO: Updating optimization_manager: rt_error            : 904.7505944862925 -> 862.2352408369602
1 day, 4:36:34.929554 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 862.2352.
1 day, 4:36:34.929621 INFO: ==============================================
1 day, 4:36:34.929683 INFO: Starting optimization step 4.
1 day, 4:36:34.929740 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:36:34.929800 INFO: Using classic extraction backend
1 day, 4:36:34.929910 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:36:34.929972 INFO: === Search parameters used ===
1 day, 4:36:34.930020 INFO: rt_error       : 862.2352408369602
1 day, 4:36:34.930074 INFO: mobility_error : 0.1
1 day, 4:36:34.930120 INFO: num_candidates : 3
1 day, 4:36:34.930169 INFO: ms1_error      : 15.0
1 day, 4:36:34.930212 INFO: ms2_error      : 15.0
1 day, 4:36:34.930251 INFO: fwhm_rt        : 3.032304525375366
1 day, 4:36:34.930289 INFO: quant_window   : 3
1 day, 4:36:34.930327 INFO: ==============================================
1 day, 4:36:34.931189 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:34.931235 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:34.931269 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 4:36:34.931291 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
1 day, 4:36:34.931986 INFO: Starting candidate selection
1 day, 4:36:40.026361 INFO: Starting candidate scoring
1 day, 4:36:40.240312 INFO: Finished candidate processing
1 day, 4:36:40.240527 INFO: Collecting candidate features
1 day, 4:36:40.255222 INFO: Collecting fragment features
1 day, 4:36:40.259791 INFO: Finished candidate scoring
1 day, 4:36:40.262996 INFO: performing precursor FDR with 47 features
1 day, 4:36:40.263046 INFO: Decoy channel: -1
1 day, 4:36:40.263073 INFO: Competetive: True
1 day, 4:36:40.267265 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:40.269868 INFO: Using random state 656817 for train-test-split
1 day, 4:36:40.282266 INFO: Test AUC: 0.541
1 day, 4:36:40.282335 INFO: Train AUC: 0.543
1 day, 4:36:40.282365 INFO: AUC difference: 0.45%
1 day, 4:36:40.506904 INFO: Resetting torch num_threads to 80
1 day, 4:36:40.507579 PROGRESS: === Extracted 3393 precursors and 37511 fragments ===
1 day, 4:36:40.508142 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:36:40.508807 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:40.508903 PROGRESS: Total precursors accumulated: 600
1 day, 4:36:40.508962 PROGRESS: Target precursors: 540 (90.00%)
1 day, 4:36:40.509011 PROGRESS: Decoy precursors: 60 (10.00%)
1 day, 4:36:40.509056 PROGRESS: 
1 day, 4:36:40.509098 PROGRESS: Precursor Summary:
1 day, 4:36:40.510181 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   501; 0.001 FDR:   501
1 day, 4:36:40.510275 PROGRESS: 
1 day, 4:36:40.510331 PROGRESS: Protein Summary:
1 day, 4:36:40.511621 PROGRESS: Channel   0:	 0.050 FDR:   474; 0.010 FDR:   474; 0.001 FDR:   474
1 day, 4:36:40.511720 PROGRESS: =========================================================================
1 day, 4:36:40.512154 INFO: Target number of precursors reached.
1 day, 4:36:40.519041 INFO: fragments_df: keeping 5000 of 37511 [sum(precursor_idx_mask)=15711 sum(mass_error_mask)=37511 stop_rank=5000
1 day, 4:36:40.527693 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:40.667272 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:40.816073 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:40.955548 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:41.639744 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:36:41.640232 INFO: Using score_cutoff 40.66190174102783 (fac=0.99, q=1)
1 day, 4:36:41.640586 INFO: Updating optimization_manager: fwhm_rt             : 3.032304525375366 -> 3.0307793617248535
1 day, 4:36:41.640670 INFO: Updating optimization_manager: fwhm_mobility       : 0.008262165822088718 -> 0.008104696869850159
1 day, 4:36:41.640724 INFO: Updating optimization_manager: score_cutoff        : 40.63398623657226 -> 40.66190174102783
1 day, 4:36:41.640782 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:41.641917 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:41.643245 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:41.644049 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:41.646371 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:41.646507 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 4:36:41.647559 INFO: Updating optimization_manager: rt_error            : 862.2352408369602 -> 862.2352408369602
1 day, 4:36:41.647682 INFO: Updating optimization_manager: classifier_version  : 3 -> 8
1 day, 4:36:41.647781 INFO: Updating optimization_manager: score_cutoff        : 40.66190174102783 -> 40.66190174102783
1 day, 4:36:41.647866 INFO: Updating optimization_manager: fwhm_rt             : 3.0307793617248535 -> 3.0307793617248535
1 day, 4:36:41.647958 INFO: Updating optimization_manager: fwhm_mobility       : 0.008104696869850159 -> 0.008104696869850159
1 day, 4:36:41.648048 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 862.2352 found after 5 searches.
