0:00:00.000026 INFO: Moved old log file ./run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/log.txt to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/log.txt
0:00:00.000140 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000174 INFO: User provided config file: config_alphadia112_rs_diaPASEF.yaml.
0:00:00.000204 INFO: User provided config dict: {}.
0:00:00.013027 PROGRESS:           _      _         ___ ___   _   
0:00:00.013086 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.013113 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013141 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013166 PROGRESS:            |_|                           
0:00:00.013185 PROGRESS: 
0:00:00.013205 PROGRESS: version: 1.12.1
0:00:00.013232 INFO: hostname: thestral
0:00:00.013279 INFO: date: 2025-10-21 09:37:01
0:00:00.013303 INFO: ================ AlphaX Environment ===============
0:00:00.013324 INFO: alphatims       : 1.0.9
0:00:00.013343 INFO: alpharaw        : 0.4.7
0:00:00.013360 INFO: alphabase       : 1.7.1
0:00:00.013379 INFO: alphapeptdeep   : 1.3.2
0:00:00.013397 INFO: directlfq       : 0.3.1
0:00:00.013413 INFO: ===================================================
0:00:00.013431 INFO: ================= Pip Environment =================
0:00:00.105314 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
0:00:00.105652 INFO: ===================================================
0:00:00.105693 INFO: Running step 'library'
0:00:00.105809 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.116845 INFO: loading additional config provided via CLI
0:00:00.116924 INFO: loading additional config provided via CLI parameters
0:00:00.117352 INFO: Updating config with 'user defined'
0:00:00.117494 INFO: Updating config with 'user defined (cli)'
0:00:00.117613 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': 0, 'target_ms2_tolerance': 0, '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_calibrateTol/library'}]
0:00:00.117873 INFO: Updating config with 'user defined'
0:00:00.117986 INFO: Updating config with 'user defined (cli)'
0:00:00.118011 INFO: Updating config with 'multistep search'
0:00:00.118048 INFO: ├──version: 1
0:00:00.118072 INFO: ├──workflow_name: None
0:00:00.118098 INFO: [32;20m├──output_directory: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library [multistep search, default: None][0m
0:00:00.118128 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
0:00:00.118148 INFO: ├──raw_paths:
0:00:00.118168 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
0:00:00.118188 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
0:00:00.118206 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
0:00:00.118228 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
0:00:00.118248 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
0:00:00.118266 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
0:00:00.118285 INFO: ├──fasta_paths:
0:00:00.118305 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.118326 INFO: ├──quant_directory: None
0:00:00.118344 INFO: ├──general
0:00:00.118366 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:00:00.118385 INFO: │   ├──transfer_step_enabled: False
0:00:00.118408 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.118426 INFO: │   ├──reuse_calibration: False
0:00:00.118445 INFO: │   ├──reuse_quant: False
0:00:00.118465 INFO: │   ├──astral_ms1: False
0:00:00.118483 INFO: │   ├──log_level: INFO
0:00:00.118502 INFO: │   ├──mmap_detector_events: False
0:00:00.118521 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.118541 INFO: │   ├──save_figures: True
0:00:00.118560 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.118580 INFO: │   ├──save_flat_library: False
0:00:00.118598 INFO: │   ├──input_library_type: base
0:00:00.118615 INFO: │   ├──save_mbr_library: True
0:00:00.118637 INFO: │   └──random_state: None
0:00:00.118654 INFO: ├──library_loading
0:00:00.118674 INFO: │   └──rt_heuristic: 180
0:00:00.118691 INFO: ├──library_prediction
0:00:00.118711 INFO: │   ├──enabled: False
0:00:00.118730 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.118748 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.118766 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.118787 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.118806 INFO: │   ├──missed_cleavages: 1
0:00:00.118824 INFO: │   ├──precursor_len:
0:00:00.118846 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.118865 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.118884 INFO: │   ├──precursor_charge:
0:00:00.118902 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.118920 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.118937 INFO: │   ├──precursor_mz:
0:00:00.118954 INFO: │   │   - 400
0:00:00.118973 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.118992 INFO: │   ├──fragment_mz:
0:00:00.119009 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.119028 INFO: │   │   - 2000
0:00:00.119047 INFO: │   ├──nce: 25.0
0:00:00.119064 INFO: │   ├──fragment_types:
0:00:00.119081 INFO: │   │   - b
0:00:00.119097 INFO: │   │   - y
0:00:00.119117 INFO: │   ├──max_fragment_charge: 2
0:00:00.119139 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.119158 INFO: │   ├──peptdeep_model_path: None
0:00:00.119178 INFO: │   └──peptdeep_model_type: generic
0:00:00.119197 INFO: ├──custom_modifications:
0:00:00.119215 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.119232 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.119251 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.119269 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.119288 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.119306 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.119325 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.119343 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.119360 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.119381 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.119400 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.119419 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.119437 INFO: │   ├──name: Label:13C(12)@K
0:00:00.119457 INFO: │   └──composition: C(12)
0:00:00.119475 INFO: ├──search
0:00:00.119493 INFO: │   ├──extraction_backend: classic
0:00:00.119511 INFO: │   [32;20m├──target_ms1_tolerance: 0 [user defined, default: 5][0m
0:00:00.119531 INFO: │   [32;20m├──target_ms2_tolerance: 0 [user defined, default: 10][0m
0:00:00.119550 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.119569 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.119589 INFO: │   ├──quant_window: 3
0:00:00.119607 INFO: │   ├──target_num_candidates: 3
0:00:00.119625 INFO: │   ├──channel_filter: 
0:00:00.119643 INFO: │   ├──exclude_shared_ions: True
0:00:00.119662 INFO: │   ├──compete_for_fragments: True
0:00:00.119680 INFO: │   ├──quant_all: True
0:00:00.119697 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.119714 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.119734 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.119752 INFO: │   ├──experimental_xic: True
0:00:00.119771 INFO: │   └──optimized_peak_group_score: False
0:00:00.119789 INFO: ├──calibration
0:00:00.119808 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.119827 INFO: │   ├──optimization_lock_target: 200
0:00:00.119846 INFO: │   ├──max_steps: 20
0:00:00.119867 INFO: │   ├──min_steps: 2
0:00:00.119884 INFO: │   ├──max_skips: 1
0:00:00.119902 INFO: │   ├──max_fragments: 5000
0:00:00.119924 INFO: │   └──min_correlation: 0.7
0:00:00.119941 INFO: ├──search_initial
0:00:00.119960 INFO: │   ├──initial_num_candidates: 1
0:00:00.119979 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.119998 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.120017 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.120035 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.120056 INFO: ├──selection_config
0:00:00.120075 INFO: │   ├──peak_len_rt: 10.0
0:00:00.120094 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.120113 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.120133 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.120151 INFO: │   ├──top_k_precursors: 3
0:00:00.120170 INFO: │   ├──kernel_size: 30
0:00:00.120188 INFO: │   ├──f_mobility: 1.0
0:00:00.120207 INFO: │   ├──f_rt: 0.99
0:00:00.120225 INFO: │   ├──center_fraction: 0.5
0:00:00.120242 INFO: │   ├──min_size_mobility: 8
0:00:00.120260 INFO: │   ├──min_size_rt: 3
0:00:00.120278 INFO: │   ├──max_size_mobility: 20
0:00:00.120296 INFO: │   ├──max_size_rt: 15
0:00:00.120315 INFO: │   ├──group_channels: False
0:00:00.120333 INFO: │   ├──use_weighted_score: True
0:00:00.120351 INFO: │   ├──join_close_candidates: False
0:00:00.120373 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.120393 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.120412 INFO: ├──scoring_config
0:00:00.120430 INFO: │   ├──score_grouped: False
0:00:00.120448 INFO: │   ├──top_k_isotopes: 3
0:00:00.120468 INFO: │   ├──reference_channel: -1
0:00:00.120485 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.120502 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.120519 INFO: ├──library_multiplexing
0:00:00.120538 INFO: │   ├──enabled: False
0:00:00.120555 INFO: │   ├──input_channel: 0
0:00:00.120573 INFO: │   └──multiplex_mapping:
0:00:00.120590 INFO: ├──multiplexing
0:00:00.120610 INFO: │   ├──enabled: False
0:00:00.120627 INFO: │   ├──target_channels: 4,8
0:00:00.120644 INFO: │   ├──decoy_channel: 12
0:00:00.120662 INFO: │   ├──reference_channel: 0
0:00:00.120681 INFO: │   └──competetive_scoring: True
0:00:00.120699 INFO: ├──fdr
0:00:00.120717 INFO: │   ├──fdr: 0.01
0:00:00.120736 INFO: │   ├──group_level: proteins
0:00:00.120754 INFO: │   ├──inference_strategy: heuristic
0:00:00.120772 INFO: │   ├──competetive_scoring: True
0:00:00.120789 INFO: │   ├──keep_decoys: False
0:00:00.120807 INFO: │   ├──channel_wise_fdr: False
0:00:00.120825 INFO: │   ├──enable_two_step_classifier: False
0:00:00.120842 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.120860 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.120878 INFO: ├──search_output
0:00:00.120897 INFO: │   ├──file_format: tsv
0:00:00.120914 INFO: │   ├──peptide_level_lfq: False
0:00:00.120932 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.120960 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.120978 INFO: │   ├──min_k_fragments: 12
0:00:00.120995 INFO: │   ├──min_correlation: 0.9
0:00:00.121013 INFO: │   ├──num_samples_quadratic: 50
0:00:00.121032 INFO: │   ├──min_nonnan: 3
0:00:00.121049 INFO: │   └──normalize_lfq: True
0:00:00.121067 INFO: ├──optimization
0:00:00.121086 INFO: │   ├──order_of_optimization: None
0:00:00.121104 INFO: │   ├──ms2_error
0:00:00.121123 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.121142 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.121162 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.121181 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.121198 INFO: │   │   ├──try_narrower_values: True
0:00:00.121217 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.121236 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.121255 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.121273 INFO: │   ├──ms1_error
0:00:00.121291 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.121310 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.121329 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.121347 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.121367 INFO: │   │   ├──try_narrower_values: False
0:00:00.121386 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.121404 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.121422 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.121440 INFO: │   ├──mobility_error
0:00:00.121459 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.121477 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.121496 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.121515 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.121533 INFO: │   │   ├──try_narrower_values: False
0:00:00.121551 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.121575 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.121593 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.121610 INFO: │   └──rt_error
0:00:00.121628 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.121647 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.121665 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.121683 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.121701 INFO: │       ├──try_narrower_values: True
0:00:00.121719 INFO: │       ├──maximal_decrease: 0.2
0:00:00.121738 INFO: │       ├──favour_narrower_optimum: True
0:00:00.121756 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.121774 INFO: ├──optimization_manager
0:00:00.121793 INFO: │   ├──fwhm_rt: 5
0:00:00.121810 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.121828 INFO: │   └──score_cutoff: 0
0:00:00.121846 INFO: ├──transfer_library
0:00:00.121864 INFO: │   ├──enabled: False
0:00:00.121883 INFO: │   ├──fragment_types:
0:00:00.121902 INFO: │   │   - b
0:00:00.121919 INFO: │   │   - y
0:00:00.121936 INFO: │   ├──max_charge: 2
0:00:00.121953 INFO: │   ├──top_k_samples: 3
0:00:00.121972 INFO: │   ├──norm_delta_max: True
0:00:00.121989 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.122007 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.122024 INFO: └──transfer_learning
0:00:00.122043 INFO:     ├──enabled: False
0:00:00.122061 INFO:     ├──batch_size: 2000
0:00:00.122078 INFO:     ├──max_lr: 0.0001
0:00:00.122095 INFO:     ├──train_fraction: 0.7
0:00:00.122113 INFO:     ├──validation_fraction: 0.2
0:00:00.122131 INFO:     ├──test_fraction: 0.1
0:00:00.122148 INFO:     ├──test_interval: 1
0:00:00.122165 INFO:     ├──lr_patience: 3
0:00:00.122184 INFO:     ├──epochs: 51
0:00:00.122203 INFO:     ├──warmup_epochs: 5
0:00:00.122220 INFO:     ├──nce: 25
0:00:00.122238 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.127002 INFO: Moved existing config file run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/frozen_config.yaml to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/frozen_config.yaml
0:00:00.127607 INFO: Registering 7 custom modifications
0:00:00.157301 INFO: Searching 6 files:
0:00:00.157370 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:00:00.157397 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
0:00:00.157419 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
0:00:00.157437 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
0:00:00.157454 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
0:00:00.157471 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
0:00:00.157488 INFO: Using 1 fasta files:
0:00:00.157506 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:00:00.157526 INFO: Using library: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:00.157544 INFO: Saving output to: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library
0:00:00.157575 PROGRESS: Loading spectral library
0:00:00.157606 PROGRESS: Loading library (type: base) from disk..
0:00:00.157639 INFO: Running DynamicLoader
0:00:00.157692 INFO: Loading .hdf library from /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:36.138304 INFO: Running PrecursorInitializer
0:00:36.138643 INFO: Running AnnotateFasta
0:00:36.285006 INFO: Dropping decoys from input library before annotation
0:00:55.809444 INFO: Running IsotopeGenerator
0:00:55.809704 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
0:00:55.809748 INFO: Running RTNormalization
0:00:55.809803 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:00:55.809850 INFO: Saving library to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/speclib.hdf
0:01:29.446061 INFO: Running DecoyGenerator
0:03:06.474304 INFO: Running FlattenLibrary
0:03:40.838478 INFO: Running InitFlatColumns
0:03:41.139115 INFO: Running LogFlatLibraryStats
0:03:41.139252 INFO: ============ Library Stats ============
0:03:41.139293 INFO: Number of precursors: 12,218,312
0:03:43.031114 INFO: 	thereof targets:6,124,046
0:03:43.031257 INFO: 	thereof decoys: 6,094,266
0:03:43.120316 INFO: Number of elution groups: 6,124,046
0:03:43.120439 INFO: 	average size: 2.00
0:03:43.407146 INFO: Number of proteins: 117,993
0:03:43.436701 INFO: Number of channels: 1 ([0])
0:03:43.436885 INFO: Isotopes Distribution for 4 isotopes
0:03:43.436914 INFO: =======================================
0:03:43.445637 PROGRESS: Starting Search Workflows
0:03:43.445818 PROGRESS: 
0:03:43.445901 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
0:03:43.445980 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/figures
0:03:43.446212 INFO: Initializing TimingManager
0:03:43.446697 INFO: Initializing RawFileManager
0:03:43.446816 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:43.446878 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:43.446924 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:43.652110 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
0:03:53.905840 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
0:03:53.910485 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:53.914356 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:53.914665 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:53.914998 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:53.916656 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:53.942342 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:53.942780 INFO: Indexing quadrupole dimension
0:03:54.510950 INFO: Transposing detector events
0:04:05.334006 INFO: Finished transposing data
0:04:05.361977 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:04:05.363286 INFO: RT (min)            : 0.0 - 70.0
0:04:05.363353 INFO: RT duration (sec)   : 4199.9
0:04:05.363390 INFO: RT duration (min)   : 70.0
0:04:05.363422 INFO: Cycle len (scans)   : 9
0:04:05.363453 INFO: Cycle len (sec)     : 0.97
0:04:05.363484 INFO: Number of cycles    : 4347
0:04:05.363515 INFO: MS2 range (m/z)     : 400.0 - 1000.0
0:04:05.363600 INFO: Creating DIA data object took: 21.916794776916504
0:04:06.901550 INFO: Initializing CalibrationManager
0:04:06.901806 INFO: Setting up calibration estimators ..
0:04:06.901866 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:04:06.901946 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'}' ..
0:04:06.902061 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:04:06.902126 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'}' ..
0:04:06.902197 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}}' ..
0:04:06.902256 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}}' ..
0:04:06.902303 INFO: Done setting up calibration estimators.
0:04:06.902416 INFO: Initializing OptimizationManager
0:04:06.902506 INFO: initial parameter: ms1_error = 30
0:04:06.902551 INFO: initial parameter: ms2_error = 30
0:04:06.902595 INFO: initial parameter: rt_error = 2099.928159
0:04:06.902635 INFO: initial parameter: mobility_error = 0.1
0:04:06.902676 INFO: initial parameter: num_candidates = 1
0:04:06.902714 INFO: initial parameter: fwhm_rt = 5
0:04:06.902753 INFO: initial parameter: fwhm_mobility = 0.01
0:04:06.902791 INFO: initial parameter: score_cutoff = 0
0:04:06.902828 INFO: initial parameter: classifier_version = -1
0:04:06.902900 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:04:06.903234 INFO: FDRManager: loading saved state not requested, will be initialized.
0:04:06.903271 INFO: Initializing FDRManager
0:04:06.903312 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:04:08.082283 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
0:04:09.260150 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:04:09.260513 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 2099.928159
0:04:09.260705 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
0:04:09.260879 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
0:04:09.260974 PROGRESS: Starting initial search for precursors.
0:04:09.261056 INFO: Starting optimization step 0.
0:04:09.261114 PROGRESS: === Extracting elution groups 0 to 200 ===
0:04:09.261182 INFO: Using classic extraction backend
0:04:09.261378 PROGRESS: Extracting batch of 390 precursors
0:04:09.261444 INFO: === Search parameters used ===
0:04:09.261490 INFO: rt_error       : 2099.928159
0:04:09.261532 INFO: mobility_error : 0.1
0:04:09.261571 INFO: num_candidates : 1
0:04:09.261608 INFO: ms1_error      : 30
0:04:09.261647 INFO: ms2_error      : 30
0:04:09.261684 INFO: fwhm_rt        : 5
0:04:09.261722 INFO: quant_window   : 3
0:04:09.261758 INFO: ==============================================
0:04:11.161987 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:04:11.162100 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:04:11.162131 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:04:11.162155 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:04:13.123498 INFO: Starting candidate selection
0:05:18.574256 INFO: Starting candidate scoring
0:09:54.329250 INFO: Finished candidate processing
0:09:54.329700 INFO: Collecting candidate features
0:09:54.740787 INFO: Collecting fragment features
0:09:55.948259 INFO: Finished candidate scoring
0:09:55.949823 INFO: performing precursor FDR with 47 features
0:09:55.949870 INFO: Decoy channel: -1
0:09:55.949892 INFO: Competetive: True
0:09:55.951206 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:55.954432 INFO: Using random state 68901 for train-test-split
0:09:55.966076 INFO: Test AUC: 0.538
0:09:55.966135 INFO: Train AUC: 0.497
0:09:55.966166 INFO: AUC difference: 8.34%
0:09:55.966189 WARNING: AUC difference > 5%. This may indicate overfitting.
0:09:56.199377 INFO: Resetting torch num_threads to 80
0:09:56.199861 PROGRESS: === Extracted 364 precursors and 3956 fragments ===
0:09:56.200309 INFO: === FDR correction performed with classifier version -1 ===
0:09:56.200813 PROGRESS: ============================= Precursor FDR =============================
0:09:56.200902 PROGRESS: Total precursors accumulated: 188
0:09:56.200972 PROGRESS: Target precursors: 178 (94.68%)
0:09:56.201023 PROGRESS: Decoy precursors: 10 (5.32%)
0:09:56.201067 PROGRESS: 
0:09:56.201109 PROGRESS: Precursor Summary:
0:09:56.201953 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:09:56.202038 PROGRESS: 
0:09:56.202098 PROGRESS: Protein Summary:
0:09:56.203007 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:09:56.203092 PROGRESS: =========================================================================
0:09:56.203349 INFO: Target number of precursors not reached yet.
0:09:56.288795 INFO: Starting optimization step 1.
0:09:56.289011 PROGRESS: === Extracting elution groups 200 to 600 ===
0:09:56.289112 INFO: Using classic extraction backend
0:09:56.289315 PROGRESS: Extracting batch of 783 precursors
0:09:56.289392 INFO: === Search parameters used ===
0:09:56.289440 INFO: rt_error       : 2099.928159
0:09:56.289482 INFO: mobility_error : 0.1
0:09:56.289523 INFO: num_candidates : 1
0:09:56.289564 INFO: ms1_error      : 30
0:09:56.289602 INFO: ms2_error      : 30
0:09:56.289640 INFO: fwhm_rt        : 5
0:09:56.289677 INFO: quant_window   : 3
0:09:56.289715 INFO: ==============================================
0:09:56.290635 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:09:56.290681 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:09:56.290715 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:09:56.290735 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:09:56.291664 INFO: Starting candidate selection
0:10:02.297934 INFO: Starting candidate scoring
0:10:02.407733 INFO: Finished candidate processing
0:10:02.407837 INFO: Collecting candidate features
0:10:02.417670 INFO: Collecting fragment features
0:10:02.420309 INFO: Finished candidate scoring
0:10:02.423198 INFO: performing precursor FDR with 47 features
0:10:02.423248 INFO: Decoy channel: -1
0:10:02.423272 INFO: Competetive: True
0:10:02.426732 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:02.429015 INFO: Using random state 504296 for train-test-split
0:10:02.437693 INFO: Test AUC: 0.498
0:10:02.437745 INFO: Train AUC: 0.505
0:10:02.437776 INFO: AUC difference: 1.38%
0:10:02.650444 INFO: Resetting torch num_threads to 80
0:10:02.651607 PROGRESS: === Extracted 1120 precursors and 12173 fragments ===
0:10:02.652049 INFO: === FDR correction performed with classifier version -1 ===
0:10:02.652591 PROGRESS: ============================= Precursor FDR =============================
0:10:02.652677 PROGRESS: Total precursors accumulated: 577
0:10:02.652736 PROGRESS: Target precursors: 551 (95.49%)
0:10:02.652792 PROGRESS: Decoy precursors: 26 (4.51%)
0:10:02.652839 PROGRESS: 
0:10:02.652882 PROGRESS: Precursor Summary:
0:10:02.653802 PROGRESS: Channel   0:	 0.050 FDR:   551; 0.010 FDR:     0; 0.001 FDR:     0
0:10:02.653890 PROGRESS: 
0:10:02.653945 PROGRESS: Protein Summary:
0:10:02.654988 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:     0; 0.001 FDR:     0
0:10:02.655075 PROGRESS: =========================================================================
0:10:02.655279 INFO: Target number of precursors not reached yet.
0:10:02.730057 INFO: Starting optimization step 2.
0:10:02.730260 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:10:02.730348 INFO: Using classic extraction backend
0:10:02.730538 PROGRESS: Extracting batch of 1576 precursors
0:10:02.730613 INFO: === Search parameters used ===
0:10:02.730664 INFO: rt_error       : 2099.928159
0:10:02.730710 INFO: mobility_error : 0.1
0:10:02.730754 INFO: num_candidates : 1
0:10:02.730797 INFO: ms1_error      : 30
0:10:02.730839 INFO: ms2_error      : 30
0:10:02.730883 INFO: fwhm_rt        : 5
0:10:02.730924 INFO: quant_window   : 3
0:10:02.730967 INFO: ==============================================
0:10:02.731858 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:10:02.731904 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:10:02.731946 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:10:02.731970 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:10:02.732747 INFO: Starting candidate selection
0:10:13.454548 INFO: Starting candidate scoring
0:10:13.644206 INFO: Finished candidate processing
0:10:13.644337 INFO: Collecting candidate features
0:10:13.657391 INFO: Collecting fragment features
0:10:13.660415 INFO: Finished candidate scoring
0:10:13.663057 INFO: performing precursor FDR with 47 features
0:10:13.663105 INFO: Decoy channel: -1
0:10:13.663130 INFO: Competetive: True
0:10:13.666524 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:13.668564 INFO: Using random state 845211 for train-test-split
0:10:13.678620 INFO: Test AUC: 0.504
0:10:13.678675 INFO: Train AUC: 0.503
0:10:13.678704 INFO: AUC difference: 0.29%
0:10:13.889827 INFO: Resetting torch num_threads to 80
0:10:13.891371 PROGRESS: === Extracted 2644 precursors and 28607 fragments ===
0:10:13.891757 INFO: === FDR correction performed with classifier version -1 ===
0:10:13.892383 PROGRESS: ============================= Precursor FDR =============================
0:10:13.892469 PROGRESS: Total precursors accumulated: 1,357
0:10:13.892529 PROGRESS: Target precursors: 1,290 (95.06%)
0:10:13.892581 PROGRESS: Decoy precursors: 67 (4.94%)
0:10:13.892628 PROGRESS: 
0:10:13.892672 PROGRESS: Precursor Summary:
0:10:13.893664 PROGRESS: Channel   0:	 0.050 FDR: 1,290; 0.010 FDR:     0; 0.001 FDR:     0
0:10:13.893754 PROGRESS: 
0:10:13.893810 PROGRESS: Protein Summary:
0:10:13.894983 PROGRESS: Channel   0:	 0.050 FDR: 1,240; 0.010 FDR:     0; 0.001 FDR:     0
0:10:13.895072 PROGRESS: =========================================================================
0:10:13.895201 INFO: Target number of precursors not reached yet.
0:10:13.977706 INFO: Starting optimization step 3.
0:10:13.977907 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:10:13.977984 INFO: Using classic extraction backend
0:10:13.978126 PROGRESS: Extracting batch of 3162 precursors
0:10:13.978196 INFO: === Search parameters used ===
0:10:13.978242 INFO: rt_error       : 2099.928159
0:10:13.978285 INFO: mobility_error : 0.1
0:10:13.978338 INFO: num_candidates : 1
0:10:13.978381 INFO: ms1_error      : 30
0:10:13.978421 INFO: ms2_error      : 30
0:10:13.978461 INFO: fwhm_rt        : 5
0:10:13.978499 INFO: quant_window   : 3
0:10:13.978537 INFO: ==============================================
0:10:13.979470 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:10:13.979516 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:10:13.979544 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:10:13.979567 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:10:13.980238 INFO: Starting candidate selection
0:10:35.218238 INFO: Starting candidate scoring
0:10:35.507802 INFO: Finished candidate processing
0:10:35.507899 INFO: Collecting candidate features
0:10:35.523344 INFO: Collecting fragment features
0:10:35.527861 INFO: Finished candidate scoring
0:10:35.538649 INFO: performing precursor FDR with 47 features
0:10:35.538710 INFO: Decoy channel: -1
0:10:35.538734 INFO: Competetive: True
0:10:35.543756 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:35.546245 INFO: Using random state 772746 for train-test-split
0:10:35.562134 INFO: Test AUC: 0.499
0:10:35.562198 INFO: Train AUC: 0.501
0:10:35.562228 INFO: AUC difference: 0.45%
0:10:36.464697 INFO: Resetting torch num_threads to 80
0:10:36.469048 PROGRESS: === Extracted 5675 precursors and 61258 fragments ===
0:10:36.469520 INFO: === FDR correction performed with classifier version -1 ===
0:10:36.470508 PROGRESS: ============================= Precursor FDR =============================
0:10:36.470595 PROGRESS: Total precursors accumulated: 2,903
0:10:36.470654 PROGRESS: Target precursors: 2,745 (94.56%)
0:10:36.470706 PROGRESS: Decoy precursors: 158 (5.44%)
0:10:36.470752 PROGRESS: 
0:10:36.470796 PROGRESS: Precursor Summary:
0:10:36.471674 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:36.471769 PROGRESS: 
0:10:36.471825 PROGRESS: Protein Summary:
0:10:36.472741 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:36.472824 PROGRESS: =========================================================================
0:10:36.473016 INFO: Target number of precursors not reached yet.
0:10:36.584078 INFO: Starting optimization step 4.
0:10:36.584301 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:10:36.584388 INFO: Using classic extraction backend
0:10:36.584542 PROGRESS: Extracting batch of 6312 precursors
0:10:36.584613 INFO: === Search parameters used ===
0:10:36.584661 INFO: rt_error       : 2099.928159
0:10:36.584703 INFO: mobility_error : 0.1
0:10:36.584746 INFO: num_candidates : 1
0:10:36.584785 INFO: ms1_error      : 30
0:10:36.584824 INFO: ms2_error      : 30
0:10:36.584866 INFO: fwhm_rt        : 5
0:10:36.584906 INFO: quant_window   : 3
0:10:36.584957 INFO: ==============================================
0:10:36.586711 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:10:36.586758 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:10:36.586789 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:10:36.586811 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:10:36.587702 INFO: Starting candidate selection
0:11:16.224233 INFO: Starting candidate scoring
0:11:16.733506 INFO: Finished candidate processing
0:11:16.733624 INFO: Collecting candidate features
0:11:16.753861 INFO: Collecting fragment features
0:11:16.759672 INFO: Finished candidate scoring
0:11:16.775154 INFO: performing precursor FDR with 47 features
0:11:16.775218 INFO: Decoy channel: -1
0:11:16.775243 INFO: Competetive: True
0:11:16.781372 INFO: Setting torch num_threads to 2 for FDR classification task
0:11:16.785904 INFO: Using random state 895197 for train-test-split
0:11:16.812635 INFO: Test AUC: 0.496
0:11:16.812718 INFO: Train AUC: 0.501
0:11:16.812748 INFO: AUC difference: 0.92%
0:11:17.028100 INFO: Resetting torch num_threads to 80
0:11:17.031185 PROGRESS: === Extracted 11704 precursors and 126135 fragments ===
0:11:17.031683 INFO: === FDR correction performed with classifier version -1 ===
0:11:17.032782 PROGRESS: ============================= Precursor FDR =============================
0:11:17.032866 PROGRESS: Total precursors accumulated: 5,987
0:11:17.032925 PROGRESS: Target precursors: 5,662 (94.57%)
0:11:17.032990 PROGRESS: Decoy precursors: 325 (5.43%)
0:11:17.033034 PROGRESS: 
0:11:17.033076 PROGRESS: Precursor Summary:
0:11:17.033940 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:11:17.034024 PROGRESS: 
0:11:17.034084 PROGRESS: Protein Summary:
0:11:17.035019 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:11:17.035101 PROGRESS: =========================================================================
0:11:17.035359 INFO: Target number of precursors not reached yet.
0:11:17.173396 INFO: Starting optimization step 5.
0:11:17.173611 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:11:17.173699 INFO: Using classic extraction backend
0:11:17.173884 PROGRESS: Extracting batch of 12615 precursors
0:11:17.173957 INFO: === Search parameters used ===
0:11:17.174008 INFO: rt_error       : 2099.928159
0:11:17.174053 INFO: mobility_error : 0.1
0:11:17.174097 INFO: num_candidates : 1
0:11:17.174138 INFO: ms1_error      : 30
0:11:17.174179 INFO: ms2_error      : 30
0:11:17.174217 INFO: fwhm_rt        : 5
0:11:17.174255 INFO: quant_window   : 3
0:11:17.174293 INFO: ==============================================
0:11:17.176691 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:11:17.176739 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:11:17.176775 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:11:17.176796 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:11:17.177609 INFO: Starting candidate selection
0:12:33.217901 INFO: Starting candidate scoring
0:12:34.209538 INFO: Finished candidate processing
0:12:34.209642 INFO: Collecting candidate features
0:12:34.232606 WARNING: height_correlation has 1 NaNs ( 0.01 % out of 12042)
0:12:34.236048 INFO: Collecting fragment features
0:12:34.245128 INFO: Finished candidate scoring
0:12:34.274684 INFO: performing precursor FDR with 47 features
0:12:34.274792 INFO: Decoy channel: -1
0:12:34.274818 INFO: Competetive: True
0:12:34.284254 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:34.288009 WARNING: dropped 1 decoy PSMs due to missing features
0:12:34.291833 INFO: Using random state 133523 for train-test-split
0:12:34.567427 INFO: Test AUC: 0.512
0:12:34.567539 INFO: Train AUC: 0.522
0:12:34.567570 INFO: AUC difference: 1.96%
0:12:34.796096 INFO: Resetting torch num_threads to 80
0:12:34.801485 PROGRESS: === Extracted 23746 precursors and 255624 fragments ===
0:12:34.802094 INFO: === FDR correction performed with classifier version -1 ===
0:12:34.804217 PROGRESS: ============================= Precursor FDR =============================
0:12:34.804315 PROGRESS: Total precursors accumulated: 12,162
0:12:34.804383 PROGRESS: Target precursors: 6,615 (54.39%)
0:12:34.804434 PROGRESS: Decoy precursors: 5,547 (45.61%)
0:12:34.804479 PROGRESS: 
0:12:34.804520 PROGRESS: Precursor Summary:
0:12:34.805478 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:12:34.805565 PROGRESS: 
0:12:34.805618 PROGRESS: Protein Summary:
0:12:34.806639 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:12:34.806722 PROGRESS: =========================================================================
0:12:34.807096 INFO: Target number of precursors not reached yet.
0:12:34.996753 INFO: Starting optimization step 6.
0:12:34.996995 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:12:34.997092 INFO: Using classic extraction backend
0:12:34.997283 PROGRESS: Extracting batch of 25223 precursors
0:12:34.997354 INFO: === Search parameters used ===
0:12:34.997401 INFO: rt_error       : 2099.928159
0:12:34.997442 INFO: mobility_error : 0.1
0:12:34.997482 INFO: num_candidates : 1
0:12:34.997520 INFO: ms1_error      : 30
0:12:34.997559 INFO: ms2_error      : 30
0:12:34.997595 INFO: fwhm_rt        : 5
0:12:34.997632 INFO: quant_window   : 3
0:12:34.997679 INFO: ==============================================
0:12:35.003744 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:12:35.003803 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:12:35.003839 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:12:35.003861 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:12:35.004666 INFO: Starting candidate selection
0:15:01.543332 INFO: Starting candidate scoring
0:15:03.474028 INFO: Finished candidate processing
0:15:03.474235 INFO: Collecting candidate features
0:15:03.554478 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 24137)
0:15:03.558736 INFO: Collecting fragment features
0:15:03.578544 INFO: Finished candidate scoring
0:15:03.647133 INFO: performing precursor FDR with 47 features
0:15:03.647288 INFO: Decoy channel: -1
0:15:03.647317 INFO: Competetive: True
0:15:03.671489 INFO: Setting torch num_threads to 2 for FDR classification task
0:15:03.683614 WARNING: dropped 1 target PSMs due to missing features
0:15:03.683776 WARNING: dropped 5 decoy PSMs due to missing features
0:15:03.691915 INFO: Using random state 129657 for train-test-split
0:15:04.574548 INFO: Test AUC: 0.559
0:15:04.574685 INFO: Train AUC: 0.573
0:15:04.574719 INFO: AUC difference: 2.30%
0:15:04.826443 INFO: Resetting torch num_threads to 80
0:15:04.838612 PROGRESS: === Extracted 47883 precursors and 515441 fragments ===
0:15:04.839523 INFO: === FDR correction performed with classifier version -1 ===
0:15:04.844844 PROGRESS: ============================= Precursor FDR =============================
0:15:04.844980 PROGRESS: Total precursors accumulated: 24,522
0:15:04.845049 PROGRESS: Target precursors: 14,611 (59.58%)
0:15:04.845106 PROGRESS: Decoy precursors: 9,911 (40.42%)
0:15:04.845156 PROGRESS: 
0:15:04.845206 PROGRESS: Precursor Summary:
0:15:04.846230 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:15:04.846343 PROGRESS: 
0:15:04.846403 PROGRESS: Protein Summary:
0:15:04.847432 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:15:04.847519 PROGRESS: =========================================================================
0:15:04.848248 INFO: Target number of precursors not reached yet.
0:15:05.179919 INFO: Starting optimization step 7.
0:15:05.180270 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:15:05.180374 INFO: Using classic extraction backend
0:15:05.180630 PROGRESS: Extracting batch of 50469 precursors
0:15:05.180722 INFO: === Search parameters used ===
0:15:05.180776 INFO: rt_error       : 2099.928159
0:15:05.180843 INFO: mobility_error : 0.1
0:15:05.180892 INFO: num_candidates : 1
0:15:05.180935 INFO: ms1_error      : 30
0:15:05.180993 INFO: ms2_error      : 30
0:15:05.181036 INFO: fwhm_rt        : 5
0:15:05.181076 INFO: quant_window   : 3
0:15:05.181115 INFO: ==============================================
0:15:05.197933 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:15:05.198085 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:15:05.198132 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:15:05.198156 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:15:05.199069 INFO: Starting candidate selection
0:19:57.735193 INFO: Starting candidate scoring
0:20:01.230809 INFO: Finished candidate processing
0:20:01.231088 INFO: Collecting candidate features
0:20:01.349854 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 48203)
0:20:01.354926 INFO: Collecting fragment features
0:20:01.387049 INFO: Finished candidate scoring
0:20:01.491191 INFO: performing precursor FDR with 47 features
0:20:01.491323 INFO: Decoy channel: -1
0:20:01.491349 INFO: Competetive: True
0:20:01.539950 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:01.563265 WARNING: dropped 2 target PSMs due to missing features
0:20:01.563395 WARNING: dropped 7 decoy PSMs due to missing features
0:20:01.582136 INFO: Using random state 868192 for train-test-split
0:20:03.434826 INFO: Test AUC: 0.565
0:20:03.434945 INFO: Train AUC: 0.591
0:20:03.434977 INFO: AUC difference: 4.51%
0:20:03.700259 INFO: Resetting torch num_threads to 80
0:20:03.767560 PROGRESS: === Extracted 96086 precursors and 1034079 fragments ===
0:20:03.768307 INFO: === FDR correction performed with classifier version -1 ===
0:20:03.779805 PROGRESS: ============================= Precursor FDR =============================
0:20:03.779944 PROGRESS: Total precursors accumulated: 49,211
0:20:03.780005 PROGRESS: Target precursors: 30,363 (61.70%)
0:20:03.780054 PROGRESS: Decoy precursors: 18,848 (38.30%)
0:20:03.780097 PROGRESS: 
0:20:03.780139 PROGRESS: Precursor Summary:
0:20:03.781491 PROGRESS: Channel   0:	 0.050 FDR:   154; 0.010 FDR:    37; 0.001 FDR:    37
0:20:03.781592 PROGRESS: 
0:20:03.781646 PROGRESS: Protein Summary:
0:20:03.782943 PROGRESS: Channel   0:	 0.050 FDR:   150; 0.010 FDR:    36; 0.001 FDR:    36
0:20:03.783034 PROGRESS: =========================================================================
0:20:03.784415 INFO: Target number of precursors not reached yet.
0:20:04.227018 INFO: Starting optimization step 8.
0:20:04.227293 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:20:04.227383 INFO: Using classic extraction backend
0:20:04.227601 PROGRESS: Extracting batch of 100931 precursors
0:20:04.227683 INFO: === Search parameters used ===
0:20:04.227731 INFO: rt_error       : 2099.928159
0:20:04.227773 INFO: mobility_error : 0.1
0:20:04.227815 INFO: num_candidates : 1
0:20:04.227855 INFO: ms1_error      : 30
0:20:04.227897 INFO: ms2_error      : 30
0:20:04.227939 INFO: fwhm_rt        : 5
0:20:04.227980 INFO: quant_window   : 3
0:20:04.228019 INFO: ==============================================
0:20:04.261379 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:20:04.261503 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:20:04.261541 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:20:04.261574 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:20:04.262559 INFO: Starting candidate selection
0:29:51.198765 INFO: Starting candidate scoring
0:29:58.388371 INFO: Finished candidate processing
0:29:58.388486 INFO: Collecting candidate features
0:29:58.686749 WARNING: intensity_correlation has 18 NaNs ( 0.02 % out of 96308)
0:29:58.687067 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 96308)
0:29:58.693849 INFO: Collecting fragment features
0:29:58.761743 INFO: Finished candidate scoring
0:29:59.108081 INFO: performing precursor FDR with 47 features
0:29:59.108438 INFO: Decoy channel: -1
0:29:59.108470 INFO: Competetive: True
0:29:59.186777 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:59.223977 WARNING: dropped 9 target PSMs due to missing features
0:29:59.224108 WARNING: dropped 18 decoy PSMs due to missing features
0:29:59.264097 INFO: Using random state 316244 for train-test-split
0:30:02.846373 INFO: Test AUC: 0.563
0:30:02.846496 INFO: Train AUC: 0.587
0:30:02.846528 INFO: AUC difference: 4.00%
0:30:03.135612 INFO: Resetting torch num_threads to 80
0:30:03.177030 PROGRESS: === Extracted 192394 precursors and 2069101 fragments ===
0:30:03.177862 INFO: === FDR correction performed with classifier version -1 ===
0:30:03.195514 PROGRESS: ============================= Precursor FDR =============================
0:30:03.195745 PROGRESS: Total precursors accumulated: 98,531
0:30:03.195811 PROGRESS: Target precursors: 59,740 (60.63%)
0:30:03.195862 PROGRESS: Decoy precursors: 38,791 (39.37%)
0:30:03.195908 PROGRESS: 
0:30:03.195951 PROGRESS: Precursor Summary:
0:30:03.197676 PROGRESS: Channel   0:	 0.050 FDR:   730; 0.010 FDR:   467; 0.001 FDR:   246
0:30:03.197783 PROGRESS: 
0:30:03.197840 PROGRESS: Protein Summary:
0:30:03.199535 PROGRESS: Channel   0:	 0.050 FDR:   675; 0.010 FDR:   438; 0.001 FDR:   238
0:30:03.199627 PROGRESS: =========================================================================
0:30:03.201454 INFO: Target number of precursors reached.
0:30:03.351091 INFO: fragments_df: keeping 4400 of 2069101 [sum(precursor_idx_mask)=5323 sum(mass_error_mask)=2069098 stop_rank=4400
0:30:03.685919 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:30:03.797838 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:03.911608 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:30:04.032166 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:04.548503 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:30:04.548936 INFO: Using score_cutoff 56.783257381439206 (fac=0.99, q=1)
0:30:04.549420 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1836166381835938
0:30:04.549501 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.011084429919719696
0:30:04.549554 INFO: Updating optimization_manager: score_cutoff        : 0 -> 56.783257381439206
0:30:04.549628 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:30:04.563644 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:04.625485 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:30:04.642297 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:04.791875 INFO: Updating optimization_manager: classifier_version  : -1 -> 8
0:30:04.792093 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:30:04.792197 INFO: Starting optimization step 9.
0:30:04.792262 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:30:04.792369 INFO: Using classic extraction backend
0:30:04.792662 PROGRESS: Extracting batch of 100530 precursors
0:30:04.792747 INFO: === Search parameters used ===
0:30:04.792798 INFO: rt_error       : 2099.928159
0:30:04.792840 INFO: mobility_error : 0.1
0:30:04.792880 INFO: num_candidates : 3
0:30:04.792919 INFO: ms1_error      : 30
0:30:04.792970 INFO: ms2_error      : 30
0:30:04.793010 INFO: fwhm_rt        : 3.1836166381835938
0:30:04.793048 INFO: quant_window   : 3
0:30:04.793101 INFO: ==============================================
0:30:04.820848 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:30:04.820981 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:30:04.821037 INFO: FWHM in RT is 3.18 seconds, sigma is 0.70
0:30:04.821062 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.14
0:30:04.829757 INFO: Starting candidate selection
0:39:44.964379 INFO: Starting candidate scoring
0:40:03.267917 INFO: Finished candidate processing
0:40:03.268321 INFO: Collecting candidate features
0:40:03.792878 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 279268)
0:40:03.805629 INFO: Collecting fragment features
0:40:03.968287 INFO: Finished candidate scoring
0:40:04.195122 INFO: performing precursor FDR with 47 features
0:40:04.195235 INFO: Decoy channel: -1
0:40:04.195262 INFO: Competetive: True
0:40:04.276665 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:04.320300 WARNING: dropped 3 target PSMs due to missing features
0:40:04.320428 WARNING: dropped 1 decoy PSMs due to missing features
0:40:04.391115 INFO: Using random state 835235 for train-test-split
0:40:08.896441 INFO: Test AUC: 0.569
0:40:08.896560 INFO: Train AUC: 0.600
0:40:08.896594 INFO: AUC difference: 5.07%
0:40:08.896620 WARNING: AUC difference > 5%. This may indicate overfitting.
0:40:09.214359 INFO: Resetting torch num_threads to 80
0:40:09.219894 PROGRESS: === Extracted 279268 precursors and 3040144 fragments ===
0:40:09.220465 INFO: === FDR correction performed with classifier version 8 ===
0:40:09.228399 PROGRESS: ============================= Precursor FDR =============================
0:40:09.228620 PROGRESS: Total precursors accumulated: 50,111
0:40:09.228682 PROGRESS: Target precursors: 32,088 (64.03%)
0:40:09.228732 PROGRESS: Decoy precursors: 18,023 (35.97%)
0:40:09.228791 PROGRESS: 
0:40:09.228834 PROGRESS: Precursor Summary:
0:40:09.230166 PROGRESS: Channel   0:	 0.050 FDR:   373; 0.010 FDR:   202; 0.001 FDR:   171
0:40:09.230255 PROGRESS: 
0:40:09.230315 PROGRESS: Protein Summary:
0:40:09.231655 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   190; 0.001 FDR:   162
0:40:09.231745 PROGRESS: =========================================================================
0:40:09.272512 INFO: Target number of precursors reached.
0:40:09.473312 INFO: fragments_df: keeping 3227 of 3040144 [sum(precursor_idx_mask)=6679 sum(mass_error_mask)=3040144 stop_rank=3227
0:40:09.762316 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:40:09.861854 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:09.955543 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:40:10.057979 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:10.410533 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:10.410946 INFO: Using score_cutoff 56.77751472129822 (fac=0.99, q=1)
0:40:10.411293 INFO: Updating optimization_manager: fwhm_rt             : 3.1836166381835938 -> 2.896853446960449
0:40:10.411369 INFO: Updating optimization_manager: fwhm_mobility       : 0.011084429919719696 -> 0.01072964258491993
0:40:10.411424 INFO: Updating optimization_manager: score_cutoff        : 56.783257381439206 -> 56.77751472129822
0:40:10.411503 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:40:10.425772 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:10.486153 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:40:10.502101 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:10.633844 INFO: === checking if optimization conditions were reached ===
0:40:10.634084 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:40:10.636225 INFO: Updating optimization_manager: ms2_error           : 30 -> 18.86732256732012
0:40:10.636325 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 18.8673.
0:40:10.636389 INFO: ==============================================
0:40:10.636473 INFO: Starting optimization step 10.
0:40:10.636530 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:40:10.636605 INFO: Using classic extraction backend
0:40:10.636786 PROGRESS: Extracting batch of 100530 precursors
0:40:10.636854 INFO: === Search parameters used ===
0:40:10.636903 INFO: rt_error       : 2099.928159
0:40:10.636956 INFO: mobility_error : 0.1
0:40:10.637017 INFO: num_candidates : 3
0:40:10.637056 INFO: ms1_error      : 30
0:40:10.637095 INFO: ms2_error      : 18.86732256732012
0:40:10.637134 INFO: fwhm_rt        : 2.896853446960449
0:40:10.637173 INFO: quant_window   : 3
0:40:10.637215 INFO: ==============================================
0:40:10.661968 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:40:10.662085 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:40:10.662133 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
0:40:10.662157 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.98
0:40:10.670967 INFO: Starting candidate selection
0:49:21.943131 INFO: Starting candidate scoring
0:49:36.177523 INFO: Finished candidate processing
0:49:36.177931 INFO: Collecting candidate features
0:49:36.703599 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 278547)
0:49:36.704065 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 278547)
0:49:36.718019 INFO: Collecting fragment features
0:49:36.889416 INFO: Finished candidate scoring
0:49:37.130918 INFO: performing precursor FDR with 47 features
0:49:37.131039 INFO: Decoy channel: -1
0:49:37.131069 INFO: Competetive: True
0:49:37.204781 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:37.248384 WARNING: dropped 3 target PSMs due to missing features
0:49:37.248513 WARNING: dropped 7 decoy PSMs due to missing features
0:49:37.320591 INFO: Using random state 835235 for train-test-split
0:49:41.836987 INFO: Test AUC: 0.566
0:49:41.837110 INFO: Train AUC: 0.596
0:49:41.837147 INFO: AUC difference: 4.97%
0:49:42.146451 INFO: Resetting torch num_threads to 80
0:49:42.152048 PROGRESS: === Extracted 278547 precursors and 2935885 fragments ===
0:49:42.152607 INFO: === FDR correction performed with classifier version 8 ===
0:49:42.160774 PROGRESS: ============================= Precursor FDR =============================
0:49:42.160991 PROGRESS: Total precursors accumulated: 49,977
0:49:42.161062 PROGRESS: Target precursors: 31,715 (63.46%)
0:49:42.161120 PROGRESS: Decoy precursors: 18,262 (36.54%)
0:49:42.161170 PROGRESS: 
0:49:42.161217 PROGRESS: Precursor Summary:
0:49:42.162545 PROGRESS: Channel   0:	 0.050 FDR:   437; 0.010 FDR:   275; 0.001 FDR:   177
0:49:42.162638 PROGRESS: 
0:49:42.162698 PROGRESS: Protein Summary:
0:49:42.164086 PROGRESS: Channel   0:	 0.050 FDR:   413; 0.010 FDR:   259; 0.001 FDR:   168
0:49:42.164181 PROGRESS: =========================================================================
0:49:42.165892 INFO: Target number of precursors reached.
0:49:42.360460 INFO: fragments_df: keeping 4287 of 2935885 [sum(precursor_idx_mask)=8964 sum(mass_error_mask)=2935885 stop_rank=4287
0:49:42.642979 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:49:42.761758 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:49:42.881815 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:49:43.001504 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:49:43.497427 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:49:43.497854 INFO: Using score_cutoff 55.6117830368042 (fac=0.99, q=1)
0:49:43.498193 INFO: Updating optimization_manager: fwhm_rt             : 2.896853446960449 -> 2.90753173828125
0:49:43.498270 INFO: Updating optimization_manager: fwhm_mobility       : 0.01072964258491993 -> 0.010003648698329926
0:49:43.498322 INFO: Updating optimization_manager: score_cutoff        : 56.77751472129822 -> 55.6117830368042
0:49:43.498385 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:49:43.510974 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:49:43.571478 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:49:43.588353 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:49:43.732962 INFO: === checking if optimization conditions were reached ===
0:49:43.733232 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:49:43.736089 INFO: Updating optimization_manager: ms2_error           : 18.86732256732012 -> 9.845600665465446
0:49:43.736199 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 9.8456.
0:49:43.736275 INFO: ==============================================
0:49:43.736357 INFO: Starting optimization step 11.
0:49:43.736423 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:49:43.736499 INFO: Using classic extraction backend
0:49:43.736711 PROGRESS: Extracting batch of 100530 precursors
0:49:43.736792 INFO: === Search parameters used ===
0:49:43.736848 INFO: rt_error       : 2099.928159
0:49:43.736913 INFO: mobility_error : 0.1
0:49:43.736983 INFO: num_candidates : 3
0:49:43.737036 INFO: ms1_error      : 30
0:49:43.737087 INFO: ms2_error      : 9.845600665465446
0:49:43.737135 INFO: fwhm_rt        : 2.90753173828125
0:49:43.737185 INFO: quant_window   : 3
0:49:43.737238 INFO: ==============================================
0:49:43.772925 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:49:43.773069 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:49:43.773126 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
0:49:43.773154 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:49:43.780643 INFO: Starting candidate selection
0:58:28.788308 INFO: Starting candidate scoring
0:58:38.238092 INFO: Finished candidate processing
0:58:38.238499 INFO: Collecting candidate features
0:58:38.763750 WARNING: intensity_correlation has 17 NaNs ( 0.01 % out of 278675)
0:58:38.764216 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 278675)
0:58:38.777068 INFO: Collecting fragment features
0:58:38.938339 INFO: Finished candidate scoring
0:58:39.166379 INFO: performing precursor FDR with 47 features
0:58:39.166500 INFO: Decoy channel: -1
0:58:39.166529 INFO: Competetive: True
0:58:39.244908 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:39.288690 WARNING: dropped 9 target PSMs due to missing features
0:58:39.288815 WARNING: dropped 10 decoy PSMs due to missing features
0:58:39.361959 INFO: Using random state 835235 for train-test-split
0:58:44.105791 INFO: Test AUC: 0.563
0:58:44.105909 INFO: Train AUC: 0.592
0:58:44.105941 INFO: AUC difference: 4.84%
0:58:44.416386 INFO: Resetting torch num_threads to 80
0:58:44.422345 PROGRESS: === Extracted 278675 precursors and 2746974 fragments ===
0:58:44.422914 INFO: === FDR correction performed with classifier version 8 ===
0:58:44.431901 PROGRESS: ============================= Precursor FDR =============================
0:58:44.432121 PROGRESS: Total precursors accumulated: 49,973
0:58:44.432190 PROGRESS: Target precursors: 31,355 (62.74%)
0:58:44.432239 PROGRESS: Decoy precursors: 18,618 (37.26%)
0:58:44.432284 PROGRESS: 
0:58:44.432326 PROGRESS: Precursor Summary:
0:58:44.433694 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   344; 0.001 FDR:   216
0:58:44.433787 PROGRESS: 
0:58:44.433842 PROGRESS: Protein Summary:
0:58:44.435217 PROGRESS: Channel   0:	 0.050 FDR:   406; 0.010 FDR:   326; 0.001 FDR:   205
0:58:44.435304 PROGRESS: =========================================================================
0:58:44.436658 INFO: Target number of precursors reached.
0:58:44.623823 INFO: fragments_df: keeping 4944 of 2746974 [sum(precursor_idx_mask)=10994 sum(mass_error_mask)=2746974 stop_rank=4944
0:58:44.914386 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:58:45.027460 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:58:45.135421 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:58:45.241978 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:58:45.840462 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:58:45.840883 INFO: Using score_cutoff 43.64952591934204 (fac=0.99, q=1)
0:58:45.841335 INFO: Updating optimization_manager: fwhm_rt             : 2.90753173828125 -> 2.4772138595581055
0:58:45.841424 INFO: Updating optimization_manager: fwhm_mobility       : 0.010003648698329926 -> 0.007825082167983055
0:58:45.841477 INFO: Updating optimization_manager: score_cutoff        : 55.6117830368042 -> 43.64952591934204
0:58:45.841541 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:58:45.854938 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:58:45.914478 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:58:45.930145 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:46.053763 INFO: === checking if optimization conditions were reached ===
0:58:46.054001 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:58:46.056537 INFO: Updating optimization_manager: ms2_error           : 9.845600665465446 -> 6.471287456658623
0:58:46.056636 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 6.4713.
0:58:46.056712 INFO: ==============================================
0:58:46.056784 INFO: Starting optimization step 12.
0:58:46.056843 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:58:46.056908 INFO: Using classic extraction backend
0:58:46.057097 PROGRESS: Extracting batch of 100530 precursors
0:58:46.057170 INFO: === Search parameters used ===
0:58:46.057218 INFO: rt_error       : 2099.928159
0:58:46.057258 INFO: mobility_error : 0.1
0:58:46.057300 INFO: num_candidates : 3
0:58:46.057340 INFO: ms1_error      : 30
0:58:46.057378 INFO: ms2_error      : 6.471287456658623
0:58:46.057417 INFO: fwhm_rt        : 2.4772138595581055
0:58:46.057459 INFO: quant_window   : 3
0:58:46.057498 INFO: ==============================================
0:58:46.082667 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:58:46.082785 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:58:46.082833 INFO: FWHM in RT is 2.48 seconds, sigma is 0.54
0:58:46.082859 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
0:58:46.091588 INFO: Starting candidate selection
1:07:21.415662 INFO: Starting candidate scoring
1:07:30.094845 INFO: Finished candidate processing
1:07:30.094954 INFO: Collecting candidate features
1:07:30.496543 WARNING: intensity_correlation has 31 NaNs ( 0.01 % out of 277936)
1:07:30.497004 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 277936)
1:07:30.509443 INFO: Collecting fragment features
1:07:30.675383 INFO: Finished candidate scoring
1:07:30.851399 INFO: performing precursor FDR with 47 features
1:07:30.851515 INFO: Decoy channel: -1
1:07:30.851542 INFO: Competetive: True
1:07:30.925657 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:30.970173 WARNING: dropped 11 target PSMs due to missing features
1:07:30.970299 WARNING: dropped 21 decoy PSMs due to missing features
1:07:31.042228 INFO: Using random state 835235 for train-test-split
1:07:35.550408 INFO: Test AUC: 0.565
1:07:35.550532 INFO: Train AUC: 0.593
1:07:35.550565 INFO: AUC difference: 4.74%
1:07:35.859030 INFO: Resetting torch num_threads to 80
1:07:35.864483 PROGRESS: === Extracted 277936 precursors and 2584004 fragments ===
1:07:35.865047 INFO: === FDR correction performed with classifier version 8 ===
1:07:35.874061 PROGRESS: ============================= Precursor FDR =============================
1:07:35.874863 PROGRESS: Total precursors accumulated: 49,874
1:07:35.874934 PROGRESS: Target precursors: 31,203 (62.56%)
1:07:35.874983 PROGRESS: Decoy precursors: 18,671 (37.44%)
1:07:35.875026 PROGRESS: 
1:07:35.875079 PROGRESS: Precursor Summary:
1:07:35.876491 PROGRESS: Channel   0:	 0.050 FDR:   454; 0.010 FDR:   337; 0.001 FDR:   238
1:07:35.876587 PROGRESS: 
1:07:35.876640 PROGRESS: Protein Summary:
1:07:35.878021 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   322; 0.001 FDR:   228
1:07:35.878120 PROGRESS: =========================================================================
1:07:35.883166 INFO: Target number of precursors reached.
1:07:36.066915 INFO: fragments_df: keeping 4755 of 2584004 [sum(precursor_idx_mask)=10431 sum(mass_error_mask)=2584004 stop_rank=4755
1:07:36.420115 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:07:37.226802 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:07:37.327935 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:07:37.438466 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:07:38.015433 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:07:38.015913 INFO: Using score_cutoff 42.59240868988037 (fac=0.99, q=1)
1:07:38.016229 INFO: Updating optimization_manager: fwhm_rt             : 2.4772138595581055 -> 2.4002151489257812
1:07:38.016307 INFO: Updating optimization_manager: fwhm_mobility       : 0.007825082167983055 -> 0.0064453077502548695
1:07:38.016360 INFO: Updating optimization_manager: score_cutoff        : 43.64952591934204 -> 42.59240868988037
1:07:38.016445 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:07:38.030656 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:07:38.091454 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:07:38.106327 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:38.237058 INFO: === checking if optimization conditions were reached ===
1:07:38.237323 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
1:07:38.240287 INFO: Updating optimization_manager: ms2_error           : 6.471287456658623 -> 5.4083277548331745
1:07:38.240391 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 5.4083.
1:07:38.240459 INFO: ==============================================
1:07:38.240534 INFO: Starting optimization step 13.
1:07:38.240599 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:07:38.240666 INFO: Using classic extraction backend
1:07:38.240896 PROGRESS: Extracting batch of 100530 precursors
1:07:38.240981 INFO: === Search parameters used ===
1:07:38.241032 INFO: rt_error       : 2099.928159
1:07:38.241073 INFO: mobility_error : 0.1
1:07:38.241114 INFO: num_candidates : 3
1:07:38.241153 INFO: ms1_error      : 30
1:07:38.241196 INFO: ms2_error      : 5.4083277548331745
1:07:38.241240 INFO: fwhm_rt        : 2.4002151489257812
1:07:38.241282 INFO: quant_window   : 3
1:07:38.241319 INFO: ==============================================
1:07:38.328010 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:07:38.328134 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:07:38.328182 INFO: FWHM in RT is 2.40 seconds, sigma is 0.53
1:07:38.328204 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.99
1:07:38.328999 INFO: Starting candidate selection
1:16:13.892000 INFO: Starting candidate scoring
1:16:21.980561 INFO: Finished candidate processing
1:16:21.980737 INFO: Collecting candidate features
1:16:22.509659 WARNING: intensity_correlation has 51 NaNs ( 0.02 % out of 277562)
1:16:22.510256 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 277562)
1:16:22.522635 INFO: Collecting fragment features
1:16:22.691731 INFO: Finished candidate scoring
1:16:22.943408 INFO: performing precursor FDR with 47 features
1:16:22.943523 INFO: Decoy channel: -1
1:16:22.943553 INFO: Competetive: True
1:16:23.026640 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:23.072471 WARNING: dropped 29 target PSMs due to missing features
1:16:23.072600 WARNING: dropped 22 decoy PSMs due to missing features
1:16:23.147133 INFO: Using random state 835235 for train-test-split
1:16:27.825011 INFO: Test AUC: 0.568
1:16:27.825133 INFO: Train AUC: 0.592
1:16:27.825169 INFO: AUC difference: 4.04%
1:16:28.141493 INFO: Resetting torch num_threads to 80
1:16:28.147060 PROGRESS: === Extracted 277562 precursors and 2496026 fragments ===
1:16:28.147824 INFO: === FDR correction performed with classifier version 8 ===
1:16:28.155921 PROGRESS: ============================= Precursor FDR =============================
1:16:28.156131 PROGRESS: Total precursors accumulated: 49,869
1:16:28.156191 PROGRESS: Target precursors: 31,192 (62.55%)
1:16:28.156239 PROGRESS: Decoy precursors: 18,677 (37.45%)
1:16:28.156282 PROGRESS: 
1:16:28.156323 PROGRESS: Precursor Summary:
1:16:28.157666 PROGRESS: Channel   0:	 0.050 FDR:   425; 0.010 FDR:   272; 0.001 FDR:   224
1:16:28.157757 PROGRESS: 
1:16:28.157810 PROGRESS: Protein Summary:
1:16:28.159233 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   257; 0.001 FDR:   212
1:16:28.159321 PROGRESS: =========================================================================
1:16:28.160634 INFO: Target number of precursors reached.
1:16:28.322764 INFO: fragments_df: keeping 4005 of 2496026 [sum(precursor_idx_mask)=8384 sum(mass_error_mask)=2496026 stop_rank=4005
1:16:28.610991 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:16:28.719391 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:16:28.820431 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:16:28.929507 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:16:29.385046 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:16:29.385476 INFO: Using score_cutoff 42.40810057296753 (fac=0.99, q=1)
1:16:29.385827 INFO: Updating optimization_manager: fwhm_rt             : 2.4002151489257812 -> 2.345280170440674
1:16:29.385906 INFO: Updating optimization_manager: fwhm_mobility       : 0.0064453077502548695 -> 0.005862523801624775
1:16:29.385963 INFO: Updating optimization_manager: score_cutoff        : 42.59240868988037 -> 42.40810057296753
1:16:29.386035 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:16:29.398942 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:16:29.459673 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:16:29.475325 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:16:29.605679 INFO: === checking if optimization conditions were reached ===
1:16:29.605936 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
1:16:29.608358 INFO: Updating optimization_manager: ms2_error           : 5.4083277548331745 -> 4.74835077085876
1:16:29.608462 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 4.7484.
1:16:29.608535 INFO: ==============================================
1:16:29.608620 INFO: Starting optimization step 14.
1:16:29.608683 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:16:29.608760 INFO: Using classic extraction backend
1:16:29.608963 PROGRESS: Extracting batch of 100530 precursors
1:16:29.609055 INFO: === Search parameters used ===
1:16:29.609111 INFO: rt_error       : 2099.928159
1:16:29.609161 INFO: mobility_error : 0.1
1:16:29.609221 INFO: num_candidates : 3
1:16:29.609270 INFO: ms1_error      : 30
1:16:29.609315 INFO: ms2_error      : 4.74835077085876
1:16:29.609363 INFO: fwhm_rt        : 2.345280170440674
1:16:29.609411 INFO: quant_window   : 3
1:16:29.609457 INFO: ==============================================
1:16:29.634471 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:16:29.634590 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:16:29.634640 INFO: FWHM in RT is 2.35 seconds, sigma is 0.52
1:16:29.634664 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.72
1:16:29.637537 INFO: Starting candidate selection
1:25:08.468988 INFO: Starting candidate scoring
1:25:16.111915 INFO: Finished candidate processing
1:25:16.112025 INFO: Collecting candidate features
1:25:16.540884 WARNING: intensity_correlation has 94 NaNs ( 0.03 % out of 276194)
1:25:16.541341 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 276194)
1:25:16.553800 INFO: Collecting fragment features
1:25:16.704818 INFO: Finished candidate scoring
1:25:16.905066 INFO: performing precursor FDR with 47 features
1:25:16.905194 INFO: Decoy channel: -1
1:25:16.905219 INFO: Competetive: True
1:25:16.987334 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:17.029548 WARNING: dropped 45 target PSMs due to missing features
1:25:17.029678 WARNING: dropped 51 decoy PSMs due to missing features
1:25:17.103572 INFO: Using random state 835235 for train-test-split
1:25:21.581179 INFO: Test AUC: 0.564
1:25:21.581401 INFO: Train AUC: 0.592
1:25:21.581439 INFO: AUC difference: 4.87%
1:25:21.900440 INFO: Resetting torch num_threads to 80
1:25:21.905975 PROGRESS: === Extracted 276194 precursors and 2322144 fragments ===
1:25:21.906555 INFO: === FDR correction performed with classifier version 8 ===
1:25:21.915263 PROGRESS: ============================= Precursor FDR =============================
1:25:21.915418 PROGRESS: Total precursors accumulated: 49,761
1:25:21.915484 PROGRESS: Target precursors: 31,165 (62.63%)
1:25:21.915535 PROGRESS: Decoy precursors: 18,596 (37.37%)
1:25:21.915581 PROGRESS: 
1:25:21.915622 PROGRESS: Precursor Summary:
1:25:21.917005 PROGRESS: Channel   0:	 0.050 FDR:   344; 0.010 FDR:   269; 0.001 FDR:   201
1:25:21.917099 PROGRESS: 
1:25:21.917154 PROGRESS: Protein Summary:
1:25:21.918549 PROGRESS: Channel   0:	 0.050 FDR:   327; 0.010 FDR:   256; 0.001 FDR:   192
1:25:21.918640 PROGRESS: =========================================================================
1:25:21.920262 INFO: Target number of precursors reached.
1:25:22.074035 INFO: fragments_df: keeping 3765 of 2322144 [sum(precursor_idx_mask)=8066 sum(mass_error_mask)=2322144 stop_rank=3765
1:25:22.392794 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:25:22.499443 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:22.603744 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:25:22.700789 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:23.129446 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:23.129869 INFO: Using score_cutoff 37.44824007568359 (fac=0.99, q=1)
1:25:23.130206 INFO: Updating optimization_manager: fwhm_rt             : 2.345280170440674 -> 2.2545197010040283
1:25:23.130283 INFO: Updating optimization_manager: fwhm_mobility       : 0.005862523801624775 -> 0.005336210131645203
1:25:23.130336 INFO: Updating optimization_manager: score_cutoff        : 42.40810057296753 -> 37.44824007568359
1:25:23.130400 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:25:23.143919 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:23.204609 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:25:23.221619 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:23.359814 INFO: === checking if optimization conditions were reached ===
1:25:23.360099 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
1:25:23.363020 INFO: Updating optimization_manager: ms2_error           : 4.74835077085876 -> 4.1821641389891715
1:25:23.363137 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 4.1822.
1:25:23.363212 INFO: ==============================================
1:25:23.363306 INFO: Starting optimization step 15.
1:25:23.363371 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:25:23.363453 INFO: Using classic extraction backend
1:25:23.363680 PROGRESS: Extracting batch of 100530 precursors
1:25:23.363761 INFO: === Search parameters used ===
1:25:23.363816 INFO: rt_error       : 2099.928159
1:25:23.363865 INFO: mobility_error : 0.1
1:25:23.363912 INFO: num_candidates : 3
1:25:23.363960 INFO: ms1_error      : 30
1:25:23.364008 INFO: ms2_error      : 4.1821641389891715
1:25:23.364059 INFO: fwhm_rt        : 2.2545197010040283
1:25:23.364106 INFO: quant_window   : 3
1:25:23.364152 INFO: ==============================================
1:25:23.398938 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:25:23.399060 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:25:23.399119 INFO: FWHM in RT is 2.25 seconds, sigma is 0.50
1:25:23.399142 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.48
1:25:23.400062 INFO: Starting candidate selection
1:33:48.257292 INFO: Starting candidate scoring
1:33:55.731305 INFO: Finished candidate processing
1:33:55.731477 INFO: Collecting candidate features
1:33:56.159114 WARNING: intensity_correlation has 72 NaNs ( 0.03 % out of 276357)
1:33:56.159563 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 276357)
1:33:56.171722 INFO: Collecting fragment features
1:33:56.326252 INFO: Finished candidate scoring
1:33:56.494798 INFO: performing precursor FDR with 47 features
1:33:56.494909 INFO: Decoy channel: -1
1:33:56.494935 INFO: Competetive: True
1:33:56.577504 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:56.621168 WARNING: dropped 36 target PSMs due to missing features
1:33:56.621293 WARNING: dropped 39 decoy PSMs due to missing features
1:33:56.694276 INFO: Using random state 835235 for train-test-split
1:34:01.537101 INFO: Test AUC: 0.564
1:34:01.537229 INFO: Train AUC: 0.593
1:34:01.537264 INFO: AUC difference: 4.81%
1:34:01.858910 INFO: Resetting torch num_threads to 80
1:34:01.891231 PROGRESS: === Extracted 276357 precursors and 2308193 fragments ===
1:34:01.891843 INFO: === FDR correction performed with classifier version 8 ===
1:34:01.900328 PROGRESS: ============================= Precursor FDR =============================
1:34:01.900541 PROGRESS: Total precursors accumulated: 49,773
1:34:01.900603 PROGRESS: Target precursors: 31,192 (62.67%)
1:34:01.900652 PROGRESS: Decoy precursors: 18,581 (37.33%)
1:34:01.900696 PROGRESS: 
1:34:01.900738 PROGRESS: Precursor Summary:
1:34:01.902052 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   245; 0.001 FDR:   207
1:34:01.902155 PROGRESS: 
1:34:01.902212 PROGRESS: Protein Summary:
1:34:01.903557 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   231; 0.001 FDR:   195
1:34:01.903644 PROGRESS: =========================================================================
1:34:01.905010 INFO: Target number of precursors reached.
1:34:02.059501 INFO: fragments_df: keeping 3445 of 2308193 [sum(precursor_idx_mask)=7207 sum(mass_error_mask)=2308193 stop_rank=3445
1:34:02.453491 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:34:02.566460 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:02.663655 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:34:02.770960 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:03.156469 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:03.156916 INFO: Using score_cutoff 35.71531105957031 (fac=0.99, q=1)
1:34:03.157259 INFO: Updating optimization_manager: fwhm_rt             : 2.2545197010040283 -> 2.335031509399414
1:34:03.157338 INFO: Updating optimization_manager: fwhm_mobility       : 0.005336210131645203 -> 0.005756530910730362
1:34:03.157391 INFO: Updating optimization_manager: score_cutoff        : 37.44824007568359 -> 35.71531105957031
1:34:03.157454 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:34:03.171108 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:03.233740 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:34:03.251029 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:03.392267 INFO: === checking if optimization conditions were reached ===
1:34:03.392551 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
1:34:03.395502 INFO: Updating optimization_manager: ms2_error           : 4.1821641389891715 -> 4.188505394725345
1:34:03.395616 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 4.1885.
1:34:03.395692 INFO: ==============================================
1:34:03.395776 INFO: Starting optimization step 16.
1:34:03.395852 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:34:03.395937 INFO: Using classic extraction backend
1:34:03.396229 PROGRESS: Extracting batch of 100530 precursors
1:34:03.396310 INFO: === Search parameters used ===
1:34:03.396364 INFO: rt_error       : 2099.928159
1:34:03.396414 INFO: mobility_error : 0.1
1:34:03.396464 INFO: num_candidates : 3
1:34:03.396512 INFO: ms1_error      : 30
1:34:03.396564 INFO: ms2_error      : 4.188505394725345
1:34:03.396613 INFO: fwhm_rt        : 2.335031509399414
1:34:03.396659 INFO: quant_window   : 3
1:34:03.396707 INFO: ==============================================
1:34:03.444751 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:34:03.444880 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:34:03.444929 INFO: FWHM in RT is 2.34 seconds, sigma is 0.51
1:34:03.444961 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.67
1:34:03.445715 INFO: Starting candidate selection
1:42:42.327449 INFO: Starting candidate scoring
1:42:49.991764 INFO: Finished candidate processing
1:42:49.991944 INFO: Collecting candidate features
1:42:50.427935 WARNING: intensity_correlation has 68 NaNs ( 0.02 % out of 277550)
1:42:50.428383 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 277550)
1:42:50.440751 INFO: Collecting fragment features
1:42:50.596219 INFO: Finished candidate scoring
1:42:50.756336 INFO: performing precursor FDR with 47 features
1:42:50.756450 INFO: Decoy channel: -1
1:42:50.756476 INFO: Competetive: True
1:42:50.832886 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:50.878867 WARNING: dropped 42 target PSMs due to missing features
1:42:50.878993 WARNING: dropped 29 decoy PSMs due to missing features
1:42:50.955260 INFO: Using random state 835235 for train-test-split
1:42:55.799750 INFO: Test AUC: 0.561
1:42:55.799869 INFO: Train AUC: 0.589
1:42:55.799902 INFO: AUC difference: 4.77%
1:42:56.121294 INFO: Resetting torch num_threads to 80
1:42:56.126846 PROGRESS: === Extracted 277550 precursors and 2328340 fragments ===
1:42:56.127407 INFO: === FDR correction performed with classifier version 8 ===
1:42:56.141809 PROGRESS: ============================= Precursor FDR =============================
1:42:56.142051 PROGRESS: Total precursors accumulated: 49,946
1:42:56.142116 PROGRESS: Target precursors: 30,962 (61.99%)
1:42:56.142165 PROGRESS: Decoy precursors: 18,984 (38.01%)
1:42:56.142209 PROGRESS: 
1:42:56.142252 PROGRESS: Precursor Summary:
1:42:56.143631 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   222; 0.001 FDR:   106
1:42:56.143719 PROGRESS: 
1:42:56.143773 PROGRESS: Protein Summary:
1:42:56.145102 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   209; 0.001 FDR:   104
1:42:56.145190 PROGRESS: =========================================================================
1:42:56.146547 INFO: Target number of precursors reached.
1:42:56.300810 INFO: fragments_df: keeping 3208 of 2328340 [sum(precursor_idx_mask)=6604 sum(mass_error_mask)=2328340 stop_rank=3208
1:42:56.600976 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:42:56.701228 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:42:56.793911 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:42:56.898538 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:42:57.249856 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:42:57.250277 INFO: Using score_cutoff 37.93220216331482 (fac=0.99, q=1)
1:42:57.250612 INFO: Updating optimization_manager: fwhm_rt             : 2.335031509399414 -> 2.3194916248321533
1:42:57.250697 INFO: Updating optimization_manager: fwhm_mobility       : 0.005756530910730362 -> 0.005857839249074459
1:42:57.250753 INFO: Updating optimization_manager: score_cutoff        : 35.71531105957031 -> 37.93220216331482
1:42:57.250810 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:42:57.263779 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:42:57.325195 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:42:57.342551 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:42:57.478106 INFO: === checking if optimization conditions were reached ===
1:42:57.478392 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
1:42:57.479527 INFO: Updating optimization_manager: ms2_error           : 4.188505394725345 -> 9.845600665465446
1:42:57.479667 INFO: Updating optimization_manager: classifier_version  : 8 -> 11
1:42:57.479774 INFO: Updating optimization_manager: score_cutoff        : 37.93220216331482 -> 43.64952591934204
1:42:57.479873 INFO: Updating optimization_manager: fwhm_rt             : 2.3194916248321533 -> 2.4772138595581055
1:42:57.479971 INFO: Updating optimization_manager: fwhm_mobility       : 0.005857839249074459 -> 0.007825082167983055
1:42:57.480067 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 9.8456 found after 8 searches.
1:42:57.480135 INFO: ==============================================
1:42:57.480214 PROGRESS: Optimization finished for ms2_error.
1:42:57.694134 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:42:57.707447 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:42:57.769047 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:42:57.786168 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:42:57.959242 INFO: Starting optimization step 0.
1:42:57.959468 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:42:57.959552 INFO: Using classic extraction backend
1:42:57.959745 PROGRESS: Extracting batch of 100530 precursors
1:42:57.959828 INFO: === Search parameters used ===
1:42:57.959884 INFO: rt_error       : 2099.928159
1:42:57.959935 INFO: mobility_error : 0.1
1:42:57.959985 INFO: num_candidates : 3
1:42:57.960034 INFO: ms1_error      : 30
1:42:57.960082 INFO: ms2_error      : 9.845600665465446
1:42:57.960130 INFO: fwhm_rt        : 2.4772138595581055
1:42:57.960178 INFO: quant_window   : 3
1:42:57.960226 INFO: ==============================================
1:42:57.990429 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:42:57.990551 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:42:57.990603 INFO: FWHM in RT is 2.48 seconds, sigma is 0.54
1:42:57.990627 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
1:42:57.991319 INFO: Starting candidate selection
1:51:31.707615 INFO: Starting candidate scoring
1:51:40.888998 INFO: Finished candidate processing
1:51:40.889186 INFO: Collecting candidate features
1:51:41.349419 WARNING: intensity_correlation has 24 NaNs ( 0.01 % out of 279167)
1:51:41.349889 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 279167)
1:51:41.362347 INFO: Collecting fragment features
1:51:41.544967 INFO: Finished candidate scoring
1:51:41.722580 INFO: performing precursor FDR with 47 features
1:51:41.722704 INFO: Decoy channel: -1
1:51:41.722730 INFO: Competetive: True
1:51:41.810410 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:41.857403 WARNING: dropped 12 target PSMs due to missing features
1:51:41.857541 WARNING: dropped 14 decoy PSMs due to missing features
1:51:41.931593 INFO: Using random state 349019 for train-test-split
1:51:46.521779 INFO: Test AUC: 0.576
1:51:46.522018 INFO: Train AUC: 0.603
1:51:46.522051 INFO: AUC difference: 4.41%
1:51:46.834558 INFO: Resetting torch num_threads to 80
1:51:46.840935 PROGRESS: === Extracted 279167 precursors and 2732764 fragments ===
1:51:46.841600 INFO: === FDR correction performed with classifier version 11 ===
1:51:46.850693 PROGRESS: ============================= Precursor FDR =============================
1:51:46.850914 PROGRESS: Total precursors accumulated: 50,038
1:51:46.850977 PROGRESS: Target precursors: 31,904 (63.76%)
1:51:46.851025 PROGRESS: Decoy precursors: 18,134 (36.24%)
1:51:46.851082 PROGRESS: 
1:51:46.851128 PROGRESS: Precursor Summary:
1:51:46.852511 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   369; 0.001 FDR:   220
1:51:46.852598 PROGRESS: 
1:51:46.852652 PROGRESS: Protein Summary:
1:51:46.854073 PROGRESS: Channel   0:	 0.050 FDR:   485; 0.010 FDR:   352; 0.001 FDR:   210
1:51:46.854170 PROGRESS: =========================================================================
1:51:46.855884 INFO: Target number of precursors reached.
1:51:47.037716 INFO: fragments_df: keeping 5000 of 2732764 [sum(precursor_idx_mask)=11514 sum(mass_error_mask)=2732764 stop_rank=5000
1:51:47.392522 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:51:47.497919 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:51:47.598319 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:51:47.710885 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:51:48.321698 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:51:48.322185 INFO: Using score_cutoff 44.350349798583984 (fac=0.99, q=1)
1:51:48.322542 INFO: Updating optimization_manager: fwhm_rt             : 2.4772138595581055 -> 2.550297975540161
1:51:48.322622 INFO: Updating optimization_manager: fwhm_mobility       : 0.007825082167983055 -> 0.007820364087820053
1:51:48.322675 INFO: Updating optimization_manager: score_cutoff        : 43.64952591934204 -> 44.350349798583984
1:51:48.322729 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:51:48.336631 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:48.398178 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:51:48.415420 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:48.557926 INFO: === checking if optimization conditions were reached ===
1:51:48.558219 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:51:48.560725 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 523.6195314406077
1:51:48.560843 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 523.6195.
1:51:48.560921 INFO: ==============================================
1:51:48.561019 INFO: Starting optimization step 1.
1:51:48.561085 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:51:48.561167 INFO: Using classic extraction backend
1:51:48.561404 PROGRESS: Extracting batch of 100530 precursors
1:51:48.561487 INFO: === Search parameters used ===
1:51:48.561546 INFO: rt_error       : 523.6195314406077
1:51:48.561600 INFO: mobility_error : 0.1
1:51:48.561650 INFO: num_candidates : 3
1:51:48.561698 INFO: ms1_error      : 30
1:51:48.561744 INFO: ms2_error      : 9.845600665465446
1:51:48.561791 INFO: fwhm_rt        : 2.550297975540161
1:51:48.561836 INFO: quant_window   : 3
1:51:48.561883 INFO: ==============================================
1:51:48.599509 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:51:48.599653 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:51:48.599715 INFO: FWHM in RT is 2.55 seconds, sigma is 0.56
1:51:48.599744 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
1:51:48.607696 INFO: Starting candidate selection
1:54:11.762721 INFO: Starting candidate scoring
1:54:21.547138 INFO: Finished candidate processing
1:54:21.547349 INFO: Collecting candidate features
1:54:21.959517 WARNING: intensity_correlation has 112 NaNs ( 0.04 % out of 267911)
1:54:21.959988 WARNING: height_correlation has 9 NaNs ( 0.00 % out of 267911)
1:54:21.971875 INFO: Collecting fragment features
1:54:22.129019 INFO: Finished candidate scoring
1:54:22.279966 INFO: performing precursor FDR with 47 features
1:54:22.280078 INFO: Decoy channel: -1
1:54:22.280102 INFO: Competetive: True
1:54:22.355161 INFO: Setting torch num_threads to 2 for FDR classification task
1:54:22.398279 WARNING: dropped 64 target PSMs due to missing features
1:54:22.398403 WARNING: dropped 56 decoy PSMs due to missing features
1:54:22.471412 INFO: Using random state 349019 for train-test-split
1:54:26.845243 INFO: Test AUC: 0.568
1:54:26.845351 INFO: Train AUC: 0.597
1:54:26.845382 INFO: AUC difference: 4.85%
1:54:27.160923 INFO: Resetting torch num_threads to 80
1:54:27.177701 PROGRESS: === Extracted 267911 precursors and 2571589 fragments ===
1:54:27.178540 INFO: === FDR correction performed with classifier version 11 ===
1:54:27.187261 PROGRESS: ============================= Precursor FDR =============================
1:54:27.187456 PROGRESS: Total precursors accumulated: 48,832
1:54:27.187517 PROGRESS: Target precursors: 30,736 (62.94%)
1:54:27.187567 PROGRESS: Decoy precursors: 18,096 (37.06%)
1:54:27.187611 PROGRESS: 
1:54:27.187657 PROGRESS: Precursor Summary:
1:54:27.189102 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   389; 0.001 FDR:   260
1:54:27.189194 PROGRESS: 
1:54:27.189251 PROGRESS: Protein Summary:
1:54:27.190665 PROGRESS: Channel   0:	 0.050 FDR:   489; 0.010 FDR:   370; 0.001 FDR:   246
1:54:27.190751 PROGRESS: =========================================================================
1:54:27.193832 INFO: Target number of precursors reached.
1:54:27.362672 INFO: fragments_df: keeping 5000 of 2571589 [sum(precursor_idx_mask)=12214 sum(mass_error_mask)=2571589 stop_rank=5000
1:54:27.716001 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:54:27.830367 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:27.937099 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:54:28.046040 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:28.653555 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:28.653987 INFO: Using score_cutoff 44.62880633239746 (fac=0.99, q=1)
1:54:28.654342 INFO: Updating optimization_manager: fwhm_rt             : 2.550297975540161 -> 2.5197629928588867
1:54:28.654422 INFO: Updating optimization_manager: fwhm_mobility       : 0.007820364087820053 -> 0.007747418247163296
1:54:28.654474 INFO: Updating optimization_manager: score_cutoff        : 44.350349798583984 -> 44.62880633239746
1:54:28.654528 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:54:28.667890 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:28.728470 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:54:28.745095 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:28.885398 INFO: === checking if optimization conditions were reached ===
1:54:28.885672 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:54:28.888148 INFO: Updating optimization_manager: rt_error            : 523.6195314406077 -> 360.77961853680256
1:54:28.888261 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 360.7796.
1:54:28.888340 INFO: ==============================================
1:54:28.888423 INFO: Starting optimization step 2.
1:54:28.888489 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:54:28.888571 INFO: Using classic extraction backend
1:54:28.888826 PROGRESS: Extracting batch of 100530 precursors
1:54:28.888909 INFO: === Search parameters used ===
1:54:28.888980 INFO: rt_error       : 360.77961853680256
1:54:28.889047 INFO: mobility_error : 0.1
1:54:28.889099 INFO: num_candidates : 3
1:54:28.889149 INFO: ms1_error      : 30
1:54:28.889197 INFO: ms2_error      : 9.845600665465446
1:54:28.889245 INFO: fwhm_rt        : 2.5197629928588867
1:54:28.889293 INFO: quant_window   : 3
1:54:28.889339 INFO: ==============================================
1:54:28.927944 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:54:28.928090 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:54:28.928149 INFO: FWHM in RT is 2.52 seconds, sigma is 0.55
1:54:28.928177 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.59
1:54:28.929348 INFO: Starting candidate selection
1:56:17.636940 INFO: Starting candidate scoring
1:56:27.572858 INFO: Finished candidate processing
1:56:27.572980 INFO: Collecting candidate features
1:56:27.945844 WARNING: intensity_correlation has 146 NaNs ( 0.05 % out of 265793)
1:56:27.946284 WARNING: height_correlation has 12 NaNs ( 0.00 % out of 265793)
1:56:27.958115 INFO: Collecting fragment features
1:56:28.108315 INFO: Finished candidate scoring
1:56:28.252618 INFO: performing precursor FDR with 47 features
1:56:28.252745 INFO: Decoy channel: -1
1:56:28.252770 INFO: Competetive: True
1:56:28.327961 INFO: Setting torch num_threads to 2 for FDR classification task
1:56:28.369170 WARNING: dropped 80 target PSMs due to missing features
1:56:28.369306 WARNING: dropped 76 decoy PSMs due to missing features
1:56:28.438008 INFO: Using random state 349019 for train-test-split
1:56:32.731458 INFO: Test AUC: 0.566
1:56:32.731576 INFO: Train AUC: 0.594
1:56:32.731608 INFO: AUC difference: 4.74%
1:56:33.042937 INFO: Resetting torch num_threads to 80
1:56:33.048279 PROGRESS: === Extracted 265793 precursors and 2522582 fragments ===
1:56:33.048821 INFO: === FDR correction performed with classifier version 11 ===
1:56:33.057172 PROGRESS: ============================= Precursor FDR =============================
1:56:33.057398 PROGRESS: Total precursors accumulated: 48,526
1:56:33.057463 PROGRESS: Target precursors: 30,280 (62.40%)
1:56:33.057512 PROGRESS: Decoy precursors: 18,246 (37.60%)
1:56:33.057556 PROGRESS: 
1:56:33.057596 PROGRESS: Precursor Summary:
1:56:33.058935 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   429; 0.001 FDR:   264
1:56:33.059023 PROGRESS: 
1:56:33.059077 PROGRESS: Protein Summary:
1:56:33.060472 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   407; 0.001 FDR:   252
1:56:33.060561 PROGRESS: =========================================================================
1:56:33.061819 INFO: Target number of precursors reached.
1:56:33.226894 INFO: fragments_df: keeping 5000 of 2522582 [sum(precursor_idx_mask)=13230 sum(mass_error_mask)=2522582 stop_rank=5000
1:56:33.437089 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:56:33.569983 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:56:33.703712 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:56:34.570357 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:56:35.182125 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:56:35.182545 INFO: Using score_cutoff 42.267093626403806 (fac=0.99, q=1)
1:56:35.182846 INFO: Updating optimization_manager: fwhm_rt             : 2.5197629928588867 -> 2.553098678588867
1:56:35.182922 INFO: Updating optimization_manager: fwhm_mobility       : 0.007747418247163296 -> 0.007735831663012505
1:56:35.182975 INFO: Updating optimization_manager: score_cutoff        : 44.62880633239746 -> 42.267093626403806
1:56:35.183026 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:56:35.190302 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:56:35.220561 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:56:35.227822 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:56:35.289201 INFO: === checking if optimization conditions were reached ===
1:56:35.289475 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:56:35.291988 INFO: Updating optimization_manager: rt_error            : 360.77961853680256 -> 264.573873755247
1:56:35.292107 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 264.5739.
1:56:35.292196 INFO: ==============================================
1:56:35.292275 INFO: Starting optimization step 3.
1:56:35.292339 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:56:35.292401 INFO: Using classic extraction backend
1:56:35.292565 PROGRESS: Extracting batch of 50061 precursors
1:56:35.292639 INFO: === Search parameters used ===
1:56:35.292693 INFO: rt_error       : 264.573873755247
1:56:35.292742 INFO: mobility_error : 0.1
1:56:35.292791 INFO: num_candidates : 3
1:56:35.292840 INFO: ms1_error      : 30
1:56:35.292886 INFO: ms2_error      : 9.845600665465446
1:56:35.292933 INFO: fwhm_rt        : 2.553098678588867
1:56:35.292995 INFO: quant_window   : 3
1:56:35.293042 INFO: ==============================================
1:56:35.310803 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:56:35.311487 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:56:35.311550 INFO: FWHM in RT is 2.55 seconds, sigma is 0.56
1:56:35.311577 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.59
1:56:35.320191 INFO: Starting candidate selection
1:57:13.932873 INFO: Starting candidate scoring
1:57:19.136986 INFO: Finished candidate processing
1:57:19.137194 INFO: Collecting candidate features
1:57:19.362088 WARNING: intensity_correlation has 91 NaNs ( 0.07 % out of 132680)
1:57:19.362431 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 132680)
1:57:19.370226 INFO: Collecting fragment features
1:57:19.444103 INFO: Finished candidate scoring
1:57:19.561768 INFO: performing precursor FDR with 47 features
1:57:19.561871 INFO: Decoy channel: -1
1:57:19.561898 INFO: Competetive: True
1:57:19.598610 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:19.620591 WARNING: dropped 49 target PSMs due to missing features
1:57:19.620716 WARNING: dropped 49 decoy PSMs due to missing features
1:57:19.640033 INFO: Using random state 349019 for train-test-split
1:57:21.738410 INFO: Test AUC: 0.560
1:57:21.738529 INFO: Train AUC: 0.599
1:57:21.738562 INFO: AUC difference: 6.47%
1:57:21.738585 WARNING: AUC difference > 5%. This may indicate overfitting.
1:57:22.009218 INFO: Resetting torch num_threads to 80
1:57:22.012227 PROGRESS: === Extracted 132680 precursors and 1251713 fragments ===
1:57:22.012731 INFO: === FDR correction performed with classifier version 11 ===
1:57:22.016397 PROGRESS: ============================= Precursor FDR =============================
1:57:22.016520 PROGRESS: Total precursors accumulated: 24,242
1:57:22.016579 PROGRESS: Target precursors: 15,161 (62.54%)
1:57:22.016629 PROGRESS: Decoy precursors: 9,081 (37.46%)
1:57:22.016671 PROGRESS: 
1:57:22.016723 PROGRESS: Precursor Summary:
1:57:22.017866 PROGRESS: Channel   0:	 0.050 FDR:   288; 0.010 FDR:   232; 0.001 FDR:   185
1:57:22.017964 PROGRESS: 
1:57:22.018018 PROGRESS: Protein Summary:
1:57:22.019226 PROGRESS: Channel   0:	 0.050 FDR:   281; 0.010 FDR:   226; 0.001 FDR:   181
1:57:22.019312 PROGRESS: =========================================================================
1:57:22.046785 INFO: Target number of precursors reached.
1:57:22.125995 INFO: fragments_df: keeping 3188 of 1251713 [sum(precursor_idx_mask)=7139 sum(mass_error_mask)=1251713 stop_rank=3188
1:57:22.329427 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:57:22.448296 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:57:22.554337 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:57:22.653891 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:57:23.004031 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:57:23.004459 INFO: Using score_cutoff 42.34185685958862 (fac=0.99, q=1)
1:57:23.004789 INFO: Updating optimization_manager: fwhm_rt             : 2.553098678588867 -> 2.5002858638763428
1:57:23.004864 INFO: Updating optimization_manager: fwhm_mobility       : 0.007735831663012505 -> 0.0076293651945889
1:57:23.004918 INFO: Updating optimization_manager: score_cutoff        : 42.267093626403806 -> 42.34185685958862
1:57:23.004983 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:57:23.012730 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:57:23.043274 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:57:23.051221 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:57:23.114632 INFO: === checking if optimization conditions were reached ===
1:57:23.114884 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:57:23.116875 INFO: Updating optimization_manager: rt_error            : 264.573873755247 -> 246.69811418250234
1:57:23.116991 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 246.6981.
1:57:23.117069 INFO: ==============================================
1:57:23.117143 INFO: Starting optimization step 4.
1:57:23.117197 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:57:23.117277 INFO: Using classic extraction backend
1:57:23.117451 PROGRESS: Extracting batch of 50061 precursors
1:57:23.117520 INFO: === Search parameters used ===
1:57:23.117566 INFO: rt_error       : 246.69811418250234
1:57:23.117607 INFO: mobility_error : 0.1
1:57:23.117646 INFO: num_candidates : 3
1:57:23.117684 INFO: ms1_error      : 30
1:57:23.117723 INFO: ms2_error      : 9.845600665465446
1:57:23.117762 INFO: fwhm_rt        : 2.5002858638763428
1:57:23.117799 INFO: quant_window   : 3
1:57:23.117837 INFO: ==============================================
1:57:23.131022 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:57:23.131124 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:57:23.131172 INFO: FWHM in RT is 2.50 seconds, sigma is 0.55
1:57:23.131194 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.54
1:57:23.140213 INFO: Starting candidate selection
1:57:57.530861 INFO: Starting candidate scoring
1:58:02.692186 INFO: Finished candidate processing
1:58:02.692434 INFO: Collecting candidate features
1:58:02.951946 WARNING: intensity_correlation has 83 NaNs ( 0.06 % out of 132542)
1:58:02.952332 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 132542)
1:58:02.960596 INFO: Collecting fragment features
1:58:03.049808 INFO: Finished candidate scoring
1:58:03.119625 INFO: performing precursor FDR with 47 features
1:58:03.119737 INFO: Decoy channel: -1
1:58:03.119763 INFO: Competetive: True
1:58:03.161166 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:03.183748 WARNING: dropped 44 target PSMs due to missing features
1:58:03.183871 WARNING: dropped 44 decoy PSMs due to missing features
1:58:03.204765 INFO: Using random state 349019 for train-test-split
1:58:05.273869 INFO: Test AUC: 0.560
1:58:05.273984 INFO: Train AUC: 0.598
1:58:05.274017 INFO: AUC difference: 6.29%
1:58:05.274040 WARNING: AUC difference > 5%. This may indicate overfitting.
1:58:05.551543 INFO: Resetting torch num_threads to 80
1:58:05.556607 PROGRESS: === Extracted 132542 precursors and 1246160 fragments ===
1:58:05.557427 INFO: === FDR correction performed with classifier version 11 ===
1:58:05.561389 PROGRESS: ============================= Precursor FDR =============================
1:58:05.561505 PROGRESS: Total precursors accumulated: 24,224
1:58:05.561565 PROGRESS: Target precursors: 15,146 (62.52%)
1:58:05.561615 PROGRESS: Decoy precursors: 9,078 (37.48%)
1:58:05.561659 PROGRESS: 
1:58:05.561701 PROGRESS: Precursor Summary:
1:58:05.562899 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   221; 0.001 FDR:   186
1:58:05.562988 PROGRESS: 
1:58:05.563042 PROGRESS: Protein Summary:
1:58:05.564301 PROGRESS: Channel   0:	 0.050 FDR:   299; 0.010 FDR:   215; 0.001 FDR:   181
1:58:05.564391 PROGRESS: =========================================================================
1:58:05.565340 INFO: Target number of precursors reached.
1:58:05.651043 INFO: fragments_df: keeping 3100 of 1246160 [sum(precursor_idx_mask)=6840 sum(mass_error_mask)=1246160 stop_rank=3100
1:58:05.890223 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:58:06.007622 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:58:06.124263 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:58:06.243370 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:58:06.650929 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:58:06.651449 INFO: Using score_cutoff 42.257404357910154 (fac=0.99, q=1)
1:58:06.651833 INFO: Updating optimization_manager: fwhm_rt             : 2.5002858638763428 -> 2.446303606033325
1:58:06.651911 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076293651945889 -> 0.0076944660395383835
1:58:06.651964 INFO: Updating optimization_manager: score_cutoff        : 42.34185685958862 -> 42.257404357910154
1:58:06.652021 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:58:06.659836 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:58:06.690151 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:58:06.698220 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:58:06.763051 INFO: === checking if optimization conditions were reached ===
1:58:06.763297 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:58:06.765414 INFO: Updating optimization_manager: rt_error            : 246.69811418250234 -> 249.59788160306368
1:58:06.765511 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 249.5979.
1:58:06.765576 INFO: ==============================================
1:58:06.765649 INFO: Starting optimization step 5.
1:58:06.765707 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:58:06.765775 INFO: Using classic extraction backend
1:58:06.765982 PROGRESS: Extracting batch of 50061 precursors
1:58:06.766053 INFO: === Search parameters used ===
1:58:06.766103 INFO: rt_error       : 249.59788160306368
1:58:06.766146 INFO: mobility_error : 0.1
1:58:06.766198 INFO: num_candidates : 3
1:58:06.766243 INFO: ms1_error      : 30
1:58:06.766283 INFO: ms2_error      : 9.845600665465446
1:58:06.766322 INFO: fwhm_rt        : 2.446303606033325
1:58:06.766364 INFO: quant_window   : 3
1:58:06.766402 INFO: ==============================================
1:58:06.779363 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:58:06.779468 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:58:06.779514 INFO: FWHM in RT is 2.45 seconds, sigma is 0.54
1:58:06.779536 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1:58:06.788257 INFO: Starting candidate selection
1:58:57.461400 INFO: Starting candidate scoring
1:59:02.751833 INFO: Finished candidate processing
1:59:02.751979 INFO: Collecting candidate features
1:59:02.933223 WARNING: intensity_correlation has 85 NaNs ( 0.06 % out of 132753)
1:59:02.933575 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 132753)
1:59:02.941413 INFO: Collecting fragment features
1:59:03.020370 INFO: Finished candidate scoring
1:59:03.090020 INFO: performing precursor FDR with 47 features
1:59:03.090132 INFO: Decoy channel: -1
1:59:03.090156 INFO: Competetive: True
1:59:03.128222 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:03.150579 WARNING: dropped 46 target PSMs due to missing features
1:59:03.150704 WARNING: dropped 44 decoy PSMs due to missing features
1:59:03.171003 INFO: Using random state 349019 for train-test-split
1:59:05.237636 INFO: Test AUC: 0.555
1:59:05.237752 INFO: Train AUC: 0.598
1:59:05.237784 INFO: AUC difference: 7.22%
1:59:05.237807 WARNING: AUC difference > 5%. This may indicate overfitting.
1:59:05.510751 INFO: Resetting torch num_threads to 80
1:59:05.513738 PROGRESS: === Extracted 132753 precursors and 1249398 fragments ===
1:59:05.514245 INFO: === FDR correction performed with classifier version 11 ===
1:59:05.517930 PROGRESS: ============================= Precursor FDR =============================
1:59:05.518048 PROGRESS: Total precursors accumulated: 24,282
1:59:05.518109 PROGRESS: Target precursors: 15,112 (62.24%)
1:59:05.518157 PROGRESS: Decoy precursors: 9,170 (37.76%)
1:59:05.518204 PROGRESS: 
1:59:05.518247 PROGRESS: Precursor Summary:
1:59:05.519360 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   215; 0.001 FDR:   184
1:59:05.519445 PROGRESS: 
1:59:05.519498 PROGRESS: Protein Summary:
1:59:05.520698 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   209; 0.001 FDR:   180
1:59:05.520783 PROGRESS: =========================================================================
1:59:05.521537 INFO: Target number of precursors reached.
1:59:05.602416 INFO: fragments_df: keeping 3005 of 1249398 [sum(precursor_idx_mask)=6700 sum(mass_error_mask)=1249398 stop_rank=3005
1:59:05.803610 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:59:05.908057 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:59:06.005927 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:59:06.105855 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:59:06.435323 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:59:06.435744 INFO: Using score_cutoff 42.2545122001648 (fac=0.99, q=1)
1:59:06.436075 INFO: Updating optimization_manager: fwhm_rt             : 2.446303606033325 -> 2.45419979095459
1:59:06.436151 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076944660395383835 -> 0.007519220467656851
1:59:06.436203 INFO: Updating optimization_manager: score_cutoff        : 42.257404357910154 -> 42.2545122001648
1:59:06.436262 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:59:06.443724 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:59:06.473862 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:59:06.481829 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:59:06.548415 INFO: === checking if optimization conditions were reached ===
1:59:06.548701 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:59:06.550148 INFO: Updating optimization_manager: rt_error            : 249.59788160306368 -> 246.69811418250234
1:59:06.550291 INFO: Updating optimization_manager: classifier_version  : 11 -> 21
1:59:06.550396 INFO: Updating optimization_manager: score_cutoff        : 42.2545122001648 -> 42.257404357910154
1:59:06.550507 INFO: Updating optimization_manager: fwhm_rt             : 2.45419979095459 -> 2.446303606033325
1:59:06.550606 INFO: Updating optimization_manager: fwhm_mobility       : 0.007519220467656851 -> 0.0076944660395383835
1:59:06.550702 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 246.6981 found after 6 searches.
1:59:06.550772 INFO: ==============================================
1:59:06.550852 PROGRESS: Optimization finished for rt_error.
1:59:06.682294 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:59:06.690170 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:59:06.720746 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:59:06.728570 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:59:06.821343 INFO: Starting optimization step 0.