1 day, 4:36:41.648109 INFO: ==============================================
1 day, 4:36:41.648177 PROGRESS: Optimization finished for rt_error.
1 day, 4:36:41.652592 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:41.653430 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:41.654730 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:41.655524 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:41.681894 INFO: Starting optimization step 0.
1 day, 4:36:41.682055 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:36:41.682133 INFO: Using classic extraction backend
1 day, 4:36:41.682272 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:36:41.682347 INFO: === Search parameters used ===
1 day, 4:36:41.682397 INFO: rt_error       : 862.2352408369602
1 day, 4:36:41.682447 INFO: mobility_error : 0.1
1 day, 4:36:41.682492 INFO: num_candidates : 3
1 day, 4:36:41.682535 INFO: ms1_error      : 15.0
1 day, 4:36:41.682576 INFO: ms2_error      : 15.0
1 day, 4:36:41.682615 INFO: fwhm_rt        : 3.0307793617248535
1 day, 4:36:41.682654 INFO: quant_window   : 3
1 day, 4:36:41.682703 INFO: ==============================================
1 day, 4:36:41.683715 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:41.683759 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:41.683801 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 4:36:41.683823 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
1 day, 4:36:41.684533 INFO: Starting candidate selection
1 day, 4:36:46.073193 INFO: Starting candidate scoring
1 day, 4:36:46.278144 INFO: Finished candidate processing
1 day, 4:36:46.278260 INFO: Collecting candidate features
1 day, 4:36:46.292164 INFO: Collecting fragment features
1 day, 4:36:46.295956 INFO: Finished candidate scoring
1 day, 4:36:46.298818 INFO: performing precursor FDR with 47 features
1 day, 4:36:46.298864 INFO: Decoy channel: -1
1 day, 4:36:46.298888 INFO: Competetive: True
1 day, 4:36:46.301964 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:46.304110 INFO: Using random state 437817 for train-test-split
1 day, 4:36:46.315012 INFO: Test AUC: 0.513
1 day, 4:36:46.315075 INFO: Train AUC: 0.549
1 day, 4:36:46.315104 INFO: AUC difference: 6.54%
1 day, 4:36:46.315126 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:36:46.533035 INFO: Resetting torch num_threads to 80
1 day, 4:36:46.533646 PROGRESS: === Extracted 3391 precursors and 37484 fragments ===
1 day, 4:36:46.534095 INFO: === FDR correction performed with classifier version 8 ===
1 day, 4:36:46.534745 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:46.534837 PROGRESS: Total precursors accumulated: 600
1 day, 4:36:46.534898 PROGRESS: Target precursors: 539 (89.83%)
1 day, 4:36:46.534947 PROGRESS: Decoy precursors: 61 (10.17%)
1 day, 4:36:46.534992 PROGRESS: 
1 day, 4:36:46.535035 PROGRESS: Precursor Summary:
1 day, 4:36:46.536092 PROGRESS: Channel   0:	 0.050 FDR:   498; 0.010 FDR:   498; 0.001 FDR:   498
1 day, 4:36:46.536192 PROGRESS: 
1 day, 4:36:46.536249 PROGRESS: Protein Summary:
1 day, 4:36:46.537521 PROGRESS: Channel   0:	 0.050 FDR:   471; 0.010 FDR:   471; 0.001 FDR:   471
1 day, 4:36:46.537616 PROGRESS: =========================================================================
1 day, 4:36:46.537762 INFO: Target number of precursors reached.