1:59:06.821537 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:59:06.821618 INFO: Using classic extraction backend
1:59:06.821772 PROGRESS: Extracting batch of 50061 precursors
1:59:06.821844 INFO: === Search parameters used ===
1:59:06.821892 INFO: rt_error       : 246.69811418250234
1:59:06.821934 INFO: mobility_error : 0.1
1:59:06.821973 INFO: num_candidates : 3
1:59:06.822012 INFO: ms1_error      : 30
1:59:06.822051 INFO: ms2_error      : 9.845600665465446
1:59:06.822088 INFO: fwhm_rt        : 2.446303606033325
1:59:06.822137 INFO: quant_window   : 3
1:59:06.822176 INFO: ==============================================
1:59:06.834753 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:59:06.834861 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:59:06.834908 INFO: FWHM in RT is 2.45 seconds, sigma is 0.54
1:59:06.834930 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1:59:06.843540 INFO: Starting candidate selection
1:59:57.443597 INFO: Starting candidate scoring
2:00:02.794860 INFO: Finished candidate processing
2:00:02.794970 INFO: Collecting candidate features
2:00:02.983574 WARNING: intensity_correlation has 93 NaNs ( 0.07 % out of 132912)
2:00:02.983939 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 132912)
2:00:02.991834 INFO: Collecting fragment features
2:00:03.068160 INFO: Finished candidate scoring
2:00:03.133332 INFO: performing precursor FDR with 47 features
2:00:03.133445 INFO: Decoy channel: -1
2:00:03.133469 INFO: Competetive: True
2:00:03.170274 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:03.191930 WARNING: dropped 50 target PSMs due to missing features
2:00:03.192055 WARNING: dropped 48 decoy PSMs due to missing features
2:00:03.211393 INFO: Using random state 27700 for train-test-split
2:00:05.412126 INFO: Test AUC: 0.567
2:00:05.412254 INFO: Train AUC: 0.618
2:00:05.412286 INFO: AUC difference: 8.33%
2:00:05.412308 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:05.683196 INFO: Resetting torch num_threads to 80
2:00:05.686203 PROGRESS: === Extracted 132912 precursors and 1249370 fragments ===
2:00:05.686706 INFO: === FDR correction performed with classifier version 21 ===
2:00:05.690363 PROGRESS: ============================= Precursor FDR =============================
2:00:05.690479 PROGRESS: Total precursors accumulated: 24,308
2:00:05.690541 PROGRESS: Target precursors: 15,586 (64.12%)
2:00:05.690603 PROGRESS: Decoy precursors: 8,722 (35.88%)
2:00:05.690667 PROGRESS: 
2:00:05.690724 PROGRESS: Precursor Summary:
2:00:05.691852 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   217; 0.001 FDR:   201
2:00:05.691939 PROGRESS: 
2:00:05.691996 PROGRESS: Protein Summary:
2:00:05.693239 PROGRESS: Channel   0:	 0.050 FDR:   318; 0.010 FDR:   211; 0.001 FDR:   196
2:00:05.693327 PROGRESS: =========================================================================
2:00:05.694272 INFO: Target number of precursors reached.
2:00:05.775894 INFO: fragments_df: keeping 2998 of 1249370 [sum(precursor_idx_mask)=6680 sum(mass_error_mask)=1249370 stop_rank=2998
2:00:05.977023 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:00:06.073907 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:00:06.168396 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:00:06.267405 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:00:06.597042 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:00:06.597465 INFO: Using score_cutoff 44.62459698944092 (fac=0.99, q=1)
2:00:06.597796 INFO: Updating optimization_manager: fwhm_rt             : 2.446303606033325 -> 2.5244457721710205
2:00:06.597873 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076944660395383835 -> 0.00783353392034769
2:00:06.597927 INFO: Updating optimization_manager: score_cutoff        : 42.257404357910154 -> 44.62459698944092
2:00:06.597982 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:00:06.605431 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:00:06.635525 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:00:06.643410 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:00:06.701759 INFO: === checking if optimization conditions were reached ===
2:00:06.702032 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
2:00:06.704162 INFO: Updating optimization_manager: ms1_error           : 30 -> 8.670566519129505
2:00:06.704271 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 8.6706.
2:00:06.704346 INFO: ==============================================
2:00:06.704427 INFO: Starting optimization step 1.
2:00:06.704490 PROGRESS: === Extracting elution groups 0 to 25400 ===
2:00:06.704559 INFO: Using classic extraction backend
2:00:06.704748 PROGRESS: Extracting batch of 50061 precursors
2:00:06.704838 INFO: === Search parameters used ===
2:00:06.704894 INFO: rt_error       : 246.69811418250234
2:00:06.704955 INFO: mobility_error : 0.1
2:00:06.705008 INFO: num_candidates : 3
2:00:06.705056 INFO: ms1_error      : 8.670566519129505
2:00:06.705103 INFO: ms2_error      : 9.845600665465446
2:00:06.705149 INFO: fwhm_rt        : 2.5244457721710205
2:00:06.705196 INFO: quant_window   : 3
2:00:06.705243 INFO: ==============================================
2:00:06.723300 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:00:06.723411 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:00:06.723465 INFO: FWHM in RT is 2.52 seconds, sigma is 0.55
2:00:06.723493 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
2:00:06.725402 INFO: Starting candidate selection
2:00:57.465790 INFO: Starting candidate scoring
2:01:01.582369 INFO: Finished candidate processing
2:01:01.582582 INFO: Collecting candidate features
2:01:01.792173 WARNING: intensity_correlation has 75 NaNs ( 0.06 % out of 132732)
2:01:01.792508 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 132732)
2:01:01.800305 INFO: Collecting fragment features
2:01:01.875799 INFO: Finished candidate scoring
2:01:01.947972 INFO: performing precursor FDR with 47 features
2:01:01.948082 INFO: Decoy channel: -1
2:01:01.948107 INFO: Competetive: True
2:01:01.984571 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:02.006291 WARNING: dropped 42 target PSMs due to missing features
2:01:02.006413 WARNING: dropped 40 decoy PSMs due to missing features
2:01:02.028883 INFO: Using random state 27700 for train-test-split
2:01:04.192400 INFO: Test AUC: 0.552
2:01:04.192514 INFO: Train AUC: 0.586
2:01:04.192545 INFO: AUC difference: 5.81%
2:01:04.192566 WARNING: AUC difference > 5%. This may indicate overfitting.
2:01:04.459027 INFO: Resetting torch num_threads to 80
2:01:04.462075 PROGRESS: === Extracted 132732 precursors and 1234583 fragments ===
2:01:04.462584 INFO: === FDR correction performed with classifier version 21 ===
2:01:04.466298 PROGRESS: ============================= Precursor FDR =============================
2:01:04.466424 PROGRESS: Total precursors accumulated: 24,336
2:01:04.466485 PROGRESS: Target precursors: 14,835 (60.96%)
2:01:04.466534 PROGRESS: Decoy precursors: 9,501 (39.04%)
2:01:04.466578 PROGRESS: 
2:01:04.466619 PROGRESS: Precursor Summary:
2:01:04.467729 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   254; 0.001 FDR:   169
2:01:04.467816 PROGRESS: 
2:01:04.467869 PROGRESS: Protein Summary:
2:01:04.469114 PROGRESS: Channel   0:	 0.050 FDR:   330; 0.010 FDR:   247; 0.001 FDR:   165
2:01:04.469201 PROGRESS: =========================================================================
2:01:04.470221 INFO: Target number of precursors reached.
2:01:04.548635 INFO: fragments_df: keeping 3422 of 1234583 [sum(precursor_idx_mask)=7828 sum(mass_error_mask)=1234577 stop_rank=3422
2:01:04.796619 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:01:04.896960 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:04.997425 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:01:05.096894 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:05.476354 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:05.476893 INFO: Using score_cutoff 40.34704205703735 (fac=0.99, q=1)
2:01:05.477311 INFO: Updating optimization_manager: fwhm_rt             : 2.5244457721710205 -> 2.4908533096313477
2:01:05.477388 INFO: Updating optimization_manager: fwhm_mobility       : 0.00783353392034769 -> 0.007597144693136215
2:01:05.477442 INFO: Updating optimization_manager: score_cutoff        : 44.62459698944092 -> 40.34704205703735
2:01:05.477502 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:01:05.485514 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:05.515753 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:01:05.523810 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:05.583905 INFO: === checking if optimization conditions were reached ===
2:01:05.584187 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
2:01:05.586769 INFO: Updating optimization_manager: ms1_error           : 8.670566519129505 -> 2.6929839117418664
2:01:05.586898 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 2.6930.
2:01:05.586974 INFO: ==============================================
2:01:05.587061 INFO: Starting optimization step 2.
2:01:05.587131 PROGRESS: === Extracting elution groups 0 to 25400 ===
2:01:05.587215 INFO: Using classic extraction backend
2:01:05.587477 PROGRESS: Extracting batch of 50061 precursors
2:01:05.587559 INFO: === Search parameters used ===
2:01:05.587613 INFO: rt_error       : 246.69811418250234
2:01:05.587663 INFO: mobility_error : 0.1
2:01:05.587711 INFO: num_candidates : 3
2:01:05.587767 INFO: ms1_error      : 2.6929839117418664
2:01:05.587815 INFO: ms2_error      : 9.845600665465446
2:01:05.587860 INFO: fwhm_rt        : 2.4908533096313477
2:01:05.587906 INFO: quant_window   : 3
2:01:05.587952 INFO: ==============================================
2:01:05.606181 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:01:05.606289 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:01:05.606342 INFO: FWHM in RT is 2.49 seconds, sigma is 0.55
2:01:05.606369 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.52
2:01:05.615052 INFO: Starting candidate selection
2:01:37.003669 INFO: Starting candidate scoring
2:01:57.022410 INFO: Finished candidate processing
2:01:57.022820 INFO: Collecting candidate features
2:01:57.251902 WARNING: intensity_correlation has 52 NaNs ( 0.04 % out of 133447)
2:01:57.252229 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 133447)
2:01:57.260062 INFO: Collecting fragment features
2:01:57.333443 INFO: Finished candidate scoring
2:01:57.427567 INFO: performing precursor FDR with 47 features
2:01:57.427677 INFO: Decoy channel: -1
2:01:57.427705 INFO: Competetive: True
2:01:57.464179 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:57.485402 WARNING: dropped 28 target PSMs due to missing features
2:01:57.485524 WARNING: dropped 29 decoy PSMs due to missing features
2:01:57.505139 INFO: Using random state 27700 for train-test-split
2:01:59.670631 INFO: Test AUC: 0.552
2:01:59.670750 INFO: Train AUC: 0.581
2:01:59.670781 INFO: AUC difference: 4.89%
2:01:59.930388 INFO: Resetting torch num_threads to 80
2:01:59.933388 PROGRESS: === Extracted 133447 precursors and 1228424 fragments ===
2:01:59.933887 INFO: === FDR correction performed with classifier version 21 ===
2:01:59.937545 PROGRESS: ============================= Precursor FDR =============================
2:01:59.937658 PROGRESS: Total precursors accumulated: 24,425
2:01:59.937717 PROGRESS: Target precursors: 14,649 (59.98%)
2:01:59.937768 PROGRESS: Decoy precursors: 9,776 (40.02%)
2:01:59.937824 PROGRESS: 
2:01:59.937869 PROGRESS: Precursor Summary:
2:01:59.938926 PROGRESS: Channel   0:	 0.050 FDR:   290; 0.010 FDR:    14; 0.001 FDR:    14
2:01:59.939013 PROGRESS: 
2:01:59.939067 PROGRESS: Protein Summary:
2:01:59.940196 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:    14; 0.001 FDR:    14
2:01:59.940283 PROGRESS: =========================================================================
2:01:59.941079 INFO: Target number of precursors not reached yet.
2:02:00.200259 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:02:00.208088 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:00.238124 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:02:00.245943 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:00.302978 INFO: === skipping optimization until target number of precursors are found ===
2:02:00.303223 PROGRESS: === Optimization of ms1_error has been skipped 1 time(s); maximum number is 1 ===
2:02:00.303319 INFO: Starting optimization step 3.
2:02:00.303382 PROGRESS: === Extracting elution groups 25400 to 51000 ===
2:02:00.303455 INFO: Using classic extraction backend
2:02:00.303634 PROGRESS: Extracting batch of 50469 precursors
2:02:00.303717 INFO: === Search parameters used ===
2:02:00.303767 INFO: rt_error       : 246.69811418250234
2:02:00.303821 INFO: mobility_error : 0.1
2:02:00.303864 INFO: num_candidates : 3
2:02:00.303904 INFO: ms1_error      : 2.6929839117418664
2:02:00.303944 INFO: ms2_error      : 9.845600665465446
2:02:00.303985 INFO: fwhm_rt        : 2.4908533096313477
2:02:00.304025 INFO: quant_window   : 3
2:02:00.304065 INFO: ==============================================
2:02:00.316926 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:02:00.317046 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:02:00.317094 INFO: FWHM in RT is 2.49 seconds, sigma is 0.55
2:02:00.317118 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.52
2:02:00.317990 INFO: Starting candidate selection
2:02:32.681049 INFO: Starting candidate scoring
2:02:36.374560 INFO: Finished candidate processing
2:02:36.374657 INFO: Collecting candidate features
2:02:36.551366 WARNING: intensity_correlation has 46 NaNs ( 0.03 % out of 134360)
2:02:36.551698 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 134360)
2:02:36.559327 INFO: Collecting fragment features
2:02:36.633361 INFO: Finished candidate scoring
2:02:36.793007 INFO: performing precursor FDR with 47 features
2:02:36.793142 INFO: Decoy channel: -1
2:02:36.793169 INFO: Competetive: True
2:02:36.882503 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:36.924065 WARNING: dropped 53 target PSMs due to missing features
2:02:36.924195 WARNING: dropped 56 decoy PSMs due to missing features
2:02:36.993427 INFO: Using random state 27700 for train-test-split
2:02:41.642142 INFO: Test AUC: 0.546
2:02:41.642266 INFO: Train AUC: 0.577
2:02:41.642298 INFO: AUC difference: 5.47%
2:02:56.986402 WARNING: AUC difference > 5%. This may indicate overfitting.
2:02:57.296525 INFO: Resetting torch num_threads to 80
2:02:57.339299 PROGRESS: === Extracted 267807 precursors and 2460254 fragments ===
2:02:57.340064 INFO: === FDR correction performed with classifier version 21 ===
2:02:57.348952 PROGRESS: ============================= Precursor FDR =============================
2:02:57.349143 PROGRESS: Total precursors accumulated: 49,047
2:02:57.349205 PROGRESS: Target precursors: 29,255 (59.65%)
2:02:57.349254 PROGRESS: Decoy precursors: 19,792 (40.35%)
2:02:57.349298 PROGRESS: 
2:02:57.349339 PROGRESS: Precursor Summary:
2:02:57.350689 PROGRESS: Channel   0:	 0.050 FDR:   524; 0.010 FDR:   409; 0.001 FDR:   320
2:02:57.350779 PROGRESS: 
2:02:57.350832 PROGRESS: Protein Summary:
2:02:57.352257 PROGRESS: Channel   0:	 0.050 FDR:   496; 0.010 FDR:   387; 0.001 FDR:   306
2:02:57.352344 PROGRESS: =========================================================================
2:02:57.353083 INFO: Target number of precursors reached.
2:02:57.526595 INFO: fragments_df: keeping 5000 of 2460254 [sum(precursor_idx_mask)=12406 sum(mass_error_mask)=2460231 stop_rank=5000
2:02:57.759521 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:02:57.868762 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:57.980215 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:02:58.095315 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:58.703219 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:58.703641 INFO: Using score_cutoff 35.09919724273682 (fac=0.99, q=1)
2:02:58.703977 INFO: Updating optimization_manager: fwhm_rt             : 2.4908533096313477 -> 2.517218589782715
2:02:58.704057 INFO: Updating optimization_manager: fwhm_mobility       : 0.007597144693136215 -> 0.0075195180252194405
2:02:58.704110 INFO: Updating optimization_manager: score_cutoff        : 40.34704205703735 -> 35.09919724273682
2:02:58.704166 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:02:58.711464 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:58.741778 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:02:58.749061 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:58.808889 INFO: === checking if optimization conditions were reached ===
2:02:58.809178 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
2:02:58.810383 INFO: Updating optimization_manager: ms1_error           : 2.6929839117418664 -> 8.670566519129505
2:02:58.810520 INFO: Updating optimization_manager: classifier_version  : 21 -> 24
2:02:58.810624 INFO: Updating optimization_manager: score_cutoff        : 35.09919724273682 -> 40.34704205703735
2:02:58.810734 INFO: Updating optimization_manager: fwhm_rt             : 2.517218589782715 -> 2.4908533096313477
2:02:58.810834 INFO: Updating optimization_manager: fwhm_mobility       : 0.0075195180252194405 -> 0.007597144693136215
2:02:58.810928 PROGRESS: ✅ ms1_error      : optimization just completed. Optimal parameter 8.6706 found after 3 searches.
2:02:58.811004 INFO: ==============================================
2:02:58.811085 PROGRESS: Optimization finished for ms1_error.
2:02:58.958503 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:02:58.965976 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:58.996527 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:02:59.003893 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:59.093035 INFO: Starting optimization step 0.
2:02:59.093219 PROGRESS: === Extracting elution groups 0 to 25400 ===
2:02:59.093291 INFO: Using classic extraction backend
2:02:59.093440 PROGRESS: Extracting batch of 50061 precursors
2:02:59.093510 INFO: === Search parameters used ===
2:02:59.093558 INFO: rt_error       : 246.69811418250234
2:02:59.093599 INFO: mobility_error : 0.1
2:02:59.093640 INFO: num_candidates : 3
2:02:59.093678 INFO: ms1_error      : 8.670566519129505
2:02:59.093716 INFO: ms2_error      : 9.845600665465446
2:02:59.093762 INFO: fwhm_rt        : 2.4908533096313477
2:02:59.093802 INFO: quant_window   : 3
2:02:59.093840 INFO: ==============================================
2:02:59.106463 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:02:59.106568 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:02:59.106613 INFO: FWHM in RT is 2.49 seconds, sigma is 0.55
2:02:59.106636 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.52
2:02:59.115409 INFO: Starting candidate selection
2:03:31.605582 INFO: Starting candidate scoring
2:03:35.679680 INFO: Finished candidate processing
2:03:35.679846 INFO: Collecting candidate features
2:03:35.884611 WARNING: intensity_correlation has 54 NaNs ( 0.04 % out of 132258)
2:03:35.884950 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 132258)
2:03:35.892548 INFO: Collecting fragment features
2:03:35.965968 INFO: Finished candidate scoring
2:03:36.033996 INFO: performing precursor FDR with 47 features
2:03:36.034106 INFO: Decoy channel: -1
2:03:36.034131 INFO: Competetive: True
2:03:36.070224 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:36.091448 WARNING: dropped 27 target PSMs due to missing features
2:03:36.091571 WARNING: dropped 35 decoy PSMs due to missing features
2:03:36.111134 INFO: Using random state 123281 for train-test-split
2:03:38.275863 INFO: Test AUC: 0.556
2:03:38.275978 INFO: Train AUC: 0.593
2:03:38.276011 INFO: AUC difference: 6.30%
2:03:38.276032 WARNING: AUC difference > 5%. This may indicate overfitting.
2:03:38.543421 INFO: Resetting torch num_threads to 80
2:03:38.546419 PROGRESS: === Extracted 132258 precursors and 1228626 fragments ===
2:03:38.546925 INFO: === FDR correction performed with classifier version 24 ===
2:03:38.550669 PROGRESS: ============================= Precursor FDR =============================
2:03:38.550784 PROGRESS: Total precursors accumulated: 24,212
2:03:38.550845 PROGRESS: Target precursors: 14,937 (61.69%)
2:03:38.550894 PROGRESS: Decoy precursors: 9,275 (38.31%)
2:03:38.550941 PROGRESS: 
2:03:38.550983 PROGRESS: Precursor Summary:
2:03:38.552078 PROGRESS: Channel   0:	 0.050 FDR:   283; 0.010 FDR:   251; 0.001 FDR:   163
2:03:38.552166 PROGRESS: 
2:03:38.552220 PROGRESS: Protein Summary:
2:03:38.553414 PROGRESS: Channel   0:	 0.050 FDR:   277; 0.010 FDR:   245; 0.001 FDR:   159
2:03:38.553502 PROGRESS: =========================================================================
2:03:38.581245 INFO: Target number of precursors reached.
2:03:38.662085 INFO: fragments_df: keeping 3380 of 1228626 [sum(precursor_idx_mask)=7662 sum(mass_error_mask)=1228624 stop_rank=3380
2:03:38.863082 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:03:38.981276 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:39.099246 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:03:39.218905 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:39.655062 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:39.655484 INFO: Using score_cutoff 40.17436231613159 (fac=0.99, q=1)
2:03:39.655815 INFO: Updating optimization_manager: fwhm_rt             : 2.4908533096313477 -> 2.5308480262756348
2:03:39.655894 INFO: Updating optimization_manager: fwhm_mobility       : 0.007597144693136215 -> 0.007441982626914978
2:03:39.655946 INFO: Updating optimization_manager: score_cutoff        : 40.34704205703735 -> 40.17436231613159
2:03:39.656000 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:03:39.663492 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:39.693745 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:03:39.701532 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:39.761301 INFO: === checking if optimization conditions were reached ===
2:03:39.761537 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2:03:39.763202 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07469232689620144
2:03:39.763297 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0747.
2:03:39.763362 INFO: ==============================================
2:03:39.763432 INFO: Starting optimization step 1.
2:03:39.763488 PROGRESS: === Extracting elution groups 0 to 25400 ===
2:03:39.763545 INFO: Using classic extraction backend
2:03:39.763713 PROGRESS: Extracting batch of 50061 precursors
2:03:39.763781 INFO: === Search parameters used ===
2:03:39.763828 INFO: rt_error       : 246.69811418250234
2:03:39.763868 INFO: mobility_error : 0.07469232689620144
2:03:39.763906 INFO: num_candidates : 3
2:03:39.763945 INFO: ms1_error      : 8.670566519129505
2:03:39.763984 INFO: ms2_error      : 9.845600665465446
2:03:39.764021 INFO: fwhm_rt        : 2.5308480262756348
2:03:39.764059 INFO: quant_window   : 3
2:03:39.764097 INFO: ==============================================
2:03:39.776573 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:03:39.776672 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:03:39.776719 INFO: FWHM in RT is 2.53 seconds, sigma is 0.56
2:03:39.776742 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.45
2:03:39.785460 INFO: Starting candidate selection
2:04:05.587361 INFO: Starting candidate scoring
2:04:09.686538 INFO: Finished candidate processing
2:04:09.686700 INFO: Collecting candidate features
2:04:09.888217 WARNING: intensity_correlation has 80 NaNs ( 0.06 % out of 130068)
2:04:09.888547 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 130068)
2:04:09.896083 INFO: Collecting fragment features
2:04:09.967556 INFO: Finished candidate scoring
2:04:10.039819 INFO: performing precursor FDR with 47 features
2:04:10.039932 INFO: Decoy channel: -1
2:04:10.039958 INFO: Competetive: True
2:04:10.074491 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:10.095565 WARNING: dropped 40 target PSMs due to missing features
2:04:10.095690 WARNING: dropped 45 decoy PSMs due to missing features
2:04:10.115011 INFO: Using random state 123281 for train-test-split
2:04:12.241477 INFO: Test AUC: 0.561
2:04:12.241593 INFO: Train AUC: 0.593
2:04:12.241624 INFO: AUC difference: 5.42%
2:04:12.241646 WARNING: AUC difference > 5%. This may indicate overfitting.
2:04:12.507998 INFO: Resetting torch num_threads to 80
2:04:12.510991 PROGRESS: === Extracted 130068 precursors and 1199031 fragments ===
2:04:12.511505 INFO: === FDR correction performed with classifier version 24 ===
2:04:12.515078 PROGRESS: ============================= Precursor FDR =============================
2:04:12.515190 PROGRESS: Total precursors accumulated: 23,919
2:04:12.515251 PROGRESS: Target precursors: 14,750 (61.67%)
2:04:12.515301 PROGRESS: Decoy precursors: 9,169 (38.33%)
2:04:12.515345 PROGRESS: 
2:04:12.515387 PROGRESS: Precursor Summary:
2:04:12.516502 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   230; 0.001 FDR:   202
2:04:12.516592 PROGRESS: 
2:04:12.516656 PROGRESS: Protein Summary:
2:04:12.517883 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   225; 0.001 FDR:   197
2:04:12.517978 PROGRESS: =========================================================================
2:04:12.518999 INFO: Target number of precursors reached.
2:04:12.597651 INFO: fragments_df: keeping 3137 of 1199031 [sum(precursor_idx_mask)=7013 sum(mass_error_mask)=1199027 stop_rank=3137
2:04:12.801902 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:04:13.738370 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:13.856472 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:04:13.974910 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:14.388182 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:14.388782 INFO: Using score_cutoff 43.64066073188782 (fac=0.99, q=1)
2:04:14.389087 INFO: Updating optimization_manager: fwhm_rt             : 2.5308480262756348 -> 2.5418572425842285
2:04:14.389166 INFO: Updating optimization_manager: fwhm_mobility       : 0.007441982626914978 -> 0.007638458628207445
2:04:14.389219 INFO: Updating optimization_manager: score_cutoff        : 40.17436231613159 -> 43.64066073188782
2:04:14.389271 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:04:14.397095 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:14.427171 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:04:14.434976 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:14.497056 INFO: === checking if optimization conditions were reached ===
2:04:14.497283 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2:04:14.499026 INFO: Updating optimization_manager: mobility_error      : 0.07469232689620144 -> 0.056761165190869316
2:04:14.499123 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0568.
2:04:14.499187 INFO: ==============================================
2:04:14.499253 INFO: Starting optimization step 2.
2:04:14.499307 PROGRESS: === Extracting elution groups 0 to 25400 ===
2:04:14.499360 INFO: Using classic extraction backend
2:04:14.499490 PROGRESS: Extracting batch of 50061 precursors
2:04:14.499555 INFO: === Search parameters used ===
2:04:14.499600 INFO: rt_error       : 246.69811418250234
2:04:14.499641 INFO: mobility_error : 0.056761165190869316
2:04:14.499680 INFO: num_candidates : 3
2:04:14.499720 INFO: ms1_error      : 8.670566519129505
2:04:14.499759 INFO: ms2_error      : 9.845600665465446
2:04:14.499796 INFO: fwhm_rt        : 2.5418572425842285
2:04:14.499835 INFO: quant_window   : 3
2:04:14.499873 INFO: ==============================================
2:04:14.527388 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:04:14.527488 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:04:14.527530 INFO: FWHM in RT is 2.54 seconds, sigma is 0.56
2:04:14.527552 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.54
2:04:14.528344 INFO: Starting candidate selection
2:04:32.590241 INFO: Starting candidate scoring
2:04:36.666631 INFO: Finished candidate processing
2:04:36.666796 INFO: Collecting candidate features
2:04:36.869155 WARNING: intensity_correlation has 86 NaNs ( 0.07 % out of 127136)
2:04:36.869483 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 127136)
2:04:36.876993 INFO: Collecting fragment features
2:04:36.946512 INFO: Finished candidate scoring
2:04:37.017255 INFO: performing precursor FDR with 47 features
2:04:37.017366 INFO: Decoy channel: -1
2:04:37.017392 INFO: Competetive: True
2:04:37.052906 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:37.074337 WARNING: dropped 37 target PSMs due to missing features
2:04:37.074463 WARNING: dropped 53 decoy PSMs due to missing features
2:04:37.093086 INFO: Using random state 123281 for train-test-split
2:04:39.229903 INFO: Test AUC: 0.558
2:04:39.230045 INFO: Train AUC: 0.594
2:04:39.230078 INFO: AUC difference: 6.11%
2:04:39.230112 WARNING: AUC difference > 5%. This may indicate overfitting.
2:04:39.505200 INFO: Resetting torch num_threads to 80
2:04:39.508370 PROGRESS: === Extracted 127136 precursors and 1154065 fragments ===
2:04:39.508901 INFO: === FDR correction performed with classifier version 24 ===
2:04:39.512731 PROGRESS: ============================= Precursor FDR =============================
2:04:39.512846 PROGRESS: Total precursors accumulated: 23,429
2:04:39.512908 PROGRESS: Target precursors: 14,522 (61.98%)
2:04:39.512983 PROGRESS: Decoy precursors: 8,907 (38.02%)
2:04:39.513033 PROGRESS: 
2:04:39.513080 PROGRESS: Precursor Summary:
2:04:39.514265 PROGRESS: Channel   0:	 0.050 FDR:   387; 0.010 FDR:   226; 0.001 FDR:   158
2:04:39.514358 PROGRESS: 
2:04:39.514413 PROGRESS: Protein Summary:
2:04:39.515641 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   220; 0.001 FDR:   154
2:04:39.515731 PROGRESS: =========================================================================
2:04:39.517348 INFO: Target number of precursors reached.
2:04:39.596031 INFO: fragments_df: keeping 2977 of 1154065 [sum(precursor_idx_mask)=6733 sum(mass_error_mask)=1154055 stop_rank=2977
2:04:39.839264 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:04:39.959515 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:40.077685 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:04:40.192742 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:40.585052 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:40.585495 INFO: Using score_cutoff 33.34941555976868 (fac=0.99, q=1)
2:04:40.585875 INFO: Updating optimization_manager: fwhm_rt             : 2.5418572425842285 -> 2.567115545272827
2:04:40.585953 INFO: Updating optimization_manager: fwhm_mobility       : 0.007638458628207445 -> 0.007596245035529137
2:04:40.586007 INFO: Updating optimization_manager: score_cutoff        : 43.64066073188782 -> 33.34941555976868
2:04:40.586073 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:04:40.593500 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:40.624405 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:04:40.632237 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:40.693871 INFO: === checking if optimization conditions were reached ===
2:04:40.694159 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2:04:40.695387 INFO: Updating optimization_manager: mobility_error      : 0.056761165190869316 -> 0.1
2:04:40.695524 INFO: Updating optimization_manager: classifier_version  : 24 -> 27
2:04:40.695628 INFO: Updating optimization_manager: score_cutoff        : 33.34941555976868 -> 40.17436231613159
2:04:40.695725 INFO: Updating optimization_manager: fwhm_rt             : 2.567115545272827 -> 2.5308480262756348
2:04:40.695820 INFO: Updating optimization_manager: fwhm_mobility       : 0.007596245035529137 -> 0.007441982626914978
2:04:40.695918 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
2:04:40.695988 INFO: ==============================================
2:04:40.696080 PROGRESS: Optimization finished for mobility_error.
2:04:40.842624 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:04:40.850535 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:40.880975 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:04:40.888736 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:40.980689 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:04:40.980918 PROGRESS: ==============================================
2:04:40.981018 PROGRESS: ms2_error      : 9.8456
2:04:40.981085 PROGRESS: rt_error       : 246.6981
2:04:40.981147 PROGRESS: ms1_error      : 8.6706
2:04:40.981202 PROGRESS: mobility_error : 0.1000
2:04:40.981254 PROGRESS: ==============================================
2:04:40.984840 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:04:42.664251 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:50.226443 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:04:52.087457 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:08.245929 INFO: Using classic extraction backend
2:05:08.246905 PROGRESS: Extracting batch of 12073114 precursors
2:05:08.247015 INFO: === Search parameters used ===
2:05:08.247069 INFO: rt_error       : 246.69811418250234
2:05:08.247116 INFO: mobility_error : 0.1
2:05:08.247164 INFO: num_candidates : 3
2:05:08.247210 INFO: ms1_error      : 8.670566519129505
2:05:08.247253 INFO: ms2_error      : 9.845600665465446
2:05:08.247294 INFO: fwhm_rt        : 2.5308480262756348
2:05:08.247338 INFO: quant_window   : 3
2:05:08.247383 INFO: ==============================================
2:05:10.924376 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:05:10.924619 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:05:10.924684 INFO: FWHM in RT is 2.53 seconds, sigma is 0.56
2:05:10.924710 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.45
2:05:10.931718 INFO: Starting candidate selection
4:01:36.190375 INFO: Removed 24527196 precursors with score below cutoff 40.17436231613159
4:01:39.675667 INFO: Starting candidate scoring
4:06:02.170841 INFO: Finished candidate processing
4:06:02.171336 INFO: Collecting candidate features
4:06:18.374518 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 9176464)
4:06:18.684023 INFO: Collecting fragment features
4:06:25.758693 INFO: Finished candidate scoring
4:06:35.830227 INFO: === Performing FDR correction with classifier version 27 ===
4:06:35.837260 INFO: performing precursor FDR with 47 features
4:06:35.837318 INFO: Decoy channel: -1
4:06:35.837348 INFO: Competetive: True
4:06:38.302172 INFO: Setting torch num_threads to 2 for FDR classification task
4:06:39.622119 WARNING: dropped 1 target PSMs due to missing features
4:06:43.147091 INFO: Using random state 579586 for train-test-split
4:09:31.358075 INFO: Test AUC: 0.568
4:09:31.358476 INFO: Train AUC: 0.569
4:09:31.358515 INFO: AUC difference: 0.10%
4:09:34.069420 INFO: Resetting torch num_threads to 80
4:09:34.398754 INFO: Removing fragments below FDR threshold
4:09:35.303848 PROGRESS: ============================= Precursor FDR =============================
4:09:35.304082 PROGRESS: Total precursors accumulated: 69,033
4:09:35.304146 PROGRESS: Target precursors: 68,350 (99.01%)
4:09:35.304197 PROGRESS: Decoy precursors: 683 (0.99%)
4:09:35.304242 PROGRESS: 
4:09:35.304285 PROGRESS: Precursor Summary:
4:09:35.328241 PROGRESS: Channel   0:	 0.050 FDR: 68,350; 0.010 FDR: 68,350; 0.001 FDR: 46,543
4:09:35.328478 PROGRESS: 
4:09:35.328540 PROGRESS: Protein Summary:
4:09:35.358983 PROGRESS: Channel   0:	 0.050 FDR: 11,007; 0.010 FDR: 11,007; 0.001 FDR: 8,676
4:09:35.359188 PROGRESS: =========================================================================
4:09:35.502807 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/psm.parquet
4:09:35.930267 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/frag.parquet
4:09:36.209604 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
4:09:36.957870 PROGRESS: 
4:09:36.958015 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
4:09:36.958087 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/figures
4:09:36.958251 INFO: Initializing TimingManager
4:09:36.958788 INFO: Initializing RawFileManager
4:09:36.958908 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:36.958966 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:36.959015 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:37.174593 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
4:09:45.833369 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
4:09:45.835505 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:45.839548 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:45.839840 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:45.840356 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:45.841677 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:45.857283 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:45.859621 INFO: Indexing quadrupole dimension
4:09:46.344498 INFO: Transposing detector events
4:09:55.275626 INFO: Finished transposing data
4:09:55.314592 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:09:55.316311 INFO: RT (min)            : 0.0 - 70.0
4:09:55.316428 INFO: RT duration (sec)   : 4199.8
4:09:55.316489 INFO: RT duration (min)   : 70.0
4:09:55.316537 INFO: Cycle len (scans)   : 9
4:09:55.316583 INFO: Cycle len (sec)     : 0.97
4:09:55.316628 INFO: Number of cycles    : 4347
4:09:55.316672 INFO: MS2 range (m/z)     : 400.0 - 1000.0
4:09:55.316802 INFO: Creating DIA data object took: 18.357895612716675
4:09:56.917894 INFO: Initializing CalibrationManager
4:09:56.918193 INFO: Setting up calibration estimators ..
4:09:56.918262 INFO: Found 1 estimator(s) in calibration group 'fragment'
4:09:56.918347 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'}' ..
4:09:56.918483 INFO: Found 3 estimator(s) in calibration group 'precursor'
4:09:56.918545 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'}' ..
4:09:56.918607 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}}' ..
4:09:56.918672 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}}' ..
4:09:56.918727 INFO: Done setting up calibration estimators.
4:09:56.918866 INFO: Initializing OptimizationManager
4:09:56.918974 INFO: initial parameter: ms1_error = 30
4:09:56.919021 INFO: initial parameter: ms2_error = 30
4:09:56.919066 INFO: initial parameter: rt_error = 2099.894844
4:09:56.919106 INFO: initial parameter: mobility_error = 0.1
4:09:56.919146 INFO: initial parameter: num_candidates = 1
4:09:56.919184 INFO: initial parameter: fwhm_rt = 5
4:09:56.919228 INFO: initial parameter: fwhm_mobility = 0.01
4:09:56.919269 INFO: initial parameter: score_cutoff = 0
4:09:56.919311 INFO: initial parameter: classifier_version = -1
4:09:56.919391 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
4:09:56.919697 INFO: FDRManager: loading saved state not requested, will be initialized.
4:09:56.919732 INFO: Initializing FDRManager
4:09:56.919777 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
4:09:58.137580 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
4:09:58.933193 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
4:09:58.933533 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 2099.894844
4:09:58.933722 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
4:09:58.933905 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
4:09:58.934003 PROGRESS: Starting initial search for precursors.
4:09:58.934086 INFO: Starting optimization step 0.
4:09:58.934147 PROGRESS: === Extracting elution groups 0 to 200 ===
4:09:58.934228 INFO: Using classic extraction backend
4:09:58.934477 PROGRESS: Extracting batch of 390 precursors
4:09:58.934550 INFO: === Search parameters used ===
4:09:58.934598 INFO: rt_error       : 2099.894844
4:09:58.934644 INFO: mobility_error : 0.1
4:09:58.934685 INFO: num_candidates : 1
4:09:58.934725 INFO: ms1_error      : 30
4:09:58.934764 INFO: ms2_error      : 30
4:09:58.934802 INFO: fwhm_rt        : 5
4:09:58.934839 INFO: quant_window   : 3
4:09:58.934877 INFO: ==============================================
4:09:58.935719 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:09:58.935763 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:09:58.935797 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:09:58.935818 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:09:58.942616 INFO: Starting candidate selection
4:10:02.922265 INFO: Starting candidate scoring
4:10:02.990605 INFO: Finished candidate processing
4:10:02.990702 INFO: Collecting candidate features
4:10:02.996851 WARNING: intensity_correlation has 1 NaNs ( 0.28 % out of 363)
4:10:03.000136 INFO: Collecting fragment features
4:10:03.002270 INFO: Finished candidate scoring
4:10:03.003083 INFO: performing precursor FDR with 47 features
4:10:03.003125 INFO: Decoy channel: -1
4:10:03.003149 INFO: Competetive: True
4:10:03.004308 INFO: Setting torch num_threads to 2 for FDR classification task
4:10:03.005432 WARNING: dropped 1 decoy PSMs due to missing features
4:10:03.007027 INFO: Using random state 239430 for train-test-split
4:10:03.015729 INFO: Test AUC: 0.348
4:10:03.015785 INFO: Train AUC: 0.550
4:10:03.015815 INFO: AUC difference: 36.63%
4:10:03.015838 WARNING: AUC difference > 5%. This may indicate overfitting.
4:10:03.234965 INFO: Resetting torch num_threads to 80
4:10:03.235425 PROGRESS: === Extracted 363 precursors and 3948 fragments ===
4:10:03.235834 INFO: === FDR correction performed with classifier version -1 ===
4:10:03.236356 PROGRESS: ============================= Precursor FDR =============================
4:10:03.236444 PROGRESS: Total precursors accumulated: 187
4:10:03.236503 PROGRESS: Target precursors: 115 (61.50%)
4:10:03.236553 PROGRESS: Decoy precursors: 72 (38.50%)
4:10:03.236598 PROGRESS: 
4:10:03.236642 PROGRESS: Precursor Summary:
4:10:03.237524 PROGRESS: Channel   0:	 0.050 FDR:    61; 0.010 FDR:    61; 0.001 FDR:    61
4:10:03.237615 PROGRESS: 
4:10:03.237678 PROGRESS: Protein Summary:
4:10:03.238647 PROGRESS: Channel   0:	 0.050 FDR:    61; 0.010 FDR:    61; 0.001 FDR:    61
4:10:03.238736 PROGRESS: =========================================================================
4:10:03.238841 INFO: Target number of precursors not reached yet.
4:10:03.304292 INFO: Starting optimization step 1.
4:10:03.304492 PROGRESS: === Extracting elution groups 200 to 600 ===
4:10:03.304565 INFO: Using classic extraction backend
4:10:03.304681 PROGRESS: Extracting batch of 783 precursors
4:10:03.304751 INFO: === Search parameters used ===
4:10:03.304801 INFO: rt_error       : 2099.894844
4:10:03.304844 INFO: mobility_error : 0.1
4:10:03.304887 INFO: num_candidates : 1
4:10:03.304928 INFO: ms1_error      : 30
4:10:03.304980 INFO: ms2_error      : 30
4:10:03.305024 INFO: fwhm_rt        : 5
4:10:03.305066 INFO: quant_window   : 3
4:10:03.305106 INFO: ==============================================
4:10:03.305793 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:10:03.305849 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:10:03.305877 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:10:03.305899 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:10:03.306575 INFO: Starting candidate selection
4:10:09.689768 INFO: Starting candidate scoring
4:10:09.812648 INFO: Finished candidate processing
4:10:09.812787 INFO: Collecting candidate features
4:10:09.823080 INFO: Collecting fragment features
4:10:09.825472 INFO: Finished candidate scoring
4:10:09.827541 INFO: performing precursor FDR with 47 features
4:10:09.827588 INFO: Decoy channel: -1
4:10:09.827613 INFO: Competetive: True
4:10:09.830440 INFO: Setting torch num_threads to 2 for FDR classification task
4:10:09.831529 WARNING: dropped 1 decoy PSMs due to missing features
4:10:09.832338 INFO: Using random state 154474 for train-test-split
4:10:09.840115 INFO: Test AUC: 0.450
4:10:09.840170 INFO: Train AUC: 0.494
4:10:09.840199 INFO: AUC difference: 9.08%
4:10:09.840219 WARNING: AUC difference > 5%. This may indicate overfitting.
4:10:10.059624 INFO: Resetting torch num_threads to 80
4:10:10.060779 PROGRESS: === Extracted 1116 precursors and 12181 fragments ===
4:10:10.061173 INFO: === FDR correction performed with classifier version -1 ===
4:10:10.061741 PROGRESS: ============================= Precursor FDR =============================
4:10:10.061830 PROGRESS: Total precursors accumulated: 575
4:10:10.061889 PROGRESS: Target precursors: 348 (60.52%)
4:10:10.061947 PROGRESS: Decoy precursors: 227 (39.48%)
4:10:10.061996 PROGRESS: 
4:10:10.062042 PROGRESS: Precursor Summary:
4:10:10.062966 PROGRESS: Channel   0:	 0.050 FDR:   182; 0.010 FDR:   182; 0.001 FDR:   182
4:10:10.063056 PROGRESS: 
4:10:10.063111 PROGRESS: Protein Summary:
4:10:10.064151 PROGRESS: Channel   0:	 0.050 FDR:   182; 0.010 FDR:   182; 0.001 FDR:   182
4:10:10.064238 PROGRESS: =========================================================================
4:10:10.064370 INFO: Target number of precursors not reached yet.
4:10:10.133571 INFO: Starting optimization step 2.
4:10:10.133774 PROGRESS: === Extracting elution groups 600 to 1400 ===
4:10:10.133847 INFO: Using classic extraction backend
4:10:10.133966 PROGRESS: Extracting batch of 1576 precursors
4:10:10.134037 INFO: === Search parameters used ===
4:10:10.134087 INFO: rt_error       : 2099.894844
4:10:10.134130 INFO: mobility_error : 0.1
4:10:10.134172 INFO: num_candidates : 1
4:10:10.134213 INFO: ms1_error      : 30
4:10:10.134252 INFO: ms2_error      : 30
4:10:10.134290 INFO: fwhm_rt        : 5
4:10:10.134330 INFO: quant_window   : 3
4:10:10.134368 INFO: ==============================================
4:10:10.135137 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:10:10.135182 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:10:10.135210 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:10:10.135232 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:10:10.135966 INFO: Starting candidate selection
4:10:21.370486 INFO: Starting candidate scoring
4:10:21.563489 INFO: Finished candidate processing
4:10:21.563620 INFO: Collecting candidate features
4:10:21.575550 INFO: Collecting fragment features
4:10:21.578530 INFO: Finished candidate scoring
4:10:21.581277 INFO: performing precursor FDR with 47 features
4:10:21.581325 INFO: Decoy channel: -1
4:10:21.581350 INFO: Competetive: True
4:10:21.584393 INFO: Setting torch num_threads to 2 for FDR classification task
4:10:21.585631 WARNING: dropped 1 decoy PSMs due to missing features
4:10:21.586525 INFO: Using random state 309883 for train-test-split
4:10:21.597271 INFO: Test AUC: 0.498
4:10:21.597331 INFO: Train AUC: 0.496
4:10:21.597361 INFO: AUC difference: 0.38%
4:10:21.810443 INFO: Resetting torch num_threads to 80
4:10:21.812064 PROGRESS: === Extracted 2636 precursors and 28710 fragments ===
4:10:21.812473 INFO: === FDR correction performed with classifier version -1 ===
4:10:21.813150 PROGRESS: ============================= Precursor FDR =============================
4:10:21.813249 PROGRESS: Total precursors accumulated: 1,353
4:10:21.813310 PROGRESS: Target precursors: 812 (60.01%)
4:10:21.813361 PROGRESS: Decoy precursors: 541 (39.99%)
4:10:21.813405 PROGRESS: 
4:10:21.813450 PROGRESS: Precursor Summary:
4:10:21.814437 PROGRESS: Channel   0:	 0.050 FDR:   396; 0.010 FDR:   396; 0.001 FDR:   396
4:10:21.814528 PROGRESS: 
4:10:21.814582 PROGRESS: Protein Summary:
4:10:21.815745 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   390; 0.001 FDR:   390
4:10:21.815837 PROGRESS: =========================================================================
4:10:21.815981 INFO: Target number of precursors reached.
4:10:21.819993 INFO: fragments_df: keeping 835 of 28710 [sum(precursor_idx_mask)=4374 sum(mass_error_mask)=28710 stop_rank=835
4:10:21.962735 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:10:22.077213 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:10:22.186137 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:10:22.294325 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:10:22.426477 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
4:10:22.426894 INFO: Using score_cutoff 32.050540763854976 (fac=0.99, q=1)
4:10:22.427217 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.3177270889282227
4:10:22.427296 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007841719314455986
4:10:22.427350 INFO: Updating optimization_manager: score_cutoff        : 0 -> 32.050540763854976
4:10:22.427407 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:10:22.428678 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:10:22.433220 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:10:22.434194 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:10:22.438814 INFO: Updating optimization_manager: classifier_version  : -1 -> 2
4:10:22.438914 PROGRESS: Required number of precursors found. Starting search parameter optimization.
4:10:22.438989 INFO: Starting optimization step 3.
4:10:22.439047 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:10:22.439101 INFO: Using classic extraction backend
4:10:22.439206 PROGRESS: Extracting batch of 2749 precursors
4:10:22.439267 INFO: === Search parameters used ===
4:10:22.439313 INFO: rt_error       : 2099.894844
4:10:22.439355 INFO: mobility_error : 0.1
4:10:22.439395 INFO: num_candidates : 3
4:10:22.439438 INFO: ms1_error      : 30
4:10:22.439478 INFO: ms2_error      : 30
4:10:22.439528 INFO: fwhm_rt        : 3.3177270889282227
4:10:22.439569 INFO: quant_window   : 3
4:10:22.439607 INFO: ==============================================
4:10:22.440733 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:10:22.440778 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:10:22.440812 INFO: FWHM in RT is 3.32 seconds, sigma is 0.73
4:10:22.440834 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.64
4:10:22.441459 INFO: Starting candidate selection
4:10:42.801605 INFO: Starting candidate scoring
4:10:43.503829 INFO: Finished candidate processing
4:10:43.503922 INFO: Collecting candidate features
4:10:43.526022 INFO: Collecting fragment features
4:10:43.534921 INFO: Finished candidate scoring
4:10:43.538571 INFO: performing precursor FDR with 47 features
4:10:43.538626 INFO: Decoy channel: -1
4:10:43.538650 INFO: Competetive: True
4:10:43.543310 INFO: Setting torch num_threads to 2 for FDR classification task
4:10:43.546474 INFO: Using random state 617692 for train-test-split
4:10:43.563880 INFO: Test AUC: 0.497
4:10:43.563954 INFO: Train AUC: 0.487
4:10:43.563986 INFO: AUC difference: 1.96%
4:10:43.783935 INFO: Resetting torch num_threads to 80
4:10:43.784621 PROGRESS: === Extracted 7570 precursors and 82769 fragments ===
4:10:43.785090 INFO: === FDR correction performed with classifier version 2 ===
4:10:43.785816 PROGRESS: ============================= Precursor FDR =============================
4:10:43.785904 PROGRESS: Total precursors accumulated: 1,375
4:10:43.785975 PROGRESS: Target precursors: 875 (63.64%)
4:10:43.786026 PROGRESS: Decoy precursors: 500 (36.36%)
4:10:43.786072 PROGRESS: 
4:10:43.786116 PROGRESS: Precursor Summary:
4:10:43.787165 PROGRESS: Channel   0:	 0.050 FDR:   602; 0.010 FDR:   602; 0.001 FDR:   602
4:10:43.787253 PROGRESS: 
4:10:43.787308 PROGRESS: Protein Summary:
4:10:43.788591 PROGRESS: Channel   0:	 0.050 FDR:   591; 0.010 FDR:   591; 0.001 FDR:   591
4:10:43.788679 PROGRESS: =========================================================================
4:10:43.788978 INFO: Target number of precursors reached.
4:10:43.799089 INFO: fragments_df: keeping 3763 of 82769 [sum(precursor_idx_mask)=19027 sum(mass_error_mask)=82769 stop_rank=3763
4:10:43.898617 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:10:44.014581 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:10:44.134300 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:10:44.249903 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:10:44.673248 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:10:44.673679 INFO: Using score_cutoff 36.641929178237916 (fac=0.99, q=1)
4:10:44.674013 INFO: Updating optimization_manager: fwhm_rt             : 3.3177270889282227 -> 3.220033645629883
4:10:44.674091 INFO: Updating optimization_manager: fwhm_mobility       : 0.007841719314455986 -> 0.007771600037813187
4:10:44.674145 INFO: Updating optimization_manager: score_cutoff        : 32.050540763854976 -> 36.641929178237916
4:10:44.674202 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:10:44.675255 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:10:44.676569 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:10:44.677346 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:10:44.679444 INFO: === checking if optimization conditions were reached ===
4:10:44.679545 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
4:10:44.681313 INFO: Updating optimization_manager: ms2_error           : 30 -> 24.37390675904184
4:10:44.681412 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 24.3739.
4:10:44.681480 INFO: ==============================================
4:10:44.681547 INFO: Starting optimization step 4.
4:10:44.681604 PROGRESS: === Extracting elution groups 0 to 600 ===
4:10:44.681662 INFO: Using classic extraction backend
4:10:44.681829 PROGRESS: Extracting batch of 1173 precursors
4:10:44.681897 INFO: === Search parameters used ===
4:10:44.681944 INFO: rt_error       : 2099.894844
4:10:44.681985 INFO: mobility_error : 0.1
4:10:44.682026 INFO: num_candidates : 3
4:10:44.682066 INFO: ms1_error      : 30
4:10:44.682106 INFO: ms2_error      : 24.37390675904184
4:10:44.682145 INFO: fwhm_rt        : 3.220033645629883
4:10:44.682185 INFO: quant_window   : 3
4:10:44.682223 INFO: ==============================================
4:10:44.683150 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:10:44.683195 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:10:44.683235 INFO: FWHM in RT is 3.22 seconds, sigma is 0.71
4:10:44.683259 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.60
4:10:44.683942 INFO: Starting candidate selection
4:10:53.969124 INFO: Starting candidate scoring
4:10:54.248426 INFO: Finished candidate processing
4:10:54.248550 INFO: Collecting candidate features
4:10:54.266339 INFO: Collecting fragment features
4:10:54.271369 INFO: Finished candidate scoring
4:10:54.273145 INFO: performing precursor FDR with 47 features
4:10:54.273188 INFO: Decoy channel: -1
4:10:54.273211 INFO: Competetive: True
4:10:54.275995 INFO: Setting torch num_threads to 2 for FDR classification task
4:10:54.278283 INFO: Using random state 617692 for train-test-split
4:10:54.288792 INFO: Test AUC: 0.450
4:10:54.288854 INFO: Train AUC: 0.483
4:10:54.288884 INFO: AUC difference: 6.69%
4:10:54.288916 WARNING: AUC difference > 5%. This may indicate overfitting.
4:10:54.498184 INFO: Resetting torch num_threads to 80
4:10:54.498699 PROGRESS: === Extracted 3215 precursors and 34755 fragments ===
4:10:54.499098 INFO: === FDR correction performed with classifier version 2 ===
4:10:54.499660 PROGRESS: ============================= Precursor FDR =============================
4:10:54.499744 PROGRESS: Total precursors accumulated: 586
4:10:54.499802 PROGRESS: Target precursors: 375 (63.99%)
4:10:54.499851 PROGRESS: Decoy precursors: 211 (36.01%)
4:10:54.499897 PROGRESS: 
4:10:54.499940 PROGRESS: Precursor Summary:
4:10:54.500881 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   273; 0.001 FDR:   273
4:10:54.500979 PROGRESS: 
4:10:54.501035 PROGRESS: Protein Summary:
4:10:54.502127 PROGRESS: Channel   0:	 0.050 FDR:   269; 0.010 FDR:   269; 0.001 FDR:   269
4:10:54.502223 PROGRESS: =========================================================================
4:10:54.502408 INFO: Target number of precursors reached.
4:10:54.507630 INFO: fragments_df: keeping 1568 of 34755 [sum(precursor_idx_mask)=8485 sum(mass_error_mask)=34755 stop_rank=1568
4:10:54.606324 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:10:54.706537 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:10:54.804868 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:10:54.903960 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:10:55.082787 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:10:55.083202 INFO: Using score_cutoff 34.57095967254639 (fac=0.99, q=1)
4:10:55.083501 INFO: Updating optimization_manager: fwhm_rt             : 3.220033645629883 -> 3.1179845333099365
4:10:55.083580 INFO: Updating optimization_manager: fwhm_mobility       : 0.007771600037813187 -> 0.007151697296649218
4:10:55.083635 INFO: Updating optimization_manager: score_cutoff        : 36.641929178237916 -> 34.57095967254639
4:10:55.083686 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:10:55.084724 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:10:55.086047 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:10:55.086808 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:10:55.088865 INFO: === checking if optimization conditions were reached ===
4:10:55.088981 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
4:10:55.090607 INFO: Updating optimization_manager: ms2_error           : 24.37390675904184 -> 19.28368564618476
4:10:55.090705 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 19.2837.
4:10:55.090769 INFO: ==============================================
4:10:55.090834 INFO: Starting optimization step 5.
4:10:55.090890 PROGRESS: === Extracting elution groups 0 to 600 ===
4:10:55.090949 INFO: Using classic extraction backend
4:10:55.091074 PROGRESS: Extracting batch of 1173 precursors
4:10:55.091140 INFO: === Search parameters used ===
4:10:55.091187 INFO: rt_error       : 2099.894844
4:10:55.091230 INFO: mobility_error : 0.1
4:10:55.091272 INFO: num_candidates : 3
4:10:55.091311 INFO: ms1_error      : 30
4:10:55.091350 INFO: ms2_error      : 19.28368564618476
4:10:55.091389 INFO: fwhm_rt        : 3.1179845333099365
4:10:55.091428 INFO: quant_window   : 3
4:10:55.091466 INFO: ==============================================
4:10:55.092234 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:10:55.092278 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:10:55.092310 INFO: FWHM in RT is 3.12 seconds, sigma is 0.69
4:10:55.092331 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.32
4:10:55.092967 INFO: Starting candidate selection
4:11:03.661628 INFO: Starting candidate scoring
4:11:03.943179 INFO: Finished candidate processing
4:11:03.943313 INFO: Collecting candidate features
4:11:03.957208 INFO: Collecting fragment features
4:11:03.960819 INFO: Finished candidate scoring
4:11:03.962595 INFO: performing precursor FDR with 47 features
4:11:03.962639 INFO: Decoy channel: -1
4:11:03.962663 INFO: Competetive: True
4:11:03.965504 INFO: Setting torch num_threads to 2 for FDR classification task
4:11:03.967452 INFO: Using random state 617692 for train-test-split
4:11:03.977456 INFO: Test AUC: 0.476
4:11:03.977513 INFO: Train AUC: 0.477
4:11:03.977544 INFO: AUC difference: 0.24%
4:11:04.188605 INFO: Resetting torch num_threads to 80
4:11:04.189131 PROGRESS: === Extracted 3241 precursors and 34519 fragments ===
4:11:04.189537 INFO: === FDR correction performed with classifier version 2 ===
4:11:04.190097 PROGRESS: ============================= Precursor FDR =============================
4:11:04.190181 PROGRESS: Total precursors accumulated: 587
4:11:04.190238 PROGRESS: Target precursors: 360 (61.33%)
4:11:04.190293 PROGRESS: Decoy precursors: 227 (38.67%)
4:11:04.190338 PROGRESS: 
4:11:04.190380 PROGRESS: Precursor Summary:
4:11:04.191310 PROGRESS: Channel   0:	 0.050 FDR:   264; 0.010 FDR:   264; 0.001 FDR:   264
4:11:04.191397 PROGRESS: 
4:11:04.191453 PROGRESS: Protein Summary:
4:11:04.192542 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   263; 0.001 FDR:   263
4:11:04.192630 PROGRESS: =========================================================================
4:11:04.192756 INFO: Target number of precursors reached.
4:11:04.197659 INFO: fragments_df: keeping 1418 of 34519 [sum(precursor_idx_mask)=8157 sum(mass_error_mask)=34519 stop_rank=1418
4:11:04.315290 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:11:04.417972 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:11:04.515504 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:11:04.615513 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:11:04.795267 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:11:04.795670 INFO: Using score_cutoff 35.645341439437864 (fac=0.99, q=1)
4:11:04.795969 INFO: Updating optimization_manager: fwhm_rt             : 3.1179845333099365 -> 2.9569640159606934
4:11:04.796046 INFO: Updating optimization_manager: fwhm_mobility       : 0.007151697296649218 -> 0.006427520886063576
4:11:04.796098 INFO: Updating optimization_manager: score_cutoff        : 34.57095967254639 -> 35.645341439437864
4:11:04.796150 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:11:04.797203 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:11:04.798516 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:11:04.799276 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:11:04.801364 INFO: === checking if optimization conditions were reached ===
4:11:04.801459 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
4:11:04.803048 INFO: Updating optimization_manager: ms2_error           : 19.28368564618476 -> 15.758386540499925
4:11:04.803145 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 15.7584.
4:11:04.803208 INFO: ==============================================
4:11:04.803271 INFO: Starting optimization step 6.
4:11:04.803326 PROGRESS: === Extracting elution groups 0 to 600 ===
4:11:04.803378 INFO: Using classic extraction backend
4:11:04.803478 PROGRESS: Extracting batch of 1173 precursors
4:11:04.803538 INFO: === Search parameters used ===
4:11:04.803584 INFO: rt_error       : 2099.894844
4:11:04.803625 INFO: mobility_error : 0.1
4:11:04.803665 INFO: num_candidates : 3
4:11:04.803706 INFO: ms1_error      : 30
4:11:04.803744 INFO: ms2_error      : 15.758386540499925
4:11:04.803784 INFO: fwhm_rt        : 2.9569640159606934
4:11:04.803822 INFO: quant_window   : 3
4:11:04.803866 INFO: ==============================================
4:11:04.804726 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:11:04.804770 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:11:04.804802 INFO: FWHM in RT is 2.96 seconds, sigma is 0.65
4:11:04.804823 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.98
4:11:04.805624 INFO: Starting candidate selection
4:11:14.076475 INFO: Starting candidate scoring
4:11:14.311081 INFO: Finished candidate processing
4:11:14.311211 INFO: Collecting candidate features
4:11:14.325859 INFO: Collecting fragment features
4:11:14.332672 INFO: Finished candidate scoring
4:11:14.334513 INFO: performing precursor FDR with 47 features
4:11:14.334557 INFO: Decoy channel: -1
4:11:14.334582 INFO: Competetive: True
4:11:14.337384 INFO: Setting torch num_threads to 2 for FDR classification task
4:11:14.339360 INFO: Using random state 617692 for train-test-split
4:11:14.349758 INFO: Test AUC: 0.488
4:11:14.349818 INFO: Train AUC: 0.479
4:11:14.349846 INFO: AUC difference: 1.77%
4:11:14.566472 INFO: Resetting torch num_threads to 80
4:11:14.566993 PROGRESS: === Extracted 3229 precursors and 33824 fragments ===
4:11:14.567389 INFO: === FDR correction performed with classifier version 2 ===
4:11:14.567943 PROGRESS: ============================= Precursor FDR =============================
4:11:14.568030 PROGRESS: Total precursors accumulated: 587
4:11:14.568088 PROGRESS: Target precursors: 372 (63.37%)
4:11:14.568136 PROGRESS: Decoy precursors: 215 (36.63%)
4:11:14.568180 PROGRESS: 
4:11:14.568223 PROGRESS: Precursor Summary:
4:11:14.569175 PROGRESS: Channel   0:	 0.050 FDR:   255; 0.010 FDR:   255; 0.001 FDR:   255
4:11:14.569264 PROGRESS: 
4:11:14.569318 PROGRESS: Protein Summary:
4:11:14.570376 PROGRESS: Channel   0:	 0.050 FDR:   254; 0.010 FDR:   254; 0.001 FDR:   254
4:11:14.570467 PROGRESS: =========================================================================
4:11:14.570602 INFO: Target number of precursors reached.
4:11:14.575234 INFO: fragments_df: keeping 1307 of 33824 [sum(precursor_idx_mask)=7628 sum(mass_error_mask)=33824 stop_rank=1307
4:11:14.676561 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:11:14.779130 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:11:14.876761 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:11:14.986506 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:11:15.180468 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:11:15.180920 INFO: Using score_cutoff 34.07248388671875 (fac=0.99, q=1)
4:11:15.181270 INFO: Updating optimization_manager: fwhm_rt             : 2.9569640159606934 -> 2.7691192626953125
4:11:15.181350 INFO: Updating optimization_manager: fwhm_mobility       : 0.006427520886063576 -> 0.005669185891747475
4:11:15.181404 INFO: Updating optimization_manager: score_cutoff        : 35.645341439437864 -> 34.07248388671875
4:11:15.181461 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:11:15.182547 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:11:15.183900 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:11:15.184705 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:11:15.187793 INFO: === checking if optimization conditions were reached ===
4:11:15.187893 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
4:11:15.189701 INFO: Updating optimization_manager: ms2_error           : 15.758386540499925 -> 13.326582126215774
4:11:15.189802 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 13.3266.
4:11:15.189885 INFO: ==============================================
4:11:15.189955 INFO: Starting optimization step 7.
4:11:15.190017 PROGRESS: === Extracting elution groups 0 to 600 ===
4:11:15.190070 INFO: Using classic extraction backend
4:11:15.190175 PROGRESS: Extracting batch of 1173 precursors
4:11:15.190256 INFO: === Search parameters used ===
4:11:15.190321 INFO: rt_error       : 2099.894844
4:11:15.190367 INFO: mobility_error : 0.1
4:11:15.190408 INFO: num_candidates : 3
4:11:15.190447 INFO: ms1_error      : 30
4:11:15.190485 INFO: ms2_error      : 13.326582126215774
4:11:15.190525 INFO: fwhm_rt        : 2.7691192626953125
4:11:15.190562 INFO: quant_window   : 3
4:11:15.190607 INFO: ==============================================
4:11:15.191597 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:11:15.191644 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:11:15.191678 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
4:11:15.191700 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.63
4:11:15.192420 INFO: Starting candidate selection
4:11:24.640451 INFO: Starting candidate scoring
4:11:24.839278 INFO: Finished candidate processing
4:11:24.839370 INFO: Collecting candidate features
4:11:24.853127 INFO: Collecting fragment features
4:11:24.857163 INFO: Finished candidate scoring
4:11:24.858948 INFO: performing precursor FDR with 47 features
4:11:24.858989 INFO: Decoy channel: -1
4:11:24.859013 INFO: Competetive: True
4:11:24.863498 INFO: Setting torch num_threads to 2 for FDR classification task
4:11:24.865902 INFO: Using random state 617692 for train-test-split
4:11:24.876855 INFO: Test AUC: 0.473
4:11:24.876911 INFO: Train AUC: 0.481
4:11:24.876950 INFO: AUC difference: 1.67%
4:11:25.950363 INFO: Resetting torch num_threads to 80
4:11:25.950900 PROGRESS: === Extracted 3231 precursors and 33232 fragments ===
4:11:25.951311 INFO: === FDR correction performed with classifier version 2 ===
4:11:25.951887 PROGRESS: ============================= Precursor FDR =============================
4:11:25.951977 PROGRESS: Total precursors accumulated: 585
4:11:25.952035 PROGRESS: Target precursors: 373 (63.76%)
4:11:25.952084 PROGRESS: Decoy precursors: 212 (36.24%)
4:11:25.952127 PROGRESS: 
4:11:25.952170 PROGRESS: Precursor Summary:
4:11:25.953114 PROGRESS: Channel   0:	 0.050 FDR:   261; 0.010 FDR:   261; 0.001 FDR:   261
4:11:25.953204 PROGRESS: 
4:11:25.953259 PROGRESS: Protein Summary:
4:11:25.954346 PROGRESS: Channel   0:	 0.050 FDR:   259; 0.010 FDR:   259; 0.001 FDR:   259
4:11:25.954434 PROGRESS: =========================================================================
4:11:25.954570 INFO: Target number of precursors reached.
4:11:25.959246 INFO: fragments_df: keeping 1304 of 33232 [sum(precursor_idx_mask)=7673 sum(mass_error_mask)=33232 stop_rank=1304
4:11:26.058041 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:11:26.157776 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:11:26.255251 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:11:26.351232 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:11:26.512773 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:11:26.513199 INFO: Using score_cutoff 31.456932014465334 (fac=0.99, q=1)
4:11:26.513512 INFO: Updating optimization_manager: fwhm_rt             : 2.7691192626953125 -> 2.6715915203094482
4:11:26.513591 INFO: Updating optimization_manager: fwhm_mobility       : 0.005669185891747475 -> 0.005252755247056484
4:11:26.513647 INFO: Updating optimization_manager: score_cutoff        : 34.07248388671875 -> 31.456932014465334
4:11:26.513699 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:11:26.514759 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:11:26.516088 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:11:26.516863 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:11:26.518928 INFO: === checking if optimization conditions were reached ===
4:11:26.519026 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
4:11:26.520674 INFO: Updating optimization_manager: ms2_error           : 13.326582126215774 -> 11.449981755899785
4:11:26.520790 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 11.4500.
4:11:26.520858 INFO: ==============================================
4:11:26.520931 INFO: Starting optimization step 8.
4:11:26.521011 PROGRESS: === Extracting elution groups 0 to 600 ===
4:11:26.521066 INFO: Using classic extraction backend
4:11:26.521200 PROGRESS: Extracting batch of 1173 precursors
4:11:26.521278 INFO: === Search parameters used ===
4:11:26.521816 INFO: rt_error       : 2099.894844
4:11:26.521861 INFO: mobility_error : 0.1
4:11:26.521901 INFO: num_candidates : 3
4:11:26.521940 INFO: ms1_error      : 30
4:11:26.521979 INFO: ms2_error      : 11.449981755899785
4:11:26.522017 INFO: fwhm_rt        : 2.6715915203094482
4:11:26.522056 INFO: quant_window   : 3
4:11:26.522094 INFO: ==============================================
4:11:26.522910 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:11:26.522955 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:11:26.522991 INFO: FWHM in RT is 2.67 seconds, sigma is 0.59
4:11:26.523013 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.44
4:11:26.523691 INFO: Starting candidate selection
4:11:34.978017 INFO: Starting candidate scoring
4:11:35.177785 INFO: Finished candidate processing
4:11:35.177917 INFO: Collecting candidate features
4:11:35.192386 INFO: Collecting fragment features
4:11:35.197650 INFO: Finished candidate scoring
4:11:35.200115 INFO: performing precursor FDR with 47 features
4:11:35.200158 INFO: Decoy channel: -1
4:11:35.200181 INFO: Competetive: True
4:11:35.203235 INFO: Setting torch num_threads to 2 for FDR classification task
4:11:35.205587 INFO: Using random state 617692 for train-test-split
4:11:35.216610 INFO: Test AUC: 0.519
4:11:35.216668 INFO: Train AUC: 0.491
4:11:35.216697 INFO: AUC difference: 5.68%
4:11:35.216718 WARNING: AUC difference > 5%. This may indicate overfitting.
4:11:35.427576 INFO: Resetting torch num_threads to 80
4:11:35.428127 PROGRESS: === Extracted 3205 precursors and 32373 fragments ===
4:11:35.428522 INFO: === FDR correction performed with classifier version 2 ===
4:11:35.429094 PROGRESS: ============================= Precursor FDR =============================
4:11:35.429181 PROGRESS: Total precursors accumulated: 584
4:11:35.429252 PROGRESS: Target precursors: 389 (66.61%)
4:11:35.429300 PROGRESS: Decoy precursors: 195 (33.39%)
4:11:35.429350 PROGRESS: 
4:11:35.429394 PROGRESS: Precursor Summary:
4:11:35.430348 PROGRESS: Channel   0:	 0.050 FDR:   272; 0.010 FDR:   272; 0.001 FDR:   272
4:11:35.430436 PROGRESS: 
4:11:35.430489 PROGRESS: Protein Summary:
4:11:35.431583 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:   270
4:11:35.431670 PROGRESS: =========================================================================
4:11:35.431798 INFO: Target number of precursors reached.
4:11:35.436434 INFO: fragments_df: keeping 1306 of 32373 [sum(precursor_idx_mask)=7847 sum(mass_error_mask)=32373 stop_rank=1306
4:11:35.535097 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:11:35.638103 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:11:35.738935 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:11:35.837933 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:11:36.001506 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:11:36.001921 INFO: Using score_cutoff 30.28695501537323 (fac=0.99, q=1)
4:11:36.002216 INFO: Updating optimization_manager: fwhm_rt             : 2.6715915203094482 -> 2.6048619747161865
4:11:36.002297 INFO: Updating optimization_manager: fwhm_mobility       : 0.005252755247056484 -> 0.004808241501450539
4:11:36.002352 INFO: Updating optimization_manager: score_cutoff        : 31.456932014465334 -> 30.28695501537323
4:11:36.002407 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:11:36.003431 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:11:36.004765 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:11:36.005542 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:11:36.007626 INFO: === checking if optimization conditions were reached ===
4:11:36.007720 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
4:11:36.009320 INFO: Updating optimization_manager: ms2_error           : 11.449981755899785 -> 10.62932191173693
4:11:36.009424 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 10.6293.
4:11:36.009511 INFO: ==============================================
4:11:36.009578 INFO: Starting optimization step 9.
4:11:36.009635 PROGRESS: === Extracting elution groups 0 to 600 ===
4:11:36.009692 INFO: Using classic extraction backend
4:11:36.009792 PROGRESS: Extracting batch of 1173 precursors
4:11:36.009854 INFO: === Search parameters used ===
4:11:36.009901 INFO: rt_error       : 2099.894844
4:11:36.009941 INFO: mobility_error : 0.1
4:11:36.009981 INFO: num_candidates : 3
4:11:36.010021 INFO: ms1_error      : 30
4:11:36.010060 INFO: ms2_error      : 10.62932191173693
4:11:36.010098 INFO: fwhm_rt        : 2.6048619747161865
4:11:36.010135 INFO: quant_window   : 3
4:11:36.010171 INFO: ==============================================
4:11:36.010950 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:11:36.010994 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:11:36.011026 INFO: FWHM in RT is 2.60 seconds, sigma is 0.57
4:11:36.011047 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.23
4:11:36.011670 INFO: Starting candidate selection
4:11:45.150193 INFO: Starting candidate scoring
4:11:45.329924 INFO: Finished candidate processing
4:11:45.330058 INFO: Collecting candidate features
4:11:45.342933 INFO: Collecting fragment features
4:11:45.347548 INFO: Finished candidate scoring
4:11:45.349568 INFO: performing precursor FDR with 47 features
4:11:45.349612 INFO: Decoy channel: -1
4:11:45.349635 INFO: Competetive: True
4:11:45.353214 INFO: Setting torch num_threads to 2 for FDR classification task
4:11:45.355165 INFO: Using random state 617692 for train-test-split
4:11:45.365322 INFO: Test AUC: 0.501
4:11:45.365380 INFO: Train AUC: 0.478
4:11:45.365409 INFO: AUC difference: 4.83%
4:11:45.579040 INFO: Resetting torch num_threads to 80
4:11:45.579576 PROGRESS: === Extracted 3233 precursors and 32241 fragments ===
4:11:45.579983 INFO: === FDR correction performed with classifier version 2 ===
4:11:45.580590 PROGRESS: ============================= Precursor FDR =============================
4:11:45.580678 PROGRESS: Total precursors accumulated: 584
4:11:45.580736 PROGRESS: Target precursors: 384 (65.75%)
4:11:45.580784 PROGRESS: Decoy precursors: 200 (34.25%)
4:11:45.580828 PROGRESS: 
4:11:45.580871 PROGRESS: Precursor Summary:
4:11:45.581832 PROGRESS: Channel   0:	 0.050 FDR:   266; 0.010 FDR:   266; 0.001 FDR:   266
4:11:45.581921 PROGRESS: 
4:11:45.581976 PROGRESS: Protein Summary:
4:11:45.583082 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   263; 0.001 FDR:   263
4:11:45.583170 PROGRESS: =========================================================================
4:11:45.583302 INFO: Target number of precursors reached.
4:11:45.587937 INFO: fragments_df: keeping 1272 of 32241 [sum(precursor_idx_mask)=7573 sum(mass_error_mask)=32241 stop_rank=1272
4:11:45.688328 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:11:45.794708 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:11:45.896591 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:11:45.996314 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:11:46.163450 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:11:46.163867 INFO: Using score_cutoff 30.12572938156128 (fac=0.99, q=1)
4:11:46.164171 INFO: Updating optimization_manager: fwhm_rt             : 2.6048619747161865 -> 2.498932123184204
4:11:46.164251 INFO: Updating optimization_manager: fwhm_mobility       : 0.004808241501450539 -> 0.004568086937069893
4:11:46.164307 INFO: Updating optimization_manager: score_cutoff        : 30.28695501537323 -> 30.12572938156128
4:11:46.164359 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:11:46.165395 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:11:46.166774 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:11:46.167534 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:11:46.169624 INFO: === checking if optimization conditions were reached ===
4:11:46.169725 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
4:11:46.171321 INFO: Updating optimization_manager: ms2_error           : 10.62932191173693 -> 9.810515608030133
4:11:46.171418 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 9.8105.
4:11:46.171481 INFO: ==============================================
4:11:46.171545 INFO: Starting optimization step 10.
4:11:46.171600 PROGRESS: === Extracting elution groups 0 to 600 ===
4:11:46.171653 INFO: Using classic extraction backend
4:11:46.171756 PROGRESS: Extracting batch of 1173 precursors
4:11:46.171819 INFO: === Search parameters used ===
4:11:46.171865 INFO: rt_error       : 2099.894844
4:11:46.171915 INFO: mobility_error : 0.1
4:11:46.171958 INFO: num_candidates : 3
4:11:46.171998 INFO: ms1_error      : 30
4:11:46.172037 INFO: ms2_error      : 9.810515608030133
4:11:46.172076 INFO: fwhm_rt        : 2.498932123184204
4:11:46.172114 INFO: quant_window   : 3
4:11:46.172152 INFO: ==============================================
4:11:46.172928 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:11:46.172985 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:11:46.173021 INFO: FWHM in RT is 2.50 seconds, sigma is 0.55
4:11:46.173043 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.12
4:11:46.174024 INFO: Starting candidate selection
4:11:55.548694 INFO: Starting candidate scoring
4:11:55.730398 INFO: Finished candidate processing
4:11:55.730580 INFO: Collecting candidate features
4:11:55.758879 INFO: Collecting fragment features
4:11:55.769670 INFO: Finished candidate scoring
4:11:55.773186 INFO: performing precursor FDR with 47 features
4:11:55.773291 INFO: Decoy channel: -1
4:11:55.773347 INFO: Competetive: True
4:11:55.780155 INFO: Setting torch num_threads to 2 for FDR classification task
4:11:55.783539 INFO: Using random state 617692 for train-test-split
4:11:55.800023 INFO: Test AUC: 0.480
4:11:55.800133 INFO: Train AUC: 0.499
4:11:55.800183 INFO: AUC difference: 3.75%
4:11:56.031872 INFO: Resetting torch num_threads to 80
4:11:56.032607 PROGRESS: === Extracted 3224 precursors and 31648 fragments ===
4:11:56.033140 INFO: === FDR correction performed with classifier version 2 ===
4:11:56.033766 PROGRESS: ============================= Precursor FDR =============================
4:11:56.033855 PROGRESS: Total precursors accumulated: 585
4:11:56.033924 PROGRESS: Target precursors: 385 (65.81%)
4:11:56.033975 PROGRESS: Decoy precursors: 200 (34.19%)
4:11:56.034019 PROGRESS: 
4:11:56.034063 PROGRESS: Precursor Summary:
4:11:56.035062 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:   265; 0.001 FDR:   265
4:11:56.035153 PROGRESS: 
4:11:56.035210 PROGRESS: Protein Summary:
4:11:56.036336 PROGRESS: Channel   0:	 0.050 FDR:   264; 0.010 FDR:   264; 0.001 FDR:   264
4:11:56.036430 PROGRESS: =========================================================================
4:11:56.036613 INFO: Target number of precursors reached.
4:11:56.041553 INFO: fragments_df: keeping 1302 of 31648 [sum(precursor_idx_mask)=7538 sum(mass_error_mask)=31648 stop_rank=1302
4:11:56.427601 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:11:56.554528 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:11:56.672826 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:11:56.774814 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:11:56.945114 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:11:56.945648 INFO: Using score_cutoff 29.25261512374878 (fac=0.99, q=1)
4:11:56.945980 INFO: Updating optimization_manager: fwhm_rt             : 2.498932123184204 -> 2.4576427936553955
4:11:56.946065 INFO: Updating optimization_manager: fwhm_mobility       : 0.004568086937069893 -> 0.004405444487929344
4:11:56.946118 INFO: Updating optimization_manager: score_cutoff        : 30.12572938156128 -> 29.25261512374878
4:11:56.946172 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:11:56.947458 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:11:56.948831 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:11:56.949619 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:11:56.951725 INFO: === checking if optimization conditions were reached ===
4:11:56.951829 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
4:11:56.953592 INFO: Updating optimization_manager: ms2_error           : 9.810515608030133 -> 9.476511420394306
4:11:56.953704 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 9.4765.
4:11:56.953780 INFO: ==============================================
4:11:56.953847 INFO: Starting optimization step 11.
4:11:56.953908 PROGRESS: === Extracting elution groups 0 to 600 ===
4:11:56.953963 INFO: Using classic extraction backend
4:11:56.954090 PROGRESS: Extracting batch of 1173 precursors
4:11:56.954154 INFO: === Search parameters used ===
4:11:56.954198 INFO: rt_error       : 2099.894844
4:11:56.954240 INFO: mobility_error : 0.1
4:11:56.954281 INFO: num_candidates : 3
4:11:56.954321 INFO: ms1_error      : 30
4:11:56.954366 INFO: ms2_error      : 9.476511420394306
4:11:56.954408 INFO: fwhm_rt        : 2.4576427936553955
4:11:56.954448 INFO: quant_window   : 3
4:11:56.954486 INFO: ==============================================
4:11:56.955444 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:11:56.955492 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:11:56.955527 INFO: FWHM in RT is 2.46 seconds, sigma is 0.54
4:11:56.955549 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.04
4:11:56.956230 INFO: Starting candidate selection
4:12:06.559185 INFO: Starting candidate scoring
4:12:06.760481 INFO: Finished candidate processing
4:12:06.760575 INFO: Collecting candidate features
4:12:06.773188 INFO: Collecting fragment features
4:12:06.778077 INFO: Finished candidate scoring
4:12:06.779863 INFO: performing precursor FDR with 47 features
4:12:06.779903 INFO: Decoy channel: -1
4:12:06.779926 INFO: Competetive: True
4:12:06.783707 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:06.786135 INFO: Using random state 617692 for train-test-split
4:12:06.797344 INFO: Test AUC: 0.499
4:12:06.797401 INFO: Train AUC: 0.492
4:12:06.797431 INFO: AUC difference: 1.48%
4:12:07.013176 INFO: Resetting torch num_threads to 80
4:12:07.013720 PROGRESS: === Extracted 3223 precursors and 31675 fragments ===
4:12:07.014186 INFO: === FDR correction performed with classifier version 2 ===
4:12:07.014761 PROGRESS: ============================= Precursor FDR =============================
4:12:07.014846 PROGRESS: Total precursors accumulated: 585
4:12:07.014905 PROGRESS: Target precursors: 387 (66.15%)
4:12:07.014955 PROGRESS: Decoy precursors: 198 (33.85%)
4:12:07.014999 PROGRESS: 
4:12:07.015041 PROGRESS: Precursor Summary:
4:12:07.015970 PROGRESS: Channel   0:	 0.050 FDR:   266; 0.010 FDR:   266; 0.001 FDR:   266
4:12:07.016055 PROGRESS: 
4:12:07.016109 PROGRESS: Protein Summary:
4:12:07.017202 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:   265; 0.001 FDR:   265
4:12:07.017291 PROGRESS: =========================================================================
4:12:07.017560 INFO: Target number of precursors reached.
4:12:07.022193 INFO: fragments_df: keeping 1290 of 31675 [sum(precursor_idx_mask)=7580 sum(mass_error_mask)=31675 stop_rank=1290
4:12:07.121689 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:12:07.222349 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:12:07.324197 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:12:07.427186 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:12:07.608901 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:12:07.609466 INFO: Using score_cutoff 29.028576375961304 (fac=0.99, q=1)
4:12:07.609871 INFO: Updating optimization_manager: fwhm_rt             : 2.4576427936553955 -> 2.504034996032715
4:12:07.609963 INFO: Updating optimization_manager: fwhm_mobility       : 0.004405444487929344 -> 0.00436017382889986
4:12:07.610020 INFO: Updating optimization_manager: score_cutoff        : 29.25261512374878 -> 29.028576375961304
4:12:07.610090 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:07.611403 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:07.612751 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:07.613556 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:07.615772 INFO: === checking if optimization conditions were reached ===
4:12:07.615897 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
4:12:07.616900 INFO: Updating optimization_manager: ms2_error           : 9.476511420394306 -> 24.37390675904184
4:12:07.617038 INFO: Updating optimization_manager: classifier_version  : 2 -> 4
4:12:07.617134 INFO: Updating optimization_manager: score_cutoff        : 29.028576375961304 -> 34.57095967254639
4:12:07.617220 INFO: Updating optimization_manager: fwhm_rt             : 2.504034996032715 -> 3.1179845333099365
4:12:07.617312 INFO: Updating optimization_manager: fwhm_mobility       : 0.00436017382889986 -> 0.007151697296649218
4:12:07.617402 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 24.3739 found after 9 searches.
4:12:07.617480 INFO: ==============================================
4:12:07.617558 PROGRESS: Optimization finished for ms2_error.
4:12:07.717529 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:07.718891 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:07.720237 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:07.721025 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:07.748895 INFO: Starting optimization step 0.
4:12:07.749073 PROGRESS: === Extracting elution groups 0 to 600 ===
4:12:07.749168 INFO: Using classic extraction backend
4:12:07.749505 PROGRESS: Extracting batch of 1173 precursors
4:12:07.749596 INFO: === Search parameters used ===
4:12:07.749650 INFO: rt_error       : 2099.894844
4:12:07.749696 INFO: mobility_error : 0.1
4:12:07.749740 INFO: num_candidates : 3
4:12:07.749781 INFO: ms1_error      : 30
4:12:07.749824 INFO: ms2_error      : 24.37390675904184
4:12:07.749863 INFO: fwhm_rt        : 3.1179845333099365
4:12:07.749902 INFO: quant_window   : 3
4:12:07.749941 INFO: ==============================================
4:12:07.751310 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:12:07.751359 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:12:07.751423 INFO: FWHM in RT is 3.12 seconds, sigma is 0.69
4:12:07.751450 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.32
4:12:07.752268 INFO: Starting candidate selection
4:12:18.273040 INFO: Starting candidate scoring
4:12:18.554152 INFO: Finished candidate processing
4:12:18.554273 INFO: Collecting candidate features
4:12:18.575946 INFO: Collecting fragment features
4:12:18.581962 INFO: Finished candidate scoring
4:12:18.584299 INFO: performing precursor FDR with 47 features
4:12:18.584367 INFO: Decoy channel: -1
4:12:18.584408 INFO: Competetive: True
4:12:18.588874 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:18.591985 INFO: Using random state 861002 for train-test-split
4:12:18.608266 INFO: Test AUC: 0.495
4:12:18.608356 INFO: Train AUC: 0.482
4:12:18.608405 INFO: AUC difference: 2.71%
4:12:18.825555 INFO: Resetting torch num_threads to 80
4:12:18.826101 PROGRESS: === Extracted 3232 precursors and 34935 fragments ===
4:12:18.826505 INFO: === FDR correction performed with classifier version 4 ===
4:12:18.827071 PROGRESS: ============================= Precursor FDR =============================
4:12:18.827157 PROGRESS: Total precursors accumulated: 589
4:12:18.827215 PROGRESS: Target precursors: 378 (64.18%)
4:12:18.827268 PROGRESS: Decoy precursors: 211 (35.82%)
4:12:18.827321 PROGRESS: 
4:12:18.827364 PROGRESS: Precursor Summary:
4:12:18.828294 PROGRESS: Channel   0:	 0.050 FDR:   272; 0.010 FDR:   272; 0.001 FDR:   272
4:12:18.828380 PROGRESS: 
4:12:18.828434 PROGRESS: Protein Summary:
4:12:18.829540 PROGRESS: Channel   0:	 0.050 FDR:   268; 0.010 FDR:   268; 0.001 FDR:   268
4:12:18.829640 PROGRESS: =========================================================================
4:12:18.829783 INFO: Target number of precursors reached.
4:12:18.834661 INFO: fragments_df: keeping 1572 of 34935 [sum(precursor_idx_mask)=8532 sum(mass_error_mask)=34935 stop_rank=1572
4:12:18.933502 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:12:19.036317 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:12:19.140136 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:12:19.259335 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:12:19.475219 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:12:19.475643 INFO: Using score_cutoff 33.078046402359014 (fac=0.99, q=1)
4:12:19.475940 INFO: Updating optimization_manager: fwhm_rt             : 3.1179845333099365 -> 3.2321088314056396
4:12:19.476017 INFO: Updating optimization_manager: fwhm_mobility       : 0.007151697296649218 -> 0.007141892798244953
4:12:19.476072 INFO: Updating optimization_manager: score_cutoff        : 34.57095967254639 -> 33.078046402359014
4:12:19.476128 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:19.477205 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:19.478513 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:19.479271 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:19.481359 INFO: === checking if optimization conditions were reached ===
4:12:19.481459 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
4:12:19.482910 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 1302.5418476286295
4:12:19.483006 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1302.5418.
4:12:19.483071 INFO: ==============================================
4:12:19.483136 INFO: Starting optimization step 1.
4:12:19.483190 PROGRESS: === Extracting elution groups 0 to 600 ===
4:12:19.483243 INFO: Using classic extraction backend
4:12:19.483348 PROGRESS: Extracting batch of 1173 precursors
4:12:19.483411 INFO: === Search parameters used ===
4:12:19.483458 INFO: rt_error       : 1302.5418476286295
4:12:19.483500 INFO: mobility_error : 0.1
4:12:19.483543 INFO: num_candidates : 3
4:12:19.483584 INFO: ms1_error      : 30
4:12:19.483623 INFO: ms2_error      : 24.37390675904184
4:12:19.483663 INFO: fwhm_rt        : 3.2321088314056396
4:12:19.483702 INFO: quant_window   : 3
4:12:19.483740 INFO: ==============================================
4:12:19.484606 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:12:19.484651 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:12:19.484684 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
4:12:19.484706 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.31
4:12:19.485409 INFO: Starting candidate selection
4:12:25.871601 INFO: Starting candidate scoring
4:12:26.158558 INFO: Finished candidate processing
4:12:26.158689 INFO: Collecting candidate features
4:12:26.172410 INFO: Collecting fragment features
4:12:26.175882 INFO: Finished candidate scoring
4:12:26.177714 INFO: performing precursor FDR with 47 features
4:12:26.177759 INFO: Decoy channel: -1
4:12:26.177783 INFO: Competetive: True
4:12:26.180519 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:26.182480 INFO: Using random state 861002 for train-test-split
4:12:26.192291 INFO: Test AUC: 0.467
4:12:26.192347 INFO: Train AUC: 0.492
4:12:26.192375 INFO: AUC difference: 5.12%
4:12:26.192398 WARNING: AUC difference > 5%. This may indicate overfitting.
4:12:26.405249 INFO: Resetting torch num_threads to 80
4:12:26.405757 PROGRESS: === Extracted 3233 precursors and 35025 fragments ===
4:12:26.406163 INFO: === FDR correction performed with classifier version 4 ===
4:12:26.406721 PROGRESS: ============================= Precursor FDR =============================
4:12:26.406806 PROGRESS: Total precursors accumulated: 588
4:12:26.406864 PROGRESS: Target precursors: 378 (64.29%)
4:12:26.406920 PROGRESS: Decoy precursors: 210 (35.71%)
4:12:26.406967 PROGRESS: 
4:12:26.407010 PROGRESS: Precursor Summary:
4:12:26.407936 PROGRESS: Channel   0:	 0.050 FDR:   271; 0.010 FDR:   271; 0.001 FDR:   271
4:12:26.408022 PROGRESS: 
4:12:26.408077 PROGRESS: Protein Summary:
4:12:26.409148 PROGRESS: Channel   0:	 0.050 FDR:   268; 0.010 FDR:   268; 0.001 FDR:   268
4:12:26.409236 PROGRESS: =========================================================================
4:12:26.409396 INFO: Target number of precursors reached.
4:12:26.414349 INFO: fragments_df: keeping 1533 of 35025 [sum(precursor_idx_mask)=8405 sum(mass_error_mask)=35025 stop_rank=1533
4:12:26.541137 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:12:26.641881 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:12:26.740113 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:12:26.839650 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:12:27.021140 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:12:27.021557 INFO: Using score_cutoff 34.19489585494995 (fac=0.99, q=1)
4:12:27.021857 INFO: Updating optimization_manager: fwhm_rt             : 3.2321088314056396 -> 3.2641265392303467
4:12:27.021936 INFO: Updating optimization_manager: fwhm_mobility       : 0.007141892798244953 -> 0.0074399178847670555
4:12:27.021990 INFO: Updating optimization_manager: score_cutoff        : 33.078046402359014 -> 34.19489585494995
4:12:27.022051 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:27.023090 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:27.024405 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:27.025211 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:27.027267 INFO: === checking if optimization conditions were reached ===
4:12:27.027368 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
4:12:27.028877 INFO: Updating optimization_manager: rt_error            : 1302.5418476286295 -> 868.4874057977572
4:12:27.028993 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 868.4874.
4:12:27.029076 INFO: ==============================================
4:12:27.029152 INFO: Starting optimization step 2.
4:12:27.029208 PROGRESS: === Extracting elution groups 0 to 600 ===
4:12:27.029261 INFO: Using classic extraction backend
4:12:27.029370 PROGRESS: Extracting batch of 1173 precursors
4:12:27.029432 INFO: === Search parameters used ===
4:12:27.029479 INFO: rt_error       : 868.4874057977572
4:12:27.029520 INFO: mobility_error : 0.1
4:12:27.029561 INFO: num_candidates : 3
4:12:27.029600 INFO: ms1_error      : 30
4:12:27.029642 INFO: ms2_error      : 24.37390675904184
4:12:27.029681 INFO: fwhm_rt        : 3.2641265392303467
4:12:27.029981 INFO: quant_window   : 3
4:12:27.030030 INFO: ==============================================
4:12:27.030818 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:12:27.030863 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:12:27.030898 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
4:12:27.030920 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.45
4:12:27.031589 INFO: Starting candidate selection
4:12:32.055444 INFO: Starting candidate scoring
4:12:32.342375 INFO: Finished candidate processing
4:12:32.342471 INFO: Collecting candidate features
4:12:32.356137 INFO: Collecting fragment features
4:12:32.359676 INFO: Finished candidate scoring
4:12:32.361466 INFO: performing precursor FDR with 47 features
4:12:32.361513 INFO: Decoy channel: -1
4:12:32.361537 INFO: Competetive: True
4:12:32.364414 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:32.366381 INFO: Using random state 861002 for train-test-split
4:12:32.376256 INFO: Test AUC: 0.487
4:12:32.376314 INFO: Train AUC: 0.494
4:12:32.376343 INFO: AUC difference: 1.40%
4:12:32.594470 INFO: Resetting torch num_threads to 80
4:12:32.595004 PROGRESS: === Extracted 3245 precursors and 35174 fragments ===
4:12:32.595405 INFO: === FDR correction performed with classifier version 4 ===
4:12:32.595968 PROGRESS: ============================= Precursor FDR =============================
4:12:32.596055 PROGRESS: Total precursors accumulated: 588
4:12:32.596115 PROGRESS: Target precursors: 387 (65.82%)
4:12:32.596165 PROGRESS: Decoy precursors: 201 (34.18%)
4:12:32.596210 PROGRESS: 
4:12:32.596253 PROGRESS: Precursor Summary:
4:12:32.597202 PROGRESS: Channel   0:	 0.050 FDR:   277; 0.010 FDR:   277; 0.001 FDR:   277
4:12:32.597293 PROGRESS: 
4:12:32.597355 PROGRESS: Protein Summary:
4:12:32.598433 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   273; 0.001 FDR:   273
4:12:32.598523 PROGRESS: =========================================================================
4:12:32.598650 INFO: Target number of precursors reached.
4:12:32.603663 INFO: fragments_df: keeping 1563 of 35174 [sum(precursor_idx_mask)=8628 sum(mass_error_mask)=35174 stop_rank=1563
4:12:32.707288 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:12:32.822752 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:12:32.941114 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:12:33.060453 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:12:33.280991 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:12:33.281413 INFO: Using score_cutoff 34.49738250274658 (fac=0.99, q=1)
4:12:33.281711 INFO: Updating optimization_manager: fwhm_rt             : 3.2641265392303467 -> 3.203296422958374
4:12:33.281789 INFO: Updating optimization_manager: fwhm_mobility       : 0.0074399178847670555 -> 0.007199667859822512
4:12:33.281844 INFO: Updating optimization_manager: score_cutoff        : 34.19489585494995 -> 34.49738250274658
4:12:33.281899 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:33.282935 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:33.284249 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:33.285027 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:33.287906 INFO: === checking if optimization conditions were reached ===
4:12:33.288009 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
4:12:33.289668 INFO: Updating optimization_manager: rt_error            : 868.4874057977572 -> 831.412233375923
4:12:33.289769 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 831.4122.
4:12:33.289835 INFO: ==============================================
4:12:33.289903 INFO: Starting optimization step 3.
4:12:33.289963 PROGRESS: === Extracting elution groups 0 to 600 ===
4:12:33.290018 INFO: Using classic extraction backend
4:12:33.290125 PROGRESS: Extracting batch of 1173 precursors
4:12:33.290205 INFO: === Search parameters used ===
4:12:33.290254 INFO: rt_error       : 831.412233375923
4:12:33.290297 INFO: mobility_error : 0.1
4:12:33.290338 INFO: num_candidates : 3
4:12:33.290377 INFO: ms1_error      : 30
4:12:33.290416 INFO: ms2_error      : 24.37390675904184
4:12:33.290456 INFO: fwhm_rt        : 3.203296422958374
4:12:33.290495 INFO: quant_window   : 3
4:12:33.290534 INFO: ==============================================
4:12:33.291759 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:12:33.291804 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:12:33.291838 INFO: FWHM in RT is 3.20 seconds, sigma is 0.70
4:12:33.291860 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.34
4:12:33.292511 INFO: Starting candidate selection
4:12:37.713894 INFO: Starting candidate scoring
4:12:38.013755 INFO: Finished candidate processing
4:12:38.013849 INFO: Collecting candidate features
4:12:38.027563 INFO: Collecting fragment features
4:12:38.031807 INFO: Finished candidate scoring
4:12:38.034182 INFO: performing precursor FDR with 47 features
4:12:38.034226 INFO: Decoy channel: -1
4:12:38.034250 INFO: Competetive: True
4:12:38.037296 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:38.039268 INFO: Using random state 861002 for train-test-split
4:12:38.049437 INFO: Test AUC: 0.481
4:12:38.049495 INFO: Train AUC: 0.493
4:12:38.049524 INFO: AUC difference: 2.49%
4:12:38.262486 INFO: Resetting torch num_threads to 80
4:12:38.263305 PROGRESS: === Extracted 3247 precursors and 35164 fragments ===
4:12:38.263716 INFO: === FDR correction performed with classifier version 4 ===
4:12:38.264315 PROGRESS: ============================= Precursor FDR =============================
4:12:38.264403 PROGRESS: Total precursors accumulated: 587
4:12:38.264460 PROGRESS: Target precursors: 388 (66.10%)
4:12:38.264508 PROGRESS: Decoy precursors: 199 (33.90%)
4:12:38.264552 PROGRESS: 
4:12:38.264593 PROGRESS: Precursor Summary:
4:12:38.265538 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   273; 0.001 FDR:   273
4:12:38.265627 PROGRESS: 
4:12:38.265683 PROGRESS: Protein Summary:
4:12:38.266750 PROGRESS: Channel   0:	 0.050 FDR:   269; 0.010 FDR:   269; 0.001 FDR:   269
4:12:38.266839 PROGRESS: =========================================================================
4:12:38.267062 INFO: Target number of precursors reached.
4:12:38.272082 INFO: fragments_df: keeping 1522 of 35164 [sum(precursor_idx_mask)=8552 sum(mass_error_mask)=35164 stop_rank=1522
4:12:38.372249 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:12:38.492713 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:12:38.615300 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:12:38.726389 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:12:38.925563 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:12:38.926130 INFO: Using score_cutoff 33.687013966369626 (fac=0.99, q=1)
4:12:38.926486 INFO: Updating optimization_manager: fwhm_rt             : 3.203296422958374 -> 3.247185468673706
4:12:38.926568 INFO: Updating optimization_manager: fwhm_mobility       : 0.007199667859822512 -> 0.007345191203057766
4:12:38.926635 INFO: Updating optimization_manager: score_cutoff        : 34.49738250274658 -> 33.687013966369626
4:12:38.926728 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:38.928080 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:38.929438 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:38.930259 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:38.933290 INFO: === checking if optimization conditions were reached ===
4:12:38.933465 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
4:12:38.934651 INFO: Updating optimization_manager: rt_error            : 831.412233375923 -> 831.412233375923
4:12:38.934784 INFO: Updating optimization_manager: classifier_version  : 4 -> 15
4:12:38.934878 INFO: Updating optimization_manager: score_cutoff        : 33.687013966369626 -> 33.687013966369626
4:12:38.934965 INFO: Updating optimization_manager: fwhm_rt             : 3.247185468673706 -> 3.247185468673706
4:12:38.935054 INFO: Updating optimization_manager: fwhm_mobility       : 0.007345191203057766 -> 0.007345191203057766
4:12:38.935146 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 831.4122 found after 4 searches.
4:12:38.935211 INFO: ==============================================
4:12:38.935302 PROGRESS: Optimization finished for rt_error.
4:12:39.037449 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:39.038947 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:39.040293 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:39.041075 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:39.069768 INFO: Starting optimization step 0.
4:12:39.069923 PROGRESS: === Extracting elution groups 0 to 600 ===
4:12:39.070007 INFO: Using classic extraction backend
4:12:39.070228 PROGRESS: Extracting batch of 1173 precursors
4:12:39.070303 INFO: === Search parameters used ===
4:12:39.070352 INFO: rt_error       : 831.412233375923
4:12:39.070395 INFO: mobility_error : 0.1
4:12:39.070438 INFO: num_candidates : 3
4:12:39.070479 INFO: ms1_error      : 30
4:12:39.070526 INFO: ms2_error      : 24.37390675904184
4:12:39.070567 INFO: fwhm_rt        : 3.247185468673706
4:12:39.070606 INFO: quant_window   : 3
4:12:39.070644 INFO: ==============================================
4:12:39.072004 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:12:39.072049 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:12:39.072090 INFO: FWHM in RT is 3.25 seconds, sigma is 0.71
4:12:39.072112 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.41
4:12:39.072874 INFO: Starting candidate selection
4:12:43.378344 INFO: Starting candidate scoring
4:12:43.658223 INFO: Finished candidate processing
4:12:43.658321 INFO: Collecting candidate features
4:12:43.672288 INFO: Collecting fragment features
4:12:43.676017 INFO: Finished candidate scoring
4:12:43.678017 INFO: performing precursor FDR with 47 features
4:12:43.678066 INFO: Decoy channel: -1
4:12:43.678089 INFO: Competetive: True
4:12:43.681955 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:43.684221 INFO: Using random state 794606 for train-test-split
4:12:43.694999 INFO: Test AUC: 0.473
4:12:43.695057 INFO: Train AUC: 0.500
4:12:43.695087 INFO: AUC difference: 5.45%
4:12:43.695109 WARNING: AUC difference > 5%. This may indicate overfitting.