1 day, 4:36:46.544412 INFO: fragments_df: keeping 5000 of 37484 [sum(precursor_idx_mask)=15566 sum(mass_error_mask)=37484 stop_rank=5000
1 day, 4:36:46.549217 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:46.687328 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:46.832699 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:46.973712 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:47.651956 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:36:47.652442 INFO: Using score_cutoff 40.65175048713684 (fac=0.99, q=1)
1 day, 4:36:47.652791 INFO: Updating optimization_manager: fwhm_rt             : 3.0307793617248535 -> 3.031545639038086
1 day, 4:36:47.652872 INFO: Updating optimization_manager: fwhm_mobility       : 0.008104696869850159 -> 0.008181547746062279
1 day, 4:36:47.652926 INFO: Updating optimization_manager: score_cutoff        : 40.66190174102783 -> 40.65175048713684
1 day, 4:36:47.652977 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:47.654123 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:47.655452 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:47.656241 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:47.658504 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:47.658608 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:36:47.659986 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07399866440646838
1 day, 4:36:47.660085 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0740.
1 day, 4:36:47.660150 INFO: ==============================================
1 day, 4:36:47.660214 INFO: Starting optimization step 1.
1 day, 4:36:47.660270 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:36:47.660328 INFO: Using classic extraction backend
1 day, 4:36:47.660455 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:36:47.660538 INFO: === Search parameters used ===
1 day, 4:36:47.660592 INFO: rt_error       : 862.2352408369602
1 day, 4:36:47.660635 INFO: mobility_error : 0.07399866440646838
1 day, 4:36:47.660676 INFO: num_candidates : 3
1 day, 4:36:47.660718 INFO: ms1_error      : 15.0
1 day, 4:36:47.660756 INFO: ms2_error      : 15.0
1 day, 4:36:47.660794 INFO: fwhm_rt        : 3.031545639038086
1 day, 4:36:47.660830 INFO: quant_window   : 3
1 day, 4:36:47.660869 INFO: ==============================================
1 day, 4:36:47.661704 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:47.661749 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:47.661782 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 4:36:47.661805 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:36:47.662491 INFO: Starting candidate selection
1 day, 4:36:51.181625 INFO: Starting candidate scoring
1 day, 4:36:51.391716 INFO: Finished candidate processing
1 day, 4:36:51.391837 INFO: Collecting candidate features
1 day, 4:36:51.406149 INFO: Collecting fragment features
1 day, 4:36:51.410283 INFO: Finished candidate scoring
1 day, 4:36:51.413040 INFO: performing precursor FDR with 47 features
1 day, 4:36:51.413085 INFO: Decoy channel: -1
1 day, 4:36:51.413110 INFO: Competetive: True
1 day, 4:36:51.416668 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:51.418852 INFO: Using random state 437817 for train-test-split
1 day, 4:36:51.430144 INFO: Test AUC: 0.543
1 day, 4:36:51.430207 INFO: Train AUC: 0.542
1 day, 4:36:51.430237 INFO: AUC difference: 0.06%
1 day, 4:36:51.647551 INFO: Resetting torch num_threads to 80
1 day, 4:36:51.648142 PROGRESS: === Extracted 3392 precursors and 37386 fragments ===
1 day, 4:36:51.648582 INFO: === FDR correction performed with classifier version 8 ===
1 day, 4:36:51.649213 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:51.649306 PROGRESS: Total precursors accumulated: 600
1 day, 4:36:51.649364 PROGRESS: Target precursors: 534 (89.00%)
1 day, 4:36:51.649413 PROGRESS: Decoy precursors: 66 (11.00%)
1 day, 4:36:51.649459 PROGRESS: 
1 day, 4:36:51.649501 PROGRESS: Precursor Summary:
1 day, 4:36:51.650569 PROGRESS: Channel   0:	 0.050 FDR:   494; 0.010 FDR:   494; 0.001 FDR:   494
1 day, 4:36:51.650665 PROGRESS: 
1 day, 4:36:51.650721 PROGRESS: Protein Summary:
1 day, 4:36:51.651967 PROGRESS: Channel   0:	 0.050 FDR:   469; 0.010 FDR:   469; 0.001 FDR:   469
1 day, 4:36:51.652061 PROGRESS: =========================================================================
1 day, 4:36:51.652212 INFO: Target number of precursors reached.