4:12:43.906977 INFO: Resetting torch num_threads to 80
4:12:43.907515 PROGRESS: === Extracted 3234 precursors and 35044 fragments ===
4:12:43.907946 INFO: === FDR correction performed with classifier version 15 ===
4:12:43.908516 PROGRESS: ============================= Precursor FDR =============================
4:12:43.908601 PROGRESS: Total precursors accumulated: 587
4:12:43.908658 PROGRESS: Target precursors: 387 (65.93%)
4:12:43.908706 PROGRESS: Decoy precursors: 200 (34.07%)
4:12:43.908748 PROGRESS: 
4:12:43.908790 PROGRESS: Precursor Summary:
4:12:43.909733 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:   270
4:12:43.909820 PROGRESS: 
4:12:43.909873 PROGRESS: Protein Summary:
4:12:43.910941 PROGRESS: Channel   0:	 0.050 FDR:   266; 0.010 FDR:   266; 0.001 FDR:   266
4:12:43.911028 PROGRESS: =========================================================================
4:12:43.911163 INFO: Target number of precursors reached.
4:12:43.916110 INFO: fragments_df: keeping 1528 of 35044 [sum(precursor_idx_mask)=8364 sum(mass_error_mask)=35044 stop_rank=1528
4:12:44.014916 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:12:44.131688 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:12:44.253412 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:12:44.378369 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:12:45.593869 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:12:45.594294 INFO: Using score_cutoff 34.49000134849548 (fac=0.99, q=1)
4:12:45.594589 INFO: Updating optimization_manager: fwhm_rt             : 3.247185468673706 -> 3.1813528537750244
4:12:45.594666 INFO: Updating optimization_manager: fwhm_mobility       : 0.007345191203057766 -> 0.007154254708439112
4:12:45.594717 INFO: Updating optimization_manager: score_cutoff        : 33.687013966369626 -> 34.49000134849548
4:12:45.594769 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:45.595809 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:45.597174 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:45.597941 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:45.599982 INFO: === checking if optimization conditions were reached ===
4:12:45.600080 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
4:12:45.601450 INFO: Updating optimization_manager: ms1_error           : 30 -> 17.25550287559626
4:12:45.601549 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 17.2555.
4:12:45.601611 INFO: ==============================================
4:12:45.601675 INFO: Starting optimization step 1.
4:12:45.601731 PROGRESS: === Extracting elution groups 0 to 600 ===
4:12:45.601792 INFO: Using classic extraction backend
4:12:45.601903 PROGRESS: Extracting batch of 1173 precursors
4:12:45.601965 INFO: === Search parameters used ===
4:12:45.602009 INFO: rt_error       : 831.412233375923
4:12:45.602049 INFO: mobility_error : 0.1
4:12:45.602087 INFO: num_candidates : 3
4:12:45.602126 INFO: ms1_error      : 17.25550287559626
4:12:45.602167 INFO: ms2_error      : 24.37390675904184
4:12:45.602209 INFO: fwhm_rt        : 3.1813528537750244
4:12:45.602246 INFO: quant_window   : 3
4:12:45.602283 INFO: ==============================================
4:12:45.603147 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:12:45.603190 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:12:45.603224 INFO: FWHM in RT is 3.18 seconds, sigma is 0.70
4:12:45.603244 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.32
4:12:45.603950 INFO: Starting candidate selection
4:12:49.482023 INFO: Starting candidate scoring
4:12:49.777642 INFO: Finished candidate processing
4:12:49.777736 INFO: Collecting candidate features
4:12:49.790970 INFO: Collecting fragment features
4:12:49.794634 INFO: Finished candidate scoring
4:12:49.797691 INFO: performing precursor FDR with 47 features
4:12:49.797738 INFO: Decoy channel: -1
4:12:49.797763 INFO: Competetive: True
4:12:49.800709 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:49.802850 INFO: Using random state 794606 for train-test-split
4:12:49.814177 INFO: Test AUC: 0.497
4:12:49.814240 INFO: Train AUC: 0.485
4:12:49.814268 INFO: AUC difference: 2.61%
4:12:50.026990 INFO: Resetting torch num_threads to 80
4:12:50.027601 PROGRESS: === Extracted 3229 precursors and 34855 fragments ===
4:12:50.028013 INFO: === FDR correction performed with classifier version 15 ===
4:12:50.028650 PROGRESS: ============================= Precursor FDR =============================
4:12:50.028742 PROGRESS: Total precursors accumulated: 589
4:12:50.028800 PROGRESS: Target precursors: 361 (61.29%)
4:12:50.028849 PROGRESS: Decoy precursors: 228 (38.71%)
4:12:50.028893 PROGRESS: 
4:12:50.028935 PROGRESS: Precursor Summary:
4:12:50.029881 PROGRESS: Channel   0:	 0.050 FDR:   224; 0.010 FDR:   224; 0.001 FDR:   224
4:12:50.029969 PROGRESS: 
4:12:50.030030 PROGRESS: Protein Summary:
4:12:50.031114 PROGRESS: Channel   0:	 0.050 FDR:   224; 0.010 FDR:   224; 0.001 FDR:   224
4:12:50.031204 PROGRESS: =========================================================================
4:12:50.031343 INFO: Target number of precursors reached.
4:12:50.036168 INFO: fragments_df: keeping 1210 of 34855 [sum(precursor_idx_mask)=6921 sum(mass_error_mask)=34855 stop_rank=1210
4:12:50.135445 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:12:50.248389 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:12:50.363871 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:12:50.485702 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:12:50.669672 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:12:50.670088 INFO: Using score_cutoff 33.55849131317139 (fac=0.99, q=1)
4:12:50.670385 INFO: Updating optimization_manager: fwhm_rt             : 3.1813528537750244 -> 3.1616716384887695
4:12:50.670463 INFO: Updating optimization_manager: fwhm_mobility       : 0.007154254708439112 -> 0.00724733667448163
4:12:50.670517 INFO: Updating optimization_manager: score_cutoff        : 34.49000134849548 -> 33.55849131317139
4:12:50.670572 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:50.671622 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:50.672990 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:50.673766 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:50.675836 INFO: === checking if optimization conditions were reached ===
4:12:50.675947 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
4:12:50.677576 INFO: Updating optimization_manager: ms1_error           : 17.25550287559626 -> 10.540351857811913
4:12:50.677678 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 10.5404.
4:12:50.677742 INFO: ==============================================
4:12:50.677809 INFO: Starting optimization step 2.
4:12:50.677867 PROGRESS: === Extracting elution groups 0 to 600 ===
4:12:50.677923 INFO: Using classic extraction backend
4:12:50.678031 PROGRESS: Extracting batch of 1173 precursors
4:12:50.678094 INFO: === Search parameters used ===
4:12:50.678140 INFO: rt_error       : 831.412233375923
4:12:50.678181 INFO: mobility_error : 0.1
4:12:50.678221 INFO: num_candidates : 3
4:12:50.678261 INFO: ms1_error      : 10.540351857811913
4:12:50.678300 INFO: ms2_error      : 24.37390675904184
4:12:50.678339 INFO: fwhm_rt        : 3.1616716384887695
4:12:50.678377 INFO: quant_window   : 3
4:12:50.678416 INFO: ==============================================
4:12:50.679295 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:12:50.679340 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:12:50.679374 INFO: FWHM in RT is 3.16 seconds, sigma is 0.69
4:12:50.679395 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.36
4:12:50.680053 INFO: Starting candidate selection
4:12:54.593150 INFO: Starting candidate scoring
4:12:54.849653 INFO: Finished candidate processing
4:12:54.849791 INFO: Collecting candidate features
4:12:54.865381 INFO: Collecting fragment features
4:12:54.869112 INFO: Finished candidate scoring
4:12:54.871574 INFO: performing precursor FDR with 47 features
4:12:54.871622 INFO: Decoy channel: -1
4:12:54.871646 INFO: Competetive: True
4:12:54.874797 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:54.876926 INFO: Using random state 794606 for train-test-split
4:12:54.888559 INFO: Test AUC: 0.458
4:12:54.888614 INFO: Train AUC: 0.491
4:12:54.888643 INFO: AUC difference: 6.70%
4:12:54.888665 WARNING: AUC difference > 5%. This may indicate overfitting.
4:12:55.105859 INFO: Resetting torch num_threads to 80
4:12:55.106428 PROGRESS: === Extracted 3250 precursors and 35031 fragments ===
4:12:55.106840 INFO: === FDR correction performed with classifier version 15 ===
4:12:55.107416 PROGRESS: ============================= Precursor FDR =============================
4:12:55.107511 PROGRESS: Total precursors accumulated: 589
4:12:55.107570 PROGRESS: Target precursors: 329 (55.86%)
4:12:55.107620 PROGRESS: Decoy precursors: 260 (44.14%)
4:12:55.107664 PROGRESS: 
4:12:55.107707 PROGRESS: Precursor Summary:
4:12:55.108630 PROGRESS: Channel   0:	 0.050 FDR:   182; 0.010 FDR:   182; 0.001 FDR:   182
4:12:55.108725 PROGRESS: 
4:12:55.108780 PROGRESS: Protein Summary:
4:12:55.109841 PROGRESS: Channel   0:	 0.050 FDR:   182; 0.010 FDR:   182; 0.001 FDR:   182
4:12:55.109931 PROGRESS: =========================================================================
4:12:55.110064 INFO: Target number of precursors not reached yet.
4:12:55.400861 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:12:55.402344 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:55.403972 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:12:55.404799 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:55.408176 INFO: === skipping optimization until target number of precursors are found ===
4:12:55.408285 PROGRESS: === Optimization of ms1_error has been skipped 1 time(s); maximum number is 1 ===
4:12:55.408379 INFO: Starting optimization step 3.
4:12:55.408439 PROGRESS: === Extracting elution groups 600 to 1400 ===
4:12:55.408494 INFO: Using classic extraction backend
4:12:55.408609 PROGRESS: Extracting batch of 1576 precursors
4:12:55.408680 INFO: === Search parameters used ===
4:12:55.408726 INFO: rt_error       : 831.412233375923
4:12:55.408769 INFO: mobility_error : 0.1
4:12:55.408808 INFO: num_candidates : 3
4:12:55.408847 INFO: ms1_error      : 10.540351857811913
4:12:55.408886 INFO: ms2_error      : 24.37390675904184
4:12:55.408925 INFO: fwhm_rt        : 3.1616716384887695
4:12:55.409016 INFO: quant_window   : 3
4:12:55.409065 INFO: ==============================================
4:12:55.410026 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:12:55.410071 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:12:55.410106 INFO: FWHM in RT is 3.16 seconds, sigma is 0.69
4:12:55.410126 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.36
4:12:55.411000 INFO: Starting candidate selection
4:13:00.099730 INFO: Starting candidate scoring
4:13:00.500095 INFO: Finished candidate processing
4:13:00.500192 INFO: Collecting candidate features
4:13:00.514227 INFO: Collecting fragment features
4:13:00.518653 INFO: Finished candidate scoring
4:13:00.523848 INFO: performing precursor FDR with 47 features
4:13:00.523902 INFO: Decoy channel: -1
4:13:00.523927 INFO: Competetive: True
4:13:00.528123 INFO: Setting torch num_threads to 2 for FDR classification task
4:13:00.530840 INFO: Using random state 794606 for train-test-split
4:13:00.549563 INFO: Test AUC: 0.505
4:13:00.549647 INFO: Train AUC: 0.490
4:13:00.549676 INFO: AUC difference: 3.17%
4:13:00.768636 INFO: Resetting torch num_threads to 80
4:13:00.770666 PROGRESS: === Extracted 7638 precursors and 82028 fragments ===
4:13:00.771069 INFO: === FDR correction performed with classifier version 15 ===
4:13:00.771751 PROGRESS: ============================= Precursor FDR =============================
4:13:00.771841 PROGRESS: Total precursors accumulated: 1,381
4:13:00.771897 PROGRESS: Target precursors: 786 (56.92%)
4:13:00.771945 PROGRESS: Decoy precursors: 595 (43.08%)
4:13:00.771988 PROGRESS: 
4:13:00.772030 PROGRESS: Precursor Summary:
4:13:00.773027 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   410; 0.001 FDR:   410
4:13:00.773117 PROGRESS: 
4:13:00.773171 PROGRESS: Protein Summary:
4:13:00.774331 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   403; 0.001 FDR:   403
4:13:00.774428 PROGRESS: =========================================================================
4:13:00.774567 INFO: Target number of precursors reached.
4:13:00.783687 INFO: fragments_df: keeping 2351 of 82028 [sum(precursor_idx_mask)=12669 sum(mass_error_mask)=82028 stop_rank=2351
4:13:00.975120 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:13:01.102845 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:13:01.234997 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:13:01.363857 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:13:01.675532 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:13:01.675952 INFO: Using score_cutoff 31.404574676513672 (fac=0.99, q=1)
4:13:01.676254 INFO: Updating optimization_manager: fwhm_rt             : 3.1616716384887695 -> 3.178529739379883
4:13:01.676332 INFO: Updating optimization_manager: fwhm_mobility       : 0.00724733667448163 -> 0.007039912976324558
4:13:01.676384 INFO: Updating optimization_manager: score_cutoff        : 33.55849131317139 -> 31.404574676513672
4:13:01.676435 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:13:01.677691 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:13:01.679889 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:13:01.680839 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:13:01.685129 INFO: === checking if optimization conditions were reached ===
4:13:01.685234 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
4:13:01.686836 INFO: Updating optimization_manager: ms1_error           : 10.540351857811913 -> 5.769193535404903
4:13:01.686939 PROGRESS: ❌ ms1_error      : optimization incomplete after 3 search(es). Will search with parameter 5.7692.
4:13:01.687003 INFO: ==============================================
4:13:01.687067 INFO: Starting optimization step 4.
4:13:01.687123 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:13:01.687176 INFO: Using classic extraction backend
4:13:01.687282 PROGRESS: Extracting batch of 2749 precursors
4:13:01.687343 INFO: === Search parameters used ===
4:13:01.687387 INFO: rt_error       : 831.412233375923
4:13:01.687429 INFO: mobility_error : 0.1
4:13:01.687468 INFO: num_candidates : 3
4:13:01.687508 INFO: ms1_error      : 5.769193535404903
4:13:01.687546 INFO: ms2_error      : 24.37390675904184
4:13:01.687585 INFO: fwhm_rt        : 3.178529739379883
4:13:01.687623 INFO: quant_window   : 3
4:13:01.687660 INFO: ==============================================
4:13:01.688760 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:13:01.688803 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:13:01.688838 INFO: FWHM in RT is 3.18 seconds, sigma is 0.70
4:13:01.688860 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.27
4:13:01.689507 INFO: Starting candidate selection
4:13:09.119703 INFO: Starting candidate scoring
4:13:09.644616 INFO: Finished candidate processing
4:13:09.644800 INFO: Collecting candidate features
4:13:09.672754 INFO: Collecting fragment features
4:13:09.681928 INFO: Finished candidate scoring
4:13:09.686164 INFO: performing precursor FDR with 47 features
4:13:09.686229 INFO: Decoy channel: -1
4:13:09.686254 INFO: Competetive: True
4:13:09.690763 INFO: Setting torch num_threads to 2 for FDR classification task
4:13:09.693928 INFO: Using random state 794606 for train-test-split
4:13:09.712779 INFO: Test AUC: 0.508
4:13:09.712860 INFO: Train AUC: 0.489
4:13:09.712891 INFO: AUC difference: 3.99%
4:13:09.939811 INFO: Resetting torch num_threads to 80
4:13:09.940515 PROGRESS: === Extracted 7623 precursors and 81672 fragments ===
4:13:09.940998 INFO: === FDR correction performed with classifier version 15 ===
4:13:09.941692 PROGRESS: ============================= Precursor FDR =============================
4:13:09.941785 PROGRESS: Total precursors accumulated: 1,379
4:13:09.941846 PROGRESS: Target precursors: 781 (56.64%)
4:13:09.941905 PROGRESS: Decoy precursors: 598 (43.36%)
4:13:09.941952 PROGRESS: 
4:13:09.941994 PROGRESS: Precursor Summary:
4:13:09.942991 PROGRESS: Channel   0:	 0.050 FDR:   384; 0.010 FDR:   384; 0.001 FDR:   384
4:13:09.943079 PROGRESS: 
4:13:09.943139 PROGRESS: Protein Summary:
4:13:09.944328 PROGRESS: Channel   0:	 0.050 FDR:   379; 0.010 FDR:   379; 0.001 FDR:   379
4:13:09.944416 PROGRESS: =========================================================================
4:13:09.944751 INFO: Target number of precursors reached.
4:13:09.953710 INFO: fragments_df: keeping 2227 of 81672 [sum(precursor_idx_mask)=11780 sum(mass_error_mask)=81672 stop_rank=2227
4:13:10.072014 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:13:10.186068 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:13:10.297100 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:13:10.408708 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:13:10.654573 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:13:10.654991 INFO: Using score_cutoff 30.46920447807312 (fac=0.99, q=1)
4:13:10.655347 INFO: Updating optimization_manager: fwhm_rt             : 3.178529739379883 -> 3.2260117530822754
4:13:10.655428 INFO: Updating optimization_manager: fwhm_mobility       : 0.007039912976324558 -> 0.006989299785345793
4:13:10.655484 INFO: Updating optimization_manager: score_cutoff        : 31.404574676513672 -> 30.46920447807312
4:13:10.655548 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:13:10.656804 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:13:10.659020 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:13:10.659978 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:13:10.664761 INFO: === checking if optimization conditions were reached ===
4:13:10.664886 PROGRESS: === Optimization of ms1_error has been performed 4 time(s); minimum number is 2 ===
4:13:10.666552 INFO: Updating optimization_manager: ms1_error           : 5.769193535404903 -> 2.761978519613881
4:13:10.666651 PROGRESS: ❌ ms1_error      : optimization incomplete after 4 search(es). Will search with parameter 2.7620.
4:13:10.666716 INFO: ==============================================
4:13:10.666789 INFO: Starting optimization step 5.
4:13:10.666848 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:13:10.666922 INFO: Using classic extraction backend
4:13:10.667203 PROGRESS: Extracting batch of 2749 precursors
4:13:10.667284 INFO: === Search parameters used ===
4:13:10.667336 INFO: rt_error       : 831.412233375923
4:13:10.667381 INFO: mobility_error : 0.1
4:13:10.667424 INFO: num_candidates : 3
4:13:10.667465 INFO: ms1_error      : 2.761978519613881
4:13:10.667506 INFO: ms2_error      : 24.37390675904184
4:13:10.667544 INFO: fwhm_rt        : 3.2260117530822754
4:13:10.667589 INFO: quant_window   : 3
4:13:10.667630 INFO: ==============================================
4:13:10.669195 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:13:10.669242 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:13:10.669297 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
4:13:10.669320 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.24
4:13:10.670043 INFO: Starting candidate selection
4:13:18.615664 INFO: Starting candidate scoring
4:13:19.120329 INFO: Finished candidate processing
4:13:19.120510 INFO: Collecting candidate features
4:13:19.150577 INFO: Collecting fragment features
4:13:19.159045 INFO: Finished candidate scoring
4:13:19.164150 INFO: performing precursor FDR with 47 features
4:13:19.164223 INFO: Decoy channel: -1
4:13:19.164248 INFO: Competetive: True
4:13:19.169163 INFO: Setting torch num_threads to 2 for FDR classification task
4:13:19.172477 INFO: Using random state 794606 for train-test-split
4:13:19.192667 INFO: Test AUC: 0.501
4:13:19.192770 INFO: Train AUC: 0.494
4:13:19.192800 INFO: AUC difference: 1.50%
4:13:19.432153 INFO: Resetting torch num_threads to 80
4:13:19.433077 PROGRESS: === Extracted 7639 precursors and 81681 fragments ===
4:13:19.433589 INFO: === FDR correction performed with classifier version 15 ===
4:13:19.434511 PROGRESS: ============================= Precursor FDR =============================
4:13:19.434606 PROGRESS: Total precursors accumulated: 1,378
4:13:19.434668 PROGRESS: Target precursors: 794 (57.62%)
4:13:19.434719 PROGRESS: Decoy precursors: 584 (42.38%)
4:13:19.434764 PROGRESS: 
4:13:19.434808 PROGRESS: Precursor Summary:
4:13:19.435849 PROGRESS: Channel   0:	 0.050 FDR:   401; 0.010 FDR:   401; 0.001 FDR:   401
4:13:19.435943 PROGRESS: 
4:13:19.436001 PROGRESS: Protein Summary:
4:13:19.437241 PROGRESS: Channel   0:	 0.050 FDR:   398; 0.010 FDR:   398; 0.001 FDR:   398
4:13:19.437338 PROGRESS: =========================================================================
4:13:19.437593 INFO: Target number of precursors reached.
4:13:19.447041 INFO: fragments_df: keeping 2560 of 81681 [sum(precursor_idx_mask)=12399 sum(mass_error_mask)=81681 stop_rank=2560
4:13:19.725163 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:13:19.838416 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:13:19.956860 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:13:20.077439 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:13:20.364714 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:13:20.365259 INFO: Using score_cutoff 26.141738090515137 (fac=0.99, q=1)
4:13:20.365606 INFO: Updating optimization_manager: fwhm_rt             : 3.2260117530822754 -> 3.1778717041015625
4:13:20.365700 INFO: Updating optimization_manager: fwhm_mobility       : 0.006989299785345793 -> 0.007356218993663788
4:13:20.365755 INFO: Updating optimization_manager: score_cutoff        : 30.46920447807312 -> 26.141738090515137
4:13:20.365810 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:13:20.367269 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:13:20.369524 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:13:20.370522 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:13:20.376530 INFO: === checking if optimization conditions were reached ===
4:13:20.376644 PROGRESS: === Optimization of ms1_error has been performed 5 time(s); minimum number is 2 ===
4:13:20.378401 INFO: Updating optimization_manager: ms1_error           : 2.761978519613881 -> 1.7083734417608665
4:13:20.378504 PROGRESS: ❌ ms1_error      : optimization incomplete after 5 search(es). Will search with parameter 1.7084.
4:13:20.378568 INFO: ==============================================
4:13:20.378634 INFO: Starting optimization step 6.
4:13:20.378690 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:13:20.378747 INFO: Using classic extraction backend
4:13:20.378872 PROGRESS: Extracting batch of 2749 precursors
4:13:20.378947 INFO: === Search parameters used ===
4:13:20.378995 INFO: rt_error       : 831.412233375923
4:13:20.379037 INFO: mobility_error : 0.1
4:13:20.379076 INFO: num_candidates : 3
4:13:20.379117 INFO: ms1_error      : 1.7083734417608665
4:13:20.379156 INFO: ms2_error      : 24.37390675904184
4:13:20.379194 INFO: fwhm_rt        : 3.1778717041015625
4:13:20.379232 INFO: quant_window   : 3
4:13:20.379272 INFO: ==============================================
4:13:20.380672 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:13:20.380716 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:13:20.380751 INFO: FWHM in RT is 3.18 seconds, sigma is 0.70
4:13:20.380772 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.41
4:13:20.381847 INFO: Starting candidate selection
4:13:28.544424 INFO: Starting candidate scoring
4:13:29.066607 INFO: Finished candidate processing
4:13:29.066700 INFO: Collecting candidate features
4:13:29.090162 INFO: Collecting fragment features
4:13:29.099385 INFO: Finished candidate scoring
4:13:29.103381 INFO: performing precursor FDR with 47 features
4:13:29.103440 INFO: Decoy channel: -1
4:13:29.103465 INFO: Competetive: True
4:13:29.108078 INFO: Setting torch num_threads to 2 for FDR classification task
4:13:29.111462 INFO: Using random state 794606 for train-test-split
4:13:29.130966 INFO: Test AUC: 0.501
4:13:29.131036 INFO: Train AUC: 0.496
4:13:29.131067 INFO: AUC difference: 1.15%
4:13:29.358490 INFO: Resetting torch num_threads to 80
4:13:29.359227 PROGRESS: === Extracted 7699 precursors and 82343 fragments ===
4:13:29.359722 INFO: === FDR correction performed with classifier version 15 ===
4:13:29.360438 PROGRESS: ============================= Precursor FDR =============================
4:13:29.360527 PROGRESS: Total precursors accumulated: 1,376
4:13:29.360593 PROGRESS: Target precursors: 819 (59.52%)
4:13:29.360645 PROGRESS: Decoy precursors: 557 (40.48%)
4:13:29.360690 PROGRESS: 
4:13:29.360734 PROGRESS: Precursor Summary:
4:13:29.361764 PROGRESS: Channel   0:	 0.050 FDR:   438; 0.010 FDR:   438; 0.001 FDR:   438
4:13:29.361858 PROGRESS: 
4:13:29.361912 PROGRESS: Protein Summary:
4:13:29.363111 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   434; 0.001 FDR:   434
4:13:29.363201 PROGRESS: =========================================================================
4:13:29.363533 INFO: Target number of precursors reached.
4:13:29.373031 INFO: fragments_df: keeping 3002 of 82343 [sum(precursor_idx_mask)=13544 sum(mass_error_mask)=82343 stop_rank=3002
4:13:29.511788 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:13:29.639861 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:13:29.777092 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:13:29.912465 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:13:30.305876 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:13:30.306308 INFO: Using score_cutoff 24.50066178302765 (fac=0.99, q=1)
4:13:30.306651 INFO: Updating optimization_manager: fwhm_rt             : 3.1778717041015625 -> 3.282142400741577
4:13:30.306731 INFO: Updating optimization_manager: fwhm_mobility       : 0.007356218993663788 -> 0.007533177733421326
4:13:30.306786 INFO: Updating optimization_manager: score_cutoff        : 26.141738090515137 -> 24.50066178302765
4:13:30.306854 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:13:30.308136 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:13:30.310402 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:13:30.311383 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:13:30.316480 INFO: === checking if optimization conditions were reached ===
4:13:30.316623 PROGRESS: === Optimization of ms1_error has been performed 6 time(s); minimum number is 2 ===
4:13:30.318313 INFO: Updating optimization_manager: ms1_error           : 1.7083734417608665 -> 0.896479238945622
4:13:30.318422 PROGRESS: ❌ ms1_error      : optimization incomplete after 6 search(es). Will search with parameter 0.8965.
4:13:30.318485 INFO: ==============================================
4:13:30.318565 INFO: Starting optimization step 7.
4:13:30.318625 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:13:30.318684 INFO: Using classic extraction backend
4:13:30.318828 PROGRESS: Extracting batch of 2749 precursors
4:13:30.318895 INFO: === Search parameters used ===
4:13:30.318940 INFO: rt_error       : 831.412233375923
4:13:30.318982 INFO: mobility_error : 0.1
4:13:30.319021 INFO: num_candidates : 3
4:13:30.319062 INFO: ms1_error      : 0.896479238945622
4:13:30.319102 INFO: ms2_error      : 24.37390675904184
4:13:30.319140 INFO: fwhm_rt        : 3.282142400741577
4:13:30.319178 INFO: quant_window   : 3
4:13:30.319216 INFO: ==============================================
4:13:30.320472 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:13:30.320515 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:13:30.320555 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
4:13:30.320575 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.49
4:13:30.321292 INFO: Starting candidate selection
4:13:38.419760 INFO: Starting candidate scoring
4:13:38.929622 INFO: Finished candidate processing
4:13:38.929753 INFO: Collecting candidate features
4:13:38.953357 INFO: Collecting fragment features
4:13:38.961543 INFO: Finished candidate scoring
4:13:38.965368 INFO: performing precursor FDR with 47 features
4:13:38.965425 INFO: Decoy channel: -1
4:13:38.965451 INFO: Competetive: True
4:13:38.969836 INFO: Setting torch num_threads to 2 for FDR classification task
4:13:38.972690 INFO: Using random state 794606 for train-test-split
4:13:38.991128 INFO: Test AUC: 0.492
4:13:38.991205 INFO: Train AUC: 0.492
4:13:38.991235 INFO: AUC difference: 0.08%
4:13:39.209385 INFO: Resetting torch num_threads to 80
4:13:39.210051 PROGRESS: === Extracted 7727 precursors and 82718 fragments ===
4:13:39.210456 INFO: === FDR correction performed with classifier version 15 ===
4:13:39.211163 PROGRESS: ============================= Precursor FDR =============================
4:13:39.211251 PROGRESS: Total precursors accumulated: 1,377
4:13:39.211309 PROGRESS: Target precursors: 844 (61.29%)
4:13:39.211359 PROGRESS: Decoy precursors: 533 (38.71%)
4:13:39.211410 PROGRESS: 
4:13:39.211455 PROGRESS: Precursor Summary:
4:13:39.212463 PROGRESS: Channel   0:	 0.050 FDR:   467; 0.010 FDR:   467; 0.001 FDR:   467
4:13:39.212553 PROGRESS: 
4:13:39.212608 PROGRESS: Protein Summary:
4:13:39.213825 PROGRESS: Channel   0:	 0.050 FDR:   461; 0.010 FDR:   461; 0.001 FDR:   461
4:13:39.213934 PROGRESS: =========================================================================
4:13:39.214092 INFO: Target number of precursors reached.
4:13:39.223331 INFO: fragments_df: keeping 3393 of 82718 [sum(precursor_idx_mask)=14575 sum(mass_error_mask)=82718 stop_rank=3393
4:13:39.322486 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:13:39.452147 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:13:39.589589 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:13:39.725660 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:13:40.126402 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:13:40.126823 INFO: Using score_cutoff 22.606499806594847 (fac=0.99, q=1)
4:13:40.127129 INFO: Updating optimization_manager: fwhm_rt             : 3.282142400741577 -> 3.28452205657959
4:13:40.127206 INFO: Updating optimization_manager: fwhm_mobility       : 0.007533177733421326 -> 0.007900062948465347
4:13:40.127261 INFO: Updating optimization_manager: score_cutoff        : 24.50066178302765 -> 22.606499806594847
4:13:40.127314 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:13:40.128357 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:13:40.129699 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:13:40.130469 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:13:40.132553 INFO: === checking if optimization conditions were reached ===
4:13:40.132651 PROGRESS: === Optimization of ms1_error has been performed 7 time(s); minimum number is 2 ===
4:13:40.134231 INFO: Updating optimization_manager: ms1_error           : 0.896479238945622 -> 0.20435124079209827
4:13:40.134329 PROGRESS: ❌ ms1_error      : optimization incomplete after 7 search(es). Will search with parameter 0.2044.
4:13:40.134392 INFO: ==============================================
4:13:40.134455 INFO: Starting optimization step 8.
4:13:40.134510 PROGRESS: === Extracting elution groups 0 to 600 ===
4:13:40.134561 INFO: Using classic extraction backend
4:13:40.134665 PROGRESS: Extracting batch of 1173 precursors
4:13:40.134728 INFO: === Search parameters used ===
4:13:40.134775 INFO: rt_error       : 831.412233375923
4:13:40.134815 INFO: mobility_error : 0.1
4:13:40.134854 INFO: num_candidates : 3
4:13:40.134891 INFO: ms1_error      : 0.20435124079209827
4:13:40.134929 INFO: ms2_error      : 24.37390675904184
4:13:40.134967 INFO: fwhm_rt        : 3.28452205657959
4:13:40.135005 INFO: quant_window   : 3
4:13:40.135048 INFO: ==============================================
4:13:40.135827 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:13:40.135870 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:13:40.135902 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
4:13:40.135923 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
4:13:40.136589 INFO: Starting candidate selection
4:13:57.355273 INFO: Starting candidate scoring
4:13:57.618301 INFO: Finished candidate processing
4:13:57.618454 INFO: Collecting candidate features
4:13:57.647845 INFO: Collecting fragment features
4:13:57.656403 INFO: Finished candidate scoring
4:13:57.659440 INFO: performing precursor FDR with 47 features
4:13:57.659546 INFO: Decoy channel: -1
4:13:57.659602 INFO: Competetive: True
4:13:57.665875 INFO: Setting torch num_threads to 2 for FDR classification task
4:13:57.670135 INFO: Using random state 794606 for train-test-split
4:13:57.687001 INFO: Test AUC: 0.485
4:13:57.687092 INFO: Train AUC: 0.499
4:13:57.687141 INFO: AUC difference: 2.83%
4:13:57.903268 INFO: Resetting torch num_threads to 80
4:13:57.903808 PROGRESS: === Extracted 3289 precursors and 35411 fragments ===
4:13:57.904207 INFO: === FDR correction performed with classifier version 15 ===
4:13:57.904769 PROGRESS: ============================= Precursor FDR =============================
4:13:57.904856 PROGRESS: Total precursors accumulated: 590
4:13:57.904912 PROGRESS: Target precursors: 366 (62.03%)
4:13:57.905034 PROGRESS: Decoy precursors: 224 (37.97%)
4:13:57.905082 PROGRESS: 
4:13:57.905126 PROGRESS: Precursor Summary:
4:13:57.906070 PROGRESS: Channel   0:	 0.050 FDR:   211; 0.010 FDR:   211; 0.001 FDR:   211
4:13:57.906164 PROGRESS: 
4:13:57.906219 PROGRESS: Protein Summary:
4:13:57.907253 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   210
4:13:57.907342 PROGRESS: =========================================================================
4:13:57.907528 INFO: Target number of precursors reached.
4:13:57.912279 INFO: fragments_df: keeping 1600 of 35411 [sum(precursor_idx_mask)=6542 sum(mass_error_mask)=35411 stop_rank=1600
4:13:58.011287 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:13:58.125777 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:13:58.244264 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:13:58.361600 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:13:58.577869 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:13:58.578289 INFO: Using score_cutoff 21.552225677490235 (fac=0.99, q=1)
4:13:58.578584 INFO: Updating optimization_manager: fwhm_rt             : 3.28452205657959 -> 3.223083972930908
4:13:58.578661 INFO: Updating optimization_manager: fwhm_mobility       : 0.007900062948465347 -> 0.0077647496946156025
4:13:58.578713 INFO: Updating optimization_manager: score_cutoff        : 22.606499806594847 -> 21.552225677490235
4:13:58.578763 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:13:58.579824 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:13:58.581187 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:13:58.581956 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:13:58.584077 INFO: === checking if optimization conditions were reached ===
4:13:58.584173 PROGRESS: === Optimization of ms1_error has been performed 8 time(s); minimum number is 2 ===
4:13:58.586294 INFO: Updating optimization_manager: ms1_error           : 0.20435124079209827 -> 0.10188931495876112
4:13:58.586391 PROGRESS: ❌ ms1_error      : optimization incomplete after 8 search(es). Will search with parameter 0.1019.
4:13:58.586454 INFO: ==============================================
4:13:58.586516 INFO: Starting optimization step 9.
4:13:58.586571 PROGRESS: === Extracting elution groups 0 to 600 ===
4:13:58.586620 INFO: Using classic extraction backend
4:13:58.586720 PROGRESS: Extracting batch of 1173 precursors
4:13:58.586781 INFO: === Search parameters used ===
4:13:58.586833 INFO: rt_error       : 831.412233375923
4:13:58.586875 INFO: mobility_error : 0.1
4:13:58.586915 INFO: num_candidates : 3
4:13:58.586954 INFO: ms1_error      : 0.10188931495876112
4:13:58.586992 INFO: ms2_error      : 24.37390675904184
4:13:58.587029 INFO: fwhm_rt        : 3.223083972930908
4:13:58.587065 INFO: quant_window   : 3
4:13:58.587101 INFO: ==============================================
4:13:58.587901 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:13:58.587944 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:13:58.587976 INFO: FWHM in RT is 3.22 seconds, sigma is 0.71
4:13:58.587996 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.60
4:13:58.588630 INFO: Starting candidate selection
4:14:02.821710 INFO: Starting candidate scoring
4:14:03.094531 INFO: Finished candidate processing
4:14:03.094682 INFO: Collecting candidate features
4:14:03.107907 INFO: Collecting fragment features
4:14:03.112014 INFO: Finished candidate scoring
4:14:03.114020 INFO: performing precursor FDR with 47 features
4:14:03.114073 INFO: Decoy channel: -1
4:14:03.114100 INFO: Competetive: True
4:14:03.117403 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:03.119579 INFO: Using random state 794606 for train-test-split
4:14:03.131310 INFO: Test AUC: 0.471
4:14:03.131371 INFO: Train AUC: 0.497
4:14:03.131401 INFO: AUC difference: 5.21%
4:14:03.131423 WARNING: AUC difference > 5%. This may indicate overfitting.
4:14:03.351030 INFO: Resetting torch num_threads to 80
4:14:03.351733 PROGRESS: === Extracted 3295 precursors and 35465 fragments ===
4:14:03.352249 INFO: === FDR correction performed with classifier version 15 ===
4:14:03.352877 PROGRESS: ============================= Precursor FDR =============================
4:14:03.352984 PROGRESS: Total precursors accumulated: 590
4:14:03.353046 PROGRESS: Target precursors: 366 (62.03%)
4:14:03.353097 PROGRESS: Decoy precursors: 224 (37.97%)
4:14:03.353142 PROGRESS: 
4:14:03.353186 PROGRESS: Precursor Summary:
4:14:03.354139 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:14:03.354229 PROGRESS: 
4:14:03.354284 PROGRESS: Protein Summary:
4:14:03.355331 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:14:03.355425 PROGRESS: =========================================================================
4:14:03.355635 INFO: Target number of precursors reached.
4:14:03.360455 INFO: fragments_df: keeping 1610 of 35465 [sum(precursor_idx_mask)=6437 sum(mass_error_mask)=35465 stop_rank=1610
4:14:03.525423 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:14:03.639417 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:03.760974 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:14:03.877254 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:04.072891 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:04.073417 INFO: Using score_cutoff 22.33981255187988 (fac=0.99, q=1)
4:14:04.073743 INFO: Updating optimization_manager: fwhm_rt             : 3.223083972930908 -> 3.257974147796631
4:14:04.073822 INFO: Updating optimization_manager: fwhm_mobility       : 0.0077647496946156025 -> 0.007873955182731152
4:14:04.073876 INFO: Updating optimization_manager: score_cutoff        : 21.552225677490235 -> 22.33981255187988
4:14:04.073931 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:14:04.075211 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:04.076662 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:14:04.077455 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:04.080147 INFO: === checking if optimization conditions were reached ===
4:14:04.080258 PROGRESS: === Optimization of ms1_error has been performed 9 time(s); minimum number is 2 ===
4:14:04.081974 INFO: Updating optimization_manager: ms1_error           : 0.10188931495876112 -> 0.06788140259905374
4:14:04.082084 PROGRESS: ❌ ms1_error      : optimization incomplete after 9 search(es). Will search with parameter 0.0679.
4:14:04.082159 INFO: ==============================================
4:14:04.082231 INFO: Starting optimization step 10.
4:14:04.082291 PROGRESS: === Extracting elution groups 0 to 600 ===
4:14:04.082346 INFO: Using classic extraction backend
4:14:04.082471 PROGRESS: Extracting batch of 1173 precursors
4:14:04.082538 INFO: === Search parameters used ===
4:14:04.082585 INFO: rt_error       : 831.412233375923
4:14:04.082628 INFO: mobility_error : 0.1
4:14:04.082669 INFO: num_candidates : 3
4:14:04.082710 INFO: ms1_error      : 0.06788140259905374
4:14:04.082750 INFO: ms2_error      : 24.37390675904184
4:14:04.082788 INFO: fwhm_rt        : 3.257974147796631
4:14:04.082828 INFO: quant_window   : 3
4:14:04.082867 INFO: ==============================================
4:14:04.083883 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:14:04.083929 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:14:04.083964 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
4:14:04.083987 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.65
4:14:04.084715 INFO: Starting candidate selection
4:14:07.586496 INFO: Starting candidate scoring
4:14:07.835762 INFO: Finished candidate processing
4:14:07.835860 INFO: Collecting candidate features
4:14:07.849506 INFO: Collecting fragment features
4:14:07.853535 INFO: Finished candidate scoring
4:14:07.855628 INFO: performing precursor FDR with 47 features
4:14:07.855673 INFO: Decoy channel: -1
4:14:07.855699 INFO: Competetive: True
4:14:07.858775 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:07.860964 INFO: Using random state 794606 for train-test-split
4:14:07.872865 INFO: Test AUC: 0.486
4:14:07.872952 INFO: Train AUC: 0.495
4:14:07.872986 INFO: AUC difference: 1.71%
4:14:08.095827 INFO: Resetting torch num_threads to 80
4:14:08.096505 PROGRESS: === Extracted 3303 precursors and 35537 fragments ===
4:14:08.097018 INFO: === FDR correction performed with classifier version 15 ===
4:14:08.097640 PROGRESS: ============================= Precursor FDR =============================
4:14:08.097733 PROGRESS: Total precursors accumulated: 590
4:14:08.097795 PROGRESS: Target precursors: 365 (61.86%)
4:14:08.097848 PROGRESS: Decoy precursors: 225 (38.14%)
4:14:08.097901 PROGRESS: 
4:14:08.097947 PROGRESS: Precursor Summary:
4:14:08.098884 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:14:08.098976 PROGRESS: 
4:14:08.099032 PROGRESS: Protein Summary:
4:14:08.100096 PROGRESS: Channel   0:	 0.050 FDR:   208; 0.010 FDR:   208; 0.001 FDR:   208
4:14:08.100188 PROGRESS: =========================================================================
4:14:08.100346 INFO: Target number of precursors reached.
4:14:08.109125 INFO: fragments_df: keeping 1633 of 35537 [sum(precursor_idx_mask)=6413 sum(mass_error_mask)=35537 stop_rank=1633
4:14:08.239824 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:14:08.353750 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:08.473415 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:14:08.590520 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:08.818136 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:08.818650 INFO: Using score_cutoff 22.134497525024415 (fac=0.99, q=1)
4:14:08.818972 INFO: Updating optimization_manager: fwhm_rt             : 3.257974147796631 -> 3.1917054653167725
4:14:08.819051 INFO: Updating optimization_manager: fwhm_mobility       : 0.007873955182731152 -> 0.007885199040174484
4:14:08.819109 INFO: Updating optimization_manager: score_cutoff        : 22.33981255187988 -> 22.134497525024415
4:14:08.819165 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:14:08.820426 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:08.821879 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:14:08.822663 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:08.825418 INFO: === checking if optimization conditions were reached ===
4:14:08.825536 PROGRESS: === Optimization of ms1_error has been performed 10 time(s); minimum number is 2 ===
4:14:08.827196 INFO: Updating optimization_manager: ms1_error           : 0.06788140259905374 -> 0.06094499964282079
4:14:08.827295 PROGRESS: ❌ ms1_error      : optimization incomplete after 10 search(es). Will search with parameter 0.0609.
4:14:08.827363 INFO: ==============================================
4:14:08.827433 INFO: Starting optimization step 11.
4:14:08.827493 PROGRESS: === Extracting elution groups 0 to 600 ===
4:14:08.827552 INFO: Using classic extraction backend
4:14:08.827680 PROGRESS: Extracting batch of 1173 precursors
4:14:08.827745 INFO: === Search parameters used ===
4:14:08.827794 INFO: rt_error       : 831.412233375923
4:14:08.827837 INFO: mobility_error : 0.1
4:14:08.827879 INFO: num_candidates : 3
4:14:08.827920 INFO: ms1_error      : 0.06094499964282079
4:14:08.827960 INFO: ms2_error      : 24.37390675904184
4:14:08.828000 INFO: fwhm_rt        : 3.1917054653167725
4:14:08.828039 INFO: quant_window   : 3
4:14:08.828079 INFO: ==============================================
4:14:08.829113 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:14:08.829160 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:14:08.829196 INFO: FWHM in RT is 3.19 seconds, sigma is 0.70
4:14:08.829220 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
4:14:08.829910 INFO: Starting candidate selection
4:14:12.874444 INFO: Starting candidate scoring
4:14:13.138179 INFO: Finished candidate processing
4:14:13.138275 INFO: Collecting candidate features
4:14:13.151628 INFO: Collecting fragment features
4:14:13.155257 INFO: Finished candidate scoring
4:14:13.157304 INFO: performing precursor FDR with 47 features
4:14:13.157347 INFO: Decoy channel: -1
4:14:13.157371 INFO: Competetive: True
4:14:13.160233 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:13.162262 INFO: Using random state 794606 for train-test-split
4:14:13.173516 INFO: Test AUC: 0.467
4:14:13.173580 INFO: Train AUC: 0.498
4:14:13.173610 INFO: AUC difference: 6.27%
4:14:13.173632 WARNING: AUC difference > 5%. This may indicate overfitting.
4:14:13.390842 INFO: Resetting torch num_threads to 80
4:14:13.391843 PROGRESS: === Extracted 3298 precursors and 35472 fragments ===
4:14:13.392268 INFO: === FDR correction performed with classifier version 15 ===
4:14:13.392847 PROGRESS: ============================= Precursor FDR =============================
4:14:13.392936 PROGRESS: Total precursors accumulated: 590
4:14:13.393005 PROGRESS: Target precursors: 365 (61.86%)
4:14:13.393055 PROGRESS: Decoy precursors: 225 (38.14%)
4:14:13.393102 PROGRESS: 
4:14:13.393148 PROGRESS: Precursor Summary:
4:14:13.394071 PROGRESS: Channel   0:	 0.050 FDR:   206; 0.010 FDR:   206; 0.001 FDR:   206
4:14:13.394159 PROGRESS: 
4:14:13.394213 PROGRESS: Protein Summary:
4:14:13.395236 PROGRESS: Channel   0:	 0.050 FDR:   206; 0.010 FDR:   206; 0.001 FDR:   206
4:14:13.395324 PROGRESS: =========================================================================
4:14:13.395612 INFO: Target number of precursors reached.
4:14:13.400316 INFO: fragments_df: keeping 1583 of 35472 [sum(precursor_idx_mask)=6318 sum(mass_error_mask)=35472 stop_rank=1583
4:14:13.500764 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:14:13.613670 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:13.733742 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:14:13.848855 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:14.074206 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:14.074644 INFO: Using score_cutoff 22.142485098838804 (fac=0.99, q=1)
4:14:14.074948 INFO: Updating optimization_manager: fwhm_rt             : 3.1917054653167725 -> 3.1660473346710205
4:14:14.075027 INFO: Updating optimization_manager: fwhm_mobility       : 0.007885199040174484 -> 0.007808351423591375
4:14:14.075083 INFO: Updating optimization_manager: score_cutoff        : 22.134497525024415 -> 22.142485098838804
4:14:14.075145 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:14:14.076235 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:14.077699 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:14:14.078480 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:14.083041 INFO: === checking if optimization conditions were reached ===
4:14:14.083169 PROGRESS: === Optimization of ms1_error has been performed 11 time(s); minimum number is 2 ===
4:14:14.084826 INFO: Updating optimization_manager: ms1_error           : 0.06094499964282079 -> 0.05920033394759892
4:14:14.084927 PROGRESS: ❌ ms1_error      : optimization incomplete after 11 search(es). Will search with parameter 0.0592.
4:14:14.085006 INFO: ==============================================
4:14:14.085081 INFO: Starting optimization step 12.
4:14:14.085142 PROGRESS: === Extracting elution groups 0 to 600 ===
4:14:14.085209 INFO: Using classic extraction backend
4:14:14.085404 PROGRESS: Extracting batch of 1173 precursors
4:14:14.085473 INFO: === Search parameters used ===
4:14:14.085518 INFO: rt_error       : 831.412233375923
4:14:14.085567 INFO: mobility_error : 0.1
4:14:14.085609 INFO: num_candidates : 3
4:14:14.085648 INFO: ms1_error      : 0.05920033394759892
4:14:14.085686 INFO: ms2_error      : 24.37390675904184
4:14:14.085724 INFO: fwhm_rt        : 3.1660473346710205
4:14:14.085763 INFO: quant_window   : 3
4:14:14.085801 INFO: ==============================================
4:14:14.087211 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:14:14.087262 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:14:14.087302 INFO: FWHM in RT is 3.17 seconds, sigma is 0.70
4:14:14.087324 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
4:14:14.088026 INFO: Starting candidate selection
4:14:18.070649 INFO: Starting candidate scoring
4:14:18.317403 INFO: Finished candidate processing
4:14:18.317500 INFO: Collecting candidate features
4:14:18.331764 INFO: Collecting fragment features
4:14:18.335840 INFO: Finished candidate scoring
4:14:18.337751 INFO: performing precursor FDR with 47 features
4:14:18.337801 INFO: Decoy channel: -1
4:14:18.337824 INFO: Competetive: True
4:14:18.341538 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:18.343823 INFO: Using random state 794606 for train-test-split
4:14:18.355683 INFO: Test AUC: 0.495
4:14:18.355741 INFO: Train AUC: 0.492
4:14:18.355771 INFO: AUC difference: 0.76%
4:14:18.572370 INFO: Resetting torch num_threads to 80
4:14:18.572911 PROGRESS: === Extracted 3294 precursors and 35410 fragments ===
4:14:18.573380 INFO: === FDR correction performed with classifier version 15 ===
4:14:18.573947 PROGRESS: ============================= Precursor FDR =============================
4:14:18.574033 PROGRESS: Total precursors accumulated: 590
4:14:18.574090 PROGRESS: Target precursors: 363 (61.53%)
4:14:18.574138 PROGRESS: Decoy precursors: 227 (38.47%)
4:14:18.574181 PROGRESS: 
4:14:18.574222 PROGRESS: Precursor Summary:
4:14:18.575137 PROGRESS: Channel   0:	 0.050 FDR:   206; 0.010 FDR:   206; 0.001 FDR:   206
4:14:18.575223 PROGRESS: 
4:14:18.575277 PROGRESS: Protein Summary:
4:14:18.576321 PROGRESS: Channel   0:	 0.050 FDR:   206; 0.010 FDR:   206; 0.001 FDR:   206
4:14:18.576407 PROGRESS: =========================================================================
4:14:18.576557 INFO: Target number of precursors reached.
4:14:18.581282 INFO: fragments_df: keeping 1590 of 35410 [sum(precursor_idx_mask)=6284 sum(mass_error_mask)=35410 stop_rank=1590
4:14:18.680395 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:14:18.793957 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:18.913249 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:14:19.008297 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:20.357690 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:20.358128 INFO: Using score_cutoff 22.15108798599243 (fac=0.99, q=1)
4:14:20.358423 INFO: Updating optimization_manager: fwhm_rt             : 3.1660473346710205 -> 3.1467480659484863
4:14:20.358504 INFO: Updating optimization_manager: fwhm_mobility       : 0.007808351423591375 -> 0.007877597585320473
4:14:20.358559 INFO: Updating optimization_manager: score_cutoff        : 22.142485098838804 -> 22.15108798599243
4:14:20.358612 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:14:20.359699 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:20.361107 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:14:20.361869 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:20.364110 INFO: === checking if optimization conditions were reached ===
4:14:20.364209 PROGRESS: === Optimization of ms1_error has been performed 12 time(s); minimum number is 2 ===
4:14:20.365759 INFO: Updating optimization_manager: ms1_error           : 0.05920033394759892 -> 0.06221550687900619
4:14:20.365861 PROGRESS: ❌ ms1_error      : optimization incomplete after 12 search(es). Will search with parameter 0.0622.
4:14:20.365930 INFO: ==============================================
4:14:20.365996 INFO: Starting optimization step 13.
4:14:20.366050 PROGRESS: === Extracting elution groups 0 to 600 ===
4:14:20.366101 INFO: Using classic extraction backend
4:14:20.366201 PROGRESS: Extracting batch of 1173 precursors
4:14:20.366261 INFO: === Search parameters used ===
4:14:20.366307 INFO: rt_error       : 831.412233375923
4:14:20.366348 INFO: mobility_error : 0.1
4:14:20.366395 INFO: num_candidates : 3
4:14:20.366435 INFO: ms1_error      : 0.06221550687900619
4:14:20.366472 INFO: ms2_error      : 24.37390675904184
4:14:20.366508 INFO: fwhm_rt        : 3.1467480659484863
4:14:20.366545 INFO: quant_window   : 3
4:14:20.366581 INFO: ==============================================
4:14:20.367387 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:14:20.367431 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:14:20.367464 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
4:14:20.367485 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.65
4:14:20.368224 INFO: Starting candidate selection
4:14:24.344776 INFO: Starting candidate scoring
4:14:24.595414 INFO: Finished candidate processing
4:14:24.596296 INFO: Collecting candidate features
4:14:24.611863 INFO: Collecting fragment features
4:14:24.615629 INFO: Finished candidate scoring
4:14:24.618793 INFO: performing precursor FDR with 47 features
4:14:24.618839 INFO: Decoy channel: -1
4:14:24.618863 INFO: Competetive: True
4:14:24.621780 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:24.623805 INFO: Using random state 794606 for train-test-split
4:14:24.635037 INFO: Test AUC: 0.518
4:14:24.635096 INFO: Train AUC: 0.490
4:14:24.635125 INFO: AUC difference: 5.66%
4:14:24.635149 WARNING: AUC difference > 5%. This may indicate overfitting.
4:14:24.848047 INFO: Resetting torch num_threads to 80
4:14:24.848617 PROGRESS: === Extracted 3300 precursors and 35483 fragments ===
4:14:24.849028 INFO: === FDR correction performed with classifier version 15 ===
4:14:24.849617 PROGRESS: ============================= Precursor FDR =============================
4:14:24.849707 PROGRESS: Total precursors accumulated: 590
4:14:24.849763 PROGRESS: Target precursors: 366 (62.03%)
4:14:24.849812 PROGRESS: Decoy precursors: 224 (37.97%)
4:14:24.849854 PROGRESS: 
4:14:24.849896 PROGRESS: Precursor Summary:
4:14:24.850824 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:14:24.850909 PROGRESS: 
4:14:24.850961 PROGRESS: Protein Summary:
4:14:24.851999 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:14:24.852091 PROGRESS: =========================================================================
4:14:24.852215 INFO: Target number of precursors reached.
4:14:24.856876 INFO: fragments_df: keeping 1608 of 35483 [sum(precursor_idx_mask)=6438 sum(mass_error_mask)=35483 stop_rank=1608
4:14:24.956029 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:14:25.059430 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:25.154631 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:14:25.250008 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:25.439122 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:25.439550 INFO: Using score_cutoff 22.513556449127197 (fac=0.99, q=1)
4:14:25.439839 INFO: Updating optimization_manager: fwhm_rt             : 3.1467480659484863 -> 3.2222843170166016
4:14:25.439916 INFO: Updating optimization_manager: fwhm_mobility       : 0.007877597585320473 -> 0.007885199040174484
4:14:25.439968 INFO: Updating optimization_manager: score_cutoff        : 22.15108798599243 -> 22.513556449127197
4:14:25.440018 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:14:25.441095 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:25.442452 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:14:25.443238 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:25.445401 INFO: === checking if optimization conditions were reached ===
4:14:25.445500 PROGRESS: === Optimization of ms1_error has been performed 13 time(s); minimum number is 2 ===
4:14:25.447029 INFO: Updating optimization_manager: ms1_error           : 0.06221550687900619 -> 0.0626598859317545
4:14:25.447127 PROGRESS: ❌ ms1_error      : optimization incomplete after 13 search(es). Will search with parameter 0.0627.
4:14:25.447198 INFO: ==============================================
4:14:25.447260 INFO: Starting optimization step 14.
4:14:25.447316 PROGRESS: === Extracting elution groups 0 to 600 ===
4:14:25.447366 INFO: Using classic extraction backend
4:14:25.447490 PROGRESS: Extracting batch of 1173 precursors
4:14:25.447552 INFO: === Search parameters used ===
4:14:25.447597 INFO: rt_error       : 831.412233375923
4:14:25.447637 INFO: mobility_error : 0.1
4:14:25.447677 INFO: num_candidates : 3
4:14:25.447716 INFO: ms1_error      : 0.0626598859317545
4:14:25.447754 INFO: ms2_error      : 24.37390675904184
4:14:25.447794 INFO: fwhm_rt        : 3.2222843170166016
4:14:25.447831 INFO: quant_window   : 3
4:14:25.447868 INFO: ==============================================
4:14:25.448787 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:14:25.448830 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:14:25.448861 INFO: FWHM in RT is 3.22 seconds, sigma is 0.71
4:14:25.448882 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
4:14:25.449519 INFO: Starting candidate selection
4:14:28.998930 INFO: Starting candidate scoring
4:14:29.264870 INFO: Finished candidate processing
4:14:29.265011 INFO: Collecting candidate features
4:14:29.278156 INFO: Collecting fragment features
4:14:29.283127 INFO: Finished candidate scoring
4:14:29.286128 INFO: performing precursor FDR with 47 features
4:14:29.286175 INFO: Decoy channel: -1
4:14:29.286200 INFO: Competetive: True
4:14:29.289383 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:29.291460 INFO: Using random state 794606 for train-test-split
4:14:29.302944 INFO: Test AUC: 0.474
4:14:29.303003 INFO: Train AUC: 0.499
4:14:29.303031 INFO: AUC difference: 4.97%
4:14:29.516551 INFO: Resetting torch num_threads to 80
4:14:29.517142 PROGRESS: === Extracted 3293 precursors and 35372 fragments ===
4:14:29.517562 INFO: === FDR correction performed with classifier version 15 ===
4:14:29.518136 PROGRESS: ============================= Precursor FDR =============================
4:14:29.518224 PROGRESS: Total precursors accumulated: 590
4:14:29.518282 PROGRESS: Target precursors: 363 (61.53%)
4:14:29.518332 PROGRESS: Decoy precursors: 227 (38.47%)
4:14:29.518377 PROGRESS: 
4:14:29.518420 PROGRESS: Precursor Summary:
4:14:29.519338 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:14:29.519427 PROGRESS: 
4:14:29.519483 PROGRESS: Protein Summary:
4:14:29.520513 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:14:29.520603 PROGRESS: =========================================================================
4:14:29.520738 INFO: Target number of precursors reached.
4:14:29.525408 INFO: fragments_df: keeping 1591 of 35372 [sum(precursor_idx_mask)=6384 sum(mass_error_mask)=35372 stop_rank=1591
4:14:29.624513 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:14:29.728647 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:29.824876 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:14:29.920876 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:30.108481 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:30.108913 INFO: Using score_cutoff 21.475324690246584 (fac=0.99, q=1)
4:14:30.109235 INFO: Updating optimization_manager: fwhm_rt             : 3.2222843170166016 -> 3.2222843170166016
4:14:30.109313 INFO: Updating optimization_manager: fwhm_mobility       : 0.007885199040174484 -> 0.007873955182731152
4:14:30.109369 INFO: Updating optimization_manager: score_cutoff        : 22.513556449127197 -> 21.475324690246584
4:14:30.109421 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:14:30.110516 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:30.111871 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:14:30.112648 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:30.114836 INFO: === checking if optimization conditions were reached ===
4:14:30.114948 PROGRESS: === Optimization of ms1_error has been performed 14 time(s); minimum number is 2 ===
4:14:30.116521 INFO: Updating optimization_manager: ms1_error           : 0.0626598859317545 -> 0.0623602792132915
4:14:30.116618 PROGRESS: ❌ ms1_error      : optimization incomplete after 14 search(es). Will search with parameter 0.0624.
4:14:30.116682 INFO: ==============================================
4:14:30.116746 INFO: Starting optimization step 15.
4:14:30.116801 PROGRESS: === Extracting elution groups 0 to 600 ===
4:14:30.116853 INFO: Using classic extraction backend
4:14:30.116961 PROGRESS: Extracting batch of 1173 precursors
4:14:30.117028 INFO: === Search parameters used ===
4:14:30.117073 INFO: rt_error       : 831.412233375923
4:14:30.117115 INFO: mobility_error : 0.1
4:14:30.117238 INFO: num_candidates : 3
4:14:30.117284 INFO: ms1_error      : 0.0623602792132915
4:14:30.117325 INFO: ms2_error      : 24.37390675904184
4:14:30.117364 INFO: fwhm_rt        : 3.2222843170166016
4:14:30.117403 INFO: quant_window   : 3
4:14:30.117441 INFO: ==============================================
4:14:30.118250 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:14:30.118294 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:14:30.118327 INFO: FWHM in RT is 3.22 seconds, sigma is 0.71
4:14:30.118348 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.65
4:14:30.118966 INFO: Starting candidate selection
4:14:33.474486 INFO: Starting candidate scoring
4:14:57.003002 INFO: Finished candidate processing
4:14:57.003216 INFO: Collecting candidate features
4:14:57.034723 INFO: Collecting fragment features
4:14:57.043751 INFO: Finished candidate scoring
4:14:57.047303 INFO: performing precursor FDR with 47 features
4:14:57.047411 INFO: Decoy channel: -1
4:14:57.047470 INFO: Competetive: True
4:14:57.054818 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:57.058955 INFO: Using random state 794606 for train-test-split
4:14:57.077556 INFO: Test AUC: 0.494
4:14:57.077654 INFO: Train AUC: 0.495
4:14:57.077702 INFO: AUC difference: 0.35%
4:14:57.299344 INFO: Resetting torch num_threads to 80
4:14:57.299911 PROGRESS: === Extracted 3287 precursors and 35316 fragments ===
4:14:57.300347 INFO: === FDR correction performed with classifier version 15 ===
4:14:57.300928 PROGRESS: ============================= Precursor FDR =============================
4:14:57.301032 PROGRESS: Total precursors accumulated: 590
4:14:57.301090 PROGRESS: Target precursors: 368 (62.37%)
4:14:57.301140 PROGRESS: Decoy precursors: 222 (37.63%)
4:14:57.301184 PROGRESS: 
4:14:57.301227 PROGRESS: Precursor Summary:
4:14:57.302158 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:14:57.302247 PROGRESS: 
4:14:57.302301 PROGRESS: Protein Summary:
4:14:57.303366 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:14:57.303454 PROGRESS: =========================================================================
4:14:57.303629 INFO: Target number of precursors reached.
4:14:57.308347 INFO: fragments_df: keeping 1601 of 35316 [sum(precursor_idx_mask)=6449 sum(mass_error_mask)=35316 stop_rank=1601
4:14:57.408576 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:14:57.516179 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:57.615213 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:14:57.711855 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:57.901275 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:57.901705 INFO: Using score_cutoff 22.15357491989136 (fac=0.99, q=1)
4:14:57.902001 INFO: Updating optimization_manager: fwhm_rt             : 3.2222843170166016 -> 3.214820384979248
4:14:57.902079 INFO: Updating optimization_manager: fwhm_mobility       : 0.007873955182731152 -> 0.007742747664451599
4:14:57.902131 INFO: Updating optimization_manager: score_cutoff        : 21.475324690246584 -> 22.15357491989136
4:14:57.902184 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:14:57.903273 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:57.904710 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:14:57.905503 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:57.907653 INFO: === checking if optimization conditions were reached ===
4:14:57.907752 PROGRESS: === Optimization of ms1_error has been performed 15 time(s); minimum number is 2 ===
4:14:57.909337 INFO: Updating optimization_manager: ms1_error           : 0.0623602792132915 -> 0.056250298841950624
4:14:57.909438 PROGRESS: ❌ ms1_error      : optimization incomplete after 15 search(es). Will search with parameter 0.0563.
4:14:57.909502 INFO: ==============================================
4:14:57.909575 INFO: Starting optimization step 16.
4:14:57.909634 PROGRESS: === Extracting elution groups 0 to 600 ===
4:14:57.909689 INFO: Using classic extraction backend
4:14:57.909811 PROGRESS: Extracting batch of 1173 precursors
4:14:57.909880 INFO: === Search parameters used ===
4:14:57.909938 INFO: rt_error       : 831.412233375923
4:14:57.909995 INFO: mobility_error : 0.1
4:14:57.910043 INFO: num_candidates : 3
4:14:57.910089 INFO: ms1_error      : 0.056250298841950624
4:14:57.910129 INFO: ms2_error      : 24.37390675904184
4:14:57.910167 INFO: fwhm_rt        : 3.214820384979248
4:14:57.910204 INFO: quant_window   : 3
4:14:57.910241 INFO: ==============================================
4:14:57.911053 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:14:57.911096 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:14:57.911129 INFO: FWHM in RT is 3.21 seconds, sigma is 0.71
4:14:57.911149 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.59
4:14:57.912012 INFO: Starting candidate selection
4:15:01.522318 INFO: Starting candidate scoring
4:15:01.765926 INFO: Finished candidate processing
4:15:01.766056 INFO: Collecting candidate features
4:15:01.780227 INFO: Collecting fragment features
4:15:01.783813 INFO: Finished candidate scoring
4:15:01.785856 INFO: performing precursor FDR with 47 features
4:15:01.785904 INFO: Decoy channel: -1
4:15:01.785928 INFO: Competetive: True
4:15:01.788825 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:01.790884 INFO: Using random state 794606 for train-test-split
4:15:01.801252 INFO: Test AUC: 0.508
4:15:01.801308 INFO: Train AUC: 0.492
4:15:01.801337 INFO: AUC difference: 3.28%
4:15:02.020064 INFO: Resetting torch num_threads to 80
4:15:02.020640 PROGRESS: === Extracted 3290 precursors and 35457 fragments ===
4:15:02.021055 INFO: === FDR correction performed with classifier version 15 ===
4:15:02.021631 PROGRESS: ============================= Precursor FDR =============================
4:15:02.021716 PROGRESS: Total precursors accumulated: 590
4:15:02.021781 PROGRESS: Target precursors: 365 (61.86%)
4:15:02.021831 PROGRESS: Decoy precursors: 225 (38.14%)
4:15:02.021875 PROGRESS: 
4:15:02.021918 PROGRESS: Precursor Summary:
4:15:02.022843 PROGRESS: Channel   0:	 0.050 FDR:   207; 0.010 FDR:   207; 0.001 FDR:   207
4:15:02.022931 PROGRESS: 
4:15:02.022987 PROGRESS: Protein Summary:
4:15:02.024034 PROGRESS: Channel   0:	 0.050 FDR:   207; 0.010 FDR:   207; 0.001 FDR:   207
4:15:02.024122 PROGRESS: =========================================================================
4:15:02.024259 INFO: Target number of precursors reached.
4:15:02.028909 INFO: fragments_df: keeping 1616 of 35457 [sum(precursor_idx_mask)=6403 sum(mass_error_mask)=35457 stop_rank=1616
4:15:02.148333 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:15:02.250432 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:02.349311 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:15:02.444659 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:02.633725 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:02.634149 INFO: Using score_cutoff 22.152495128631593 (fac=0.99, q=1)
4:15:02.634442 INFO: Updating optimization_manager: fwhm_rt             : 3.214820384979248 -> 3.225486993789673
4:15:02.634529 INFO: Updating optimization_manager: fwhm_mobility       : 0.007742747664451599 -> 0.007885199040174484
4:15:02.634585 INFO: Updating optimization_manager: score_cutoff        : 22.15357491989136 -> 22.152495128631593
4:15:02.634639 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:15:02.635702 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:02.637070 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:15:02.637852 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:02.640075 INFO: === checking if optimization conditions were reached ===
4:15:02.640177 PROGRESS: === Optimization of ms1_error has been performed 16 time(s); minimum number is 2 ===
4:15:02.641737 INFO: Updating optimization_manager: ms1_error           : 0.056250298841950624 -> 0.05783593812309967
4:15:02.641835 PROGRESS: ❌ ms1_error      : optimization incomplete after 16 search(es). Will search with parameter 0.0578.
4:15:02.641899 INFO: ==============================================
4:15:02.641963 INFO: Starting optimization step 17.
4:15:02.642019 PROGRESS: === Extracting elution groups 0 to 600 ===
4:15:02.642071 INFO: Using classic extraction backend
4:15:02.642174 PROGRESS: Extracting batch of 1173 precursors
4:15:02.642237 INFO: === Search parameters used ===
4:15:02.642282 INFO: rt_error       : 831.412233375923
4:15:02.642324 INFO: mobility_error : 0.1
4:15:02.642365 INFO: num_candidates : 3
4:15:02.642402 INFO: ms1_error      : 0.05783593812309967
4:15:02.642441 INFO: ms2_error      : 24.37390675904184
4:15:02.642477 INFO: fwhm_rt        : 3.225486993789673
4:15:02.642515 INFO: quant_window   : 3
4:15:02.642553 INFO: ==============================================
4:15:02.643345 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:15:02.643388 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:15:02.643421 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
4:15:02.643442 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
4:15:02.644103 INFO: Starting candidate selection
4:15:06.827732 INFO: Starting candidate scoring
4:15:07.082819 INFO: Finished candidate processing
4:15:07.082951 INFO: Collecting candidate features
4:15:07.096668 INFO: Collecting fragment features
4:15:07.100251 INFO: Finished candidate scoring
4:15:07.102248 INFO: performing precursor FDR with 47 features
4:15:07.102294 INFO: Decoy channel: -1
4:15:07.102319 INFO: Competetive: True
4:15:07.105149 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:07.107135 INFO: Using random state 794606 for train-test-split
4:15:07.118124 INFO: Test AUC: 0.479
4:15:07.118181 INFO: Train AUC: 0.494
4:15:07.118211 INFO: AUC difference: 3.01%
4:15:07.338536 INFO: Resetting torch num_threads to 80
4:15:07.339077 PROGRESS: === Extracted 3284 precursors and 35421 fragments ===
4:15:07.339483 INFO: === FDR correction performed with classifier version 15 ===
4:15:07.340064 PROGRESS: ============================= Precursor FDR =============================
4:15:07.340156 PROGRESS: Total precursors accumulated: 590
4:15:07.340214 PROGRESS: Target precursors: 367 (62.20%)
4:15:07.340263 PROGRESS: Decoy precursors: 223 (37.80%)
4:15:07.340308 PROGRESS: 
4:15:07.340351 PROGRESS: Precursor Summary:
4:15:07.341304 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   210
4:15:07.341396 PROGRESS: 
4:15:07.341450 PROGRESS: Protein Summary:
4:15:07.342505 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   210
4:15:07.342596 PROGRESS: =========================================================================
4:15:07.342732 INFO: Target number of precursors reached.
4:15:07.347425 INFO: fragments_df: keeping 1600 of 35421 [sum(precursor_idx_mask)=6436 sum(mass_error_mask)=35421 stop_rank=1600
4:15:07.451294 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:15:07.559494 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:07.659630 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:15:07.755303 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:07.938884 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:07.939304 INFO: Using score_cutoff 21.482334609603882 (fac=0.99, q=1)
4:15:07.939599 INFO: Updating optimization_manager: fwhm_rt             : 3.225486993789673 -> 3.2357983589172363
4:15:07.939683 INFO: Updating optimization_manager: fwhm_mobility       : 0.007885199040174484 -> 0.007811994291841984
4:15:07.939738 INFO: Updating optimization_manager: score_cutoff        : 22.152495128631593 -> 21.482334609603882
4:15:07.939789 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:15:07.940848 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:07.942206 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:15:07.942980 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:07.945128 INFO: === checking if optimization conditions were reached ===
4:15:07.945225 PROGRESS: === Optimization of ms1_error has been performed 17 time(s); minimum number is 2 ===
4:15:07.946835 INFO: Updating optimization_manager: ms1_error           : 0.05783593812309967 -> 0.05822671246563424
4:15:07.946932 PROGRESS: ❌ ms1_error      : optimization incomplete after 17 search(es). Will search with parameter 0.0582.
4:15:07.946996 INFO: ==============================================
4:15:07.947062 INFO: Starting optimization step 18.
4:15:07.947119 PROGRESS: === Extracting elution groups 0 to 600 ===
4:15:07.947171 INFO: Using classic extraction backend
4:15:07.947272 PROGRESS: Extracting batch of 1173 precursors
4:15:07.947337 INFO: === Search parameters used ===
4:15:07.947394 INFO: rt_error       : 831.412233375923
4:15:07.947438 INFO: mobility_error : 0.1
4:15:07.947479 INFO: num_candidates : 3
4:15:07.947525 INFO: ms1_error      : 0.05822671246563424
4:15:07.947566 INFO: ms2_error      : 24.37390675904184
4:15:07.947607 INFO: fwhm_rt        : 3.2357983589172363
4:15:07.947646 INFO: quant_window   : 3
4:15:07.947684 INFO: ==============================================
4:15:07.949102 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:15:07.949147 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:15:07.949179 INFO: FWHM in RT is 3.24 seconds, sigma is 0.71
4:15:07.949199 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
4:15:07.949861 INFO: Starting candidate selection
4:15:11.757063 INFO: Starting candidate scoring
4:15:12.023281 INFO: Finished candidate processing
4:15:12.023374 INFO: Collecting candidate features
4:15:12.036101 INFO: Collecting fragment features
4:15:12.039806 INFO: Finished candidate scoring
4:15:12.041692 INFO: performing precursor FDR with 47 features
4:15:12.041736 INFO: Decoy channel: -1
4:15:12.041760 INFO: Competetive: True
4:15:12.045261 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:12.047641 INFO: Using random state 794606 for train-test-split
4:15:12.058835 INFO: Test AUC: 0.504
4:15:12.058890 INFO: Train AUC: 0.490
4:15:12.058921 INFO: AUC difference: 2.96%
4:15:12.278681 INFO: Resetting torch num_threads to 80
4:15:12.279261 PROGRESS: === Extracted 3284 precursors and 35394 fragments ===
4:15:12.279737 INFO: === FDR correction performed with classifier version 15 ===
4:15:12.280313 PROGRESS: ============================= Precursor FDR =============================
4:15:12.280398 PROGRESS: Total precursors accumulated: 590
4:15:12.280457 PROGRESS: Target precursors: 368 (62.37%)
4:15:12.280506 PROGRESS: Decoy precursors: 222 (37.63%)
4:15:12.280551 PROGRESS: 
4:15:12.280593 PROGRESS: Precursor Summary:
4:15:12.281520 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   210
4:15:12.281609 PROGRESS: 
4:15:12.281663 PROGRESS: Protein Summary:
4:15:12.282716 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   210
4:15:12.282803 PROGRESS: =========================================================================
4:15:12.283044 INFO: Target number of precursors reached.
4:15:12.287857 INFO: fragments_df: keeping 1608 of 35394 [sum(precursor_idx_mask)=6462 sum(mass_error_mask)=35394 stop_rank=1608
4:15:12.387426 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:15:12.507568 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:12.626588 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:15:12.745286 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:12.964262 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:12.964683 INFO: Using score_cutoff 20.31514855670929 (fac=0.99, q=1)
4:15:12.965018 INFO: Updating optimization_manager: fwhm_rt             : 3.2357983589172363 -> 3.268490791320801
4:15:12.965099 INFO: Updating optimization_manager: fwhm_mobility       : 0.007811994291841984 -> 0.007767566479742527
4:15:12.965152 INFO: Updating optimization_manager: score_cutoff        : 21.482334609603882 -> 20.31514855670929
4:15:12.965209 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:15:12.966284 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:12.967622 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:15:12.968394 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:12.970574 INFO: === checking if optimization conditions were reached ===
4:15:12.970685 PROGRESS: === Optimization of ms1_error has been performed 18 time(s); minimum number is 2 ===
4:15:12.972326 INFO: Updating optimization_manager: ms1_error           : 0.05822671246563424 -> 0.058014911501835
4:15:12.972425 PROGRESS: ❌ ms1_error      : optimization incomplete after 18 search(es). Will search with parameter 0.0580.
4:15:12.972488 INFO: ==============================================
4:15:12.972557 INFO: Starting optimization step 19.
4:15:12.972721 PROGRESS: === Extracting elution groups 0 to 600 ===
4:15:12.972784 INFO: Using classic extraction backend
4:15:12.972930 PROGRESS: Extracting batch of 1173 precursors
4:15:12.973007 INFO: === Search parameters used ===
4:15:12.973054 INFO: rt_error       : 831.412233375923
4:15:12.973095 INFO: mobility_error : 0.1
4:15:12.973136 INFO: num_candidates : 3
4:15:12.973176 INFO: ms1_error      : 0.058014911501835
4:15:12.973216 INFO: ms2_error      : 24.37390675904184
4:15:12.973254 INFO: fwhm_rt        : 3.268490791320801
4:15:12.973293 INFO: quant_window   : 3
4:15:12.973332 INFO: ==============================================
4:15:12.974256 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:15:12.974299 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:15:12.974339 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
4:15:12.974360 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.60
4:15:12.975059 INFO: Starting candidate selection
4:15:17.457608 INFO: Starting candidate scoring
4:15:17.702216 INFO: Finished candidate processing
4:15:17.702971 INFO: Collecting candidate features
4:15:17.716104 INFO: Collecting fragment features
4:15:17.719565 INFO: Finished candidate scoring
4:15:17.721920 INFO: performing precursor FDR with 47 features
4:15:17.722018 INFO: Decoy channel: -1
4:15:17.722074 INFO: Competetive: True
4:15:17.727854 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:17.731589 INFO: Using random state 794606 for train-test-split
4:15:17.748136 INFO: Test AUC: 0.525
4:15:17.748226 INFO: Train AUC: 0.486
4:15:17.748274 INFO: AUC difference: 8.10%
4:15:17.748312 WARNING: AUC difference > 5%. This may indicate overfitting.
4:15:17.968575 INFO: Resetting torch num_threads to 80
4:15:17.969131 PROGRESS: === Extracted 3284 precursors and 35397 fragments ===
4:15:17.969536 INFO: === FDR correction performed with classifier version 15 ===
4:15:17.970100 PROGRESS: ============================= Precursor FDR =============================
4:15:17.970187 PROGRESS: Total precursors accumulated: 590
4:15:17.970245 PROGRESS: Target precursors: 370 (62.71%)
4:15:17.970295 PROGRESS: Decoy precursors: 220 (37.29%)
4:15:17.970348 PROGRESS: 
4:15:17.970393 PROGRESS: Precursor Summary:
4:15:17.971303 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   210
4:15:17.971400 PROGRESS: 
4:15:17.971455 PROGRESS: Protein Summary:
4:15:17.972513 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   210
4:15:17.972600 PROGRESS: =========================================================================
4:15:17.972731 INFO: Target number of precursors reached.
4:15:17.977361 INFO: fragments_df: keeping 1594 of 35397 [sum(precursor_idx_mask)=6456 sum(mass_error_mask)=35397 stop_rank=1594
4:15:18.076446 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:15:18.180184 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:18.277945 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:15:18.372719 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:18.557877 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:18.558295 INFO: Using score_cutoff 20.317897073364257 (fac=0.99, q=1)
4:15:18.558590 INFO: Updating optimization_manager: fwhm_rt             : 3.268490791320801 -> 3.3044421672821045
4:15:18.558673 INFO: Updating optimization_manager: fwhm_mobility       : 0.007767566479742527 -> 0.0077377501875162125
4:15:18.558726 INFO: Updating optimization_manager: score_cutoff        : 20.31514855670929 -> 20.317897073364257
4:15:18.558778 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:15:18.559845 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:18.561201 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:15:18.561962 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:18.564080 INFO: === checking if optimization conditions were reached ===
4:15:18.564179 PROGRESS: === Optimization of ms1_error has been performed 19 time(s); minimum number is 2 ===
4:15:18.565760 INFO: Updating optimization_manager: ms1_error           : 0.058014911501835 -> 0.0592737055907031
4:15:18.565859 PROGRESS: ❌ ms1_error      : optimization incomplete after 19 search(es). Will search with parameter 0.0593.
4:15:18.565924 INFO: ==============================================
4:15:18.565987 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
4:15:18.566078 INFO: Starting optimization step 0.
4:15:18.566139 PROGRESS: === Extracting elution groups 0 to 600 ===
4:15:18.566191 INFO: Using classic extraction backend
4:15:18.566296 PROGRESS: Extracting batch of 1173 precursors
4:15:18.566359 INFO: === Search parameters used ===
4:15:18.566404 INFO: rt_error       : 831.412233375923
4:15:18.566447 INFO: mobility_error : 0.1
4:15:18.566487 INFO: num_candidates : 3
4:15:18.566527 INFO: ms1_error      : 0.0592737055907031
4:15:18.566566 INFO: ms2_error      : 24.37390675904184
4:15:18.566604 INFO: fwhm_rt        : 3.3044421672821045
4:15:18.566644 INFO: quant_window   : 3
4:15:18.566682 INFO: ==============================================
4:15:18.567457 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:15:18.567504 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:15:18.567540 INFO: FWHM in RT is 3.30 seconds, sigma is 0.73
4:15:18.567562 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.59
4:15:18.568203 INFO: Starting candidate selection
4:15:22.795189 INFO: Starting candidate scoring
4:15:23.046503 INFO: Finished candidate processing
4:15:23.046686 INFO: Collecting candidate features
4:15:23.061877 INFO: Collecting fragment features
4:15:23.065417 INFO: Finished candidate scoring
4:15:23.067139 INFO: performing precursor FDR with 47 features
4:15:23.067183 INFO: Decoy channel: -1
4:15:23.067208 INFO: Competetive: True
4:15:23.070119 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:23.072069 INFO: Using random state 794606 for train-test-split
4:15:23.083102 INFO: Test AUC: 0.489
4:15:23.083165 INFO: Train AUC: 0.497
4:15:23.083194 INFO: AUC difference: 1.63%
4:15:23.295631 INFO: Resetting torch num_threads to 80
4:15:23.296161 PROGRESS: === Extracted 3287 precursors and 35433 fragments ===
4:15:23.296573 INFO: === FDR correction performed with classifier version 15 ===
4:15:23.297151 PROGRESS: ============================= Precursor FDR =============================
4:15:23.297239 PROGRESS: Total precursors accumulated: 590
4:15:23.297297 PROGRESS: Target precursors: 372 (63.05%)
4:15:23.297345 PROGRESS: Decoy precursors: 218 (36.95%)
4:15:23.297389 PROGRESS: 
4:15:23.297430 PROGRESS: Precursor Summary:
4:15:23.298330 PROGRESS: Channel   0:	 0.050 FDR:   212; 0.010 FDR:   212; 0.001 FDR:   212
4:15:23.298416 PROGRESS: 
4:15:23.298470 PROGRESS: Protein Summary:
4:15:23.299497 PROGRESS: Channel   0:	 0.050 FDR:   212; 0.010 FDR:   212; 0.001 FDR:   212
4:15:23.299582 PROGRESS: =========================================================================
4:15:23.299708 INFO: Target number of precursors reached.
4:15:23.304299 INFO: fragments_df: keeping 1619 of 35433 [sum(precursor_idx_mask)=6506 sum(mass_error_mask)=35433 stop_rank=1619
4:15:23.403329 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:15:23.520171 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:23.638332 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:15:23.757192 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:23.987245 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:23.987670 INFO: Using score_cutoff 20.32537441635132 (fac=0.99, q=1)
4:15:23.987967 INFO: Updating optimization_manager: fwhm_rt             : 3.3044421672821045 -> 3.2815091609954834
4:15:23.988052 INFO: Updating optimization_manager: fwhm_mobility       : 0.0077377501875162125 -> 0.007767566479742527
4:15:23.988107 INFO: Updating optimization_manager: score_cutoff        : 20.317897073364257 -> 20.32537441635132
4:15:23.988159 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:15:23.989247 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:23.990594 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:15:23.991357 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:23.993500 INFO: === checking if optimization conditions were reached ===
4:15:23.993599 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
4:15:23.994914 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.09716966921634441
4:15:23.995008 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0972.
4:15:23.995072 INFO: ==============================================
4:15:23.995135 INFO: Starting optimization step 1.
4:15:23.995189 PROGRESS: === Extracting elution groups 0 to 600 ===
4:15:23.995244 INFO: Using classic extraction backend
4:15:23.995348 PROGRESS: Extracting batch of 1173 precursors
4:15:23.995413 INFO: === Search parameters used ===
4:15:23.995460 INFO: rt_error       : 831.412233375923
4:15:23.995500 INFO: mobility_error : 0.09716966921634441
4:15:23.995539 INFO: num_candidates : 3
4:15:23.995584 INFO: ms1_error      : 0.0592737055907031
4:15:23.995625 INFO: ms2_error      : 24.37390675904184
4:15:23.995665 INFO: fwhm_rt        : 3.2815091609954834
4:15:23.995704 INFO: quant_window   : 3
4:15:23.995743 INFO: ==============================================
4:15:23.996716 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:15:23.996761 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:15:23.996794 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
4:15:23.996814 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.60
4:15:23.997511 INFO: Starting candidate selection
4:15:28.086928 INFO: Starting candidate scoring
4:15:28.331376 INFO: Finished candidate processing
4:15:28.331572 INFO: Collecting candidate features
4:15:28.345157 INFO: Collecting fragment features
4:15:28.349053 INFO: Finished candidate scoring
4:15:28.350816 INFO: performing precursor FDR with 47 features
4:15:28.350869 INFO: Decoy channel: -1
4:15:28.350893 INFO: Competetive: True
4:15:28.354038 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:28.356014 INFO: Using random state 794606 for train-test-split
4:15:28.366485 INFO: Test AUC: 0.499
4:15:28.366546 INFO: Train AUC: 0.492
4:15:28.366575 INFO: AUC difference: 1.38%
4:15:28.583759 INFO: Resetting torch num_threads to 80
4:15:28.584296 PROGRESS: === Extracted 3281 precursors and 35258 fragments ===
4:15:28.584704 INFO: === FDR correction performed with classifier version 15 ===
4:15:28.585277 PROGRESS: ============================= Precursor FDR =============================
4:15:28.585366 PROGRESS: Total precursors accumulated: 588
4:15:28.585423 PROGRESS: Target precursors: 369 (62.76%)
4:15:28.585472 PROGRESS: Decoy precursors: 219 (37.24%)
4:15:28.585515 PROGRESS: 
4:15:28.585557 PROGRESS: Precursor Summary:
4:15:28.586472 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:15:28.586558 PROGRESS: 
4:15:28.586612 PROGRESS: Protein Summary:
4:15:28.587630 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:   209
4:15:28.587717 PROGRESS: =========================================================================
4:15:28.587862 INFO: Target number of precursors reached.
4:15:28.592520 INFO: fragments_df: keeping 1598 of 35258 [sum(precursor_idx_mask)=6408 sum(mass_error_mask)=35258 stop_rank=1598
4:15:28.838902 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:15:28.955975 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:29.075092 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:15:29.174245 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:29.362949 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:29.363359 INFO: Using score_cutoff 22.00701780395508 (fac=0.99, q=1)
4:15:29.363654 INFO: Updating optimization_manager: fwhm_rt             : 3.2815091609954834 -> 3.284703493118286
4:15:29.363731 INFO: Updating optimization_manager: fwhm_mobility       : 0.007767566479742527 -> 0.00789401400834322
4:15:29.363786 INFO: Updating optimization_manager: score_cutoff        : 20.32537441635132 -> 22.00701780395508
4:15:29.363838 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:15:29.364881 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:29.366232 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:15:29.366996 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:29.369814 INFO: === checking if optimization conditions were reached ===
4:15:29.369914 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
4:15:29.371294 INFO: Updating optimization_manager: mobility_error      : 0.09716966921634441 -> 0.09922484285883783
4:15:29.371393 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0992.
4:15:29.371458 INFO: ==============================================
4:15:29.371523 INFO: Starting optimization step 2.
4:15:29.371590 PROGRESS: === Extracting elution groups 0 to 600 ===
4:15:29.371644 INFO: Using classic extraction backend
4:15:29.371748 PROGRESS: Extracting batch of 1173 precursors
4:15:29.371812 INFO: === Search parameters used ===
4:15:29.371859 INFO: rt_error       : 831.412233375923
4:15:29.371903 INFO: mobility_error : 0.09922484285883783
4:15:29.371945 INFO: num_candidates : 3
4:15:29.371985 INFO: ms1_error      : 0.0592737055907031
4:15:29.372024 INFO: ms2_error      : 24.37390675904184
4:15:29.372063 INFO: fwhm_rt        : 3.284703493118286
4:15:29.372102 INFO: quant_window   : 3
4:15:29.372140 INFO: ==============================================
4:15:29.373170 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:15:29.373217 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:15:29.373250 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
4:15:29.373272 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
4:15:29.374138 INFO: Starting candidate selection
4:15:33.324006 INFO: Starting candidate scoring
4:15:57.004817 INFO: Finished candidate processing
4:15:57.004963 INFO: Collecting candidate features
4:15:57.040459 INFO: Collecting fragment features
4:15:57.049802 INFO: Finished candidate scoring
4:15:57.053722 INFO: performing precursor FDR with 47 features
4:15:57.053841 INFO: Decoy channel: -1
4:15:57.053901 INFO: Competetive: True
4:15:57.060563 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:57.064273 INFO: Using random state 794606 for train-test-split
4:15:57.081813 INFO: Test AUC: 0.498
4:15:57.081917 INFO: Train AUC: 0.491
4:15:57.081967 INFO: AUC difference: 1.49%
4:15:57.309080 INFO: Resetting torch num_threads to 80
4:15:57.309794 PROGRESS: === Extracted 3288 precursors and 35433 fragments ===
4:15:57.310337 INFO: === FDR correction performed with classifier version 15 ===
4:15:57.310991 PROGRESS: ============================= Precursor FDR =============================
4:15:57.311084 PROGRESS: Total precursors accumulated: 590
4:15:57.311146 PROGRESS: Target precursors: 366 (62.03%)
4:15:57.311200 PROGRESS: Decoy precursors: 224 (37.97%)
4:15:57.311248 PROGRESS: 
4:15:57.311293 PROGRESS: Precursor Summary:
4:15:57.312245 PROGRESS: Channel   0:	 0.050 FDR:   208; 0.010 FDR:   208; 0.001 FDR:   208
4:15:57.312343 PROGRESS: 
4:15:57.312402 PROGRESS: Protein Summary:
4:15:57.313516 PROGRESS: Channel   0:	 0.050 FDR:   208; 0.010 FDR:   208; 0.001 FDR:   208
4:15:57.313613 PROGRESS: =========================================================================
4:15:57.313781 INFO: Target number of precursors reached.
4:15:57.318673 INFO: fragments_df: keeping 1598 of 35433 [sum(precursor_idx_mask)=6354 sum(mass_error_mask)=35433 stop_rank=1598
4:15:57.648887 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:15:57.752061 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:57.852224 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:15:57.950284 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:58.144615 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:58.145144 INFO: Using score_cutoff 20.603188936614988 (fac=0.99, q=1)
4:15:58.145469 INFO: Updating optimization_manager: fwhm_rt             : 3.284703493118286 -> 3.2815091609954834
4:15:58.145550 INFO: Updating optimization_manager: fwhm_mobility       : 0.00789401400834322 -> 0.007887627929449081
4:15:58.145605 INFO: Updating optimization_manager: score_cutoff        : 22.00701780395508 -> 20.603188936614988
4:15:58.145660 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:15:58.146942 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:58.148296 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:15:58.149078 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:58.151289 INFO: === checking if optimization conditions were reached ===
4:15:58.151393 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
4:15:58.152234 INFO: Updating optimization_manager: mobility_error      : 0.09922484285883783 -> 0.1
4:15:58.152357 INFO: Updating optimization_manager: classifier_version  : 15 -> 36
4:15:58.152449 INFO: Updating optimization_manager: score_cutoff        : 20.603188936614988 -> 20.32537441635132
4:15:58.152535 INFO: Updating optimization_manager: fwhm_rt             : 3.2815091609954834 -> 3.2815091609954834
4:15:58.152616 INFO: Updating optimization_manager: fwhm_mobility       : 0.007887627929449081 -> 0.007767566479742527
4:15:58.152696 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
4:15:58.152757 INFO: ==============================================
4:15:58.152820 PROGRESS: Optimization finished for mobility_error.
4:15:58.252562 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:15:58.253968 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:58.255348 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:15:58.256130 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:58.285798 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
4:15:58.285983 PROGRESS: ==============================================
4:15:58.286066 PROGRESS: ms2_error      : 24.3739
4:15:58.286131 PROGRESS: rt_error       : 831.4122
4:15:58.286195 PROGRESS: ms1_error      : 0.0593
4:15:58.286242 PROGRESS: mobility_error : 0.1000
4:15:58.286286 PROGRESS: ==============================================
4:15:58.287314 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:16:00.241070 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:16:07.760920 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:16:09.374881 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:16:27.463313 INFO: Using classic extraction backend
4:16:27.464286 PROGRESS: Extracting batch of 12073114 precursors
4:16:27.464449 INFO: === Search parameters used ===
4:16:27.464509 INFO: rt_error       : 831.412233375923
4:16:27.464556 INFO: mobility_error : 0.1
4:16:27.464604 INFO: num_candidates : 3
4:16:27.464647 INFO: ms1_error      : 0.0592737055907031
4:16:27.464689 INFO: ms2_error      : 24.37390675904184
4:16:27.464729 INFO: fwhm_rt        : 3.2815091609954834
4:16:27.464768 INFO: quant_window   : 3
4:16:27.464809 INFO: ==============================================
4:16:31.565897 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:16:31.566114 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:16:31.566192 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
4:16:31.566222 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.60
4:16:31.567868 INFO: Starting candidate selection
11:16:15.087545 INFO: Removed 742743 precursors with score below cutoff 20.32537441635132
11:16:18.758512 INFO: Starting candidate scoring
11:42:26.903221 INFO: Finished candidate processing
11:42:26.904637 INFO: Collecting candidate features
11:44:51.139139 INFO: Collecting fragment features
11:45:48.551785 INFO: Finished candidate scoring
11:46:31.055805 INFO: === Performing FDR correction with classifier version 36 ===
11:46:31.075266 INFO: performing precursor FDR with 47 features
11:46:31.075323 INFO: Decoy channel: -1
11:46:31.075356 INFO: Competetive: True
11:46:44.345675 INFO: Setting torch num_threads to 2 for FDR classification task
11:47:23.795018 INFO: Using random state 350205 for train-test-split
12:00:11.879518 INFO: Test AUC: 0.574
12:00:11.879796 INFO: Train AUC: 0.575
12:00:11.879841 INFO: AUC difference: 0.12%
12:00:17.946928 INFO: Resetting torch num_threads to 80
12:00:18.580091 INFO: Removing fragments below FDR threshold
12:00:21.788056 PROGRESS: ============================= Precursor FDR =============================
12:00:21.788283 PROGRESS: Total precursors accumulated: 39,711
12:00:21.788348 PROGRESS: Target precursors: 39,318 (99.01%)
12:00:21.788402 PROGRESS: Decoy precursors: 393 (0.99%)
12:00:21.788449 PROGRESS: 
12:00:21.788492 PROGRESS: Precursor Summary:
12:00:21.800083 PROGRESS: Channel   0:	 0.050 FDR: 39,318; 0.010 FDR: 39,318; 0.001 FDR: 22,556
12:00:21.800309 PROGRESS: 
12:00:21.800367 PROGRESS: Protein Summary:
12:00:21.817185 PROGRESS: Channel   0:	 0.050 FDR: 8,065; 0.010 FDR: 8,065; 0.001 FDR: 5,824
12:00:21.817377 PROGRESS: =========================================================================
12:00:22.276139 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/psm.parquet
12:00:22.528317 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/frag.parquet
12:00:22.706838 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
12:00:23.232197 PROGRESS: 
12:00:23.232347 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
12:00:23.232439 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/figures
12:00:23.232762 INFO: Initializing TimingManager
12:00:23.233300 INFO: Initializing RawFileManager
12:00:23.233413 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:23.233467 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:23.233514 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:23.442227 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
12:00:32.439195 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
12:00:32.442004 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:32.444570 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:32.444757 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:32.445137 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:32.446732 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:32.458913 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:32.459357 INFO: Indexing quadrupole dimension
12:00:32.946556 INFO: Transposing detector events
12:00:41.824717 INFO: Finished transposing data
12:00:41.862392 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
12:00:41.863600 INFO: RT (min)            : 0.0 - 70.0
12:00:41.863693 INFO: RT duration (sec)   : 4199.8
12:00:41.863746 INFO: RT duration (min)   : 70.0
12:00:41.863794 INFO: Cycle len (scans)   : 9
12:00:41.863842 INFO: Cycle len (sec)     : 0.97
12:00:41.863887 INFO: Number of cycles    : 4347
12:00:41.863933 INFO: MS2 range (m/z)     : 400.0 - 1000.0
12:00:41.864057 INFO: Creating DIA data object took: 18.630643606185913
12:00:43.434457 INFO: Initializing CalibrationManager
12:00:43.434729 INFO: Setting up calibration estimators ..
12:00:43.434788 INFO: Found 1 estimator(s) in calibration group 'fragment'
12:00:43.434871 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'}' ..
12:00:43.434953 INFO: Found 3 estimator(s) in calibration group 'precursor'
12:00:43.435012 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'}' ..
12:00:43.435068 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}}' ..
12:00:43.435129 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}}' ..
12:00:43.435178 INFO: Done setting up calibration estimators.
12:00:43.435303 INFO: Initializing OptimizationManager
12:00:43.435395 INFO: initial parameter: ms1_error = 30
12:00:43.435440 INFO: initial parameter: ms2_error = 30
12:00:43.435483 INFO: initial parameter: rt_error = 2099.8992935
12:00:43.435524 INFO: initial parameter: mobility_error = 0.1
12:00:43.435565 INFO: initial parameter: num_candidates = 1
12:00:43.435605 INFO: initial parameter: fwhm_rt = 5
12:00:43.436235 INFO: initial parameter: fwhm_mobility = 0.01
12:00:43.436280 INFO: initial parameter: score_cutoff = 0
12:00:43.436319 INFO: initial parameter: classifier_version = -1
12:00:43.436393 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
12:00:43.436690 INFO: FDRManager: loading saved state not requested, will be initialized.
12:00:43.436722 INFO: Initializing FDRManager
12:00:43.436772 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
12:00:44.648409 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
12:00:45.426072 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
12:00:45.426426 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 2099.8992935
12:00:45.426612 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
12:00:45.426798 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
12:00:45.426888 PROGRESS: Starting initial search for precursors.
12:00:45.426969 INFO: Starting optimization step 0.
12:00:45.427029 PROGRESS: === Extracting elution groups 0 to 200 ===
12:00:45.427098 INFO: Using classic extraction backend
12:00:45.427325 PROGRESS: Extracting batch of 390 precursors
12:00:45.427396 INFO: === Search parameters used ===
12:00:45.427443 INFO: rt_error       : 2099.8992935
12:00:45.427484 INFO: mobility_error : 0.1
12:00:45.427525 INFO: num_candidates : 1
12:00:45.427565 INFO: ms1_error      : 30
12:00:45.427604 INFO: ms2_error      : 30
12:00:45.427644 INFO: fwhm_rt        : 5
12:00:45.427682 INFO: quant_window   : 3
12:00:45.427720 INFO: ==============================================
12:00:45.428534 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:00:45.428577 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:00:45.428611 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
12:00:45.428632 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
12:00:45.429896 INFO: Starting candidate selection
12:00:49.428882 INFO: Starting candidate scoring
12:00:49.494713 INFO: Finished candidate processing
12:00:49.494805 INFO: Collecting candidate features
12:00:49.503840 INFO: Collecting fragment features
12:00:49.505969 INFO: Finished candidate scoring
12:00:49.506772 INFO: performing precursor FDR with 47 features
12:00:49.506813 INFO: Decoy channel: -1
12:00:49.506838 INFO: Competetive: True
12:00:49.507969 INFO: Setting torch num_threads to 2 for FDR classification task
12:00:49.510406 INFO: Using random state 978255 for train-test-split
12:00:49.518842 INFO: Test AUC: 0.495
12:00:49.518899 INFO: Train AUC: 0.519
12:00:49.518930 INFO: AUC difference: 4.68%
12:00:49.748346 INFO: Resetting torch num_threads to 80
12:00:49.748781 PROGRESS: === Extracted 363 precursors and 3936 fragments ===
12:00:49.749195 INFO: === FDR correction performed with classifier version -1 ===
12:00:49.749715 PROGRESS: ============================= Precursor FDR =============================
12:00:49.749802 PROGRESS: Total precursors accumulated: 188
12:00:49.749860 PROGRESS: Target precursors: 122 (64.89%)
12:00:49.749910 PROGRESS: Decoy precursors: 66 (35.11%)
12:00:49.749958 PROGRESS: 
12:00:49.750005 PROGRESS: Precursor Summary:
12:00:49.750880 PROGRESS: Channel   0:	 0.050 FDR:    77; 0.010 FDR:    77; 0.001 FDR:    77
12:00:49.750965 PROGRESS: 
12:00:49.751028 PROGRESS: Protein Summary:
12:00:49.751999 PROGRESS: Channel   0:	 0.050 FDR:    77; 0.010 FDR:    77; 0.001 FDR:    77
12:00:49.752086 PROGRESS: =========================================================================
12:00:49.752188 INFO: Target number of precursors not reached yet.
12:00:49.817171 INFO: Starting optimization step 1.
12:00:49.817366 PROGRESS: === Extracting elution groups 200 to 600 ===
12:00:49.817438 INFO: Using classic extraction backend
12:00:49.817552 PROGRESS: Extracting batch of 783 precursors
12:00:49.817621 INFO: === Search parameters used ===
12:00:49.817683 INFO: rt_error       : 2099.8992935
12:00:49.817727 INFO: mobility_error : 0.1
12:00:49.817769 INFO: num_candidates : 1
12:00:49.817811 INFO: ms1_error      : 30
12:00:49.817850 INFO: ms2_error      : 30
12:00:49.817889 INFO: fwhm_rt        : 5
12:00:49.817927 INFO: quant_window   : 3
12:00:49.817965 INFO: ==============================================
12:00:49.818625 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:00:49.818669 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:00:49.818697 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
12:00:49.818718 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
12:00:49.819371 INFO: Starting candidate selection
12:00:57.435606 INFO: Starting candidate scoring
12:00:57.560935 INFO: Finished candidate processing
12:00:57.561045 INFO: Collecting candidate features
12:00:57.571049 INFO: Collecting fragment features
12:00:57.573418 INFO: Finished candidate scoring
12:00:57.575342 INFO: performing precursor FDR with 47 features
12:00:57.575388 INFO: Decoy channel: -1
12:00:57.575412 INFO: Competetive: True
12:00:57.578433 INFO: Setting torch num_threads to 2 for FDR classification task
12:00:57.580233 INFO: Using random state 138195 for train-test-split
12:00:57.588224 INFO: Test AUC: 0.529
12:00:57.588280 INFO: Train AUC: 0.503
12:00:57.588310 INFO: AUC difference: 5.02%
12:00:57.588331 WARNING: AUC difference > 5%. This may indicate overfitting.
12:00:58.960649 INFO: Resetting torch num_threads to 80
12:00:58.961875 PROGRESS: === Extracted 1117 precursors and 12174 fragments ===
12:00:58.962265 INFO: === FDR correction performed with classifier version -1 ===
12:00:58.962890 PROGRESS: ============================= Precursor FDR =============================
12:00:58.962981 PROGRESS: Total precursors accumulated: 576
12:00:58.963040 PROGRESS: Target precursors: 363 (63.02%)
12:00:58.963096 PROGRESS: Decoy precursors: 213 (36.98%)
12:00:58.963145 PROGRESS: 
12:00:58.963188 PROGRESS: Precursor Summary:
12:00:58.964143 PROGRESS: Channel   0:	 0.050 FDR:   232; 0.010 FDR:   232; 0.001 FDR:   232
12:00:58.964234 PROGRESS: 
12:00:58.964288 PROGRESS: Protein Summary:
12:00:58.965386 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:   229
12:00:58.965479 PROGRESS: =========================================================================
12:00:58.965613 INFO: Target number of precursors reached.
12:00:58.968274 INFO: fragments_df: keeping 471 of 12174 [sum(precursor_idx_mask)=2560 sum(mass_error_mask)=12174 stop_rank=471
12:00:59.085805 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:00:59.183120 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:00:59.281005 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:00:59.378044 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:00:59.481710 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
12:00:59.482100 INFO: Using score_cutoff 38.27957726554871 (fac=0.99, q=1)
12:00:59.482391 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.454655647277832
12:00:59.482470 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007902481593191624
12:00:59.482526 INFO: Updating optimization_manager: score_cutoff        : 0 -> 38.27957726554871
12:00:59.482585 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:00:59.483653 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:00:59.485008 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:00:59.485806 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:00:59.488013 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
12:00:59.488108 PROGRESS: Required number of precursors found. Starting search parameter optimization.
12:00:59.488183 INFO: Starting optimization step 2.
12:00:59.488240 PROGRESS: === Extracting elution groups 0 to 600 ===
12:00:59.488295 INFO: Using classic extraction backend
12:00:59.488399 PROGRESS: Extracting batch of 1173 precursors
12:00:59.488470 INFO: === Search parameters used ===
12:00:59.488517 INFO: rt_error       : 2099.8992935
12:00:59.488558 INFO: mobility_error : 0.1
12:00:59.488599 INFO: num_candidates : 3
12:00:59.488638 INFO: ms1_error      : 30
12:00:59.488677 INFO: ms2_error      : 30
12:00:59.488716 INFO: fwhm_rt        : 3.454655647277832
12:00:59.488756 INFO: quant_window   : 3
12:00:59.488793 INFO: ==============================================
12:00:59.489636 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:00:59.489681 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:00:59.489715 INFO: FWHM in RT is 3.45 seconds, sigma is 0.76
12:00:59.489738 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
12:00:59.490412 INFO: Starting candidate selection
12:01:08.899108 INFO: Starting candidate scoring
12:01:09.214684 INFO: Finished candidate processing
12:01:09.214776 INFO: Collecting candidate features
12:01:09.226981 INFO: Collecting fragment features
12:01:09.230644 INFO: Finished candidate scoring
12:01:09.233080 INFO: performing precursor FDR with 47 features
12:01:09.233127 INFO: Decoy channel: -1
12:01:09.233151 INFO: Competetive: True
12:01:09.236037 INFO: Setting torch num_threads to 2 for FDR classification task
12:01:09.237980 INFO: Using random state 63794 for train-test-split
12:01:09.248366 INFO: Test AUC: 0.501
12:01:09.248423 INFO: Train AUC: 0.500
12:01:09.248450 INFO: AUC difference: 0.33%
12:01:09.465921 INFO: Resetting torch num_threads to 80
12:01:09.466454 PROGRESS: === Extracted 3219 precursors and 35188 fragments ===
12:01:09.466843 INFO: === FDR correction performed with classifier version 1 ===
12:01:09.467419 PROGRESS: ============================= Precursor FDR =============================
12:01:09.467509 PROGRESS: Total precursors accumulated: 588
12:01:09.467568 PROGRESS: Target precursors: 433 (73.64%)
12:01:09.467617 PROGRESS: Decoy precursors: 155 (26.36%)
12:01:09.467660 PROGRESS: 
12:01:09.467703 PROGRESS: Precursor Summary:
12:01:09.468678 PROGRESS: Channel   0:	 0.050 FDR:   358; 0.010 FDR:   358; 0.001 FDR:   358
12:01:09.468768 PROGRESS: 
12:01:09.468822 PROGRESS: Protein Summary:
12:01:09.469970 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   355
12:01:09.470062 PROGRESS: =========================================================================
12:01:09.470192 INFO: Target number of precursors reached.
12:01:09.475880 INFO: fragments_df: keeping 2179 of 35188 [sum(precursor_idx_mask)=11145 sum(mass_error_mask)=35188 stop_rank=2179
12:01:09.578315 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:01:09.683885 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:01:09.789842 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:01:09.895548 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:01:10.137035 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:01:10.137452 INFO: Using score_cutoff 39.401085546112064 (fac=0.99, q=1)
12:01:10.137751 INFO: Updating optimization_manager: fwhm_rt             : 3.454655647277832 -> 3.370589017868042
12:01:10.137840 INFO: Updating optimization_manager: fwhm_mobility       : 0.007902481593191624 -> 0.007943905889987946
12:01:10.137897 INFO: Updating optimization_manager: score_cutoff        : 38.27957726554871 -> 39.401085546112064
12:01:10.137948 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:01:10.138991 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:01:10.140339 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:01:10.141122 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:01:10.143155 INFO: === checking if optimization conditions were reached ===
12:01:10.143251 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
12:01:10.144783 INFO: Updating optimization_manager: ms2_error           : 30 -> 22.46883142682328
12:01:10.144880 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 22.4688.
12:01:10.144958 INFO: ==============================================
12:01:10.145026 INFO: Starting optimization step 3.
12:01:10.145084 PROGRESS: === Extracting elution groups 0 to 600 ===
12:01:10.145139 INFO: Using classic extraction backend
12:01:10.145244 PROGRESS: Extracting batch of 1173 precursors
12:01:10.145306 INFO: === Search parameters used ===
12:01:10.145351 INFO: rt_error       : 2099.8992935
12:01:10.145392 INFO: mobility_error : 0.1
12:01:10.145430 INFO: num_candidates : 3
12:01:10.145468 INFO: ms1_error      : 30
12:01:10.145511 INFO: ms2_error      : 22.46883142682328
12:01:10.145552 INFO: fwhm_rt        : 3.370589017868042
12:01:10.145590 INFO: quant_window   : 3
12:01:10.145627 INFO: ==============================================
12:01:10.146413 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:01:10.146457 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:01:10.146490 INFO: FWHM in RT is 3.37 seconds, sigma is 0.74
12:01:10.146511 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.68
12:01:10.147152 INFO: Starting candidate selection
12:01:18.845665 INFO: Starting candidate scoring
12:01:19.108001 INFO: Finished candidate processing
12:01:19.108097 INFO: Collecting candidate features
12:01:19.120564 INFO: Collecting fragment features
12:01:19.124252 INFO: Finished candidate scoring
12:01:19.126723 INFO: performing precursor FDR with 47 features
12:01:19.126770 INFO: Decoy channel: -1
12:01:19.126795 INFO: Competetive: True
12:01:19.129820 INFO: Setting torch num_threads to 2 for FDR classification task
12:01:19.131831 INFO: Using random state 63794 for train-test-split
12:01:19.143196 INFO: Test AUC: 0.513
12:01:19.143256 INFO: Train AUC: 0.501
12:01:19.143286 INFO: AUC difference: 2.39%
12:01:19.364887 INFO: Resetting torch num_threads to 80
12:01:19.365449 PROGRESS: === Extracted 3210 precursors and 34541 fragments ===
12:01:19.365846 INFO: === FDR correction performed with classifier version 1 ===
12:01:19.366435 PROGRESS: ============================= Precursor FDR =============================
12:01:19.366524 PROGRESS: Total precursors accumulated: 587
12:01:19.366582 PROGRESS: Target precursors: 429 (73.08%)
12:01:19.366634 PROGRESS: Decoy precursors: 158 (26.92%)
12:01:19.366679 PROGRESS: 
12:01:19.366724 PROGRESS: Precursor Summary:
12:01:19.367714 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   352; 0.001 FDR:   352
12:01:19.367805 PROGRESS: 
12:01:19.367862 PROGRESS: Protein Summary:
12:01:19.369029 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   350; 0.001 FDR:   350
12:01:19.369121 PROGRESS: =========================================================================
12:01:19.369338 INFO: Target number of precursors reached.
12:01:19.374904 INFO: fragments_df: keeping 1924 of 34541 [sum(precursor_idx_mask)=10829 sum(mass_error_mask)=34541 stop_rank=1924
12:01:19.473980 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:01:19.596139 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:01:19.722285 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:01:19.848192 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:01:20.064291 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:01:20.064711 INFO: Using score_cutoff 36.408320312118526 (fac=0.99, q=1)
12:01:20.065022 INFO: Updating optimization_manager: fwhm_rt             : 3.370589017868042 -> 3.1294116973876953
12:01:20.065107 INFO: Updating optimization_manager: fwhm_mobility       : 0.007943905889987946 -> 0.006916288286447525
12:01:20.065162 INFO: Updating optimization_manager: score_cutoff        : 39.401085546112064 -> 36.408320312118526
12:01:20.065216 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:01:20.066264 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:01:20.067628 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:01:20.068419 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:01:20.074410 INFO: === checking if optimization conditions were reached ===
12:01:20.074520 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
12:01:20.076228 INFO: Updating optimization_manager: ms2_error           : 22.46883142682328 -> 17.97690003499437
12:01:20.076329 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 17.9769.
12:01:20.076392 INFO: ==============================================
12:01:20.076462 INFO: Starting optimization step 4.
12:01:20.076518 PROGRESS: === Extracting elution groups 0 to 600 ===
12:01:20.076741 INFO: Using classic extraction backend
12:01:20.076854 PROGRESS: Extracting batch of 1173 precursors
12:01:20.076916 INFO: === Search parameters used ===
12:01:20.076975 INFO: rt_error       : 2099.8992935
12:01:20.077020 INFO: mobility_error : 0.1
12:01:20.077061 INFO: num_candidates : 3
12:01:20.077100 INFO: ms1_error      : 30
12:01:20.077139 INFO: ms2_error      : 17.97690003499437
12:01:20.077177 INFO: fwhm_rt        : 3.1294116973876953
12:01:20.077215 INFO: quant_window   : 3
12:01:20.077253 INFO: ==============================================
12:01:20.078269 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:01:20.078314 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:01:20.078347 INFO: FWHM in RT is 3.13 seconds, sigma is 0.69
12:01:20.078368 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.21
12:01:20.078989 INFO: Starting candidate selection
12:01:57.452766 INFO: Starting candidate scoring
12:01:57.722925 INFO: Finished candidate processing
12:01:57.723018 INFO: Collecting candidate features
12:01:57.738279 INFO: Collecting fragment features
12:01:57.742689 INFO: Finished candidate scoring
12:01:57.744834 INFO: performing precursor FDR with 47 features
12:01:57.744879 INFO: Decoy channel: -1
12:01:57.744905 INFO: Competetive: True
12:01:57.748671 INFO: Setting torch num_threads to 2 for FDR classification task
12:01:57.751207 INFO: Using random state 63794 for train-test-split
12:01:57.762499 INFO: Test AUC: 0.513
12:01:57.762559 INFO: Train AUC: 0.503
12:01:57.762590 INFO: AUC difference: 1.97%
12:01:57.990409 INFO: Resetting torch num_threads to 80
12:01:57.990997 PROGRESS: === Extracted 3222 precursors and 34006 fragments ===
12:01:57.991451 INFO: === FDR correction performed with classifier version 1 ===
12:01:57.992026 PROGRESS: ============================= Precursor FDR =============================
12:01:57.992116 PROGRESS: Total precursors accumulated: 587
12:01:57.992179 PROGRESS: Target precursors: 438 (74.62%)
12:01:57.992230 PROGRESS: Decoy precursors: 149 (25.38%)
12:01:57.992275 PROGRESS: 
12:01:57.992318 PROGRESS: Precursor Summary:
12:01:57.993319 PROGRESS: Channel   0:	 0.050 FDR:   357; 0.010 FDR:   357; 0.001 FDR:   357
12:01:57.993412 PROGRESS: 
12:01:57.993468 PROGRESS: Protein Summary:
12:01:57.994627 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   354; 0.001 FDR:   354
12:01:57.994720 PROGRESS: =========================================================================
12:01:57.994906 INFO: Target number of precursors reached.
12:01:58.000412 INFO: fragments_df: keeping 1948 of 34006 [sum(precursor_idx_mask)=10899 sum(mass_error_mask)=34005 stop_rank=1948
12:01:58.100420 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:01:58.235061 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:01:58.362865 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:01:58.495670 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:01:58.760366 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:01:58.760816 INFO: Using score_cutoff 32.79650159454346 (fac=0.99, q=1)
12:01:58.761184 INFO: Updating optimization_manager: fwhm_rt             : 3.1294116973876953 -> 3.0073013305664062
12:01:58.761275 INFO: Updating optimization_manager: fwhm_mobility       : 0.006916288286447525 -> 0.006072926335036755
12:01:58.761342 INFO: Updating optimization_manager: score_cutoff        : 36.408320312118526 -> 32.79650159454346
12:01:58.761421 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:01:58.762527 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:01:58.763919 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:01:58.764737 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:01:58.767014 INFO: === checking if optimization conditions were reached ===
12:01:58.767145 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
12:01:58.768940 INFO: Updating optimization_manager: ms2_error           : 17.97690003499437 -> 15.67040364427005
12:01:58.769062 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 15.6704.
12:01:58.769142 INFO: ==============================================
12:01:58.769228 INFO: Starting optimization step 5.
12:01:58.769298 PROGRESS: === Extracting elution groups 0 to 600 ===
12:01:58.769374 INFO: Using classic extraction backend
12:01:58.769579 PROGRESS: Extracting batch of 1173 precursors
12:01:58.769663 INFO: === Search parameters used ===
12:01:58.769722 INFO: rt_error       : 2099.8992935
12:01:58.769778 INFO: mobility_error : 0.1
12:01:58.769831 INFO: num_candidates : 3
12:01:58.769886 INFO: ms1_error      : 30
12:01:58.769938 INFO: ms2_error      : 15.67040364427005
12:01:58.769988 INFO: fwhm_rt        : 3.0073013305664062
12:01:58.770040 INFO: quant_window   : 3
12:01:58.770090 INFO: ==============================================
12:01:58.771225 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:01:58.771272 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:01:58.771333 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
12:01:58.771364 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.82
12:01:58.772089 INFO: Starting candidate selection
12:02:07.753206 INFO: Starting candidate scoring
12:02:07.978571 INFO: Finished candidate processing
12:02:07.978709 INFO: Collecting candidate features
12:02:07.992047 INFO: Collecting fragment features
12:02:07.996629 INFO: Finished candidate scoring
12:02:07.998595 INFO: performing precursor FDR with 47 features
12:02:07.998640 INFO: Decoy channel: -1
12:02:07.998664 INFO: Competetive: True
12:02:08.001638 INFO: Setting torch num_threads to 2 for FDR classification task
12:02:08.003621 INFO: Using random state 63794 for train-test-split
12:02:08.014456 INFO: Test AUC: 0.520
12:02:08.014513 INFO: Train AUC: 0.487
12:02:08.014543 INFO: AUC difference: 6.67%
12:02:08.014565 WARNING: AUC difference > 5%. This may indicate overfitting.
12:02:08.233314 INFO: Resetting torch num_threads to 80
12:02:08.233845 PROGRESS: === Extracted 3205 precursors and 33310 fragments ===
12:02:08.234242 INFO: === FDR correction performed with classifier version 1 ===
12:02:08.234804 PROGRESS: ============================= Precursor FDR =============================
12:02:08.234891 PROGRESS: Total precursors accumulated: 587
12:02:08.235267 PROGRESS: Target precursors: 432 (73.59%)
12:02:08.235328 PROGRESS: Decoy precursors: 155 (26.41%)
12:02:08.235373 PROGRESS: 
12:02:08.235418 PROGRESS: Precursor Summary:
12:02:08.236380 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:   345; 0.001 FDR:   345
12:02:08.236469 PROGRESS: 
12:02:08.236522 PROGRESS: Protein Summary:
12:02:08.237666 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   343; 0.001 FDR:   343
12:02:08.237756 PROGRESS: =========================================================================
12:02:08.237888 INFO: Target number of precursors reached.
12:02:08.243091 INFO: fragments_df: keeping 1807 of 33310 [sum(precursor_idx_mask)=10179 sum(mass_error_mask)=33310 stop_rank=1807
12:02:08.341744 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:02:08.470554 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:02:08.595453 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:02:08.721951 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:02:08.966710 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:02:08.967124 INFO: Using score_cutoff 34.91461441955566 (fac=0.99, q=1)
12:02:08.967421 INFO: Updating optimization_manager: fwhm_rt             : 3.0073013305664062 -> 2.8445539474487305
12:02:08.967500 INFO: Updating optimization_manager: fwhm_mobility       : 0.006072926335036755 -> 0.00576012535020709
12:02:08.967562 INFO: Updating optimization_manager: score_cutoff        : 32.79650159454346 -> 34.91461441955566
12:02:08.967618 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:02:08.968646 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:02:08.969980 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:02:08.970752 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:02:08.972854 INFO: === checking if optimization conditions were reached ===
12:02:08.972958 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
12:02:08.974629 INFO: Updating optimization_manager: ms2_error           : 15.67040364427005 -> 13.699795071938036
12:02:08.974731 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 13.6998.
12:02:08.974794 INFO: ==============================================
12:02:08.974859 INFO: Starting optimization step 6.
12:02:08.974915 PROGRESS: === Extracting elution groups 0 to 600 ===
12:02:08.974967 INFO: Using classic extraction backend
12:02:08.975067 PROGRESS: Extracting batch of 1173 precursors
12:02:08.975130 INFO: === Search parameters used ===
12:02:08.975176 INFO: rt_error       : 2099.8992935
12:02:08.975218 INFO: mobility_error : 0.1
12:02:08.975259 INFO: num_candidates : 3
12:02:08.975297 INFO: ms1_error      : 30
12:02:08.975336 INFO: ms2_error      : 13.699795071938036
12:02:08.975381 INFO: fwhm_rt        : 2.8445539474487305
12:02:08.975423 INFO: quant_window   : 3
12:02:08.975463 INFO: ==============================================
12:02:08.976235 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:02:08.976278 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:02:08.976310 INFO: FWHM in RT is 2.84 seconds, sigma is 0.63
12:02:08.976332 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.67
12:02:08.977029 INFO: Starting candidate selection
12:02:18.243712 INFO: Starting candidate scoring
12:02:57.070089 INFO: Finished candidate processing
12:02:57.070333 INFO: Collecting candidate features
12:02:57.097946 INFO: Collecting fragment features
12:02:57.106084 INFO: Finished candidate scoring
12:02:57.109135 INFO: performing precursor FDR with 47 features
12:02:57.109239 INFO: Decoy channel: -1
12:02:57.109296 INFO: Competetive: True
12:02:57.115463 INFO: Setting torch num_threads to 2 for FDR classification task
12:02:57.120011 INFO: Using random state 63794 for train-test-split
12:02:57.138310 INFO: Test AUC: 0.521
12:02:57.138405 INFO: Train AUC: 0.496
12:02:57.138453 INFO: AUC difference: 5.02%
12:02:57.138488 WARNING: AUC difference > 5%. This may indicate overfitting.
12:02:57.364475 INFO: Resetting torch num_threads to 80
12:02:57.364999 PROGRESS: === Extracted 3208 precursors and 32946 fragments ===
12:02:57.365389 INFO: === FDR correction performed with classifier version 1 ===
12:02:57.365940 PROGRESS: ============================= Precursor FDR =============================
12:02:57.366027 PROGRESS: Total precursors accumulated: 586
12:02:57.366084 PROGRESS: Target precursors: 425 (72.53%)
12:02:57.366132 PROGRESS: Decoy precursors: 161 (27.47%)
12:02:57.366174 PROGRESS: 
12:02:57.366216 PROGRESS: Precursor Summary:
12:02:57.367150 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   354; 0.001 FDR:   354
12:02:57.367240 PROGRESS: 
12:02:57.367294 PROGRESS: Protein Summary:
12:02:57.368403 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   352; 0.001 FDR:   352
12:02:57.368491 PROGRESS: =========================================================================
12:02:57.368628 INFO: Target number of precursors reached.
12:02:57.373758 INFO: fragments_df: keeping 1861 of 32946 [sum(precursor_idx_mask)=10466 sum(mass_error_mask)=32946 stop_rank=1861
12:02:57.472337 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:02:57.590775 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:02:57.695504 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:02:57.805471 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:02:58.015383 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:02:58.015813 INFO: Using score_cutoff 31.98747322368622 (fac=0.99, q=1)
12:02:58.016119 INFO: Updating optimization_manager: fwhm_rt             : 2.8445539474487305 -> 2.8054165840148926
12:02:58.016202 INFO: Updating optimization_manager: fwhm_mobility       : 0.00576012535020709 -> 0.005359012633562088
12:02:58.016260 INFO: Updating optimization_manager: score_cutoff        : 34.91461441955566 -> 31.98747322368622
12:02:58.016313 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:02:58.017359 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:02:58.018696 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:02:58.019464 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:02:58.021587 INFO: === checking if optimization conditions were reached ===
12:02:58.021687 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
12:02:58.023412 INFO: Updating optimization_manager: ms2_error           : 13.699795071938036 -> 11.763852990414211
12:02:58.023515 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 11.7639.
12:02:58.023582 INFO: ==============================================
12:02:58.023648 INFO: Starting optimization step 7.
12:02:58.023704 PROGRESS: === Extracting elution groups 0 to 600 ===
12:02:58.023757 INFO: Using classic extraction backend
12:02:58.023867 PROGRESS: Extracting batch of 1173 precursors
12:02:58.023929 INFO: === Search parameters used ===
12:02:58.023974 INFO: rt_error       : 2099.8992935
12:02:58.024015 INFO: mobility_error : 0.1
12:02:58.024057 INFO: num_candidates : 3
12:02:58.024096 INFO: ms1_error      : 30
12:02:58.024135 INFO: ms2_error      : 11.763852990414211
12:02:58.024173 INFO: fwhm_rt        : 2.8054165840148926
12:02:58.024211 INFO: quant_window   : 3
12:02:58.024249 INFO: ==============================================
12:02:58.025044 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:02:58.025091 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:02:58.025124 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
12:02:58.025146 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.49
12:02:58.025835 INFO: Starting candidate selection
12:03:07.605438 INFO: Starting candidate scoring
12:03:07.847775 INFO: Finished candidate processing
12:03:07.847870 INFO: Collecting candidate features
12:03:07.861224 INFO: Collecting fragment features
12:03:07.866071 INFO: Finished candidate scoring
12:03:07.867749 INFO: performing precursor FDR with 47 features
12:03:07.867791 INFO: Decoy channel: -1
12:03:07.867814 INFO: Competetive: True
12:03:07.870599 INFO: Setting torch num_threads to 2 for FDR classification task
12:03:07.872563 INFO: Using random state 63794 for train-test-split
12:03:07.882447 INFO: Test AUC: 0.521
12:03:07.882506 INFO: Train AUC: 0.497
12:03:07.882535 INFO: AUC difference: 4.73%
12:03:08.102652 INFO: Resetting torch num_threads to 80
12:03:08.103175 PROGRESS: === Extracted 3217 precursors and 32383 fragments ===
12:03:08.103579 INFO: === FDR correction performed with classifier version 1 ===
12:03:08.104136 PROGRESS: ============================= Precursor FDR =============================
12:03:08.104226 PROGRESS: Total precursors accumulated: 589
12:03:08.104286 PROGRESS: Target precursors: 432 (73.34%)
12:03:08.104335 PROGRESS: Decoy precursors: 157 (26.66%)
12:03:08.104381 PROGRESS: 
12:03:08.104432 PROGRESS: Precursor Summary:
12:03:08.105404 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   350; 0.001 FDR:   350
12:03:08.105495 PROGRESS: 
12:03:08.105550 PROGRESS: Protein Summary:
12:03:08.106663 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   348
12:03:08.106759 PROGRESS: =========================================================================
12:03:08.106932 INFO: Target number of precursors reached.
12:03:08.112039 INFO: fragments_df: keeping 1768 of 32383 [sum(precursor_idx_mask)=10142 sum(mass_error_mask)=32383 stop_rank=1768
12:03:08.211982 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:03:08.340805 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:03:08.465697 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:03:08.597065 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:03:08.833149 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:03:08.833559 INFO: Using score_cutoff 31.77285651569366 (fac=0.99, q=1)
12:03:08.833862 INFO: Updating optimization_manager: fwhm_rt             : 2.8054165840148926 -> 2.696725368499756
12:03:08.833941 INFO: Updating optimization_manager: fwhm_mobility       : 0.005359012633562088 -> 0.005060289986431599
12:03:08.833996 INFO: Updating optimization_manager: score_cutoff        : 31.98747322368622 -> 31.77285651569366
12:03:08.834049 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:03:08.835091 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:03:08.836405 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:03:08.837392 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:03:08.839494 INFO: === checking if optimization conditions were reached ===
12:03:08.839591 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
12:03:08.841267 INFO: Updating optimization_manager: ms2_error           : 11.763852990414211 -> 10.451594630104939
12:03:08.841368 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 10.4516.
12:03:08.841433 INFO: ==============================================
12:03:08.841499 INFO: Starting optimization step 8.
12:03:08.841559 PROGRESS: === Extracting elution groups 0 to 600 ===
12:03:08.841613 INFO: Using classic extraction backend
12:03:08.841717 PROGRESS: Extracting batch of 1173 precursors
12:03:08.841780 INFO: === Search parameters used ===
12:03:08.841827 INFO: rt_error       : 2099.8992935
12:03:08.841870 INFO: mobility_error : 0.1
12:03:08.841912 INFO: num_candidates : 3
12:03:08.841952 INFO: ms1_error      : 30
12:03:08.841992 INFO: ms2_error      : 10.451594630104939
12:03:08.842030 INFO: fwhm_rt        : 2.696725368499756
12:03:08.842069 INFO: quant_window   : 3
12:03:08.842108 INFO: ==============================================
12:03:08.842902 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:03:08.842949 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:03:08.842983 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
12:03:08.843004 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.35
12:03:08.843687 INFO: Starting candidate selection
12:03:17.686244 INFO: Starting candidate scoring
12:03:17.906096 INFO: Finished candidate processing
12:03:17.906227 INFO: Collecting candidate features
12:03:17.919790 INFO: Collecting fragment features
12:03:17.923939 INFO: Finished candidate scoring
12:03:17.925682 INFO: performing precursor FDR with 47 features
12:03:17.925724 INFO: Decoy channel: -1
12:03:17.925748 INFO: Competetive: True
12:03:17.928715 INFO: Setting torch num_threads to 2 for FDR classification task
12:03:17.930703 INFO: Using random state 63794 for train-test-split
12:03:17.941408 INFO: Test AUC: 0.498
12:03:17.941467 INFO: Train AUC: 0.492
12:03:17.941495 INFO: AUC difference: 1.12%
12:03:18.159589 INFO: Resetting torch num_threads to 80
12:03:18.160104 PROGRESS: === Extracted 3220 precursors and 32066 fragments ===
12:03:18.160513 INFO: === FDR correction performed with classifier version 1 ===
12:03:18.161083 PROGRESS: ============================= Precursor FDR =============================
12:03:18.161172 PROGRESS: Total precursors accumulated: 589
12:03:18.161231 PROGRESS: Target precursors: 418 (70.97%)
12:03:18.161287 PROGRESS: Decoy precursors: 171 (29.03%)
12:03:18.161333 PROGRESS: 
12:03:18.161376 PROGRESS: Precursor Summary:
12:03:18.162333 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   338; 0.001 FDR:   338
12:03:18.162421 PROGRESS: 
12:03:18.162475 PROGRESS: Protein Summary:
12:03:18.163594 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   336; 0.001 FDR:   336
12:03:18.163681 PROGRESS: =========================================================================
12:03:18.163808 INFO: Target number of precursors reached.
12:03:18.168710 INFO: fragments_df: keeping 1659 of 32066 [sum(precursor_idx_mask)=9697 sum(mass_error_mask)=32066 stop_rank=1659
12:03:18.286533 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:03:18.408567 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:03:18.532358 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:03:18.659118 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:03:18.890615 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:03:18.891022 INFO: Using score_cutoff 30.24422956123352 (fac=0.99, q=1)
12:03:18.891315 INFO: Updating optimization_manager: fwhm_rt             : 2.696725368499756 -> 2.534274101257324
12:03:18.891393 INFO: Updating optimization_manager: fwhm_mobility       : 0.005060289986431599 -> 0.004624363966286182
12:03:18.891448 INFO: Updating optimization_manager: score_cutoff        : 31.77285651569366 -> 30.24422956123352
12:03:18.891846 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:03:18.892878 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:03:18.894196 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:03:18.894959 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:03:18.897108 INFO: === checking if optimization conditions were reached ===
12:03:18.897203 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
12:03:18.898829 INFO: Updating optimization_manager: ms2_error           : 10.451594630104939 -> 9.203412154797988
12:03:18.898927 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 9.2034.
12:03:18.898992 INFO: ==============================================
12:03:18.899055 INFO: Starting optimization step 9.
12:03:18.899109 PROGRESS: === Extracting elution groups 0 to 600 ===
12:03:18.899161 INFO: Using classic extraction backend
12:03:18.899260 PROGRESS: Extracting batch of 1173 precursors
12:03:18.899323 INFO: === Search parameters used ===
12:03:18.899372 INFO: rt_error       : 2099.8992935
12:03:18.899413 INFO: mobility_error : 0.1
12:03:18.899455 INFO: num_candidates : 3
12:03:18.899494 INFO: ms1_error      : 30
12:03:18.899534 INFO: ms2_error      : 9.203412154797988
12:03:18.899571 INFO: fwhm_rt        : 2.534274101257324
12:03:18.899615 INFO: quant_window   : 3
12:03:18.899655 INFO: ==============================================
12:03:18.900418 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:03:18.900463 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:03:18.900498 INFO: FWHM in RT is 2.53 seconds, sigma is 0.56
12:03:18.900520 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.14
12:03:18.901186 INFO: Starting candidate selection
12:03:57.434452 INFO: Starting candidate scoring
12:03:57.672784 INFO: Finished candidate processing
12:03:57.672930 INFO: Collecting candidate features
12:03:57.685787 INFO: Collecting fragment features
12:03:57.689594 INFO: Finished candidate scoring
12:03:57.691748 INFO: performing precursor FDR with 47 features
12:03:57.691790 INFO: Decoy channel: -1
12:03:57.691814 INFO: Competetive: True
12:03:57.694689 INFO: Setting torch num_threads to 2 for FDR classification task
12:03:57.696624 INFO: Using random state 63794 for train-test-split
12:03:57.706952 INFO: Test AUC: 0.491
12:03:57.707014 INFO: Train AUC: 0.487
12:03:57.707042 INFO: AUC difference: 0.78%
12:03:57.926073 INFO: Resetting torch num_threads to 80
12:03:57.926903 PROGRESS: === Extracted 3233 precursors and 31724 fragments ===
12:03:57.927309 INFO: === FDR correction performed with classifier version 1 ===
12:03:57.927872 PROGRESS: ============================= Precursor FDR =============================
12:03:57.927959 PROGRESS: Total precursors accumulated: 587
12:03:57.928018 PROGRESS: Target precursors: 408 (69.51%)
12:03:57.928065 PROGRESS: Decoy precursors: 179 (30.49%)
12:03:57.928108 PROGRESS: 
12:03:57.928151 PROGRESS: Precursor Summary:
12:03:57.929119 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   337; 0.001 FDR:   337
12:03:57.929209 PROGRESS: 
12:03:57.929263 PROGRESS: Protein Summary:
12:03:57.930382 PROGRESS: Channel   0:	 0.050 FDR:   335; 0.010 FDR:   335; 0.001 FDR:   335
12:03:57.930470 PROGRESS: =========================================================================
12:03:57.930694 INFO: Target number of precursors reached.
12:03:57.935593 INFO: fragments_df: keeping 1590 of 31724 [sum(precursor_idx_mask)=9565 sum(mass_error_mask)=31724 stop_rank=1590
12:03:58.035136 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:03:58.159808 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:03:58.284059 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:03:58.411382 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:03:58.632284 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:03:58.632695 INFO: Using score_cutoff 29.383346001434326 (fac=0.99, q=1)
12:03:58.632999 INFO: Updating optimization_manager: fwhm_rt             : 2.534274101257324 -> 2.547919273376465
12:03:58.633083 INFO: Updating optimization_manager: fwhm_mobility       : 0.004624363966286182 -> 0.00438930606469512
12:03:58.633136 INFO: Updating optimization_manager: score_cutoff        : 30.24422956123352 -> 29.383346001434326
12:03:58.633194 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:03:58.634248 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:03:58.635561 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:03:58.636314 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:03:58.638731 INFO: === checking if optimization conditions were reached ===
12:03:58.638828 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
12:03:58.640500 INFO: Updating optimization_manager: ms2_error           : 9.203412154797988 -> 8.563797856189629
12:03:58.640600 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 8.5638.
12:03:58.640665 INFO: ==============================================
12:03:58.640731 INFO: Starting optimization step 10.
12:03:58.640786 PROGRESS: === Extracting elution groups 0 to 600 ===
12:03:58.640841 INFO: Using classic extraction backend
12:03:58.640956 PROGRESS: Extracting batch of 1173 precursors
12:03:58.641034 INFO: === Search parameters used ===
12:03:58.641082 INFO: rt_error       : 2099.8992935
12:03:58.641124 INFO: mobility_error : 0.1
12:03:58.641166 INFO: num_candidates : 3
12:03:58.641210 INFO: ms1_error      : 30
12:03:58.641252 INFO: ms2_error      : 8.563797856189629
12:03:58.641290 INFO: fwhm_rt        : 2.547919273376465
12:03:58.641328 INFO: quant_window   : 3
12:03:58.641367 INFO: ==============================================
12:03:58.642723 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:03:58.642769 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:03:58.642805 INFO: FWHM in RT is 2.55 seconds, sigma is 0.56
12:03:58.642827 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 2.04
12:03:58.643516 INFO: Starting candidate selection
12:04:08.267840 INFO: Starting candidate scoring
12:04:08.448008 INFO: Finished candidate processing
12:04:08.448146 INFO: Collecting candidate features
12:04:08.461822 INFO: Collecting fragment features
12:04:08.466887 INFO: Finished candidate scoring
12:04:08.468719 INFO: performing precursor FDR with 47 features
12:04:08.468764 INFO: Decoy channel: -1
12:04:08.468789 INFO: Competetive: True
12:04:08.472506 INFO: Setting torch num_threads to 2 for FDR classification task
12:04:08.474865 INFO: Using random state 63794 for train-test-split
12:04:08.486561 INFO: Test AUC: 0.462
12:04:08.486621 INFO: Train AUC: 0.497
12:04:08.486652 INFO: AUC difference: 7.08%
12:04:08.486675 WARNING: AUC difference > 5%. This may indicate overfitting.
12:04:08.706717 INFO: Resetting torch num_threads to 80
12:04:08.707250 PROGRESS: === Extracted 3223 precursors and 31203 fragments ===
12:04:08.707699 INFO: === FDR correction performed with classifier version 1 ===
12:04:08.708256 PROGRESS: ============================= Precursor FDR =============================
12:04:08.708343 PROGRESS: Total precursors accumulated: 586
12:04:08.708403 PROGRESS: Target precursors: 403 (68.77%)
12:04:08.708452 PROGRESS: Decoy precursors: 183 (31.23%)
12:04:08.708495 PROGRESS: 
12:04:08.708538 PROGRESS: Precursor Summary:
12:04:08.709486 PROGRESS: Channel   0:	 0.050 FDR:   333; 0.010 FDR:   333; 0.001 FDR:   333
12:04:08.709576 PROGRESS: 
12:04:08.709630 PROGRESS: Protein Summary:
12:04:08.710744 PROGRESS: Channel   0:	 0.050 FDR:   332; 0.010 FDR:   332; 0.001 FDR:   332
12:04:08.710831 PROGRESS: =========================================================================
12:04:08.710988 INFO: Target number of precursors reached.
12:04:08.715870 INFO: fragments_df: keeping 1525 of 31203 [sum(precursor_idx_mask)=9329 sum(mass_error_mask)=31203 stop_rank=1525
12:04:08.814464 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:04:08.926123 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:04:09.028322 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:04:09.132418 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:04:09.314343 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:04:09.314754 INFO: Using score_cutoff 29.416046017456054 (fac=0.99, q=1)
12:04:09.315075 INFO: Updating optimization_manager: fwhm_rt             : 2.547919273376465 -> 2.4361138343811035
12:04:09.315154 INFO: Updating optimization_manager: fwhm_mobility       : 0.00438930606469512 -> 0.004115695599466562
12:04:09.315210 INFO: Updating optimization_manager: score_cutoff        : 29.383346001434326 -> 29.416046017456054
12:04:09.315266 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:04:09.316295 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:04:09.317616 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:04:09.318381 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:04:09.320487 INFO: === checking if optimization conditions were reached ===
12:04:09.320593 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
12:04:09.322248 INFO: Updating optimization_manager: ms2_error           : 8.563797856189629 -> 7.963910467349246
12:04:09.322354 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 7.9639.
12:04:09.322423 INFO: ==============================================
12:04:09.322489 INFO: Starting optimization step 11.
12:04:09.322545 PROGRESS: === Extracting elution groups 0 to 600 ===
12:04:09.322601 INFO: Using classic extraction backend
12:04:09.322754 PROGRESS: Extracting batch of 1173 precursors
12:04:09.322820 INFO: === Search parameters used ===
12:04:09.322866 INFO: rt_error       : 2099.8992935
12:04:09.322907 INFO: mobility_error : 0.1
12:04:09.322950 INFO: num_candidates : 3
12:04:09.322989 INFO: ms1_error      : 30
12:04:09.323028 INFO: ms2_error      : 7.963910467349246
12:04:09.323067 INFO: fwhm_rt        : 2.4361138343811035
12:04:09.323115 INFO: quant_window   : 3
12:04:09.323155 INFO: ==============================================
12:04:09.324038 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:04:09.324082 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:04:09.324119 INFO: FWHM in RT is 2.44 seconds, sigma is 0.54
12:04:09.324140 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.91
12:04:09.324796 INFO: Starting candidate selection
12:04:57.423272 INFO: Starting candidate scoring
12:04:57.620705 INFO: Finished candidate processing
12:04:57.620797 INFO: Collecting candidate features
12:04:57.633372 INFO: Collecting fragment features
12:04:57.637264 INFO: Finished candidate scoring
12:04:57.638925 INFO: performing precursor FDR with 47 features
12:04:57.638967 INFO: Decoy channel: -1
12:04:57.638991 INFO: Competetive: True
12:04:57.641763 INFO: Setting torch num_threads to 2 for FDR classification task
12:04:57.643702 INFO: Using random state 63794 for train-test-split
12:04:57.653638 INFO: Test AUC: 0.518
12:04:57.653692 INFO: Train AUC: 0.482
12:04:57.653721 INFO: AUC difference: 7.35%
12:04:57.653741 WARNING: AUC difference > 5%. This may indicate overfitting.
12:04:57.873527 INFO: Resetting torch num_threads to 80
12:04:57.874049 PROGRESS: === Extracted 3218 precursors and 30441 fragments ===
12:04:57.874449 INFO: === FDR correction performed with classifier version 1 ===
12:04:57.875015 PROGRESS: ============================= Precursor FDR =============================
12:04:57.875102 PROGRESS: Total precursors accumulated: 587
12:04:57.875160 PROGRESS: Target precursors: 409 (69.68%)
12:04:57.875209 PROGRESS: Decoy precursors: 178 (30.32%)
12:04:57.875386 PROGRESS: 
12:04:57.875436 PROGRESS: Precursor Summary:
12:04:57.876392 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   336; 0.001 FDR:   336
12:04:57.876479 PROGRESS: 
12:04:57.876532 PROGRESS: Protein Summary:
12:04:57.877662 PROGRESS: Channel   0:	 0.050 FDR:   334; 0.010 FDR:   334; 0.001 FDR:   334
12:04:57.877752 PROGRESS: =========================================================================
12:04:57.877893 INFO: Target number of precursors reached.
12:04:57.882694 INFO: fragments_df: keeping 1507 of 30441 [sum(precursor_idx_mask)=9226 sum(mass_error_mask)=30441 stop_rank=1507
12:04:57.981948 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:04:58.106820 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:04:58.221341 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:04:58.324611 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:04:58.508061 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:04:58.508468 INFO: Using score_cutoff 29.664440757751464 (fac=0.99, q=1)
12:04:58.508764 INFO: Updating optimization_manager: fwhm_rt             : 2.4361138343811035 -> 2.3112311363220215
12:04:58.508849 INFO: Updating optimization_manager: fwhm_mobility       : 0.004115695599466562 -> 0.003789931535720825
12:04:58.508904 INFO: Updating optimization_manager: score_cutoff        : 29.416046017456054 -> 29.664440757751464
12:04:58.508968 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:04:58.509999 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:04:58.511309 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:04:58.512063 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:04:58.514242 INFO: === checking if optimization conditions were reached ===
12:04:58.514338 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
12:04:58.515942 INFO: Updating optimization_manager: ms2_error           : 7.963910467349246 -> 6.954090712272618
12:04:58.516041 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 6.9541.
12:04:58.516105 INFO: ==============================================
12:04:58.516169 INFO: Starting optimization step 12.
12:04:58.516225 PROGRESS: === Extracting elution groups 0 to 600 ===
12:04:58.516286 INFO: Using classic extraction backend
12:04:58.516388 PROGRESS: Extracting batch of 1173 precursors
12:04:58.516451 INFO: === Search parameters used ===
12:04:58.516497 INFO: rt_error       : 2099.8992935
12:04:58.516538 INFO: mobility_error : 0.1
12:04:58.516578 INFO: num_candidates : 3
12:04:58.516618 INFO: ms1_error      : 30
12:04:58.516656 INFO: ms2_error      : 6.954090712272618
12:04:58.516694 INFO: fwhm_rt        : 2.3112311363220215
12:04:58.516731 INFO: quant_window   : 3
12:04:58.516770 INFO: ==============================================
12:04:58.517647 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:04:58.517693 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:04:58.517727 INFO: FWHM in RT is 2.31 seconds, sigma is 0.51
12:04:58.517749 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.76
12:04:58.518384 INFO: Starting candidate selection
12:05:07.726948 INFO: Starting candidate scoring
12:05:07.923175 INFO: Finished candidate processing
12:05:07.923272 INFO: Collecting candidate features
12:05:07.935328 INFO: Collecting fragment features
12:05:07.939127 INFO: Finished candidate scoring
12:05:07.940724 INFO: performing precursor FDR with 47 features
12:05:07.940768 INFO: Decoy channel: -1
12:05:07.940791 INFO: Competetive: True
12:05:07.943561 INFO: Setting torch num_threads to 2 for FDR classification task
12:05:07.945523 INFO: Using random state 63794 for train-test-split
12:05:07.955670 INFO: Test AUC: 0.514
12:05:07.955729 INFO: Train AUC: 0.476
12:05:07.955757 INFO: AUC difference: 7.87%
12:05:07.955779 WARNING: AUC difference > 5%. This may indicate overfitting.
12:05:08.176354 INFO: Resetting torch num_threads to 80
12:05:08.176881 PROGRESS: === Extracted 3227 precursors and 29837 fragments ===
12:05:08.177287 INFO: === FDR correction performed with classifier version 1 ===
12:05:08.177838 PROGRESS: ============================= Precursor FDR =============================
12:05:08.177924 PROGRESS: Total precursors accumulated: 586
12:05:08.177982 PROGRESS: Target precursors: 397 (67.75%)
12:05:08.178032 PROGRESS: Decoy precursors: 189 (32.25%)
12:05:08.178077 PROGRESS: 
12:05:08.178119 PROGRESS: Precursor Summary:
12:05:08.179060 PROGRESS: Channel   0:	 0.050 FDR:   332; 0.010 FDR:   332; 0.001 FDR:   332
12:05:08.179149 PROGRESS: 
12:05:08.179204 PROGRESS: Protein Summary:
12:05:08.180321 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:   331; 0.001 FDR:   331
12:05:08.180409 PROGRESS: =========================================================================
12:05:08.180538 INFO: Target number of precursors reached.
12:05:08.185071 INFO: fragments_df: keeping 1476 of 29837 [sum(precursor_idx_mask)=8858 sum(mass_error_mask)=29837 stop_rank=1476
12:05:08.285247 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:05:08.410421 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:05:08.534194 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:05:08.655341 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:05:08.865682 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:05:08.866099 INFO: Using score_cutoff 30.38531334171295 (fac=0.99, q=1)
12:05:08.866396 INFO: Updating optimization_manager: fwhm_rt             : 2.3112311363220215 -> 2.244647979736328
12:05:08.866475 INFO: Updating optimization_manager: fwhm_mobility       : 0.003789931535720825 -> 0.0034056142903864384
12:05:08.866527 INFO: Updating optimization_manager: score_cutoff        : 29.664440757751464 -> 30.38531334171295
12:05:08.866577 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:05:08.867593 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:05:08.868895 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:05:08.869662 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:05:08.871736 INFO: === checking if optimization conditions were reached ===
12:05:08.871829 PROGRESS: === Optimization of ms2_error has been performed 11 time(s); minimum number is 2 ===
12:05:08.873466 INFO: Updating optimization_manager: ms2_error           : 6.954090712272618 -> 6.3411982204094635
12:05:08.873567 PROGRESS: ❌ ms2_error      : optimization incomplete after 11 search(es). Will search with parameter 6.3412.
12:05:08.873630 INFO: ==============================================
12:05:08.873695 INFO: Starting optimization step 13.
12:05:08.873748 PROGRESS: === Extracting elution groups 0 to 600 ===
12:05:08.873799 INFO: Using classic extraction backend
12:05:08.873901 PROGRESS: Extracting batch of 1173 precursors
12:05:08.873963 INFO: === Search parameters used ===
12:05:08.874008 INFO: rt_error       : 2099.8992935
12:05:08.874056 INFO: mobility_error : 0.1
12:05:08.874099 INFO: num_candidates : 3
12:05:08.874139 INFO: ms1_error      : 30
12:05:08.874179 INFO: ms2_error      : 6.3411982204094635
12:05:08.874218 INFO: fwhm_rt        : 2.244647979736328
12:05:08.874256 INFO: quant_window   : 3
12:05:08.874295 INFO: ==============================================
12:05:08.875135 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:05:08.875179 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:05:08.875213 INFO: FWHM in RT is 2.24 seconds, sigma is 0.49
12:05:08.875237 INFO: FWHM in mobility is 0.003 1/K_0, sigma is 1.58
12:05:08.875902 INFO: Starting candidate selection
12:05:18.474515 INFO: Starting candidate scoring
12:05:18.658481 INFO: Finished candidate processing
12:05:18.658662 INFO: Collecting candidate features
12:05:18.673050 INFO: Collecting fragment features
12:05:18.677411 INFO: Finished candidate scoring
12:05:18.679128 INFO: performing precursor FDR with 47 features
12:05:18.679172 INFO: Decoy channel: -1
12:05:18.679196 INFO: Competetive: True
12:05:18.682085 INFO: Setting torch num_threads to 2 for FDR classification task
12:05:18.684035 INFO: Using random state 63794 for train-test-split
12:05:18.694400 INFO: Test AUC: 0.482
12:05:18.694458 INFO: Train AUC: 0.491
12:05:18.694489 INFO: AUC difference: 1.69%
12:05:18.913306 INFO: Resetting torch num_threads to 80
12:05:18.913814 PROGRESS: === Extracted 3224 precursors and 29628 fragments ===
12:05:18.914212 INFO: === FDR correction performed with classifier version 1 ===
12:05:18.914763 PROGRESS: ============================= Precursor FDR =============================
12:05:18.914850 PROGRESS: Total precursors accumulated: 584
12:05:18.914912 PROGRESS: Target precursors: 403 (69.01%)
12:05:18.914962 PROGRESS: Decoy precursors: 181 (30.99%)
12:05:18.915007 PROGRESS: 
12:05:18.915050 PROGRESS: Precursor Summary:
12:05:18.915982 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   326; 0.001 FDR:   326
12:05:18.916069 PROGRESS: 
12:05:18.916124 PROGRESS: Protein Summary:
12:05:18.917236 PROGRESS: Channel   0:	 0.050 FDR:   325; 0.010 FDR:   325; 0.001 FDR:   325
12:05:18.917326 PROGRESS: =========================================================================
12:05:18.917457 INFO: Target number of precursors reached.
12:05:18.921983 INFO: fragments_df: keeping 1496 of 29628 [sum(precursor_idx_mask)=8651 sum(mass_error_mask)=29628 stop_rank=1496
12:05:19.038534 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:05:19.162616 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:05:19.286536 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:05:19.413490 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:05:19.622857 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:05:19.623267 INFO: Using score_cutoff 28.591424345970154 (fac=0.99, q=1)
12:05:19.623560 INFO: Updating optimization_manager: fwhm_rt             : 2.244647979736328 -> 2.177638292312622
12:05:19.623638 INFO: Updating optimization_manager: fwhm_mobility       : 0.0034056142903864384 -> 0.0034249855671077967
12:05:19.623691 INFO: Updating optimization_manager: score_cutoff        : 30.38531334171295 -> 28.591424345970154
12:05:19.623742 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:05:19.624766 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:05:19.626096 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:05:19.626848 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:05:19.629145 INFO: === checking if optimization conditions were reached ===
12:05:19.629241 PROGRESS: === Optimization of ms2_error has been performed 12 time(s); minimum number is 2 ===
12:05:19.630867 INFO: Updating optimization_manager: ms2_error           : 6.3411982204094635 -> 6.051533278601659
12:05:19.630966 PROGRESS: ❌ ms2_error      : optimization incomplete after 12 search(es). Will search with parameter 6.0515.
12:05:19.631046 INFO: ==============================================
12:05:19.631113 INFO: Starting optimization step 14.
12:05:19.631169 PROGRESS: === Extracting elution groups 0 to 600 ===
12:05:19.631221 INFO: Using classic extraction backend
12:05:19.631324 PROGRESS: Extracting batch of 1173 precursors
12:05:19.631383 INFO: === Search parameters used ===
12:05:19.631428 INFO: rt_error       : 2099.8992935
12:05:19.631468 INFO: mobility_error : 0.1
12:05:19.631507 INFO: num_candidates : 3
12:05:19.631546 INFO: ms1_error      : 30
12:05:19.631583 INFO: ms2_error      : 6.051533278601659
12:05:19.631621 INFO: fwhm_rt        : 2.177638292312622
12:05:19.631657 INFO: quant_window   : 3
12:05:19.631695 INFO: ==============================================
12:05:19.632542 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:05:19.632586 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:05:19.632619 INFO: FWHM in RT is 2.18 seconds, sigma is 0.48
12:05:19.632640 INFO: FWHM in mobility is 0.003 1/K_0, sigma is 1.59
12:05:19.633350 INFO: Starting candidate selection
12:05:57.445047 INFO: Starting candidate scoring
12:05:57.629667 INFO: Finished candidate processing
12:05:57.629799 INFO: Collecting candidate features
12:05:57.639298 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3232)
12:05:57.642430 INFO: Collecting fragment features
12:05:57.646593 INFO: Finished candidate scoring
12:05:57.648312 INFO: performing precursor FDR with 47 features
12:05:57.648356 INFO: Decoy channel: -1
12:05:57.648380 INFO: Competetive: True
12:05:57.651106 INFO: Setting torch num_threads to 2 for FDR classification task
12:05:57.652357 WARNING: dropped 1 decoy PSMs due to missing features
12:05:57.653337 INFO: Using random state 63794 for train-test-split
12:05:57.663538 INFO: Test AUC: 0.479
12:05:57.663595 INFO: Train AUC: 0.493
12:05:57.663624 INFO: AUC difference: 2.89%
12:05:59.231257 INFO: Resetting torch num_threads to 80
12:05:59.231961 PROGRESS: === Extracted 3232 precursors and 29551 fragments ===
12:05:59.232361 INFO: === FDR correction performed with classifier version 1 ===
12:05:59.232969 PROGRESS: ============================= Precursor FDR =============================
12:05:59.233064 PROGRESS: Total precursors accumulated: 585
12:05:59.233121 PROGRESS: Target precursors: 413 (70.60%)
12:05:59.233170 PROGRESS: Decoy precursors: 172 (29.40%)
12:05:59.233212 PROGRESS: 
12:05:59.233263 PROGRESS: Precursor Summary:
12:05:59.234239 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   341; 0.001 FDR:   341
12:05:59.234333 PROGRESS: 
12:05:59.234386 PROGRESS: Protein Summary:
12:05:59.235508 PROGRESS: Channel   0:	 0.050 FDR:   340; 0.010 FDR:   340; 0.001 FDR:   340
12:05:59.235598 PROGRESS: =========================================================================
12:05:59.235735 INFO: Target number of precursors reached.
12:05:59.240414 INFO: fragments_df: keeping 1586 of 29551 [sum(precursor_idx_mask)=8955 sum(mass_error_mask)=29551 stop_rank=1586
12:05:59.340465 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:05:59.446452 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:05:59.569587 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:05:59.692084 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:05:59.878062 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:05:59.878497 INFO: Using score_cutoff 27.911818542480468 (fac=0.99, q=1)
12:05:59.878793 INFO: Updating optimization_manager: fwhm_rt             : 2.177638292312622 -> 2.1551144123077393
12:05:59.878871 INFO: Updating optimization_manager: fwhm_mobility       : 0.0034249855671077967 -> 0.0034684943966567516
12:05:59.878924 INFO: Updating optimization_manager: score_cutoff        : 28.591424345970154 -> 27.911818542480468
12:05:59.878982 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:05:59.880031 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:05:59.881599 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:05:59.882374 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:05:59.884501 INFO: === checking if optimization conditions were reached ===
12:05:59.884594 PROGRESS: === Optimization of ms2_error has been performed 13 time(s); minimum number is 2 ===
12:05:59.885291 INFO: Updating optimization_manager: ms2_error           : 6.051533278601659 -> 30.0
12:05:59.885409 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
12:05:59.885498 INFO: Updating optimization_manager: score_cutoff        : 27.911818542480468 -> 39.401085546112064
12:05:59.885580 INFO: Updating optimization_manager: fwhm_rt             : 2.1551144123077393 -> 3.370589017868042
12:05:59.885661 INFO: Updating optimization_manager: fwhm_mobility       : 0.0034684943966567516 -> 0.007943905889987946
12:05:59.885739 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 30.0000 found after 13 searches.
12:05:59.885796 INFO: ==============================================
12:05:59.885859 PROGRESS: Optimization finished for ms2_error.
12:05:59.986876 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:05:59.988003 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:05:59.989353 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:05:59.990133 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:06:00.016984 INFO: Starting optimization step 0.
12:06:00.017120 PROGRESS: === Extracting elution groups 0 to 600 ===
12:06:00.017191 INFO: Using classic extraction backend
12:06:00.017309 PROGRESS: Extracting batch of 1173 precursors
12:06:00.017378 INFO: === Search parameters used ===
12:06:00.017425 INFO: rt_error       : 2099.8992935
12:06:00.017467 INFO: mobility_error : 0.1
12:06:00.017507 INFO: num_candidates : 3
12:06:00.017547 INFO: ms1_error      : 30
12:06:00.017587 INFO: ms2_error      : 30.0
12:06:00.017626 INFO: fwhm_rt        : 3.370589017868042
12:06:00.017665 INFO: quant_window   : 3
12:06:00.017706 INFO: ==============================================
12:06:00.018641 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:06:00.018688 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:06:00.018726 INFO: FWHM in RT is 3.37 seconds, sigma is 0.74
12:06:00.018748 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.68
12:06:00.019386 INFO: Starting candidate selection
12:06:09.016550 INFO: Starting candidate scoring
12:06:09.351965 INFO: Finished candidate processing
12:06:09.352062 INFO: Collecting candidate features
12:06:09.365480 INFO: Collecting fragment features
12:06:09.369348 INFO: Finished candidate scoring
12:06:09.371933 INFO: performing precursor FDR with 47 features
12:06:09.371980 INFO: Decoy channel: -1
12:06:09.372004 INFO: Competetive: True
12:06:09.375656 INFO: Setting torch num_threads to 2 for FDR classification task
12:06:09.378044 INFO: Using random state 272074 for train-test-split
12:06:09.388763 INFO: Test AUC: 0.484
12:06:09.388821 INFO: Train AUC: 0.501
12:06:09.388852 INFO: AUC difference: 3.37%
12:06:09.610927 INFO: Resetting torch num_threads to 80
12:06:09.611508 PROGRESS: === Extracted 3236 precursors and 35346 fragments ===
12:06:09.611969 INFO: === FDR correction performed with classifier version 2 ===
12:06:09.612571 PROGRESS: ============================= Precursor FDR =============================
12:06:09.612666 PROGRESS: Total precursors accumulated: 588
12:06:09.612727 PROGRESS: Target precursors: 425 (72.28%)
12:06:09.612775 PROGRESS: Decoy precursors: 163 (27.72%)
12:06:09.612818 PROGRESS: 
12:06:09.612861 PROGRESS: Precursor Summary:
12:06:09.613879 PROGRESS: Channel   0:	 0.050 FDR:   344; 0.010 FDR:   344; 0.001 FDR:   344
12:06:09.613972 PROGRESS: 
12:06:09.614028 PROGRESS: Protein Summary:
12:06:09.615160 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   341; 0.001 FDR:   341
12:06:09.615260 PROGRESS: =========================================================================
12:06:09.615402 INFO: Target number of precursors reached.
12:06:09.620971 INFO: fragments_df: keeping 2087 of 35346 [sum(precursor_idx_mask)=10714 sum(mass_error_mask)=35346 stop_rank=2087
12:06:09.719681 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:06:09.833112 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:06:09.938017 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:06:10.045971 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:06:10.278126 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:06:10.278549 INFO: Using score_cutoff 37.37864308776856 (fac=0.99, q=1)
12:06:10.278876 INFO: Updating optimization_manager: fwhm_rt             : 3.370589017868042 -> 3.4837563037872314
12:06:10.278955 INFO: Updating optimization_manager: fwhm_mobility       : 0.007943905889987946 -> 0.008120144717395306
12:06:10.279009 INFO: Updating optimization_manager: score_cutoff        : 39.401085546112064 -> 37.37864308776856
12:06:10.279066 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:06:10.280132 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:06:10.281491 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:06:10.282274 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:06:10.284382 INFO: === checking if optimization conditions were reached ===
12:06:10.284492 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
12:06:10.286030 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 1299.0031601092892
12:06:10.286129 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1299.0032.
12:06:10.286191 INFO: ==============================================
12:06:10.286259 INFO: Starting optimization step 1.
12:06:10.286318 PROGRESS: === Extracting elution groups 0 to 600 ===
12:06:10.286375 INFO: Using classic extraction backend
12:06:10.286525 PROGRESS: Extracting batch of 1173 precursors
12:06:10.286590 INFO: === Search parameters used ===
12:06:10.286636 INFO: rt_error       : 1299.0031601092892
12:06:10.286678 INFO: mobility_error : 0.1
12:06:10.286718 INFO: num_candidates : 3
12:06:10.286758 INFO: ms1_error      : 30
12:06:10.286797 INFO: ms2_error      : 30.0
12:06:10.286834 INFO: fwhm_rt        : 3.4837563037872314
12:06:10.286870 INFO: quant_window   : 3
12:06:10.286908 INFO: ==============================================
12:06:10.287778 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:06:10.287822 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:06:10.287863 INFO: FWHM in RT is 3.48 seconds, sigma is 0.77
12:06:10.287885 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.77
12:06:10.288560 INFO: Starting candidate selection
12:06:16.845297 INFO: Starting candidate scoring
12:06:17.177403 INFO: Finished candidate processing
12:06:17.177589 INFO: Collecting candidate features
12:06:17.197665 INFO: Collecting fragment features
12:06:17.201562 INFO: Finished candidate scoring
12:06:17.204330 INFO: performing precursor FDR with 47 features
12:06:17.204373 INFO: Decoy channel: -1
12:06:17.204397 INFO: Competetive: True
12:06:17.207414 INFO: Setting torch num_threads to 2 for FDR classification task
12:06:17.209462 INFO: Using random state 272074 for train-test-split
12:06:17.221082 INFO: Test AUC: 0.492
12:06:17.221142 INFO: Train AUC: 0.496
12:06:17.221171 INFO: AUC difference: 0.73%
12:06:17.439689 INFO: Resetting torch num_threads to 80
12:06:17.440248 PROGRESS: === Extracted 3231 precursors and 35339 fragments ===
12:06:17.440650 INFO: === FDR correction performed with classifier version 2 ===
12:06:17.441237 PROGRESS: ============================= Precursor FDR =============================
12:06:17.441328 PROGRESS: Total precursors accumulated: 589
12:06:17.441387 PROGRESS: Target precursors: 427 (72.50%)
12:06:17.441444 PROGRESS: Decoy precursors: 162 (27.50%)
12:06:17.441491 PROGRESS: 
12:06:17.441535 PROGRESS: Precursor Summary:
12:06:17.442513 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   354; 0.001 FDR:   354
12:06:17.442602 PROGRESS: 
12:06:17.442657 PROGRESS: Protein Summary:
12:06:17.443787 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   351; 0.001 FDR:   351
12:06:17.443877 PROGRESS: =========================================================================
12:06:17.444006 INFO: Target number of precursors reached.
12:06:17.449480 INFO: fragments_df: keeping 2075 of 35339 [sum(precursor_idx_mask)=11072 sum(mass_error_mask)=35339 stop_rank=2075
12:06:17.548338 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:06:17.670444 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:06:17.799521 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:06:17.928166 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:06:18.188968 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:06:18.189384 INFO: Using score_cutoff 36.8387777835846 (fac=0.99, q=1)
12:06:18.189681 INFO: Updating optimization_manager: fwhm_rt             : 3.4837563037872314 -> 3.423060894012451
12:06:18.189759 INFO: Updating optimization_manager: fwhm_mobility       : 0.008120144717395306 -> 0.00820249319076538
12:06:18.189811 INFO: Updating optimization_manager: score_cutoff        : 37.37864308776856 -> 36.8387777835846
12:06:18.189871 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:06:18.190927 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:06:18.192268 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:06:18.193046 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:06:18.195165 INFO: === checking if optimization conditions were reached ===
12:06:18.195263 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
12:06:18.196828 INFO: Updating optimization_manager: rt_error            : 1299.0031601092892 -> 873.650439883446
12:06:18.196926 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 873.6504.
12:06:18.197003 INFO: ==============================================
12:06:18.197072 INFO: Starting optimization step 2.
12:06:18.197127 PROGRESS: === Extracting elution groups 0 to 600 ===
12:06:18.197182 INFO: Using classic extraction backend
12:06:18.197284 PROGRESS: Extracting batch of 1173 precursors
12:06:18.197345 INFO: === Search parameters used ===
12:06:18.197390 INFO: rt_error       : 873.650439883446
12:06:18.197433 INFO: mobility_error : 0.1
12:06:18.197471 INFO: num_candidates : 3
12:06:18.197511 INFO: ms1_error      : 30
12:06:18.197550 INFO: ms2_error      : 30.0
12:06:18.197588 INFO: fwhm_rt        : 3.423060894012451
12:06:18.197626 INFO: quant_window   : 3
12:06:18.197669 INFO: ==============================================
12:06:18.198471 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:06:18.198515 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:06:18.198547 INFO: FWHM in RT is 3.42 seconds, sigma is 0.75
12:06:18.198569 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
12:06:18.199203 INFO: Starting candidate selection
12:06:57.448021 INFO: Starting candidate scoring
12:06:57.782880 INFO: Finished candidate processing
12:06:57.783015 INFO: Collecting candidate features
12:06:57.797401 INFO: Collecting fragment features
12:06:57.800981 INFO: Finished candidate scoring
12:06:57.803197 INFO: performing precursor FDR with 47 features
12:06:57.803239 INFO: Decoy channel: -1
12:06:57.803263 INFO: Competetive: True
12:06:57.806225 INFO: Setting torch num_threads to 2 for FDR classification task
12:06:57.808227 INFO: Using random state 272074 for train-test-split
12:06:57.819680 INFO: Test AUC: 0.483
12:06:57.819739 INFO: Train AUC: 0.494
12:06:57.819767 INFO: AUC difference: 2.06%
12:06:58.038116 INFO: Resetting torch num_threads to 80
12:06:58.038702 PROGRESS: === Extracted 3244 precursors and 35376 fragments ===
12:06:58.039101 INFO: === FDR correction performed with classifier version 2 ===
12:06:58.039665 PROGRESS: ============================= Precursor FDR =============================
12:06:58.039756 PROGRESS: Total precursors accumulated: 589
12:06:58.039819 PROGRESS: Target precursors: 425 (72.16%)
12:06:58.039868 PROGRESS: Decoy precursors: 164 (27.84%)
12:06:58.039912 PROGRESS: 
12:06:58.039955 PROGRESS: Precursor Summary:
12:06:58.040928 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   350; 0.001 FDR:   350
12:06:58.041031 PROGRESS: 
12:06:58.041087 PROGRESS: Protein Summary:
12:06:58.042223 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   348
12:06:58.042314 PROGRESS: =========================================================================
12:06:58.042444 INFO: Target number of precursors reached.
12:06:58.048029 INFO: fragments_df: keeping 2065 of 35376 [sum(precursor_idx_mask)=10939 sum(mass_error_mask)=35376 stop_rank=2065
12:06:58.146784 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:06:58.269434 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:06:58.397249 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:06:58.509086 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:06:58.737919 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:06:58.738335 INFO: Using score_cutoff 37.69231281852722 (fac=0.99, q=1)
12:06:58.738637 INFO: Updating optimization_manager: fwhm_rt             : 3.423060894012451 -> 3.4142472743988037
12:06:58.738718 INFO: Updating optimization_manager: fwhm_mobility       : 0.00820249319076538 -> 0.008039599284529686
12:06:58.738771 INFO: Updating optimization_manager: score_cutoff        : 36.8387777835846 -> 37.69231281852722
12:06:58.738822 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:06:58.739875 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:06:58.741242 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:06:58.742019 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:06:58.744157 INFO: === checking if optimization conditions were reached ===
12:06:58.744257 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
12:06:58.745914 INFO: Updating optimization_manager: rt_error            : 873.650439883446 -> 808.5439287624014
12:06:58.746015 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 808.5439.
12:06:58.746080 INFO: ==============================================
12:06:58.746146 INFO: Starting optimization step 3.
12:06:58.746202 PROGRESS: === Extracting elution groups 0 to 600 ===
12:06:58.746256 INFO: Using classic extraction backend
12:06:58.746359 PROGRESS: Extracting batch of 1173 precursors
12:06:58.746421 INFO: === Search parameters used ===
12:06:58.746477 INFO: rt_error       : 808.5439287624014
12:06:58.746522 INFO: mobility_error : 0.1
12:06:58.746563 INFO: num_candidates : 3
12:06:58.746603 INFO: ms1_error      : 30
12:06:58.746643 INFO: ms2_error      : 30.0
12:06:58.746681 INFO: fwhm_rt        : 3.4142472743988037
12:06:58.746721 INFO: quant_window   : 3
12:06:58.746759 INFO: ==============================================
12:06:58.747556 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:06:58.747601 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:06:58.747639 INFO: FWHM in RT is 3.41 seconds, sigma is 0.75
12:06:58.747662 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.73
12:06:58.748335 INFO: Starting candidate selection
12:07:02.516010 INFO: Starting candidate scoring
12:07:02.852030 INFO: Finished candidate processing
12:07:02.852128 INFO: Collecting candidate features
12:07:02.881090 INFO: Collecting fragment features
12:07:02.889184 INFO: Finished candidate scoring
12:07:02.892577 INFO: performing precursor FDR with 47 features
12:07:02.892673 INFO: Decoy channel: -1
12:07:02.892730 INFO: Competetive: True
12:07:02.898828 INFO: Setting torch num_threads to 2 for FDR classification task
12:07:02.902793 INFO: Using random state 272074 for train-test-split
12:07:02.918871 INFO: Test AUC: 0.493
12:07:02.918966 INFO: Train AUC: 0.485
12:07:02.919015 INFO: AUC difference: 1.58%
12:07:03.147625 INFO: Resetting torch num_threads to 80
12:07:03.148191 PROGRESS: === Extracted 3240 precursors and 35360 fragments ===
12:07:03.148592 INFO: === FDR correction performed with classifier version 2 ===
12:07:03.149243 PROGRESS: ============================= Precursor FDR =============================
12:07:03.149345 PROGRESS: Total precursors accumulated: 588
12:07:03.149406 PROGRESS: Target precursors: 423 (71.94%)
12:07:03.149459 PROGRESS: Decoy precursors: 165 (28.06%)
12:07:03.149507 PROGRESS: 
12:07:03.149554 PROGRESS: Precursor Summary:
12:07:03.150560 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   351; 0.001 FDR:   351
12:07:03.150651 PROGRESS: 
12:07:03.150708 PROGRESS: Protein Summary:
12:07:03.151876 PROGRESS: Channel   0:	 0.050 FDR:   349; 0.010 FDR:   349; 0.001 FDR:   349
12:07:03.151966 PROGRESS: =========================================================================
12:07:03.152116 INFO: Target number of precursors reached.
12:07:03.157803 INFO: fragments_df: keeping 2108 of 35360 [sum(precursor_idx_mask)=10975 sum(mass_error_mask)=35360 stop_rank=2108
12:07:03.257540 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:07:03.366465 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:07:03.477588 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:07:03.584842 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:07:03.819406 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:07:03.819823 INFO: Using score_cutoff 37.503697357177735 (fac=0.99, q=1)
12:07:03.820124 INFO: Updating optimization_manager: fwhm_rt             : 3.4142472743988037 -> 3.391397476196289
12:07:03.820204 INFO: Updating optimization_manager: fwhm_mobility       : 0.008039599284529686 -> 0.007957196794450283
12:07:03.820259 INFO: Updating optimization_manager: score_cutoff        : 37.69231281852722 -> 37.503697357177735
12:07:03.820312 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:07:03.821374 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:07:03.822779 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:07:03.823552 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:07:03.825670 INFO: === checking if optimization conditions were reached ===
12:07:03.825771 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
12:07:03.827423 INFO: Updating optimization_manager: rt_error            : 808.5439287624014 -> 799.3762494159641
12:07:03.827527 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 799.3762.
12:07:03.827592 INFO: ==============================================
12:07:03.827656 INFO: Starting optimization step 4.
12:07:03.827710 PROGRESS: === Extracting elution groups 0 to 600 ===
12:07:03.827762 INFO: Using classic extraction backend
12:07:03.827861 PROGRESS: Extracting batch of 1173 precursors
12:07:03.827922 INFO: === Search parameters used ===
12:07:03.827969 INFO: rt_error       : 799.3762494159641
12:07:03.828012 INFO: mobility_error : 0.1
12:07:03.828058 INFO: num_candidates : 3
12:07:03.828099 INFO: ms1_error      : 30
12:07:03.828137 INFO: ms2_error      : 30.0
12:07:03.828175 INFO: fwhm_rt        : 3.391397476196289
12:07:03.828213 INFO: quant_window   : 3
12:07:03.828251 INFO: ==============================================
12:07:03.829054 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:07:03.829099 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:07:03.829133 INFO: FWHM in RT is 3.39 seconds, sigma is 0.75
12:07:03.829155 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.69
12:07:03.829840 INFO: Starting candidate selection
12:07:07.995275 INFO: Starting candidate scoring
12:07:08.327001 INFO: Finished candidate processing
12:07:08.327096 INFO: Collecting candidate features
12:07:08.339671 INFO: Collecting fragment features
12:07:08.343062 INFO: Finished candidate scoring
12:07:08.344971 INFO: performing precursor FDR with 47 features
12:07:08.345018 INFO: Decoy channel: -1
12:07:08.345042 INFO: Competetive: True
12:07:08.347886 INFO: Setting torch num_threads to 2 for FDR classification task
12:07:08.349886 INFO: Using random state 272074 for train-test-split
12:07:08.360172 INFO: Test AUC: 0.487
12:07:08.360229 INFO: Train AUC: 0.494
12:07:08.360257 INFO: AUC difference: 1.38%
12:07:08.583402 INFO: Resetting torch num_threads to 80
12:07:08.583958 PROGRESS: === Extracted 3227 precursors and 35252 fragments ===
12:07:08.584361 INFO: === FDR correction performed with classifier version 2 ===
12:07:08.584927 PROGRESS: ============================= Precursor FDR =============================
12:07:08.585027 PROGRESS: Total precursors accumulated: 589
12:07:08.585084 PROGRESS: Target precursors: 423 (71.82%)
12:07:08.585136 PROGRESS: Decoy precursors: 166 (28.18%)
12:07:08.585186 PROGRESS: 
12:07:08.585232 PROGRESS: Precursor Summary:
12:07:08.586204 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   350; 0.001 FDR:   350
12:07:08.586295 PROGRESS: 
12:07:08.586352 PROGRESS: Protein Summary:
12:07:08.587494 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   348
12:07:08.587583 PROGRESS: =========================================================================
12:07:08.587721 INFO: Target number of precursors reached.
12:07:08.593297 INFO: fragments_df: keeping 2076 of 35252 [sum(precursor_idx_mask)=10869 sum(mass_error_mask)=35252 stop_rank=2076
12:07:08.692351 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:07:08.807058 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:07:08.917241 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:07:09.023670 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:07:09.259215 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:07:09.259629 INFO: Using score_cutoff 37.50170114822387 (fac=0.99, q=1)
12:07:09.259926 INFO: Updating optimization_manager: fwhm_rt             : 3.391397476196289 -> 3.4255318641662598
12:07:09.260004 INFO: Updating optimization_manager: fwhm_mobility       : 0.007957196794450283 -> 0.00807250291109085
12:07:09.260056 INFO: Updating optimization_manager: score_cutoff        : 37.503697357177735 -> 37.50170114822387
12:07:09.260106 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:07:09.261160 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:07:09.262537 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:07:09.263313 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:07:09.265388 INFO: === checking if optimization conditions were reached ===
12:07:09.265487 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
12:07:09.266447 INFO: Updating optimization_manager: rt_error            : 799.3762494159641 -> 799.3762494159641
12:07:09.266567 INFO: Updating optimization_manager: classifier_version  : 2 -> 19
12:07:09.266657 INFO: Updating optimization_manager: score_cutoff        : 37.50170114822387 -> 37.50170114822387
12:07:09.266742 INFO: Updating optimization_manager: fwhm_rt             : 3.4255318641662598 -> 3.4255318641662598
12:07:09.266829 INFO: Updating optimization_manager: fwhm_mobility       : 0.00807250291109085 -> 0.00807250291109085
12:07:09.266909 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 799.3762 found after 5 searches.
12:07:09.266968 INFO: ==============================================
12:07:09.267032 PROGRESS: Optimization finished for rt_error.
12:07:09.366028 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:07:09.367128 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:07:09.368464 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:07:09.369242 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:07:09.395709 INFO: Starting optimization step 0.
12:07:09.395846 PROGRESS: === Extracting elution groups 0 to 600 ===
12:07:09.395926 INFO: Using classic extraction backend
12:07:09.396036 PROGRESS: Extracting batch of 1173 precursors
12:07:09.396104 INFO: === Search parameters used ===
12:07:09.396152 INFO: rt_error       : 799.3762494159641
12:07:09.396194 INFO: mobility_error : 0.1
12:07:09.396235 INFO: num_candidates : 3
12:07:09.396275 INFO: ms1_error      : 30
12:07:09.396313 INFO: ms2_error      : 30.0
12:07:09.396352 INFO: fwhm_rt        : 3.4255318641662598
12:07:09.396389 INFO: quant_window   : 3
12:07:09.396452 INFO: ==============================================
12:07:09.397337 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:07:09.397382 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:07:09.397417 INFO: FWHM in RT is 3.43 seconds, sigma is 0.75
12:07:09.397438 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.74
12:07:09.398130 INFO: Starting candidate selection
12:07:13.801365 INFO: Starting candidate scoring
12:07:14.147974 INFO: Finished candidate processing
12:07:14.148106 INFO: Collecting candidate features
12:07:14.162603 INFO: Collecting fragment features
12:07:14.166137 INFO: Finished candidate scoring
12:07:14.168013 INFO: performing precursor FDR with 47 features
12:07:14.168054 INFO: Decoy channel: -1
12:07:14.168077 INFO: Competetive: True
12:07:14.170931 INFO: Setting torch num_threads to 2 for FDR classification task
12:07:14.172925 INFO: Using random state 379583 for train-test-split
12:07:14.183790 INFO: Test AUC: 0.506
12:07:14.183849 INFO: Train AUC: 0.493
12:07:14.183878 INFO: AUC difference: 2.70%
12:07:14.404802 INFO: Resetting torch num_threads to 80
12:07:14.405358 PROGRESS: === Extracted 3227 precursors and 35277 fragments ===
12:07:14.405762 INFO: === FDR correction performed with classifier version 19 ===
12:07:14.406311 PROGRESS: ============================= Precursor FDR =============================
12:07:14.406401 PROGRESS: Total precursors accumulated: 590
12:07:14.406461 PROGRESS: Target precursors: 425 (72.03%)
12:07:14.406511 PROGRESS: Decoy precursors: 165 (27.97%)
12:07:14.406557 PROGRESS: 
12:07:14.406600 PROGRESS: Precursor Summary:
12:07:14.407550 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   355
12:07:14.407639 PROGRESS: 
12:07:14.407693 PROGRESS: Protein Summary:
12:07:14.408832 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   353; 0.001 FDR:   353
12:07:14.408921 PROGRESS: =========================================================================
12:07:14.409085 INFO: Target number of precursors reached.
12:07:14.414573 INFO: fragments_df: keeping 2052 of 35277 [sum(precursor_idx_mask)=10911 sum(mass_error_mask)=35277 stop_rank=2052
12:07:14.531644 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:07:14.655887 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:07:14.784662 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:07:14.913081 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:07:15.187113 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:07:15.187525 INFO: Using score_cutoff 37.92645036392212 (fac=0.99, q=1)
12:07:15.187828 INFO: Updating optimization_manager: fwhm_rt             : 3.4255318641662598 -> 3.4840452671051025
12:07:15.187909 INFO: Updating optimization_manager: fwhm_mobility       : 0.00807250291109085 -> 0.008057864382863045
12:07:15.187964 INFO: Updating optimization_manager: score_cutoff        : 37.50170114822387 -> 37.92645036392212
12:07:15.188016 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:07:15.189059 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:07:15.190385 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:07:15.191146 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:07:15.193229 INFO: === checking if optimization conditions were reached ===
12:07:15.193457 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
12:07:15.194832 INFO: Updating optimization_manager: ms1_error           : 30 -> 18.749738850669043
12:07:15.194927 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 18.7497.
12:07:15.194991 INFO: ==============================================
12:07:15.195055 INFO: Starting optimization step 1.
12:07:15.195112 PROGRESS: === Extracting elution groups 0 to 600 ===
12:07:15.195167 INFO: Using classic extraction backend
12:07:15.195268 PROGRESS: Extracting batch of 1173 precursors
12:07:15.195331 INFO: === Search parameters used ===
12:07:15.195377 INFO: rt_error       : 799.3762494159641
12:07:15.195417 INFO: mobility_error : 0.1
12:07:15.195456 INFO: num_candidates : 3
12:07:15.195496 INFO: ms1_error      : 18.749738850669043
12:07:15.195535 INFO: ms2_error      : 30.0
12:07:15.195572 INFO: fwhm_rt        : 3.4840452671051025
12:07:15.195612 INFO: quant_window   : 3
12:07:15.195650 INFO: ==============================================
12:07:15.196421 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:07:15.196465 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:07:15.196498 INFO: FWHM in RT is 3.48 seconds, sigma is 0.77
12:07:15.196519 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.74
12:07:15.197282 INFO: Starting candidate selection
12:07:57.439807 INFO: Starting candidate scoring
12:07:57.751920 INFO: Finished candidate processing
12:07:57.752057 INFO: Collecting candidate features
12:07:57.764751 INFO: Collecting fragment features
12:07:57.768522 INFO: Finished candidate scoring
12:07:57.770285 INFO: performing precursor FDR with 47 features
12:07:57.770331 INFO: Decoy channel: -1
12:07:57.770355 INFO: Competetive: True
12:07:57.775982 INFO: Setting torch num_threads to 2 for FDR classification task
12:07:57.777990 INFO: Using random state 379583 for train-test-split
12:07:57.788146 INFO: Test AUC: 0.482
12:07:57.788205 INFO: Train AUC: 0.493
12:07:57.788237 INFO: AUC difference: 2.20%
12:07:58.011176 INFO: Resetting torch num_threads to 80
12:07:58.011715 PROGRESS: === Extracted 3226 precursors and 35291 fragments ===
12:07:58.012124 INFO: === FDR correction performed with classifier version 19 ===
12:07:58.012686 PROGRESS: ============================= Precursor FDR =============================
12:07:58.012775 PROGRESS: Total precursors accumulated: 589
12:07:58.012842 PROGRESS: Target precursors: 392 (66.55%)
12:07:58.012894 PROGRESS: Decoy precursors: 197 (33.45%)
12:07:58.012951 PROGRESS: 
12:07:58.013002 PROGRESS: Precursor Summary:
12:07:58.013958 PROGRESS: Channel   0:	 0.050 FDR:   292; 0.010 FDR:   292; 0.001 FDR:   292
12:07:58.014047 PROGRESS: 
12:07:58.014106 PROGRESS: Protein Summary:
12:07:58.015203 PROGRESS: Channel   0:	 0.050 FDR:   291; 0.010 FDR:   291; 0.001 FDR:   291
12:07:58.015291 PROGRESS: =========================================================================
12:07:58.015423 INFO: Target number of precursors reached.
12:07:58.020552 INFO: fragments_df: keeping 1699 of 35291 [sum(precursor_idx_mask)=8982 sum(mass_error_mask)=35291 stop_rank=1699
12:07:58.122669 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:07:58.240803 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:07:58.363951 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:07:58.485083 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:07:58.723292 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:07:58.723700 INFO: Using score_cutoff 36.261402271270754 (fac=0.99, q=1)
12:07:58.723993 INFO: Updating optimization_manager: fwhm_rt             : 3.4840452671051025 -> 3.5024960041046143
12:07:58.724073 INFO: Updating optimization_manager: fwhm_mobility       : 0.008057864382863045 -> 0.007790553383529186
12:07:58.724128 INFO: Updating optimization_manager: score_cutoff        : 37.92645036392212 -> 36.261402271270754
12:07:58.724190 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:07:58.725238 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:07:58.726554 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:07:58.727316 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:07:58.729462 INFO: === checking if optimization conditions were reached ===
12:07:58.729562 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
12:07:58.731095 INFO: Updating optimization_manager: ms1_error           : 18.749738850669043 -> 12.624706120291913
12:07:58.731194 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 12.6247.
12:07:58.731259 INFO: ==============================================
12:07:58.731323 INFO: Starting optimization step 2.
12:07:58.731378 PROGRESS: === Extracting elution groups 0 to 600 ===
12:07:58.731429 INFO: Using classic extraction backend
12:07:58.731533 PROGRESS: Extracting batch of 1173 precursors
12:07:58.731595 INFO: === Search parameters used ===
12:07:58.731643 INFO: rt_error       : 799.3762494159641
12:07:58.731685 INFO: mobility_error : 0.1
12:07:58.731726 INFO: num_candidates : 3
12:07:58.731765 INFO: ms1_error      : 12.624706120291913
12:07:58.731805 INFO: ms2_error      : 30.0
12:07:58.731844 INFO: fwhm_rt        : 3.5024960041046143
12:07:58.731891 INFO: quant_window   : 3
12:07:58.731931 INFO: ==============================================
12:07:58.732826 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:07:58.732871 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:07:58.732906 INFO: FWHM in RT is 3.50 seconds, sigma is 0.77
12:07:58.732929 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
12:07:58.733612 INFO: Starting candidate selection
12:08:03.044682 INFO: Starting candidate scoring
12:08:03.340101 INFO: Finished candidate processing
12:08:03.340218 INFO: Collecting candidate features
12:08:03.353739 INFO: Collecting fragment features
12:08:03.357638 INFO: Finished candidate scoring
12:08:03.359443 INFO: performing precursor FDR with 47 features
12:08:03.359485 INFO: Decoy channel: -1
12:08:03.359509 INFO: Competetive: True
12:08:03.363043 INFO: Setting torch num_threads to 2 for FDR classification task
12:08:03.365482 INFO: Using random state 379583 for train-test-split
12:08:03.377822 INFO: Test AUC: 0.458
12:08:03.377881 INFO: Train AUC: 0.501
12:08:03.377912 INFO: AUC difference: 8.46%
12:08:03.377934 WARNING: AUC difference > 5%. This may indicate overfitting.
12:08:03.595058 INFO: Resetting torch num_threads to 80
12:08:03.595613 PROGRESS: === Extracted 3232 precursors and 35212 fragments ===
12:08:03.596072 INFO: === FDR correction performed with classifier version 19 ===
12:08:03.596642 PROGRESS: ============================= Precursor FDR =============================
12:08:03.596730 PROGRESS: Total precursors accumulated: 591
12:08:03.596793 PROGRESS: Target precursors: 373 (63.11%)
12:08:03.596843 PROGRESS: Decoy precursors: 218 (36.89%)
12:08:03.596887 PROGRESS: 
12:08:03.596928 PROGRESS: Precursor Summary:
12:08:03.597866 PROGRESS: Channel   0:	 0.050 FDR:   240; 0.010 FDR:   240; 0.001 FDR:   240
12:08:03.597955 PROGRESS: 
12:08:03.598013 PROGRESS: Protein Summary:
12:08:03.599764 PROGRESS: Channel   0:	 0.050 FDR:   239; 0.010 FDR:   239; 0.001 FDR:   239
12:08:03.599855 PROGRESS: =========================================================================
12:08:03.600085 INFO: Target number of precursors reached.
12:08:03.604842 INFO: fragments_df: keeping 1284 of 35212 [sum(precursor_idx_mask)=7327 sum(mass_error_mask)=35212 stop_rank=1284
12:08:03.703917 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:08:03.822443 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:08:03.939978 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:08:04.038078 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:08:04.205250 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:08:04.205663 INFO: Using score_cutoff 35.865423759841924 (fac=0.99, q=1)
12:08:04.205983 INFO: Updating optimization_manager: fwhm_rt             : 3.5024960041046143 -> 3.561790704727173
12:08:04.206063 INFO: Updating optimization_manager: fwhm_mobility       : 0.007790553383529186 -> 0.007607827428728342
12:08:04.206118 INFO: Updating optimization_manager: score_cutoff        : 36.261402271270754 -> 35.865423759841924
12:08:04.206174 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:08:04.207211 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:08:04.208510 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:08:04.209290 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:08:04.211494 INFO: === checking if optimization conditions were reached ===
12:08:04.211604 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
12:08:04.213181 INFO: Updating optimization_manager: ms1_error           : 12.624706120291913 -> 7.664843302591144
12:08:04.213281 PROGRESS: ❌ ms1_error      : optimization incomplete after 3 search(es). Will search with parameter 7.6648.
12:08:04.213345 INFO: ==============================================
12:08:04.213416 INFO: Starting optimization step 3.
12:08:04.213477 PROGRESS: === Extracting elution groups 0 to 600 ===
12:08:04.213546 INFO: Using classic extraction backend
12:08:04.213713 PROGRESS: Extracting batch of 1173 precursors
12:08:04.213789 INFO: === Search parameters used ===
12:08:04.213838 INFO: rt_error       : 799.3762494159641
12:08:04.213881 INFO: mobility_error : 0.1
12:08:04.213923 INFO: num_candidates : 3
12:08:04.213962 INFO: ms1_error      : 7.664843302591144
12:08:04.214001 INFO: ms2_error      : 30.0
12:08:04.214038 INFO: fwhm_rt        : 3.561790704727173
12:08:04.214076 INFO: quant_window   : 3
12:08:04.214113 INFO: ==============================================
12:08:04.215008 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:08:04.215053 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:08:04.215092 INFO: FWHM in RT is 3.56 seconds, sigma is 0.78
12:08:04.215116 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.53
12:08:04.215803 INFO: Starting candidate selection
12:08:08.016381 INFO: Starting candidate scoring
12:08:08.311761 INFO: Finished candidate processing
12:08:08.311894 INFO: Collecting candidate features
12:08:08.325691 INFO: Collecting fragment features
12:08:08.329280 INFO: Finished candidate scoring
12:08:08.330986 INFO: performing precursor FDR with 47 features
12:08:08.331028 INFO: Decoy channel: -1
12:08:08.331051 INFO: Competetive: True
12:08:08.333879 INFO: Setting torch num_threads to 2 for FDR classification task
12:08:08.335847 INFO: Using random state 379583 for train-test-split
12:08:08.346676 INFO: Test AUC: 0.511
12:08:08.346740 INFO: Train AUC: 0.499
12:08:08.346770 INFO: AUC difference: 2.42%
12:08:08.565313 INFO: Resetting torch num_threads to 80
12:08:08.565844 PROGRESS: === Extracted 3230 precursors and 35119 fragments ===
12:08:08.566243 INFO: === FDR correction performed with classifier version 19 ===
12:08:08.566821 PROGRESS: ============================= Precursor FDR =============================
12:08:08.566915 PROGRESS: Total precursors accumulated: 589
12:08:08.566975 PROGRESS: Target precursors: 354 (60.10%)
12:08:08.567024 PROGRESS: Decoy precursors: 235 (39.90%)
12:08:08.567072 PROGRESS: 
12:08:08.567117 PROGRESS: Precursor Summary:
12:08:08.568031 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   189
12:08:08.568120 PROGRESS: 
12:08:08.568175 PROGRESS: Protein Summary:
12:08:08.569219 PROGRESS: Channel   0:	 0.050 FDR:   188; 0.010 FDR:   188; 0.001 FDR:   188
12:08:08.569315 PROGRESS: =========================================================================
12:08:08.569447 INFO: Target number of precursors not reached yet.
12:08:08.643650 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:08:08.644803 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:08:08.646365 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:08:08.647186 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:08:08.650753 INFO: === skipping optimization until target number of precursors are found ===
12:08:08.650864 PROGRESS: === Optimization of ms1_error has been skipped 1 time(s); maximum number is 1 ===
12:08:08.650945 INFO: Starting optimization step 4.
12:08:08.651006 PROGRESS: === Extracting elution groups 600 to 1400 ===
12:08:08.651062 INFO: Using classic extraction backend
12:08:08.651168 PROGRESS: Extracting batch of 1576 precursors
12:08:08.651236 INFO: === Search parameters used ===
12:08:08.651283 INFO: rt_error       : 799.3762494159641
12:08:08.651324 INFO: mobility_error : 0.1
12:08:08.651363 INFO: num_candidates : 3
12:08:08.651401 INFO: ms1_error      : 7.664843302591144
12:08:08.651439 INFO: ms2_error      : 30.0
12:08:08.651479 INFO: fwhm_rt        : 3.561790704727173
12:08:08.651517 INFO: quant_window   : 3
12:08:08.651555 INFO: ==============================================
12:08:08.653212 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:08:08.653259 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:08:08.653294 INFO: FWHM in RT is 3.56 seconds, sigma is 0.78
12:08:08.653315 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.53
12:08:08.653965 INFO: Starting candidate selection
12:08:13.498527 INFO: Starting candidate scoring
12:08:13.863956 INFO: Finished candidate processing
12:08:13.864054 INFO: Collecting candidate features
12:08:13.878340 INFO: Collecting fragment features
12:08:13.883113 INFO: Finished candidate scoring
12:08:13.887786 INFO: performing precursor FDR with 47 features
12:08:13.887848 INFO: Decoy channel: -1
12:08:13.887872 INFO: Competetive: True
12:08:13.892086 INFO: Setting torch num_threads to 2 for FDR classification task
12:08:13.894881 INFO: Using random state 379583 for train-test-split
12:08:13.911911 INFO: Test AUC: 0.506
12:08:13.911997 INFO: Train AUC: 0.493
12:08:13.912025 INFO: AUC difference: 2.59%
12:08:14.125063 INFO: Resetting torch num_threads to 80
12:08:14.126901 PROGRESS: === Extracted 7589 precursors and 82299 fragments ===
12:08:14.127293 INFO: === FDR correction performed with classifier version 19 ===
12:08:14.127942 PROGRESS: ============================= Precursor FDR =============================
12:08:14.128032 PROGRESS: Total precursors accumulated: 1,375
12:08:14.128091 PROGRESS: Target precursors: 828 (60.22%)
12:08:14.128140 PROGRESS: Decoy precursors: 547 (39.78%)
12:08:14.128184 PROGRESS: 
12:08:14.128225 PROGRESS: Precursor Summary:
12:08:14.129239 PROGRESS: Channel   0:	 0.050 FDR:   437; 0.010 FDR:   437; 0.001 FDR:   437
12:08:14.129335 PROGRESS: 
12:08:14.129392 PROGRESS: Protein Summary:
12:08:14.130580 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   434; 0.001 FDR:   434
12:08:14.130671 PROGRESS: =========================================================================
12:08:14.130805 INFO: Target number of precursors reached.
12:08:14.140076 INFO: fragments_df: keeping 2299 of 82299 [sum(precursor_idx_mask)=13148 sum(mass_error_mask)=82299 stop_rank=2299
12:08:14.257037 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:08:14.363661 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:08:14.472278 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:08:14.584099 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:08:14.839211 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:08:14.839632 INFO: Using score_cutoff 31.25972335281372 (fac=0.99, q=1)
12:08:14.839946 INFO: Updating optimization_manager: fwhm_rt             : 3.561790704727173 -> 3.539198637008667
12:08:14.840026 INFO: Updating optimization_manager: fwhm_mobility       : 0.007607827428728342 -> 0.00753869628533721
12:08:14.840080 INFO: Updating optimization_manager: score_cutoff        : 35.865423759841924 -> 31.25972335281372
12:08:14.840133 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:08:14.841357 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:08:14.843570 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:08:14.844524 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:08:14.848850 INFO: === checking if optimization conditions were reached ===
12:08:14.848961 PROGRESS: === Optimization of ms1_error has been performed 4 time(s); minimum number is 2 ===
12:08:14.850523 INFO: Updating optimization_manager: ms1_error           : 7.664843302591144 -> 3.9350741146526436
12:08:14.850620 PROGRESS: ❌ ms1_error      : optimization incomplete after 4 search(es). Will search with parameter 3.9351.
12:08:14.850683 INFO: ==============================================
12:08:14.850747 INFO: Starting optimization step 5.
12:08:14.850803 PROGRESS: === Extracting elution groups 0 to 1400 ===
12:08:14.850857 INFO: Using classic extraction backend
12:08:14.850957 PROGRESS: Extracting batch of 2749 precursors
12:08:14.851018 INFO: === Search parameters used ===
12:08:14.851063 INFO: rt_error       : 799.3762494159641
12:08:14.851109 INFO: mobility_error : 0.1
12:08:14.851152 INFO: num_candidates : 3
12:08:14.851191 INFO: ms1_error      : 3.9350741146526436
12:08:14.851231 INFO: ms2_error      : 30.0
12:08:14.851269 INFO: fwhm_rt        : 3.539198637008667
12:08:14.851308 INFO: quant_window   : 3
12:08:14.851346 INFO: ==============================================
12:08:14.852418 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:08:14.852462 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:08:14.852495 INFO: FWHM in RT is 3.54 seconds, sigma is 0.78
12:08:14.852516 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.50
12:08:14.853160 INFO: Starting candidate selection
12:08:57.452535 INFO: Starting candidate scoring
12:08:58.061656 INFO: Finished candidate processing
12:08:58.061748 INFO: Collecting candidate features
12:08:58.083130 INFO: Collecting fragment features
12:08:58.089920 INFO: Finished candidate scoring
12:08:58.093453 INFO: performing precursor FDR with 47 features
12:08:58.093508 INFO: Decoy channel: -1
12:08:58.093532 INFO: Competetive: True
12:08:58.097105 INFO: Setting torch num_threads to 2 for FDR classification task
12:08:58.099829 INFO: Using random state 379583 for train-test-split
12:08:58.118394 INFO: Test AUC: 0.495
12:08:58.118470 INFO: Train AUC: 0.498
12:08:58.118500 INFO: AUC difference: 0.57%
12:08:58.333755 INFO: Resetting torch num_threads to 80
12:08:58.334402 PROGRESS: === Extracted 7601 precursors and 82417 fragments ===
12:08:58.334807 INFO: === FDR correction performed with classifier version 19 ===
12:08:58.335472 PROGRESS: ============================= Precursor FDR =============================
12:08:58.335562 PROGRESS: Total precursors accumulated: 1,375
12:08:58.335619 PROGRESS: Target precursors: 764 (55.56%)
12:08:58.335668 PROGRESS: Decoy precursors: 611 (44.44%)
12:08:58.335712 PROGRESS: 
12:08:58.335755 PROGRESS: Precursor Summary:
12:08:58.336673 PROGRESS: Channel   0:	 0.050 FDR:   262; 0.010 FDR:   262; 0.001 FDR:   262
12:08:58.336762 PROGRESS: 
12:08:58.336816 PROGRESS: Protein Summary:
12:08:58.337906 PROGRESS: Channel   0:	 0.050 FDR:   259; 0.010 FDR:   259; 0.001 FDR:   259
12:08:58.338007 PROGRESS: =========================================================================
12:08:58.338176 INFO: Target number of precursors reached.
12:08:58.346340 INFO: fragments_df: keeping 1295 of 82417 [sum(precursor_idx_mask)=7915 sum(mass_error_mask)=82417 stop_rank=1295
12:08:58.463960 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:08:58.573355 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:08:58.674660 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:08:58.767588 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:08:58.934669 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:08:58.935084 INFO: Using score_cutoff 31.662235220718383 (fac=0.99, q=1)
12:08:58.935378 INFO: Updating optimization_manager: fwhm_rt             : 3.539198637008667 -> 3.520721435546875
12:08:58.935457 INFO: Updating optimization_manager: fwhm_mobility       : 0.00753869628533721 -> 0.007369320373982191
12:08:58.935512 INFO: Updating optimization_manager: score_cutoff        : 31.25972335281372 -> 31.662235220718383
12:08:58.935564 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:08:58.936775 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:08:58.939050 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:08:58.940003 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:08:58.944278 INFO: === checking if optimization conditions were reached ===
12:08:58.944383 PROGRESS: === Optimization of ms1_error has been performed 5 time(s); minimum number is 2 ===
12:08:58.945944 INFO: Updating optimization_manager: ms1_error           : 3.9350741146526436 -> 2.796243797417394
12:08:58.946043 PROGRESS: ❌ ms1_error      : optimization incomplete after 5 search(es). Will search with parameter 2.7962.
12:08:58.946120 INFO: ==============================================
12:08:58.946188 INFO: Starting optimization step 6.
12:08:58.946245 PROGRESS: === Extracting elution groups 0 to 1400 ===
12:08:58.946298 INFO: Using classic extraction backend
12:08:58.946402 PROGRESS: Extracting batch of 2749 precursors
12:08:58.946467 INFO: === Search parameters used ===
12:08:58.946515 INFO: rt_error       : 799.3762494159641
12:08:58.946557 INFO: mobility_error : 0.1
12:08:58.946598 INFO: num_candidates : 3
12:08:58.946637 INFO: ms1_error      : 2.796243797417394
12:08:58.946680 INFO: ms2_error      : 30.0
12:08:58.946720 INFO: fwhm_rt        : 3.520721435546875
12:08:58.946759 INFO: quant_window   : 3
12:08:58.946795 INFO: ==============================================
12:08:58.947899 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:08:58.947945 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:08:58.947979 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
12:08:58.948001 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.42
12:08:58.948638 INFO: Starting candidate selection
12:09:06.999411 INFO: Starting candidate scoring
12:09:07.605468 INFO: Finished candidate processing
12:09:07.605562 INFO: Collecting candidate features
12:09:07.623546 INFO: Collecting fragment features
12:09:07.629813 INFO: Finished candidate scoring
12:09:07.633337 INFO: performing precursor FDR with 47 features
12:09:07.633393 INFO: Decoy channel: -1
12:09:07.633417 INFO: Competetive: True
12:09:07.636983 INFO: Setting torch num_threads to 2 for FDR classification task
12:09:07.639686 INFO: Using random state 379583 for train-test-split
12:09:07.658780 INFO: Test AUC: 0.490
12:09:07.658860 INFO: Train AUC: 0.493
12:09:07.658890 INFO: AUC difference: 0.54%
12:09:07.879244 INFO: Resetting torch num_threads to 80
12:09:07.879912 PROGRESS: === Extracted 7606 precursors and 82622 fragments ===
12:09:07.880306 INFO: === FDR correction performed with classifier version 19 ===
12:09:07.880967 PROGRESS: ============================= Precursor FDR =============================
12:09:07.881057 PROGRESS: Total precursors accumulated: 1,376
12:09:07.881121 PROGRESS: Target precursors: 737 (53.56%)
12:09:07.881170 PROGRESS: Decoy precursors: 639 (46.44%)
12:09:07.881212 PROGRESS: 
12:09:07.881261 PROGRESS: Precursor Summary:
12:09:07.882166 PROGRESS: Channel   0:	 0.050 FDR:   166; 0.010 FDR:   166; 0.001 FDR:   166
12:09:07.882255 PROGRESS: 
12:09:07.882309 PROGRESS: Protein Summary:
12:09:07.883326 PROGRESS: Channel   0:	 0.050 FDR:   166; 0.010 FDR:   166; 0.001 FDR:   166
12:09:07.883414 PROGRESS: =========================================================================
12:09:07.883561 INFO: Target number of precursors not reached yet.