1 day, 4:36:51.658947 INFO: fragments_df: keeping 5000 of 37386 [sum(precursor_idx_mask)=15486 sum(mass_error_mask)=37386 stop_rank=5000
1 day, 4:36:51.663803 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:51.801931 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:51.950606 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:52.090163 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:52.771325 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:36:52.771802 INFO: Using score_cutoff 40.63190958709717 (fac=0.99, q=1)
1 day, 4:36:52.772122 INFO: Updating optimization_manager: fwhm_rt             : 3.031545639038086 -> 3.0331368446350098
1 day, 4:36:52.772203 INFO: Updating optimization_manager: fwhm_mobility       : 0.008181547746062279 -> 0.008149951696395874
1 day, 4:36:52.772261 INFO: Updating optimization_manager: score_cutoff        : 40.65175048713684 -> 40.63190958709717
1 day, 4:36:52.772316 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:52.773450 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:52.774781 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:52.775570 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:52.777836 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:52.777938 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:36:52.779405 INFO: Updating optimization_manager: mobility_error      : 0.07399866440646838 -> 0.06548262576323442
1 day, 4:36:52.779519 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0655.
1 day, 4:36:52.779588 INFO: ==============================================
1 day, 4:36:52.779655 INFO: Starting optimization step 2.
1 day, 4:36:52.779713 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:36:52.779766 INFO: Using classic extraction backend
1 day, 4:36:52.779876 PROGRESS: Extracting batch of 1194 precursors
1 day, 4:36:52.779940 INFO: === Search parameters used ===
1 day, 4:36:52.779987 INFO: rt_error       : 862.2352408369602
1 day, 4:36:52.780029 INFO: mobility_error : 0.06548262576323442
1 day, 4:36:52.780075 INFO: num_candidates : 3
1 day, 4:36:52.780117 INFO: ms1_error      : 15.0
1 day, 4:36:52.780156 INFO: ms2_error      : 15.0
1 day, 4:36:52.780196 INFO: fwhm_rt        : 3.0331368446350098
1 day, 4:36:52.780236 INFO: quant_window   : 3
1 day, 4:36:52.780275 INFO: ==============================================
1 day, 4:36:52.781096 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:52.781143 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:52.781178 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 4:36:52.781202 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.78
1 day, 4:36:52.781898 INFO: Starting candidate selection
1 day, 4:36:55.716947 INFO: Starting candidate scoring
1 day, 4:36:55.959500 INFO: Finished candidate processing
1 day, 4:36:55.959617 INFO: Collecting candidate features
1 day, 4:36:55.972713 INFO: Collecting fragment features
1 day, 4:36:55.976538 INFO: Finished candidate scoring
1 day, 4:36:55.979023 INFO: performing precursor FDR with 47 features
1 day, 4:36:55.979071 INFO: Decoy channel: -1
1 day, 4:36:55.979100 INFO: Competetive: True
1 day, 4:36:55.982410 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:55.984614 INFO: Using random state 437817 for train-test-split
1 day, 4:36:55.995819 INFO: Test AUC: 0.573
1 day, 4:36:55.995889 INFO: Train AUC: 0.542
1 day, 4:36:55.995918 INFO: AUC difference: 5.76%
1 day, 4:36:55.995940 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:36:56.217775 INFO: Resetting torch num_threads to 80
1 day, 4:36:56.218392 PROGRESS: === Extracted 3387 precursors and 37252 fragments ===
1 day, 4:36:56.218831 INFO: === FDR correction performed with classifier version 8 ===
1 day, 4:36:56.219424 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:56.219512 PROGRESS: Total precursors accumulated: 600
1 day, 4:36:56.219569 PROGRESS: Target precursors: 535 (89.17%)
1 day, 4:36:56.219616 PROGRESS: Decoy precursors: 65 (10.83%)
1 day, 4:36:56.219666 PROGRESS: 
1 day, 4:36:56.219723 PROGRESS: Precursor Summary:
1 day, 4:36:56.220775 PROGRESS: Channel   0:	 0.050 FDR:   493; 0.010 FDR:   493; 0.001 FDR:   493
1 day, 4:36:56.220866 PROGRESS: 
1 day, 4:36:56.220922 PROGRESS: Protein Summary:
1 day, 4:36:56.222188 PROGRESS: Channel   0:	 0.050 FDR:   468; 0.010 FDR:   468; 0.001 FDR:   468
1 day, 4:36:56.222281 PROGRESS: =========================================================================
1 day, 4:36:56.222426 INFO: Target number of precursors reached.