12:09:07.984472 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:09:07.985825 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:09:07.988326 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:09:07.989341 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:09:07.994358 INFO: === skipping optimization until target number of precursors are found ===
12:09:07.994466 PROGRESS: === Optimization of ms1_error has been skipped 1 time(s); maximum number is 1 ===
12:09:07.994545 INFO: Starting optimization step 7.
12:09:07.994610 PROGRESS: === Extracting elution groups 1400 to 3000 ===
12:09:07.994666 INFO: Using classic extraction backend
12:09:07.994773 PROGRESS: Extracting batch of 3162 precursors
12:09:07.994840 INFO: === Search parameters used ===
12:09:07.994889 INFO: rt_error       : 799.3762494159641
12:09:07.994930 INFO: mobility_error : 0.1
12:09:07.994971 INFO: num_candidates : 3
12:09:07.995021 INFO: ms1_error      : 2.796243797417394
12:09:07.995062 INFO: ms2_error      : 30.0
12:09:07.995101 INFO: fwhm_rt        : 3.520721435546875
12:09:07.995138 INFO: quant_window   : 3
12:09:07.995176 INFO: ==============================================
12:09:07.996166 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:09:07.996210 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:09:07.996244 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
12:09:07.996266 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.42
12:09:07.996896 INFO: Starting candidate selection
12:09:57.440306 INFO: Starting candidate scoring
12:09:58.134637 INFO: Finished candidate processing
12:09:58.134784 INFO: Collecting candidate features
12:09:58.189222 INFO: Collecting fragment features
12:09:58.200956 INFO: Finished candidate scoring
12:09:58.218215 INFO: performing precursor FDR with 47 features
12:09:58.218305 INFO: Decoy channel: -1
12:09:58.218329 INFO: Competetive: True
12:09:58.224788 INFO: Setting torch num_threads to 2 for FDR classification task
12:09:58.229427 INFO: Using random state 379583 for train-test-split
12:09:58.357178 INFO: Test AUC: 0.505
12:09:58.357284 INFO: Train AUC: 0.499
12:09:58.357314 INFO: AUC difference: 1.20%
12:09:58.586582 INFO: Resetting torch num_threads to 80
12:09:58.592435 PROGRESS: === Extracted 16463 precursors and 178792 fragments ===
12:09:58.592877 INFO: === FDR correction performed with classifier version 19 ===
12:09:58.593768 PROGRESS: ============================= Precursor FDR =============================
12:09:58.593861 PROGRESS: Total precursors accumulated: 2,953
12:09:58.593922 PROGRESS: Target precursors: 1,534 (51.95%)
12:09:58.593973 PROGRESS: Decoy precursors: 1,419 (48.05%)
12:09:58.594018 PROGRESS: 
12:09:58.594060 PROGRESS: Precursor Summary:
12:09:58.594923 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
12:09:58.595012 PROGRESS: 
12:09:58.595068 PROGRESS: Protein Summary:
12:09:58.596001 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
12:09:58.596088 PROGRESS: =========================================================================
12:09:58.596272 INFO: Target number of precursors not reached yet.
12:09:58.694892 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:09:58.696613 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:09:58.702303 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:09:58.703749 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:09:58.712033 INFO: === skipping optimization until target number of precursors are found ===
12:09:58.712158 PROGRESS: === Optimization of ms1_error has been skipped 2 time(s); maximum number is 1 ===
12:09:58.712384 INFO: Updating optimization_manager: ms1_error           : 2.796243797417394 -> 3.9350741146526436
12:09:58.712490 INFO: Updating optimization_manager: classifier_version  : 19 -> 25
12:09:58.712582 INFO: Updating optimization_manager: score_cutoff        : 31.662235220718383 -> 31.662235220718383
12:09:58.712671 INFO: Updating optimization_manager: fwhm_rt             : 3.520721435546875 -> 3.520721435546875
12:09:58.712755 INFO: Updating optimization_manager: fwhm_mobility       : 0.007369320373982191 -> 0.007369320373982191
12:09:58.712839 PROGRESS: ✅ ms1_error      : optimization complete (batch_substantially_bigger). Optimal parameter 3.9351 found after 5 searches.
12:09:58.712925 PROGRESS: Optimization finished for ms1_error.
12:09:58.839918 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:09:58.841467 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:09:58.843741 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:09:58.844708 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:09:58.872777 INFO: Starting optimization step 0.
12:09:58.872922 PROGRESS: === Extracting elution groups 0 to 1400 ===
12:09:58.873039 INFO: Using classic extraction backend
12:09:58.873281 PROGRESS: Extracting batch of 2749 precursors
12:09:58.873365 INFO: === Search parameters used ===
12:09:58.873418 INFO: rt_error       : 799.3762494159641
12:09:58.873463 INFO: mobility_error : 0.1
12:09:58.873507 INFO: num_candidates : 3
12:09:58.873548 INFO: ms1_error      : 3.9350741146526436
12:09:58.873590 INFO: ms2_error      : 30.0
12:09:58.873629 INFO: fwhm_rt        : 3.520721435546875
12:09:58.873668 INFO: quant_window   : 3
12:09:58.873707 INFO: ==============================================
12:09:58.874871 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:09:58.874916 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:09:58.874957 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
12:09:58.874979 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.42
12:09:58.875742 INFO: Starting candidate selection
12:10:07.038879 INFO: Starting candidate scoring
12:10:07.635225 INFO: Finished candidate processing
12:10:07.635322 INFO: Collecting candidate features
12:10:07.653749 INFO: Collecting fragment features
12:10:07.660192 INFO: Finished candidate scoring
12:10:07.663997 INFO: performing precursor FDR with 47 features
12:10:07.664050 INFO: Decoy channel: -1
12:10:07.664074 INFO: Competetive: True
12:10:07.668358 INFO: Setting torch num_threads to 2 for FDR classification task
12:10:07.671398 INFO: Using random state 634715 for train-test-split
12:10:07.689456 INFO: Test AUC: 0.504
12:10:07.689540 INFO: Train AUC: 0.489
12:10:07.689571 INFO: AUC difference: 3.03%
12:10:07.904507 INFO: Resetting torch num_threads to 80
12:10:07.905179 PROGRESS: === Extracted 7599 precursors and 82556 fragments ===
12:10:07.905630 INFO: === FDR correction performed with classifier version 25 ===
12:10:07.906333 PROGRESS: ============================= Precursor FDR =============================
12:10:07.906424 PROGRESS: Total precursors accumulated: 1,375
12:10:07.906482 PROGRESS: Target precursors: 769 (55.93%)
12:10:07.906530 PROGRESS: Decoy precursors: 606 (44.07%)
12:10:07.906576 PROGRESS: 
12:10:07.906621 PROGRESS: Precursor Summary:
12:10:07.907561 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   246; 0.001 FDR:   246
12:10:07.907651 PROGRESS: 
12:10:07.907706 PROGRESS: Protein Summary:
12:10:07.908786 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:   243; 0.001 FDR:   243
12:10:07.908883 PROGRESS: =========================================================================
12:10:07.909161 INFO: Target number of precursors reached.
12:10:07.917128 INFO: fragments_df: keeping 1217 of 82556 [sum(precursor_idx_mask)=7376 sum(mass_error_mask)=82556 stop_rank=1217
12:10:08.034099 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:10:08.127521 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:10:08.227563 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:10:08.324846 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:10:08.484805 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:10:08.485230 INFO: Using score_cutoff 32.85143453979492 (fac=0.99, q=1)
12:10:08.485556 INFO: Updating optimization_manager: fwhm_rt             : 3.520721435546875 -> 3.475355863571167
12:10:08.485638 INFO: Updating optimization_manager: fwhm_mobility       : 0.007369320373982191 -> 0.007677293382585049
12:10:08.485698 INFO: Updating optimization_manager: score_cutoff        : 31.662235220718383 -> 32.85143453979492
12:10:08.485751 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:10:08.486960 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:10:08.489218 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:10:08.490169 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:10:08.494571 INFO: === checking if optimization conditions were reached ===
12:10:08.494689 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
12:10:08.496023 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.09218507201027858
12:10:08.496124 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0922.
12:10:08.496191 INFO: ==============================================
12:10:08.496258 INFO: Starting optimization step 1.
12:10:08.496313 PROGRESS: === Extracting elution groups 0 to 1400 ===
12:10:08.496367 INFO: Using classic extraction backend
12:10:08.496477 PROGRESS: Extracting batch of 2749 precursors
12:10:08.496541 INFO: === Search parameters used ===
12:10:08.496588 INFO: rt_error       : 799.3762494159641
12:10:08.496629 INFO: mobility_error : 0.09218507201027858
12:10:08.496668 INFO: num_candidates : 3
12:10:08.496709 INFO: ms1_error      : 3.9350741146526436
12:10:08.496750 INFO: ms2_error      : 30.0
12:10:08.496792 INFO: fwhm_rt        : 3.475355863571167
12:10:08.496831 INFO: quant_window   : 3
12:10:08.496869 INFO: ==============================================
12:10:08.498077 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:10:08.498123 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:10:08.498157 INFO: FWHM in RT is 3.48 seconds, sigma is 0.76
12:10:08.498178 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.56
12:10:08.498786 INFO: Starting candidate selection
12:10:16.135410 INFO: Starting candidate scoring
12:10:16.734581 INFO: Finished candidate processing
12:10:16.734775 INFO: Collecting candidate features
12:10:16.755232 INFO: Collecting fragment features
12:10:16.761981 INFO: Finished candidate scoring
12:10:16.765684 INFO: performing precursor FDR with 47 features
12:10:16.765743 INFO: Decoy channel: -1
12:10:16.765766 INFO: Competetive: True
12:10:16.769437 INFO: Setting torch num_threads to 2 for FDR classification task
12:10:16.772195 INFO: Using random state 634715 for train-test-split
12:10:16.789979 INFO: Test AUC: 0.510
12:10:16.790059 INFO: Train AUC: 0.494
12:10:16.790087 INFO: AUC difference: 3.36%
12:10:17.004347 INFO: Resetting torch num_threads to 80
12:10:17.005002 PROGRESS: === Extracted 7544 precursors and 81942 fragments ===
12:10:17.005399 INFO: === FDR correction performed with classifier version 25 ===
12:10:17.006043 PROGRESS: ============================= Precursor FDR =============================
12:10:17.006130 PROGRESS: Total precursors accumulated: 1,365
12:10:17.006188 PROGRESS: Target precursors: 767 (56.19%)
12:10:17.006243 PROGRESS: Decoy precursors: 598 (43.81%)
12:10:17.006289 PROGRESS: 
12:10:17.006336 PROGRESS: Precursor Summary:
12:10:17.007259 PROGRESS: Channel   0:	 0.050 FDR:   247; 0.010 FDR:   247; 0.001 FDR:   247
12:10:17.007346 PROGRESS: 
12:10:17.007398 PROGRESS: Protein Summary:
12:10:17.008456 PROGRESS: Channel   0:	 0.050 FDR:   244; 0.010 FDR:   244; 0.001 FDR:   244
12:10:17.008542 PROGRESS: =========================================================================
12:10:17.008718 INFO: Target number of precursors reached.
12:10:17.016784 INFO: fragments_df: keeping 1228 of 81942 [sum(precursor_idx_mask)=7565 sum(mass_error_mask)=81942 stop_rank=1228
12:10:17.134701 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:10:17.227044 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:10:17.326671 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:10:17.424008 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:10:17.585453 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:10:17.585865 INFO: Using score_cutoff 32.90790363464356 (fac=0.99, q=1)
12:10:17.586157 INFO: Updating optimization_manager: fwhm_rt             : 3.475355863571167 -> 3.5314621925354004
12:10:17.586235 INFO: Updating optimization_manager: fwhm_mobility       : 0.007677293382585049 -> 0.007629680912941694
12:10:17.586289 INFO: Updating optimization_manager: score_cutoff        : 32.85143453979492 -> 32.90790363464356
12:10:17.586350 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:10:17.587553 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:10:17.589794 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:10:17.590747 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:10:17.594861 INFO: === checking if optimization conditions were reached ===
12:10:17.594963 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
12:10:17.596336 INFO: Updating optimization_manager: mobility_error      : 0.09218507201027858 -> 0.08387058534750436
12:10:17.596433 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0839.
12:10:17.596500 INFO: ==============================================
12:10:17.596568 INFO: Starting optimization step 2.
12:10:17.596623 PROGRESS: === Extracting elution groups 0 to 1400 ===
12:10:17.596676 INFO: Using classic extraction backend
12:10:17.596778 PROGRESS: Extracting batch of 2749 precursors
12:10:17.596839 INFO: === Search parameters used ===
12:10:17.596884 INFO: rt_error       : 799.3762494159641
12:10:17.596925 INFO: mobility_error : 0.08387058534750436
12:10:17.596980 INFO: num_candidates : 3
12:10:17.597027 INFO: ms1_error      : 3.9350741146526436
12:10:17.597068 INFO: ms2_error      : 30.0
12:10:17.597106 INFO: fwhm_rt        : 3.5314621925354004
12:10:17.597152 INFO: quant_window   : 3
12:10:17.597191 INFO: ==============================================
12:10:17.598371 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:10:17.598419 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:10:17.598453 INFO: FWHM in RT is 3.53 seconds, sigma is 0.78
12:10:17.598474 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.54
12:10:17.599112 INFO: Starting candidate selection
12:10:57.453728 INFO: Starting candidate scoring
12:10:58.056984 INFO: Finished candidate processing
12:10:58.057085 INFO: Collecting candidate features
12:10:58.075187 INFO: Collecting fragment features
12:10:58.081948 INFO: Finished candidate scoring
12:10:58.085450 INFO: performing precursor FDR with 47 features
12:10:58.085504 INFO: Decoy channel: -1
12:10:58.085527 INFO: Competetive: True
12:10:58.089133 INFO: Setting torch num_threads to 2 for FDR classification task
12:10:58.091825 INFO: Using random state 634715 for train-test-split
12:10:58.109169 INFO: Test AUC: 0.518
12:10:58.109243 INFO: Train AUC: 0.490
12:10:58.109272 INFO: AUC difference: 5.75%
12:10:58.109294 WARNING: AUC difference > 5%. This may indicate overfitting.
12:10:58.324436 INFO: Resetting torch num_threads to 80
12:10:58.325103 PROGRESS: === Extracted 7530 precursors and 81745 fragments ===
12:10:58.325509 INFO: === FDR correction performed with classifier version 25 ===
12:10:58.326177 PROGRESS: ============================= Precursor FDR =============================
12:10:58.326269 PROGRESS: Total precursors accumulated: 1,358
12:10:58.326326 PROGRESS: Target precursors: 741 (54.57%)
12:10:58.326374 PROGRESS: Decoy precursors: 617 (45.43%)
12:10:58.326418 PROGRESS: 
12:10:58.326461 PROGRESS: Precursor Summary:
12:10:58.327375 PROGRESS: Channel   0:	 0.050 FDR:   244; 0.010 FDR:   244; 0.001 FDR:   244
12:10:58.327462 PROGRESS: 
12:10:58.327516 PROGRESS: Protein Summary:
12:10:58.328571 PROGRESS: Channel   0:	 0.050 FDR:   241; 0.010 FDR:   241; 0.001 FDR:   241
12:10:58.328659 PROGRESS: =========================================================================
12:10:58.328802 INFO: Target number of precursors reached.
12:10:58.336535 INFO: fragments_df: keeping 1207 of 81745 [sum(precursor_idx_mask)=7461 sum(mass_error_mask)=81744 stop_rank=1207
12:10:58.455388 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:11:00.019531 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:11:00.120922 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:11:00.218415 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:11:00.380604 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:11:00.381030 INFO: Using score_cutoff 33.4070356716156 (fac=0.99, q=1)
12:11:00.381329 INFO: Updating optimization_manager: fwhm_rt             : 3.5314621925354004 -> 3.4890692234039307
12:11:00.381407 INFO: Updating optimization_manager: fwhm_mobility       : 0.007629680912941694 -> 0.007613331079483032
12:11:00.381463 INFO: Updating optimization_manager: score_cutoff        : 32.90790363464356 -> 33.4070356716156
12:11:00.381514 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:11:00.382755 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:11:00.385039 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:11:00.386022 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:11:00.390446 INFO: === checking if optimization conditions were reached ===
12:11:00.390560 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
12:11:00.391227 INFO: Updating optimization_manager: mobility_error      : 0.08387058534750436 -> 0.09218507201027858
12:11:00.391345 INFO: Updating optimization_manager: classifier_version  : 25 -> 29
12:11:00.391437 INFO: Updating optimization_manager: score_cutoff        : 33.4070356716156 -> 32.90790363464356
12:11:00.391521 INFO: Updating optimization_manager: fwhm_rt             : 3.4890692234039307 -> 3.5314621925354004
12:11:00.391601 INFO: Updating optimization_manager: fwhm_mobility       : 0.007613331079483032 -> 0.007629680912941694
12:11:00.391680 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0922 found after 3 searches.
12:11:00.391747 INFO: ==============================================
12:11:00.391812 PROGRESS: Optimization finished for mobility_error.
12:11:00.530725 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:11:00.532026 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:11:00.534316 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:11:00.535301 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:11:00.564996 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
12:11:00.565146 PROGRESS: ==============================================
12:11:00.565215 PROGRESS: ms2_error      : 30.0000
12:11:00.565271 PROGRESS: rt_error       : 799.3762
12:11:00.565327 PROGRESS: ms1_error      : 3.9351
12:11:00.565372 PROGRESS: mobility_error : 0.0922
12:11:00.565415 PROGRESS: ==============================================
12:11:00.566013 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:11:02.203001 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:11:09.758839 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:11:11.420445 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:11:28.221170 INFO: Using classic extraction backend
12:11:28.221993 PROGRESS: Extracting batch of 12073114 precursors
12:11:28.222114 INFO: === Search parameters used ===
12:11:28.222168 INFO: rt_error       : 799.3762494159641
12:11:28.222224 INFO: mobility_error : 0.09218507201027858
12:11:28.222269 INFO: num_candidates : 3
12:11:28.222311 INFO: ms1_error      : 3.9350741146526436
12:11:28.222352 INFO: ms2_error      : 30.0
12:11:28.222394 INFO: fwhm_rt        : 3.5314621925354004
12:11:28.222435 INFO: quant_window   : 3
12:11:28.222474 INFO: ==============================================
12:11:30.960965 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:11:30.961100 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:11:30.961149 INFO: FWHM in RT is 3.53 seconds, sigma is 0.78
12:11:30.961171 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.54
12:11:30.963173 INFO: Starting candidate selection
19:02:56.148652 INFO: Removed 2010384 precursors with score below cutoff 32.90790363464356
19:02:59.116493 INFO: Starting candidate scoring
19:33:55.338433 INFO: Finished candidate processing
19:33:55.338918 INFO: Collecting candidate features
19:34:41.125695 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31551631)
19:34:42.198597 INFO: Collecting fragment features
19:35:03.524797 INFO: Finished candidate scoring
19:35:52.518875 INFO: === Performing FDR correction with classifier version 29 ===
19:35:52.561577 INFO: performing precursor FDR with 47 features
19:35:52.561652 INFO: Decoy channel: -1
19:35:52.561682 INFO: Competetive: True
19:36:00.158043 INFO: Setting torch num_threads to 2 for FDR classification task
19:36:03.947774 WARNING: dropped 1 target PSMs due to missing features
19:36:17.045950 INFO: Using random state 267254 for train-test-split
19:46:33.980528 INFO: Test AUC: 0.571
19:46:33.980897 INFO: Train AUC: 0.572
19:46:33.980957 INFO: AUC difference: 0.19%
19:46:39.612955 INFO: Resetting torch num_threads to 80
19:46:40.247204 INFO: Removing fragments below FDR threshold
19:46:43.011406 PROGRESS: ============================= Precursor FDR =============================
19:46:43.011662 PROGRESS: Total precursors accumulated: 29,435
19:46:43.011729 PROGRESS: Target precursors: 29,144 (99.01%)
19:46:43.011780 PROGRESS: Decoy precursors: 291 (0.99%)
19:46:43.011828 PROGRESS: 
19:46:43.011872 PROGRESS: Precursor Summary:
19:46:43.018330 PROGRESS: Channel   0:	 0.050 FDR: 29,144; 0.010 FDR: 29,144; 0.001 FDR:    27
19:46:43.018479 PROGRESS: 
19:46:43.018535 PROGRESS: Protein Summary:
19:46:43.028078 PROGRESS: Channel   0:	 0.050 FDR: 6,706; 0.010 FDR: 6,706; 0.001 FDR:    26
19:46:43.028239 PROGRESS: =========================================================================
19:46:43.323696 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/psm.parquet
19:46:43.563890 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/frag.parquet
19:46:43.715062 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
19:46:44.456938 PROGRESS: 
19:46:44.457097 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
19:46:44.457175 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/figures
19:46:44.457335 INFO: Initializing TimingManager
19:46:44.457978 INFO: Initializing RawFileManager
19:46:44.458086 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:46:44.458322 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:46:44.458378 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:46:44.672395 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
19:46:53.274674 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
19:46:53.283570 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:46:53.285954 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:46:53.286309 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:46:53.286666 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:46:53.288070 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:46:53.301233 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:46:53.301419 INFO: Indexing quadrupole dimension
19:46:53.756418 INFO: Transposing detector events
19:47:03.369775 INFO: Finished transposing data
19:47:03.394333 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:47:03.395260 INFO: RT (min)            : 0.0 - 70.0
19:47:03.395306 INFO: RT duration (sec)   : 4199.8
19:47:03.395330 INFO: RT duration (min)   : 70.0
19:47:03.395352 INFO: Cycle len (scans)   : 9
19:47:03.395371 INFO: Cycle len (sec)     : 0.97
19:47:03.395391 INFO: Number of cycles    : 4347
19:47:03.395411 INFO: MS2 range (m/z)     : 400.0 - 1000.0
19:47:03.395465 INFO: Creating DIA data object took: 18.9373881816864
19:47:04.967320 INFO: Initializing CalibrationManager
19:47:04.967599 INFO: Setting up calibration estimators ..
19:47:04.967664 INFO: Found 1 estimator(s) in calibration group 'fragment'
19:47:04.967749 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'}' ..
19:47:04.967826 INFO: Found 3 estimator(s) in calibration group 'precursor'
19:47:04.967887 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'}' ..
19:47:04.967946 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}}' ..
19:47:04.968009 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}}' ..
19:47:04.968060 INFO: Done setting up calibration estimators.
19:47:04.968202 INFO: Initializing OptimizationManager
19:47:04.968300 INFO: initial parameter: ms1_error = 30
19:47:04.968348 INFO: initial parameter: ms2_error = 30
19:47:04.968392 INFO: initial parameter: rt_error = 2099.891532
19:47:04.968432 INFO: initial parameter: mobility_error = 0.1
19:47:04.968474 INFO: initial parameter: num_candidates = 1
19:47:04.968512 INFO: initial parameter: fwhm_rt = 5
19:47:04.968552 INFO: initial parameter: fwhm_mobility = 0.01
19:47:04.968590 INFO: initial parameter: score_cutoff = 0
19:47:04.968626 INFO: initial parameter: classifier_version = -1
19:47:04.968703 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
19:47:04.969025 INFO: FDRManager: loading saved state not requested, will be initialized.
19:47:04.969062 INFO: Initializing FDRManager
19:47:04.969112 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
19:47:06.175038 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
19:47:06.916531 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
19:47:06.916879 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 2099.891532
19:47:06.917077 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
19:47:06.917257 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
19:47:06.917355 PROGRESS: Starting initial search for precursors.
19:47:06.917440 INFO: Starting optimization step 0.
19:47:06.917500 PROGRESS: === Extracting elution groups 0 to 200 ===
19:47:06.917579 INFO: Using classic extraction backend
19:47:06.917795 PROGRESS: Extracting batch of 390 precursors
19:47:06.917869 INFO: === Search parameters used ===
19:47:06.917920 INFO: rt_error       : 2099.891532
19:47:06.917963 INFO: mobility_error : 0.1
19:47:06.918007 INFO: num_candidates : 1
19:47:06.918048 INFO: ms1_error      : 30
19:47:06.918087 INFO: ms2_error      : 30
19:47:06.918124 INFO: fwhm_rt        : 5
19:47:06.918163 INFO: quant_window   : 3
19:47:06.918200 INFO: ==============================================
19:47:06.919106 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:47:06.919151 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:47:06.919186 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
19:47:06.919209 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
19:47:06.920480 INFO: Starting candidate selection
19:47:10.632619 INFO: Starting candidate scoring
19:47:10.690973 INFO: Finished candidate processing
19:47:10.691068 INFO: Collecting candidate features
19:47:10.700133 INFO: Collecting fragment features
19:47:10.702398 INFO: Finished candidate scoring
19:47:10.703234 INFO: performing precursor FDR with 47 features
19:47:10.703278 INFO: Decoy channel: -1
19:47:10.703301 INFO: Competetive: True
19:47:10.704554 INFO: Setting torch num_threads to 2 for FDR classification task
19:47:10.707062 INFO: Using random state 976138 for train-test-split
19:47:10.715334 INFO: Test AUC: 0.547
19:47:10.715391 INFO: Train AUC: 0.508
19:47:10.715422 INFO: AUC difference: 7.67%
19:47:10.715443 WARNING: AUC difference > 5%. This may indicate overfitting.
19:47:10.934745 INFO: Resetting torch num_threads to 80
19:47:10.935198 PROGRESS: === Extracted 364 precursors and 3956 fragments ===
19:47:10.935596 INFO: === FDR correction performed with classifier version -1 ===
19:47:10.936129 PROGRESS: ============================= Precursor FDR =============================
19:47:10.936221 PROGRESS: Total precursors accumulated: 187
19:47:10.936282 PROGRESS: Target precursors: 129 (68.98%)
19:47:10.936335 PROGRESS: Decoy precursors: 58 (31.02%)
19:47:10.936378 PROGRESS: 
19:47:10.936419 PROGRESS: Precursor Summary:
19:47:10.937305 PROGRESS: Channel   0:	 0.050 FDR:    97; 0.010 FDR:    97; 0.001 FDR:    97
19:47:10.937398 PROGRESS: 
19:47:10.937462 PROGRESS: Protein Summary:
19:47:10.938432 PROGRESS: Channel   0:	 0.050 FDR:    97; 0.010 FDR:    97; 0.001 FDR:    97
19:47:10.938520 PROGRESS: =========================================================================
19:47:10.938622 INFO: Target number of precursors not reached yet.
19:47:11.004340 INFO: Starting optimization step 1.
19:47:11.004539 PROGRESS: === Extracting elution groups 200 to 600 ===
19:47:11.004611 INFO: Using classic extraction backend
19:47:11.004727 PROGRESS: Extracting batch of 783 precursors
19:47:11.004797 INFO: === Search parameters used ===
19:47:11.004847 INFO: rt_error       : 2099.891532
19:47:11.004891 INFO: mobility_error : 0.1
19:47:11.004935 INFO: num_candidates : 1
19:47:11.004994 INFO: ms1_error      : 30
19:47:11.005035 INFO: ms2_error      : 30
19:47:11.005075 INFO: fwhm_rt        : 5
19:47:11.005116 INFO: quant_window   : 3
19:47:11.005156 INFO: ==============================================
19:47:11.005872 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:47:11.005929 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:47:11.005957 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
19:47:11.005977 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
19:47:11.006613 INFO: Starting candidate selection
19:47:16.797011 INFO: Starting candidate scoring
19:47:16.910920 INFO: Finished candidate processing
19:47:16.911048 INFO: Collecting candidate features
19:47:16.920821 INFO: Collecting fragment features
19:47:16.923294 INFO: Finished candidate scoring
19:47:16.925462 INFO: performing precursor FDR with 47 features
19:47:16.925508 INFO: Decoy channel: -1
19:47:16.925533 INFO: Competetive: True
19:47:16.928334 INFO: Setting torch num_threads to 2 for FDR classification task
19:47:16.930108 INFO: Using random state 525688 for train-test-split
19:47:16.938084 INFO: Test AUC: 0.480
19:47:16.938141 INFO: Train AUC: 0.518
19:47:16.938169 INFO: AUC difference: 7.51%
19:47:16.938190 WARNING: AUC difference > 5%. This may indicate overfitting.
19:47:17.150409 INFO: Resetting torch num_threads to 80
19:47:17.151621 PROGRESS: === Extracted 1117 precursors and 12152 fragments ===
19:47:17.152014 INFO: === FDR correction performed with classifier version -1 ===
19:47:17.152588 PROGRESS: ============================= Precursor FDR =============================
19:47:17.152684 PROGRESS: Total precursors accumulated: 575
19:47:17.152741 PROGRESS: Target precursors: 399 (69.39%)
19:47:17.152799 PROGRESS: Decoy precursors: 176 (30.61%)
19:47:17.152846 PROGRESS: 
19:47:17.152889 PROGRESS: Precursor Summary:
19:47:17.153874 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   284; 0.001 FDR:   284
19:47:17.153964 PROGRESS: 
19:47:17.154019 PROGRESS: Protein Summary:
19:47:17.155107 PROGRESS: Channel   0:	 0.050 FDR:   281; 0.010 FDR:   281; 0.001 FDR:   281
19:47:17.155198 PROGRESS: =========================================================================
19:47:17.155330 INFO: Target number of precursors reached.
19:47:17.158148 INFO: fragments_df: keeping 592 of 12152 [sum(precursor_idx_mask)=3175 sum(mass_error_mask)=12152 stop_rank=592
19:47:17.257179 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:47:17.382295 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:47:17.506686 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:47:17.628692 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:47:17.763950 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
19:47:17.764360 INFO: Using score_cutoff 38.185333943939206 (fac=0.99, q=1)
19:47:17.764672 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.3577704429626465
19:47:17.764755 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008048195391893387
19:47:17.764810 INFO: Updating optimization_manager: score_cutoff        : 0 -> 38.185333943939206
19:47:17.764875 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:47:17.765940 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:47:17.767349 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:47:17.768134 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:47:17.770491 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
19:47:17.770587 PROGRESS: Required number of precursors found. Starting search parameter optimization.
19:47:17.770663 INFO: Starting optimization step 2.
19:47:17.770725 PROGRESS: === Extracting elution groups 0 to 600 ===
19:47:17.770780 INFO: Using classic extraction backend
19:47:17.770882 PROGRESS: Extracting batch of 1173 precursors
19:47:17.770944 INFO: === Search parameters used ===
19:47:17.770988 INFO: rt_error       : 2099.891532
19:47:17.771031 INFO: mobility_error : 0.1
19:47:17.771072 INFO: num_candidates : 3
19:47:17.771110 INFO: ms1_error      : 30
19:47:17.771149 INFO: ms2_error      : 30
19:47:17.771188 INFO: fwhm_rt        : 3.3577704429626465
19:47:17.771227 INFO: quant_window   : 3
19:47:17.771273 INFO: ==============================================
19:47:17.772118 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:47:17.772164 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:47:17.772198 INFO: FWHM in RT is 3.36 seconds, sigma is 0.74
19:47:17.772221 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.73
19:47:17.772862 INFO: Starting candidate selection
19:47:27.042063 INFO: Starting candidate scoring
19:47:27.357474 INFO: Finished candidate processing
19:47:27.357608 INFO: Collecting candidate features
19:47:27.371737 INFO: Collecting fragment features
19:47:27.376211 INFO: Finished candidate scoring
19:47:27.378662 INFO: performing precursor FDR with 47 features
19:47:27.378705 INFO: Decoy channel: -1
19:47:27.378729 INFO: Competetive: True
19:47:27.382085 INFO: Setting torch num_threads to 2 for FDR classification task
19:47:27.384090 INFO: Using random state 492759 for train-test-split
19:47:57.115919 INFO: Test AUC: 0.501
19:47:57.116105 INFO: Train AUC: 0.490
19:47:57.116178 INFO: AUC difference: 2.36%
19:47:57.360313 INFO: Resetting torch num_threads to 80
19:47:57.360859 PROGRESS: === Extracted 3241 precursors and 35464 fragments ===
19:47:57.361268 INFO: === FDR correction performed with classifier version 1 ===
19:47:57.361844 PROGRESS: ============================= Precursor FDR =============================
19:47:57.361936 PROGRESS: Total precursors accumulated: 588
19:47:57.361993 PROGRESS: Target precursors: 455 (77.38%)
19:47:57.362041 PROGRESS: Decoy precursors: 133 (22.62%)
19:47:57.362085 PROGRESS: 
19:47:57.362126 PROGRESS: Precursor Summary:
19:47:57.363098 PROGRESS: Channel   0:	 0.050 FDR:   402; 0.010 FDR:   402; 0.001 FDR:   402
19:47:57.363187 PROGRESS: 
19:47:57.363241 PROGRESS: Protein Summary:
19:47:57.364383 PROGRESS: Channel   0:	 0.050 FDR:   396; 0.010 FDR:   396; 0.001 FDR:   396
19:47:57.364477 PROGRESS: =========================================================================
19:47:57.364612 INFO: Target number of precursors reached.
19:47:57.370863 INFO: fragments_df: keeping 2488 of 35464 [sum(precursor_idx_mask)=12679 sum(mass_error_mask)=35464 stop_rank=2488
19:47:57.487581 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:47:57.620012 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:47:57.751130 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:47:57.879864 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:47:58.211839 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:47:58.212251 INFO: Using score_cutoff 38.12340097389221 (fac=0.99, q=1)
19:47:58.212551 INFO: Updating optimization_manager: fwhm_rt             : 3.3577704429626465 -> 3.317265272140503
19:47:58.212640 INFO: Updating optimization_manager: fwhm_mobility       : 0.008048195391893387 -> 0.008012180216610432
19:47:58.212696 INFO: Updating optimization_manager: score_cutoff        : 38.185333943939206 -> 38.12340097389221
19:47:58.212747 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:47:58.213782 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:47:58.215128 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:47:58.215875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:47:58.217921 INFO: === checking if optimization conditions were reached ===
19:47:58.218025 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
19:47:58.219617 INFO: Updating optimization_manager: ms2_error           : 30 -> 23.759473807561974
19:47:58.219717 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 23.7595.
19:47:58.219781 INFO: ==============================================
19:47:58.219846 INFO: Starting optimization step 3.
19:47:58.219901 PROGRESS: === Extracting elution groups 0 to 600 ===
19:47:58.219954 INFO: Using classic extraction backend
19:47:58.220060 PROGRESS: Extracting batch of 1173 precursors
19:47:58.220124 INFO: === Search parameters used ===
19:47:58.220184 INFO: rt_error       : 2099.891532
19:47:58.220227 INFO: mobility_error : 0.1
19:47:58.220267 INFO: num_candidates : 3
19:47:58.220305 INFO: ms1_error      : 30
19:47:58.220349 INFO: ms2_error      : 23.759473807561974
19:47:58.220387 INFO: fwhm_rt        : 3.317265272140503
19:47:58.220428 INFO: quant_window   : 3
19:47:58.220466 INFO: ==============================================
19:47:58.221293 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:47:58.221338 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:47:58.221370 INFO: FWHM in RT is 3.32 seconds, sigma is 0.73
19:47:58.221390 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.72
19:47:58.222043 INFO: Starting candidate selection
19:48:06.414652 INFO: Starting candidate scoring
19:48:06.685446 INFO: Finished candidate processing
19:48:06.685540 INFO: Collecting candidate features
19:48:06.701014 INFO: Collecting fragment features
19:48:06.704695 INFO: Finished candidate scoring
19:48:06.706778 INFO: performing precursor FDR with 47 features
19:48:06.706824 INFO: Decoy channel: -1
19:48:06.706849 INFO: Competetive: True
19:48:06.711636 INFO: Setting torch num_threads to 2 for FDR classification task
19:48:06.715057 INFO: Using random state 492759 for train-test-split
19:48:06.731957 INFO: Test AUC: 0.514
19:48:06.732049 INFO: Train AUC: 0.490
19:48:06.732097 INFO: AUC difference: 4.75%
19:48:06.952938 INFO: Resetting torch num_threads to 80
19:48:06.953523 PROGRESS: === Extracted 3228 precursors and 34850 fragments ===
19:48:06.953907 INFO: === FDR correction performed with classifier version 1 ===
19:48:06.954461 PROGRESS: ============================= Precursor FDR =============================
19:48:06.954550 PROGRESS: Total precursors accumulated: 586
19:48:06.954606 PROGRESS: Target precursors: 455 (77.65%)
19:48:06.954655 PROGRESS: Decoy precursors: 131 (22.35%)
19:48:06.954700 PROGRESS: 
19:48:06.954740 PROGRESS: Precursor Summary:
19:48:06.955712 PROGRESS: Channel   0:	 0.050 FDR:   404; 0.010 FDR:   404; 0.001 FDR:   404
19:48:06.955800 PROGRESS: 
19:48:06.955855 PROGRESS: Protein Summary:
19:48:06.957039 PROGRESS: Channel   0:	 0.050 FDR:   398; 0.010 FDR:   398; 0.001 FDR:   398
19:48:06.957131 PROGRESS: =========================================================================
19:48:06.957267 INFO: Target number of precursors reached.
19:48:06.963253 INFO: fragments_df: keeping 2331 of 34850 [sum(precursor_idx_mask)=12511 sum(mass_error_mask)=34850 stop_rank=2331
19:48:07.062113 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:48:07.194253 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:48:07.325034 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:48:07.459524 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:48:07.764287 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:48:07.764688 INFO: Using score_cutoff 37.04360355834961 (fac=0.99, q=1)
19:48:07.765000 INFO: Updating optimization_manager: fwhm_rt             : 3.317265272140503 -> 3.2259907722473145
19:48:07.765082 INFO: Updating optimization_manager: fwhm_mobility       : 0.008012180216610432 -> 0.007147967349737883
19:48:07.765136 INFO: Updating optimization_manager: score_cutoff        : 38.12340097389221 -> 37.04360355834961
19:48:07.765190 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:48:07.766208 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:48:07.767561 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:48:07.768323 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:48:07.770399 INFO: === checking if optimization conditions were reached ===
19:48:07.770499 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
19:48:07.772328 INFO: Updating optimization_manager: ms2_error           : 23.759473807561974 -> 18.722742581271117
19:48:07.772428 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 18.7227.
19:48:07.772509 INFO: ==============================================
19:48:07.772577 INFO: Starting optimization step 4.
19:48:07.772634 PROGRESS: === Extracting elution groups 0 to 600 ===
19:48:07.772694 INFO: Using classic extraction backend
19:48:07.772798 PROGRESS: Extracting batch of 1173 precursors
19:48:07.772859 INFO: === Search parameters used ===
19:48:07.772905 INFO: rt_error       : 2099.891532
19:48:07.772951 INFO: mobility_error : 0.1
19:48:07.772995 INFO: num_candidates : 3
19:48:07.773039 INFO: ms1_error      : 30
19:48:07.773081 INFO: ms2_error      : 18.722742581271117
19:48:07.773119 INFO: fwhm_rt        : 3.2259907722473145
19:48:07.773158 INFO: quant_window   : 3
19:48:07.773196 INFO: ==============================================
19:48:07.773985 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:48:07.774029 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:48:07.774062 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
19:48:07.774082 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.32
19:48:07.774709 INFO: Starting candidate selection
19:48:16.374717 INFO: Starting candidate scoring
19:48:16.593291 INFO: Finished candidate processing
19:48:16.593399 INFO: Collecting candidate features
19:48:16.603219 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3228)
19:48:16.607956 INFO: Collecting fragment features
19:48:16.611613 INFO: Finished candidate scoring
19:48:16.613618 INFO: performing precursor FDR with 47 features
19:48:16.613665 INFO: Decoy channel: -1
19:48:16.613694 INFO: Competetive: True
19:48:16.616589 INFO: Setting torch num_threads to 2 for FDR classification task
19:48:16.617896 WARNING: dropped 1 target PSMs due to missing features
19:48:16.618971 INFO: Using random state 492759 for train-test-split
19:48:16.628880 INFO: Test AUC: 0.525
19:48:16.628939 INFO: Train AUC: 0.487
19:48:16.628982 INFO: AUC difference: 7.95%
19:48:16.629004 WARNING: AUC difference > 5%. This may indicate overfitting.
19:48:16.851133 INFO: Resetting torch num_threads to 80
19:48:16.851728 PROGRESS: === Extracted 3228 precursors and 34174 fragments ===
19:48:16.852127 INFO: === FDR correction performed with classifier version 1 ===
19:48:16.852711 PROGRESS: ============================= Precursor FDR =============================
19:48:16.852803 PROGRESS: Total precursors accumulated: 587
19:48:16.852862 PROGRESS: Target precursors: 453 (77.17%)
19:48:16.852910 PROGRESS: Decoy precursors: 134 (22.83%)
19:48:16.852967 PROGRESS: 
19:48:16.853013 PROGRESS: Precursor Summary:
19:48:16.853963 PROGRESS: Channel   0:	 0.050 FDR:   399; 0.010 FDR:   399; 0.001 FDR:   399
19:48:16.854048 PROGRESS: 
19:48:16.854102 PROGRESS: Protein Summary:
19:48:16.855232 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   395; 0.001 FDR:   395
19:48:16.855318 PROGRESS: =========================================================================
19:48:16.855558 INFO: Target number of precursors reached.
19:48:16.861326 INFO: fragments_df: keeping 2244 of 34174 [sum(precursor_idx_mask)=12196 sum(mass_error_mask)=34174 stop_rank=2244
19:48:16.960305 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:48:17.089247 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:48:17.217822 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:48:17.351789 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:48:17.654185 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:48:17.654612 INFO: Using score_cutoff 33.827149134063724 (fac=0.99, q=1)
19:48:17.654908 INFO: Updating optimization_manager: fwhm_rt             : 3.2259907722473145 -> 3.0079333782196045
19:48:17.654986 INFO: Updating optimization_manager: fwhm_mobility       : 0.007147967349737883 -> 0.006325251888483763
19:48:17.655039 INFO: Updating optimization_manager: score_cutoff        : 37.04360355834961 -> 33.827149134063724
19:48:17.655094 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:48:17.656127 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:48:17.657490 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:48:17.658249 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:48:17.660299 INFO: === checking if optimization conditions were reached ===
19:48:17.660401 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
19:48:17.662161 INFO: Updating optimization_manager: ms2_error           : 18.722742581271117 -> 15.988192888579047
19:48:17.662260 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 15.9882.
19:48:17.662324 INFO: ==============================================
19:48:17.662391 INFO: Starting optimization step 5.
19:48:17.662447 PROGRESS: === Extracting elution groups 0 to 600 ===
19:48:17.662502 INFO: Using classic extraction backend
19:48:17.662605 PROGRESS: Extracting batch of 1173 precursors
19:48:17.662669 INFO: === Search parameters used ===
19:48:17.662716 INFO: rt_error       : 2099.891532
19:48:17.662757 INFO: mobility_error : 0.1
19:48:17.662796 INFO: num_candidates : 3
19:48:17.662835 INFO: ms1_error      : 30
19:48:17.662875 INFO: ms2_error      : 15.988192888579047
19:48:17.662914 INFO: fwhm_rt        : 3.0079333782196045
19:48:17.662952 INFO: quant_window   : 3
19:48:17.662991 INFO: ==============================================
19:48:17.665030 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:48:17.665083 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:48:17.665117 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
19:48:17.665138 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.93
19:48:17.665769 INFO: Starting candidate selection
19:48:57.456939 INFO: Starting candidate scoring
19:48:57.680077 INFO: Finished candidate processing
19:48:57.680218 INFO: Collecting candidate features
19:48:57.693193 INFO: Collecting fragment features
19:48:57.697204 INFO: Finished candidate scoring
19:48:57.699129 INFO: performing precursor FDR with 47 features
19:48:57.699169 INFO: Decoy channel: -1
19:48:57.699191 INFO: Competetive: True
19:48:57.702497 INFO: Setting torch num_threads to 2 for FDR classification task
19:48:57.704799 INFO: Using random state 492759 for train-test-split
19:48:57.715533 INFO: Test AUC: 0.487
19:48:57.715589 INFO: Train AUC: 0.505
19:48:57.715619 INFO: AUC difference: 3.69%
19:48:57.932739 INFO: Resetting torch num_threads to 80
19:48:57.933331 PROGRESS: === Extracted 3232 precursors and 33621 fragments ===
19:48:57.933788 INFO: === FDR correction performed with classifier version 1 ===
19:48:57.934347 PROGRESS: ============================= Precursor FDR =============================
19:48:57.934432 PROGRESS: Total precursors accumulated: 588
19:48:57.934497 PROGRESS: Target precursors: 460 (78.23%)
19:48:57.934548 PROGRESS: Decoy precursors: 128 (21.77%)
19:48:57.934593 PROGRESS: 
19:48:57.934635 PROGRESS: Precursor Summary:
19:48:57.935589 PROGRESS: Channel   0:	 0.050 FDR:   406; 0.010 FDR:   406; 0.001 FDR:   406
19:48:57.935674 PROGRESS: 
19:48:57.935728 PROGRESS: Protein Summary:
19:48:57.936873 PROGRESS: Channel   0:	 0.050 FDR:   401; 0.010 FDR:   401; 0.001 FDR:   401
19:48:57.936968 PROGRESS: =========================================================================
19:48:57.937125 INFO: Target number of precursors reached.
19:48:57.942693 INFO: fragments_df: keeping 2154 of 33621 [sum(precursor_idx_mask)=12117 sum(mass_error_mask)=33621 stop_rank=2154
19:48:58.041803 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:48:58.170633 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:48:58.299872 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:48:58.432904 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:48:58.718020 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:48:58.718443 INFO: Using score_cutoff 34.77744025611877 (fac=0.99, q=1)
19:48:58.718766 INFO: Updating optimization_manager: fwhm_rt             : 3.0079333782196045 -> 2.830536127090454
19:48:58.718852 INFO: Updating optimization_manager: fwhm_mobility       : 0.006325251888483763 -> 0.005631548352539539
19:48:58.718905 INFO: Updating optimization_manager: score_cutoff        : 33.827149134063724 -> 34.77744025611877
19:48:58.718966 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:48:58.719997 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:48:58.721335 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:48:58.722106 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:48:58.724329 INFO: === checking if optimization conditions were reached ===
19:48:58.724432 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
19:48:58.726287 INFO: Updating optimization_manager: ms2_error           : 15.988192888579047 -> 13.771991082054932
19:48:58.726385 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 13.7720.
19:48:58.726449 INFO: ==============================================
19:48:58.726515 INFO: Starting optimization step 6.
19:48:58.726570 PROGRESS: === Extracting elution groups 0 to 600 ===
19:48:58.726626 INFO: Using classic extraction backend
19:48:58.726784 PROGRESS: Extracting batch of 1173 precursors
19:48:58.726849 INFO: === Search parameters used ===
19:48:58.726895 INFO: rt_error       : 2099.891532
19:48:58.726936 INFO: mobility_error : 0.1
19:48:58.726975 INFO: num_candidates : 3
19:48:58.727013 INFO: ms1_error      : 30
19:48:58.727049 INFO: ms2_error      : 13.771991082054932
19:48:58.727092 INFO: fwhm_rt        : 2.830536127090454
19:48:58.727131 INFO: quant_window   : 3
19:48:58.727170 INFO: ==============================================
19:48:58.728069 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:48:58.728112 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:48:58.728152 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
19:48:58.728173 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.61
19:48:58.728828 INFO: Starting candidate selection
19:49:07.551965 INFO: Starting candidate scoring
19:49:07.788517 INFO: Finished candidate processing
19:49:07.788662 INFO: Collecting candidate features
19:49:07.800842 INFO: Collecting fragment features
19:49:07.804392 INFO: Finished candidate scoring
19:49:07.806207 INFO: performing precursor FDR with 47 features
19:49:07.806250 INFO: Decoy channel: -1
19:49:07.806274 INFO: Competetive: True
19:49:07.809209 INFO: Setting torch num_threads to 2 for FDR classification task
19:49:07.811132 INFO: Using random state 492759 for train-test-split
19:49:07.821054 INFO: Test AUC: 0.493
19:49:07.821111 INFO: Train AUC: 0.499
19:49:07.821140 INFO: AUC difference: 1.36%
19:49:08.034634 INFO: Resetting torch num_threads to 80
19:49:08.035158 PROGRESS: === Extracted 3229 precursors and 33034 fragments ===
19:49:08.035561 INFO: === FDR correction performed with classifier version 1 ===
19:49:08.036110 PROGRESS: ============================= Precursor FDR =============================
19:49:08.036195 PROGRESS: Total precursors accumulated: 589
19:49:08.036253 PROGRESS: Target precursors: 460 (78.10%)
19:49:08.036303 PROGRESS: Decoy precursors: 129 (21.90%)
19:49:08.036347 PROGRESS: 
19:49:08.036389 PROGRESS: Precursor Summary:
19:49:08.037366 PROGRESS: Channel   0:	 0.050 FDR:   400; 0.010 FDR:   400; 0.001 FDR:   400
19:49:08.037454 PROGRESS: 
19:49:08.037509 PROGRESS: Protein Summary:
19:49:08.038648 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   395; 0.001 FDR:   395
19:49:08.038738 PROGRESS: =========================================================================
19:49:08.038871 INFO: Target number of precursors reached.
19:49:08.044522 INFO: fragments_df: keeping 2068 of 33034 [sum(precursor_idx_mask)=11836 sum(mass_error_mask)=33034 stop_rank=2068
19:49:08.142978 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:49:08.256868 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:49:08.365041 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:49:08.472830 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:49:08.700125 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:49:08.700541 INFO: Using score_cutoff 32.95586714515686 (fac=0.99, q=1)
19:49:08.700842 INFO: Updating optimization_manager: fwhm_rt             : 2.830536127090454 -> 2.739436388015747
19:49:08.700919 INFO: Updating optimization_manager: fwhm_mobility       : 0.005631548352539539 -> 0.005140152759850025
19:49:08.700983 INFO: Updating optimization_manager: score_cutoff        : 34.77744025611877 -> 32.95586714515686
19:49:08.701037 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:49:08.702063 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:49:08.703384 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:49:08.704138 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:49:08.706171 INFO: === checking if optimization conditions were reached ===
19:49:08.706274 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
19:49:08.707979 INFO: Updating optimization_manager: ms2_error           : 13.771991082054932 -> 11.890621311236481
19:49:08.708074 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 11.8906.
19:49:08.708136 INFO: ==============================================
19:49:08.708204 INFO: Starting optimization step 7.
19:49:08.708259 PROGRESS: === Extracting elution groups 0 to 600 ===
19:49:08.708311 INFO: Using classic extraction backend
19:49:08.708421 PROGRESS: Extracting batch of 1173 precursors
19:49:08.708486 INFO: === Search parameters used ===
19:49:08.708532 INFO: rt_error       : 2099.891532
19:49:08.708573 INFO: mobility_error : 0.1
19:49:08.708613 INFO: num_candidates : 3
19:49:08.708653 INFO: ms1_error      : 30
19:49:08.708691 INFO: ms2_error      : 11.890621311236481
19:49:08.708729 INFO: fwhm_rt        : 2.739436388015747
19:49:08.708768 INFO: quant_window   : 3
19:49:08.708807 INFO: ==============================================
19:49:08.709611 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:49:08.709657 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:49:08.709692 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
19:49:08.709715 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.38
19:49:08.710323 INFO: Starting candidate selection
19:49:17.567256 INFO: Starting candidate scoring
19:49:17.791419 INFO: Finished candidate processing
19:49:17.791515 INFO: Collecting candidate features
19:49:17.818983 INFO: Collecting fragment features
19:49:17.827982 INFO: Finished candidate scoring
19:49:17.830824 INFO: performing precursor FDR with 47 features
19:49:17.830924 INFO: Decoy channel: -1
19:49:17.830983 INFO: Competetive: True
19:49:17.836928 INFO: Setting torch num_threads to 2 for FDR classification task
19:49:17.841207 INFO: Using random state 492759 for train-test-split
19:49:17.856828 INFO: Test AUC: 0.472
19:49:17.856919 INFO: Train AUC: 0.509
19:49:17.856980 INFO: AUC difference: 7.26%
19:49:17.857016 WARNING: AUC difference > 5%. This may indicate overfitting.
19:49:18.082109 INFO: Resetting torch num_threads to 80
19:49:18.082656 PROGRESS: === Extracted 3228 precursors and 32495 fragments ===
19:49:18.083058 INFO: === FDR correction performed with classifier version 1 ===
19:49:18.083632 PROGRESS: ============================= Precursor FDR =============================
19:49:18.083717 PROGRESS: Total precursors accumulated: 588
19:49:18.083775 PROGRESS: Target precursors: 451 (76.70%)
19:49:18.083823 PROGRESS: Decoy precursors: 137 (23.30%)
19:49:18.083867 PROGRESS: 
19:49:18.083909 PROGRESS: Precursor Summary:
19:49:18.084867 PROGRESS: Channel   0:	 0.050 FDR:   391; 0.010 FDR:   391; 0.001 FDR:   391
19:49:18.084961 PROGRESS: 
19:49:18.085019 PROGRESS: Protein Summary:
19:49:18.086185 PROGRESS: Channel   0:	 0.050 FDR:   386; 0.010 FDR:   386; 0.001 FDR:   386
19:49:18.086283 PROGRESS: =========================================================================
19:49:18.086433 INFO: Target number of precursors reached.
19:49:18.091769 INFO: fragments_df: keeping 1987 of 32495 [sum(precursor_idx_mask)=11388 sum(mass_error_mask)=32495 stop_rank=1987
19:49:18.191271 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:49:18.298223 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:49:18.404601 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:49:18.514296 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:49:18.733966 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:49:18.734393 INFO: Using score_cutoff 31.43016779136658 (fac=0.99, q=1)
19:49:18.734705 INFO: Updating optimization_manager: fwhm_rt             : 2.739436388015747 -> 2.66349458694458
19:49:18.734784 INFO: Updating optimization_manager: fwhm_mobility       : 0.005140152759850025 -> 0.004993121139705181
19:49:18.734836 INFO: Updating optimization_manager: score_cutoff        : 32.95586714515686 -> 31.43016779136658
19:49:18.734887 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:49:18.735915 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:49:18.737247 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:49:18.738011 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:49:18.740248 INFO: === checking if optimization conditions were reached ===
19:49:18.740344 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
19:49:18.742056 INFO: Updating optimization_manager: ms2_error           : 11.890621311236481 -> 10.217496387716707
19:49:18.742164 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 10.2175.
19:49:18.742229 INFO: ==============================================
19:49:18.742294 INFO: Starting optimization step 8.
19:49:18.742349 PROGRESS: === Extracting elution groups 0 to 600 ===
19:49:18.742402 INFO: Using classic extraction backend
19:49:18.742504 PROGRESS: Extracting batch of 1173 precursors
19:49:18.742564 INFO: === Search parameters used ===
19:49:18.742609 INFO: rt_error       : 2099.891532
19:49:18.742647 INFO: mobility_error : 0.1
19:49:18.742688 INFO: num_candidates : 3
19:49:18.742725 INFO: ms1_error      : 30
19:49:18.742762 INFO: ms2_error      : 10.217496387716707
19:49:18.742799 INFO: fwhm_rt        : 2.66349458694458
19:49:18.742835 INFO: quant_window   : 3
19:49:18.742872 INFO: ==============================================
19:49:18.743658 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:49:18.743705 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:49:18.743737 INFO: FWHM in RT is 2.66 seconds, sigma is 0.59
19:49:18.743758 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.32
19:49:18.744374 INFO: Starting candidate selection
19:49:57.449939 INFO: Starting candidate scoring
19:49:57.625320 INFO: Finished candidate processing
19:49:57.625452 INFO: Collecting candidate features
19:49:57.638368 INFO: Collecting fragment features
19:49:57.642732 INFO: Finished candidate scoring
19:49:57.644452 INFO: performing precursor FDR with 47 features
19:49:57.644492 INFO: Decoy channel: -1
19:49:57.644518 INFO: Competetive: True
19:49:57.647479 INFO: Setting torch num_threads to 2 for FDR classification task
19:49:57.649522 INFO: Using random state 492759 for train-test-split
19:49:57.659580 INFO: Test AUC: 0.473
19:49:57.659636 INFO: Train AUC: 0.508
19:49:57.659665 INFO: AUC difference: 6.88%
19:49:57.659688 WARNING: AUC difference > 5%. This may indicate overfitting.
19:49:57.879915 INFO: Resetting torch num_threads to 80
19:49:57.880436 PROGRESS: === Extracted 3221 precursors and 31992 fragments ===
19:49:57.880825 INFO: === FDR correction performed with classifier version 1 ===
19:49:57.881405 PROGRESS: ============================= Precursor FDR =============================
19:49:57.882137 PROGRESS: Total precursors accumulated: 589
19:49:57.882197 PROGRESS: Target precursors: 450 (76.40%)
19:49:57.882253 PROGRESS: Decoy precursors: 139 (23.60%)
19:49:57.882300 PROGRESS: 
19:49:57.882343 PROGRESS: Precursor Summary:
19:49:57.883318 PROGRESS: Channel   0:	 0.050 FDR:   388; 0.010 FDR:   388; 0.001 FDR:   388
19:49:57.883404 PROGRESS: 
19:49:57.883458 PROGRESS: Protein Summary:
19:49:57.884612 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   383; 0.001 FDR:   383
19:49:57.884697 PROGRESS: =========================================================================
19:49:57.884831 INFO: Target number of precursors reached.
19:49:57.890080 INFO: fragments_df: keeping 1950 of 31992 [sum(precursor_idx_mask)=10983 sum(mass_error_mask)=31992 stop_rank=1950
19:49:57.990080 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:49:58.103184 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:49:58.212026 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:49:58.322467 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:49:58.535462 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:49:58.535882 INFO: Using score_cutoff 30.64566048603058 (fac=0.99, q=1)
19:49:58.536175 INFO: Updating optimization_manager: fwhm_rt             : 2.66349458694458 -> 2.6230406761169434
19:49:58.536252 INFO: Updating optimization_manager: fwhm_mobility       : 0.004993121139705181 -> 0.0045813387259840965
19:49:58.536305 INFO: Updating optimization_manager: score_cutoff        : 31.43016779136658 -> 30.64566048603058
19:49:58.536363 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:49:58.537397 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:49:58.538708 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:49:58.539463 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:49:58.541510 INFO: === checking if optimization conditions were reached ===
19:49:58.541603 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
19:49:58.543277 INFO: Updating optimization_manager: ms2_error           : 10.217496387716707 -> 9.826913442197853
19:49:58.543375 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 9.8269.
19:49:58.543438 INFO: ==============================================
19:49:58.543502 INFO: Starting optimization step 9.
19:49:58.543557 PROGRESS: === Extracting elution groups 0 to 600 ===
19:49:58.543610 INFO: Using classic extraction backend
19:49:58.543714 PROGRESS: Extracting batch of 1173 precursors
19:49:58.543776 INFO: === Search parameters used ===
19:49:58.543825 INFO: rt_error       : 2099.891532
19:49:58.543867 INFO: mobility_error : 0.1
19:49:58.543909 INFO: num_candidates : 3
19:49:58.543949 INFO: ms1_error      : 30
19:49:58.543988 INFO: ms2_error      : 9.826913442197853
19:49:58.544027 INFO: fwhm_rt        : 2.6230406761169434
19:49:58.544065 INFO: quant_window   : 3
19:49:58.544110 INFO: ==============================================
19:49:58.544883 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:49:58.544927 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:49:58.544968 INFO: FWHM in RT is 2.62 seconds, sigma is 0.58
19:49:58.544989 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.13
19:49:58.545679 INFO: Starting candidate selection
19:50:07.419569 INFO: Starting candidate scoring
19:50:07.587621 INFO: Finished candidate processing
19:50:07.587753 INFO: Collecting candidate features
19:50:07.600702 INFO: Collecting fragment features
19:50:07.604642 INFO: Finished candidate scoring
19:50:07.606406 INFO: performing precursor FDR with 47 features
19:50:07.606450 INFO: Decoy channel: -1
19:50:07.606477 INFO: Competetive: True
19:50:07.609237 INFO: Setting torch num_threads to 2 for FDR classification task
19:50:07.611181 INFO: Using random state 492759 for train-test-split
19:50:07.621641 INFO: Test AUC: 0.522
19:50:07.621698 INFO: Train AUC: 0.493
19:50:07.621727 INFO: AUC difference: 5.98%
19:50:07.621749 WARNING: AUC difference > 5%. This may indicate overfitting.
19:50:07.845946 INFO: Resetting torch num_threads to 80
19:50:07.846470 PROGRESS: === Extracted 3249 precursors and 31792 fragments ===
19:50:07.846869 INFO: === FDR correction performed with classifier version 1 ===
19:50:07.847414 PROGRESS: ============================= Precursor FDR =============================
19:50:07.847500 PROGRESS: Total precursors accumulated: 587
19:50:07.847559 PROGRESS: Target precursors: 443 (75.47%)
19:50:07.847608 PROGRESS: Decoy precursors: 144 (24.53%)
19:50:07.847651 PROGRESS: 
19:50:07.847693 PROGRESS: Precursor Summary:
19:50:07.848646 PROGRESS: Channel   0:	 0.050 FDR:   380; 0.010 FDR:   380; 0.001 FDR:   380
19:50:07.848734 PROGRESS: 
19:50:07.848789 PROGRESS: Protein Summary:
19:50:07.849946 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   377; 0.001 FDR:   377
19:50:07.850037 PROGRESS: =========================================================================
19:50:07.850167 INFO: Target number of precursors reached.
19:50:07.855206 INFO: fragments_df: keeping 1903 of 31792 [sum(precursor_idx_mask)=10760 sum(mass_error_mask)=31792 stop_rank=1903
19:50:07.976101 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:50:08.096633 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:50:08.203217 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:50:08.313111 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:50:08.525692 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:50:08.526119 INFO: Using score_cutoff 31.201776550483704 (fac=0.99, q=1)
19:50:08.526430 INFO: Updating optimization_manager: fwhm_rt             : 2.6230406761169434 -> 2.576249837875366
19:50:08.526509 INFO: Updating optimization_manager: fwhm_mobility       : 0.0045813387259840965 -> 0.004268290475010872
19:50:08.526563 INFO: Updating optimization_manager: score_cutoff        : 30.64566048603058 -> 31.201776550483704
19:50:08.526618 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:50:08.527648 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:50:08.528987 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:50:08.529755 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:50:08.531871 INFO: === checking if optimization conditions were reached ===
19:50:08.531969 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
19:50:08.532676 INFO: Updating optimization_manager: ms2_error           : 9.826913442197853 -> 15.988192888579047
19:50:08.532801 INFO: Updating optimization_manager: classifier_version  : 1 -> 5
19:50:08.532902 INFO: Updating optimization_manager: score_cutoff        : 31.201776550483704 -> 34.77744025611877
19:50:08.533005 INFO: Updating optimization_manager: fwhm_rt             : 2.576249837875366 -> 2.830536127090454
19:50:08.533100 INFO: Updating optimization_manager: fwhm_mobility       : 0.004268290475010872 -> 0.005631548352539539
19:50:08.533189 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 15.9882 found after 8 searches.
19:50:08.533264 INFO: ==============================================
19:50:08.533333 PROGRESS: Optimization finished for ms2_error.
19:50:08.635285 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:50:08.636398 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:50:08.637731 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:50:08.638528 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:50:08.666496 INFO: Starting optimization step 0.
19:50:08.666639 PROGRESS: === Extracting elution groups 0 to 600 ===
19:50:08.666707 INFO: Using classic extraction backend
19:50:08.666813 PROGRESS: Extracting batch of 1173 precursors
19:50:08.666878 INFO: === Search parameters used ===
19:50:08.666934 INFO: rt_error       : 2099.891532
19:50:08.666978 INFO: mobility_error : 0.1
19:50:08.667018 INFO: num_candidates : 3
19:50:08.667058 INFO: ms1_error      : 30
19:50:08.667098 INFO: ms2_error      : 15.988192888579047
19:50:08.667136 INFO: fwhm_rt        : 2.830536127090454
19:50:08.667174 INFO: quant_window   : 3
19:50:08.667211 INFO: ==============================================
19:50:08.668018 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:50:08.668067 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:50:08.668102 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
19:50:08.668124 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.61
19:50:08.668758 INFO: Starting candidate selection
19:50:18.218009 INFO: Starting candidate scoring
19:50:18.416881 INFO: Finished candidate processing
19:50:18.416990 INFO: Collecting candidate features
19:50:18.430581 INFO: Collecting fragment features
19:50:18.434600 INFO: Finished candidate scoring
19:50:18.436849 INFO: performing precursor FDR with 47 features
19:50:18.436893 INFO: Decoy channel: -1
19:50:18.436924 INFO: Competetive: True
19:50:18.439833 INFO: Setting torch num_threads to 2 for FDR classification task
19:50:18.441819 INFO: Using random state 709881 for train-test-split
19:50:18.452746 INFO: Test AUC: 0.478
19:50:18.452804 INFO: Train AUC: 0.499
19:50:18.452840 INFO: AUC difference: 4.23%
19:50:18.675389 INFO: Resetting torch num_threads to 80
19:50:18.676348 PROGRESS: === Extracted 3244 precursors and 33634 fragments ===
19:50:18.676798 INFO: === FDR correction performed with classifier version 5 ===
19:50:18.677457 PROGRESS: ============================= Precursor FDR =============================
19:50:18.677555 PROGRESS: Total precursors accumulated: 589
19:50:18.677626 PROGRESS: Target precursors: 449 (76.23%)
19:50:18.677686 PROGRESS: Decoy precursors: 140 (23.77%)
19:50:18.677742 PROGRESS: 
19:50:18.677795 PROGRESS: Precursor Summary:
19:50:18.678902 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   390; 0.001 FDR:   390
19:50:18.678999 PROGRESS: 
19:50:18.679067 PROGRESS: Protein Summary:
19:50:18.680286 PROGRESS: Channel   0:	 0.050 FDR:   384; 0.010 FDR:   384; 0.001 FDR:   384
19:50:18.680384 PROGRESS: =========================================================================
19:50:18.680668 INFO: Target number of precursors reached.
19:50:18.686125 INFO: fragments_df: keeping 2095 of 33634 [sum(precursor_idx_mask)=11651 sum(mass_error_mask)=33634 stop_rank=2095
19:50:18.786024 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:50:18.897412 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:50:19.026987 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:50:19.158698 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:50:19.426762 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:50:19.427808 INFO: Using score_cutoff 34.46983226623536 (fac=0.99, q=1)
19:50:19.428361 INFO: Updating optimization_manager: fwhm_rt             : 2.830536127090454 -> 2.805129051208496
19:50:19.428457 INFO: Updating optimization_manager: fwhm_mobility       : 0.005631548352539539 -> 0.005569363944232464
19:50:19.428529 INFO: Updating optimization_manager: score_cutoff        : 34.77744025611877 -> 34.46983226623536
19:50:19.428611 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:50:19.430392 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:50:19.431769 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:50:19.432571 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:50:19.434906 INFO: === checking if optimization conditions were reached ===
19:50:19.435043 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
19:50:19.436853 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 1298.2570108600808
19:50:19.436969 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1298.2570.
19:50:19.437059 INFO: ==============================================
19:50:19.437150 INFO: Starting optimization step 1.
19:50:19.437227 PROGRESS: === Extracting elution groups 0 to 600 ===
19:50:19.437314 INFO: Using classic extraction backend
19:50:19.437589 PROGRESS: Extracting batch of 1173 precursors
19:50:19.437675 INFO: === Search parameters used ===
19:50:19.437737 INFO: rt_error       : 1298.2570108600808
19:50:19.437790 INFO: mobility_error : 0.1
19:50:19.437842 INFO: num_candidates : 3
19:50:19.437892 INFO: ms1_error      : 30
19:50:19.437948 INFO: ms2_error      : 15.988192888579047
19:50:19.437999 INFO: fwhm_rt        : 2.805129051208496
19:50:19.438048 INFO: quant_window   : 3
19:50:19.438097 INFO: ==============================================
19:50:19.439514 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:50:57.087488 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:50:57.087744 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
19:50:57.087788 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.58
19:50:57.088785 INFO: Starting candidate selection
19:51:04.142602 INFO: Starting candidate scoring
19:51:04.350898 INFO: Finished candidate processing
19:51:04.350999 INFO: Collecting candidate features
19:51:04.364084 INFO: Collecting fragment features
19:51:04.367853 INFO: Finished candidate scoring
19:51:04.369608 INFO: performing precursor FDR with 47 features
19:51:04.369652 INFO: Decoy channel: -1
19:51:04.369676 INFO: Competetive: True
19:51:04.372911 INFO: Setting torch num_threads to 2 for FDR classification task
19:51:04.375067 INFO: Using random state 709881 for train-test-split
19:51:04.385615 INFO: Test AUC: 0.483
19:51:04.385673 INFO: Train AUC: 0.502
19:51:04.385703 INFO: AUC difference: 3.95%
19:51:04.598255 INFO: Resetting torch num_threads to 80
19:51:04.598812 PROGRESS: === Extracted 3235 precursors and 33561 fragments ===
19:51:04.599239 INFO: === FDR correction performed with classifier version 5 ===
19:51:04.599798 PROGRESS: ============================= Precursor FDR =============================
19:51:04.599882 PROGRESS: Total precursors accumulated: 590
19:51:04.599940 PROGRESS: Target precursors: 454 (76.95%)
19:51:04.599988 PROGRESS: Decoy precursors: 136 (23.05%)
19:51:04.600031 PROGRESS: 
19:51:04.600072 PROGRESS: Precursor Summary:
19:51:04.601044 PROGRESS: Channel   0:	 0.050 FDR:   394; 0.010 FDR:   394; 0.001 FDR:   394
19:51:04.601131 PROGRESS: 
19:51:04.601184 PROGRESS: Protein Summary:
19:51:04.602316 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   389; 0.001 FDR:   389
19:51:04.602409 PROGRESS: =========================================================================
19:51:04.602539 INFO: Target number of precursors reached.
19:51:04.608084 INFO: fragments_df: keeping 2140 of 33561 [sum(precursor_idx_mask)=11719 sum(mass_error_mask)=33561 stop_rank=2140
19:51:04.706622 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:51:04.822564 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:51:04.932233 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:51:05.041865 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:51:05.279764 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:51:05.280188 INFO: Using score_cutoff 33.202604961776736 (fac=0.99, q=1)
19:51:05.280501 INFO: Updating optimization_manager: fwhm_rt             : 2.805129051208496 -> 2.797199010848999
19:51:05.280582 INFO: Updating optimization_manager: fwhm_mobility       : 0.005569363944232464 -> 0.005498791113495827
19:51:05.280640 INFO: Updating optimization_manager: score_cutoff        : 34.46983226623536 -> 33.202604961776736
19:51:05.280696 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:51:05.281728 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:51:05.283044 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:51:05.283794 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:51:05.285959 INFO: === checking if optimization conditions were reached ===
19:51:05.286065 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
19:51:05.287704 INFO: Updating optimization_manager: rt_error            : 1298.2570108600808 -> 856.060816780817
19:51:05.287806 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 856.0608.
19:51:05.287874 INFO: ==============================================
19:51:05.287941 INFO: Starting optimization step 2.
19:51:05.288001 PROGRESS: === Extracting elution groups 0 to 600 ===
19:51:05.288064 INFO: Using classic extraction backend
19:51:05.288174 PROGRESS: Extracting batch of 1173 precursors
19:51:05.288239 INFO: === Search parameters used ===
19:51:05.288291 INFO: rt_error       : 856.060816780817
19:51:05.288339 INFO: mobility_error : 0.1
19:51:05.288383 INFO: num_candidates : 3
19:51:05.288427 INFO: ms1_error      : 30
19:51:05.288469 INFO: ms2_error      : 15.988192888579047
19:51:05.288511 INFO: fwhm_rt        : 2.797199010848999
19:51:05.288553 INFO: quant_window   : 3
19:51:05.288595 INFO: ==============================================
19:51:05.289401 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:51:05.289451 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:51:05.289487 INFO: FWHM in RT is 2.80 seconds, sigma is 0.61
19:51:05.289511 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
19:51:05.290125 INFO: Starting candidate selection
19:51:10.074903 INFO: Starting candidate scoring
19:51:10.293351 INFO: Finished candidate processing
19:51:10.293448 INFO: Collecting candidate features
19:51:10.306262 INFO: Collecting fragment features
19:51:10.309825 INFO: Finished candidate scoring
19:51:10.311572 INFO: performing precursor FDR with 47 features
19:51:10.311614 INFO: Decoy channel: -1
19:51:10.311637 INFO: Competetive: True
19:51:10.314549 INFO: Setting torch num_threads to 2 for FDR classification task
19:51:10.316460 INFO: Using random state 709881 for train-test-split
19:51:10.326094 INFO: Test AUC: 0.516
19:51:10.326153 INFO: Train AUC: 0.492
19:51:10.326182 INFO: AUC difference: 4.88%
19:51:10.538523 INFO: Resetting torch num_threads to 80
19:51:10.539069 PROGRESS: === Extracted 3220 precursors and 33298 fragments ===
19:51:10.539458 INFO: === FDR correction performed with classifier version 5 ===
19:51:10.540010 PROGRESS: ============================= Precursor FDR =============================
19:51:10.540095 PROGRESS: Total precursors accumulated: 589
19:51:10.540153 PROGRESS: Target precursors: 455 (77.25%)
19:51:10.540201 PROGRESS: Decoy precursors: 134 (22.75%)
19:51:10.540246 PROGRESS: 
19:51:10.540288 PROGRESS: Precursor Summary:
19:51:10.541255 PROGRESS: Channel   0:	 0.050 FDR:   396; 0.010 FDR:   396; 0.001 FDR:   396
19:51:10.541341 PROGRESS: 
19:51:10.541402 PROGRESS: Protein Summary:
19:51:10.542515 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   390; 0.001 FDR:   390
19:51:10.542601 PROGRESS: =========================================================================
19:51:10.542722 INFO: Target number of precursors reached.
19:51:10.548080 INFO: fragments_df: keeping 2079 of 33298 [sum(precursor_idx_mask)=11683 sum(mass_error_mask)=33298 stop_rank=2079
19:51:10.646603 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:51:10.762525 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:51:10.868979 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:51:10.978315 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:51:11.216337 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:51:11.216756 INFO: Using score_cutoff 34.19612153434753 (fac=0.99, q=1)
19:51:11.217068 INFO: Updating optimization_manager: fwhm_rt             : 2.797199010848999 -> 2.76077938079834
19:51:11.217153 INFO: Updating optimization_manager: fwhm_mobility       : 0.005498791113495827 -> 0.005464652553200722
19:51:11.217208 INFO: Updating optimization_manager: score_cutoff        : 33.202604961776736 -> 34.19612153434753
19:51:11.217268 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:51:11.218289 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:51:11.219599 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:51:11.220371 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:51:11.222746 INFO: === checking if optimization conditions were reached ===
19:51:11.222855 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
19:51:11.224562 INFO: Updating optimization_manager: rt_error            : 856.060816780817 -> 795.4438422320949
19:51:11.224662 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 795.4438.
19:51:11.224729 INFO: ==============================================
19:51:11.224796 INFO: Starting optimization step 3.
19:51:11.224852 PROGRESS: === Extracting elution groups 0 to 600 ===
19:51:11.224905 INFO: Using classic extraction backend
19:51:11.225018 PROGRESS: Extracting batch of 1173 precursors
19:51:11.225087 INFO: === Search parameters used ===
19:51:11.225139 INFO: rt_error       : 795.4438422320949
19:51:11.225180 INFO: mobility_error : 0.1
19:51:11.225219 INFO: num_candidates : 3
19:51:11.225258 INFO: ms1_error      : 30
19:51:11.225301 INFO: ms2_error      : 15.988192888579047
19:51:11.225341 INFO: fwhm_rt        : 2.76077938079834
19:51:11.225379 INFO: quant_window   : 3
19:51:11.225417 INFO: ==============================================
19:51:11.226269 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:51:11.226319 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:51:11.226352 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
19:51:11.226373 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
19:51:11.226971 INFO: Starting candidate selection
19:51:15.740949 INFO: Starting candidate scoring
19:51:15.978881 INFO: Finished candidate processing
19:51:15.978976 INFO: Collecting candidate features
19:51:15.992261 INFO: Collecting fragment features
19:51:15.996106 INFO: Finished candidate scoring
19:51:15.997781 INFO: performing precursor FDR with 47 features
19:51:15.997824 INFO: Decoy channel: -1
19:51:15.997849 INFO: Competetive: True
19:51:16.000564 INFO: Setting torch num_threads to 2 for FDR classification task
19:51:16.002503 INFO: Using random state 709881 for train-test-split
19:51:16.012645 INFO: Test AUC: 0.507
19:51:16.012705 INFO: Train AUC: 0.501
19:51:16.012734 INFO: AUC difference: 1.33%
19:51:16.230513 INFO: Resetting torch num_threads to 80
19:51:16.231037 PROGRESS: === Extracted 3242 precursors and 33521 fragments ===
19:51:16.231431 INFO: === FDR correction performed with classifier version 5 ===
19:51:16.231986 PROGRESS: ============================= Precursor FDR =============================
19:51:16.232072 PROGRESS: Total precursors accumulated: 590
19:51:16.232135 PROGRESS: Target precursors: 451 (76.44%)
19:51:16.232185 PROGRESS: Decoy precursors: 139 (23.56%)
19:51:16.232229 PROGRESS: 
19:51:16.232271 PROGRESS: Precursor Summary:
19:51:16.233228 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   390; 0.001 FDR:   390
19:51:16.233316 PROGRESS: 
19:51:16.233372 PROGRESS: Protein Summary:
19:51:16.234489 PROGRESS: Channel   0:	 0.050 FDR:   384; 0.010 FDR:   384; 0.001 FDR:   384
19:51:16.234576 PROGRESS: =========================================================================
19:51:16.234708 INFO: Target number of precursors reached.
19:51:16.240195 INFO: fragments_df: keeping 2004 of 33521 [sum(precursor_idx_mask)=11601 sum(mass_error_mask)=33521 stop_rank=2004
19:51:16.339460 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:51:16.446549 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:51:16.556067 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:51:16.665308 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:51:16.897857 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:51:16.898280 INFO: Using score_cutoff 34.05011651229858 (fac=0.99, q=1)
19:51:16.898576 INFO: Updating optimization_manager: fwhm_rt             : 2.76077938079834 -> 2.8051891326904297
19:51:16.898655 INFO: Updating optimization_manager: fwhm_mobility       : 0.005464652553200722 -> 0.005522722844034433
19:51:16.898724 INFO: Updating optimization_manager: score_cutoff        : 34.19612153434753 -> 34.05011651229858
19:51:16.898779 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:51:16.899786 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:51:16.901097 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:51:16.901845 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:51:16.903961 INFO: === checking if optimization conditions were reached ===
19:51:16.904057 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
19:51:16.905714 INFO: Updating optimization_manager: rt_error            : 795.4438422320949 -> 755.7809624350052
19:51:16.905813 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 755.7810.
19:51:16.905878 INFO: ==============================================
19:51:16.905942 INFO: Starting optimization step 4.
19:51:16.905997 PROGRESS: === Extracting elution groups 0 to 600 ===
19:51:16.906051 INFO: Using classic extraction backend
19:51:16.906152 PROGRESS: Extracting batch of 1173 precursors
19:51:16.906212 INFO: === Search parameters used ===
19:51:16.906257 INFO: rt_error       : 755.7809624350052
19:51:16.906298 INFO: mobility_error : 0.1
19:51:16.906337 INFO: num_candidates : 3
19:51:16.906376 INFO: ms1_error      : 30
19:51:16.906416 INFO: ms2_error      : 15.988192888579047
19:51:16.906462 INFO: fwhm_rt        : 2.8051891326904297
19:51:16.906503 INFO: quant_window   : 3
19:51:16.906545 INFO: ==============================================
19:51:16.907388 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:51:16.907434 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:51:16.907467 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
19:51:16.907488 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.56
19:51:16.908125 INFO: Starting candidate selection
19:51:57.447503 INFO: Starting candidate scoring
19:51:57.676953 INFO: Finished candidate processing
19:51:57.677710 INFO: Collecting candidate features
19:51:57.689905 INFO: Collecting fragment features
19:51:57.693825 INFO: Finished candidate scoring
19:51:57.695459 INFO: performing precursor FDR with 47 features
19:51:57.695502 INFO: Decoy channel: -1
19:51:57.695526 INFO: Competetive: True
19:51:57.698646 INFO: Setting torch num_threads to 2 for FDR classification task
19:51:57.700570 INFO: Using random state 709881 for train-test-split
19:51:57.709945 INFO: Test AUC: 0.518
19:51:57.710002 INFO: Train AUC: 0.495
19:51:57.710030 INFO: AUC difference: 4.68%
19:51:57.920876 INFO: Resetting torch num_threads to 80
19:51:57.921408 PROGRESS: === Extracted 3233 precursors and 33492 fragments ===
19:51:57.921803 INFO: === FDR correction performed with classifier version 5 ===
19:51:57.922353 PROGRESS: ============================= Precursor FDR =============================
19:51:57.922440 PROGRESS: Total precursors accumulated: 589
19:51:57.922498 PROGRESS: Target precursors: 454 (77.08%)
19:51:57.922546 PROGRESS: Decoy precursors: 135 (22.92%)
19:51:57.922589 PROGRESS: 
19:51:57.922631 PROGRESS: Precursor Summary:
19:51:57.923593 PROGRESS: Channel   0:	 0.050 FDR:   394; 0.010 FDR:   394; 0.001 FDR:   394
19:51:57.923680 PROGRESS: 
19:51:57.923736 PROGRESS: Protein Summary:
19:51:57.924858 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   389; 0.001 FDR:   389
19:51:57.924957 PROGRESS: =========================================================================
19:51:57.925090 INFO: Target number of precursors reached.
19:51:57.930480 INFO: fragments_df: keeping 1990 of 33492 [sum(precursor_idx_mask)=11695 sum(mass_error_mask)=33492 stop_rank=1990
19:51:58.029881 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:51:58.158159 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:51:58.285641 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:51:59.997497 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:52:00.267188 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:52:00.267599 INFO: Using score_cutoff 33.208105582809445 (fac=0.99, q=1)
19:52:00.267893 INFO: Updating optimization_manager: fwhm_rt             : 2.8051891326904297 -> 2.8766660690307617
19:52:00.267971 INFO: Updating optimization_manager: fwhm_mobility       : 0.005522722844034433 -> 0.005556361749768257
19:52:00.268023 INFO: Updating optimization_manager: score_cutoff        : 34.05011651229858 -> 33.208105582809445
19:52:00.268072 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:52:00.269126 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:52:00.270503 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:52:00.271276 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:52:00.273380 INFO: === checking if optimization conditions were reached ===
19:52:00.273482 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
19:52:00.274375 INFO: Updating optimization_manager: rt_error            : 755.7809624350052 -> 755.7809624350052
19:52:00.274493 INFO: Updating optimization_manager: classifier_version  : 5 -> 14
19:52:00.274583 INFO: Updating optimization_manager: score_cutoff        : 33.208105582809445 -> 33.208105582809445
19:52:00.274666 INFO: Updating optimization_manager: fwhm_rt             : 2.8766660690307617 -> 2.8766660690307617
19:52:00.274744 INFO: Updating optimization_manager: fwhm_mobility       : 0.005556361749768257 -> 0.005556361749768257
19:52:00.274828 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 755.7810 found after 5 searches.
19:52:00.274888 INFO: ==============================================
19:52:00.274950 PROGRESS: Optimization finished for rt_error.
19:52:00.373975 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:52:00.375066 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:52:00.376396 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:52:00.377177 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:52:00.403244 INFO: Starting optimization step 0.
19:52:00.403376 PROGRESS: === Extracting elution groups 0 to 600 ===
19:52:00.403446 INFO: Using classic extraction backend
19:52:00.403556 PROGRESS: Extracting batch of 1173 precursors
19:52:00.403626 INFO: === Search parameters used ===
19:52:00.403673 INFO: rt_error       : 755.7809624350052
19:52:00.403717 INFO: mobility_error : 0.1
19:52:00.403761 INFO: num_candidates : 3
19:52:00.403802 INFO: ms1_error      : 30
19:52:00.403841 INFO: ms2_error      : 15.988192888579047
19:52:00.403881 INFO: fwhm_rt        : 2.8766660690307617
19:52:00.403919 INFO: quant_window   : 3
19:52:00.403959 INFO: ==============================================
19:52:00.404771 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:52:00.404817 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:52:00.404851 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
19:52:00.404873 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.58
19:52:00.405518 INFO: Starting candidate selection
19:52:04.170022 INFO: Starting candidate scoring
19:52:04.427109 INFO: Finished candidate processing
19:52:04.427246 INFO: Collecting candidate features
19:52:04.440217 INFO: Collecting fragment features
19:52:04.443781 INFO: Finished candidate scoring
19:52:04.446891 INFO: performing precursor FDR with 47 features
19:52:04.446937 INFO: Decoy channel: -1
19:52:04.446963 INFO: Competetive: True
19:52:04.449766 INFO: Setting torch num_threads to 2 for FDR classification task
19:52:04.451763 INFO: Using random state 208306 for train-test-split
19:52:04.462648 INFO: Test AUC: 0.510
19:52:04.462709 INFO: Train AUC: 0.495
19:52:04.462737 INFO: AUC difference: 2.99%
19:52:04.681054 INFO: Resetting torch num_threads to 80
19:52:04.681648 PROGRESS: === Extracted 3250 precursors and 33612 fragments ===
19:52:04.682045 INFO: === FDR correction performed with classifier version 14 ===
19:52:04.682622 PROGRESS: ============================= Precursor FDR =============================
19:52:04.682707 PROGRESS: Total precursors accumulated: 589
19:52:04.682763 PROGRESS: Target precursors: 446 (75.72%)
19:52:04.682811 PROGRESS: Decoy precursors: 143 (24.28%)
19:52:04.682855 PROGRESS: 
19:52:04.682897 PROGRESS: Precursor Summary:
19:52:04.683879 PROGRESS: Channel   0:	 0.050 FDR:   392; 0.010 FDR:   392; 0.001 FDR:   392
19:52:04.683964 PROGRESS: 
19:52:04.684018 PROGRESS: Protein Summary:
19:52:04.685193 PROGRESS: Channel   0:	 0.050 FDR:   387; 0.010 FDR:   387; 0.001 FDR:   387
19:52:04.685280 PROGRESS: =========================================================================
19:52:04.685407 INFO: Target number of precursors reached.
19:52:04.690980 INFO: fragments_df: keeping 2014 of 33612 [sum(precursor_idx_mask)=11625 sum(mass_error_mask)=33612 stop_rank=2014
19:52:04.807815 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:52:04.917358 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:52:05.026273 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:52:05.137681 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:52:05.367244 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:52:05.367666 INFO: Using score_cutoff 33.97181332969666 (fac=0.99, q=1)
19:52:05.367967 INFO: Updating optimization_manager: fwhm_rt             : 2.8766660690307617 -> 2.886812210083008
19:52:05.368044 INFO: Updating optimization_manager: fwhm_mobility       : 0.005556361749768257 -> 0.005736518185585737
19:52:05.368097 INFO: Updating optimization_manager: score_cutoff        : 33.208105582809445 -> 33.97181332969666
19:52:05.368148 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:52:05.369207 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:52:05.370555 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:52:05.371323 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:52:05.373405 INFO: === checking if optimization conditions were reached ===
19:52:05.373507 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
19:52:05.374877 INFO: Updating optimization_manager: ms1_error           : 30 -> 19.01623898392613
19:52:05.374978 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 19.0162.
19:52:05.375040 INFO: ==============================================
19:52:05.375103 INFO: Starting optimization step 1.
19:52:05.375158 PROGRESS: === Extracting elution groups 0 to 600 ===
19:52:05.375209 INFO: Using classic extraction backend
19:52:05.375310 PROGRESS: Extracting batch of 1173 precursors
19:52:05.375370 INFO: === Search parameters used ===
19:52:05.375414 INFO: rt_error       : 755.7809624350052
19:52:05.375455 INFO: mobility_error : 0.1
19:52:05.375501 INFO: num_candidates : 3
19:52:05.375542 INFO: ms1_error      : 19.01623898392613
19:52:05.375581 INFO: ms2_error      : 15.988192888579047
19:52:05.375620 INFO: fwhm_rt        : 2.886812210083008
19:52:05.375661 INFO: quant_window   : 3
19:52:05.375699 INFO: ==============================================
19:52:05.376508 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:52:05.376552 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:52:05.376585 INFO: FWHM in RT is 2.89 seconds, sigma is 0.63
19:52:05.376606 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.66
19:52:05.377246 INFO: Starting candidate selection
19:52:08.588938 INFO: Starting candidate scoring
19:52:08.798546 INFO: Finished candidate processing
19:52:08.798693 INFO: Collecting candidate features
19:52:08.814001 INFO: Collecting fragment features
19:52:08.818043 INFO: Finished candidate scoring
19:52:08.820981 INFO: performing precursor FDR with 47 features
19:52:08.821028 INFO: Decoy channel: -1
19:52:08.821053 INFO: Competetive: True
19:52:08.824005 INFO: Setting torch num_threads to 2 for FDR classification task
19:52:08.826062 INFO: Using random state 208306 for train-test-split
19:52:08.837238 INFO: Test AUC: 0.532
19:52:08.837294 INFO: Train AUC: 0.487
19:52:08.837322 INFO: AUC difference: 9.24%
19:52:08.837344 WARNING: AUC difference > 5%. This may indicate overfitting.
19:52:09.057998 INFO: Resetting torch num_threads to 80
19:52:09.058591 PROGRESS: === Extracted 3247 precursors and 33523 fragments ===
19:52:09.058984 INFO: === FDR correction performed with classifier version 14 ===
19:52:09.059561 PROGRESS: ============================= Precursor FDR =============================
19:52:09.059650 PROGRESS: Total precursors accumulated: 589
19:52:09.059707 PROGRESS: Target precursors: 415 (70.46%)
19:52:09.059756 PROGRESS: Decoy precursors: 174 (29.54%)
19:52:09.059799 PROGRESS: 
19:52:09.059841 PROGRESS: Precursor Summary:
19:52:09.060786 PROGRESS: Channel   0:	 0.050 FDR:   330; 0.010 FDR:   330; 0.001 FDR:   330
19:52:09.060872 PROGRESS: 
19:52:09.060926 PROGRESS: Protein Summary:
19:52:09.062050 PROGRESS: Channel   0:	 0.050 FDR:   329; 0.010 FDR:   329; 0.001 FDR:   329
19:52:09.062140 PROGRESS: =========================================================================
19:52:09.062273 INFO: Target number of precursors reached.
19:52:09.067472 INFO: fragments_df: keeping 1681 of 33523 [sum(precursor_idx_mask)=9834 sum(mass_error_mask)=33523 stop_rank=1681
19:52:09.166045 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:52:09.272214 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:52:09.381482 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:52:09.492657 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:52:09.696232 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:52:09.696652 INFO: Using score_cutoff 32.71739472427368 (fac=0.99, q=1)
19:52:09.696961 INFO: Updating optimization_manager: fwhm_rt             : 2.886812210083008 -> 2.9424285888671875
19:52:09.697043 INFO: Updating optimization_manager: fwhm_mobility       : 0.005736518185585737 -> 0.005704914219677448
19:52:09.697096 INFO: Updating optimization_manager: score_cutoff        : 33.97181332969666 -> 32.71739472427368
19:52:09.697148 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:52:09.698197 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:52:09.699537 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:52:09.700306 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:52:09.702414 INFO: === checking if optimization conditions were reached ===
19:52:09.702512 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
19:52:09.704036 INFO: Updating optimization_manager: ms1_error           : 19.01623898392613 -> 13.17629657164724
19:52:09.704134 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 13.1763.
19:52:09.704197 INFO: ==============================================
19:52:09.704269 INFO: Starting optimization step 2.
19:52:09.704326 PROGRESS: === Extracting elution groups 0 to 600 ===
19:52:09.704378 INFO: Using classic extraction backend
19:52:09.704481 PROGRESS: Extracting batch of 1173 precursors
19:52:09.704542 INFO: === Search parameters used ===
19:52:09.704588 INFO: rt_error       : 755.7809624350052
19:52:09.704628 INFO: mobility_error : 0.1
19:52:09.704668 INFO: num_candidates : 3
19:52:09.704706 INFO: ms1_error      : 13.17629657164724
19:52:09.704744 INFO: ms2_error      : 15.988192888579047
19:52:09.704782 INFO: fwhm_rt        : 2.9424285888671875
19:52:09.704821 INFO: quant_window   : 3
19:52:09.704859 INFO: ==============================================
19:52:09.705784 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:52:09.705831 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:52:09.705865 INFO: FWHM in RT is 2.94 seconds, sigma is 0.65
19:52:09.705887 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.65
19:52:09.706511 INFO: Starting candidate selection
19:52:13.172914 INFO: Starting candidate scoring
19:52:13.375458 INFO: Finished candidate processing
19:52:13.375594 INFO: Collecting candidate features
19:52:13.391958 INFO: Collecting fragment features
19:52:13.396300 INFO: Finished candidate scoring
19:52:13.400839 INFO: performing precursor FDR with 47 features
19:52:13.400900 INFO: Decoy channel: -1
19:52:13.400925 INFO: Competetive: True
19:52:13.404955 INFO: Setting torch num_threads to 2 for FDR classification task
19:52:13.407324 INFO: Using random state 208306 for train-test-split
19:52:13.420286 INFO: Test AUC: 0.517
19:52:13.420357 INFO: Train AUC: 0.493
19:52:13.420387 INFO: AUC difference: 4.80%
19:52:13.662822 INFO: Resetting torch num_threads to 80
19:52:13.669422 PROGRESS: === Extracted 3229 precursors and 33216 fragments ===
19:52:13.670257 INFO: === FDR correction performed with classifier version 14 ===
19:52:13.671826 PROGRESS: ============================= Precursor FDR =============================
19:52:13.671942 PROGRESS: Total precursors accumulated: 588
19:52:13.672003 PROGRESS: Target precursors: 399 (67.86%)
19:52:13.672053 PROGRESS: Decoy precursors: 189 (32.14%)
19:52:13.672099 PROGRESS: 
19:52:13.672142 PROGRESS: Precursor Summary:
19:52:13.673197 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   285; 0.001 FDR:   285
19:52:13.673305 PROGRESS: 
19:52:13.673380 PROGRESS: Protein Summary:
19:52:13.674519 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   284; 0.001 FDR:   284
19:52:13.674611 PROGRESS: =========================================================================
19:52:13.675279 INFO: Target number of precursors reached.
19:52:13.680622 INFO: fragments_df: keeping 1429 of 33216 [sum(precursor_idx_mask)=8316 sum(mass_error_mask)=33216 stop_rank=1429
19:52:13.792024 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:52:13.930337 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:52:14.060205 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:52:14.178692 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:52:14.361007 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:52:14.361548 INFO: Using score_cutoff 32.394728155517576 (fac=0.99, q=1)
19:52:14.361876 INFO: Updating optimization_manager: fwhm_rt             : 2.9424285888671875 -> 2.9260520935058594
19:52:14.361958 INFO: Updating optimization_manager: fwhm_mobility       : 0.005704914219677448 -> 0.005741032771766186
19:52:14.362013 INFO: Updating optimization_manager: score_cutoff        : 32.71739472427368 -> 32.394728155517576
19:52:14.362068 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:52:14.363392 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:52:14.364825 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:52:14.365695 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:52:14.368395 INFO: === checking if optimization conditions were reached ===
19:52:14.368515 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
19:52:14.369417 INFO: Updating optimization_manager: ms1_error           : 13.17629657164724 -> 19.01623898392613
19:52:14.369541 INFO: Updating optimization_manager: classifier_version  : 14 -> 16
19:52:14.369635 INFO: Updating optimization_manager: score_cutoff        : 32.394728155517576 -> 32.71739472427368
19:52:14.369719 INFO: Updating optimization_manager: fwhm_rt             : 2.9260520935058594 -> 2.9424285888671875
19:52:14.369797 INFO: Updating optimization_manager: fwhm_mobility       : 0.005741032771766186 -> 0.005704914219677448
19:52:14.369872 PROGRESS: ✅ ms1_error      : optimization just completed. Optimal parameter 19.0162 found after 3 searches.
19:52:14.370070 INFO: ==============================================
19:52:14.370138 PROGRESS: Optimization finished for ms1_error.
19:52:14.476427 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:52:14.478822 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:52:14.480222 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:52:14.481032 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:52:14.512453 INFO: Starting optimization step 0.
19:52:14.512650 PROGRESS: === Extracting elution groups 0 to 600 ===
19:52:14.512778 INFO: Using classic extraction backend
19:52:14.513198 PROGRESS: Extracting batch of 1173 precursors
19:52:14.513314 INFO: === Search parameters used ===
19:52:14.513370 INFO: rt_error       : 755.7809624350052
19:52:14.513414 INFO: mobility_error : 0.1
19:52:14.513457 INFO: num_candidates : 3
19:52:14.513501 INFO: ms1_error      : 19.01623898392613
19:52:14.513541 INFO: ms2_error      : 15.988192888579047
19:52:14.513590 INFO: fwhm_rt        : 2.9424285888671875
19:52:14.513637 INFO: quant_window   : 3
19:52:14.513685 INFO: ==============================================
19:52:14.515503 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:52:14.515551 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:52:14.515614 INFO: FWHM in RT is 2.94 seconds, sigma is 0.65
19:52:14.515637 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.65
19:52:14.516439 INFO: Starting candidate selection
19:52:17.653704 INFO: Starting candidate scoring
19:52:17.866344 INFO: Finished candidate processing
19:52:17.866444 INFO: Collecting candidate features
19:52:17.879416 INFO: Collecting fragment features
19:52:17.883193 INFO: Finished candidate scoring
19:52:17.885457 INFO: performing precursor FDR with 47 features
19:52:17.885503 INFO: Decoy channel: -1
19:52:17.885528 INFO: Competetive: True
19:52:17.888878 INFO: Setting torch num_threads to 2 for FDR classification task
19:52:17.891119 INFO: Using random state 891237 for train-test-split
19:52:17.902053 INFO: Test AUC: 0.472
19:52:17.902112 INFO: Train AUC: 0.492
19:52:17.902142 INFO: AUC difference: 4.11%
19:52:18.126628 INFO: Resetting torch num_threads to 80
19:52:18.127244 PROGRESS: === Extracted 3242 precursors and 33451 fragments ===
19:52:18.127704 INFO: === FDR correction performed with classifier version 16 ===
19:52:18.128279 PROGRESS: ============================= Precursor FDR =============================
19:52:18.128381 PROGRESS: Total precursors accumulated: 588
19:52:18.128440 PROGRESS: Target precursors: 412 (70.07%)
19:52:18.128490 PROGRESS: Decoy precursors: 176 (29.93%)
19:52:18.128534 PROGRESS: 
19:52:18.128578 PROGRESS: Precursor Summary:
19:52:18.129550 PROGRESS: Channel   0:	 0.050 FDR:   329; 0.010 FDR:   329; 0.001 FDR:   329
19:52:18.129640 PROGRESS: 
19:52:18.129696 PROGRESS: Protein Summary:
19:52:18.130808 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   328; 0.001 FDR:   328
19:52:18.130897 PROGRESS: =========================================================================
19:52:18.131055 INFO: Target number of precursors reached.
19:52:18.136257 INFO: fragments_df: keeping 1719 of 33451 [sum(precursor_idx_mask)=9784 sum(mass_error_mask)=33451 stop_rank=1719
19:52:18.235265 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:52:18.358393 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:52:18.483636 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:52:18.610384 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:52:18.851475 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:52:18.851907 INFO: Using score_cutoff 32.798316000366206 (fac=0.99, q=1)
19:52:18.852233 INFO: Updating optimization_manager: fwhm_rt             : 2.9424285888671875 -> 2.9057669639587402
19:52:18.852312 INFO: Updating optimization_manager: fwhm_mobility       : 0.005704914219677448 -> 0.005617247428745031
19:52:18.852371 INFO: Updating optimization_manager: score_cutoff        : 32.71739472427368 -> 32.798316000366206
19:52:18.852422 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:52:18.853510 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:52:18.854851 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:52:18.855619 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:52:18.857786 INFO: === checking if optimization conditions were reached ===
19:52:18.857892 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
19:52:18.859220 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.09967724455321438
19:52:18.859323 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0997.
19:52:18.859386 INFO: ==============================================
19:52:18.859449 INFO: Starting optimization step 1.
19:52:18.859505 PROGRESS: === Extracting elution groups 0 to 600 ===
19:52:18.859559 INFO: Using classic extraction backend
19:52:18.859674 PROGRESS: Extracting batch of 1173 precursors
19:52:18.859736 INFO: === Search parameters used ===
19:52:18.859779 INFO: rt_error       : 755.7809624350052
19:52:18.859820 INFO: mobility_error : 0.09967724455321438
19:52:18.859858 INFO: num_candidates : 3
19:52:18.859897 INFO: ms1_error      : 19.01623898392613
19:52:18.859934 INFO: ms2_error      : 15.988192888579047
19:52:18.859974 INFO: fwhm_rt        : 2.9057669639587402
19:52:18.860015 INFO: quant_window   : 3
19:52:18.860054 INFO: ==============================================
19:52:18.860878 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:52:57.081281 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:52:57.081465 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
19:52:57.081539 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.61
19:52:57.082576 INFO: Starting candidate selection
19:53:00.321042 INFO: Starting candidate scoring
19:53:00.529040 INFO: Finished candidate processing
19:53:00.529171 INFO: Collecting candidate features
19:53:00.541833 INFO: Collecting fragment features
19:53:00.545709 INFO: Finished candidate scoring
19:53:00.547817 INFO: performing precursor FDR with 47 features
19:53:00.547861 INFO: Decoy channel: -1
19:53:00.547886 INFO: Competetive: True
19:53:00.550734 INFO: Setting torch num_threads to 2 for FDR classification task
19:53:00.552736 INFO: Using random state 891237 for train-test-split
19:53:00.563005 INFO: Test AUC: 0.476
19:53:00.563063 INFO: Train AUC: 0.493
19:53:00.563093 INFO: AUC difference: 3.45%
19:53:00.788314 INFO: Resetting torch num_threads to 80
19:53:00.788850 PROGRESS: === Extracted 3263 precursors and 33628 fragments ===
19:53:00.789261 INFO: === FDR correction performed with classifier version 16 ===
19:53:00.789838 PROGRESS: ============================= Precursor FDR =============================
19:53:00.789925 PROGRESS: Total precursors accumulated: 589
19:53:00.789983 PROGRESS: Target precursors: 414 (70.29%)
19:53:00.790032 PROGRESS: Decoy precursors: 175 (29.71%)
19:53:00.790085 PROGRESS: 
19:53:00.790129 PROGRESS: Precursor Summary:
19:53:00.791081 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   324
19:53:00.791170 PROGRESS: 
19:53:00.791226 PROGRESS: Protein Summary:
19:53:00.792336 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   322; 0.001 FDR:   322
19:53:00.792427 PROGRESS: =========================================================================
19:53:00.792573 INFO: Target number of precursors reached.
19:53:00.797776 INFO: fragments_df: keeping 1714 of 33628 [sum(precursor_idx_mask)=9692 sum(mass_error_mask)=33628 stop_rank=1714
19:53:00.896569 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:53:00.999005 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:53:01.108322 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:53:01.215140 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:53:01.415294 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:53:01.415720 INFO: Using score_cutoff 33.14618975830078 (fac=0.99, q=1)
19:53:01.416013 INFO: Updating optimization_manager: fwhm_rt             : 2.9057669639587402 -> 2.888808012008667
19:53:01.416092 INFO: Updating optimization_manager: fwhm_mobility       : 0.005617247428745031 -> 0.005777257960289717
19:53:01.416145 INFO: Updating optimization_manager: score_cutoff        : 32.798316000366206 -> 33.14618975830078
19:53:01.416197 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:53:01.417289 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:53:01.418627 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:53:01.419384 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:53:01.421432 INFO: === checking if optimization conditions were reached ===
19:53:01.421533 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
19:53:01.422924 INFO: Updating optimization_manager: mobility_error      : 0.09967724455321438 -> 0.09822112663331535
19:53:01.423022 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0982.
19:53:01.423085 INFO: ==============================================
19:53:01.423148 INFO: Starting optimization step 2.
19:53:01.423204 PROGRESS: === Extracting elution groups 0 to 600 ===
19:53:01.423258 INFO: Using classic extraction backend
19:53:01.423369 PROGRESS: Extracting batch of 1173 precursors
19:53:01.423433 INFO: === Search parameters used ===
19:53:01.423480 INFO: rt_error       : 755.7809624350052
19:53:01.423524 INFO: mobility_error : 0.09822112663331535
19:53:01.423565 INFO: num_candidates : 3
19:53:01.423604 INFO: ms1_error      : 19.01623898392613
19:53:01.423643 INFO: ms2_error      : 15.988192888579047
19:53:01.423681 INFO: fwhm_rt        : 2.888808012008667
19:53:01.423719 INFO: quant_window   : 3
19:53:01.423758 INFO: ==============================================
19:53:01.424584 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:53:01.424630 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:53:01.424668 INFO: FWHM in RT is 2.89 seconds, sigma is 0.63
19:53:01.424691 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.68
19:53:01.425378 INFO: Starting candidate selection
19:53:04.536134 INFO: Starting candidate scoring
19:53:04.731030 INFO: Finished candidate processing
19:53:04.731161 INFO: Collecting candidate features
19:53:04.745210 INFO: Collecting fragment features
19:53:04.748828 INFO: Finished candidate scoring
19:53:04.750846 INFO: performing precursor FDR with 47 features
19:53:04.750892 INFO: Decoy channel: -1
19:53:04.750916 INFO: Competetive: True
19:53:04.753814 INFO: Setting torch num_threads to 2 for FDR classification task
19:53:04.755824 INFO: Using random state 891237 for train-test-split
19:53:04.766835 INFO: Test AUC: 0.473
19:53:04.766898 INFO: Train AUC: 0.495
19:53:04.766928 INFO: AUC difference: 4.39%
19:53:04.989081 INFO: Resetting torch num_threads to 80
19:53:04.989662 PROGRESS: === Extracted 3265 precursors and 33598 fragments ===
19:53:04.990062 INFO: === FDR correction performed with classifier version 16 ===
19:53:04.990626 PROGRESS: ============================= Precursor FDR =============================
19:53:04.990725 PROGRESS: Total precursors accumulated: 589
19:53:04.990783 PROGRESS: Target precursors: 410 (69.61%)
19:53:04.990832 PROGRESS: Decoy precursors: 179 (30.39%)
19:53:04.990875 PROGRESS: 
19:53:04.990917 PROGRESS: Precursor Summary:
19:53:04.991855 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   324
19:53:04.991939 PROGRESS: 
19:53:04.991994 PROGRESS: Protein Summary:
19:53:04.993110 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   323; 0.001 FDR:   323
19:53:04.993201 PROGRESS: =========================================================================
19:53:04.993349 INFO: Target number of precursors reached.
19:53:04.998441 INFO: fragments_df: keeping 1718 of 33598 [sum(precursor_idx_mask)=9654 sum(mass_error_mask)=33598 stop_rank=1718
19:53:05.106588 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
19:53:05.228158 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
19:53:05.352240 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
19:53:05.481085 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
19:53:05.714481 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
19:53:05.714915 INFO: Using score_cutoff 33.07764404869079 (fac=0.99, q=1)
19:53:05.715211 INFO: Updating optimization_manager: fwhm_rt             : 2.888808012008667 -> 2.923825263977051
19:53:05.715289 INFO: Updating optimization_manager: fwhm_mobility       : 0.005777257960289717 -> 0.0059150205925107
19:53:05.715342 INFO: Updating optimization_manager: score_cutoff        : 33.14618975830078 -> 33.07764404869079
19:53:05.715397 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:53:05.716467 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:53:05.717830 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:53:05.718603 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:53:05.720660 INFO: === checking if optimization conditions were reached ===
19:53:05.720760 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
19:53:05.721454 INFO: Updating optimization_manager: mobility_error      : 0.09822112663331535 -> 0.1
19:53:05.721575 INFO: Updating optimization_manager: classifier_version  : 16 -> 18
19:53:05.721666 INFO: Updating optimization_manager: score_cutoff        : 33.07764404869079 -> 32.798316000366206
19:53:05.721750 INFO: Updating optimization_manager: fwhm_rt             : 2.923825263977051 -> 2.9057669639587402
19:53:05.721831 INFO: Updating optimization_manager: fwhm_mobility       : 0.0059150205925107 -> 0.005617247428745031
19:53:05.721911 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
19:53:05.721967 INFO: ==============================================
19:53:05.722035 PROGRESS: Optimization finished for mobility_error.
19:53:05.820477 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:53:05.821627 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:53:05.822956 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:53:05.823718 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:53:05.850089 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
19:53:05.850240 PROGRESS: ==============================================
19:53:05.850323 PROGRESS: ms2_error      : 15.9882
19:53:05.850382 PROGRESS: rt_error       : 755.7810
19:53:05.850434 PROGRESS: ms1_error      : 19.0162
19:53:05.850480 PROGRESS: mobility_error : 0.1000
19:53:05.850522 PROGRESS: ==============================================
19:53:05.851337 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
19:53:07.322896 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
19:53:14.487912 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
19:53:15.970086 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
19:53:32.193291 INFO: Using classic extraction backend
19:53:32.194118 PROGRESS: Extracting batch of 12073114 precursors
19:53:32.194263 INFO: === Search parameters used ===
19:53:32.194321 INFO: rt_error       : 755.7809624350052
19:53:32.194371 INFO: mobility_error : 0.1
19:53:32.194424 INFO: num_candidates : 3
19:53:32.194471 INFO: ms1_error      : 19.01623898392613
19:53:32.194510 INFO: ms2_error      : 15.988192888579047
19:53:32.194549 INFO: fwhm_rt        : 2.9057669639587402
19:53:32.194587 INFO: quant_window   : 3
19:53:32.194624 INFO: ==============================================
19:53:34.943397 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:53:34.943525 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:53:34.943581 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
19:53:34.943608 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.61
19:53:34.944850 INFO: Starting candidate selection
1 day, 2:42:22.614951 INFO: Removed 2017188 precursors with score below cutoff 32.798316000366206
1 day, 2:42:25.340933 INFO: Starting candidate scoring
1 day, 3:02:35.794198 INFO: Finished candidate processing
1 day, 3:02:35.794748 INFO: Collecting candidate features
1 day, 3:03:21.468732 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 31774963)
1 day, 3:03:22.549928 INFO: Collecting fragment features
1 day, 3:03:43.670171 INFO: Finished candidate scoring
1 day, 3:04:27.193525 INFO: === Performing FDR correction with classifier version 18 ===
1 day, 3:04:27.203738 INFO: performing precursor FDR with 47 features
1 day, 3:04:27.203794 INFO: Decoy channel: -1
1 day, 3:04:27.203830 INFO: Competetive: True
1 day, 3:04:34.744301 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:04:39.332084 WARNING: dropped 2 target PSMs due to missing features
1 day, 3:04:39.332224 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 3:04:52.571079 INFO: Using random state 407830 for train-test-split
1 day, 3:14:20.636995 INFO: Test AUC: 0.578
1 day, 3:14:20.637254 INFO: Train AUC: 0.578
1 day, 3:14:20.637295 INFO: AUC difference: 0.08%
1 day, 3:14:26.293249 INFO: Resetting torch num_threads to 80
1 day, 3:14:26.956753 INFO: Removing fragments below FDR threshold
1 day, 3:14:30.344962 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:14:30.345213 PROGRESS: Total precursors accumulated: 47,542
1 day, 3:14:30.345278 PROGRESS: Target precursors: 47,072 (99.01%)
1 day, 3:14:30.345331 PROGRESS: Decoy precursors: 470 (0.99%)
1 day, 3:14:30.345378 PROGRESS: 
1 day, 3:14:30.345422 PROGRESS: Precursor Summary:
1 day, 3:14:30.360276 PROGRESS: Channel   0:	 0.050 FDR: 47,072; 0.010 FDR: 47,072; 0.001 FDR: 28,210
1 day, 3:14:30.360506 PROGRESS: 
1 day, 3:14:30.360569 PROGRESS: Protein Summary:
1 day, 3:14:30.381548 PROGRESS: Channel   0:	 0.050 FDR: 8,696; 0.010 FDR: 8,696; 0.001 FDR: 6,396
1 day, 3:14:30.381762 PROGRESS: =========================================================================
1 day, 3:14:30.681560 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/psm.parquet
1 day, 3:14:31.023677 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/frag.parquet
1 day, 3:14:31.220380 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 3:14:31.738323 PROGRESS: 
1 day, 3:14:31.738464 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
1 day, 3:14:31.738534 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/figures
1 day, 3:14:31.739716 INFO: Initializing TimingManager
1 day, 3:14:31.740227 INFO: Initializing RawFileManager
1 day, 3:14:31.740338 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:31.740390 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:31.740431 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:31.952961 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, 3:14:41.685137 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
1 day, 3:14:41.686244 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:41.688413 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:41.688650 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:41.689046 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:41.690496 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:41.703713 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:41.703906 INFO: Indexing quadrupole dimension
1 day, 3:14:42.174395 INFO: Transposing detector events
1 day, 3:14:51.700635 INFO: Finished transposing data
1 day, 3:14:51.738286 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 3:14:51.739583 INFO: RT (min)            : 0.0 - 70.0
1 day, 3:14:51.739702 INFO: RT duration (sec)   : 4199.9
1 day, 3:14:51.739760 INFO: RT duration (min)   : 70.0
1 day, 3:14:51.739811 INFO: Cycle len (scans)   : 9
1 day, 3:14:51.739858 INFO: Cycle len (sec)     : 0.97
1 day, 3:14:51.739905 INFO: Number of cycles    : 4347
1 day, 3:14:51.739950 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 3:14:51.740083 INFO: Creating DIA data object took: 19.99973750114441
1 day, 3:14:53.335273 INFO: Initializing CalibrationManager
1 day, 3:14:53.335563 INFO: Setting up calibration estimators ..
1 day, 3:14:53.335632 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 3:14:53.335735 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, 3:14:53.335830 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 3:14:53.335894 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, 3:14:53.335953 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, 3:14:53.336018 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, 3:14:53.336068 INFO: Done setting up calibration estimators.
1 day, 3:14:53.336203 INFO: Initializing OptimizationManager
1 day, 3:14:53.336304 INFO: initial parameter: ms1_error = 30
1 day, 3:14:53.336353 INFO: initial parameter: ms2_error = 30
1 day, 3:14:53.336397 INFO: initial parameter: rt_error = 2099.9331315
1 day, 3:14:53.336437 INFO: initial parameter: mobility_error = 0.1
1 day, 3:14:53.336476 INFO: initial parameter: num_candidates = 1
1 day, 3:14:53.336515 INFO: initial parameter: fwhm_rt = 5
1 day, 3:14:53.336556 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 3:14:53.336596 INFO: initial parameter: score_cutoff = 0
1 day, 3:14:53.336635 INFO: initial parameter: classifier_version = -1
1 day, 3:14:53.336712 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 3:14:53.337667 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 3:14:53.337716 INFO: Initializing FDRManager
1 day, 3:14:53.337768 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 3:14:54.553554 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
1 day, 3:14:55.312318 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 3:14:55.312675 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 2099.9331315
1 day, 3:14:55.312887 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 3:14:55.313079 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 3:14:55.313166 PROGRESS: Starting initial search for precursors.
1 day, 3:14:55.313255 INFO: Starting optimization step 0.
1 day, 3:14:55.313317 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 3:14:55.313381 INFO: Using classic extraction backend
1 day, 3:14:55.313603 PROGRESS: Extracting batch of 390 precursors
1 day, 3:14:55.313676 INFO: === Search parameters used ===
1 day, 3:14:55.313726 INFO: rt_error       : 2099.9331315
1 day, 3:14:55.313769 INFO: mobility_error : 0.1
1 day, 3:14:55.313809 INFO: num_candidates : 1
1 day, 3:14:55.313849 INFO: ms1_error      : 30
1 day, 3:14:55.313888 INFO: ms2_error      : 30
1 day, 3:14:55.313925 INFO: fwhm_rt        : 5
1 day, 3:14:55.313965 INFO: quant_window   : 3
1 day, 3:14:55.314003 INFO: ==============================================
1 day, 3:14:55.315101 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:14:55.315145 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:14:55.315199 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 3:14:55.315222 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 3:14:55.316144 INFO: Starting candidate selection
1 day, 3:14:59.119739 INFO: Starting candidate scoring
1 day, 3:14:59.185951 INFO: Finished candidate processing
1 day, 3:14:59.186049 INFO: Collecting candidate features
1 day, 3:14:59.195226 INFO: Collecting fragment features
1 day, 3:14:59.197385 INFO: Finished candidate scoring
1 day, 3:14:59.198120 INFO: performing precursor FDR with 47 features
1 day, 3:14:59.198163 INFO: Decoy channel: -1
1 day, 3:14:59.198188 INFO: Competetive: True
1 day, 3:14:59.199648 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:14:59.202083 INFO: Using random state 128458 for train-test-split
1 day, 3:14:59.210488 INFO: Test AUC: 0.483
1 day, 3:14:59.210545 INFO: Train AUC: 0.497
1 day, 3:14:59.210576 INFO: AUC difference: 2.84%
1 day, 3:14:59.434895 INFO: Resetting torch num_threads to 80
1 day, 3:14:59.435333 PROGRESS: === Extracted 364 precursors and 3938 fragments ===
1 day, 3:14:59.435734 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:14:59.436253 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:14:59.436343 PROGRESS: Total precursors accumulated: 187
1 day, 3:14:59.436404 PROGRESS: Target precursors: 161 (86.10%)
1 day, 3:14:59.436455 PROGRESS: Decoy precursors: 26 (13.90%)
1 day, 3:14:59.436501 PROGRESS: 
1 day, 3:14:59.436548 PROGRESS: Precursor Summary:
1 day, 3:14:59.437459 PROGRESS: Channel   0:	 0.050 FDR:   149; 0.010 FDR:   149; 0.001 FDR:   149
1 day, 3:14:59.437552 PROGRESS: 
1 day, 3:14:59.437615 PROGRESS: Protein Summary:
1 day, 3:14:59.438635 PROGRESS: Channel   0:	 0.050 FDR:   149; 0.010 FDR:   149; 0.001 FDR:   149
1 day, 3:14:59.438728 PROGRESS: =========================================================================
1 day, 3:14:59.438827 INFO: Target number of precursors not reached yet.
1 day, 3:14:59.504315 INFO: Starting optimization step 1.
1 day, 3:14:59.504503 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 3:14:59.504576 INFO: Using classic extraction backend
1 day, 3:14:59.504696 PROGRESS: Extracting batch of 783 precursors
1 day, 3:14:59.504767 INFO: === Search parameters used ===
1 day, 3:14:59.504818 INFO: rt_error       : 2099.9331315
1 day, 3:14:59.504862 INFO: mobility_error : 0.1
1 day, 3:14:59.504905 INFO: num_candidates : 1
1 day, 3:14:59.504989 INFO: ms1_error      : 30
1 day, 3:14:59.505041 INFO: ms2_error      : 30
1 day, 3:14:59.505082 INFO: fwhm_rt        : 5
1 day, 3:14:59.505121 INFO: quant_window   : 3
1 day, 3:14:59.505162 INFO: ==============================================
1 day, 3:14:59.505803 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:14:59.505859 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:14:59.505887 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 3:14:59.505909 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 3:14:59.506632 INFO: Starting candidate selection
1 day, 3:15:05.512233 INFO: Starting candidate scoring
1 day, 3:15:05.610199 INFO: Finished candidate processing
1 day, 3:15:05.610295 INFO: Collecting candidate features
1 day, 3:15:05.619663 INFO: Collecting fragment features
1 day, 3:15:05.621966 INFO: Finished candidate scoring
1 day, 3:15:05.623832 INFO: performing precursor FDR with 47 features
1 day, 3:15:05.623878 INFO: Decoy channel: -1
1 day, 3:15:05.623904 INFO: Competetive: True
1 day, 3:15:05.626756 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:15:05.628416 INFO: Using random state 826422 for train-test-split
1 day, 3:15:05.636863 INFO: Test AUC: 0.497
1 day, 3:15:05.636923 INFO: Train AUC: 0.510
1 day, 3:15:05.636971 INFO: AUC difference: 2.60%
1 day, 3:15:05.844528 INFO: Resetting torch num_threads to 80
1 day, 3:15:05.845690 PROGRESS: === Extracted 1114 precursors and 12160 fragments ===
1 day, 3:15:05.846076 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:15:05.846618 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:15:05.846707 PROGRESS: Total precursors accumulated: 574
1 day, 3:15:05.846766 PROGRESS: Target precursors: 498 (86.76%)
1 day, 3:15:05.846824 PROGRESS: Decoy precursors: 76 (13.24%)
1 day, 3:15:05.846871 PROGRESS: 
1 day, 3:15:05.846914 PROGRESS: Precursor Summary:
1 day, 3:15:05.847923 PROGRESS: Channel   0:	 0.050 FDR:   472; 0.010 FDR:   472; 0.001 FDR:   472
1 day, 3:15:05.848011 PROGRESS: 
1 day, 3:15:05.848065 PROGRESS: Protein Summary:
1 day, 3:15:05.849261 PROGRESS: Channel   0:	 0.050 FDR:   464; 0.010 FDR:   464; 0.001 FDR:   464
1 day, 3:15:05.849353 PROGRESS: =========================================================================
1 day, 3:15:05.849498 INFO: Target number of precursors reached.
1 day, 3:15:05.852570 INFO: fragments_df: keeping 973 of 12160 [sum(precursor_idx_mask)=5283 sum(mass_error_mask)=12160 stop_rank=973
1 day, 3:15:05.953277 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:06.083628 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:06.222721 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:06.352983 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:06.491394 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 3:15:06.491812 INFO: Using score_cutoff 33.34244627609253 (fac=0.99, q=1)
1 day, 3:15:06.492129 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.196465015411377
1 day, 3:15:06.492208 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007966334000229836
1 day, 3:15:06.492263 INFO: Updating optimization_manager: score_cutoff        : 0 -> 33.34244627609253
1 day, 3:15:06.492328 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:06.493398 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:06.494711 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:06.495479 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:06.497634 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
1 day, 3:15:06.497734 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 3:15:06.497808 INFO: Starting optimization step 2.
1 day, 3:15:06.497868 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:15:06.497923 INFO: Using classic extraction backend
1 day, 3:15:06.498026 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:15:06.498091 INFO: === Search parameters used ===
1 day, 3:15:06.498140 INFO: rt_error       : 2099.9331315
1 day, 3:15:06.498183 INFO: mobility_error : 0.1
1 day, 3:15:06.498224 INFO: num_candidates : 3
1 day, 3:15:06.498821 INFO: ms1_error      : 30
1 day, 3:15:06.498866 INFO: ms2_error      : 30
1 day, 3:15:06.498908 INFO: fwhm_rt        : 3.196465015411377
1 day, 3:15:06.498948 INFO: quant_window   : 3
1 day, 3:15:06.498986 INFO: ==============================================
1 day, 3:15:06.499827 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:15:06.499870 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:15:06.499905 INFO: FWHM in RT is 3.20 seconds, sigma is 0.70
1 day, 3:15:06.499927 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.70
1 day, 3:15:06.500562 INFO: Starting candidate selection
1 day, 3:15:15.553601 INFO: Starting candidate scoring
1 day, 3:15:15.857766 INFO: Finished candidate processing
1 day, 3:15:15.857871 INFO: Collecting candidate features
1 day, 3:15:15.870553 INFO: Collecting fragment features
1 day, 3:15:15.874068 INFO: Finished candidate scoring
1 day, 3:15:15.875741 INFO: performing precursor FDR with 47 features
1 day, 3:15:15.875782 INFO: Decoy channel: -1
1 day, 3:15:15.875806 INFO: Competetive: True
1 day, 3:15:15.878495 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:15:15.880438 INFO: Using random state 20749 for train-test-split
1 day, 3:15:15.890071 INFO: Test AUC: 0.520
1 day, 3:15:15.890126 INFO: Train AUC: 0.494
1 day, 3:15:15.890156 INFO: AUC difference: 5.24%
1 day, 3:15:15.890179 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:15:16.102403 INFO: Resetting torch num_threads to 80
1 day, 3:15:16.102913 PROGRESS: === Extracted 3251 precursors and 35527 fragments ===
1 day, 3:15:16.103317 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:15:16.103872 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:15:16.103962 PROGRESS: Total precursors accumulated: 588
1 day, 3:15:16.104020 PROGRESS: Target precursors: 541 (92.01%)
1 day, 3:15:16.104070 PROGRESS: Decoy precursors: 47 (7.99%)
1 day, 3:15:16.104115 PROGRESS: 
1 day, 3:15:16.104158 PROGRESS: Precursor Summary:
1 day, 3:15:16.105165 PROGRESS: Channel   0:	 0.050 FDR:   527; 0.010 FDR:   527; 0.001 FDR:   527
1 day, 3:15:16.105254 PROGRESS: 
1 day, 3:15:16.105309 PROGRESS: Protein Summary:
1 day, 3:15:16.106511 PROGRESS: Channel   0:	 0.050 FDR:   517; 0.010 FDR:   517; 0.001 FDR:   517
1 day, 3:15:16.106601 PROGRESS: =========================================================================
1 day, 3:15:16.106727 INFO: Target number of precursors reached.
1 day, 3:15:16.113167 INFO: fragments_df: keeping 3212 of 35527 [sum(precursor_idx_mask)=16601 sum(mass_error_mask)=35527 stop_rank=3212
1 day, 3:15:16.229883 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:16.346394 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:16.461484 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:16.579404 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:16.935362 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:15:16.935774 INFO: Using score_cutoff 35.565659740448 (fac=0.99, q=1)
1 day, 3:15:16.936075 INFO: Updating optimization_manager: fwhm_rt             : 3.196465015411377 -> 3.086374282836914
1 day, 3:15:16.936162 INFO: Updating optimization_manager: fwhm_mobility       : 0.007966334000229836 -> 0.00781641248613596
1 day, 3:15:16.936220 INFO: Updating optimization_manager: score_cutoff        : 33.34244627609253 -> 35.565659740448
1 day, 3:15:16.936275 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:16.937305 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:16.938622 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:16.939369 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:16.941440 INFO: === checking if optimization conditions were reached ===
1 day, 3:15:16.941547 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:15:16.943209 INFO: Updating optimization_manager: ms2_error           : 30 -> 23.394477525116994
1 day, 3:15:16.943310 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 23.3945.
1 day, 3:15:16.943377 INFO: ==============================================
1 day, 3:15:16.943442 INFO: Starting optimization step 3.
1 day, 3:15:16.943498 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:15:16.943552 INFO: Using classic extraction backend
1 day, 3:15:16.943652 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:15:16.943717 INFO: === Search parameters used ===
1 day, 3:15:16.943764 INFO: rt_error       : 2099.9331315
1 day, 3:15:16.943809 INFO: mobility_error : 0.1
1 day, 3:15:16.943852 INFO: num_candidates : 3
1 day, 3:15:16.943895 INFO: ms1_error      : 30
1 day, 3:15:16.944038 INFO: ms2_error      : 23.394477525116994
1 day, 3:15:16.944086 INFO: fwhm_rt        : 3.086374282836914
1 day, 3:15:16.944127 INFO: quant_window   : 3
1 day, 3:15:16.944165 INFO: ==============================================
1 day, 3:15:16.944950 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:15:16.944997 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:15:16.945031 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
1 day, 3:15:16.945057 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
1 day, 3:15:16.945743 INFO: Starting candidate selection
1 day, 3:15:57.417810 INFO: Starting candidate scoring
1 day, 3:15:57.701059 INFO: Finished candidate processing
1 day, 3:15:57.701162 INFO: Collecting candidate features
1 day, 3:15:57.729950 INFO: Collecting fragment features
1 day, 3:15:57.742709 INFO: Finished candidate scoring
1 day, 3:15:57.746747 INFO: performing precursor FDR with 47 features
1 day, 3:15:57.746845 INFO: Decoy channel: -1
1 day, 3:15:57.746901 INFO: Competetive: True
1 day, 3:15:57.752381 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:15:57.755534 INFO: Using random state 20749 for train-test-split
1 day, 3:15:57.772569 INFO: Test AUC: 0.492
1 day, 3:15:57.772667 INFO: Train AUC: 0.497
1 day, 3:15:57.772715 INFO: AUC difference: 0.87%
1 day, 3:15:57.990097 INFO: Resetting torch num_threads to 80
1 day, 3:15:57.990914 PROGRESS: === Extracted 3229 precursors and 34753 fragments ===
1 day, 3:15:57.991318 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:15:57.991872 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:15:57.991963 PROGRESS: Total precursors accumulated: 588
1 day, 3:15:57.992021 PROGRESS: Target precursors: 539 (91.67%)
1 day, 3:15:57.992071 PROGRESS: Decoy precursors: 49 (8.33%)
1 day, 3:15:57.992115 PROGRESS: 
1 day, 3:15:57.992157 PROGRESS: Precursor Summary:
1 day, 3:15:57.993174 PROGRESS: Channel   0:	 0.050 FDR:   527; 0.010 FDR:   527; 0.001 FDR:   527
1 day, 3:15:57.993266 PROGRESS: 
1 day, 3:15:57.993320 PROGRESS: Protein Summary:
1 day, 3:15:57.994529 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   516; 0.001 FDR:   516
1 day, 3:15:57.994619 PROGRESS: =========================================================================
1 day, 3:15:57.994833 INFO: Target number of precursors reached.
1 day, 3:15:58.001091 INFO: fragments_df: keeping 3108 of 34753 [sum(precursor_idx_mask)=16378 sum(mass_error_mask)=34753 stop_rank=3108
1 day, 3:15:58.100256 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:58.224282 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:58.339965 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:58.459862 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:58.809721 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:15:58.810144 INFO: Using score_cutoff 34.345858467864986 (fac=0.99, q=1)
1 day, 3:15:58.810447 INFO: Updating optimization_manager: fwhm_rt             : 3.086374282836914 -> 2.843061923980713
1 day, 3:15:58.810536 INFO: Updating optimization_manager: fwhm_mobility       : 0.00781641248613596 -> 0.006918610073626041
1 day, 3:15:58.810590 INFO: Updating optimization_manager: score_cutoff        : 35.565659740448 -> 34.345858467864986
1 day, 3:15:58.810647 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:58.811692 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:58.813022 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:58.813784 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:58.815983 INFO: === checking if optimization conditions were reached ===
1 day, 3:15:58.816082 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:15:58.817889 INFO: Updating optimization_manager: ms2_error           : 23.394477525116994 -> 19.00109113653737
1 day, 3:15:58.817990 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 19.0011.
1 day, 3:15:58.818054 INFO: ==============================================
1 day, 3:15:58.818118 INFO: Starting optimization step 4.
1 day, 3:15:58.818179 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:15:58.818239 INFO: Using classic extraction backend
1 day, 3:15:58.818348 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:15:58.818414 INFO: === Search parameters used ===
1 day, 3:15:58.818461 INFO: rt_error       : 2099.9331315
1 day, 3:15:58.818503 INFO: mobility_error : 0.1
1 day, 3:15:58.818543 INFO: num_candidates : 3
1 day, 3:15:58.818584 INFO: ms1_error      : 30
1 day, 3:15:58.818623 INFO: ms2_error      : 19.00109113653737
1 day, 3:15:58.818663 INFO: fwhm_rt        : 2.843061923980713
1 day, 3:15:58.818703 INFO: quant_window   : 3
1 day, 3:15:58.818741 INFO: ==============================================
1 day, 3:15:58.820829 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:15:58.820873 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:15:58.820908 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
1 day, 3:15:58.820930 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.21
1 day, 3:15:58.822562 INFO: Starting candidate selection
1 day, 3:16:08.045740 INFO: Starting candidate scoring
1 day, 3:16:08.282260 INFO: Finished candidate processing
1 day, 3:16:08.282370 INFO: Collecting candidate features
1 day, 3:16:08.296648 INFO: Collecting fragment features
1 day, 3:16:08.300517 INFO: Finished candidate scoring
1 day, 3:16:08.302507 INFO: performing precursor FDR with 47 features
1 day, 3:16:08.302563 INFO: Decoy channel: -1
1 day, 3:16:08.302588 INFO: Competetive: True
1 day, 3:16:08.306129 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:16:08.308411 INFO: Using random state 20749 for train-test-split
1 day, 3:16:08.318657 INFO: Test AUC: 0.509
1 day, 3:16:08.318713 INFO: Train AUC: 0.499
1 day, 3:16:08.318744 INFO: AUC difference: 2.02%
1 day, 3:16:08.533767 INFO: Resetting torch num_threads to 80
1 day, 3:16:08.534309 PROGRESS: === Extracted 3233 precursors and 34325 fragments ===
1 day, 3:16:08.534763 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:16:08.535324 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:16:08.535414 PROGRESS: Total precursors accumulated: 587
1 day, 3:16:08.535475 PROGRESS: Target precursors: 544 (92.67%)
1 day, 3:16:08.535525 PROGRESS: Decoy precursors: 43 (7.33%)
1 day, 3:16:08.535570 PROGRESS: 
1 day, 3:16:08.535613 PROGRESS: Precursor Summary:
1 day, 3:16:08.536614 PROGRESS: Channel   0:	 0.050 FDR:   531; 0.010 FDR:   531; 0.001 FDR:   531
1 day, 3:16:08.536703 PROGRESS: 
1 day, 3:16:08.536757 PROGRESS: Protein Summary:
1 day, 3:16:08.537996 PROGRESS: Channel   0:	 0.050 FDR:   520; 0.010 FDR:   520; 0.001 FDR:   520
1 day, 3:16:08.538089 PROGRESS: =========================================================================
1 day, 3:16:08.538229 INFO: Target number of precursors reached.
1 day, 3:16:08.544477 INFO: fragments_df: keeping 3044 of 34325 [sum(precursor_idx_mask)=16289 sum(mass_error_mask)=34325 stop_rank=3044
1 day, 3:16:08.643356 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:16:08.766528 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:16:08.882228 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:16:08.999606 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:16:09.339826 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:16:09.340247 INFO: Using score_cutoff 34.262432281494135 (fac=0.99, q=1)
1 day, 3:16:09.340577 INFO: Updating optimization_manager: fwhm_rt             : 2.843061923980713 -> 2.807823657989502
1 day, 3:16:09.340657 INFO: Updating optimization_manager: fwhm_mobility       : 0.006918610073626041 -> 0.0062845926731824875
1 day, 3:16:09.340710 INFO: Updating optimization_manager: score_cutoff        : 34.345858467864986 -> 34.262432281494135
1 day, 3:16:09.340767 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:16:09.341819 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:16:09.343145 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:16:09.343902 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:16:09.346012 INFO: === checking if optimization conditions were reached ===
1 day, 3:16:09.346129 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:16:09.347948 INFO: Updating optimization_manager: ms2_error           : 19.00109113653737 -> 17.253616366314823
1 day, 3:16:09.348051 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 17.2536.
1 day, 3:16:09.348117 INFO: ==============================================
1 day, 3:16:09.348186 INFO: Starting optimization step 5.
1 day, 3:16:09.348244 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:16:09.348303 INFO: Using classic extraction backend
1 day, 3:16:09.348459 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:16:09.348526 INFO: === Search parameters used ===
1 day, 3:16:09.348575 INFO: rt_error       : 2099.9331315
1 day, 3:16:09.348618 INFO: mobility_error : 0.1
1 day, 3:16:09.348659 INFO: num_candidates : 3
1 day, 3:16:09.348699 INFO: ms1_error      : 30
1 day, 3:16:09.348743 INFO: ms2_error      : 17.253616366314823
1 day, 3:16:09.348783 INFO: fwhm_rt        : 2.807823657989502
1 day, 3:16:09.348821 INFO: quant_window   : 3
1 day, 3:16:09.348861 INFO: ==============================================
1 day, 3:16:09.349785 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:16:09.349834 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:16:09.349873 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 3:16:09.349896 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.92
1 day, 3:16:09.350564 INFO: Starting candidate selection
1 day, 3:16:18.640948 INFO: Starting candidate scoring
1 day, 3:16:18.908884 INFO: Finished candidate processing
1 day, 3:16:18.909118 INFO: Collecting candidate features
1 day, 3:16:18.923573 INFO: Collecting fragment features
1 day, 3:16:18.927326 INFO: Finished candidate scoring
1 day, 3:16:18.929059 INFO: performing precursor FDR with 47 features
1 day, 3:16:18.929106 INFO: Decoy channel: -1
1 day, 3:16:18.929132 INFO: Competetive: True
1 day, 3:16:18.932049 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:16:18.934014 INFO: Using random state 20749 for train-test-split
1 day, 3:16:57.055440 INFO: Test AUC: 0.504
1 day, 3:16:57.055624 INFO: Train AUC: 0.503
1 day, 3:16:57.055697 INFO: AUC difference: 0.31%
1 day, 3:16:57.299105 INFO: Resetting torch num_threads to 80
1 day, 3:16:57.299636 PROGRESS: === Extracted 3226 precursors and 33922 fragments ===
1 day, 3:16:57.300030 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:16:57.300580 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:16:57.300678 PROGRESS: Total precursors accumulated: 587
1 day, 3:16:57.300740 PROGRESS: Target precursors: 543 (92.50%)
1 day, 3:16:57.300789 PROGRESS: Decoy precursors: 44 (7.50%)
1 day, 3:16:57.300832 PROGRESS: 
1 day, 3:16:57.300873 PROGRESS: Precursor Summary:
1 day, 3:16:57.301868 PROGRESS: Channel   0:	 0.050 FDR:   531; 0.010 FDR:   531; 0.001 FDR:   531
1 day, 3:16:57.301963 PROGRESS: 
1 day, 3:16:57.302017 PROGRESS: Protein Summary:
1 day, 3:16:57.303232 PROGRESS: Channel   0:	 0.050 FDR:   521; 0.010 FDR:   521; 0.001 FDR:   521
1 day, 3:16:57.303322 PROGRESS: =========================================================================
1 day, 3:16:57.303454 INFO: Target number of precursors reached.
1 day, 3:16:57.309816 INFO: fragments_df: keeping 3038 of 33922 [sum(precursor_idx_mask)=15997 sum(mass_error_mask)=33922 stop_rank=3038
1 day, 3:16:57.408482 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:16:57.523619 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:16:57.639772 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:16:57.759074 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:16:58.098960 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:16:58.099384 INFO: Using score_cutoff 33.69806309509278 (fac=0.99, q=1)
1 day, 3:16:58.099696 INFO: Updating optimization_manager: fwhm_rt             : 2.807823657989502 -> 2.749605655670166
1 day, 3:16:58.099784 INFO: Updating optimization_manager: fwhm_mobility       : 0.0062845926731824875 -> 0.006098787300288677
1 day, 3:16:58.099846 INFO: Updating optimization_manager: score_cutoff        : 34.262432281494135 -> 33.69806309509278
1 day, 3:16:58.099907 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:16:58.100955 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:16:58.102273 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:16:58.103034 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:16:58.105315 INFO: === checking if optimization conditions were reached ===
1 day, 3:16:58.105417 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
1 day, 3:16:58.107236 INFO: Updating optimization_manager: ms2_error           : 17.253616366314823 -> 15.150790181198603
1 day, 3:16:58.107365 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 15.1508.
1 day, 3:16:58.107433 INFO: ==============================================
1 day, 3:16:58.107503 INFO: Starting optimization step 6.
1 day, 3:16:58.107564 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:16:58.107626 INFO: Using classic extraction backend
1 day, 3:16:58.107735 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:16:58.107802 INFO: === Search parameters used ===
1 day, 3:16:58.107853 INFO: rt_error       : 2099.9331315
1 day, 3:16:58.107899 INFO: mobility_error : 0.1
1 day, 3:16:58.107944 INFO: num_candidates : 3
1 day, 3:16:58.107989 INFO: ms1_error      : 30
1 day, 3:16:58.108032 INFO: ms2_error      : 15.150790181198603
1 day, 3:16:58.108082 INFO: fwhm_rt        : 2.749605655670166
1 day, 3:16:58.108128 INFO: quant_window   : 3
1 day, 3:16:58.108171 INFO: ==============================================
1 day, 3:16:58.109003 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:16:58.109054 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:16:58.109090 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 3:16:58.109114 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.83
1 day, 3:16:58.109721 INFO: Starting candidate selection
1 day, 3:17:07.268688 INFO: Starting candidate scoring
1 day, 3:17:07.477120 INFO: Finished candidate processing
1 day, 3:17:07.477252 INFO: Collecting candidate features
1 day, 3:17:07.490719 INFO: Collecting fragment features
1 day, 3:17:07.494452 INFO: Finished candidate scoring
1 day, 3:17:07.496204 INFO: performing precursor FDR with 47 features
1 day, 3:17:07.496251 INFO: Decoy channel: -1
1 day, 3:17:07.496277 INFO: Competetive: True
1 day, 3:17:07.499129 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:17:07.501096 INFO: Using random state 20749 for train-test-split
1 day, 3:17:07.511213 INFO: Test AUC: 0.486
1 day, 3:17:07.511270 INFO: Train AUC: 0.503
1 day, 3:17:07.511300 INFO: AUC difference: 3.29%
1 day, 3:17:07.725565 INFO: Resetting torch num_threads to 80
1 day, 3:17:07.726078 PROGRESS: === Extracted 3223 precursors and 33519 fragments ===
1 day, 3:17:07.726473 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:17:07.727022 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:17:07.727111 PROGRESS: Total precursors accumulated: 587
1 day, 3:17:07.727168 PROGRESS: Target precursors: 537 (91.48%)
1 day, 3:17:07.727218 PROGRESS: Decoy precursors: 50 (8.52%)
1 day, 3:17:07.727263 PROGRESS: 
1 day, 3:17:07.727305 PROGRESS: Precursor Summary:
1 day, 3:17:07.728295 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   525; 0.001 FDR:   525
1 day, 3:17:07.728384 PROGRESS: 
1 day, 3:17:07.728438 PROGRESS: Protein Summary:
1 day, 3:17:07.729653 PROGRESS: Channel   0:	 0.050 FDR:   514; 0.010 FDR:   514; 0.001 FDR:   514
1 day, 3:17:07.729744 PROGRESS: =========================================================================
1 day, 3:17:07.729889 INFO: Target number of precursors reached.
1 day, 3:17:07.736190 INFO: fragments_df: keeping 2879 of 33519 [sum(precursor_idx_mask)=15619 sum(mass_error_mask)=33519 stop_rank=2879
1 day, 3:17:07.838135 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:07.952461 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:08.067412 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:08.182511 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:08.499687 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:17:08.500104 INFO: Using score_cutoff 33.29776643829346 (fac=0.99, q=1)
1 day, 3:17:08.500412 INFO: Updating optimization_manager: fwhm_rt             : 2.749605655670166 -> 2.631718635559082
1 day, 3:17:08.500497 INFO: Updating optimization_manager: fwhm_mobility       : 0.006098787300288677 -> 0.0056068613193929195
1 day, 3:17:08.500556 INFO: Updating optimization_manager: score_cutoff        : 33.69806309509278 -> 33.29776643829346
1 day, 3:17:08.500613 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:08.501642 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:08.502965 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:08.503720 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:08.505813 INFO: === checking if optimization conditions were reached ===
1 day, 3:17:08.505917 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
1 day, 3:17:08.507698 INFO: Updating optimization_manager: ms2_error           : 15.150790181198603 -> 13.983095797037157
1 day, 3:17:08.507802 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 13.9831.
1 day, 3:17:08.507872 INFO: ==============================================
1 day, 3:17:08.507944 INFO: Starting optimization step 7.
1 day, 3:17:08.508006 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:17:08.508064 INFO: Using classic extraction backend
1 day, 3:17:08.508179 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:17:08.508250 INFO: === Search parameters used ===
1 day, 3:17:08.508305 INFO: rt_error       : 2099.9331315
1 day, 3:17:08.508353 INFO: mobility_error : 0.1
1 day, 3:17:08.508401 INFO: num_candidates : 3
1 day, 3:17:08.508446 INFO: ms1_error      : 30
1 day, 3:17:08.508491 INFO: ms2_error      : 13.983095797037157
1 day, 3:17:08.508542 INFO: fwhm_rt        : 2.631718635559082
1 day, 3:17:08.508585 INFO: quant_window   : 3
1 day, 3:17:08.508630 INFO: ==============================================
1 day, 3:17:08.509447 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:17:08.509497 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:17:08.509534 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
1 day, 3:17:08.509560 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.60
1 day, 3:17:08.516003 INFO: Starting candidate selection
1 day, 3:17:17.122844 INFO: Starting candidate scoring
1 day, 3:17:17.311405 INFO: Finished candidate processing
1 day, 3:17:17.311540 INFO: Collecting candidate features
1 day, 3:17:17.324850 INFO: Collecting fragment features
1 day, 3:17:17.328657 INFO: Finished candidate scoring
1 day, 3:17:17.330412 INFO: performing precursor FDR with 47 features
1 day, 3:17:17.330457 INFO: Decoy channel: -1
1 day, 3:17:17.330484 INFO: Competetive: True
1 day, 3:17:17.333789 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:17:17.335722 INFO: Using random state 20749 for train-test-split
1 day, 3:17:17.345582 INFO: Test AUC: 0.492
1 day, 3:17:17.345640 INFO: Train AUC: 0.503
1 day, 3:17:17.345670 INFO: AUC difference: 2.30%
1 day, 3:17:17.564894 INFO: Resetting torch num_threads to 80
1 day, 3:17:17.565415 PROGRESS: === Extracted 3237 precursors and 33153 fragments ===
1 day, 3:17:17.565807 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:17:17.566366 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:17:17.566458 PROGRESS: Total precursors accumulated: 587
1 day, 3:17:17.566517 PROGRESS: Target precursors: 538 (91.65%)
1 day, 3:17:17.566567 PROGRESS: Decoy precursors: 49 (8.35%)
1 day, 3:17:17.566611 PROGRESS: 
1 day, 3:17:17.566652 PROGRESS: Precursor Summary:
1 day, 3:17:17.567645 PROGRESS: Channel   0:	 0.050 FDR:   526; 0.010 FDR:   526; 0.001 FDR:   526
1 day, 3:17:17.567735 PROGRESS: 
1 day, 3:17:17.567791 PROGRESS: Protein Summary:
1 day, 3:17:17.568994 PROGRESS: Channel   0:	 0.050 FDR:   515; 0.010 FDR:   515; 0.001 FDR:   515
1 day, 3:17:17.569096 PROGRESS: =========================================================================
1 day, 3:17:17.569223 INFO: Target number of precursors reached.
1 day, 3:17:17.575438 INFO: fragments_df: keeping 2870 of 33153 [sum(precursor_idx_mask)=15495 sum(mass_error_mask)=33153 stop_rank=2870
1 day, 3:17:17.692607 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:17.810097 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:17.924915 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:18.039975 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:18.354640 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:17:18.355055 INFO: Using score_cutoff 31.881718769073487 (fac=0.99, q=1)
1 day, 3:17:18.355359 INFO: Updating optimization_manager: fwhm_rt             : 2.631718635559082 -> 2.5770270824432373
1 day, 3:17:18.355439 INFO: Updating optimization_manager: fwhm_mobility       : 0.0056068613193929195 -> 0.0051518213003873825
1 day, 3:17:18.355493 INFO: Updating optimization_manager: score_cutoff        : 33.29776643829346 -> 31.881718769073487
1 day, 3:17:18.355544 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:18.356560 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:18.357882 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:18.358634 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:18.360751 INFO: === checking if optimization conditions were reached ===
1 day, 3:17:18.360853 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
1 day, 3:17:18.362646 INFO: Updating optimization_manager: ms2_error           : 13.983095797037157 -> 12.411939333756102
1 day, 3:17:18.362755 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 12.4119.
1 day, 3:17:18.362823 INFO: ==============================================
1 day, 3:17:18.362887 INFO: Starting optimization step 8.
1 day, 3:17:18.362944 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:17:18.363000 INFO: Using classic extraction backend
1 day, 3:17:18.363103 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:17:18.363165 INFO: === Search parameters used ===
1 day, 3:17:18.363212 INFO: rt_error       : 2099.9331315
1 day, 3:17:18.363253 INFO: mobility_error : 0.1
1 day, 3:17:18.363294 INFO: num_candidates : 3
1 day, 3:17:18.363335 INFO: ms1_error      : 30
1 day, 3:17:18.363378 INFO: ms2_error      : 12.411939333756102
1 day, 3:17:18.363418 INFO: fwhm_rt        : 2.5770270824432373
1 day, 3:17:18.363457 INFO: quant_window   : 3
1 day, 3:17:18.363497 INFO: ==============================================
1 day, 3:17:18.364333 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:17:18.364378 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:17:18.364411 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
1 day, 3:17:18.364433 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.39
1 day, 3:17:18.365071 INFO: Starting candidate selection
1 day, 3:17:57.406047 INFO: Starting candidate scoring
1 day, 3:17:57.628808 INFO: Finished candidate processing
1 day, 3:17:57.628907 INFO: Collecting candidate features
1 day, 3:17:57.641882 INFO: Collecting fragment features
1 day, 3:17:57.645928 INFO: Finished candidate scoring
1 day, 3:17:57.647582 INFO: performing precursor FDR with 47 features
1 day, 3:17:57.647626 INFO: Decoy channel: -1
1 day, 3:17:57.647651 INFO: Competetive: True
1 day, 3:17:57.651892 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:17:57.654195 INFO: Using random state 20749 for train-test-split
1 day, 3:17:57.665147 INFO: Test AUC: 0.515
1 day, 3:17:57.665204 INFO: Train AUC: 0.483
1 day, 3:17:57.665235 INFO: AUC difference: 6.50%
1 day, 3:17:57.665256 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:17:57.881917 INFO: Resetting torch num_threads to 80
1 day, 3:17:57.882503 PROGRESS: === Extracted 3231 precursors and 32831 fragments ===
1 day, 3:17:57.882959 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:17:57.883506 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:17:57.883593 PROGRESS: Total precursors accumulated: 586
1 day, 3:17:57.883650 PROGRESS: Target precursors: 534 (91.13%)
1 day, 3:17:57.883707 PROGRESS: Decoy precursors: 52 (8.87%)
1 day, 3:17:57.883753 PROGRESS: 
1 day, 3:17:57.883796 PROGRESS: Precursor Summary:
1 day, 3:17:57.884795 PROGRESS: Channel   0:	 0.050 FDR:   524; 0.010 FDR:   524; 0.001 FDR:   524
1 day, 3:17:57.884886 PROGRESS: 
1 day, 3:17:57.884952 PROGRESS: Protein Summary:
1 day, 3:17:57.886240 PROGRESS: Channel   0:	 0.050 FDR:   513; 0.010 FDR:   513; 0.001 FDR:   513
1 day, 3:17:57.886330 PROGRESS: =========================================================================
1 day, 3:17:57.886544 INFO: Target number of precursors reached.
1 day, 3:17:57.892635 INFO: fragments_df: keeping 2819 of 32831 [sum(precursor_idx_mask)=15228 sum(mass_error_mask)=32831 stop_rank=2819
1 day, 3:17:57.991691 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:58.133869 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:58.249928 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:58.368134 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:58.675429 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:17:58.675851 INFO: Using score_cutoff 31.673810989379884 (fac=0.99, q=1)
1 day, 3:17:58.676181 INFO: Updating optimization_manager: fwhm_rt             : 2.5770270824432373 -> 2.5265238285064697
1 day, 3:17:58.676261 INFO: Updating optimization_manager: fwhm_mobility       : 0.0051518213003873825 -> 0.005107354372739792
1 day, 3:17:58.676321 INFO: Updating optimization_manager: score_cutoff        : 31.881718769073487 -> 31.673810989379884
1 day, 3:17:58.676382 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:58.677419 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:58.678728 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:58.679482 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:58.681575 INFO: === checking if optimization conditions were reached ===
1 day, 3:17:58.681692 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
1 day, 3:17:58.683502 INFO: Updating optimization_manager: ms2_error           : 12.411939333756102 -> 11.427736538060342
1 day, 3:17:58.683602 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 11.4277.
1 day, 3:17:58.683666 INFO: ==============================================
1 day, 3:17:58.683737 INFO: Starting optimization step 9.
1 day, 3:17:58.683794 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:17:58.683850 INFO: Using classic extraction backend
1 day, 3:17:58.684005 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:17:58.684070 INFO: === Search parameters used ===
1 day, 3:17:58.684118 INFO: rt_error       : 2099.9331315
1 day, 3:17:58.684158 INFO: mobility_error : 0.1
1 day, 3:17:58.684199 INFO: num_candidates : 3
1 day, 3:17:58.684236 INFO: ms1_error      : 30
1 day, 3:17:58.684276 INFO: ms2_error      : 11.427736538060342
1 day, 3:17:58.684315 INFO: fwhm_rt        : 2.5265238285064697
1 day, 3:17:58.684355 INFO: quant_window   : 3
1 day, 3:17:58.684400 INFO: ==============================================
1 day, 3:17:58.685306 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:17:58.685351 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:17:58.685391 INFO: FWHM in RT is 2.53 seconds, sigma is 0.56
1 day, 3:17:58.685414 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.37
1 day, 3:17:58.686057 INFO: Starting candidate selection
1 day, 3:18:08.303611 INFO: Starting candidate scoring
1 day, 3:18:08.506847 INFO: Finished candidate processing
1 day, 3:18:08.506986 INFO: Collecting candidate features
1 day, 3:18:08.520859 INFO: Collecting fragment features
1 day, 3:18:08.525523 INFO: Finished candidate scoring
1 day, 3:18:08.527249 INFO: performing precursor FDR with 47 features
1 day, 3:18:08.527292 INFO: Decoy channel: -1
1 day, 3:18:08.527321 INFO: Competetive: True
1 day, 3:18:08.530136 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:18:08.532057 INFO: Using random state 20749 for train-test-split
1 day, 3:18:08.542202 INFO: Test AUC: 0.510
1 day, 3:18:08.542259 INFO: Train AUC: 0.492
1 day, 3:18:08.542289 INFO: AUC difference: 3.83%
1 day, 3:18:08.755176 INFO: Resetting torch num_threads to 80
1 day, 3:18:08.755686 PROGRESS: === Extracted 3231 precursors and 32488 fragments ===
1 day, 3:18:08.756097 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:18:08.756651 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:18:08.756739 PROGRESS: Total precursors accumulated: 586
1 day, 3:18:08.756798 PROGRESS: Target precursors: 536 (91.47%)
1 day, 3:18:08.756849 PROGRESS: Decoy precursors: 50 (8.53%)
1 day, 3:18:08.756895 PROGRESS: 
1 day, 3:18:08.756937 PROGRESS: Precursor Summary:
1 day, 3:18:08.757927 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   525; 0.001 FDR:   525
1 day, 3:18:08.758016 PROGRESS: 
1 day, 3:18:08.758072 PROGRESS: Protein Summary:
1 day, 3:18:08.759279 PROGRESS: Channel   0:	 0.050 FDR:   514; 0.010 FDR:   514; 0.001 FDR:   514
1 day, 3:18:08.759369 PROGRESS: =========================================================================
1 day, 3:18:08.759494 INFO: Target number of precursors reached.
1 day, 3:18:08.765459 INFO: fragments_df: keeping 2846 of 32488 [sum(precursor_idx_mask)=15081 sum(mass_error_mask)=32488 stop_rank=2846
1 day, 3:18:08.864173 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:08.978683 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:09.093668 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:09.213295 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:18:11.303388 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:18:11.303813 INFO: Using score_cutoff 30.455863851928708 (fac=0.99, q=1)
1 day, 3:18:11.304117 INFO: Updating optimization_manager: fwhm_rt             : 2.5265238285064697 -> 2.5164783000946045
1 day, 3:18:11.304197 INFO: Updating optimization_manager: fwhm_mobility       : 0.005107354372739792 -> 0.004832361824810505
1 day, 3:18:11.304252 INFO: Updating optimization_manager: score_cutoff        : 31.673810989379884 -> 30.455863851928708
1 day, 3:18:11.304301 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:11.305394 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:11.306742 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:11.307498 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:18:11.309639 INFO: === checking if optimization conditions were reached ===
1 day, 3:18:11.309744 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
1 day, 3:18:11.311568 INFO: Updating optimization_manager: ms2_error           : 11.427736538060342 -> 10.068475492419308
1 day, 3:18:11.311670 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 10.0685.
1 day, 3:18:11.311734 INFO: ==============================================
1 day, 3:18:11.311799 INFO: Starting optimization step 10.
1 day, 3:18:11.311854 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:18:11.311906 INFO: Using classic extraction backend
1 day, 3:18:11.312006 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:18:11.312078 INFO: === Search parameters used ===
1 day, 3:18:11.312125 INFO: rt_error       : 2099.9331315
1 day, 3:18:11.312167 INFO: mobility_error : 0.1
1 day, 3:18:11.312207 INFO: num_candidates : 3
1 day, 3:18:11.312245 INFO: ms1_error      : 30
1 day, 3:18:11.312283 INFO: ms2_error      : 10.068475492419308
1 day, 3:18:11.312323 INFO: fwhm_rt        : 2.5164783000946045
1 day, 3:18:11.312362 INFO: quant_window   : 3
1 day, 3:18:11.312400 INFO: ==============================================
1 day, 3:18:11.313216 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:18:11.313264 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:18:11.313299 INFO: FWHM in RT is 2.52 seconds, sigma is 0.55
1 day, 3:18:11.313323 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.24
1 day, 3:18:11.313944 INFO: Starting candidate selection
1 day, 3:18:19.854861 INFO: Starting candidate scoring
1 day, 3:18:20.025305 INFO: Finished candidate processing
1 day, 3:18:20.025411 INFO: Collecting candidate features
1 day, 3:18:20.037948 INFO: Collecting fragment features
1 day, 3:18:20.042502 INFO: Finished candidate scoring
1 day, 3:18:20.045959 INFO: performing precursor FDR with 47 features
1 day, 3:18:20.046007 INFO: Decoy channel: -1
1 day, 3:18:20.046031 INFO: Competetive: True
1 day, 3:18:20.049097 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:18:20.051168 INFO: Using random state 20749 for train-test-split
1 day, 3:18:20.061437 INFO: Test AUC: 0.504
1 day, 3:18:20.061496 INFO: Train AUC: 0.498
1 day, 3:18:20.061526 INFO: AUC difference: 1.23%
1 day, 3:18:20.276874 INFO: Resetting torch num_threads to 80
1 day, 3:18:20.277456 PROGRESS: === Extracted 3234 precursors and 32124 fragments ===
1 day, 3:18:20.277850 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:18:20.278448 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:18:20.278546 PROGRESS: Total precursors accumulated: 586
1 day, 3:18:20.278604 PROGRESS: Target precursors: 531 (90.61%)
1 day, 3:18:20.278654 PROGRESS: Decoy precursors: 55 (9.39%)
1 day, 3:18:20.278698 PROGRESS: 
1 day, 3:18:20.278742 PROGRESS: Precursor Summary:
1 day, 3:18:20.279803 PROGRESS: Channel   0:	 0.050 FDR:   519; 0.010 FDR:   519; 0.001 FDR:   519
1 day, 3:18:20.279896 PROGRESS: 
1 day, 3:18:20.279952 PROGRESS: Protein Summary:
1 day, 3:18:20.281185 PROGRESS: Channel   0:	 0.050 FDR:   509; 0.010 FDR:   509; 0.001 FDR:   509
1 day, 3:18:20.281278 PROGRESS: =========================================================================
1 day, 3:18:20.281424 INFO: Target number of precursors reached.
1 day, 3:18:20.287425 INFO: fragments_df: keeping 2757 of 32124 [sum(precursor_idx_mask)=14839 sum(mass_error_mask)=32124 stop_rank=2757
1 day, 3:18:20.386719 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:20.499214 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:20.615063 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:20.734214 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:18:21.039285 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:18:21.039709 INFO: Using score_cutoff 30.151421857452394 (fac=0.99, q=1)
1 day, 3:18:21.040015 INFO: Updating optimization_manager: fwhm_rt             : 2.5164783000946045 -> 2.4519705772399902
1 day, 3:18:21.040096 INFO: Updating optimization_manager: fwhm_mobility       : 0.004832361824810505 -> 0.004633096978068352
1 day, 3:18:21.040149 INFO: Updating optimization_manager: score_cutoff        : 30.455863851928708 -> 30.151421857452394
1 day, 3:18:21.040202 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:21.041265 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:21.042633 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:21.043411 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:18:21.045592 INFO: === checking if optimization conditions were reached ===
1 day, 3:18:21.045696 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
1 day, 3:18:21.047527 INFO: Updating optimization_manager: ms2_error           : 10.068475492419308 -> 9.711889690442028
1 day, 3:18:21.047637 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 9.7119.
1 day, 3:18:21.047702 INFO: ==============================================
1 day, 3:18:21.047764 INFO: Starting optimization step 11.
1 day, 3:18:21.047820 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:18:21.047872 INFO: Using classic extraction backend
1 day, 3:18:21.047976 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:18:21.048040 INFO: === Search parameters used ===
1 day, 3:18:21.048086 INFO: rt_error       : 2099.9331315
1 day, 3:18:21.048128 INFO: mobility_error : 0.1
1 day, 3:18:21.048168 INFO: num_candidates : 3
1 day, 3:18:21.048206 INFO: ms1_error      : 30
1 day, 3:18:57.028589 INFO: ms2_error      : 9.711889690442028
1 day, 3:18:57.028673 INFO: fwhm_rt        : 2.4519705772399902
1 day, 3:18:57.028725 INFO: quant_window   : 3
1 day, 3:18:57.028767 INFO: ==============================================
1 day, 3:18:57.030106 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:18:57.030157 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:18:57.030197 INFO: FWHM in RT is 2.45 seconds, sigma is 0.54
1 day, 3:18:57.030220 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.15
1 day, 3:18:57.030988 INFO: Starting candidate selection
1 day, 3:19:05.075126 INFO: Starting candidate scoring
1 day, 3:19:05.237390 INFO: Finished candidate processing
1 day, 3:19:05.237484 INFO: Collecting candidate features
1 day, 3:19:05.246539 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3256)
1 day, 3:19:05.249719 INFO: Collecting fragment features
1 day, 3:19:05.253358 INFO: Finished candidate scoring
1 day, 3:19:05.256092 INFO: performing precursor FDR with 47 features
1 day, 3:19:05.256139 INFO: Decoy channel: -1
1 day, 3:19:05.256163 INFO: Competetive: True
1 day, 3:19:05.259322 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:19:05.260585 WARNING: dropped 1 target PSMs due to missing features
1 day, 3:19:05.261615 INFO: Using random state 20749 for train-test-split
1 day, 3:19:05.271376 INFO: Test AUC: 0.513
1 day, 3:19:05.271434 INFO: Train AUC: 0.498
1 day, 3:19:05.271466 INFO: AUC difference: 2.87%
1 day, 3:19:05.484142 INFO: Resetting torch num_threads to 80
1 day, 3:19:05.484714 PROGRESS: === Extracted 3256 precursors and 31973 fragments ===
1 day, 3:19:05.485121 INFO: === FDR correction performed with classifier version 1 ===
1 day, 3:19:05.485708 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:19:05.485803 PROGRESS: Total precursors accumulated: 586
1 day, 3:19:05.485862 PROGRESS: Target precursors: 533 (90.96%)
1 day, 3:19:05.485911 PROGRESS: Decoy precursors: 53 (9.04%)
1 day, 3:19:05.485963 PROGRESS: 
1 day, 3:19:05.486011 PROGRESS: Precursor Summary:
1 day, 3:19:05.487053 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:   522; 0.001 FDR:   522
1 day, 3:19:05.487146 PROGRESS: 
1 day, 3:19:05.487201 PROGRESS: Protein Summary:
1 day, 3:19:05.488405 PROGRESS: Channel   0:	 0.050 FDR:   512; 0.010 FDR:   512; 0.001 FDR:   512
1 day, 3:19:05.488499 PROGRESS: =========================================================================
1 day, 3:19:05.488623 INFO: Target number of precursors reached.
1 day, 3:19:05.494514 INFO: fragments_df: keeping 2696 of 31973 [sum(precursor_idx_mask)=14845 sum(mass_error_mask)=31973 stop_rank=2696
1 day, 3:19:05.594048 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:19:05.707165 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:19:05.829658 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:19:05.948451 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:19:06.301326 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:19:06.301754 INFO: Using score_cutoff 29.45884154548645 (fac=0.99, q=1)
1 day, 3:19:06.302060 INFO: Updating optimization_manager: fwhm_rt             : 2.4519705772399902 -> 2.3596067428588867
1 day, 3:19:06.302138 INFO: Updating optimization_manager: fwhm_mobility       : 0.004633096978068352 -> 0.004369107075035572
1 day, 3:19:06.302190 INFO: Updating optimization_manager: score_cutoff        : 30.151421857452394 -> 29.45884154548645
1 day, 3:19:06.302240 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:19:06.303298 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:19:06.304641 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:19:06.305423 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:19:06.307545 INFO: === checking if optimization conditions were reached ===
1 day, 3:19:06.307646 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
1 day, 3:19:06.308315 INFO: Updating optimization_manager: ms2_error           : 9.711889690442028 -> 19.00109113653737
1 day, 3:19:06.308435 INFO: Updating optimization_manager: classifier_version  : 1 -> 4
1 day, 3:19:06.308526 INFO: Updating optimization_manager: score_cutoff        : 29.45884154548645 -> 34.262432281494135
1 day, 3:19:06.308610 INFO: Updating optimization_manager: fwhm_rt             : 2.3596067428588867 -> 2.807823657989502
1 day, 3:19:06.308690 INFO: Updating optimization_manager: fwhm_mobility       : 0.004369107075035572 -> 0.0062845926731824875
1 day, 3:19:06.308769 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 19.0011 found after 10 searches.
1 day, 3:19:06.308828 INFO: ==============================================
1 day, 3:19:06.308890 PROGRESS: Optimization finished for ms2_error.
1 day, 3:19:06.407460 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:19:06.408556 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:19:06.409909 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:19:06.410671 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:19:06.437758 INFO: Starting optimization step 0.
1 day, 3:19:06.437904 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:19:06.437986 INFO: Using classic extraction backend
1 day, 3:19:06.438094 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:19:06.438161 INFO: === Search parameters used ===
1 day, 3:19:06.438208 INFO: rt_error       : 2099.9331315
1 day, 3:19:06.438251 INFO: mobility_error : 0.1
1 day, 3:19:06.438291 INFO: num_candidates : 3
1 day, 3:19:06.438332 INFO: ms1_error      : 30
1 day, 3:19:06.438371 INFO: ms2_error      : 19.00109113653737
1 day, 3:19:06.438411 INFO: fwhm_rt        : 2.807823657989502
1 day, 3:19:06.438452 INFO: quant_window   : 3
1 day, 3:19:06.438490 INFO: ==============================================
1 day, 3:19:06.439259 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:19:06.439303 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:19:06.439337 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 3:19:06.439358 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.92
1 day, 3:19:06.440012 INFO: Starting candidate selection
1 day, 3:19:15.268641 INFO: Starting candidate scoring
1 day, 3:19:15.497015 INFO: Finished candidate processing
1 day, 3:19:15.497151 INFO: Collecting candidate features
1 day, 3:19:15.512110 INFO: Collecting fragment features
1 day, 3:19:15.516040 INFO: Finished candidate scoring
1 day, 3:19:15.518836 INFO: performing precursor FDR with 47 features
1 day, 3:19:15.518885 INFO: Decoy channel: -1
1 day, 3:19:15.518910 INFO: Competetive: True
1 day, 3:19:15.522745 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:19:15.524794 INFO: Using random state 962548 for train-test-split
1 day, 3:19:15.535116 INFO: Test AUC: 0.487
1 day, 3:19:15.535175 INFO: Train AUC: 0.491
1 day, 3:19:15.535204 INFO: AUC difference: 0.92%
1 day, 3:19:15.748037 INFO: Resetting torch num_threads to 80
1 day, 3:19:15.748597 PROGRESS: === Extracted 3240 precursors and 34369 fragments ===
1 day, 3:19:15.749008 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:19:15.749584 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:19:15.749672 PROGRESS: Total precursors accumulated: 587
1 day, 3:19:15.749735 PROGRESS: Target precursors: 535 (91.14%)
1 day, 3:19:15.749785 PROGRESS: Decoy precursors: 52 (8.86%)
1 day, 3:19:15.749829 PROGRESS: 
1 day, 3:19:15.749873 PROGRESS: Precursor Summary:
1 day, 3:19:15.750876 PROGRESS: Channel   0:	 0.050 FDR:   523; 0.010 FDR:   523; 0.001 FDR:   523
1 day, 3:19:15.750967 PROGRESS: 
1 day, 3:19:15.751029 PROGRESS: Protein Summary:
1 day, 3:19:15.752263 PROGRESS: Channel   0:	 0.050 FDR:   513; 0.010 FDR:   513; 0.001 FDR:   513
1 day, 3:19:15.752356 PROGRESS: =========================================================================
1 day, 3:19:15.752489 INFO: Target number of precursors reached.
1 day, 3:19:15.759053 INFO: fragments_df: keeping 2970 of 34369 [sum(precursor_idx_mask)=15866 sum(mass_error_mask)=34369 stop_rank=2970
1 day, 3:19:15.876055 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:19:15.995334 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:19:16.110533 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:19:16.228992 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:19:16.552067 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:19:16.552481 INFO: Using score_cutoff 34.12967536010742 (fac=0.99, q=1)
1 day, 3:19:16.552783 INFO: Updating optimization_manager: fwhm_rt             : 2.807823657989502 -> 2.8190267086029053
1 day, 3:19:16.552872 INFO: Updating optimization_manager: fwhm_mobility       : 0.0062845926731824875 -> 0.006458178628236055
1 day, 3:19:16.552928 INFO: Updating optimization_manager: score_cutoff        : 34.262432281494135 -> 34.12967536010742
1 day, 3:19:16.552991 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:19:16.554038 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:19:16.555383 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:19:16.556155 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:19:16.558231 INFO: === checking if optimization conditions were reached ===
1 day, 3:19:16.558340 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:19:16.559919 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 1363.4823322836044
1 day, 3:19:16.560020 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1363.4823.
1 day, 3:19:16.560085 INFO: ==============================================
1 day, 3:19:16.560150 INFO: Starting optimization step 1.
1 day, 3:19:16.560206 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:19:16.560260 INFO: Using classic extraction backend
1 day, 3:19:16.560361 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:19:16.560422 INFO: === Search parameters used ===
1 day, 3:19:16.560471 INFO: rt_error       : 1363.4823322836044
1 day, 3:19:16.560513 INFO: mobility_error : 0.1
1 day, 3:19:16.560555 INFO: num_candidates : 3
1 day, 3:19:16.560593 INFO: ms1_error      : 30
1 day, 3:19:16.560635 INFO: ms2_error      : 19.00109113653737
1 day, 3:19:16.560674 INFO: fwhm_rt        : 2.8190267086029053
1 day, 3:19:16.560713 INFO: quant_window   : 3
1 day, 3:19:16.560751 INFO: ==============================================
1 day, 3:19:16.561566 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:19:16.561615 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:19:16.561650 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 3:19:16.561673 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.00
1 day, 3:19:16.562319 INFO: Starting candidate selection
1 day, 3:19:57.426581 INFO: Starting candidate scoring
1 day, 3:19:57.660718 INFO: Finished candidate processing
1 day, 3:19:57.660815 INFO: Collecting candidate features
1 day, 3:19:57.673804 INFO: Collecting fragment features
1 day, 3:19:57.677429 INFO: Finished candidate scoring
1 day, 3:19:57.679785 INFO: performing precursor FDR with 47 features
1 day, 3:19:57.679833 INFO: Decoy channel: -1
1 day, 3:19:57.679859 INFO: Competetive: True
1 day, 3:19:57.682970 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:19:57.685003 INFO: Using random state 962548 for train-test-split
1 day, 3:19:57.695096 INFO: Test AUC: 0.484
1 day, 3:19:57.695154 INFO: Train AUC: 0.494
1 day, 3:19:57.695184 INFO: AUC difference: 2.15%
1 day, 3:19:57.912049 INFO: Resetting torch num_threads to 80
1 day, 3:19:57.912652 PROGRESS: === Extracted 3226 precursors and 34221 fragments ===
1 day, 3:19:57.913063 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:19:57.913621 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:19:57.913723 PROGRESS: Total precursors accumulated: 587
1 day, 3:19:57.913781 PROGRESS: Target precursors: 535 (91.14%)
1 day, 3:19:57.913829 PROGRESS: Decoy precursors: 52 (8.86%)
1 day, 3:19:57.913874 PROGRESS: 
1 day, 3:19:57.913918 PROGRESS: Precursor Summary:
1 day, 3:19:57.914922 PROGRESS: Channel   0:	 0.050 FDR:   521; 0.010 FDR:   521; 0.001 FDR:   521
1 day, 3:19:57.915014 PROGRESS: 
1 day, 3:19:57.915069 PROGRESS: Protein Summary:
1 day, 3:19:57.916269 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   511; 0.001 FDR:   511
1 day, 3:19:57.916362 PROGRESS: =========================================================================
1 day, 3:19:57.916502 INFO: Target number of precursors reached.
1 day, 3:19:57.922834 INFO: fragments_df: keeping 2997 of 34221 [sum(precursor_idx_mask)=15863 sum(mass_error_mask)=34221 stop_rank=2997
1 day, 3:19:58.024010 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:19:58.159124 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:19:58.271297 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:19:58.390171 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:19:58.717620 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:19:58.718030 INFO: Using score_cutoff 33.77381842803955 (fac=0.99, q=1)
1 day, 3:19:58.718336 INFO: Updating optimization_manager: fwhm_rt             : 2.8190267086029053 -> 2.815311908721924
1 day, 3:19:58.718416 INFO: Updating optimization_manager: fwhm_mobility       : 0.006458178628236055 -> 0.006444400176405907
1 day, 3:19:58.718482 INFO: Updating optimization_manager: score_cutoff        : 34.12967536010742 -> 33.77381842803955
1 day, 3:19:58.718537 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:19:58.719575 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:19:58.720918 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:19:58.721698 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:19:58.723777 INFO: === checking if optimization conditions were reached ===
1 day, 3:19:58.723877 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:19:58.725570 INFO: Updating optimization_manager: rt_error            : 1363.4823322836044 -> 906.6618163562267
1 day, 3:19:58.725670 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 906.6618.
1 day, 3:19:58.725736 INFO: ==============================================
1 day, 3:19:58.725799 INFO: Starting optimization step 2.
1 day, 3:19:58.725856 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:19:58.725907 INFO: Using classic extraction backend
1 day, 3:19:58.726011 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:19:58.726072 INFO: === Search parameters used ===
1 day, 3:19:58.726117 INFO: rt_error       : 906.6618163562267
1 day, 3:19:58.726158 INFO: mobility_error : 0.1
1 day, 3:19:58.726197 INFO: num_candidates : 3
1 day, 3:19:58.726236 INFO: ms1_error      : 30
1 day, 3:19:58.726275 INFO: ms2_error      : 19.00109113653737
1 day, 3:19:58.726320 INFO: fwhm_rt        : 2.815311908721924
1 day, 3:19:58.726362 INFO: quant_window   : 3
1 day, 3:19:58.726400 INFO: ==============================================
1 day, 3:19:58.727247 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:19:58.727290 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:19:58.727324 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 3:19:58.727346 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.99
1 day, 3:19:58.728012 INFO: Starting candidate selection
1 day, 3:20:03.217216 INFO: Starting candidate scoring
1 day, 3:20:03.451958 INFO: Finished candidate processing
1 day, 3:20:03.452090 INFO: Collecting candidate features
1 day, 3:20:03.466002 INFO: Collecting fragment features
1 day, 3:20:03.474246 INFO: Finished candidate scoring
1 day, 3:20:03.477777 INFO: performing precursor FDR with 47 features
1 day, 3:20:03.477914 INFO: Decoy channel: -1
1 day, 3:20:03.477943 INFO: Competetive: True
1 day, 3:20:03.481812 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:20:03.484319 INFO: Using random state 962548 for train-test-split
1 day, 3:20:03.495402 INFO: Test AUC: 0.484
1 day, 3:20:03.495474 INFO: Train AUC: 0.498
1 day, 3:20:03.495503 INFO: AUC difference: 2.65%
1 day, 3:20:03.711581 INFO: Resetting torch num_threads to 80
1 day, 3:20:03.712190 PROGRESS: === Extracted 3226 precursors and 34220 fragments ===
1 day, 3:20:03.712596 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:20:03.713196 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:20:03.713289 PROGRESS: Total precursors accumulated: 587
1 day, 3:20:03.713350 PROGRESS: Target precursors: 538 (91.65%)
1 day, 3:20:03.713402 PROGRESS: Decoy precursors: 49 (8.35%)
1 day, 3:20:03.713452 PROGRESS: 
1 day, 3:20:03.713496 PROGRESS: Precursor Summary:
1 day, 3:20:03.714538 PROGRESS: Channel   0:	 0.050 FDR:   524; 0.010 FDR:   524; 0.001 FDR:   524
1 day, 3:20:03.714632 PROGRESS: 
1 day, 3:20:03.714687 PROGRESS: Protein Summary:
1 day, 3:20:03.715901 PROGRESS: Channel   0:	 0.050 FDR:   514; 0.010 FDR:   514; 0.001 FDR:   514
1 day, 3:20:03.715997 PROGRESS: =========================================================================
1 day, 3:20:03.716244 INFO: Target number of precursors reached.
1 day, 3:20:03.722521 INFO: fragments_df: keeping 3011 of 34220 [sum(precursor_idx_mask)=16006 sum(mass_error_mask)=34220 stop_rank=3011
1 day, 3:20:03.824892 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:03.946864 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:04.064302 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:04.186637 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:04.526304 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:20:04.526736 INFO: Using score_cutoff 33.95819894142151 (fac=0.99, q=1)
1 day, 3:20:04.527056 INFO: Updating optimization_manager: fwhm_rt             : 2.815311908721924 -> 2.823535680770874
1 day, 3:20:04.527139 INFO: Updating optimization_manager: fwhm_mobility       : 0.006444400176405907 -> 0.006316567305475473
1 day, 3:20:04.527193 INFO: Updating optimization_manager: score_cutoff        : 33.77381842803955 -> 33.95819894142151
1 day, 3:20:04.527248 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:04.528317 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:04.529683 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:04.530458 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:04.532569 INFO: === checking if optimization conditions were reached ===
1 day, 3:20:04.532673 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:20:04.534496 INFO: Updating optimization_manager: rt_error            : 906.6618163562267 -> 825.5910466043107
1 day, 3:20:04.534599 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 825.5910.
1 day, 3:20:04.534662 INFO: ==============================================
1 day, 3:20:04.534725 INFO: Starting optimization step 3.
1 day, 3:20:04.534787 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:20:04.534842 INFO: Using classic extraction backend
1 day, 3:20:04.534957 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:20:04.535021 INFO: === Search parameters used ===
1 day, 3:20:04.535068 INFO: rt_error       : 825.5910466043107
1 day, 3:20:04.535112 INFO: mobility_error : 0.1
1 day, 3:20:04.535151 INFO: num_candidates : 3
1 day, 3:20:04.535190 INFO: ms1_error      : 30
1 day, 3:20:04.535230 INFO: ms2_error      : 19.00109113653737
1 day, 3:20:04.535267 INFO: fwhm_rt        : 2.823535680770874
1 day, 3:20:04.535304 INFO: quant_window   : 3
1 day, 3:20:04.535341 INFO: ==============================================
1 day, 3:20:04.536390 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:20:04.536433 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:20:04.536466 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 3:20:04.536487 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.93
1 day, 3:20:04.537395 INFO: Starting candidate selection
1 day, 3:20:08.762963 INFO: Starting candidate scoring
1 day, 3:20:08.997331 INFO: Finished candidate processing
1 day, 3:20:08.997582 INFO: Collecting candidate features
1 day, 3:20:09.030180 INFO: Collecting fragment features
1 day, 3:20:09.041646 INFO: Finished candidate scoring
1 day, 3:20:09.046678 INFO: performing precursor FDR with 47 features
1 day, 3:20:09.046787 INFO: Decoy channel: -1
1 day, 3:20:09.046844 INFO: Competetive: True
1 day, 3:20:09.059894 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:20:09.065580 INFO: Using random state 962548 for train-test-split
1 day, 3:20:09.085168 INFO: Test AUC: 0.505
1 day, 3:20:09.085261 INFO: Train AUC: 0.496
1 day, 3:20:09.085297 INFO: AUC difference: 1.78%
1 day, 3:20:09.336851 INFO: Resetting torch num_threads to 80
1 day, 3:20:09.337754 PROGRESS: === Extracted 3222 precursors and 34192 fragments ===
1 day, 3:20:09.338435 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:20:09.339115 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:20:09.339206 PROGRESS: Total precursors accumulated: 587
1 day, 3:20:09.339272 PROGRESS: Target precursors: 534 (90.97%)
1 day, 3:20:09.339328 PROGRESS: Decoy precursors: 53 (9.03%)
1 day, 3:20:09.339375 PROGRESS: 
1 day, 3:20:09.339418 PROGRESS: Precursor Summary:
1 day, 3:20:09.340503 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:   522; 0.001 FDR:   522
1 day, 3:20:09.340594 PROGRESS: 
1 day, 3:20:09.340649 PROGRESS: Protein Summary:
1 day, 3:20:09.342060 PROGRESS: Channel   0:	 0.050 FDR:   512; 0.010 FDR:   512; 0.001 FDR:   512
1 day, 3:20:09.342166 PROGRESS: =========================================================================
1 day, 3:20:09.342540 INFO: Target number of precursors reached.
1 day, 3:20:09.349559 INFO: fragments_df: keeping 2941 of 34192 [sum(precursor_idx_mask)=15978 sum(mass_error_mask)=34192 stop_rank=2941
1 day, 3:20:09.453683 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:09.588734 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:09.714689 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:09.839194 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:10.171427 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:20:10.171958 INFO: Using score_cutoff 34.15852212409973 (fac=0.99, q=1)
1 day, 3:20:10.172350 INFO: Updating optimization_manager: fwhm_rt             : 2.823535680770874 -> 2.7887887954711914
1 day, 3:20:10.172430 INFO: Updating optimization_manager: fwhm_mobility       : 0.006316567305475473 -> 0.006267342250794172
1 day, 3:20:10.172483 INFO: Updating optimization_manager: score_cutoff        : 33.95819894142151 -> 34.15852212409973
1 day, 3:20:10.172549 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:10.173872 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:10.175254 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:10.176032 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:10.178211 INFO: === checking if optimization conditions were reached ===
1 day, 3:20:10.178354 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 3:20:10.180358 INFO: Updating optimization_manager: rt_error            : 825.5910466043107 -> 789.4513662798012
1 day, 3:20:10.180471 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 789.4514.
1 day, 3:20:10.180536 INFO: ==============================================
1 day, 3:20:10.180622 INFO: Starting optimization step 4.
1 day, 3:20:10.180684 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:20:10.180752 INFO: Using classic extraction backend
1 day, 3:20:10.181072 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:20:10.181154 INFO: === Search parameters used ===
1 day, 3:20:10.181205 INFO: rt_error       : 789.4513662798012
1 day, 3:20:10.181248 INFO: mobility_error : 0.1
1 day, 3:20:10.181288 INFO: num_candidates : 3
1 day, 3:20:10.181328 INFO: ms1_error      : 30
1 day, 3:20:10.181369 INFO: ms2_error      : 19.00109113653737
1 day, 3:20:10.181430 INFO: fwhm_rt        : 2.7887887954711914
1 day, 3:20:10.181473 INFO: quant_window   : 3
1 day, 3:20:10.181513 INFO: ==============================================
1 day, 3:20:10.182694 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:20:10.182742 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:20:10.182792 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 3:20:10.182817 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.91
1 day, 3:20:10.183566 INFO: Starting candidate selection
1 day, 3:20:14.868478 INFO: Starting candidate scoring
1 day, 3:20:15.114016 INFO: Finished candidate processing
1 day, 3:20:15.114112 INFO: Collecting candidate features
1 day, 3:20:15.126868 INFO: Collecting fragment features
1 day, 3:20:15.130494 INFO: Finished candidate scoring
1 day, 3:20:15.132420 INFO: performing precursor FDR with 47 features
1 day, 3:20:15.132467 INFO: Decoy channel: -1
1 day, 3:20:15.132493 INFO: Competetive: True
1 day, 3:20:15.135428 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:20:15.137429 INFO: Using random state 962548 for train-test-split
1 day, 3:20:15.147369 INFO: Test AUC: 0.498
1 day, 3:20:15.147427 INFO: Train AUC: 0.497
1 day, 3:20:15.147457 INFO: AUC difference: 0.22%
1 day, 3:20:15.365807 INFO: Resetting torch num_threads to 80
1 day, 3:20:15.366385 PROGRESS: === Extracted 3225 precursors and 34210 fragments ===
1 day, 3:20:15.366800 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:20:15.367361 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:20:15.367449 PROGRESS: Total precursors accumulated: 587
1 day, 3:20:15.367509 PROGRESS: Target precursors: 541 (92.16%)
1 day, 3:20:15.367568 PROGRESS: Decoy precursors: 46 (7.84%)
1 day, 3:20:15.367617 PROGRESS: 
1 day, 3:20:15.367661 PROGRESS: Precursor Summary:
1 day, 3:20:15.368712 PROGRESS: Channel   0:	 0.050 FDR:   528; 0.010 FDR:   528; 0.001 FDR:   528
1 day, 3:20:15.368805 PROGRESS: 
1 day, 3:20:15.368862 PROGRESS: Protein Summary:
1 day, 3:20:15.370092 PROGRESS: Channel   0:	 0.050 FDR:   518; 0.010 FDR:   518; 0.001 FDR:   518
1 day, 3:20:15.370188 PROGRESS: =========================================================================
1 day, 3:20:15.370336 INFO: Target number of precursors reached.
1 day, 3:20:15.376730 INFO: fragments_df: keeping 2987 of 34210 [sum(precursor_idx_mask)=16093 sum(mass_error_mask)=34210 stop_rank=2987
1 day, 3:20:15.475399 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:15.622860 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:15.765124 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:15.908435 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:16.300544 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:20:16.300987 INFO: Using score_cutoff 33.57827250595093 (fac=0.99, q=1)
1 day, 3:20:16.301298 INFO: Updating optimization_manager: fwhm_rt             : 2.7887887954711914 -> 2.8087069988250732
1 day, 3:20:16.301378 INFO: Updating optimization_manager: fwhm_mobility       : 0.006267342250794172 -> 0.006294857710599899
1 day, 3:20:16.301431 INFO: Updating optimization_manager: score_cutoff        : 34.15852212409973 -> 33.57827250595093
1 day, 3:20:16.301489 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:16.302527 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:16.303864 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:16.304623 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:16.306669 INFO: === checking if optimization conditions were reached ===
1 day, 3:20:16.306778 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 3:20:16.307750 INFO: Updating optimization_manager: rt_error            : 789.4513662798012 -> 789.4513662798012
1 day, 3:20:16.307878 INFO: Updating optimization_manager: classifier_version  : 4 -> 16
1 day, 3:20:16.307972 INFO: Updating optimization_manager: score_cutoff        : 33.57827250595093 -> 33.57827250595093
1 day, 3:20:16.308056 INFO: Updating optimization_manager: fwhm_rt             : 2.8087069988250732 -> 2.8087069988250732
1 day, 3:20:16.308138 INFO: Updating optimization_manager: fwhm_mobility       : 0.006294857710599899 -> 0.006294857710599899
1 day, 3:20:16.308219 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 789.4514 found after 5 searches.
1 day, 3:20:16.308279 INFO: ==============================================
1 day, 3:20:16.308343 PROGRESS: Optimization finished for rt_error.
1 day, 3:20:16.407060 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:16.408170 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:16.409514 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:16.410270 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:16.439135 INFO: Starting optimization step 0.
1 day, 3:20:16.439286 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:20:16.439358 INFO: Using classic extraction backend
1 day, 3:20:16.439476 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:20:16.439548 INFO: === Search parameters used ===
1 day, 3:20:16.439596 INFO: rt_error       : 789.4513662798012
1 day, 3:20:16.439642 INFO: mobility_error : 0.1
1 day, 3:20:16.439685 INFO: num_candidates : 3
1 day, 3:20:16.439726 INFO: ms1_error      : 30
1 day, 3:20:16.439765 INFO: ms2_error      : 19.00109113653737
1 day, 3:20:16.439807 INFO: fwhm_rt        : 2.8087069988250732
1 day, 3:20:16.439847 INFO: quant_window   : 3
1 day, 3:20:16.439886 INFO: ==============================================
1 day, 3:20:16.440636 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:20:16.440682 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:20:16.440716 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 3:20:16.440737 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.92
1 day, 3:20:16.441370 INFO: Starting candidate selection
1 day, 3:20:26.084131 INFO: Starting candidate scoring
1 day, 3:20:26.338820 INFO: Finished candidate processing
1 day, 3:20:26.338921 INFO: Collecting candidate features
1 day, 3:20:26.352047 INFO: Collecting fragment features
1 day, 3:20:26.355609 INFO: Finished candidate scoring
1 day, 3:20:26.357430 INFO: performing precursor FDR with 47 features
1 day, 3:20:26.357477 INFO: Decoy channel: -1
1 day, 3:20:26.357501 INFO: Competetive: True
1 day, 3:20:26.360322 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:20:26.362293 INFO: Using random state 366794 for train-test-split
1 day, 3:20:26.371718 INFO: Test AUC: 0.506
1 day, 3:20:26.371775 INFO: Train AUC: 0.496
1 day, 3:20:26.371805 INFO: AUC difference: 2.01%
1 day, 3:20:26.589128 INFO: Resetting torch num_threads to 80
1 day, 3:20:26.589690 PROGRESS: === Extracted 3224 precursors and 34211 fragments ===
1 day, 3:20:26.590098 INFO: === FDR correction performed with classifier version 16 ===
1 day, 3:20:26.590657 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:20:26.590747 PROGRESS: Total precursors accumulated: 587
1 day, 3:20:26.590804 PROGRESS: Target precursors: 537 (91.48%)
1 day, 3:20:26.590855 PROGRESS: Decoy precursors: 50 (8.52%)
1 day, 3:20:26.590901 PROGRESS: 
1 day, 3:20:26.590945 PROGRESS: Precursor Summary:
1 day, 3:20:26.591956 PROGRESS: Channel   0:	 0.050 FDR:   526; 0.010 FDR:   526; 0.001 FDR:   526
1 day, 3:20:26.592055 PROGRESS: 
1 day, 3:20:26.592111 PROGRESS: Protein Summary:
1 day, 3:20:26.593344 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   516; 0.001 FDR:   516
1 day, 3:20:26.593437 PROGRESS: =========================================================================
1 day, 3:20:26.593578 INFO: Target number of precursors reached.
1 day, 3:20:26.599907 INFO: fragments_df: keeping 2943 of 34211 [sum(precursor_idx_mask)=16037 sum(mass_error_mask)=34211 stop_rank=2943
1 day, 3:20:26.698523 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:26.844389 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:26.986305 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:27.128124 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:27.518524 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:20:27.518949 INFO: Using score_cutoff 33.56067106246948 (fac=0.99, q=1)
1 day, 3:20:27.519257 INFO: Updating optimization_manager: fwhm_rt             : 2.8087069988250732 -> 2.823286533355713
1 day, 3:20:27.519338 INFO: Updating optimization_manager: fwhm_mobility       : 0.006294857710599899 -> 0.006324484013020992
1 day, 3:20:27.519391 INFO: Updating optimization_manager: score_cutoff        : 33.57827250595093 -> 33.56067106246948
1 day, 3:20:27.519442 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:27.520468 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:27.521812 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:27.522574 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:27.524691 INFO: === checking if optimization conditions were reached ===
1 day, 3:20:27.524799 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:20:27.526223 INFO: Updating optimization_manager: ms1_error           : 30 -> 18.167462017469568
1 day, 3:20:27.526325 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 18.1675.
1 day, 3:20:27.526389 INFO: ==============================================
1 day, 3:20:27.526455 INFO: Starting optimization step 1.
1 day, 3:20:27.526513 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:20:27.526566 INFO: Using classic extraction backend
1 day, 3:20:27.526675 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:20:27.526739 INFO: === Search parameters used ===
1 day, 3:20:27.526787 INFO: rt_error       : 789.4513662798012
1 day, 3:20:27.526831 INFO: mobility_error : 0.1
1 day, 3:20:27.526871 INFO: num_candidates : 3
1 day, 3:20:27.526910 INFO: ms1_error      : 18.167462017469568
1 day, 3:20:27.526950 INFO: ms2_error      : 19.00109113653737
1 day, 3:20:27.526989 INFO: fwhm_rt        : 2.823286533355713
1 day, 3:20:27.527028 INFO: quant_window   : 3
1 day, 3:20:27.527071 INFO: ==============================================
1 day, 3:20:27.527849 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:20:27.527894 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:20:27.527929 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 3:20:27.527952 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.93
1 day, 3:20:27.528608 INFO: Starting candidate selection
1 day, 3:20:31.593572 INFO: Starting candidate scoring
1 day, 3:20:31.835142 INFO: Finished candidate processing
1 day, 3:20:31.835237 INFO: Collecting candidate features
1 day, 3:20:31.847543 INFO: Collecting fragment features
1 day, 3:20:31.850994 INFO: Finished candidate scoring
1 day, 3:20:31.852778 INFO: performing precursor FDR with 47 features
1 day, 3:20:31.852823 INFO: Decoy channel: -1
1 day, 3:20:31.852847 INFO: Competetive: True
1 day, 3:20:31.855919 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:20:31.857922 INFO: Using random state 366794 for train-test-split
1 day, 3:20:31.867749 INFO: Test AUC: 0.489
1 day, 3:20:31.867807 INFO: Train AUC: 0.508
1 day, 3:20:31.867837 INFO: AUC difference: 3.66%
1 day, 3:20:32.084740 INFO: Resetting torch num_threads to 80
1 day, 3:20:32.085307 PROGRESS: === Extracted 3240 precursors and 34265 fragments ===
1 day, 3:20:32.085714 INFO: === FDR correction performed with classifier version 16 ===
1 day, 3:20:32.086284 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:20:32.086380 PROGRESS: Total precursors accumulated: 588
1 day, 3:20:32.086438 PROGRESS: Target precursors: 514 (87.41%)
1 day, 3:20:32.086489 PROGRESS: Decoy precursors: 74 (12.59%)
1 day, 3:20:32.086534 PROGRESS: 
1 day, 3:20:32.086579 PROGRESS: Precursor Summary:
1 day, 3:20:32.087568 PROGRESS: Channel   0:	 0.050 FDR:   490; 0.010 FDR:   490; 0.001 FDR:   490
1 day, 3:20:32.087658 PROGRESS: 
1 day, 3:20:32.087714 PROGRESS: Protein Summary:
1 day, 3:20:32.088894 PROGRESS: Channel   0:	 0.050 FDR:   480; 0.010 FDR:   480; 0.001 FDR:   480
1 day, 3:20:32.088997 PROGRESS: =========================================================================
1 day, 3:20:32.089152 INFO: Target number of precursors reached.
1 day, 3:20:32.095429 INFO: fragments_df: keeping 2705 of 34265 [sum(precursor_idx_mask)=15010 sum(mass_error_mask)=34265 stop_rank=2705
1 day, 3:20:32.195078 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:32.329818 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:32.468228 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:32.606704 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:32.961757 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:20:32.962178 INFO: Using score_cutoff 32.46078379669189 (fac=0.99, q=1)
1 day, 3:20:32.962481 INFO: Updating optimization_manager: fwhm_rt             : 2.823286533355713 -> 2.7674288749694824
1 day, 3:20:32.962570 INFO: Updating optimization_manager: fwhm_mobility       : 0.006324484013020992 -> 0.006125140003859997
1 day, 3:20:32.962625 INFO: Updating optimization_manager: score_cutoff        : 33.56067106246948 -> 32.46078379669189
1 day, 3:20:32.962677 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:32.963699 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:32.965026 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:32.965785 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:32.967854 INFO: === checking if optimization conditions were reached ===
1 day, 3:20:32.967955 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:20:32.969543 INFO: Updating optimization_manager: ms1_error           : 18.167462017469568 -> 11.397324983085603
1 day, 3:20:32.969644 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 11.3973.
1 day, 3:20:32.969707 INFO: ==============================================
1 day, 3:20:32.969773 INFO: Starting optimization step 2.
1 day, 3:20:32.969831 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:20:32.969886 INFO: Using classic extraction backend
1 day, 3:20:32.969995 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:20:32.970059 INFO: === Search parameters used ===
1 day, 3:20:32.970104 INFO: rt_error       : 789.4513662798012
1 day, 3:20:32.970148 INFO: mobility_error : 0.1
1 day, 3:20:32.970189 INFO: num_candidates : 3
1 day, 3:20:32.970228 INFO: ms1_error      : 11.397324983085603
1 day, 3:20:32.970274 INFO: ms2_error      : 19.00109113653737
1 day, 3:20:32.970316 INFO: fwhm_rt        : 2.7674288749694824
1 day, 3:20:32.970354 INFO: quant_window   : 3
1 day, 3:20:32.970392 INFO: ==============================================
1 day, 3:20:32.971160 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:20:32.971203 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:20:32.971236 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 3:20:32.971256 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.84
1 day, 3:20:32.971883 INFO: Starting candidate selection
1 day, 3:20:37.390895 INFO: Starting candidate scoring
1 day, 3:20:37.595929 INFO: Finished candidate processing
1 day, 3:20:37.596025 INFO: Collecting candidate features
1 day, 3:20:37.610638 INFO: Collecting fragment features
1 day, 3:20:37.615134 INFO: Finished candidate scoring
1 day, 3:20:37.617553 INFO: performing precursor FDR with 47 features
1 day, 3:20:37.617601 INFO: Decoy channel: -1
1 day, 3:20:37.617629 INFO: Competetive: True
1 day, 3:20:37.620911 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:20:37.623070 INFO: Using random state 366794 for train-test-split
1 day, 3:20:37.635428 INFO: Test AUC: 0.497
1 day, 3:20:37.635496 INFO: Train AUC: 0.494
1 day, 3:20:37.635526 INFO: AUC difference: 0.63%
1 day, 3:20:37.854435 INFO: Resetting torch num_threads to 80
1 day, 3:20:37.855188 PROGRESS: === Extracted 3257 precursors and 34321 fragments ===
1 day, 3:20:37.855694 INFO: === FDR correction performed with classifier version 16 ===
1 day, 3:20:37.856340 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:20:37.856432 PROGRESS: Total precursors accumulated: 589
1 day, 3:20:37.856492 PROGRESS: Target precursors: 475 (80.65%)
1 day, 3:20:37.856540 PROGRESS: Decoy precursors: 114 (19.35%)
1 day, 3:20:37.856586 PROGRESS: 
1 day, 3:20:37.856630 PROGRESS: Precursor Summary:
1 day, 3:20:37.857659 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   430; 0.001 FDR:   430
1 day, 3:20:37.857752 PROGRESS: 
1 day, 3:20:37.857808 PROGRESS: Protein Summary:
1 day, 3:20:37.859001 PROGRESS: Channel   0:	 0.050 FDR:   423; 0.010 FDR:   423; 0.001 FDR:   423
1 day, 3:20:37.859093 PROGRESS: =========================================================================
1 day, 3:20:37.859261 INFO: Target number of precursors reached.
1 day, 3:20:37.865678 INFO: fragments_df: keeping 2372 of 34321 [sum(precursor_idx_mask)=13052 sum(mass_error_mask)=34321 stop_rank=2372
1 day, 3:20:38.139423 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:38.254862 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:38.369987 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:38.486059 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:38.747361 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:20:38.747879 INFO: Using score_cutoff 30.221431093597413 (fac=0.99, q=1)
1 day, 3:20:38.748213 INFO: Updating optimization_manager: fwhm_rt             : 2.7674288749694824 -> 2.8675951957702637
1 day, 3:20:38.748292 INFO: Updating optimization_manager: fwhm_mobility       : 0.006125140003859997 -> 0.0063261911273002625
1 day, 3:20:38.748345 INFO: Updating optimization_manager: score_cutoff        : 32.46078379669189 -> 30.221431093597413
1 day, 3:20:38.748397 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:38.749668 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:38.751017 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:38.751777 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:38.753943 INFO: === checking if optimization conditions were reached ===
1 day, 3:20:38.754048 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:20:38.755704 INFO: Updating optimization_manager: ms1_error           : 11.397324983085603 -> 6.480397909394132
1 day, 3:20:38.755804 PROGRESS: ❌ ms1_error      : optimization incomplete after 3 search(es). Will search with parameter 6.4804.
1 day, 3:20:38.755868 INFO: ==============================================
1 day, 3:20:38.755934 INFO: Starting optimization step 3.
1 day, 3:20:38.755992 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:20:38.756056 INFO: Using classic extraction backend
1 day, 3:20:38.756181 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:20:38.756244 INFO: === Search parameters used ===
1 day, 3:20:38.756292 INFO: rt_error       : 789.4513662798012
1 day, 3:20:38.756333 INFO: mobility_error : 0.1
1 day, 3:20:38.756374 INFO: num_candidates : 3
1 day, 3:20:38.756413 INFO: ms1_error      : 6.480397909394132
1 day, 3:20:38.756451 INFO: ms2_error      : 19.00109113653737
1 day, 3:20:38.756497 INFO: fwhm_rt        : 2.8675951957702637
1 day, 3:20:38.756536 INFO: quant_window   : 3
1 day, 3:20:38.756575 INFO: ==============================================
1 day, 3:20:38.757515 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:20:38.757563 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:20:38.757600 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:20:38.757623 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.93
1 day, 3:20:38.758284 INFO: Starting candidate selection
1 day, 3:20:43.006485 INFO: Starting candidate scoring
1 day, 3:20:43.209684 INFO: Finished candidate processing
1 day, 3:20:43.209815 INFO: Collecting candidate features
1 day, 3:20:43.223571 INFO: Collecting fragment features
1 day, 3:20:43.227298 INFO: Finished candidate scoring
1 day, 3:20:43.229534 INFO: performing precursor FDR with 47 features
1 day, 3:20:43.229592 INFO: Decoy channel: -1
1 day, 3:20:43.229617 INFO: Competetive: True
1 day, 3:20:43.233170 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:20:43.235183 INFO: Using random state 366794 for train-test-split
1 day, 3:20:43.245914 INFO: Test AUC: 0.531
1 day, 3:20:43.245974 INFO: Train AUC: 0.503
1 day, 3:20:43.246006 INFO: AUC difference: 5.48%
1 day, 3:20:43.246029 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:20:43.465074 INFO: Resetting torch num_threads to 80
1 day, 3:20:43.465635 PROGRESS: === Extracted 3238 precursors and 33999 fragments ===
1 day, 3:20:43.466042 INFO: === FDR correction performed with classifier version 16 ===
1 day, 3:20:43.466607 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:20:43.466702 PROGRESS: Total precursors accumulated: 589
1 day, 3:20:43.466762 PROGRESS: Target precursors: 444 (75.38%)
1 day, 3:20:43.466813 PROGRESS: Decoy precursors: 145 (24.62%)
1 day, 3:20:43.466858 PROGRESS: 
1 day, 3:20:43.466903 PROGRESS: Precursor Summary:
1 day, 3:20:43.467851 PROGRESS: Channel   0:	 0.050 FDR:   370; 0.010 FDR:   370; 0.001 FDR:   370
1 day, 3:20:43.467940 PROGRESS: 
1 day, 3:20:43.468001 PROGRESS: Protein Summary:
1 day, 3:20:43.469152 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   365; 0.001 FDR:   365
1 day, 3:20:43.469244 PROGRESS: =========================================================================
1 day, 3:20:43.469388 INFO: Target number of precursors reached.