1 day, 4:36:56.229118 INFO: fragments_df: keeping 5000 of 37252 [sum(precursor_idx_mask)=15425 sum(mass_error_mask)=37252 stop_rank=5000
1 day, 4:36:56.233985 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:56.374533 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:56.524483 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:56.666055 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:57.354501 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:36:57.354993 INFO: Using score_cutoff 39.002629655456545 (fac=0.99, q=1)
1 day, 4:36:57.355309 INFO: Updating optimization_manager: fwhm_rt             : 3.0331368446350098 -> 3.032315969467163
1 day, 4:36:57.355387 INFO: Updating optimization_manager: fwhm_mobility       : 0.008149951696395874 -> 0.00810976792126894
1 day, 4:36:57.355440 INFO: Updating optimization_manager: score_cutoff        : 40.63190958709717 -> 39.002629655456545
1 day, 4:36:57.355490 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:57.356609 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:57.357931 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:57.358715 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:57.361002 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:57.361103 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:36:57.361801 INFO: Updating optimization_manager: mobility_error      : 0.06548262576323442 -> 0.1
1 day, 4:36:57.361920 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1 day, 4:36:57.362009 INFO: Updating optimization_manager: score_cutoff        : 39.002629655456545 -> 40.65175048713684
1 day, 4:36:57.362101 INFO: Updating optimization_manager: fwhm_rt             : 3.032315969467163 -> 3.031545639038086
1 day, 4:36:57.362185 INFO: Updating optimization_manager: fwhm_mobility       : 0.00810976792126894 -> 0.008181547746062279
1 day, 4:36:57.362266 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 4:36:57.362324 INFO: ==============================================
1 day, 4:36:57.362386 PROGRESS: Optimization finished for mobility_error.
1 day, 4:36:57.366806 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:57.367645 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:57.368928 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:57.369700 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:57.397765 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 4:36:57.397910 PROGRESS: ==============================================
1 day, 4:36:57.397995 PROGRESS: ms2_error      : 15.0000
1 day, 4:36:57.398077 PROGRESS: ms1_error      : 15.0000
1 day, 4:36:57.398135 PROGRESS: rt_error       : 862.2352
1 day, 4:36:57.398181 PROGRESS: mobility_error : 0.1000
1 day, 4:36:57.398224 PROGRESS: ==============================================
1 day, 4:36:57.399161 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:36:57.424718 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:36:57.521539 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:36:57.547618 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:36:57.820995 INFO: Using classic extraction backend
1 day, 4:36:57.821418 PROGRESS: Extracting batch of 180112 precursors
1 day, 4:36:57.821508 INFO: === Search parameters used ===
1 day, 4:36:57.821566 INFO: rt_error       : 862.2352408369602
1 day, 4:36:57.821613 INFO: mobility_error : 0.1
1 day, 4:36:57.821658 INFO: num_candidates : 3
1 day, 4:36:57.821700 INFO: ms1_error      : 15.0
1 day, 4:36:57.821740 INFO: ms2_error      : 15.0
1 day, 4:36:57.821781 INFO: fwhm_rt        : 3.031545639038086
1 day, 4:36:57.821822 INFO: quant_window   : 3
1 day, 4:36:57.821861 INFO: ==============================================
1 day, 4:36:57.858958 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:57.859116 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:57.859161 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 4:36:57.859201 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 4:36:57.860206 INFO: Starting candidate selection
1 day, 4:44:40.970982 INFO: Removed 33932 precursors with score below cutoff 40.65175048713684
1 day, 4:44:41.328804 INFO: Starting candidate scoring
1 day, 4:45:01.564308 INFO: Finished candidate processing
1 day, 4:45:01.564545 INFO: Collecting candidate features
1 day, 4:45:02.252028 INFO: Collecting fragment features
1 day, 4:45:02.562371 INFO: Finished candidate scoring
1 day, 4:45:02.832504 INFO: === Performing FDR correction with classifier version 9 ===
1 day, 4:45:02.834687 INFO: performing precursor FDR with 47 features
1 day, 4:45:02.834769 INFO: Decoy channel: -1
1 day, 4:45:02.834793 INFO: Competetive: True