1 day, 3:20:43.474674 INFO: fragments_df: keeping 2054 of 33999 [sum(precursor_idx_mask)=11068 sum(mass_error_mask)=33998 stop_rank=2054
1 day, 3:20:43.574425 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:43.702711 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:43.832243 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:43.961304 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:44.232215 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:20:44.232639 INFO: Using score_cutoff 28.73697842903137 (fac=0.99, q=1)
1 day, 3:20:44.232939 INFO: Updating optimization_manager: fwhm_rt             : 2.8675951957702637 -> 2.818246841430664
1 day, 3:20:44.233032 INFO: Updating optimization_manager: fwhm_mobility       : 0.0063261911273002625 -> 0.0064054518006742
1 day, 3:20:44.233086 INFO: Updating optimization_manager: score_cutoff        : 30.221431093597413 -> 28.73697842903137
1 day, 3:20:44.233139 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:44.234169 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:44.235475 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:44.236231 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:44.238323 INFO: === checking if optimization conditions were reached ===
1 day, 3:20:44.238435 PROGRESS: === Optimization of ms1_error has been performed 4 time(s); minimum number is 2 ===
1 day, 3:20:44.240283 INFO: Updating optimization_manager: ms1_error           : 6.480397909394132 -> 2.9984193949036255
1 day, 3:20:44.240383 PROGRESS: ❌ ms1_error      : optimization incomplete after 4 search(es). Will search with parameter 2.9984.
1 day, 3:20:44.240447 INFO: ==============================================
1 day, 3:20:44.240515 INFO: Starting optimization step 4.
1 day, 3:20:44.240573 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:20:44.240626 INFO: Using classic extraction backend
1 day, 3:20:44.240734 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:20:44.240798 INFO: === Search parameters used ===
1 day, 3:20:44.240844 INFO: rt_error       : 789.4513662798012
1 day, 3:20:44.240884 INFO: mobility_error : 0.1
1 day, 3:20:44.240924 INFO: num_candidates : 3
1 day, 3:20:44.240988 INFO: ms1_error      : 2.9984193949036255
1 day, 3:20:44.241031 INFO: ms2_error      : 19.00109113653737
1 day, 3:20:44.241072 INFO: fwhm_rt        : 2.818246841430664
1 day, 3:20:44.241112 INFO: quant_window   : 3
1 day, 3:20:44.241155 INFO: ==============================================
1 day, 3:20:44.241925 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:20:44.241968 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:20:44.242001 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 3:20:44.242024 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.97
1 day, 3:20:44.247745 INFO: Starting candidate selection
1 day, 3:20:48.422044 INFO: Starting candidate scoring
1 day, 3:20:48.647991 INFO: Finished candidate processing
1 day, 3:20:48.648130 INFO: Collecting candidate features
1 day, 3:20:48.660698 INFO: Collecting fragment features
1 day, 3:20:48.664959 INFO: Finished candidate scoring
1 day, 3:20:48.666729 INFO: performing precursor FDR with 47 features
1 day, 3:20:48.666772 INFO: Decoy channel: -1
1 day, 3:20:48.666796 INFO: Competetive: True
1 day, 3:20:48.669608 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:20:48.671606 INFO: Using random state 366794 for train-test-split
1 day, 3:20:48.681936 INFO: Test AUC: 0.480
1 day, 3:20:48.681992 INFO: Train AUC: 0.497
1 day, 3:20:48.682021 INFO: AUC difference: 3.42%
1 day, 3:20:48.896826 INFO: Resetting torch num_threads to 80
1 day, 3:20:48.897374 PROGRESS: === Extracted 3263 precursors and 34191 fragments ===
1 day, 3:20:48.897782 INFO: === FDR correction performed with classifier version 16 ===
1 day, 3:20:48.898345 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:20:48.898443 PROGRESS: Total precursors accumulated: 590
1 day, 3:20:48.898504 PROGRESS: Target precursors: 363 (61.53%)
1 day, 3:20:48.898554 PROGRESS: Decoy precursors: 227 (38.47%)
1 day, 3:20:48.898600 PROGRESS: 
1 day, 3:20:48.898642 PROGRESS: Precursor Summary:
1 day, 3:20:48.899557 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   210
1 day, 3:20:48.899645 PROGRESS: 
1 day, 3:20:48.899702 PROGRESS: Protein Summary:
1 day, 3:20:48.900720 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   210
1 day, 3:20:48.900810 PROGRESS: =========================================================================
1 day, 3:20:48.900955 INFO: Target number of precursors reached.
1 day, 3:20:48.905402 INFO: fragments_df: keeping 1203 of 34191 [sum(precursor_idx_mask)=6410 sum(mass_error_mask)=34191 stop_rank=1203
1 day, 3:20:49.024489 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:49.147275 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:49.269067 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:49.390259 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:49.577240 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:20:49.577651 INFO: Using score_cutoff 28.596123828506467 (fac=0.99, q=1)
1 day, 3:20:49.577942 INFO: Updating optimization_manager: fwhm_rt             : 2.818246841430664 -> 2.9883103370666504
1 day, 3:20:49.578022 INFO: Updating optimization_manager: fwhm_mobility       : 0.0064054518006742 -> 0.0063438694924116135
1 day, 3:20:49.578088 INFO: Updating optimization_manager: score_cutoff        : 28.73697842903137 -> 28.596123828506467
1 day, 3:20:49.578142 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:49.579166 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:49.580498 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:49.581262 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:49.583424 INFO: === checking if optimization conditions were reached ===
1 day, 3:20:49.583524 PROGRESS: === Optimization of ms1_error has been performed 5 time(s); minimum number is 2 ===
1 day, 3:20:49.585694 INFO: Updating optimization_manager: ms1_error           : 2.9984193949036255 -> 6.480397909394132
1 day, 3:20:49.585875 INFO: Updating optimization_manager: classifier_version  : 16 -> 20
1 day, 3:20:49.585969 INFO: Updating optimization_manager: score_cutoff        : 28.596123828506467 -> 28.73697842903137
1 day, 3:20:49.586053 INFO: Updating optimization_manager: fwhm_rt             : 2.9883103370666504 -> 2.818246841430664
1 day, 3:20:49.586133 INFO: Updating optimization_manager: fwhm_mobility       : 0.0063438694924116135 -> 0.0064054518006742
1 day, 3:20:49.586212 PROGRESS: ✅ ms1_error      : optimization just completed. Optimal parameter 6.4804 found after 5 searches.
1 day, 3:20:49.586270 INFO: ==============================================
1 day, 3:20:49.586335 PROGRESS: Optimization finished for ms1_error.
1 day, 3:20:49.685422 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:49.686505 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:49.687836 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:49.688609 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:49.713601 INFO: Starting optimization step 0.
1 day, 3:20:49.713739 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:20:49.713807 INFO: Using classic extraction backend
1 day, 3:20:49.713923 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:20:49.713992 INFO: === Search parameters used ===
1 day, 3:20:49.714039 INFO: rt_error       : 789.4513662798012
1 day, 3:20:49.714080 INFO: mobility_error : 0.1
1 day, 3:20:49.714120 INFO: num_candidates : 3
1 day, 3:20:49.714161 INFO: ms1_error      : 6.480397909394132
1 day, 3:20:49.714200 INFO: ms2_error      : 19.00109113653737
1 day, 3:20:49.714239 INFO: fwhm_rt        : 2.818246841430664
1 day, 3:20:49.714278 INFO: quant_window   : 3
1 day, 3:20:49.714315 INFO: ==============================================
1 day, 3:20:49.715070 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:20:49.715114 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:20:49.715147 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 3:20:49.715170 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.97
1 day, 3:20:49.715817 INFO: Starting candidate selection
1 day, 3:20:54.200823 INFO: Starting candidate scoring
1 day, 3:20:54.400236 INFO: Finished candidate processing
1 day, 3:20:54.400368 INFO: Collecting candidate features
1 day, 3:20:54.415388 INFO: Collecting fragment features
1 day, 3:20:54.419120 INFO: Finished candidate scoring
1 day, 3:20:54.420853 INFO: performing precursor FDR with 47 features
1 day, 3:20:54.420897 INFO: Decoy channel: -1
1 day, 3:20:54.420922 INFO: Competetive: True
1 day, 3:20:54.423988 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:20:54.425976 INFO: Using random state 151924 for train-test-split
1 day, 3:20:54.436254 INFO: Test AUC: 0.511
1 day, 3:20:54.436313 INFO: Train AUC: 0.490
1 day, 3:20:54.436342 INFO: AUC difference: 4.28%
1 day, 3:20:54.654888 INFO: Resetting torch num_threads to 80
1 day, 3:20:54.655432 PROGRESS: === Extracted 3234 precursors and 33864 fragments ===
1 day, 3:20:54.655846 INFO: === FDR correction performed with classifier version 20 ===
1 day, 3:20:54.656409 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:20:54.656499 PROGRESS: Total precursors accumulated: 589
1 day, 3:20:54.656557 PROGRESS: Target precursors: 430 (73.01%)
1 day, 3:20:54.656608 PROGRESS: Decoy precursors: 159 (26.99%)
1 day, 3:20:54.656653 PROGRESS: 
1 day, 3:20:54.656704 PROGRESS: Precursor Summary:
1 day, 3:20:54.657655 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   365; 0.001 FDR:   365
1 day, 3:20:54.657743 PROGRESS: 
1 day, 3:20:54.657799 PROGRESS: Protein Summary:
1 day, 3:20:54.658915 PROGRESS: Channel   0:	 0.050 FDR:   359; 0.010 FDR:   359; 0.001 FDR:   359
1 day, 3:20:54.659006 PROGRESS: =========================================================================
1 day, 3:20:54.659217 INFO: Target number of precursors reached.
1 day, 3:20:54.664542 INFO: fragments_df: keeping 2059 of 33864 [sum(precursor_idx_mask)=11034 sum(mass_error_mask)=33864 stop_rank=2059
1 day, 3:20:54.763892 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:54.889467 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:55.019064 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:55.148913 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:55.423995 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:20:55.424418 INFO: Using score_cutoff 29.140532247161865 (fac=0.99, q=1)
1 day, 3:20:55.424724 INFO: Updating optimization_manager: fwhm_rt             : 2.818246841430664 -> 2.891063690185547
1 day, 3:20:55.424803 INFO: Updating optimization_manager: fwhm_mobility       : 0.0064054518006742 -> 0.006300922948867083
1 day, 3:20:55.424855 INFO: Updating optimization_manager: score_cutoff        : 28.73697842903137 -> 29.140532247161865
1 day, 3:20:55.424906 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:20:55.425954 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:20:55.427262 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:20:55.428029 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:20:55.430416 INFO: === checking if optimization conditions were reached ===
1 day, 3:20:55.430519 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:20:55.431834 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0976525875200309
1 day, 3:20:55.431931 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0977.
1 day, 3:20:55.431996 INFO: ==============================================
1 day, 3:20:55.432081 INFO: Starting optimization step 1.
1 day, 3:20:55.432140 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:20:55.432195 INFO: Using classic extraction backend
1 day, 3:20:55.432306 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:20:55.432373 INFO: === Search parameters used ===
1 day, 3:20:55.432421 INFO: rt_error       : 789.4513662798012
1 day, 3:20:55.432462 INFO: mobility_error : 0.0976525875200309
1 day, 3:20:55.432504 INFO: num_candidates : 3
1 day, 3:20:55.432544 INFO: ms1_error      : 6.480397909394132
1 day, 3:20:55.432583 INFO: ms2_error      : 19.00109113653737
1 day, 3:20:55.432621 INFO: fwhm_rt        : 2.891063690185547
1 day, 3:20:55.432659 INFO: quant_window   : 3
1 day, 3:20:55.432700 INFO: ==============================================
1 day, 3:20:55.434847 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:20:55.434896 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:20:55.434931 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 3:20:55.434953 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.92
1 day, 3:20:55.435611 INFO: Starting candidate selection
1 day, 3:20:59.802810 INFO: Starting candidate scoring
1 day, 3:21:00.007529 INFO: Finished candidate processing
1 day, 3:21:00.007638 INFO: Collecting candidate features
1 day, 3:21:00.020486 INFO: Collecting fragment features
1 day, 3:21:00.024581 INFO: Finished candidate scoring
1 day, 3:21:00.026385 INFO: performing precursor FDR with 47 features
1 day, 3:21:00.026434 INFO: Decoy channel: -1
1 day, 3:21:00.026460 INFO: Competetive: True
1 day, 3:21:00.029959 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:21:00.032393 INFO: Using random state 151924 for train-test-split
1 day, 3:21:00.043699 INFO: Test AUC: 0.504
1 day, 3:21:00.043760 INFO: Train AUC: 0.491
1 day, 3:21:00.043796 INFO: AUC difference: 2.46%
1 day, 3:21:00.263968 INFO: Resetting torch num_threads to 80
1 day, 3:21:00.264545 PROGRESS: === Extracted 3254 precursors and 34170 fragments ===
1 day, 3:21:00.265024 INFO: === FDR correction performed with classifier version 20 ===
1 day, 3:21:00.265616 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:21:00.265706 PROGRESS: Total precursors accumulated: 589
1 day, 3:21:00.265768 PROGRESS: Target precursors: 427 (72.50%)
1 day, 3:21:00.265819 PROGRESS: Decoy precursors: 162 (27.50%)
1 day, 3:21:00.265866 PROGRESS: 
1 day, 3:21:00.265909 PROGRESS: Precursor Summary:
1 day, 3:21:00.266847 PROGRESS: Channel   0:	 0.050 FDR:   358; 0.010 FDR:   358; 0.001 FDR:   358
1 day, 3:21:00.266936 PROGRESS: 
1 day, 3:21:00.266990 PROGRESS: Protein Summary:
1 day, 3:21:00.268097 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   353; 0.001 FDR:   353
1 day, 3:21:00.268185 PROGRESS: =========================================================================
1 day, 3:21:00.268340 INFO: Target number of precursors reached.
1 day, 3:21:00.273834 INFO: fragments_df: keeping 2008 of 34170 [sum(precursor_idx_mask)=10744 sum(mass_error_mask)=34170 stop_rank=2008
1 day, 3:21:00.373086 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:21:00.501711 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:21:00.630672 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:21:00.759721 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:21:01.027775 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:21:01.028197 INFO: Using score_cutoff 31.32882032546997 (fac=0.99, q=1)
1 day, 3:21:01.028536 INFO: Updating optimization_manager: fwhm_rt             : 2.891063690185547 -> 2.9547476768493652
1 day, 3:21:01.028617 INFO: Updating optimization_manager: fwhm_mobility       : 0.006300922948867083 -> 0.006361478008329868
1 day, 3:21:01.028671 INFO: Updating optimization_manager: score_cutoff        : 29.140532247161865 -> 31.32882032546997
1 day, 3:21:01.028727 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:21:01.029784 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:21:01.031103 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:21:01.031871 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:21:01.034412 INFO: === checking if optimization conditions were reached ===
1 day, 3:21:01.034526 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:21:01.035949 INFO: Updating optimization_manager: mobility_error      : 0.0976525875200309 -> 0.09878232404560083
1 day, 3:21:01.036048 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0988.
1 day, 3:21:01.036112 INFO: ==============================================
1 day, 3:21:01.036181 INFO: Starting optimization step 2.
1 day, 3:21:01.036238 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 3:21:01.036296 INFO: Using classic extraction backend
1 day, 3:21:01.036453 PROGRESS: Extracting batch of 1173 precursors
1 day, 3:21:01.036518 INFO: === Search parameters used ===
1 day, 3:21:01.036564 INFO: rt_error       : 789.4513662798012
1 day, 3:21:01.036607 INFO: mobility_error : 0.09878232404560083
1 day, 3:21:01.036660 INFO: num_candidates : 3
1 day, 3:21:01.036703 INFO: ms1_error      : 6.480397909394132
1 day, 3:21:01.036742 INFO: ms2_error      : 19.00109113653737
1 day, 3:21:01.036780 INFO: fwhm_rt        : 2.9547476768493652
1 day, 3:21:01.036821 INFO: quant_window   : 3
1 day, 3:21:01.036859 INFO: ==============================================
1 day, 3:21:01.037844 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:21:01.037889 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:21:01.037929 INFO: FWHM in RT is 2.95 seconds, sigma is 0.65
1 day, 3:21:01.037951 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.95
1 day, 3:21:01.038629 INFO: Starting candidate selection
1 day, 3:21:05.559833 INFO: Starting candidate scoring
1 day, 3:21:05.775671 INFO: Finished candidate processing
1 day, 3:21:05.775769 INFO: Collecting candidate features
1 day, 3:21:05.796019 INFO: Collecting fragment features
1 day, 3:21:05.804073 INFO: Finished candidate scoring
1 day, 3:21:05.806791 INFO: performing precursor FDR with 47 features
1 day, 3:21:05.806889 INFO: Decoy channel: -1
1 day, 3:21:05.806945 INFO: Competetive: True
1 day, 3:21:05.813158 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:21:05.817385 INFO: Using random state 151924 for train-test-split
1 day, 3:21:05.833350 INFO: Test AUC: 0.443
1 day, 3:21:05.833443 INFO: Train AUC: 0.508
1 day, 3:21:05.833492 INFO: AUC difference: 12.80%
1 day, 3:21:05.833530 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:21:06.053928 INFO: Resetting torch num_threads to 80
1 day, 3:21:06.054471 PROGRESS: === Extracted 3231 precursors and 33857 fragments ===
1 day, 3:21:06.054867 INFO: === FDR correction performed with classifier version 20 ===
1 day, 3:21:06.055412 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:21:06.055501 PROGRESS: Total precursors accumulated: 589
1 day, 3:21:06.055559 PROGRESS: Target precursors: 427 (72.50%)
1 day, 3:21:06.055608 PROGRESS: Decoy precursors: 162 (27.50%)
1 day, 3:21:06.055652 PROGRESS: 
1 day, 3:21:06.055695 PROGRESS: Precursor Summary:
1 day, 3:21:06.056633 PROGRESS: Channel   0:	 0.050 FDR:   360; 0.010 FDR:   360; 0.001 FDR:   360
1 day, 3:21:06.056723 PROGRESS: 
1 day, 3:21:06.056779 PROGRESS: Protein Summary:
1 day, 3:21:06.057912 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   354; 0.001 FDR:   354
1 day, 3:21:06.058003 PROGRESS: =========================================================================
1 day, 3:21:06.058129 INFO: Target number of precursors reached.
1 day, 3:21:06.063461 INFO: fragments_df: keeping 1963 of 33857 [sum(precursor_idx_mask)=10724 sum(mass_error_mask)=33857 stop_rank=1963
1 day, 3:21:06.162403 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:21:06.269701 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:21:06.377960 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:21:06.483781 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:21:06.707076 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:21:06.707495 INFO: Using score_cutoff 28.006395994377137 (fac=0.99, q=1)
1 day, 3:21:06.707798 INFO: Updating optimization_manager: fwhm_rt             : 2.9547476768493652 -> 3.004807949066162
1 day, 3:21:06.707878 INFO: Updating optimization_manager: fwhm_mobility       : 0.006361478008329868 -> 0.006218419410288334
1 day, 3:21:06.707931 INFO: Updating optimization_manager: score_cutoff        : 31.32882032546997 -> 28.006395994377137
1 day, 3:21:06.707983 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:21:06.709017 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:21:06.710348 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:21:06.711100 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:21:06.713491 INFO: === checking if optimization conditions were reached ===
1 day, 3:21:06.713601 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:21:06.714288 INFO: Updating optimization_manager: mobility_error      : 0.09878232404560083 -> 0.1
1 day, 3:21:06.714409 INFO: Updating optimization_manager: classifier_version  : 20 -> 22
1 day, 3:21:06.714500 INFO: Updating optimization_manager: score_cutoff        : 28.006395994377137 -> 29.140532247161865
1 day, 3:21:06.714593 INFO: Updating optimization_manager: fwhm_rt             : 3.004807949066162 -> 2.891063690185547
1 day, 3:21:06.714675 INFO: Updating optimization_manager: fwhm_mobility       : 0.006218419410288334 -> 0.006300922948867083
1 day, 3:21:06.714754 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 3:21:06.714813 INFO: ==============================================
1 day, 3:21:06.714876 PROGRESS: Optimization finished for mobility_error.
1 day, 3:21:06.813844 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:21:06.814988 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:21:06.816352 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:21:06.817140 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:21:06.842668 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 3:21:06.842809 PROGRESS: ==============================================
1 day, 3:21:06.842888 PROGRESS: ms2_error      : 19.0011
1 day, 3:21:06.842956 PROGRESS: rt_error       : 789.4514
1 day, 3:21:06.843015 PROGRESS: ms1_error      : 6.4804
1 day, 3:21:06.843070 PROGRESS: mobility_error : 0.1000
1 day, 3:21:06.843118 PROGRESS: ==============================================
1 day, 3:21:06.844114 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:21:08.430545 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:21:15.722837 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:21:17.248518 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:21:34.991684 INFO: Using classic extraction backend
1 day, 3:21:34.992686 PROGRESS: Extracting batch of 12073114 precursors
1 day, 3:21:34.992847 INFO: === Search parameters used ===
1 day, 3:21:34.992911 INFO: rt_error       : 789.4513662798012
1 day, 3:21:34.992976 INFO: mobility_error : 0.1
1 day, 3:21:34.993029 INFO: num_candidates : 3
1 day, 3:21:34.993078 INFO: ms1_error      : 6.480397909394132
1 day, 3:21:34.993119 INFO: ms2_error      : 19.00109113653737
1 day, 3:21:34.993163 INFO: fwhm_rt        : 2.891063690185547
1 day, 3:21:34.993205 INFO: quant_window   : 3
1 day, 3:21:34.993244 INFO: ==============================================
1 day, 3:21:37.726223 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:21:37.726347 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:21:37.726404 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 3:21:37.726430 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.92
1 day, 3:21:37.733359 INFO: Starting candidate selection
1 day, 11:59:25.841152 INFO: Removed 1433332 precursors with score below cutoff 29.140532247161865
1 day, 11:59:28.672717 INFO: Starting candidate scoring
1 day, 12:20:16.669811 INFO: Finished candidate processing
1 day, 12:20:16.670250 INFO: Collecting candidate features
1 day, 12:21:03.181074 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 32390465)
1 day, 12:21:04.278639 INFO: Collecting fragment features
1 day, 12:21:25.861459 INFO: Finished candidate scoring
1 day, 12:22:03.427824 INFO: === Performing FDR correction with classifier version 22 ===
1 day, 12:22:03.435151 INFO: performing precursor FDR with 47 features
1 day, 12:22:03.435204 INFO: Decoy channel: -1
1 day, 12:22:03.435233 INFO: Competetive: True
1 day, 12:22:10.936484 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:22:15.560024 WARNING: dropped 4 target PSMs due to missing features
1 day, 12:22:15.560323 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 12:22:28.778561 INFO: Using random state 170018 for train-test-split
1 day, 12:32:14.204646 INFO: Test AUC: 0.573
1 day, 12:32:14.204919 INFO: Train AUC: 0.574
1 day, 12:32:14.204982 INFO: AUC difference: 0.04%
1 day, 12:32:20.371845 INFO: Resetting torch num_threads to 80
1 day, 12:32:21.036863 INFO: Removing fragments below FDR threshold
1 day, 12:32:24.078605 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:32:24.079029 PROGRESS: Total precursors accumulated: 37,653
1 day, 12:32:24.079110 PROGRESS: Target precursors: 37,281 (99.01%)
1 day, 12:32:24.079167 PROGRESS: Decoy precursors: 372 (0.99%)
1 day, 12:32:24.079220 PROGRESS: 
1 day, 12:32:24.079269 PROGRESS: Precursor Summary:
1 day, 12:32:24.088127 PROGRESS: Channel   0:	 0.050 FDR: 37,281; 0.010 FDR: 37,281; 0.001 FDR:    11
1 day, 12:32:24.088334 PROGRESS: 
1 day, 12:32:24.088398 PROGRESS: Protein Summary:
1 day, 12:32:24.100034 PROGRESS: Channel   0:	 0.050 FDR: 7,637; 0.010 FDR: 7,637; 0.001 FDR:    10
1 day, 12:32:24.100244 PROGRESS: =========================================================================
1 day, 12:32:24.626538 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/psm.parquet
1 day, 12:32:24.934575 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/frag.parquet
1 day, 12:32:25.105882 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 12:32:25.625389 PROGRESS: 
1 day, 12:32:25.625543 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
1 day, 12:32:25.625614 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/figures
1 day, 12:32:25.625787 INFO: Initializing TimingManager
1 day, 12:32:25.626670 INFO: Initializing RawFileManager
1 day, 12:32:25.626780 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:25.626842 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:25.626884 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:25.839793 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, 12:32:37.406321 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
1 day, 12:32:37.407393 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:37.409761 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:37.410001 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:37.410374 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:37.411763 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:37.419865 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:37.420058 INFO: Indexing quadrupole dimension
1 day, 12:32:37.878807 INFO: Transposing detector events
1 day, 12:32:46.760378 INFO: Finished transposing data
1 day, 12:32:46.801129 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 12:32:46.802252 INFO: RT (min)            : 0.0 - 70.0
1 day, 12:32:46.802361 INFO: RT duration (sec)   : 4199.8
1 day, 12:32:46.802427 INFO: RT duration (min)   : 70.0
1 day, 12:32:46.802485 INFO: Cycle len (scans)   : 9
1 day, 12:32:46.802539 INFO: Cycle len (sec)     : 0.97
1 day, 12:32:46.802612 INFO: Number of cycles    : 4347
1 day, 12:32:46.802665 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 12:32:46.802732 INFO: Creating DIA data object took: 21.175963878631592
1 day, 12:32:47.986422 INFO: Initializing CalibrationManager
1 day, 12:32:47.986692 INFO: Setting up calibration estimators ..
1 day, 12:32:47.986751 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 12:32:47.986841 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, 12:32:47.986924 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 12:32:47.986985 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, 12:32:47.987042 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, 12:32:47.987103 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, 12:32:47.987153 INFO: Done setting up calibration estimators.
1 day, 12:32:47.987264 INFO: Initializing OptimizationManager
1 day, 12:32:47.987358 INFO: initial parameter: ms1_error = 30
1 day, 12:32:47.987407 INFO: initial parameter: ms2_error = 30
1 day, 12:32:47.987452 INFO: initial parameter: rt_error = 2099.9231665
1 day, 12:32:47.987496 INFO: initial parameter: mobility_error = 0.1
1 day, 12:32:47.987536 INFO: initial parameter: num_candidates = 1
1 day, 12:32:47.987576 INFO: initial parameter: fwhm_rt = 5
1 day, 12:32:47.987617 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 12:32:47.987655 INFO: initial parameter: score_cutoff = 0
1 day, 12:32:47.987694 INFO: initial parameter: classifier_version = -1
1 day, 12:32:47.987764 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 12:32:47.988007 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 12:32:47.988043 INFO: Initializing FDRManager
1 day, 12:32:47.988082 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 12:32:49.199646 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
1 day, 12:32:49.952479 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 12:32:49.952851 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 2099.9231665
1 day, 12:32:49.953091 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 12:32:49.953286 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 12:32:49.953396 PROGRESS: Starting initial search for precursors.
1 day, 12:32:49.953492 INFO: Starting optimization step 0.
1 day, 12:32:49.953557 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 12:32:49.953624 INFO: Using classic extraction backend
1 day, 12:32:49.953827 PROGRESS: Extracting batch of 390 precursors
1 day, 12:32:49.953901 INFO: === Search parameters used ===
1 day, 12:32:49.953976 INFO: rt_error       : 2099.9231665
1 day, 12:32:49.954029 INFO: mobility_error : 0.1
1 day, 12:32:49.954074 INFO: num_candidates : 1
1 day, 12:32:49.954119 INFO: ms1_error      : 30
1 day, 12:32:49.954160 INFO: ms2_error      : 30
1 day, 12:32:49.954202 INFO: fwhm_rt        : 5
1 day, 12:32:49.954244 INFO: quant_window   : 3
1 day, 12:32:49.954288 INFO: ==============================================
1 day, 12:32:49.955116 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:32:49.955161 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:32:49.955195 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 12:32:49.955220 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 12:32:49.956137 INFO: Starting candidate selection
1 day, 12:32:53.982524 INFO: Starting candidate scoring
1 day, 12:32:54.049106 INFO: Finished candidate processing
1 day, 12:32:54.049205 INFO: Collecting candidate features
1 day, 12:32:54.058484 INFO: Collecting fragment features
1 day, 12:32:54.060784 INFO: Finished candidate scoring
1 day, 12:32:54.061679 INFO: performing precursor FDR with 47 features
1 day, 12:32:54.061728 INFO: Decoy channel: -1
1 day, 12:32:54.061753 INFO: Competetive: True
1 day, 12:32:54.062934 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:32:54.065397 INFO: Using random state 898731 for train-test-split
1 day, 12:32:54.074630 INFO: Test AUC: 0.546
1 day, 12:32:54.074688 INFO: Train AUC: 0.531
1 day, 12:32:54.074723 INFO: AUC difference: 2.80%
1 day, 12:32:54.315203 INFO: Resetting torch num_threads to 80
1 day, 12:32:54.315653 PROGRESS: === Extracted 363 precursors and 3919 fragments ===
1 day, 12:32:54.316078 INFO: === FDR correction performed with classifier version -1 ===
1 day, 12:32:54.316599 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:32:54.316694 PROGRESS: Total precursors accumulated: 188
1 day, 12:32:54.316758 PROGRESS: Target precursors: 140 (74.47%)
1 day, 12:32:54.316814 PROGRESS: Decoy precursors: 48 (25.53%)
1 day, 12:32:54.316866 PROGRESS: 
1 day, 12:32:54.316916 PROGRESS: Precursor Summary:
1 day, 12:32:54.317817 PROGRESS: Channel   0:	 0.050 FDR:   104; 0.010 FDR:   104; 0.001 FDR:   104
1 day, 12:32:54.317909 PROGRESS: 
1 day, 12:32:54.317976 PROGRESS: Protein Summary:
1 day, 12:32:54.318990 PROGRESS: Channel   0:	 0.050 FDR:   104; 0.010 FDR:   104; 0.001 FDR:   104
1 day, 12:32:54.319088 PROGRESS: =========================================================================
1 day, 12:32:54.319208 INFO: Target number of precursors not reached yet.
1 day, 12:32:54.384573 INFO: Starting optimization step 1.
1 day, 12:32:54.384770 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 12:32:54.384847 INFO: Using classic extraction backend
1 day, 12:32:54.384994 PROGRESS: Extracting batch of 783 precursors
1 day, 12:32:54.385079 INFO: === Search parameters used ===
1 day, 12:32:54.385134 INFO: rt_error       : 2099.9231665
1 day, 12:32:54.385183 INFO: mobility_error : 0.1
1 day, 12:32:54.385231 INFO: num_candidates : 1
1 day, 12:32:54.385279 INFO: ms1_error      : 30
1 day, 12:32:54.385324 INFO: ms2_error      : 30
1 day, 12:32:54.385368 INFO: fwhm_rt        : 5
1 day, 12:32:54.385412 INFO: quant_window   : 3
1 day, 12:32:54.385455 INFO: ==============================================
1 day, 12:32:54.386146 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:32:54.386195 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:32:54.386227 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 12:32:54.386255 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 12:32:54.386936 INFO: Starting candidate selection
1 day, 12:33:00.124609 INFO: Starting candidate scoring
1 day, 12:33:00.252831 INFO: Finished candidate processing
1 day, 12:33:00.252999 INFO: Collecting candidate features
1 day, 12:33:00.275196 INFO: Collecting fragment features
1 day, 12:33:00.281402 INFO: Finished candidate scoring
1 day, 12:33:00.286526 INFO: performing precursor FDR with 47 features
1 day, 12:33:00.286635 INFO: Decoy channel: -1
1 day, 12:33:00.286697 INFO: Competetive: True
1 day, 12:33:00.291978 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:33:00.294786 INFO: Using random state 684512 for train-test-split
1 day, 12:33:00.307880 INFO: Test AUC: 0.513
1 day, 12:33:00.307971 INFO: Train AUC: 0.516
1 day, 12:33:00.308020 INFO: AUC difference: 0.57%
1 day, 12:33:00.529927 INFO: Resetting torch num_threads to 80
1 day, 12:33:00.531339 PROGRESS: === Extracted 1117 precursors and 12127 fragments ===
1 day, 12:33:00.531731 INFO: === FDR correction performed with classifier version -1 ===
1 day, 12:33:00.532294 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:33:00.532388 PROGRESS: Total precursors accumulated: 576
1 day, 12:33:00.532451 PROGRESS: Target precursors: 420 (72.92%)
1 day, 12:33:00.532507 PROGRESS: Decoy precursors: 156 (27.08%)
1 day, 12:33:00.532555 PROGRESS: 
1 day, 12:33:00.532599 PROGRESS: Precursor Summary:
1 day, 12:33:00.533571 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   323; 0.001 FDR:   323
1 day, 12:33:00.533664 PROGRESS: 
1 day, 12:33:00.533721 PROGRESS: Protein Summary:
1 day, 12:33:00.534842 PROGRESS: Channel   0:	 0.050 FDR:   319; 0.010 FDR:   319; 0.001 FDR:   319
1 day, 12:33:00.534934 PROGRESS: =========================================================================
1 day, 12:33:00.535085 INFO: Target number of precursors reached.
1 day, 12:33:00.537929 INFO: fragments_df: keeping 628 of 12127 [sum(precursor_idx_mask)=3630 sum(mass_error_mask)=12127 stop_rank=628
1 day, 12:33:00.639121 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:00.766308 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:00.891970 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:01.018045 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:01.171451 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 12:33:01.171940 INFO: Using score_cutoff 36.71055034332275 (fac=0.99, q=1)
1 day, 12:33:01.172347 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1881227493286133
1 day, 12:33:01.172432 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007786293514072895
1 day, 12:33:01.172487 INFO: Updating optimization_manager: score_cutoff        : 0 -> 36.71055034332275
1 day, 12:33:01.172559 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:01.173687 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:01.175293 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:01.176099 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:01.178918 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
1 day, 12:33:01.179020 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 12:33:01.179127 INFO: Starting optimization step 2.
1 day, 12:33:01.179196 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:33:01.179267 INFO: Using classic extraction backend
1 day, 12:33:01.179483 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:33:01.179553 INFO: === Search parameters used ===
1 day, 12:33:01.179600 INFO: rt_error       : 2099.9231665
1 day, 12:33:01.179642 INFO: mobility_error : 0.1
1 day, 12:33:01.179685 INFO: num_candidates : 3
1 day, 12:33:01.179725 INFO: ms1_error      : 30
1 day, 12:33:01.179765 INFO: ms2_error      : 30
1 day, 12:33:01.179806 INFO: fwhm_rt        : 3.1881227493286133
1 day, 12:33:01.179844 INFO: quant_window   : 3
1 day, 12:33:01.179884 INFO: ==============================================
1 day, 12:33:01.181247 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:33:01.181294 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:33:01.181336 INFO: FWHM in RT is 3.19 seconds, sigma is 0.70
1 day, 12:33:01.181360 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 12:33:01.182140 INFO: Starting candidate selection
1 day, 12:33:10.623486 INFO: Starting candidate scoring
1 day, 12:33:10.936567 INFO: Finished candidate processing
1 day, 12:33:10.936701 INFO: Collecting candidate features
1 day, 12:33:10.950989 INFO: Collecting fragment features
1 day, 12:33:10.954944 INFO: Finished candidate scoring
1 day, 12:33:10.956879 INFO: performing precursor FDR with 47 features
1 day, 12:33:10.956925 INFO: Decoy channel: -1
1 day, 12:33:10.956960 INFO: Competetive: True
1 day, 12:33:10.960436 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:33:10.962613 INFO: Using random state 298934 for train-test-split
1 day, 12:33:10.973402 INFO: Test AUC: 0.519
1 day, 12:33:10.973459 INFO: Train AUC: 0.508
1 day, 12:33:10.973490 INFO: AUC difference: 2.11%
1 day, 12:33:11.184342 INFO: Resetting torch num_threads to 80
1 day, 12:33:11.184888 PROGRESS: === Extracted 3211 precursors and 35045 fragments ===
1 day, 12:33:11.185325 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:33:11.185911 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:33:11.186001 PROGRESS: Total precursors accumulated: 589
1 day, 12:33:11.186058 PROGRESS: Target precursors: 470 (79.80%)
1 day, 12:33:11.186106 PROGRESS: Decoy precursors: 119 (20.20%)
1 day, 12:33:11.186149 PROGRESS: 
1 day, 12:33:11.186193 PROGRESS: Precursor Summary:
1 day, 12:33:11.187154 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   410; 0.001 FDR:   410
1 day, 12:33:11.187241 PROGRESS: 
1 day, 12:33:11.187295 PROGRESS: Protein Summary:
1 day, 12:33:11.188433 PROGRESS: Channel   0:	 0.050 FDR:   405; 0.010 FDR:   405; 0.001 FDR:   405
1 day, 12:33:11.188522 PROGRESS: =========================================================================
1 day, 12:33:11.188648 INFO: Target number of precursors reached.
1 day, 12:33:11.194374 INFO: fragments_df: keeping 2453 of 35045 [sum(precursor_idx_mask)=12749 sum(mass_error_mask)=35045 stop_rank=2453
1 day, 12:33:11.292970 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:11.402272 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:11.512701 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:11.623062 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:13.913144 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:33:13.913566 INFO: Using score_cutoff 39.2322150604248 (fac=0.99, q=1)
1 day, 12:33:13.913868 INFO: Updating optimization_manager: fwhm_rt             : 3.1881227493286133 -> 3.1703996658325195
1 day, 12:33:13.913956 INFO: Updating optimization_manager: fwhm_mobility       : 0.007786293514072895 -> 0.007842330262064934
1 day, 12:33:13.914011 INFO: Updating optimization_manager: score_cutoff        : 36.71055034332275 -> 39.2322150604248
1 day, 12:33:13.914064 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:13.915118 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:13.916488 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:13.917259 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:13.919364 INFO: === checking if optimization conditions were reached ===
1 day, 12:33:13.919465 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
1 day, 12:33:13.921072 INFO: Updating optimization_manager: ms2_error           : 30 -> 25.255712833228486
1 day, 12:33:13.921173 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 25.2557.
1 day, 12:33:13.921237 INFO: ==============================================
1 day, 12:33:13.921299 INFO: Starting optimization step 3.
1 day, 12:33:13.921354 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:33:13.921404 INFO: Using classic extraction backend
1 day, 12:33:13.921504 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:33:13.921565 INFO: === Search parameters used ===
1 day, 12:33:13.921608 INFO: rt_error       : 2099.9231665
1 day, 12:33:13.921671 INFO: mobility_error : 0.1
1 day, 12:33:13.921710 INFO: num_candidates : 3
1 day, 12:33:13.921750 INFO: ms1_error      : 30
1 day, 12:33:13.921796 INFO: ms2_error      : 25.255712833228486
1 day, 12:33:13.921840 INFO: fwhm_rt        : 3.1703996658325195
1 day, 12:33:13.921885 INFO: quant_window   : 3
1 day, 12:33:13.921924 INFO: ==============================================
1 day, 12:33:13.922747 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:33:13.922791 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:33:13.922825 INFO: FWHM in RT is 3.17 seconds, sigma is 0.70
1 day, 12:33:13.922845 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.64
1 day, 12:33:13.923560 INFO: Starting candidate selection
1 day, 12:33:23.002118 INFO: Starting candidate scoring
1 day, 12:33:23.294810 INFO: Finished candidate processing
1 day, 12:33:23.294918 INFO: Collecting candidate features
1 day, 12:33:23.307967 INFO: Collecting fragment features
1 day, 12:33:23.311917 INFO: Finished candidate scoring
1 day, 12:33:23.315702 INFO: performing precursor FDR with 47 features
1 day, 12:33:23.315748 INFO: Decoy channel: -1
1 day, 12:33:23.315773 INFO: Competetive: True
1 day, 12:33:23.319120 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:33:23.321259 INFO: Using random state 298934 for train-test-split
1 day, 12:33:23.331592 INFO: Test AUC: 0.522
1 day, 12:33:23.331649 INFO: Train AUC: 0.504
1 day, 12:33:23.331678 INFO: AUC difference: 3.67%
1 day, 12:33:23.544265 INFO: Resetting torch num_threads to 80
1 day, 12:33:23.544840 PROGRESS: === Extracted 3213 precursors and 34714 fragments ===
1 day, 12:33:23.545242 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:33:23.545851 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:33:23.545942 PROGRESS: Total precursors accumulated: 587
1 day, 12:33:23.546000 PROGRESS: Target precursors: 458 (78.02%)
1 day, 12:33:23.546050 PROGRESS: Decoy precursors: 129 (21.98%)
1 day, 12:33:23.546094 PROGRESS: 
1 day, 12:33:23.546136 PROGRESS: Precursor Summary:
1 day, 12:33:23.547137 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   410; 0.001 FDR:   410
1 day, 12:33:23.547227 PROGRESS: 
1 day, 12:33:23.547281 PROGRESS: Protein Summary:
1 day, 12:33:23.548425 PROGRESS: Channel   0:	 0.050 FDR:   405; 0.010 FDR:   405; 0.001 FDR:   405
1 day, 12:33:23.548513 PROGRESS: =========================================================================
1 day, 12:33:23.548643 INFO: Target number of precursors reached.
1 day, 12:33:23.554619 INFO: fragments_df: keeping 2333 of 34714 [sum(precursor_idx_mask)=12627 sum(mass_error_mask)=34714 stop_rank=2333
1 day, 12:33:23.653664 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:23.756934 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:23.867426 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:23.977121 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:24.230926 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:33:24.231346 INFO: Using score_cutoff 37.22514807128906 (fac=0.99, q=1)
1 day, 12:33:24.231644 INFO: Updating optimization_manager: fwhm_rt             : 3.1703996658325195 -> 3.0772931575775146
1 day, 12:33:24.231721 INFO: Updating optimization_manager: fwhm_mobility       : 0.007842330262064934 -> 0.007328680716454983
1 day, 12:33:24.231774 INFO: Updating optimization_manager: score_cutoff        : 39.2322150604248 -> 37.22514807128906
1 day, 12:33:24.231823 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:24.232859 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:24.234288 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:24.235065 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:24.237117 INFO: === checking if optimization conditions were reached ===
1 day, 12:33:24.237217 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
1 day, 12:33:24.238910 INFO: Updating optimization_manager: ms2_error           : 25.255712833228486 -> 21.20784327193157
1 day, 12:33:24.239015 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 21.2078.
1 day, 12:33:24.239078 INFO: ==============================================
1 day, 12:33:24.239141 INFO: Starting optimization step 4.
1 day, 12:33:24.239194 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:33:24.239252 INFO: Using classic extraction backend
1 day, 12:33:24.239356 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:33:24.239416 INFO: === Search parameters used ===
1 day, 12:33:24.239462 INFO: rt_error       : 2099.9231665
1 day, 12:33:24.239504 INFO: mobility_error : 0.1
1 day, 12:33:24.239543 INFO: num_candidates : 3
1 day, 12:33:24.239581 INFO: ms1_error      : 30
1 day, 12:33:24.239619 INFO: ms2_error      : 21.20784327193157
1 day, 12:33:24.239657 INFO: fwhm_rt        : 3.0772931575775146
1 day, 12:33:24.239695 INFO: quant_window   : 3
1 day, 12:33:24.239734 INFO: ==============================================
1 day, 12:33:24.240558 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:33:24.240603 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:33:24.240636 INFO: FWHM in RT is 3.08 seconds, sigma is 0.68
1 day, 12:33:24.240657 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.40
1 day, 12:33:24.241311 INFO: Starting candidate selection
1 day, 12:33:32.769763 INFO: Starting candidate scoring
1 day, 12:33:33.008360 INFO: Finished candidate processing
1 day, 12:33:33.008493 INFO: Collecting candidate features
1 day, 12:33:33.022990 INFO: Collecting fragment features
1 day, 12:33:33.026802 INFO: Finished candidate scoring
1 day, 12:33:33.029735 INFO: performing precursor FDR with 47 features
1 day, 12:33:33.029784 INFO: Decoy channel: -1
1 day, 12:33:33.029808 INFO: Competetive: True
1 day, 12:33:33.032725 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:33:33.034771 INFO: Using random state 298934 for train-test-split
1 day, 12:33:33.045801 INFO: Test AUC: 0.460
1 day, 12:33:33.045861 INFO: Train AUC: 0.511
1 day, 12:33:33.045890 INFO: AUC difference: 9.90%
1 day, 12:33:33.045912 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 12:33:33.254836 INFO: Resetting torch num_threads to 80
1 day, 12:33:33.255429 PROGRESS: === Extracted 3229 precursors and 34518 fragments ===
1 day, 12:33:33.255819 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:33:33.256386 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:33:33.256483 PROGRESS: Total precursors accumulated: 588
1 day, 12:33:33.256540 PROGRESS: Target precursors: 464 (78.91%)
1 day, 12:33:33.256588 PROGRESS: Decoy precursors: 124 (21.09%)
1 day, 12:33:33.256633 PROGRESS: 
1 day, 12:33:33.256674 PROGRESS: Precursor Summary:
1 day, 12:33:33.257708 PROGRESS: Channel   0:	 0.050 FDR:   414; 0.010 FDR:   414; 0.001 FDR:   414
1 day, 12:33:33.257798 PROGRESS: 
1 day, 12:33:33.257853 PROGRESS: Protein Summary:
1 day, 12:33:33.259019 PROGRESS: Channel   0:	 0.050 FDR:   409; 0.010 FDR:   409; 0.001 FDR:   409
1 day, 12:33:33.259111 PROGRESS: =========================================================================
1 day, 12:33:33.259236 INFO: Target number of precursors reached.
1 day, 12:33:33.264965 INFO: fragments_df: keeping 2320 of 34518 [sum(precursor_idx_mask)=12663 sum(mass_error_mask)=34518 stop_rank=2320
1 day, 12:33:33.364044 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:33.472299 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:33.586676 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:33.699592 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:33.953427 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:33:33.953851 INFO: Using score_cutoff 35.97550468711853 (fac=0.99, q=1)
1 day, 12:33:33.954149 INFO: Updating optimization_manager: fwhm_rt             : 3.0772931575775146 -> 3.012362480163574
1 day, 12:33:33.954234 INFO: Updating optimization_manager: fwhm_mobility       : 0.007328680716454983 -> 0.006678048055619001
1 day, 12:33:33.954287 INFO: Updating optimization_manager: score_cutoff        : 37.22514807128906 -> 35.97550468711853
1 day, 12:33:33.954336 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:33.955385 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:33.956731 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:33.957546 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:33.959765 INFO: === checking if optimization conditions were reached ===
1 day, 12:33:33.959869 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
1 day, 12:33:33.961655 INFO: Updating optimization_manager: ms2_error           : 21.20784327193157 -> 17.62190467828678
1 day, 12:33:33.961760 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 17.6219.
1 day, 12:33:33.961823 INFO: ==============================================
1 day, 12:33:33.961885 INFO: Starting optimization step 5.
1 day, 12:33:33.961939 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:33:33.961990 INFO: Using classic extraction backend
1 day, 12:33:33.962092 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:33:33.962153 INFO: === Search parameters used ===
1 day, 12:33:33.962198 INFO: rt_error       : 2099.9231665
1 day, 12:33:33.962238 INFO: mobility_error : 0.1
1 day, 12:33:33.962277 INFO: num_candidates : 3
1 day, 12:33:33.962317 INFO: ms1_error      : 30
1 day, 12:33:33.962355 INFO: ms2_error      : 17.62190467828678
1 day, 12:33:33.962392 INFO: fwhm_rt        : 3.012362480163574
1 day, 12:33:33.962429 INFO: quant_window   : 3
1 day, 12:33:33.962466 INFO: ==============================================
1 day, 12:33:33.963273 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:33:33.963315 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:33:33.963349 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 12:33:33.963372 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.10
1 day, 12:33:33.964004 INFO: Starting candidate selection
1 day, 12:33:42.864868 INFO: Starting candidate scoring
1 day, 12:33:43.079461 INFO: Finished candidate processing
1 day, 12:33:43.079570 INFO: Collecting candidate features
1 day, 12:33:43.092469 INFO: Collecting fragment features
1 day, 12:33:43.096479 INFO: Finished candidate scoring
1 day, 12:33:43.099148 INFO: performing precursor FDR with 47 features
1 day, 12:33:43.099194 INFO: Decoy channel: -1
1 day, 12:33:43.099218 INFO: Competetive: True
1 day, 12:33:43.102656 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:33:43.104639 INFO: Using random state 298934 for train-test-split
1 day, 12:33:43.114845 INFO: Test AUC: 0.509
1 day, 12:33:43.114903 INFO: Train AUC: 0.507
1 day, 12:33:43.114932 INFO: AUC difference: 0.36%
1 day, 12:33:43.325034 INFO: Resetting torch num_threads to 80
1 day, 12:33:43.325620 PROGRESS: === Extracted 3224 precursors and 34000 fragments ===
1 day, 12:33:43.326010 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:33:43.326578 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:33:43.326663 PROGRESS: Total precursors accumulated: 589
1 day, 12:33:43.326726 PROGRESS: Target precursors: 472 (80.14%)
1 day, 12:33:43.326776 PROGRESS: Decoy precursors: 117 (19.86%)
1 day, 12:33:43.326821 PROGRESS: 
1 day, 12:33:43.326864 PROGRESS: Precursor Summary:
1 day, 12:33:43.327853 PROGRESS: Channel   0:	 0.050 FDR:   415; 0.010 FDR:   415; 0.001 FDR:   415
1 day, 12:33:43.327943 PROGRESS: 
1 day, 12:33:43.327997 PROGRESS: Protein Summary:
1 day, 12:33:43.329170 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   410; 0.001 FDR:   410
1 day, 12:33:43.329262 PROGRESS: =========================================================================
1 day, 12:33:43.329403 INFO: Target number of precursors reached.
1 day, 12:33:43.335088 INFO: fragments_df: keeping 2254 of 34000 [sum(precursor_idx_mask)=12568 sum(mass_error_mask)=34000 stop_rank=2254
1 day, 12:33:43.434870 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:43.542585 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:43.650542 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:43.761847 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:44.013811 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:33:44.014228 INFO: Using score_cutoff 33.85579132232667 (fac=0.99, q=1)
1 day, 12:33:44.014529 INFO: Updating optimization_manager: fwhm_rt             : 3.012362480163574 -> 2.863037347793579
1 day, 12:33:44.014608 INFO: Updating optimization_manager: fwhm_mobility       : 0.006678048055619001 -> 0.005966446828097105
1 day, 12:33:44.014662 INFO: Updating optimization_manager: score_cutoff        : 35.97550468711853 -> 33.85579132232667
1 day, 12:33:44.014721 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:44.015757 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:44.017116 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:44.017881 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:44.019976 INFO: === checking if optimization conditions were reached ===
1 day, 12:33:44.020074 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
1 day, 12:33:44.021826 INFO: Updating optimization_manager: ms2_error           : 17.62190467828678 -> 15.65170738607732
1 day, 12:33:44.021927 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 15.6517.
1 day, 12:33:44.021989 INFO: ==============================================
1 day, 12:33:44.022053 INFO: Starting optimization step 6.
1 day, 12:33:44.022108 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:33:44.022160 INFO: Using classic extraction backend
1 day, 12:33:44.022264 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:33:44.022323 INFO: === Search parameters used ===
1 day, 12:33:44.022368 INFO: rt_error       : 2099.9231665
1 day, 12:33:44.022412 INFO: mobility_error : 0.1
1 day, 12:33:44.022453 INFO: num_candidates : 3
1 day, 12:33:44.022492 INFO: ms1_error      : 30
1 day, 12:33:44.022532 INFO: ms2_error      : 15.65170738607732
1 day, 12:33:44.022570 INFO: fwhm_rt        : 2.863037347793579
1 day, 12:33:44.022616 INFO: quant_window   : 3
1 day, 12:33:44.022657 INFO: ==============================================
1 day, 12:33:44.023468 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:33:44.023513 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:33:44.023546 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 12:33:44.023568 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.77
1 day, 12:33:44.029949 INFO: Starting candidate selection
1 day, 12:33:52.402154 INFO: Starting candidate scoring
1 day, 12:33:52.618498 INFO: Finished candidate processing
1 day, 12:33:52.618632 INFO: Collecting candidate features
1 day, 12:33:52.631282 INFO: Collecting fragment features
1 day, 12:33:52.635571 INFO: Finished candidate scoring
1 day, 12:33:52.638003 INFO: performing precursor FDR with 47 features
1 day, 12:33:52.638048 INFO: Decoy channel: -1
1 day, 12:33:52.638072 INFO: Competetive: True
1 day, 12:33:52.640974 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:33:52.642952 INFO: Using random state 298934 for train-test-split
1 day, 12:33:52.652993 INFO: Test AUC: 0.481
1 day, 12:33:52.653051 INFO: Train AUC: 0.515
1 day, 12:33:52.653079 INFO: AUC difference: 6.59%
1 day, 12:33:52.653102 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 12:33:52.864818 INFO: Resetting torch num_threads to 80
1 day, 12:33:52.865449 PROGRESS: === Extracted 3217 precursors and 33606 fragments ===
1 day, 12:33:52.865840 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:33:52.866408 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:33:52.866502 PROGRESS: Total precursors accumulated: 585
1 day, 12:33:52.866560 PROGRESS: Target precursors: 459 (78.46%)
1 day, 12:33:52.866608 PROGRESS: Decoy precursors: 126 (21.54%)
1 day, 12:33:52.866654 PROGRESS: 
1 day, 12:33:52.866696 PROGRESS: Precursor Summary:
1 day, 12:33:52.867686 PROGRESS: Channel   0:	 0.050 FDR:   414; 0.010 FDR:   414; 0.001 FDR:   414
1 day, 12:33:52.867778 PROGRESS: 
1 day, 12:33:52.867832 PROGRESS: Protein Summary:
1 day, 12:33:52.869004 PROGRESS: Channel   0:	 0.050 FDR:   408; 0.010 FDR:   408; 0.001 FDR:   408
1 day, 12:33:52.869092 PROGRESS: =========================================================================
1 day, 12:33:52.869230 INFO: Target number of precursors reached.
1 day, 12:33:52.875265 INFO: fragments_df: keeping 2171 of 33606 [sum(precursor_idx_mask)=12446 sum(mass_error_mask)=33606 stop_rank=2171
1 day, 12:33:52.974442 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:53.099711 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:53.225900 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:53.339168 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:53.584227 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:33:53.584641 INFO: Using score_cutoff 31.667250177383423 (fac=0.99, q=1)
1 day, 12:33:53.584938 INFO: Updating optimization_manager: fwhm_rt             : 2.863037347793579 -> 2.8779819011688232
1 day, 12:33:53.585029 INFO: Updating optimization_manager: fwhm_mobility       : 0.005966446828097105 -> 0.00553581677377224
1 day, 12:33:53.585083 INFO: Updating optimization_manager: score_cutoff        : 33.85579132232667 -> 31.667250177383423
1 day, 12:33:53.585136 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:33:53.586168 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:33:53.587516 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:33:53.588277 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:33:53.590389 INFO: === checking if optimization conditions were reached ===
1 day, 12:33:53.590494 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
1 day, 12:33:53.592232 INFO: Updating optimization_manager: ms2_error           : 15.65170738607732 -> 13.83888176474647
1 day, 12:33:53.592333 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 13.8389.
1 day, 12:33:53.592396 INFO: ==============================================
1 day, 12:33:53.592460 INFO: Starting optimization step 7.
1 day, 12:33:53.592515 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:33:53.592570 INFO: Using classic extraction backend
1 day, 12:33:53.592671 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:33:53.592741 INFO: === Search parameters used ===
1 day, 12:33:53.592791 INFO: rt_error       : 2099.9231665
1 day, 12:33:53.592833 INFO: mobility_error : 0.1
1 day, 12:33:53.592873 INFO: num_candidates : 3
1 day, 12:33:53.592913 INFO: ms1_error      : 30
1 day, 12:33:53.592967 INFO: ms2_error      : 13.83888176474647
1 day, 12:33:53.593011 INFO: fwhm_rt        : 2.8779819011688232
1 day, 12:33:53.593051 INFO: quant_window   : 3
1 day, 12:33:53.593091 INFO: ==============================================
1 day, 12:33:53.593911 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:33:53.593958 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:33:53.593990 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1 day, 12:33:53.594014 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.57
1 day, 12:33:53.594645 INFO: Starting candidate selection
1 day, 12:34:01.830419 INFO: Starting candidate scoring
1 day, 12:34:02.035823 INFO: Finished candidate processing
1 day, 12:34:02.035919 INFO: Collecting candidate features
1 day, 12:34:02.048148 INFO: Collecting fragment features
1 day, 12:34:02.051921 INFO: Finished candidate scoring
1 day, 12:34:02.054152 INFO: performing precursor FDR with 47 features
1 day, 12:34:02.054196 INFO: Decoy channel: -1
1 day, 12:34:02.054220 INFO: Competetive: True
1 day, 12:34:02.057189 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:34:02.059193 INFO: Using random state 298934 for train-test-split
1 day, 12:34:02.069194 INFO: Test AUC: 0.496
1 day, 12:34:02.069254 INFO: Train AUC: 0.511
1 day, 12:34:02.069283 INFO: AUC difference: 2.83%
1 day, 12:34:02.283434 INFO: Resetting torch num_threads to 80
1 day, 12:34:02.284023 PROGRESS: === Extracted 3221 precursors and 33050 fragments ===
1 day, 12:34:02.284418 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:34:02.285002 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:34:02.285100 PROGRESS: Total precursors accumulated: 587
1 day, 12:34:02.285158 PROGRESS: Target precursors: 463 (78.88%)
1 day, 12:34:02.285208 PROGRESS: Decoy precursors: 124 (21.12%)
1 day, 12:34:02.285256 PROGRESS: 
1 day, 12:34:02.285301 PROGRESS: Precursor Summary:
1 day, 12:34:02.286283 PROGRESS: Channel   0:	 0.050 FDR:   413; 0.010 FDR:   413; 0.001 FDR:   413
1 day, 12:34:02.286375 PROGRESS: 
1 day, 12:34:02.286431 PROGRESS: Protein Summary:
1 day, 12:34:02.287590 PROGRESS: Channel   0:	 0.050 FDR:   408; 0.010 FDR:   408; 0.001 FDR:   408
1 day, 12:34:02.287689 PROGRESS: =========================================================================
1 day, 12:34:02.287826 INFO: Target number of precursors reached.
1 day, 12:34:02.293599 INFO: fragments_df: keeping 2129 of 33050 [sum(precursor_idx_mask)=12165 sum(mass_error_mask)=33050 stop_rank=2129
1 day, 12:34:02.411668 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:02.520776 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:02.630098 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:02.743246 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:02.979118 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:34:02.979541 INFO: Using score_cutoff 32.83964369659424 (fac=0.99, q=1)
1 day, 12:34:02.979841 INFO: Updating optimization_manager: fwhm_rt             : 2.8779819011688232 -> 2.638012170791626
1 day, 12:34:02.979919 INFO: Updating optimization_manager: fwhm_mobility       : 0.00553581677377224 -> 0.0051279678009450436
1 day, 12:34:02.979973 INFO: Updating optimization_manager: score_cutoff        : 31.667250177383423 -> 32.83964369659424
1 day, 12:34:02.980025 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:02.981063 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:02.982471 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:02.983239 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:02.985402 INFO: === checking if optimization conditions were reached ===
1 day, 12:34:02.985506 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
1 day, 12:34:02.987250 INFO: Updating optimization_manager: ms2_error           : 13.83888176474647 -> 11.567750494983589
1 day, 12:34:02.987360 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 11.5678.
1 day, 12:34:02.987424 INFO: ==============================================
1 day, 12:34:02.987489 INFO: Starting optimization step 8.
1 day, 12:34:02.987546 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:34:02.987599 INFO: Using classic extraction backend
1 day, 12:34:02.987702 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:34:02.987764 INFO: === Search parameters used ===
1 day, 12:34:02.987816 INFO: rt_error       : 2099.9231665
1 day, 12:34:02.987858 INFO: mobility_error : 0.1
1 day, 12:34:02.987899 INFO: num_candidates : 3
1 day, 12:34:02.987941 INFO: ms1_error      : 30
1 day, 12:34:02.987981 INFO: ms2_error      : 11.567750494983589
1 day, 12:34:02.988021 INFO: fwhm_rt        : 2.638012170791626
1 day, 12:34:02.988060 INFO: quant_window   : 3
1 day, 12:34:02.988099 INFO: ==============================================
1 day, 12:34:02.988904 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:34:02.988957 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:34:02.988993 INFO: FWHM in RT is 2.64 seconds, sigma is 0.58
1 day, 12:34:02.989016 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.38
1 day, 12:34:02.989666 INFO: Starting candidate selection
1 day, 12:34:11.347564 INFO: Starting candidate scoring
1 day, 12:34:11.541990 INFO: Finished candidate processing
1 day, 12:34:11.542088 INFO: Collecting candidate features
1 day, 12:34:11.554896 INFO: Collecting fragment features
1 day, 12:34:11.558628 INFO: Finished candidate scoring
1 day, 12:34:11.560872 INFO: performing precursor FDR with 47 features
1 day, 12:34:11.560916 INFO: Decoy channel: -1
1 day, 12:34:11.560950 INFO: Competetive: True
1 day, 12:34:11.563939 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:34:11.565987 INFO: Using random state 298934 for train-test-split
1 day, 12:34:11.575940 INFO: Test AUC: 0.517
1 day, 12:34:11.576002 INFO: Train AUC: 0.494
1 day, 12:34:11.576032 INFO: AUC difference: 4.65%
1 day, 12:34:11.796714 INFO: Resetting torch num_threads to 80
1 day, 12:34:11.797325 PROGRESS: === Extracted 3256 precursors and 32886 fragments ===
1 day, 12:34:11.797727 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:34:11.798326 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:34:11.798418 PROGRESS: Total precursors accumulated: 587
1 day, 12:34:11.798476 PROGRESS: Target precursors: 453 (77.17%)
1 day, 12:34:11.798534 PROGRESS: Decoy precursors: 134 (22.83%)
1 day, 12:34:11.798581 PROGRESS: 
1 day, 12:34:11.798625 PROGRESS: Precursor Summary:
1 day, 12:34:11.799601 PROGRESS: Channel   0:	 0.050 FDR:   398; 0.010 FDR:   398; 0.001 FDR:   398
1 day, 12:34:11.799691 PROGRESS: 
1 day, 12:34:11.799748 PROGRESS: Protein Summary:
1 day, 12:34:11.800910 PROGRESS: Channel   0:	 0.050 FDR:   393; 0.010 FDR:   393; 0.001 FDR:   393
1 day, 12:34:11.801011 PROGRESS: =========================================================================
1 day, 12:34:11.801264 INFO: Target number of precursors reached.
1 day, 12:34:11.806755 INFO: fragments_df: keeping 2001 of 32886 [sum(precursor_idx_mask)=11508 sum(mass_error_mask)=32886 stop_rank=2001
1 day, 12:34:11.908610 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:12.044026 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:12.173973 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:12.312723 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:12.583717 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:34:12.584163 INFO: Using score_cutoff 31.18334471912384 (fac=0.99, q=1)
1 day, 12:34:12.584465 INFO: Updating optimization_manager: fwhm_rt             : 2.638012170791626 -> 2.5859246253967285
1 day, 12:34:12.584543 INFO: Updating optimization_manager: fwhm_mobility       : 0.0051279678009450436 -> 0.004675213247537613
1 day, 12:34:12.584598 INFO: Updating optimization_manager: score_cutoff        : 32.83964369659424 -> 31.18334471912384
1 day, 12:34:12.584653 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:12.585738 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:12.587086 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:12.587853 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:12.589945 INFO: === checking if optimization conditions were reached ===
1 day, 12:34:12.590051 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
1 day, 12:34:12.591865 INFO: Updating optimization_manager: ms2_error           : 11.567750494983589 -> 9.987774995204571
1 day, 12:34:12.591964 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 9.9878.
1 day, 12:34:12.592030 INFO: ==============================================
1 day, 12:34:12.592097 INFO: Starting optimization step 9.
1 day, 12:34:12.592155 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:34:12.592214 INFO: Using classic extraction backend
1 day, 12:34:12.592330 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:34:12.592396 INFO: === Search parameters used ===
1 day, 12:34:12.592443 INFO: rt_error       : 2099.9231665
1 day, 12:34:12.592485 INFO: mobility_error : 0.1
1 day, 12:34:12.592529 INFO: num_candidates : 3
1 day, 12:34:12.592571 INFO: ms1_error      : 30
1 day, 12:34:12.592611 INFO: ms2_error      : 9.987774995204571
1 day, 12:34:12.592650 INFO: fwhm_rt        : 2.5859246253967285
1 day, 12:34:12.592688 INFO: quant_window   : 3
1 day, 12:34:12.592733 INFO: ==============================================
1 day, 12:34:12.593567 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:34:12.593613 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:34:12.593647 INFO: FWHM in RT is 2.59 seconds, sigma is 0.57
1 day, 12:34:12.593668 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.17
1 day, 12:34:12.594323 INFO: Starting candidate selection
1 day, 12:34:20.446630 INFO: Starting candidate scoring
1 day, 12:34:20.616175 INFO: Finished candidate processing
1 day, 12:34:20.616279 INFO: Collecting candidate features
1 day, 12:34:20.630924 INFO: Collecting fragment features
1 day, 12:34:20.635364 INFO: Finished candidate scoring
1 day, 12:34:20.637488 INFO: performing precursor FDR with 47 features
1 day, 12:34:20.637531 INFO: Decoy channel: -1
1 day, 12:34:20.637558 INFO: Competetive: True
1 day, 12:34:20.640988 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:34:20.643323 INFO: Using random state 298934 for train-test-split
1 day, 12:34:20.654968 INFO: Test AUC: 0.495
1 day, 12:34:20.655031 INFO: Train AUC: 0.505
1 day, 12:34:20.655065 INFO: AUC difference: 1.88%
1 day, 12:34:20.877994 INFO: Resetting torch num_threads to 80
1 day, 12:34:20.878592 PROGRESS: === Extracted 3229 precursors and 31886 fragments ===
1 day, 12:34:20.879046 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:34:20.879619 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:34:20.879707 PROGRESS: Total precursors accumulated: 585
1 day, 12:34:20.879766 PROGRESS: Target precursors: 454 (77.61%)
1 day, 12:34:20.879817 PROGRESS: Decoy precursors: 131 (22.39%)
1 day, 12:34:20.879861 PROGRESS: 
1 day, 12:34:20.879904 PROGRESS: Precursor Summary:
1 day, 12:34:20.880890 PROGRESS: Channel   0:	 0.050 FDR:   396; 0.010 FDR:   396; 0.001 FDR:   396
1 day, 12:34:20.880986 PROGRESS: 
1 day, 12:34:20.881047 PROGRESS: Protein Summary:
1 day, 12:34:20.882209 PROGRESS: Channel   0:	 0.050 FDR:   393; 0.010 FDR:   393; 0.001 FDR:   393
1 day, 12:34:20.882301 PROGRESS: =========================================================================
1 day, 12:34:20.882555 INFO: Target number of precursors reached.
1 day, 12:34:20.887970 INFO: fragments_df: keeping 1898 of 31886 [sum(precursor_idx_mask)=11248 sum(mass_error_mask)=31886 stop_rank=1898
1 day, 12:34:20.987017 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:21.105044 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:21.215583 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:21.327891 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:21.544615 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:34:21.545062 INFO: Using score_cutoff 30.873869092941284 (fac=0.99, q=1)
1 day, 12:34:21.545435 INFO: Updating optimization_manager: fwhm_rt             : 2.5859246253967285 -> 2.434283971786499
1 day, 12:34:21.545517 INFO: Updating optimization_manager: fwhm_mobility       : 0.004675213247537613 -> 0.004130763933062553
1 day, 12:34:21.545569 INFO: Updating optimization_manager: score_cutoff        : 31.18334471912384 -> 30.873869092941284
1 day, 12:34:21.545623 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:21.546657 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:21.548002 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:21.548761 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:21.550930 INFO: === checking if optimization conditions were reached ===
1 day, 12:34:21.551037 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
1 day, 12:34:21.552792 INFO: Updating optimization_manager: ms2_error           : 9.987774995204571 -> 8.996203009560706
1 day, 12:34:21.552891 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 8.9962.
1 day, 12:34:21.552964 INFO: ==============================================
1 day, 12:34:21.553034 INFO: Starting optimization step 10.
1 day, 12:34:21.553091 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:34:21.553151 INFO: Using classic extraction backend
1 day, 12:34:21.553310 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:34:21.553376 INFO: === Search parameters used ===
1 day, 12:34:21.553430 INFO: rt_error       : 2099.9231665
1 day, 12:34:21.553474 INFO: mobility_error : 0.1
1 day, 12:34:21.553515 INFO: num_candidates : 3
1 day, 12:34:21.553554 INFO: ms1_error      : 30
1 day, 12:34:21.553594 INFO: ms2_error      : 8.996203009560706
1 day, 12:34:21.553632 INFO: fwhm_rt        : 2.434283971786499
1 day, 12:34:21.553669 INFO: quant_window   : 3
1 day, 12:34:21.553707 INFO: ==============================================
1 day, 12:34:21.554633 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:34:21.554676 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:34:21.554714 INFO: FWHM in RT is 2.43 seconds, sigma is 0.54
1 day, 12:34:21.554738 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.92
1 day, 12:34:21.555473 INFO: Starting candidate selection
1 day, 12:34:29.991891 INFO: Starting candidate scoring
1 day, 12:34:30.183366 INFO: Finished candidate processing
1 day, 12:34:30.183497 INFO: Collecting candidate features
1 day, 12:34:30.197487 INFO: Collecting fragment features
1 day, 12:34:30.201299 INFO: Finished candidate scoring
1 day, 12:34:30.203298 INFO: performing precursor FDR with 47 features
1 day, 12:34:30.203343 INFO: Decoy channel: -1
1 day, 12:34:30.203374 INFO: Competetive: True
1 day, 12:34:30.206213 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:34:30.208215 INFO: Using random state 298934 for train-test-split
1 day, 12:34:30.218662 INFO: Test AUC: 0.528
1 day, 12:34:30.218722 INFO: Train AUC: 0.493
1 day, 12:34:30.218758 INFO: AUC difference: 7.11%
1 day, 12:34:30.218787 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 12:34:30.438985 INFO: Resetting torch num_threads to 80
1 day, 12:34:30.439580 PROGRESS: === Extracted 3225 precursors and 31129 fragments ===
1 day, 12:34:30.440003 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:34:30.440599 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:34:30.440697 PROGRESS: Total precursors accumulated: 585
1 day, 12:34:30.440771 PROGRESS: Target precursors: 459 (78.46%)
1 day, 12:34:30.440833 PROGRESS: Decoy precursors: 126 (21.54%)
1 day, 12:34:30.440890 PROGRESS: 
1 day, 12:34:30.441042 PROGRESS: Precursor Summary:
1 day, 12:34:30.442145 PROGRESS: Channel   0:	 0.050 FDR:   391; 0.010 FDR:   391; 0.001 FDR:   391
1 day, 12:34:30.442252 PROGRESS: 
1 day, 12:34:30.442322 PROGRESS: Protein Summary:
1 day, 12:34:30.443557 PROGRESS: Channel   0:	 0.050 FDR:   387; 0.010 FDR:   387; 0.001 FDR:   387
1 day, 12:34:30.443655 PROGRESS: =========================================================================
1 day, 12:34:30.443834 INFO: Target number of precursors reached.
1 day, 12:34:30.449234 INFO: fragments_df: keeping 1921 of 31129 [sum(precursor_idx_mask)=10931 sum(mass_error_mask)=31129 stop_rank=1921
1 day, 12:34:30.547927 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:30.667441 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:30.775120 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:30.887492 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:31.108798 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:34:31.109221 INFO: Using score_cutoff 28.052676315307618 (fac=0.99, q=1)
1 day, 12:34:31.109521 INFO: Updating optimization_manager: fwhm_rt             : 2.434283971786499 -> 2.33250093460083
1 day, 12:34:31.109601 INFO: Updating optimization_manager: fwhm_mobility       : 0.004130763933062553 -> 0.003933974076062441
1 day, 12:34:31.109654 INFO: Updating optimization_manager: score_cutoff        : 30.873869092941284 -> 28.052676315307618
1 day, 12:34:31.109706 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:31.110729 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:31.112069 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:31.112816 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:31.114961 INFO: === checking if optimization conditions were reached ===
1 day, 12:34:31.115059 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
1 day, 12:34:31.116829 INFO: Updating optimization_manager: ms2_error           : 8.996203009560706 -> 8.166996757180048
1 day, 12:34:31.116940 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 8.1670.
1 day, 12:34:31.117024 INFO: ==============================================
1 day, 12:34:31.117092 INFO: Starting optimization step 11.
1 day, 12:34:31.117148 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:34:31.117203 INFO: Using classic extraction backend
1 day, 12:34:31.117312 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:34:31.117397 INFO: === Search parameters used ===
1 day, 12:34:31.117448 INFO: rt_error       : 2099.9231665
1 day, 12:34:31.117490 INFO: mobility_error : 0.1
1 day, 12:34:31.117529 INFO: num_candidates : 3
1 day, 12:34:31.117567 INFO: ms1_error      : 30
1 day, 12:34:31.117604 INFO: ms2_error      : 8.166996757180048
1 day, 12:34:31.117641 INFO: fwhm_rt        : 2.33250093460083
1 day, 12:34:31.117678 INFO: quant_window   : 3
1 day, 12:34:31.117715 INFO: ==============================================
1 day, 12:34:31.118511 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:34:31.118554 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:34:31.118587 INFO: FWHM in RT is 2.33 seconds, sigma is 0.51
1 day, 12:34:31.118608 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.82
1 day, 12:34:31.119236 INFO: Starting candidate selection
1 day, 12:34:39.773290 INFO: Starting candidate scoring
1 day, 12:34:39.931069 INFO: Finished candidate processing
1 day, 12:34:39.931160 INFO: Collecting candidate features
1 day, 12:34:39.943283 INFO: Collecting fragment features
1 day, 12:34:39.946972 INFO: Finished candidate scoring
1 day, 12:34:39.948889 INFO: performing precursor FDR with 47 features
1 day, 12:34:39.948930 INFO: Decoy channel: -1
1 day, 12:34:39.948962 INFO: Competetive: True
1 day, 12:34:39.951809 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:34:39.953804 INFO: Using random state 298934 for train-test-split
1 day, 12:34:39.963558 INFO: Test AUC: 0.513
1 day, 12:34:39.963615 INFO: Train AUC: 0.495
1 day, 12:34:39.963643 INFO: AUC difference: 3.53%
1 day, 12:34:40.184685 INFO: Resetting torch num_threads to 80
1 day, 12:34:40.185236 PROGRESS: === Extracted 3228 precursors and 31175 fragments ===
1 day, 12:34:40.185632 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:34:40.186205 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:34:40.186294 PROGRESS: Total precursors accumulated: 586
1 day, 12:34:40.186352 PROGRESS: Target precursors: 453 (77.30%)
1 day, 12:34:40.186403 PROGRESS: Decoy precursors: 133 (22.70%)
1 day, 12:34:40.186454 PROGRESS: 
1 day, 12:34:40.186499 PROGRESS: Precursor Summary:
1 day, 12:34:40.187466 PROGRESS: Channel   0:	 0.050 FDR:   388; 0.010 FDR:   388; 0.001 FDR:   388
1 day, 12:34:40.187554 PROGRESS: 
1 day, 12:34:40.187608 PROGRESS: Protein Summary:
1 day, 12:34:40.188754 PROGRESS: Channel   0:	 0.050 FDR:   384; 0.010 FDR:   384; 0.001 FDR:   384
1 day, 12:34:40.188840 PROGRESS: =========================================================================
1 day, 12:34:40.188999 INFO: Target number of precursors reached.
1 day, 12:34:40.194437 INFO: fragments_df: keeping 1869 of 31175 [sum(precursor_idx_mask)=10836 sum(mass_error_mask)=31175 stop_rank=1869
1 day, 12:34:40.293365 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:40.406108 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:40.514700 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:40.631108 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:40.847625 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:34:40.848028 INFO: Using score_cutoff 28.76692990951538 (fac=0.99, q=1)
1 day, 12:34:40.848326 INFO: Updating optimization_manager: fwhm_rt             : 2.33250093460083 -> 2.374906539916992
1 day, 12:34:40.848404 INFO: Updating optimization_manager: fwhm_mobility       : 0.003933974076062441 -> 0.004007873125374317
1 day, 12:34:40.848457 INFO: Updating optimization_manager: score_cutoff        : 28.052676315307618 -> 28.76692990951538
1 day, 12:34:40.848507 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:40.849566 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:40.850921 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:40.851681 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:40.853778 INFO: === checking if optimization conditions were reached ===
1 day, 12:34:40.853875 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
1 day, 12:34:40.855529 INFO: Updating optimization_manager: ms2_error           : 8.166996757180048 -> 7.8841927473643585
1 day, 12:34:40.855626 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 7.8842.
1 day, 12:34:40.855689 INFO: ==============================================
1 day, 12:34:40.855751 INFO: Starting optimization step 12.
1 day, 12:34:40.855809 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:34:40.855863 INFO: Using classic extraction backend
1 day, 12:34:40.855963 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:34:40.856024 INFO: === Search parameters used ===
1 day, 12:34:40.856069 INFO: rt_error       : 2099.9231665
1 day, 12:34:40.856109 INFO: mobility_error : 0.1
1 day, 12:34:40.856149 INFO: num_candidates : 3
1 day, 12:34:40.856187 INFO: ms1_error      : 30
1 day, 12:34:40.856225 INFO: ms2_error      : 7.8841927473643585
1 day, 12:34:40.856262 INFO: fwhm_rt        : 2.374906539916992
1 day, 12:34:40.856300 INFO: quant_window   : 3
1 day, 12:34:40.856337 INFO: ==============================================
1 day, 12:34:40.857198 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:34:40.857246 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:34:40.857288 INFO: FWHM in RT is 2.37 seconds, sigma is 0.52
1 day, 12:34:40.857312 INFO: FWHM in mobility is 0.004 1/K_0, sigma is 1.86
1 day, 12:34:40.857931 INFO: Starting candidate selection
1 day, 12:34:49.611136 INFO: Starting candidate scoring
1 day, 12:34:49.779672 INFO: Finished candidate processing
1 day, 12:34:49.779907 INFO: Collecting candidate features
1 day, 12:34:49.794052 INFO: Collecting fragment features
1 day, 12:34:49.798440 INFO: Finished candidate scoring
1 day, 12:34:49.800664 INFO: performing precursor FDR with 47 features
1 day, 12:34:49.800717 INFO: Decoy channel: -1
1 day, 12:34:49.800742 INFO: Competetive: True
1 day, 12:34:49.804022 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:34:49.806285 INFO: Using random state 298934 for train-test-split
1 day, 12:34:49.818658 INFO: Test AUC: 0.518
1 day, 12:34:49.818730 INFO: Train AUC: 0.498
1 day, 12:34:49.818760 INFO: AUC difference: 3.95%
1 day, 12:34:50.040250 INFO: Resetting torch num_threads to 80
1 day, 12:34:50.040999 PROGRESS: === Extracted 3210 precursors and 30507 fragments ===
1 day, 12:34:50.041503 INFO: === FDR correction performed with classifier version 1 ===
1 day, 12:34:50.042167 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:34:50.042258 PROGRESS: Total precursors accumulated: 587
1 day, 12:34:50.042320 PROGRESS: Target precursors: 457 (77.85%)
1 day, 12:34:50.042372 PROGRESS: Decoy precursors: 130 (22.15%)
1 day, 12:34:50.042421 PROGRESS: 
1 day, 12:34:50.042471 PROGRESS: Precursor Summary:
1 day, 12:34:50.043488 PROGRESS: Channel   0:	 0.050 FDR:   393; 0.010 FDR:   393; 0.001 FDR:   393
1 day, 12:34:50.043582 PROGRESS: 
1 day, 12:34:50.043641 PROGRESS: Protein Summary:
1 day, 12:34:50.044813 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   389; 0.001 FDR:   389
1 day, 12:34:50.044905 PROGRESS: =========================================================================
1 day, 12:34:50.045098 INFO: Target number of precursors reached.
1 day, 12:34:50.050517 INFO: fragments_df: keeping 1867 of 30507 [sum(precursor_idx_mask)=10793 sum(mass_error_mask)=30507 stop_rank=1867
1 day, 12:34:50.343245 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:50.477462 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:50.609613 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:50.728704 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:50.942984 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:34:50.943511 INFO: Using score_cutoff 29.571922073364256 (fac=0.99, q=1)
1 day, 12:34:50.943844 INFO: Updating optimization_manager: fwhm_rt             : 2.374906539916992 -> 2.262693405151367
1 day, 12:34:50.943928 INFO: Updating optimization_manager: fwhm_mobility       : 0.004007873125374317 -> 0.0037658922374248505
1 day, 12:34:50.943986 INFO: Updating optimization_manager: score_cutoff        : 28.76692990951538 -> 29.571922073364256
1 day, 12:34:50.944043 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:50.945288 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:50.946638 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:50.947417 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:50.949563 INFO: === checking if optimization conditions were reached ===
1 day, 12:34:50.949677 PROGRESS: === Optimization of ms2_error has been performed 11 time(s); minimum number is 2 ===
1 day, 12:34:50.950530 INFO: Updating optimization_manager: ms2_error           : 7.8841927473643585 -> 15.65170738607732
1 day, 12:34:50.950653 INFO: Updating optimization_manager: classifier_version  : 1 -> 6
1 day, 12:34:50.950747 INFO: Updating optimization_manager: score_cutoff        : 29.571922073364256 -> 31.667250177383423
1 day, 12:34:50.950832 INFO: Updating optimization_manager: fwhm_rt             : 2.262693405151367 -> 2.8779819011688232
1 day, 12:34:50.950926 INFO: Updating optimization_manager: fwhm_mobility       : 0.0037658922374248505 -> 0.00553581677377224
1 day, 12:34:50.951011 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 15.6517 found after 11 searches.
1 day, 12:34:50.951074 INFO: ==============================================
1 day, 12:34:50.951139 PROGRESS: Optimization finished for ms2_error.
1 day, 12:34:51.113272 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:34:51.114991 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:34:51.116368 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:34:51.117164 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:34:51.146620 INFO: Starting optimization step 0.
1 day, 12:34:51.146792 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:34:51.146872 INFO: Using classic extraction backend
1 day, 12:34:51.147005 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:34:51.147082 INFO: === Search parameters used ===
1 day, 12:34:51.147135 INFO: rt_error       : 2099.9231665
1 day, 12:34:51.147180 INFO: mobility_error : 0.1
1 day, 12:34:51.147224 INFO: num_candidates : 3
1 day, 12:34:51.147268 INFO: ms1_error      : 30
1 day, 12:34:51.147311 INFO: ms2_error      : 15.65170738607732
1 day, 12:34:51.147353 INFO: fwhm_rt        : 2.8779819011688232
1 day, 12:34:51.147393 INFO: quant_window   : 3
1 day, 12:34:51.147434 INFO: ==============================================
1 day, 12:34:51.148383 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:34:51.148431 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:34:51.148468 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1 day, 12:34:51.148491 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.57
1 day, 12:34:51.149282 INFO: Starting candidate selection
1 day, 12:34:59.892145 INFO: Starting candidate scoring
1 day, 12:35:00.095836 INFO: Finished candidate processing
1 day, 12:35:00.095934 INFO: Collecting candidate features
1 day, 12:35:00.109050 INFO: Collecting fragment features
1 day, 12:35:00.113653 INFO: Finished candidate scoring
1 day, 12:35:00.115606 INFO: performing precursor FDR with 47 features
1 day, 12:35:00.115651 INFO: Decoy channel: -1
1 day, 12:35:00.115682 INFO: Competetive: True
1 day, 12:35:00.118600 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:00.121214 INFO: Using random state 314585 for train-test-split
1 day, 12:35:00.137794 INFO: Test AUC: 0.501
1 day, 12:35:00.137892 INFO: Train AUC: 0.509
1 day, 12:35:00.137956 INFO: AUC difference: 1.56%
1 day, 12:35:00.354779 INFO: Resetting torch num_threads to 80
1 day, 12:35:00.355386 PROGRESS: === Extracted 3234 precursors and 33558 fragments ===
1 day, 12:35:00.355822 INFO: === FDR correction performed with classifier version 6 ===
1 day, 12:35:00.356439 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:00.356538 PROGRESS: Total precursors accumulated: 589
1 day, 12:35:00.356620 PROGRESS: Target precursors: 460 (78.10%)
1 day, 12:35:00.356685 PROGRESS: Decoy precursors: 129 (21.90%)
1 day, 12:35:00.356743 PROGRESS: 
1 day, 12:35:00.356798 PROGRESS: Precursor Summary:
1 day, 12:35:00.357882 PROGRESS: Channel   0:	 0.050 FDR:   400; 0.010 FDR:   400; 0.001 FDR:   400
1 day, 12:35:00.357983 PROGRESS: 
1 day, 12:35:00.358055 PROGRESS: Protein Summary:
1 day, 12:35:00.359274 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   395; 0.001 FDR:   395
1 day, 12:35:00.359376 PROGRESS: =========================================================================
1 day, 12:35:00.359555 INFO: Target number of precursors reached.
1 day, 12:35:00.365009 INFO: fragments_df: keeping 2078 of 33558 [sum(precursor_idx_mask)=11869 sum(mass_error_mask)=33558 stop_rank=2078
1 day, 12:35:00.464286 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:00.578386 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:00.688124 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:00.798033 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:01.031358 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:01.031798 INFO: Using score_cutoff 34.583625995635984 (fac=0.99, q=1)
1 day, 12:35:01.032128 INFO: Updating optimization_manager: fwhm_rt             : 2.8779819011688232 -> 2.8005359172821045
1 day, 12:35:01.032219 INFO: Updating optimization_manager: fwhm_mobility       : 0.00553581677377224 -> 0.005595320835709572
1 day, 12:35:01.032297 INFO: Updating optimization_manager: score_cutoff        : 31.667250177383423 -> 34.583625995635984
1 day, 12:35:01.032363 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:01.033435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:01.034784 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:01.035569 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:01.037718 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:01.037829 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 12:35:01.039391 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 1302.9503378862496
1 day, 12:35:01.039500 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1302.9503.
1 day, 12:35:01.039578 INFO: ==============================================
1 day, 12:35:01.039661 INFO: Starting optimization step 1.
1 day, 12:35:01.039732 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:01.039798 INFO: Using classic extraction backend
1 day, 12:35:01.039923 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:01.040001 INFO: === Search parameters used ===
1 day, 12:35:01.040059 INFO: rt_error       : 1302.9503378862496
1 day, 12:35:01.040112 INFO: mobility_error : 0.1
1 day, 12:35:01.040162 INFO: num_candidates : 3
1 day, 12:35:01.040215 INFO: ms1_error      : 30
1 day, 12:35:01.040264 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:01.040323 INFO: fwhm_rt        : 2.8005359172821045
1 day, 12:35:01.040375 INFO: quant_window   : 3
1 day, 12:35:01.040424 INFO: ==============================================
1 day, 12:35:01.041461 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:01.041509 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:01.041553 INFO: FWHM in RT is 2.80 seconds, sigma is 0.62
1 day, 12:35:01.041589 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.60
1 day, 12:35:01.042197 INFO: Starting candidate selection
1 day, 12:35:08.072011 INFO: Starting candidate scoring
1 day, 12:35:08.325919 INFO: Finished candidate processing
1 day, 12:35:08.326077 INFO: Collecting candidate features
1 day, 12:35:08.356103 INFO: Collecting fragment features
1 day, 12:35:08.364842 INFO: Finished candidate scoring
1 day, 12:35:08.368036 INFO: performing precursor FDR with 47 features
1 day, 12:35:08.368143 INFO: Decoy channel: -1
1 day, 12:35:08.368201 INFO: Competetive: True
1 day, 12:35:08.374090 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:08.377171 INFO: Using random state 314585 for train-test-split
1 day, 12:35:08.392199 INFO: Test AUC: 0.501
1 day, 12:35:08.392292 INFO: Train AUC: 0.515
1 day, 12:35:08.392340 INFO: AUC difference: 2.69%
1 day, 12:35:08.607528 INFO: Resetting torch num_threads to 80
1 day, 12:35:08.608068 PROGRESS: === Extracted 3224 precursors and 33363 fragments ===
1 day, 12:35:08.608475 INFO: === FDR correction performed with classifier version 6 ===
1 day, 12:35:08.609057 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:08.609148 PROGRESS: Total precursors accumulated: 588
1 day, 12:35:08.609209 PROGRESS: Target precursors: 465 (79.08%)
1 day, 12:35:08.609271 PROGRESS: Decoy precursors: 123 (20.92%)
1 day, 12:35:08.609318 PROGRESS: 
1 day, 12:35:08.609364 PROGRESS: Precursor Summary:
1 day, 12:35:08.610341 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   403; 0.001 FDR:   403
1 day, 12:35:08.610429 PROGRESS: 
1 day, 12:35:08.610484 PROGRESS: Protein Summary:
1 day, 12:35:08.611628 PROGRESS: Channel   0:	 0.050 FDR:   397; 0.010 FDR:   397; 0.001 FDR:   397
1 day, 12:35:08.611719 PROGRESS: =========================================================================
1 day, 12:35:08.611865 INFO: Target number of precursors reached.
1 day, 12:35:08.617494 INFO: fragments_df: keeping 2082 of 33363 [sum(precursor_idx_mask)=11984 sum(mass_error_mask)=33363 stop_rank=2082
1 day, 12:35:08.734916 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:08.869998 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:08.995548 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:09.128241 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:09.405991 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:09.406420 INFO: Using score_cutoff 32.99317632751465 (fac=0.99, q=1)
1 day, 12:35:09.406722 INFO: Updating optimization_manager: fwhm_rt             : 2.8005359172821045 -> 2.813856840133667
1 day, 12:35:09.406801 INFO: Updating optimization_manager: fwhm_mobility       : 0.005595320835709572 -> 0.005538898520171642
1 day, 12:35:09.406855 INFO: Updating optimization_manager: score_cutoff        : 34.583625995635984 -> 32.99317632751465
1 day, 12:35:09.406907 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:09.407938 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:09.409251 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:09.410002 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:09.412056 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:09.412154 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 12:35:09.413771 INFO: Updating optimization_manager: rt_error            : 1302.9503378862496 -> 899.9977528863399
1 day, 12:35:09.413872 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 899.9978.
1 day, 12:35:09.413937 INFO: ==============================================
1 day, 12:35:09.414001 INFO: Starting optimization step 2.
1 day, 12:35:09.414056 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:09.414108 INFO: Using classic extraction backend
1 day, 12:35:09.414222 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:09.414288 INFO: === Search parameters used ===
1 day, 12:35:09.414334 INFO: rt_error       : 899.9977528863399
1 day, 12:35:09.414375 INFO: mobility_error : 0.1
1 day, 12:35:09.414419 INFO: num_candidates : 3
1 day, 12:35:09.414459 INFO: ms1_error      : 30
1 day, 12:35:09.414498 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:09.414536 INFO: fwhm_rt        : 2.813856840133667
1 day, 12:35:09.414575 INFO: quant_window   : 3
1 day, 12:35:09.414613 INFO: ==============================================
1 day, 12:35:09.415406 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:09.415451 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:09.415485 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 12:35:09.415508 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.57
1 day, 12:35:09.416395 INFO: Starting candidate selection
1 day, 12:35:14.523385 INFO: Starting candidate scoring
1 day, 12:35:14.740512 INFO: Finished candidate processing
1 day, 12:35:14.741441 INFO: Collecting candidate features
1 day, 12:35:14.754752 INFO: Collecting fragment features
1 day, 12:35:14.759041 INFO: Finished candidate scoring
1 day, 12:35:14.760913 INFO: performing precursor FDR with 47 features
1 day, 12:35:14.760972 INFO: Decoy channel: -1
1 day, 12:35:14.760998 INFO: Competetive: True
1 day, 12:35:14.763911 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:14.765954 INFO: Using random state 314585 for train-test-split
1 day, 12:35:14.776233 INFO: Test AUC: 0.476
1 day, 12:35:14.776290 INFO: Train AUC: 0.517
1 day, 12:35:14.776319 INFO: AUC difference: 7.95%
1 day, 12:35:14.776342 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 12:35:14.988617 INFO: Resetting torch num_threads to 80
1 day, 12:35:14.989183 PROGRESS: === Extracted 3221 precursors and 33395 fragments ===
1 day, 12:35:14.989591 INFO: === FDR correction performed with classifier version 6 ===
1 day, 12:35:14.990140 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:14.990229 PROGRESS: Total precursors accumulated: 587
1 day, 12:35:14.990287 PROGRESS: Target precursors: 456 (77.68%)
1 day, 12:35:14.990335 PROGRESS: Decoy precursors: 131 (22.32%)
1 day, 12:35:14.990380 PROGRESS: 
1 day, 12:35:14.990426 PROGRESS: Precursor Summary:
1 day, 12:35:14.991387 PROGRESS: Channel   0:	 0.050 FDR:   402; 0.010 FDR:   402; 0.001 FDR:   402
1 day, 12:35:14.991475 PROGRESS: 
1 day, 12:35:14.991531 PROGRESS: Protein Summary:
1 day, 12:35:14.992663 PROGRESS: Channel   0:	 0.050 FDR:   396; 0.010 FDR:   396; 0.001 FDR:   396
1 day, 12:35:14.992770 PROGRESS: =========================================================================
1 day, 12:35:14.993001 INFO: Target number of precursors reached.
1 day, 12:35:14.998426 INFO: fragments_df: keeping 2064 of 33395 [sum(precursor_idx_mask)=11985 sum(mass_error_mask)=33395 stop_rank=2064
1 day, 12:35:15.101053 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:15.216136 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:15.324302 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:15.436411 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:15.675758 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:15.676168 INFO: Using score_cutoff 33.19290292854309 (fac=0.99, q=1)
1 day, 12:35:15.676471 INFO: Updating optimization_manager: fwhm_rt             : 2.813856840133667 -> 2.8263440132141113
1 day, 12:35:15.676549 INFO: Updating optimization_manager: fwhm_mobility       : 0.005538898520171642 -> 0.005604940466582775
1 day, 12:35:15.676606 INFO: Updating optimization_manager: score_cutoff        : 32.99317632751465 -> 33.19290292854309
1 day, 12:35:15.676659 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:15.677702 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:15.679008 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:15.679758 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:15.681791 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:15.681892 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 12:35:15.683579 INFO: Updating optimization_manager: rt_error            : 899.9977528863399 -> 814.5305851660243
1 day, 12:35:15.683675 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 814.5306.
1 day, 12:35:15.683739 INFO: ==============================================
1 day, 12:35:15.683807 INFO: Starting optimization step 3.
1 day, 12:35:15.683863 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:15.683917 INFO: Using classic extraction backend
1 day, 12:35:15.684018 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:15.684083 INFO: === Search parameters used ===
1 day, 12:35:15.684130 INFO: rt_error       : 814.5305851660243
1 day, 12:35:15.684172 INFO: mobility_error : 0.1
1 day, 12:35:15.684214 INFO: num_candidates : 3
1 day, 12:35:15.684254 INFO: ms1_error      : 30
1 day, 12:35:15.684293 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:15.684342 INFO: fwhm_rt        : 2.8263440132141113
1 day, 12:35:15.684381 INFO: quant_window   : 3
1 day, 12:35:15.684419 INFO: ==============================================
1 day, 12:35:15.686397 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:15.686446 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:15.686480 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1 day, 12:35:15.686502 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.60
1 day, 12:35:15.687205 INFO: Starting candidate selection
1 day, 12:35:21.006868 INFO: Starting candidate scoring
1 day, 12:35:21.219990 INFO: Finished candidate processing
1 day, 12:35:21.220121 INFO: Collecting candidate features
1 day, 12:35:21.234200 INFO: Collecting fragment features
1 day, 12:35:21.238170 INFO: Finished candidate scoring
1 day, 12:35:21.240052 INFO: performing precursor FDR with 47 features
1 day, 12:35:21.240094 INFO: Decoy channel: -1
1 day, 12:35:21.240119 INFO: Competetive: True
1 day, 12:35:21.244025 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:21.246390 INFO: Using random state 314585 for train-test-split
1 day, 12:35:21.256919 INFO: Test AUC: 0.506
1 day, 12:35:21.256989 INFO: Train AUC: 0.511
1 day, 12:35:21.257024 INFO: AUC difference: 1.12%
1 day, 12:35:21.473272 INFO: Resetting torch num_threads to 80
1 day, 12:35:21.473834 PROGRESS: === Extracted 3222 precursors and 33414 fragments ===
1 day, 12:35:21.474280 INFO: === FDR correction performed with classifier version 6 ===
1 day, 12:35:21.474840 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:21.474925 PROGRESS: Total precursors accumulated: 588
1 day, 12:35:21.474983 PROGRESS: Target precursors: 458 (77.89%)
1 day, 12:35:21.475039 PROGRESS: Decoy precursors: 130 (22.11%)
1 day, 12:35:21.475085 PROGRESS: 
1 day, 12:35:21.475127 PROGRESS: Precursor Summary:
1 day, 12:35:21.476086 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   403; 0.001 FDR:   403
1 day, 12:35:21.476172 PROGRESS: 
1 day, 12:35:21.476226 PROGRESS: Protein Summary:
1 day, 12:35:21.477360 PROGRESS: Channel   0:	 0.050 FDR:   397; 0.010 FDR:   397; 0.001 FDR:   397
1 day, 12:35:21.477446 PROGRESS: =========================================================================
1 day, 12:35:21.477585 INFO: Target number of precursors reached.
1 day, 12:35:21.483096 INFO: fragments_df: keeping 2033 of 33414 [sum(precursor_idx_mask)=11998 sum(mass_error_mask)=33414 stop_rank=2033
1 day, 12:35:21.582322 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:21.697328 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:21.808210 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:21.919179 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:22.155243 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:22.155660 INFO: Using score_cutoff 33.360554457092285 (fac=0.99, q=1)
1 day, 12:35:22.155985 INFO: Updating optimization_manager: fwhm_rt             : 2.8263440132141113 -> 2.84551739692688
1 day, 12:35:22.156062 INFO: Updating optimization_manager: fwhm_mobility       : 0.005604940466582775 -> 0.0054546743631362915
1 day, 12:35:22.156115 INFO: Updating optimization_manager: score_cutoff        : 33.19290292854309 -> 33.360554457092285
1 day, 12:35:22.156177 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:22.157221 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:22.158528 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:22.159286 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:22.161838 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:22.161948 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 12:35:22.163652 INFO: Updating optimization_manager: rt_error            : 814.5305851660243 -> 782.7188284603353
1 day, 12:35:22.163755 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 782.7188.
1 day, 12:35:22.163820 INFO: ==============================================
1 day, 12:35:22.163889 INFO: Starting optimization step 4.
1 day, 12:35:22.163945 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:22.164001 INFO: Using classic extraction backend
1 day, 12:35:22.164152 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:22.164217 INFO: === Search parameters used ===
1 day, 12:35:22.164264 INFO: rt_error       : 782.7188284603353
1 day, 12:35:22.164305 INFO: mobility_error : 0.1
1 day, 12:35:22.164346 INFO: num_candidates : 3
1 day, 12:35:22.164384 INFO: ms1_error      : 30
1 day, 12:35:22.164422 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:22.164460 INFO: fwhm_rt        : 2.84551739692688
1 day, 12:35:22.164503 INFO: quant_window   : 3
1 day, 12:35:22.164541 INFO: ==============================================
1 day, 12:35:22.165538 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:22.165584 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:22.165626 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 12:35:22.165648 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
1 day, 12:35:22.166299 INFO: Starting candidate selection
1 day, 12:35:26.265055 INFO: Starting candidate scoring
1 day, 12:35:26.487307 INFO: Finished candidate processing
1 day, 12:35:26.487439 INFO: Collecting candidate features
1 day, 12:35:26.502386 INFO: Collecting fragment features
1 day, 12:35:26.506185 INFO: Finished candidate scoring
1 day, 12:35:26.508034 INFO: performing precursor FDR with 47 features
1 day, 12:35:26.508077 INFO: Decoy channel: -1
1 day, 12:35:26.508100 INFO: Competetive: True
1 day, 12:35:26.510899 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:26.512861 INFO: Using random state 314585 for train-test-split
1 day, 12:35:26.523336 INFO: Test AUC: 0.510
1 day, 12:35:26.523394 INFO: Train AUC: 0.508
1 day, 12:35:26.523422 INFO: AUC difference: 0.39%
1 day, 12:35:26.734785 INFO: Resetting torch num_threads to 80
1 day, 12:35:26.735312 PROGRESS: === Extracted 3225 precursors and 33421 fragments ===
1 day, 12:35:26.735700 INFO: === FDR correction performed with classifier version 6 ===
1 day, 12:35:26.736251 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:26.736337 PROGRESS: Total precursors accumulated: 588
1 day, 12:35:26.736393 PROGRESS: Target precursors: 459 (78.06%)
1 day, 12:35:26.736442 PROGRESS: Decoy precursors: 129 (21.94%)
1 day, 12:35:26.736485 PROGRESS: 
1 day, 12:35:26.736528 PROGRESS: Precursor Summary:
1 day, 12:35:26.737511 PROGRESS: Channel   0:	 0.050 FDR:   404; 0.010 FDR:   404; 0.001 FDR:   404
1 day, 12:35:26.737600 PROGRESS: 
1 day, 12:35:26.737655 PROGRESS: Protein Summary:
1 day, 12:35:26.738806 PROGRESS: Channel   0:	 0.050 FDR:   399; 0.010 FDR:   399; 0.001 FDR:   399
1 day, 12:35:26.738895 PROGRESS: =========================================================================
1 day, 12:35:26.739025 INFO: Target number of precursors reached.