1 day, 4:45:02.965746 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:45:03.168309 INFO: Using random state 65977 for train-test-split
1 day, 4:45:11.857032 INFO: Test AUC: 0.749
1 day, 4:45:11.857200 INFO: Train AUC: 0.752
1 day, 4:45:11.857235 INFO: AUC difference: 0.42%
1 day, 4:45:12.298754 INFO: Resetting torch num_threads to 80
1 day, 4:45:12.319872 INFO: Removing fragments below FDR threshold
1 day, 4:45:12.427432 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:45:12.427744 PROGRESS: Total precursors accumulated: 77,858
1 day, 4:45:12.427835 PROGRESS: Target precursors: 77,088 (99.01%)
1 day, 4:45:12.427889 PROGRESS: Decoy precursors: 770 (0.99%)
1 day, 4:45:12.427936 PROGRESS: 
1 day, 4:45:12.427983 PROGRESS: Precursor Summary:
1 day, 4:45:12.469856 PROGRESS: Channel   0:	 0.050 FDR: 77,088; 0.010 FDR: 77,088; 0.001 FDR: 71,315
1 day, 4:45:12.470206 PROGRESS: 
1 day, 4:45:12.470271 PROGRESS: Protein Summary:
1 day, 4:45:12.523296 PROGRESS: Channel   0:	 0.050 FDR: 8,663; 0.010 FDR: 8,663; 0.001 FDR: 8,521
1 day, 4:45:12.523613 PROGRESS: =========================================================================
1 day, 4:45:12.529204 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/psm.parquet
1 day, 4:45:12.867514 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/frag.parquet
1 day, 4:45:13.161378 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 4:45:14.657340 PROGRESS: Processing search outputs
1 day, 4:45:14.657481 PROGRESS: Performing protein grouping and FDR
1 day, 4:45:14.657517 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 4:45:14.723506 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 4:45:14.793720 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 4:45:14.855662 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 4:45:14.926328 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 4:45:14.986140 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 4:45:15.052523 INFO: Building combined output
1 day, 4:45:15.102979 INFO: Performing protein inference
1 day, 4:45:15.647539 INFO: Inference strategy: library. Using library grouping for protein inference
1 day, 4:45:15.650203 INFO: Performing protein FDR
1 day, 4:45:19.328612 INFO: Normalizing q-values using 8,879 targets and 2,726 decoys
1 day, 4:45:19.331400 INFO: Test AUC: 1.000
1 day, 4:45:19.331452 INFO: Train AUC: 1.000
1 day, 4:45:19.331485 INFO: AUC difference: 0.01%
1 day, 4:45:20.036838 PROGRESS: ================ Protein FDR =================
1 day, 4:45:20.037016 PROGRESS: Unique protein groups in output
1 day, 4:45:20.037048 PROGRESS:   1% protein FDR: 8,872
1 day, 4:45:20.037068 PROGRESS: 
1 day, 4:45:20.037087 PROGRESS: Unique precursor in output
1 day, 4:45:20.037106 PROGRESS:   1% protein FDR: 90,440
1 day, 4:45:20.037124 PROGRESS: ================================================
1 day, 4:45:20.112106 PROGRESS: Building search statistics
1 day, 4:45:20.242765 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
1 day, 4:45:20.243012 INFO: Initializing OptimizationManager
1 day, 4:45:20.243342 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
1 day, 4:45:20.243420 INFO: Initializing CalibrationManager
1 day, 4:45:20.243668 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
1 day, 4:45:20.243744 INFO: Initializing RawFileManager
1 day, 4:45:20.277772 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
1 day, 4:45:20.278007 INFO: Initializing OptimizationManager
1 day, 4:45:20.278251 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
1 day, 4:45:20.278325 INFO: Initializing CalibrationManager
1 day, 4:45:20.278546 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
1 day, 4:45:20.278624 INFO: Initializing RawFileManager
1 day, 4:45:20.311430 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
1 day, 4:45:20.311659 INFO: Initializing OptimizationManager
1 day, 4:45:20.311888 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
1 day, 4:45:20.311959 INFO: Initializing CalibrationManager
1 day, 4:45:20.312176 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
1 day, 4:45:20.312252 INFO: Initializing RawFileManager
1 day, 4:45:20.347318 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
1 day, 4:45:20.347538 INFO: Initializing OptimizationManager
1 day, 4:45:20.347774 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
1 day, 4:45:20.347847 INFO: Initializing CalibrationManager
1 day, 4:45:20.348069 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
1 day, 4:45:20.348142 INFO: Initializing RawFileManager
1 day, 4:45:20.380736 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
1 day, 4:45:20.380968 INFO: Initializing OptimizationManager
1 day, 4:45:20.381200 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
1 day, 4:45:20.381272 INFO: Initializing CalibrationManager
1 day, 4:45:20.381499 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
1 day, 4:45:20.381573 INFO: Initializing RawFileManager
1 day, 4:45:20.414016 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
1 day, 4:45:20.414258 INFO: Initializing OptimizationManager
1 day, 4:45:20.414505 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
1 day, 4:45:20.414577 INFO: Initializing CalibrationManager
1 day, 4:45:20.414782 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
1 day, 4:45:20.414861 INFO: Initializing RawFileManager
1 day, 4:45:20.417443 INFO: Writing stat output to disk
1 day, 4:45:20.417512 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/stat.tsv to disk
1 day, 4:45:20.426106 PROGRESS: Building internal statistics
1 day, 4:45:20.426498 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
1 day, 4:45:20.426548 INFO: Initializing TimingManager
1 day, 4:45:20.427016 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
1 day, 4:45:20.427057 INFO: Initializing TimingManager
1 day, 4:45:20.427246 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
1 day, 4:45:20.427284 INFO: Initializing TimingManager
1 day, 4:45:20.427464 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
1 day, 4:45:20.427501 INFO: Initializing TimingManager
1 day, 4:45:20.427680 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
1 day, 4:45:20.427717 INFO: Initializing TimingManager
1 day, 4:45:20.427891 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
1 day, 4:45:20.427925 INFO: Initializing TimingManager
1 day, 4:45:20.428388 INFO: Writing internal output to disk
1 day, 4:45:20.428433 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/internal.tsv to disk
1 day, 4:45:20.429019 PROGRESS: Performing label free quantification
1 day, 4:45:20.528736 INFO: Accumulating fragment data
1 day, 4:45:20.528937 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 4:45:20.584106 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 4:45:21.870607 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 4:45:23.064659 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 4:45:24.264633 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 4:45:25.515158 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 4:45:26.950095 PROGRESS: Performing label free quantification on the precursor level
1 day, 4:45:26.950281 INFO: Filtering fragments by quality
1 day, 4:45:27.228783 INFO: Performing label-free quantification using directLFQ
1 day, 4:45:28.269449 INFO: 90440 lfq-groups total
1 day, 4:47:05.524632 INFO: using 80 processes
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1 day, 4:48:01.092545 INFO: lfq-object 89300
1 day, 4:48:01.155080 INFO: lfq-object 89800
1 day, 4:48:01.163253 INFO: lfq-object 90000
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1 day, 4:48:01.318832 INFO: lfq-object 90400
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1 day, 4:48:13.434400 INFO: Writing precursor output to disk
1 day, 4:48:13.434676 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/precursor.matrix.tsv to disk
1 day, 4:48:13.938740 PROGRESS: Performing label free quantification on the pg level
1 day, 4:48:13.938858 INFO: Filtering fragments by quality
1 day, 4:48:14.228891 INFO: Performing label-free quantification using directLFQ
1 day, 4:48:14.682068 INFO: 8872 lfq-groups total
1 day, 4:49:36.600804 INFO: using 80 processes
1 day, 4:49:36.713216 INFO: lfq-object 0
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1 day, 4:49:36.994291 INFO: lfq-object 700
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1 day, 4:49:37.625509 INFO: lfq-object 1000
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1 day, 4:49:40.114394 INFO: lfq-object 7600
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1 day, 4:49:40.434047 INFO: lfq-object 8500
1 day, 4:49:40.545579 INFO: lfq-object 8800
1 day, 4:49:40.598407 INFO: lfq-object 8700
1 day, 4:49:44.899304 INFO: Writing pg output to disk
1 day, 4:49:44.899503 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/pg.matrix.tsv to disk
1 day, 4:49:45.142253 INFO: Writing psm output to disk
1 day, 4:49:45.142428 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR/precursors.tsv to disk
1 day, 4:50:11.889408 PROGRESS: Building MBR spectral library
1 day, 4:50:11.981690 INFO: Running MbrLibraryBuilder
1 day, 4:50:12.224055 INFO: MBR spectral library contains 90,440 precursors, 8,872 proteins
1 day, 4:50:12.224211 INFO: Writing MBR spectral library to disk
1 day, 4:50:12.899895 PROGRESS: =================== Search Finished ===================