1 day, 12:35:26.744445 INFO: fragments_df: keeping 2075 of 33421 [sum(precursor_idx_mask)=12020 sum(mass_error_mask)=33421 stop_rank=2075
1 day, 12:35:26.843853 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:26.952959 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:27.063256 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:27.174604 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:27.418846 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:27.419259 INFO: Using score_cutoff 33.348848057556154 (fac=0.99, q=1)
1 day, 12:35:27.419555 INFO: Updating optimization_manager: fwhm_rt             : 2.84551739692688 -> 2.8473119735717773
1 day, 12:35:27.419633 INFO: Updating optimization_manager: fwhm_mobility       : 0.0054546743631362915 -> 0.005456320475786924
1 day, 12:35:27.419694 INFO: Updating optimization_manager: score_cutoff        : 33.360554457092285 -> 33.348848057556154
1 day, 12:35:27.419747 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:27.420761 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:27.422084 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:27.422838 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:27.424863 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:27.424965 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 12:35:27.425913 INFO: Updating optimization_manager: rt_error            : 782.7188284603353 -> 782.7188284603353
1 day, 12:35:27.426029 INFO: Updating optimization_manager: classifier_version  : 6 -> 17
1 day, 12:35:27.426118 INFO: Updating optimization_manager: score_cutoff        : 33.348848057556154 -> 33.348848057556154
1 day, 12:35:27.426198 INFO: Updating optimization_manager: fwhm_rt             : 2.8473119735717773 -> 2.8473119735717773
1 day, 12:35:27.426275 INFO: Updating optimization_manager: fwhm_mobility       : 0.005456320475786924 -> 0.005456320475786924
1 day, 12:35:27.426351 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 782.7188 found after 5 searches.
1 day, 12:35:27.426417 INFO: ==============================================
1 day, 12:35:27.426481 PROGRESS: Optimization finished for rt_error.
1 day, 12:35:27.525480 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:27.526563 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:27.527864 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:27.528634 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:27.555216 INFO: Starting optimization step 0.
1 day, 12:35:27.555350 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:27.555419 INFO: Using classic extraction backend
1 day, 12:35:27.555528 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:27.555597 INFO: === Search parameters used ===
1 day, 12:35:27.555645 INFO: rt_error       : 782.7188284603353
1 day, 12:35:27.555693 INFO: mobility_error : 0.1
1 day, 12:35:27.555734 INFO: num_candidates : 3
1 day, 12:35:27.555775 INFO: ms1_error      : 30
1 day, 12:35:27.555815 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:27.555854 INFO: fwhm_rt        : 2.8473119735717773
1 day, 12:35:27.555893 INFO: quant_window   : 3
1 day, 12:35:27.555933 INFO: ==============================================
1 day, 12:35:27.556895 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:27.556949 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:27.556986 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 12:35:27.557007 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
1 day, 12:35:27.557690 INFO: Starting candidate selection
1 day, 12:35:31.908247 INFO: Starting candidate scoring
1 day, 12:35:32.139149 INFO: Finished candidate processing
1 day, 12:35:32.139334 INFO: Collecting candidate features
1 day, 12:35:32.154611 INFO: Collecting fragment features
1 day, 12:35:32.159075 INFO: Finished candidate scoring
1 day, 12:35:32.160962 INFO: performing precursor FDR with 47 features
1 day, 12:35:32.161011 INFO: Decoy channel: -1
1 day, 12:35:32.161037 INFO: Competetive: True
1 day, 12:35:32.163821 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:32.165835 INFO: Using random state 231642 for train-test-split
1 day, 12:35:32.176547 INFO: Test AUC: 0.515
1 day, 12:35:32.176606 INFO: Train AUC: 0.505
1 day, 12:35:32.176635 INFO: AUC difference: 1.97%
1 day, 12:35:32.389797 INFO: Resetting torch num_threads to 80
1 day, 12:35:32.390306 PROGRESS: === Extracted 3221 precursors and 33404 fragments ===
1 day, 12:35:32.390713 INFO: === FDR correction performed with classifier version 17 ===
1 day, 12:35:32.391266 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:32.391351 PROGRESS: Total precursors accumulated: 587
1 day, 12:35:32.391407 PROGRESS: Target precursors: 456 (77.68%)
1 day, 12:35:32.391455 PROGRESS: Decoy precursors: 131 (22.32%)
1 day, 12:35:32.391500 PROGRESS: 
1 day, 12:35:32.391541 PROGRESS: Precursor Summary:
1 day, 12:35:32.392507 PROGRESS: Channel   0:	 0.050 FDR:   401; 0.010 FDR:   401; 0.001 FDR:   401
1 day, 12:35:32.392594 PROGRESS: 
1 day, 12:35:32.392648 PROGRESS: Protein Summary:
1 day, 12:35:32.393809 PROGRESS: Channel   0:	 0.050 FDR:   396; 0.010 FDR:   396; 0.001 FDR:   396
1 day, 12:35:32.393898 PROGRESS: =========================================================================
1 day, 12:35:32.394031 INFO: Target number of precursors reached.
1 day, 12:35:32.399771 INFO: fragments_df: keeping 2056 of 33404 [sum(precursor_idx_mask)=11872 sum(mass_error_mask)=33404 stop_rank=2056
1 day, 12:35:32.498828 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:32.607284 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:32.718393 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:32.829057 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:33.072799 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:33.073225 INFO: Using score_cutoff 33.339465293884274 (fac=0.99, q=1)
1 day, 12:35:33.073525 INFO: Updating optimization_manager: fwhm_rt             : 2.8473119735717773 -> 2.849106550216675
1 day, 12:35:33.073610 INFO: Updating optimization_manager: fwhm_mobility       : 0.005456320475786924 -> 0.005499923136085272
1 day, 12:35:33.073665 INFO: Updating optimization_manager: score_cutoff        : 33.348848057556154 -> 33.339465293884274
1 day, 12:35:33.073718 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:33.074733 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:33.076039 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:33.076785 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:33.079388 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:33.079490 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
1 day, 12:35:33.080881 INFO: Updating optimization_manager: ms1_error           : 30 -> 19.706368216936717
1 day, 12:35:33.080984 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 19.7064.
1 day, 12:35:33.081048 INFO: ==============================================
1 day, 12:35:33.081111 INFO: Starting optimization step 1.
1 day, 12:35:33.081166 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:33.081216 INFO: Using classic extraction backend
1 day, 12:35:33.081327 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:33.081389 INFO: === Search parameters used ===
1 day, 12:35:33.081434 INFO: rt_error       : 782.7188284603353
1 day, 12:35:33.081475 INFO: mobility_error : 0.1
1 day, 12:35:33.081515 INFO: num_candidates : 3
1 day, 12:35:33.081554 INFO: ms1_error      : 19.706368216936717
1 day, 12:35:33.081598 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:33.081637 INFO: fwhm_rt        : 2.849106550216675
1 day, 12:35:33.081674 INFO: quant_window   : 3
1 day, 12:35:33.081711 INFO: ==============================================
1 day, 12:35:33.082598 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:33.082642 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:33.082675 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 12:35:33.082696 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.55
1 day, 12:35:33.083323 INFO: Starting candidate selection
1 day, 12:35:37.418480 INFO: Starting candidate scoring
1 day, 12:35:37.619277 INFO: Finished candidate processing
1 day, 12:35:37.619372 INFO: Collecting candidate features
1 day, 12:35:37.632412 INFO: Collecting fragment features
1 day, 12:35:37.636088 INFO: Finished candidate scoring
1 day, 12:35:37.637868 INFO: performing precursor FDR with 47 features
1 day, 12:35:37.637910 INFO: Decoy channel: -1
1 day, 12:35:37.637935 INFO: Competetive: True
1 day, 12:35:37.640645 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:37.642612 INFO: Using random state 231642 for train-test-split
1 day, 12:35:37.652924 INFO: Test AUC: 0.532
1 day, 12:35:37.652989 INFO: Train AUC: 0.499
1 day, 12:35:37.653019 INFO: AUC difference: 6.67%
1 day, 12:35:37.653041 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 12:35:37.871630 INFO: Resetting torch num_threads to 80
1 day, 12:35:37.872167 PROGRESS: === Extracted 3214 precursors and 33248 fragments ===
1 day, 12:35:37.872563 INFO: === FDR correction performed with classifier version 17 ===
1 day, 12:35:37.873136 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:37.873224 PROGRESS: Total precursors accumulated: 589
1 day, 12:35:37.873282 PROGRESS: Target precursors: 426 (72.33%)
1 day, 12:35:37.873331 PROGRESS: Decoy precursors: 163 (27.67%)
1 day, 12:35:37.873374 PROGRESS: 
1 day, 12:35:37.873415 PROGRESS: Precursor Summary:
1 day, 12:35:37.874369 PROGRESS: Channel   0:	 0.050 FDR:   349; 0.010 FDR:   349; 0.001 FDR:   349
1 day, 12:35:37.874456 PROGRESS: 
1 day, 12:35:37.874510 PROGRESS: Protein Summary:
1 day, 12:35:37.875629 PROGRESS: Channel   0:	 0.050 FDR:   347; 0.010 FDR:   347; 0.001 FDR:   347
1 day, 12:35:37.875716 PROGRESS: =========================================================================
1 day, 12:35:37.875846 INFO: Target number of precursors reached.
1 day, 12:35:37.880912 INFO: fragments_df: keeping 1799 of 33248 [sum(precursor_idx_mask)=10288 sum(mass_error_mask)=33248 stop_rank=1799
1 day, 12:35:37.980409 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:38.086312 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:38.192785 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:38.300550 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:38.511665 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:38.512074 INFO: Using score_cutoff 31.212379989624022 (fac=0.99, q=1)
1 day, 12:35:38.512383 INFO: Updating optimization_manager: fwhm_rt             : 2.849106550216675 -> 2.7854177951812744
1 day, 12:35:38.512459 INFO: Updating optimization_manager: fwhm_mobility       : 0.005499923136085272 -> 0.005414838902652264
1 day, 12:35:38.512511 INFO: Updating optimization_manager: score_cutoff        : 33.339465293884274 -> 31.212379989624022
1 day, 12:35:38.512561 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:38.513584 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:38.514893 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:38.515641 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:38.517765 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:38.517866 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
1 day, 12:35:38.519401 INFO: Updating optimization_manager: ms1_error           : 19.706368216936717 -> 12.452928035004609
1 day, 12:35:38.519497 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 12.4529.
1 day, 12:35:38.519559 INFO: ==============================================
1 day, 12:35:38.519623 INFO: Starting optimization step 2.
1 day, 12:35:38.519685 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:38.519738 INFO: Using classic extraction backend
1 day, 12:35:38.519841 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:38.519910 INFO: === Search parameters used ===
1 day, 12:35:38.519957 INFO: rt_error       : 782.7188284603353
1 day, 12:35:38.519999 INFO: mobility_error : 0.1
1 day, 12:35:38.520039 INFO: num_candidates : 3
1 day, 12:35:38.520078 INFO: ms1_error      : 12.452928035004609
1 day, 12:35:38.520118 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:38.520157 INFO: fwhm_rt        : 2.7854177951812744
1 day, 12:35:38.520195 INFO: quant_window   : 3
1 day, 12:35:38.520233 INFO: ==============================================
1 day, 12:35:38.521129 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:38.521175 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:38.521208 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 12:35:38.521230 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.51
1 day, 12:35:38.521875 INFO: Starting candidate selection
1 day, 12:35:42.583867 INFO: Starting candidate scoring
1 day, 12:35:42.794290 INFO: Finished candidate processing
1 day, 12:35:42.794417 INFO: Collecting candidate features
1 day, 12:35:42.805854 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3220)
1 day, 12:35:42.809079 INFO: Collecting fragment features
1 day, 12:35:42.813629 INFO: Finished candidate scoring
1 day, 12:35:42.815433 INFO: performing precursor FDR with 47 features
1 day, 12:35:42.815476 INFO: Decoy channel: -1
1 day, 12:35:42.815499 INFO: Competetive: True
1 day, 12:35:42.818703 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:42.819940 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 12:35:42.820877 INFO: Using random state 231642 for train-test-split
1 day, 12:35:42.831167 INFO: Test AUC: 0.525
1 day, 12:35:42.831226 INFO: Train AUC: 0.499
1 day, 12:35:42.831255 INFO: AUC difference: 5.24%
1 day, 12:35:42.831277 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 12:35:43.048703 INFO: Resetting torch num_threads to 80
1 day, 12:35:43.049245 PROGRESS: === Extracted 3220 precursors and 33138 fragments ===
1 day, 12:35:43.049642 INFO: === FDR correction performed with classifier version 17 ===
1 day, 12:35:43.050257 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:43.050346 PROGRESS: Total precursors accumulated: 590
1 day, 12:35:43.050404 PROGRESS: Target precursors: 401 (67.97%)
1 day, 12:35:43.050453 PROGRESS: Decoy precursors: 189 (32.03%)
1 day, 12:35:43.050498 PROGRESS: 
1 day, 12:35:43.050540 PROGRESS: Precursor Summary:
1 day, 12:35:43.051489 PROGRESS: Channel   0:	 0.050 FDR:   300; 0.010 FDR:   300; 0.001 FDR:   300
1 day, 12:35:43.051578 PROGRESS: 
1 day, 12:35:43.051640 PROGRESS: Protein Summary:
1 day, 12:35:43.052726 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   298; 0.001 FDR:   298
1 day, 12:35:43.052815 PROGRESS: =========================================================================
1 day, 12:35:43.052953 INFO: Target number of precursors reached.
1 day, 12:35:43.057915 INFO: fragments_df: keeping 1482 of 33138 [sum(precursor_idx_mask)=8800 sum(mass_error_mask)=33138 stop_rank=1482
1 day, 12:35:43.158196 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:43.266986 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:43.371320 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:43.476215 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:43.664304 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:43.664727 INFO: Using score_cutoff 30.14893792591095 (fac=0.99, q=1)
1 day, 12:35:43.665037 INFO: Updating optimization_manager: fwhm_rt             : 2.7854177951812744 -> 2.814425468444824
1 day, 12:35:43.665119 INFO: Updating optimization_manager: fwhm_mobility       : 0.005414838902652264 -> 0.005584824364632368
1 day, 12:35:43.665173 INFO: Updating optimization_manager: score_cutoff        : 31.212379989624022 -> 30.14893792591095
1 day, 12:35:43.665226 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:43.666262 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:43.667572 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:43.668332 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:43.670889 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:43.671001 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
1 day, 12:35:43.671754 INFO: Updating optimization_manager: ms1_error           : 12.452928035004609 -> 19.706368216936717
1 day, 12:35:43.671875 INFO: Updating optimization_manager: classifier_version  : 17 -> 19
1 day, 12:35:43.671967 INFO: Updating optimization_manager: score_cutoff        : 30.14893792591095 -> 31.212379989624022
1 day, 12:35:43.672050 INFO: Updating optimization_manager: fwhm_rt             : 2.814425468444824 -> 2.7854177951812744
1 day, 12:35:43.672131 INFO: Updating optimization_manager: fwhm_mobility       : 0.005584824364632368 -> 0.005414838902652264
1 day, 12:35:43.672209 PROGRESS: ✅ ms1_error      : optimization just completed. Optimal parameter 19.7064 found after 3 searches.
1 day, 12:35:43.672269 INFO: ==============================================
1 day, 12:35:43.672333 PROGRESS: Optimization finished for ms1_error.
1 day, 12:35:43.771634 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:43.772743 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:43.774071 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:43.774834 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:43.802346 INFO: Starting optimization step 0.
1 day, 12:35:43.802483 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:43.802551 INFO: Using classic extraction backend
1 day, 12:35:43.802660 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:43.802729 INFO: === Search parameters used ===
1 day, 12:35:43.802786 INFO: rt_error       : 782.7188284603353
1 day, 12:35:43.802830 INFO: mobility_error : 0.1
1 day, 12:35:43.802872 INFO: num_candidates : 3
1 day, 12:35:43.802912 INFO: ms1_error      : 19.706368216936717
1 day, 12:35:43.802951 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:43.802989 INFO: fwhm_rt        : 2.7854177951812744
1 day, 12:35:43.803027 INFO: quant_window   : 3
1 day, 12:35:43.803065 INFO: ==============================================
1 day, 12:35:43.803794 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:43.803839 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:43.803871 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 12:35:43.803892 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.51
1 day, 12:35:43.804546 INFO: Starting candidate selection
1 day, 12:35:48.188823 INFO: Starting candidate scoring
1 day, 12:35:48.396010 INFO: Finished candidate processing
1 day, 12:35:48.396142 INFO: Collecting candidate features
1 day, 12:35:48.411674 INFO: Collecting fragment features
1 day, 12:35:48.415497 INFO: Finished candidate scoring
1 day, 12:35:48.417474 INFO: performing precursor FDR with 47 features
1 day, 12:35:48.417525 INFO: Decoy channel: -1
1 day, 12:35:48.417549 INFO: Competetive: True
1 day, 12:35:48.420405 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:48.422395 INFO: Using random state 242117 for train-test-split
1 day, 12:35:48.433305 INFO: Test AUC: 0.504
1 day, 12:35:48.433361 INFO: Train AUC: 0.502
1 day, 12:35:48.433391 INFO: AUC difference: 0.48%
1 day, 12:35:48.652642 INFO: Resetting torch num_threads to 80
1 day, 12:35:48.653214 PROGRESS: === Extracted 3213 precursors and 33213 fragments ===
1 day, 12:35:48.653624 INFO: === FDR correction performed with classifier version 19 ===
1 day, 12:35:48.654190 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:48.654276 PROGRESS: Total precursors accumulated: 589
1 day, 12:35:48.654341 PROGRESS: Target precursors: 427 (72.50%)
1 day, 12:35:48.654391 PROGRESS: Decoy precursors: 162 (27.50%)
1 day, 12:35:48.654437 PROGRESS: 
1 day, 12:35:48.654480 PROGRESS: Precursor Summary:
1 day, 12:35:48.655437 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   350; 0.001 FDR:   350
1 day, 12:35:48.655523 PROGRESS: 
1 day, 12:35:48.655576 PROGRESS: Protein Summary:
1 day, 12:35:48.656687 PROGRESS: Channel   0:	 0.050 FDR:   347; 0.010 FDR:   347; 0.001 FDR:   347
1 day, 12:35:48.656775 PROGRESS: =========================================================================
1 day, 12:35:48.656918 INFO: Target number of precursors reached.
1 day, 12:35:48.662105 INFO: fragments_df: keeping 1761 of 33213 [sum(precursor_idx_mask)=10222 sum(mass_error_mask)=33213 stop_rank=1761
1 day, 12:35:48.778904 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:48.880582 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:48.988058 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:49.095241 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:49.296037 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:49.296451 INFO: Using score_cutoff 30.94897650203705 (fac=0.99, q=1)
1 day, 12:35:49.296745 INFO: Updating optimization_manager: fwhm_rt             : 2.7854177951812744 -> 2.8171794414520264
1 day, 12:35:49.296824 INFO: Updating optimization_manager: fwhm_mobility       : 0.005414838902652264 -> 0.005509057082235813
1 day, 12:35:49.296878 INFO: Updating optimization_manager: score_cutoff        : 31.212379989624022 -> 30.94897650203705
1 day, 12:35:49.296931 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:49.298022 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:49.299326 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:49.300079 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:49.302130 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:49.302226 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 12:35:49.303520 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.10096501891499265
1 day, 12:35:49.303617 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.1010.
1 day, 12:35:49.303687 INFO: ==============================================
1 day, 12:35:49.303753 INFO: Starting optimization step 1.
1 day, 12:35:49.303808 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:49.303859 INFO: Using classic extraction backend
1 day, 12:35:49.303961 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:49.304024 INFO: === Search parameters used ===
1 day, 12:35:49.304069 INFO: rt_error       : 782.7188284603353
1 day, 12:35:49.304109 INFO: mobility_error : 0.10096501891499265
1 day, 12:35:49.304149 INFO: num_candidates : 3
1 day, 12:35:49.304189 INFO: ms1_error      : 19.706368216936717
1 day, 12:35:49.304227 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:49.304266 INFO: fwhm_rt        : 2.8171794414520264
1 day, 12:35:49.304304 INFO: quant_window   : 3
1 day, 12:35:49.304342 INFO: ==============================================
1 day, 12:35:49.305282 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:49.305328 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:49.305362 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 12:35:49.305382 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.56
1 day, 12:35:49.306050 INFO: Starting candidate selection
1 day, 12:35:53.568468 INFO: Starting candidate scoring
1 day, 12:35:53.765018 INFO: Finished candidate processing
1 day, 12:35:53.765157 INFO: Collecting candidate features
1 day, 12:35:53.779459 INFO: Collecting fragment features
1 day, 12:35:53.783278 INFO: Finished candidate scoring
1 day, 12:35:53.785145 INFO: performing precursor FDR with 47 features
1 day, 12:35:53.785192 INFO: Decoy channel: -1
1 day, 12:35:53.785224 INFO: Competetive: True
1 day, 12:35:53.788157 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:53.790166 INFO: Using random state 242117 for train-test-split
1 day, 12:35:53.800812 INFO: Test AUC: 0.496
1 day, 12:35:53.800872 INFO: Train AUC: 0.509
1 day, 12:35:53.800910 INFO: AUC difference: 2.65%
1 day, 12:35:54.019205 INFO: Resetting torch num_threads to 80
1 day, 12:35:54.019758 PROGRESS: === Extracted 3219 precursors and 33316 fragments ===
1 day, 12:35:54.020188 INFO: === FDR correction performed with classifier version 19 ===
1 day, 12:35:54.020794 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:54.020890 PROGRESS: Total precursors accumulated: 589
1 day, 12:35:54.020972 PROGRESS: Target precursors: 430 (73.01%)
1 day, 12:35:54.021039 PROGRESS: Decoy precursors: 159 (26.99%)
1 day, 12:35:54.021096 PROGRESS: 
1 day, 12:35:54.021161 PROGRESS: Precursor Summary:
1 day, 12:35:54.022214 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   355
1 day, 12:35:54.022312 PROGRESS: 
1 day, 12:35:54.022382 PROGRESS: Protein Summary:
1 day, 12:35:54.023569 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   352; 0.001 FDR:   352
1 day, 12:35:54.023667 PROGRESS: =========================================================================
1 day, 12:35:54.023936 INFO: Target number of precursors reached.
1 day, 12:35:54.029093 INFO: fragments_df: keeping 1792 of 33316 [sum(precursor_idx_mask)=10471 sum(mass_error_mask)=33316 stop_rank=1792
1 day, 12:35:54.128436 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:54.229294 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:54.337513 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:54.445035 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:54.661517 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:35:54.661955 INFO: Using score_cutoff 30.62014261894226 (fac=0.99, q=1)
1 day, 12:35:54.662282 INFO: Updating optimization_manager: fwhm_rt             : 2.8171794414520264 -> 2.833570957183838
1 day, 12:35:54.662371 INFO: Updating optimization_manager: fwhm_mobility       : 0.005509057082235813 -> 0.005500505678355694
1 day, 12:35:54.662439 INFO: Updating optimization_manager: score_cutoff        : 30.94897650203705 -> 30.62014261894226
1 day, 12:35:54.662511 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:54.663589 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:35:54.664959 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:35:54.665754 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:35:54.668799 INFO: === checking if optimization conditions were reached ===
1 day, 12:35:54.668912 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 12:35:54.670373 INFO: Updating optimization_manager: mobility_error      : 0.10096501891499265 -> 0.10031388203784757
1 day, 12:35:54.670481 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.1003.
1 day, 12:35:54.670561 INFO: ==============================================
1 day, 12:35:54.670649 INFO: Starting optimization step 2.
1 day, 12:35:54.670724 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 12:35:54.670797 INFO: Using classic extraction backend
1 day, 12:35:54.670928 PROGRESS: Extracting batch of 1173 precursors
1 day, 12:35:54.671008 INFO: === Search parameters used ===
1 day, 12:35:54.671068 INFO: rt_error       : 782.7188284603353
1 day, 12:35:54.671124 INFO: mobility_error : 0.10031388203784757
1 day, 12:35:54.671178 INFO: num_candidates : 3
1 day, 12:35:54.671232 INFO: ms1_error      : 19.706368216936717
1 day, 12:35:54.671284 INFO: ms2_error      : 15.65170738607732
1 day, 12:35:54.671347 INFO: fwhm_rt        : 2.833570957183838
1 day, 12:35:54.671402 INFO: quant_window   : 3
1 day, 12:35:54.671454 INFO: ==============================================
1 day, 12:35:54.672607 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:35:54.672654 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:35:54.672698 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1 day, 12:35:54.672732 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.55
1 day, 12:35:54.673445 INFO: Starting candidate selection
1 day, 12:35:58.798077 INFO: Starting candidate scoring
1 day, 12:35:58.989430 INFO: Finished candidate processing
1 day, 12:35:58.989563 INFO: Collecting candidate features
1 day, 12:35:59.000442 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3222)
1 day, 12:35:59.003784 INFO: Collecting fragment features
1 day, 12:35:59.007730 INFO: Finished candidate scoring
1 day, 12:35:59.009552 INFO: performing precursor FDR with 47 features
1 day, 12:35:59.009596 INFO: Decoy channel: -1
1 day, 12:35:59.009624 INFO: Competetive: True
1 day, 12:35:59.012450 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 12:35:59.013750 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 12:35:59.014753 INFO: Using random state 242117 for train-test-split
1 day, 12:35:59.025255 INFO: Test AUC: 0.521
1 day, 12:35:59.025314 INFO: Train AUC: 0.506
1 day, 12:35:59.025344 INFO: AUC difference: 3.15%
1 day, 12:35:59.243209 INFO: Resetting torch num_threads to 80
1 day, 12:35:59.243837 PROGRESS: === Extracted 3222 precursors and 33369 fragments ===
1 day, 12:35:59.244239 INFO: === FDR correction performed with classifier version 19 ===
1 day, 12:35:59.244832 PROGRESS: ============================= Precursor FDR =============================
1 day, 12:35:59.244920 PROGRESS: Total precursors accumulated: 589
1 day, 12:35:59.244992 PROGRESS: Target precursors: 432 (73.34%)
1 day, 12:35:59.245043 PROGRESS: Decoy precursors: 157 (26.66%)
1 day, 12:35:59.245087 PROGRESS: 
1 day, 12:35:59.245130 PROGRESS: Precursor Summary:
1 day, 12:35:59.246105 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   354; 0.001 FDR:   354
1 day, 12:35:59.246192 PROGRESS: 
1 day, 12:35:59.246247 PROGRESS: Protein Summary:
1 day, 12:35:59.247370 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   351; 0.001 FDR:   351
1 day, 12:35:59.247460 PROGRESS: =========================================================================
1 day, 12:35:59.247612 INFO: Target number of precursors reached.
1 day, 12:35:59.252848 INFO: fragments_df: keeping 1797 of 33369 [sum(precursor_idx_mask)=10507 sum(mass_error_mask)=33369 stop_rank=1797
1 day, 12:35:59.352168 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:35:59.454143 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:36:01.787278 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:36:01.916499 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:36:02.159073 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 12:36:02.159510 INFO: Using score_cutoff 31.427057518959046 (fac=0.99, q=1)
1 day, 12:36:02.159817 INFO: Updating optimization_manager: fwhm_rt             : 2.833570957183838 -> 2.8389482498168945
1 day, 12:36:02.159895 INFO: Updating optimization_manager: fwhm_mobility       : 0.005500505678355694 -> 0.005604233592748642
1 day, 12:36:02.159947 INFO: Updating optimization_manager: score_cutoff        : 30.62014261894226 -> 31.427057518959046
1 day, 12:36:02.159998 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:36:02.161121 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:36:02.162518 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:36:02.163295 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:36:02.165489 INFO: === checking if optimization conditions were reached ===
1 day, 12:36:02.165594 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 12:36:02.166269 INFO: Updating optimization_manager: mobility_error      : 0.10031388203784757 -> 0.10096501891499265
1 day, 12:36:02.166388 INFO: Updating optimization_manager: classifier_version  : 19 -> 22
1 day, 12:36:02.166477 INFO: Updating optimization_manager: score_cutoff        : 31.427057518959046 -> 30.62014261894226
1 day, 12:36:02.166559 INFO: Updating optimization_manager: fwhm_rt             : 2.8389482498168945 -> 2.833570957183838
1 day, 12:36:02.166639 INFO: Updating optimization_manager: fwhm_mobility       : 0.005604233592748642 -> 0.005500505678355694
1 day, 12:36:02.166716 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1010 found after 3 searches.
1 day, 12:36:02.166774 INFO: ==============================================
1 day, 12:36:02.166835 PROGRESS: Optimization finished for mobility_error.
1 day, 12:36:02.266105 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:36:02.267205 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:36:02.268549 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:36:02.269332 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:36:02.295179 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 12:36:02.295312 PROGRESS: ==============================================
1 day, 12:36:02.295379 PROGRESS: ms2_error      : 15.6517
1 day, 12:36:02.295431 PROGRESS: rt_error       : 782.7188
1 day, 12:36:02.295479 PROGRESS: ms1_error      : 19.7064
1 day, 12:36:02.295522 PROGRESS: mobility_error : 0.1010
1 day, 12:36:02.295564 PROGRESS: ==============================================
1 day, 12:36:02.296133 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 12:36:03.872017 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 12:36:11.146692 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 12:36:12.659145 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 12:36:30.027671 INFO: Using classic extraction backend
1 day, 12:36:30.028284 PROGRESS: Extracting batch of 12073114 precursors
1 day, 12:36:30.028382 INFO: === Search parameters used ===
1 day, 12:36:30.028439 INFO: rt_error       : 782.7188284603353
1 day, 12:36:30.028488 INFO: mobility_error : 0.10096501891499265
1 day, 12:36:30.028542 INFO: num_candidates : 3
1 day, 12:36:30.028587 INFO: ms1_error      : 19.706368216936717
1 day, 12:36:30.028631 INFO: ms2_error      : 15.65170738607732
1 day, 12:36:30.028676 INFO: fwhm_rt        : 2.833570957183838
1 day, 12:36:30.028717 INFO: quant_window   : 3
1 day, 12:36:30.028760 INFO: ==============================================
1 day, 12:36:32.717042 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 12:36:32.717164 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 12:36:32.717210 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1 day, 12:36:32.717233 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.55
1 day, 12:36:32.718169 INFO: Starting candidate selection
1 day, 19:41:23.467643 INFO: Removed 1340017 precursors with score below cutoff 30.62014261894226
1 day, 19:41:26.449571 INFO: Starting candidate scoring
1 day, 20:02:11.648800 INFO: Finished candidate processing
1 day, 20:02:11.649812 INFO: Collecting candidate features
1 day, 20:03:13.560456 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 32477010)
1 day, 20:03:13.589193 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 32477010)
1 day, 20:03:14.671198 INFO: Collecting fragment features
1 day, 20:03:36.231239 INFO: Finished candidate scoring
1 day, 20:04:23.422994 INFO: === Performing FDR correction with classifier version 22 ===
1 day, 20:04:23.469320 INFO: performing precursor FDR with 47 features
1 day, 20:04:23.469419 INFO: Decoy channel: -1
1 day, 20:04:23.469475 INFO: Competetive: True
1 day, 20:04:31.348214 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:04:35.991147 WARNING: dropped 6 target PSMs due to missing features
1 day, 20:04:35.991295 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 20:04:49.325093 INFO: Using random state 134147 for train-test-split
1 day, 20:14:33.657447 INFO: Test AUC: 0.577
1 day, 20:14:33.657714 INFO: Train AUC: 0.578
1 day, 20:14:33.657756 INFO: AUC difference: 0.14%
1 day, 20:14:39.470879 INFO: Resetting torch num_threads to 80
1 day, 20:14:40.148912 INFO: Removing fragments below FDR threshold
1 day, 20:14:43.758838 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:14:43.759130 PROGRESS: Total precursors accumulated: 48,877
1 day, 20:14:43.759198 PROGRESS: Target precursors: 48,394 (99.01%)
1 day, 20:14:43.759251 PROGRESS: Decoy precursors: 483 (0.99%)
1 day, 20:14:43.759306 PROGRESS: 
1 day, 20:14:43.759353 PROGRESS: Precursor Summary:
1 day, 20:14:43.773755 PROGRESS: Channel   0:	 0.050 FDR: 48,394; 0.010 FDR: 48,394; 0.001 FDR: 26,709
1 day, 20:14:43.773998 PROGRESS: 
1 day, 20:14:43.774057 PROGRESS: Protein Summary:
1 day, 20:14:43.799981 PROGRESS: Channel   0:	 0.050 FDR: 8,842; 0.010 FDR: 8,842; 0.001 FDR: 6,255
1 day, 20:14:43.800221 PROGRESS: =========================================================================
1 day, 20:14:44.260465 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/psm.parquet
1 day, 20:14:44.686902 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/frag.parquet
1 day, 20:14:44.914433 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:15:23.425394 PROGRESS: Processing search outputs
1 day, 20:15:23.425622 PROGRESS: Performing protein grouping and FDR
1 day, 20:15:23.425663 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 20:15:23.547269 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 20:15:23.593052 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 20:15:23.609132 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:15:23.632674 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:15:23.651376 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:15:23.674842 INFO: Building combined output
1 day, 20:15:23.694516 INFO: Performing protein inference
1 day, 20:15:23.980137 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1 day, 20:15:41.904609 INFO: Performing protein FDR
1 day, 20:15:45.758317 INFO: Normalizing q-values using 12,362 targets and 2,055 decoys
1 day, 20:15:45.761389 INFO: Test AUC: 0.883
1 day, 20:15:45.761446 INFO: Train AUC: 0.880
1 day, 20:15:45.761482 INFO: AUC difference: 0.43%
1 day, 20:15:46.218373 PROGRESS: ================ Protein FDR =================
1 day, 20:15:46.218518 PROGRESS: Unique protein groups in output
1 day, 20:15:46.218549 PROGRESS:   1% protein FDR: 7,424
1 day, 20:15:46.218573 PROGRESS: 
1 day, 20:15:46.218594 PROGRESS: Unique precursor in output
1 day, 20:15:46.218614 PROGRESS:   1% protein FDR: 73,677
1 day, 20:15:46.218634 PROGRESS: ================================================
1 day, 20:15:46.263505 PROGRESS: Building search statistics
1 day, 20:15:46.333951 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
1 day, 20:15:46.334334 INFO: Initializing OptimizationManager
1 day, 20:15:46.334728 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
1 day, 20:15:46.334814 INFO: Initializing CalibrationManager
1 day, 20:15:46.335227 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
1 day, 20:15:46.335312 INFO: Initializing RawFileManager
1 day, 20:15:46.353949 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
1 day, 20:15:46.354287 INFO: Initializing OptimizationManager
1 day, 20:15:46.354520 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
1 day, 20:15:46.354605 INFO: Initializing CalibrationManager
1 day, 20:15:46.355050 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
1 day, 20:15:46.355139 INFO: Initializing RawFileManager
1 day, 20:15:46.371685 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
1 day, 20:15:46.371842 INFO: Initializing OptimizationManager
1 day, 20:15:46.372169 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
1 day, 20:15:46.372251 INFO: Initializing CalibrationManager
1 day, 20:15:46.372614 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
1 day, 20:15:46.372699 INFO: Initializing RawFileManager
1 day, 20:15:46.391632 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
1 day, 20:15:46.391817 INFO: Initializing OptimizationManager
1 day, 20:15:46.392029 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
1 day, 20:15:46.392106 INFO: Initializing CalibrationManager
1 day, 20:15:46.392298 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
1 day, 20:15:46.392376 INFO: Initializing RawFileManager
1 day, 20:15:46.410173 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
1 day, 20:15:46.410354 INFO: Initializing OptimizationManager
1 day, 20:15:46.410562 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
1 day, 20:15:46.410637 INFO: Initializing CalibrationManager
1 day, 20:15:46.410829 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
1 day, 20:15:46.410907 INFO: Initializing RawFileManager
1 day, 20:15:46.430415 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
1 day, 20:15:46.430601 INFO: Initializing OptimizationManager
1 day, 20:15:46.430811 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
1 day, 20:15:46.430887 INFO: Initializing CalibrationManager
1 day, 20:15:46.431076 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
1 day, 20:15:46.431168 INFO: Initializing RawFileManager
1 day, 20:15:46.433523 INFO: Writing stat output to disk
1 day, 20:15:46.433599 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/stat.tsv to disk
1 day, 20:15:46.439745 PROGRESS: Building internal statistics
1 day, 20:15:46.440159 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
1 day, 20:15:46.440209 INFO: Initializing TimingManager
1 day, 20:15:46.440650 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
1 day, 20:15:46.440698 INFO: Initializing TimingManager
1 day, 20:15:46.440897 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
1 day, 20:15:46.440940 INFO: Initializing TimingManager
1 day, 20:15:46.441131 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
1 day, 20:15:46.441173 INFO: Initializing TimingManager
1 day, 20:15:46.441346 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
1 day, 20:15:46.441386 INFO: Initializing TimingManager
1 day, 20:15:46.441555 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
1 day, 20:15:46.441595 INFO: Initializing TimingManager
1 day, 20:15:46.441975 INFO: Writing internal output to disk
1 day, 20:15:46.442021 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/internal.tsv to disk
1 day, 20:15:46.442470 PROGRESS: Performing label free quantification
1 day, 20:15:46.491948 INFO: Accumulating fragment data
1 day, 20:15:46.492102 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 20:15:46.727210 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 20:15:47.594393 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 20:15:48.342896 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:15:49.185409 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:15:50.010365 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:15:51.132814 PROGRESS: Performing label free quantification on the precursor level
1 day, 20:15:51.132962 INFO: Filtering fragments by quality
1 day, 20:15:51.342853 INFO: Performing label-free quantification using directLFQ
1 day, 20:15:52.498792 INFO: 73677 lfq-groups total
1 day, 20:17:13.378261 INFO: using 80 processes
1 day, 20:17:13.563644 INFO: lfq-object 0
1 day, 20:17:13.662306 INFO: lfq-object 100
1 day, 20:17:13.701760 INFO: lfq-object 300
1 day, 20:17:13.742561 INFO: lfq-object 500
1 day, 20:17:13.768534 INFO: lfq-object 700
1 day, 20:17:13.769857 INFO: lfq-object 200
1 day, 20:17:13.822323 INFO: lfq-object 400
1 day, 20:17:13.844908 INFO: lfq-object 600
1 day, 20:17:13.873686 INFO: lfq-object 800
1 day, 20:17:13.888398 INFO: lfq-object 1000
1 day, 20:17:13.916627 INFO: lfq-object 1200
1 day, 20:17:13.953351 INFO: lfq-object 1400
1 day, 20:17:13.979884 INFO: lfq-object 900
1 day, 20:17:14.003376 INFO: lfq-object 1100
1 day, 20:17:14.017661 INFO: lfq-object 1300
1 day, 20:17:14.070553 INFO: lfq-object 1500
1 day, 20:17:14.127831 INFO: lfq-object 1700
1 day, 20:17:14.162440 INFO: lfq-object 1900
1 day, 20:17:14.178636 INFO: lfq-object 1600
1 day, 20:17:14.221881 INFO: lfq-object 2100
1 day, 20:17:14.235669 INFO: lfq-object 1800
1 day, 20:17:14.276079 INFO: lfq-object 2000
1 day, 20:17:14.325448 INFO: lfq-object 2200
1 day, 20:17:14.427984 INFO: lfq-object 2300
1 day, 20:17:14.450114 INFO: lfq-object 2400
1 day, 20:17:14.554807 INFO: lfq-object 2500
1 day, 20:17:14.597000 INFO: lfq-object 2600
1 day, 20:17:14.697164 INFO: lfq-object 2700
1 day, 20:17:14.738601 INFO: lfq-object 2800
1 day, 20:17:14.842703 INFO: lfq-object 2900
1 day, 20:17:14.909010 INFO: lfq-object 3100
1 day, 20:17:14.942797 INFO: lfq-object 3300
1 day, 20:17:14.946961 INFO: lfq-object 3000
1 day, 20:17:15.007771 INFO: lfq-object 3500
1 day, 20:17:15.011830 INFO: lfq-object 3200
1 day, 20:17:15.042338 INFO: lfq-object 3700
1 day, 20:17:15.048282 INFO: lfq-object 3400
1 day, 20:17:15.106486 INFO: lfq-object 3600
1 day, 20:17:15.152683 INFO: lfq-object 3800
1 day, 20:17:15.208633 INFO: lfq-object 4000
1 day, 20:17:15.240472 INFO: lfq-object 4200
1 day, 20:17:15.253892 INFO: lfq-object 3900
1 day, 20:17:15.307075 INFO: lfq-object 4100
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1 day, 20:17:15.345111 INFO: lfq-object 4300
1 day, 20:17:15.433239 INFO: lfq-object 4500
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1 day, 20:17:15.573422 INFO: lfq-object 4900
1 day, 20:17:15.623447 INFO: lfq-object 5100
1 day, 20:17:15.642867 INFO: lfq-object 4800
1 day, 20:17:15.679430 INFO: lfq-object 5000
1 day, 20:17:15.723613 INFO: lfq-object 5200
1 day, 20:17:15.790548 INFO: lfq-object 5400
1 day, 20:17:15.825729 INFO: lfq-object 5300
1 day, 20:17:15.829325 INFO: lfq-object 5600
1 day, 20:17:15.860950 INFO: lfq-object 5800
1 day, 20:17:15.920197 INFO: lfq-object 5500
1 day, 20:17:15.933372 INFO: lfq-object 5700
1 day, 20:17:15.964608 INFO: lfq-object 5900
1 day, 20:17:16.050375 INFO: lfq-object 6100
1 day, 20:17:16.067989 INFO: lfq-object 6000
1 day, 20:17:16.107020 INFO: lfq-object 6300
1 day, 20:17:16.133279 INFO: lfq-object 6500
1 day, 20:17:16.152826 INFO: lfq-object 6200
1 day, 20:17:16.214575 INFO: lfq-object 6400
1 day, 20:17:16.216553 INFO: lfq-object 6700
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1 day, 20:17:19.578240 INFO: lfq-object 7000
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1 day, 20:17:19.680957 INFO: lfq-object 7100
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1 day, 20:17:19.771135 INFO: lfq-object 7300
1 day, 20:17:19.834107 INFO: lfq-object 7500
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1 day, 20:17:19.933667 INFO: lfq-object 7600
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1 day, 20:17:20.047610 INFO: lfq-object 8000
1 day, 20:17:20.105626 INFO: lfq-object 8200
1 day, 20:17:20.167425 INFO: lfq-object 8400
1 day, 20:17:20.205823 INFO: lfq-object 8300
1 day, 20:17:20.273876 INFO: lfq-object 8500
1 day, 20:17:20.296070 INFO: lfq-object 8600
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1 day, 20:17:20.649156 INFO: lfq-object 9000
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1 day, 20:17:20.772848 INFO: lfq-object 9200
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1 day, 20:17:20.879066 INFO: lfq-object 9400
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1 day, 20:17:21.019167 INFO: lfq-object 10000
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1 day, 20:17:21.067768 INFO: lfq-object 10200
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1 day, 20:17:22.033956 INFO: lfq-object 12200
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1 day, 20:17:22.179908 INFO: lfq-object 13000
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1 day, 20:17:22.966689 INFO: lfq-object 14200
1 day, 20:17:22.995518 INFO: lfq-object 14400
1 day, 20:17:23.017254 INFO: lfq-object 14600
1 day, 20:17:23.070892 INFO: lfq-object 14300
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1 day, 20:17:23.372313 INFO: lfq-object 15400
1 day, 20:17:23.449881 INFO: lfq-object 15600
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1 day, 20:17:23.544930 INFO: lfq-object 16000
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1 day, 20:17:23.590348 INFO: lfq-object 16200
1 day, 20:17:23.597182 INFO: lfq-object 15900
1 day, 20:17:23.642215 INFO: lfq-object 16100
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1 day, 20:17:23.730241 INFO: lfq-object 16500
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1 day, 20:17:23.803832 INFO: lfq-object 16900
1 day, 20:17:23.834303 INFO: lfq-object 16600
1 day, 20:17:23.845170 INFO: lfq-object 17100
1 day, 20:17:23.863343 INFO: lfq-object 16800
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1 day, 20:17:23.948407 INFO: lfq-object 17200
1 day, 20:17:23.993176 INFO: lfq-object 17400
1 day, 20:17:24.042555 INFO: lfq-object 17600
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1 day, 20:17:24.094010 INFO: lfq-object 17500
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1 day, 20:18:04.665753 INFO: Writing precursor output to disk
1 day, 20:18:04.666029 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/precursor.matrix.tsv to disk
1 day, 20:18:04.961702 PROGRESS: Performing label free quantification on the pg level
1 day, 20:18:04.961821 INFO: Filtering fragments by quality
1 day, 20:18:05.182903 INFO: Performing label-free quantification using directLFQ
1 day, 20:18:05.452385 INFO: 7424 lfq-groups total
1 day, 20:19:14.198494 INFO: using 80 processes
1 day, 20:19:14.287338 INFO: lfq-object 0
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1 day, 20:19:24.563531 INFO: Writing pg output to disk
1 day, 20:19:24.563687 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/pg.matrix.tsv to disk
1 day, 20:19:24.698076 INFO: Writing psm output to disk
1 day, 20:19:24.698215 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/precursors.tsv to disk
1 day, 20:19:38.523829 PROGRESS: Building MBR spectral library
1 day, 20:19:38.580483 INFO: Running MbrLibraryBuilder
1 day, 20:19:40.656498 INFO: MBR spectral library contains 73,677 precursors, 7,424 proteins
1 day, 20:19:40.656637 INFO: Writing MBR spectral library to disk
1 day, 20:19:41.529884 PROGRESS: =================== Search Finished ===================
1 day, 20:19:43.198505 INFO: Running step 'mbr'
1 day, 20:19:43.202688 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 7.5754825, 'target_ms2_tolerance': 17.494642}})
1 day, 20:19:43.202922 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
1 day, 20:19:43.215109 INFO: loading additional config provided via CLI
1 day, 20:19:43.215196 INFO: loading additional config provided via CLI parameters
1 day, 20:19:43.215647 INFO: Updating config with 'user defined'
1 day, 20:19:43.215845 INFO: Updating config with 'user defined (cli)'
1 day, 20:19:43.216043 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': 0, 'target_ms2_tolerance': 0, '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': 7.5754825, 'target_ms2_tolerance': 17.494642}, '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_calibrateTol/library/speclib.mbr.hdf', 'output_directory': 'run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol'}]
1 day, 20:19:43.216326 INFO: Updating config with 'user defined'
1 day, 20:19:43.216446 INFO: Updating config with 'user defined (cli)'
1 day, 20:19:43.216471 INFO: Updating config with 'multistep search'
1 day, 20:19:43.216516 INFO: ├──version: 1
1 day, 20:19:43.216542 INFO: ├──workflow_name: None
1 day, 20:19:43.216563 INFO: [32;20m├──output_directory: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol [multistep search, default: None][0m
1 day, 20:19:43.216589 INFO: [32;20m├──library_path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/speclib.mbr.hdf [multistep search, default: None][0m
1 day, 20:19:43.216612 INFO: ├──raw_paths:
1 day, 20:19:43.216632 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
1 day, 20:19:43.216651 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
1 day, 20:19:43.216672 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
1 day, 20:19:43.216689 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
1 day, 20:19:43.216706 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
1 day, 20:19:43.216725 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
1 day, 20:19:43.216744 INFO: ├──fasta_paths:
1 day, 20:19:43.216765 INFO: ├──quant_directory: None
1 day, 20:19:43.216783 INFO: ├──general
1 day, 20:19:43.216803 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
1 day, 20:19:43.216823 INFO: │   ├──transfer_step_enabled: False
1 day, 20:19:43.216842 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
1 day, 20:19:43.216862 INFO: │   ├──reuse_calibration: False
1 day, 20:19:43.216880 INFO: │   ├──reuse_quant: False
1 day, 20:19:43.216899 INFO: │   ├──astral_ms1: False
1 day, 20:19:43.216917 INFO: │   ├──log_level: INFO
1 day, 20:19:43.216937 INFO: │   ├──mmap_detector_events: False
1 day, 20:19:43.218780 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
1 day, 20:19:43.218831 INFO: │   ├──save_figures: True
1 day, 20:19:43.218852 INFO: │   ├──save_library: True
1 day, 20:19:43.218873 INFO: │   ├──save_flat_library: False
1 day, 20:19:43.218893 INFO: │   ├──input_library_type: base
1 day, 20:19:43.218911 INFO: │   ├──save_mbr_library: True
1 day, 20:19:43.218929 INFO: │   └──random_state: None
1 day, 20:19:43.218953 INFO: ├──library_loading
1 day, 20:19:43.218976 INFO: │   └──rt_heuristic: 180
1 day, 20:19:43.218997 INFO: ├──library_prediction
1 day, 20:19:43.219016 INFO: │   ├──enabled: False
1 day, 20:19:43.219035 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
1 day, 20:19:43.219053 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
1 day, 20:19:43.219071 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
1 day, 20:19:43.219089 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
1 day, 20:19:43.219108 INFO: │   ├──missed_cleavages: 1
1 day, 20:19:43.219126 INFO: │   ├──precursor_len:
1 day, 20:19:43.219144 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
1 day, 20:19:43.219165 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
1 day, 20:19:43.219183 INFO: │   ├──precursor_charge:
1 day, 20:19:43.219207 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
1 day, 20:19:43.219225 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
1 day, 20:19:43.219242 INFO: │   ├──precursor_mz:
1 day, 20:19:43.219261 INFO: │   │   - 400
1 day, 20:19:43.219280 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
1 day, 20:19:43.219301 INFO: │   ├──fragment_mz:
1 day, 20:19:43.219318 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
1 day, 20:19:43.219338 INFO: │   │   - 2000
1 day, 20:19:43.219357 INFO: │   ├──nce: 25.0
1 day, 20:19:43.219374 INFO: │   ├──fragment_types:
1 day, 20:19:43.219393 INFO: │   │   - b
1 day, 20:19:43.219410 INFO: │   │   - y
1 day, 20:19:43.219429 INFO: │   ├──max_fragment_charge: 2
1 day, 20:19:43.219447 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
1 day, 20:19:43.219466 INFO: │   ├──peptdeep_model_path: None
1 day, 20:19:43.219484 INFO: │   └──peptdeep_model_type: generic
1 day, 20:19:43.219503 INFO: ├──custom_modifications:
1 day, 20:19:43.219524 INFO: │   ├──name: Dimethyl:d12@K
1 day, 20:19:43.219543 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 20:19:43.219563 INFO: │   ├──name: Dimethyl:d12@Any_N-term
1 day, 20:19:43.219581 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 20:19:43.219604 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
1 day, 20:19:43.219625 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 20:19:43.219644 INFO: │   ├──name: mTRAQ:d12@K
1 day, 20:19:43.219664 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
1 day, 20:19:43.219684 INFO: │   ├──name: mTRAQ:d12@Any_N-term
1 day, 20:19:43.219704 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1 day, 20:19:43.219723 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
1 day, 20:19:43.219743 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1 day, 20:19:43.219762 INFO: │   ├──name: Label:13C(12)@K
1 day, 20:19:43.219780 INFO: │   └──composition: C(12)
1 day, 20:19:43.219800 INFO: ├──search
1 day, 20:19:43.219818 INFO: │   ├──extraction_backend: classic
1 day, 20:19:43.219852 INFO: │   [32;20m├──target_ms1_tolerance: 7.5754825 [multistep search, default: 5][0m
1 day, 20:19:43.219873 INFO: │   [32;20m├──target_ms2_tolerance: 17.494642 [multistep search, default: 10][0m
1 day, 20:19:43.219893 INFO: │   ├──target_rt_tolerance: 0.0
1 day, 20:19:43.219910 INFO: │   ├──target_mobility_tolerance: 0.0
1 day, 20:19:43.219930 INFO: │   ├──quant_window: 3
1 day, 20:19:43.219949 INFO: │   ├──target_num_candidates: 3
1 day, 20:19:43.219967 INFO: │   ├──channel_filter: 
1 day, 20:19:43.219985 INFO: │   ├──exclude_shared_ions: True
1 day, 20:19:43.220003 INFO: │   ├──compete_for_fragments: True
1 day, 20:19:43.220021 INFO: │   ├──quant_all: True
1 day, 20:19:43.220037 INFO: │   ├──top_k_fragments_selection: 12
1 day, 20:19:43.220055 INFO: │   ├──top_k_fragments_scoring: 12
1 day, 20:19:43.220073 INFO: │   ├──min_fragment_intensity: 0.01
1 day, 20:19:43.220090 INFO: │   ├──experimental_xic: True
1 day, 20:19:43.220108 INFO: │   └──optimized_peak_group_score: False
1 day, 20:19:43.220126 INFO: ├──calibration
1 day, 20:19:43.220145 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
1 day, 20:19:43.220163 INFO: │   ├──optimization_lock_target: 200
1 day, 20:19:43.220180 INFO: │   ├──max_steps: 20
1 day, 20:19:43.220199 INFO: │   ├──min_steps: 2
1 day, 20:19:43.220217 INFO: │   ├──max_skips: 1
1 day, 20:19:43.220234 INFO: │   ├──max_fragments: 5000
1 day, 20:19:43.220253 INFO: │   └──min_correlation: 0.7
1 day, 20:19:43.220270 INFO: ├──search_initial
1 day, 20:19:43.220289 INFO: │   ├──initial_num_candidates: 1
1 day, 20:19:43.220306 INFO: │   ├──initial_ms1_tolerance: 30
1 day, 20:19:43.220327 INFO: │   ├──initial_ms2_tolerance: 30
1 day, 20:19:43.220346 INFO: │   ├──initial_mobility_tolerance: 0.1
1 day, 20:19:43.220363 INFO: │   └──initial_rt_tolerance: 0.5
1 day, 20:19:43.220380 INFO: ├──selection_config
1 day, 20:19:43.220398 INFO: │   ├──peak_len_rt: 10.0
1 day, 20:19:43.220415 INFO: │   ├──sigma_scale_rt: 0.5
1 day, 20:19:43.220433 INFO: │   ├──peak_len_mobility: 0.01
1 day, 20:19:43.220451 INFO: │   ├──sigma_scale_mobility: 1.0
1 day, 20:19:43.220469 INFO: │   ├──top_k_precursors: 3
1 day, 20:19:43.220487 INFO: │   ├──kernel_size: 30
1 day, 20:19:43.220504 INFO: │   ├──f_mobility: 1.0
1 day, 20:19:43.220523 INFO: │   ├──f_rt: 0.99
1 day, 20:19:43.220542 INFO: │   ├──center_fraction: 0.5
1 day, 20:19:43.220563 INFO: │   ├──min_size_mobility: 8
1 day, 20:19:43.220582 INFO: │   ├──min_size_rt: 3
1 day, 20:19:43.220599 INFO: │   ├──max_size_mobility: 20
1 day, 20:19:43.220618 INFO: │   ├──max_size_rt: 15
1 day, 20:19:43.220637 INFO: │   ├──group_channels: False
1 day, 20:19:43.220656 INFO: │   ├──use_weighted_score: True
1 day, 20:19:43.220674 INFO: │   ├──join_close_candidates: False
1 day, 20:19:43.220692 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
1 day, 20:19:43.220711 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
1 day, 20:19:43.220729 INFO: ├──scoring_config
1 day, 20:19:43.220749 INFO: │   ├──score_grouped: False
1 day, 20:19:43.220768 INFO: │   ├──top_k_isotopes: 3
1 day, 20:19:43.220787 INFO: │   ├──reference_channel: -1
1 day, 20:19:43.220805 INFO: │   ├──precursor_mz_tolerance: 10
1 day, 20:19:43.220823 INFO: │   └──fragment_mz_tolerance: 15
1 day, 20:19:43.220840 INFO: ├──library_multiplexing
1 day, 20:19:43.220858 INFO: │   ├──enabled: False
1 day, 20:19:43.220878 INFO: │   ├──input_channel: 0
1 day, 20:19:43.220896 INFO: │   └──multiplex_mapping:
1 day, 20:19:43.220915 INFO: ├──multiplexing
1 day, 20:19:43.220934 INFO: │   ├──enabled: False
1 day, 20:19:43.220985 INFO: │   ├──target_channels: 4,8
1 day, 20:19:43.221005 INFO: │   ├──decoy_channel: 12
1 day, 20:19:43.221025 INFO: │   ├──reference_channel: 0
1 day, 20:19:43.221043 INFO: │   └──competetive_scoring: True
1 day, 20:19:43.221062 INFO: ├──fdr
1 day, 20:19:43.221082 INFO: │   ├──fdr: 0.01
1 day, 20:19:43.221100 INFO: │   ├──group_level: proteins
1 day, 20:19:43.221120 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
1 day, 20:19:43.221139 INFO: │   ├──competetive_scoring: True
1 day, 20:19:43.221159 INFO: │   ├──keep_decoys: False
1 day, 20:19:43.221177 INFO: │   ├──channel_wise_fdr: False
1 day, 20:19:43.221195 INFO: │   ├──enable_two_step_classifier: False
1 day, 20:19:43.221214 INFO: │   ├──two_step_classifier_max_iterations: 5
1 day, 20:19:43.221234 INFO: │   └──enable_nn_hyperparameter_tuning: False
1 day, 20:19:43.221256 INFO: ├──search_output
1 day, 20:19:43.221274 INFO: │   ├──file_format: tsv
1 day, 20:19:43.221293 INFO: │   ├──peptide_level_lfq: False
1 day, 20:19:43.221312 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
1 day, 20:19:43.221330 INFO: │   ├──save_fragment_quant_matrix: False
1 day, 20:19:43.221349 INFO: │   ├──min_k_fragments: 12
1 day, 20:19:43.221367 INFO: │   ├──min_correlation: 0.9
1 day, 20:19:43.221386 INFO: │   ├──num_samples_quadratic: 50
1 day, 20:19:43.221403 INFO: │   ├──min_nonnan: 3
1 day, 20:19:43.221421 INFO: │   └──normalize_lfq: True
1 day, 20:19:43.221441 INFO: ├──optimization
1 day, 20:19:43.221459 INFO: │   ├──order_of_optimization: None
1 day, 20:19:43.221477 INFO: │   ├──ms2_error
1 day, 20:19:43.221501 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 20:19:43.221522 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 20:19:43.221541 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 20:19:43.221560 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 20:19:43.221578 INFO: │   │   ├──try_narrower_values: True
1 day, 20:19:43.221597 INFO: │   │   ├──maximal_decrease: 0.5
1 day, 20:19:43.221616 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 20:19:43.221634 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 20:19:43.221652 INFO: │   ├──ms1_error
1 day, 20:19:43.221670 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 20:19:43.221689 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 20:19:43.221708 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 20:19:43.221726 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 20:19:43.221745 INFO: │   │   ├──try_narrower_values: False
1 day, 20:19:43.221763 INFO: │   │   ├──maximal_decrease: 0.2
1 day, 20:19:43.221780 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 20:19:43.221799 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 20:19:43.221816 INFO: │   ├──mobility_error
1 day, 20:19:43.221835 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 20:19:43.221853 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 20:19:43.221871 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 20:19:43.221890 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 20:19:43.221907 INFO: │   │   ├──try_narrower_values: False
1 day, 20:19:43.221926 INFO: │   │   ├──maximal_decrease: 0.2
1 day, 20:19:43.221944 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 20:19:43.221962 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 20:19:43.221980 INFO: │   └──rt_error
1 day, 20:19:43.221998 INFO: │       ├──targeted_update_percentile_range: 0.95
1 day, 20:19:43.222017 INFO: │       ├──targeted_update_factor: 1.0
1 day, 20:19:43.222035 INFO: │       ├──automatic_update_percentile_range: 0.99
1 day, 20:19:43.222053 INFO: │       ├──automatic_update_factor: 1.1
1 day, 20:19:43.222072 INFO: │       ├──try_narrower_values: True
1 day, 20:19:43.222090 INFO: │       ├──maximal_decrease: 0.2
1 day, 20:19:43.222108 INFO: │       ├──favour_narrower_optimum: True
1 day, 20:19:43.222126 INFO: │       └──maximum_decrease_from_maximum: 0.1
1 day, 20:19:43.222143 INFO: ├──optimization_manager
1 day, 20:19:43.222161 INFO: │   ├──fwhm_rt: 5
1 day, 20:19:43.222179 INFO: │   ├──fwhm_mobility: 0.01
1 day, 20:19:43.222199 INFO: │   └──score_cutoff: 0
1 day, 20:19:43.222220 INFO: ├──transfer_library
1 day, 20:19:43.222239 INFO: │   ├──enabled: False
1 day, 20:19:43.222256 INFO: │   ├──fragment_types:
1 day, 20:19:43.222274 INFO: │   │   - b
1 day, 20:19:43.222293 INFO: │   │   - y
1 day, 20:19:43.222311 INFO: │   ├──max_charge: 2
1 day, 20:19:43.222329 INFO: │   ├──top_k_samples: 3
1 day, 20:19:43.222348 INFO: │   ├──norm_delta_max: True
1 day, 20:19:43.222367 INFO: │   ├──precursor_correlation_cutoff: 0.5
1 day, 20:19:43.222386 INFO: │   └──fragment_correlation_ratio: 0.75
1 day, 20:19:43.222404 INFO: └──transfer_learning
1 day, 20:19:43.222425 INFO:     ├──enabled: False
1 day, 20:19:43.222443 INFO:     ├──batch_size: 2000
1 day, 20:19:43.222461 INFO:     ├──max_lr: 0.0001
1 day, 20:19:43.222481 INFO:     ├──train_fraction: 0.7
1 day, 20:19:43.222500 INFO:     ├──validation_fraction: 0.2
1 day, 20:19:43.222521 INFO:     ├──test_fraction: 0.1
1 day, 20:19:43.222538 INFO:     ├──test_interval: 1
1 day, 20:19:43.222561 INFO:     ├──lr_patience: 3
1 day, 20:19:43.222578 INFO:     ├──epochs: 51
1 day, 20:19:43.222597 INFO:     ├──warmup_epochs: 5
1 day, 20:19:43.222615 INFO:     ├──nce: 25
1 day, 20:19:43.222633 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
1 day, 20:19:43.228309 INFO: Moved existing config file run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/frozen_config.yaml to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/frozen_config.yaml
1 day, 20:19:43.229551 INFO: Registering 7 custom modifications
1 day, 20:19:43.248277 INFO: Searching 6 files:
1 day, 20:19:43.248354 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:43.248379 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:19:43.248399 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:19:43.248416 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:19:43.248433 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:19:43.248451 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:19:43.248467 INFO: Using 0 fasta files:
1 day, 20:19:43.248486 INFO: Using library: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/speclib.mbr.hdf
1 day, 20:19:43.248506 INFO: Saving output to: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol
1 day, 20:19:43.248544 PROGRESS: Loading spectral library
1 day, 20:19:43.248583 PROGRESS: Loading library (type: base) from disk..
1 day, 20:19:43.248628 INFO: Running DynamicLoader
1 day, 20:19:43.248696 INFO: Loading .hdf library from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/speclib.mbr.hdf
1 day, 20:19:43.589138 INFO: Running PrecursorInitializer
1 day, 20:19:43.589413 INFO: Running AnnotateFasta
1 day, 20:19:43.589775 INFO: Dropping decoys from input library before annotation
1 day, 20:19:43.599828 INFO: Running IsotopeGenerator
1 day, 20:19:43.600121 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
1 day, 20:19:43.600173 INFO: Running RTNormalization
1 day, 20:19:43.604433 INFO: Saving library to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/speclib.hdf
1 day, 20:19:44.136282 INFO: Running DecoyGenerator
1 day, 20:19:48.979938 INFO: Running FlattenLibrary
1 day, 20:19:50.247618 INFO: Running InitFlatColumns
1 day, 20:19:50.253289 INFO: Running LogFlatLibraryStats
1 day, 20:19:50.253393 INFO: ============ Library Stats ============
1 day, 20:19:50.253422 INFO: Number of precursors: 147,346
1 day, 20:19:50.275710 INFO: 	thereof targets:73,677
1 day, 20:19:50.275833 INFO: 	thereof decoys: 73,669
1 day, 20:19:50.277166 INFO: Number of elution groups: 73,677
1 day, 20:19:50.277236 INFO: 	average size: 2.00
1 day, 20:19:50.281260 INFO: Number of proteins: 7,424
1 day, 20:19:50.281938 INFO: Number of channels: 1 ([0])
1 day, 20:19:50.282026 INFO: Isotopes Distribution for 4 isotopes
1 day, 20:19:50.282052 INFO: =======================================
1 day, 20:19:50.282110 PROGRESS: Starting Search Workflows
1 day, 20:19:50.282164 PROGRESS: 
1 day, 20:19:50.282229 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
1 day, 20:19:50.282289 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/figures
1 day, 20:19:50.282524 INFO: Initializing TimingManager
1 day, 20:19:50.283809 INFO: Initializing RawFileManager
1 day, 20:19:50.283932 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:50.283988 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:50.284050 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:50.492818 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, 20:19:55.338521 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
1 day, 20:19:55.339917 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:55.341829 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:55.342047 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:55.342437 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:55.343878 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:55.356167 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:19:55.356671 INFO: Indexing quadrupole dimension
1 day, 20:19:55.816951 INFO: Transposing detector events
1 day, 20:20:05.291873 INFO: Finished transposing data
1 day, 20:20:05.328876 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 20:20:05.330509 INFO: RT (min)            : 0.0 - 70.0
1 day, 20:20:05.330613 INFO: RT duration (sec)   : 4199.9
1 day, 20:20:05.330692 INFO: RT duration (min)   : 70.0
1 day, 20:20:05.330762 INFO: Cycle len (scans)   : 9
1 day, 20:20:05.330828 INFO: Cycle len (sec)     : 0.97
1 day, 20:20:05.330890 INFO: Number of cycles    : 4347
1 day, 20:20:05.330951 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 20:20:05.331103 INFO: Creating DIA data object took: 15.047155857086182
1 day, 20:20:05.375910 INFO: Initializing CalibrationManager
1 day, 20:20:05.376193 INFO: Setting up calibration estimators ..
1 day, 20:20:05.376269 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 20:20:05.376386 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, 20:20:05.376484 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 20:20:05.376557 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, 20:20:05.376630 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, 20:20:05.376709 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, 20:20:05.376771 INFO: Done setting up calibration estimators.
1 day, 20:20:05.376914 INFO: Initializing OptimizationManager
1 day, 20:20:05.377034 INFO: initial parameter: ms1_error = 30
1 day, 20:20:05.377094 INFO: initial parameter: ms2_error = 30
1 day, 20:20:05.377156 INFO: initial parameter: rt_error = 2099.928159
1 day, 20:20:05.377213 INFO: initial parameter: mobility_error = 0.1
1 day, 20:20:05.377270 INFO: initial parameter: num_candidates = 1
1 day, 20:20:05.377326 INFO: initial parameter: fwhm_rt = 5
1 day, 20:20:05.377382 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 20:20:05.377437 INFO: initial parameter: score_cutoff = 0
1 day, 20:20:05.377491 INFO: initial parameter: classifier_version = -1
1 day, 20:20:05.377585 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 20:20:05.377958 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 20:20:05.377997 INFO: Initializing FDRManager
1 day, 20:20:05.378068 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 20:20:05.396097 PROGRESS: Initializing spectral library: 73,677 target precursors potentially observable (0 removed)
1 day, 20:20:05.408952 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 20:20:05.409330 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 2099.928159
1 day, 20:20:05.409444 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 20:20:05.409635 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 20:20:05.409755 PROGRESS: Starting initial search for precursors.
1 day, 20:20:05.409865 INFO: Starting optimization step 0.
1 day, 20:20:05.409941 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 20:20:05.410030 INFO: Using classic extraction backend
1 day, 20:20:05.410247 PROGRESS: Extracting batch of 399 precursors
1 day, 20:20:05.410334 INFO: === Search parameters used ===
1 day, 20:20:05.410394 INFO: rt_error       : 2099.928159
1 day, 20:20:05.410452 INFO: mobility_error : 0.1
1 day, 20:20:05.410508 INFO: num_candidates : 1
1 day, 20:20:05.410563 INFO: ms1_error      : 30
1 day, 20:20:05.410618 INFO: ms2_error      : 30
1 day, 20:20:05.410674 INFO: fwhm_rt        : 5
1 day, 20:20:05.410729 INFO: quant_window   : 3
1 day, 20:20:05.410784 INFO: ==============================================
1 day, 20:20:05.411757 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:20:05.411806 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:20:05.411853 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:20:05.411882 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:20:05.415250 INFO: Starting candidate selection
1 day, 20:20:09.391054 INFO: Starting candidate scoring
1 day, 20:20:09.498586 INFO: Finished candidate processing
1 day, 20:20:09.498838 INFO: Collecting candidate features
1 day, 20:20:09.508202 INFO: Collecting fragment features
1 day, 20:20:09.510560 INFO: Finished candidate scoring
1 day, 20:20:09.511544 INFO: performing precursor FDR with 47 features
1 day, 20:20:09.511585 INFO: Decoy channel: -1
1 day, 20:20:09.511611 INFO: Competetive: True
1 day, 20:20:09.512886 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:20:09.515713 INFO: Using random state 693154 for train-test-split
1 day, 20:20:09.524703 INFO: Test AUC: 0.500
1 day, 20:20:09.524762 INFO: Train AUC: 0.500
1 day, 20:20:09.524795 INFO: AUC difference: 0.00%
1 day, 20:20:09.778773 INFO: Resetting torch num_threads to 80
1 day, 20:20:09.779248 PROGRESS: === Extracted 399 precursors and 4585 fragments ===
1 day, 20:20:09.779654 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:20:09.780210 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:20:09.780302 PROGRESS: Total precursors accumulated: 200
1 day, 20:20:09.780360 PROGRESS: Target precursors: 200 (100.00%)
1 day, 20:20:09.780411 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 20:20:09.780456 PROGRESS: 
1 day, 20:20:09.780499 PROGRESS: Precursor Summary:
1 day, 20:20:09.781458 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 20:20:09.781547 PROGRESS: 
1 day, 20:20:09.781606 PROGRESS: Protein Summary:
1 day, 20:20:09.782727 PROGRESS: Channel   0:	 0.050 FDR:   193; 0.010 FDR:   193; 0.001 FDR:   193
1 day, 20:20:09.782815 PROGRESS: =========================================================================
1 day, 20:20:09.782904 INFO: Target number of precursors reached.
1 day, 20:20:09.784962 INFO: fragments_df: keeping 1351 of 4585 [sum(precursor_idx_mask)=2294 sum(mass_error_mask)=4585 stop_rank=1351
1 day, 20:20:09.787784 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:09.899890 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:10.018030 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:10.138253 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:10.341205 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 20:20:10.341641 INFO: Using score_cutoff 48.27712223625183 (fac=0.99, q=1)
1 day, 20:20:10.342008 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1514105796813965
1 day, 20:20:10.342089 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010037988424301147
1 day, 20:20:10.342141 INFO: Updating optimization_manager: score_cutoff        : 0 -> 48.27712223625183
1 day, 20:20:10.342197 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:10.343152 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:10.344079 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:10.344747 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:10.345982 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 20:20:10.346079 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 20:20:10.346154 INFO: Starting optimization step 1.
1 day, 20:20:10.346211 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 20:20:10.346266 INFO: Using classic extraction backend
1 day, 20:20:10.346368 PROGRESS: Extracting batch of 399 precursors
1 day, 20:20:10.346428 INFO: === Search parameters used ===
1 day, 20:20:10.346474 INFO: rt_error       : 2099.928159
1 day, 20:20:10.346515 INFO: mobility_error : 0.1
1 day, 20:20:10.346555 INFO: num_candidates : 3
1 day, 20:20:10.346595 INFO: ms1_error      : 30
1 day, 20:20:10.346634 INFO: ms2_error      : 30
1 day, 20:20:10.346671 INFO: fwhm_rt        : 3.1514105796813965
1 day, 20:20:10.346709 INFO: quant_window   : 3
1 day, 20:20:10.346747 INFO: ==============================================
1 day, 20:20:10.347430 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:20:10.347475 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:20:10.347509 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
1 day, 20:20:10.347531 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.66
1 day, 20:20:10.348155 INFO: Starting candidate selection
1 day, 20:20:13.883613 INFO: Starting candidate scoring
1 day, 20:20:14.074921 INFO: Finished candidate processing
1 day, 20:20:14.075016 INFO: Collecting candidate features
1 day, 20:20:14.084696 INFO: Collecting fragment features
1 day, 20:20:14.087412 INFO: Finished candidate scoring
1 day, 20:20:14.088483 INFO: performing precursor FDR with 47 features
1 day, 20:20:14.088525 INFO: Decoy channel: -1
1 day, 20:20:14.088550 INFO: Competetive: True
1 day, 20:20:14.091326 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:20:14.093073 INFO: Using random state 655647 for train-test-split
1 day, 20:20:14.101114 INFO: Test AUC: 0.496
1 day, 20:20:14.101171 INFO: Train AUC: 0.499
1 day, 20:20:14.101200 INFO: AUC difference: 0.65%
1 day, 20:20:14.313649 INFO: Resetting torch num_threads to 80
1 day, 20:20:14.314135 PROGRESS: === Extracted 1139 precursors and 13049 fragments ===
1 day, 20:20:14.314535 INFO: === FDR correction performed with classifier version 0 ===
1 day, 20:20:14.315062 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:20:14.315154 PROGRESS: Total precursors accumulated: 200
1 day, 20:20:14.315212 PROGRESS: Target precursors: 198 (99.00%)
1 day, 20:20:14.315261 PROGRESS: Decoy precursors: 2 (1.00%)
1 day, 20:20:14.315306 PROGRESS: 
1 day, 20:20:14.315348 PROGRESS: Precursor Summary:
1 day, 20:20:14.316201 PROGRESS: Channel   0:	 0.050 FDR:   198; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:20:14.316292 PROGRESS: 
1 day, 20:20:14.316347 PROGRESS: Protein Summary:
1 day, 20:20:14.317313 PROGRESS: Channel   0:	 0.050 FDR:   191; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:20:14.317400 PROGRESS: =========================================================================
1 day, 20:20:14.317530 INFO: Target number of precursors not reached yet.
1 day, 20:20:14.320918 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:14.321846 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:14.322969 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:14.323706 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:14.325331 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:20:14.325446 INFO: Starting optimization step 2.
1 day, 20:20:14.325512 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 20:20:14.325571 INFO: Using classic extraction backend
1 day, 20:20:14.325671 PROGRESS: Extracting batch of 795 precursors
1 day, 20:20:14.325737 INFO: === Search parameters used ===
1 day, 20:20:14.325784 INFO: rt_error       : 2099.928159
1 day, 20:20:14.325827 INFO: mobility_error : 0.1
1 day, 20:20:14.325868 INFO: num_candidates : 3
1 day, 20:20:14.325906 INFO: ms1_error      : 30
1 day, 20:20:14.325951 INFO: ms2_error      : 30
1 day, 20:20:14.325990 INFO: fwhm_rt        : 3.1514105796813965
1 day, 20:20:14.326030 INFO: quant_window   : 3
1 day, 20:20:14.326068 INFO: ==============================================
1 day, 20:20:14.326743 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:20:14.326791 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:20:14.326825 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
1 day, 20:20:14.326846 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.66
1 day, 20:20:14.327438 INFO: Starting candidate selection
1 day, 20:20:20.700236 INFO: Starting candidate scoring
1 day, 20:20:20.950471 INFO: Finished candidate processing
1 day, 20:20:20.950583 INFO: Collecting candidate features
1 day, 20:20:20.962352 INFO: Collecting fragment features
1 day, 20:20:20.965713 INFO: Finished candidate scoring
1 day, 20:20:20.968791 INFO: performing precursor FDR with 47 features
1 day, 20:20:20.968841 INFO: Decoy channel: -1
1 day, 20:20:20.968867 INFO: Competetive: True
1 day, 20:20:20.972723 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:20:20.975023 INFO: Using random state 655647 for train-test-split
1 day, 20:20:20.985580 INFO: Test AUC: 0.500
1 day, 20:20:20.985638 INFO: Train AUC: 0.499
1 day, 20:20:20.985667 INFO: AUC difference: 0.26%
1 day, 20:20:21.202663 INFO: Resetting torch num_threads to 80
1 day, 20:20:21.204302 PROGRESS: === Extracted 3420 precursors and 38957 fragments ===
1 day, 20:20:21.204707 INFO: === FDR correction performed with classifier version 0 ===
1 day, 20:20:21.205312 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:20:21.205400 PROGRESS: Total precursors accumulated: 600
1 day, 20:20:21.205457 PROGRESS: Target precursors: 594 (99.00%)
1 day, 20:20:21.205506 PROGRESS: Decoy precursors: 6 (1.00%)
1 day, 20:20:21.205551 PROGRESS: 
1 day, 20:20:21.205593 PROGRESS: Precursor Summary:
1 day, 20:20:21.206489 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:20:21.206583 PROGRESS: 
1 day, 20:20:21.206637 PROGRESS: Protein Summary:
1 day, 20:20:21.207687 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:20:21.207774 PROGRESS: =========================================================================
1 day, 20:20:21.207919 INFO: Target number of precursors not reached yet.
1 day, 20:20:21.212274 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:21.213309 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:21.214874 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:21.215715 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:21.219235 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:20:21.219350 INFO: Starting optimization step 3.
1 day, 20:20:21.219416 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 20:20:21.219487 INFO: Using classic extraction backend
1 day, 20:20:21.219592 PROGRESS: Extracting batch of 1588 precursors
1 day, 20:20:21.219661 INFO: === Search parameters used ===
1 day, 20:20:21.219707 INFO: rt_error       : 2099.928159
1 day, 20:20:21.219748 INFO: mobility_error : 0.1
1 day, 20:20:21.219790 INFO: num_candidates : 3
1 day, 20:20:21.219833 INFO: ms1_error      : 30
1 day, 20:20:21.219873 INFO: ms2_error      : 30
1 day, 20:20:21.219911 INFO: fwhm_rt        : 3.1514105796813965
1 day, 20:20:21.219949 INFO: quant_window   : 3
1 day, 20:20:21.219987 INFO: ==============================================
1 day, 20:20:21.220816 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:20:21.220861 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:20:21.220895 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
1 day, 20:20:21.220916 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.66
1 day, 20:20:21.221492 INFO: Starting candidate selection
1 day, 20:20:33.645071 INFO: Starting candidate scoring
1 day, 20:20:34.111800 INFO: Finished candidate processing
1 day, 20:20:34.111897 INFO: Collecting candidate features
1 day, 20:20:34.126722 INFO: Collecting fragment features
1 day, 20:20:34.133365 INFO: Finished candidate scoring
1 day, 20:20:34.138903 INFO: performing precursor FDR with 47 features
1 day, 20:20:34.138962 INFO: Decoy channel: -1
1 day, 20:20:34.138988 INFO: Competetive: True
1 day, 20:20:34.144306 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:20:34.147244 INFO: Using random state 655647 for train-test-split
1 day, 20:20:34.164342 INFO: Test AUC: 0.499
1 day, 20:20:34.164412 INFO: Train AUC: 0.499
1 day, 20:20:34.164442 INFO: AUC difference: 0.08%
1 day, 20:20:34.388278 INFO: Resetting torch num_threads to 80
1 day, 20:20:34.390408 PROGRESS: === Extracted 7908 precursors and 89728 fragments ===
1 day, 20:20:34.391627 INFO: === FDR correction performed with classifier version 0 ===
1 day, 20:20:34.392307 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:20:34.392395 PROGRESS: Total precursors accumulated: 1,400
1 day, 20:20:34.392451 PROGRESS: Target precursors: 1,387 (99.07%)
1 day, 20:20:34.392501 PROGRESS: Decoy precursors: 13 (0.93%)
1 day, 20:20:34.392553 PROGRESS: 
1 day, 20:20:34.392598 PROGRESS: Precursor Summary:
1 day, 20:20:34.393754 PROGRESS: Channel   0:	 0.050 FDR: 1,387; 0.010 FDR: 1,387; 0.001 FDR:     0
1 day, 20:20:34.393846 PROGRESS: 
1 day, 20:20:34.393900 PROGRESS: Protein Summary:
1 day, 20:20:34.395357 PROGRESS: Channel   0:	 0.050 FDR: 1,144; 0.010 FDR: 1,144; 0.001 FDR:     0
1 day, 20:20:34.395448 PROGRESS: =========================================================================
1 day, 20:20:34.395614 INFO: Target number of precursors reached.
1 day, 20:20:34.414946 INFO: fragments_df: keeping 5000 of 89728 [sum(precursor_idx_mask)=44966 sum(mass_error_mask)=89728 stop_rank=5000
1 day, 20:20:34.421959 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:34.636163 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:34.854650 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:35.068125 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:35.749422 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:20:35.749843 INFO: Using score_cutoff 48.86724677810669 (fac=0.99, q=1)
1 day, 20:20:35.750173 INFO: Updating optimization_manager: fwhm_rt             : 3.1514105796813965 -> 3.2676074504852295
1 day, 20:20:35.750252 INFO: Updating optimization_manager: fwhm_mobility       : 0.010037988424301147 -> 0.010110636241734028
1 day, 20:20:35.750304 INFO: Updating optimization_manager: score_cutoff        : 48.27712223625183 -> 48.86724677810669
1 day, 20:20:35.750358 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:35.751406 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:35.752810 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:35.753579 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:35.755672 INFO: === checking if optimization conditions were reached ===
1 day, 20:20:35.757293 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.494642
1 day, 20:20:35.757394 INFO: Updating optimization_manager: classifier_version  : 0 -> 3
1 day, 20:20:35.757457 PROGRESS: ❌ ms2_error      : 17.4946 > 17.4946 or insufficient steps taken.
1 day, 20:20:35.758553 INFO: Updating optimization_manager: ms1_error           : 30 -> 10.481372630190874
1 day, 20:20:35.758651 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
1 day, 20:20:35.758711 PROGRESS: ❌ ms1_error      : 10.4814 > 7.5755 or insufficient steps taken.
1 day, 20:20:35.758764 INFO: ==============================================
1 day, 20:20:35.758823 INFO: Starting optimization step 4.
1 day, 20:20:35.758878 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:20:35.758932 INFO: Using classic extraction backend
1 day, 20:20:35.759062 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:20:35.759123 INFO: === Search parameters used ===
1 day, 20:20:35.759168 INFO: rt_error       : 2099.928159
1 day, 20:20:35.759210 INFO: mobility_error : 0.1
1 day, 20:20:35.759251 INFO: num_candidates : 3
1 day, 20:20:35.759291 INFO: ms1_error      : 10.481372630190874
1 day, 20:20:35.759331 INFO: ms2_error      : 17.494642
1 day, 20:20:35.759376 INFO: fwhm_rt        : 3.2676074504852295
1 day, 20:20:35.759416 INFO: quant_window   : 3
1 day, 20:20:35.759454 INFO: ==============================================
1 day, 20:20:35.760377 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:20:35.760423 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:20:35.760456 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 20:20:35.760480 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.69
1 day, 20:20:35.761689 INFO: Starting candidate selection
1 day, 20:20:44.672745 INFO: Starting candidate scoring
1 day, 20:20:44.922673 INFO: Finished candidate processing
1 day, 20:20:44.922865 INFO: Collecting candidate features
1 day, 20:20:44.952642 INFO: Collecting fragment features
1 day, 20:20:44.962524 INFO: Finished candidate scoring
1 day, 20:20:44.965857 INFO: performing precursor FDR with 47 features
1 day, 20:20:44.965959 INFO: Decoy channel: -1
1 day, 20:20:44.966015 INFO: Competetive: True
1 day, 20:20:44.974308 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:20:44.978396 INFO: Using random state 903373 for train-test-split
1 day, 20:20:44.996237 INFO: Test AUC: 0.492
1 day, 20:20:44.996329 INFO: Train AUC: 0.496
1 day, 20:20:44.996381 INFO: AUC difference: 0.77%
1 day, 20:20:45.216392 INFO: Resetting torch num_threads to 80
1 day, 20:20:45.216975 PROGRESS: === Extracted 3400 precursors and 37926 fragments ===
1 day, 20:20:45.217442 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:20:45.218078 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:20:45.218165 PROGRESS: Total precursors accumulated: 600
1 day, 20:20:45.218224 PROGRESS: Target precursors: 569 (94.83%)
1 day, 20:20:45.218275 PROGRESS: Decoy precursors: 31 (5.17%)
1 day, 20:20:45.218319 PROGRESS: 
1 day, 20:20:45.218359 PROGRESS: Precursor Summary:
1 day, 20:20:45.219182 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:20:45.219267 PROGRESS: 
1 day, 20:20:45.219319 PROGRESS: Protein Summary:
1 day, 20:20:45.220209 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:20:45.220293 PROGRESS: =========================================================================
1 day, 20:20:45.221493 INFO: Target number of precursors not reached yet.
1 day, 20:20:45.227516 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:45.228666 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:45.230232 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:45.231051 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:45.234481 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:20:45.234608 INFO: Starting optimization step 5.
1 day, 20:20:45.234676 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 20:20:45.234740 INFO: Using classic extraction backend
1 day, 20:20:45.234860 PROGRESS: Extracting batch of 1588 precursors
1 day, 20:20:45.234932 INFO: === Search parameters used ===
1 day, 20:20:45.234979 INFO: rt_error       : 2099.928159
1 day, 20:20:45.235022 INFO: mobility_error : 0.1
1 day, 20:20:45.235062 INFO: num_candidates : 3
1 day, 20:20:45.235100 INFO: ms1_error      : 10.481372630190874
1 day, 20:20:45.235139 INFO: ms2_error      : 17.494642
1 day, 20:20:45.235179 INFO: fwhm_rt        : 3.2676074504852295
1 day, 20:20:45.235218 INFO: quant_window   : 3
1 day, 20:20:45.235256 INFO: ==============================================
1 day, 20:20:45.236151 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:20:45.236198 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:20:45.236238 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 20:20:45.236260 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.69
1 day, 20:20:45.237035 INFO: Starting candidate selection
1 day, 20:20:56.941990 INFO: Starting candidate scoring
1 day, 20:20:57.222677 INFO: Finished candidate processing
1 day, 20:20:57.222785 INFO: Collecting candidate features
1 day, 20:20:57.237324 INFO: Collecting fragment features
1 day, 20:20:57.242281 INFO: Finished candidate scoring
1 day, 20:20:57.246981 INFO: performing precursor FDR with 47 features
1 day, 20:20:57.247034 INFO: Decoy channel: -1
1 day, 20:20:57.247060 INFO: Competetive: True
1 day, 20:20:57.252584 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:20:57.255390 INFO: Using random state 903373 for train-test-split
1 day, 20:20:57.271353 INFO: Test AUC: 0.496
1 day, 20:20:57.271428 INFO: Train AUC: 0.497
1 day, 20:20:57.271458 INFO: AUC difference: 0.13%
1 day, 20:20:57.487201 INFO: Resetting torch num_threads to 80
1 day, 20:20:57.489162 PROGRESS: === Extracted 7901 precursors and 87736 fragments ===
1 day, 20:20:57.489568 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:20:57.490223 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:20:57.490309 PROGRESS: Total precursors accumulated: 1,400
1 day, 20:20:57.490366 PROGRESS: Target precursors: 1,333 (95.21%)
1 day, 20:20:57.490416 PROGRESS: Decoy precursors: 67 (4.79%)
1 day, 20:20:57.490465 PROGRESS: 
1 day, 20:20:57.490516 PROGRESS: Precursor Summary:
1 day, 20:20:57.491368 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 20:20:57.491454 PROGRESS: 
1 day, 20:20:57.491507 PROGRESS: Protein Summary:
1 day, 20:20:57.492440 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 20:20:57.492524 PROGRESS: =========================================================================
1 day, 20:20:57.492672 INFO: Target number of precursors not reached yet.
1 day, 20:20:57.500086 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:20:57.501292 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:20:57.503682 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:20:57.504672 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:20:57.509874 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:20:57.510000 INFO: Starting optimization step 6.
1 day, 20:20:57.510063 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 20:20:57.510125 INFO: Using classic extraction backend
1 day, 20:20:57.510228 PROGRESS: Extracting batch of 3184 precursors
1 day, 20:20:57.510305 INFO: === Search parameters used ===
1 day, 20:20:57.510352 INFO: rt_error       : 2099.928159
1 day, 20:20:57.510395 INFO: mobility_error : 0.1
1 day, 20:20:57.510434 INFO: num_candidates : 3
1 day, 20:20:57.510473 INFO: ms1_error      : 10.481372630190874
1 day, 20:20:57.510517 INFO: ms2_error      : 17.494642
1 day, 20:20:57.510558 INFO: fwhm_rt        : 3.2676074504852295
1 day, 20:20:57.510595 INFO: quant_window   : 3
1 day, 20:20:57.510632 INFO: ==============================================
1 day, 20:20:57.511608 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:20:57.511654 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:20:57.511687 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 20:20:57.511709 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.69
1 day, 20:20:57.512375 INFO: Starting candidate selection
1 day, 20:21:17.786309 INFO: Starting candidate scoring
1 day, 20:21:18.321298 INFO: Finished candidate processing
1 day, 20:21:18.321398 INFO: Collecting candidate features
1 day, 20:21:18.341168 INFO: Collecting fragment features
1 day, 20:21:18.348757 INFO: Finished candidate scoring
1 day, 20:21:18.357934 INFO: performing precursor FDR with 47 features
1 day, 20:21:18.358021 INFO: Decoy channel: -1
1 day, 20:21:18.358048 INFO: Competetive: True
1 day, 20:21:18.365424 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:21:18.369754 INFO: Using random state 903373 for train-test-split
1 day, 20:21:18.493847 INFO: Test AUC: 0.694
1 day, 20:21:18.493947 INFO: Train AUC: 0.701
1 day, 20:21:18.493977 INFO: AUC difference: 0.95%
1 day, 20:21:18.716867 INFO: Resetting torch num_threads to 80
1 day, 20:21:18.719898 PROGRESS: === Extracted 16961 precursors and 188523 fragments ===
1 day, 20:21:18.720331 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:21:18.721235 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:21:18.721330 PROGRESS: Total precursors accumulated: 3,000
1 day, 20:21:18.721388 PROGRESS: Target precursors: 2,619 (87.30%)
1 day, 20:21:18.721438 PROGRESS: Decoy precursors: 381 (12.70%)
1 day, 20:21:18.721485 PROGRESS: 
1 day, 20:21:18.721528 PROGRESS: Precursor Summary:
1 day, 20:21:18.722366 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:21:18.722453 PROGRESS: 
1 day, 20:21:18.722507 PROGRESS: Protein Summary:
1 day, 20:21:18.723410 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:21:18.723497 PROGRESS: =========================================================================
1 day, 20:21:18.723729 INFO: Target number of precursors not reached yet.
1 day, 20:21:18.735664 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:21:18.737245 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:21:18.742042 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:21:18.743384 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:21:18.751817 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:21:18.751955 INFO: Starting optimization step 7.
1 day, 20:21:18.752022 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 20:21:18.752085 INFO: Using classic extraction backend
1 day, 20:21:18.752222 PROGRESS: Extracting batch of 6376 precursors
1 day, 20:21:18.752298 INFO: === Search parameters used ===
1 day, 20:21:18.752347 INFO: rt_error       : 2099.928159
1 day, 20:21:18.752394 INFO: mobility_error : 0.1
1 day, 20:21:18.752437 INFO: num_candidates : 3
1 day, 20:21:18.752480 INFO: ms1_error      : 10.481372630190874
1 day, 20:21:18.752523 INFO: ms2_error      : 17.494642
1 day, 20:21:18.752563 INFO: fwhm_rt        : 3.2676074504852295
1 day, 20:21:18.752604 INFO: quant_window   : 3
1 day, 20:21:18.752645 INFO: ==============================================
1 day, 20:21:18.754225 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:21:18.754283 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:21:18.754318 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 20:21:18.754343 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.69
1 day, 20:21:18.755089 INFO: Starting candidate selection
1 day, 20:21:59.827462 INFO: Starting candidate scoring
1 day, 20:22:00.879864 INFO: Finished candidate processing
1 day, 20:22:00.880579 INFO: Collecting candidate features
1 day, 20:22:00.915472 INFO: Collecting fragment features
1 day, 20:22:00.929061 INFO: Finished candidate scoring
1 day, 20:22:00.948661 INFO: performing precursor FDR with 47 features
1 day, 20:22:00.948779 INFO: Decoy channel: -1
1 day, 20:22:00.948805 INFO: Competetive: True
1 day, 20:22:00.960939 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:00.969255 INFO: Using random state 903373 for train-test-split
1 day, 20:22:01.420781 INFO: Test AUC: 0.743
1 day, 20:22:01.420879 INFO: Train AUC: 0.745
1 day, 20:22:01.420912 INFO: AUC difference: 0.28%
1 day, 20:22:01.667552 INFO: Resetting torch num_threads to 80
1 day, 20:22:01.674894 PROGRESS: === Extracted 35090 precursors and 390856 fragments ===
1 day, 20:22:01.675466 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:22:01.676714 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:01.676809 PROGRESS: Total precursors accumulated: 6,199
1 day, 20:22:01.676874 PROGRESS: Target precursors: 5,895 (95.10%)
1 day, 20:22:01.677264 PROGRESS: Decoy precursors: 304 (4.90%)
1 day, 20:22:01.677329 PROGRESS: 
1 day, 20:22:01.677379 PROGRESS: Precursor Summary:
1 day, 20:22:01.679749 PROGRESS: Channel   0:	 0.050 FDR: 5,881; 0.010 FDR: 4,735; 0.001 FDR:     0
1 day, 20:22:01.679845 PROGRESS: 
1 day, 20:22:01.679908 PROGRESS: Protein Summary:
1 day, 20:22:01.682647 PROGRESS: Channel   0:	 0.050 FDR: 3,381; 0.010 FDR: 2,850; 0.001 FDR:     0
1 day, 20:22:01.682745 PROGRESS: =========================================================================
1 day, 20:22:01.683092 INFO: Target number of precursors reached.
1 day, 20:22:01.759616 INFO: fragments_df: keeping 5000 of 390856 [sum(precursor_idx_mask)=150636 sum(mass_error_mask)=390856 stop_rank=5000
1 day, 20:22:01.771890 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:02.427922 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:03.083804 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:03.729926 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:04.414075 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:04.414574 INFO: Using score_cutoff 45.604452495574954 (fac=0.99, q=1)
1 day, 20:22:04.415064 INFO: Updating optimization_manager: fwhm_rt             : 3.2676074504852295 -> 2.93937611579895
1 day, 20:22:04.415145 INFO: Updating optimization_manager: fwhm_mobility       : 0.010110636241734028 -> 0.009056027978658676
1 day, 20:22:04.415198 INFO: Updating optimization_manager: score_cutoff        : 48.86724677810669 -> 45.604452495574954
1 day, 20:22:04.415252 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:04.416360 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:04.417716 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:04.418468 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:04.420796 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:04.422387 INFO: Updating optimization_manager: ms2_error           : 17.494642 -> 17.494642
1 day, 20:22:04.422497 INFO: Updating optimization_manager: classifier_version  : 3 -> 7
1 day, 20:22:04.422564 PROGRESS: ✅ ms2_error      : 17.4946 <= 17.4946
1 day, 20:22:04.424148 INFO: Updating optimization_manager: ms1_error           : 10.481372630190874 -> 7.5754825
1 day, 20:22:04.424240 INFO: Updating optimization_manager: classifier_version  : 7 -> 7
1 day, 20:22:04.424309 PROGRESS: ✅ ms1_error      : 7.5755 <= 7.5755
1 day, 20:22:04.424363 INFO: ==============================================
1 day, 20:22:04.424433 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 20:22:04.428442 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:04.429277 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:04.430578 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:04.431319 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:04.433449 INFO: Starting optimization step 0.
1 day, 20:22:04.433544 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:04.433617 INFO: Using classic extraction backend
1 day, 20:22:04.433810 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:04.433885 INFO: === Search parameters used ===
1 day, 20:22:04.433933 INFO: rt_error       : 2099.928159
1 day, 20:22:04.433975 INFO: mobility_error : 0.1
1 day, 20:22:04.434016 INFO: num_candidates : 3
1 day, 20:22:04.434055 INFO: ms1_error      : 7.5754825
1 day, 20:22:04.434093 INFO: ms2_error      : 17.494642
1 day, 20:22:04.434129 INFO: fwhm_rt        : 2.93937611579895
1 day, 20:22:04.434168 INFO: quant_window   : 3
1 day, 20:22:04.434206 INFO: ==============================================
1 day, 20:22:04.435135 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:04.435181 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:04.435221 INFO: FWHM in RT is 2.94 seconds, sigma is 0.65
1 day, 20:22:04.435243 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.20
1 day, 20:22:04.435967 INFO: Starting candidate selection
1 day, 20:22:13.635399 INFO: Starting candidate scoring
1 day, 20:22:13.869879 INFO: Finished candidate processing
1 day, 20:22:13.869980 INFO: Collecting candidate features
1 day, 20:22:13.882516 INFO: Collecting fragment features
1 day, 20:22:13.886170 INFO: Finished candidate scoring
1 day, 20:22:13.888196 INFO: performing precursor FDR with 47 features
1 day, 20:22:13.888241 INFO: Decoy channel: -1
1 day, 20:22:13.888266 INFO: Competetive: True
1 day, 20:22:13.891562 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:13.893854 INFO: Using random state 502199 for train-test-split
1 day, 20:22:13.906184 INFO: Test AUC: 0.741
1 day, 20:22:13.906242 INFO: Train AUC: 0.753
1 day, 20:22:13.906274 INFO: AUC difference: 1.61%
1 day, 20:22:14.124163 INFO: Resetting torch num_threads to 80
1 day, 20:22:14.124701 PROGRESS: === Extracted 3383 precursors and 37725 fragments ===
1 day, 20:22:14.125141 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:22:14.125708 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:14.125794 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:14.125852 PROGRESS: Target precursors: 567 (94.50%)
1 day, 20:22:14.125902 PROGRESS: Decoy precursors: 33 (5.50%)
1 day, 20:22:14.125947 PROGRESS: 
1 day, 20:22:14.125992 PROGRESS: Precursor Summary:
1 day, 20:22:14.126954 PROGRESS: Channel   0:	 0.050 FDR:   563; 0.010 FDR:   479; 0.001 FDR:     0
1 day, 20:22:14.127046 PROGRESS: 
1 day, 20:22:14.127102 PROGRESS: Protein Summary:
1 day, 20:22:14.128270 PROGRESS: Channel   0:	 0.050 FDR:   508; 0.010 FDR:   436; 0.001 FDR:     0
1 day, 20:22:14.128367 PROGRESS: =========================================================================
1 day, 20:22:14.128683 INFO: Target number of precursors reached.
1 day, 20:22:14.135256 INFO: fragments_df: keeping 5000 of 37725 [sum(precursor_idx_mask)=15149 sum(mass_error_mask)=37725 stop_rank=5000
1 day, 20:22:14.139579 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:14.278832 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:14.414935 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:14.553289 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:15.232664 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:15.233138 INFO: Using score_cutoff 43.207262271881106 (fac=0.99, q=1)
1 day, 20:22:15.233445 INFO: Updating optimization_manager: fwhm_rt             : 2.93937611579895 -> 2.894702672958374
1 day, 20:22:15.233524 INFO: Updating optimization_manager: fwhm_mobility       : 0.009056027978658676 -> 0.009028720669448376
1 day, 20:22:15.233580 INFO: Updating optimization_manager: score_cutoff        : 45.604452495574954 -> 43.207262271881106
1 day, 20:22:15.233634 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:15.234668 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:15.236003 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:15.236759 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:15.238954 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:15.239061 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:22:15.240675 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 515.7000908443479
1 day, 20:22:15.240770 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 515.7001.
1 day, 20:22:15.240834 INFO: ==============================================
1 day, 20:22:15.240901 INFO: Starting optimization step 1.
1 day, 20:22:15.240966 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:15.241024 INFO: Using classic extraction backend
1 day, 20:22:15.241127 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:15.241189 INFO: === Search parameters used ===
1 day, 20:22:15.241236 INFO: rt_error       : 515.7000908443479
1 day, 20:22:15.241278 INFO: mobility_error : 0.1
1 day, 20:22:15.241320 INFO: num_candidates : 3
1 day, 20:22:15.241361 INFO: ms1_error      : 7.5754825
1 day, 20:22:15.241400 INFO: ms2_error      : 17.494642
1 day, 20:22:15.241440 INFO: fwhm_rt        : 2.894702672958374
1 day, 20:22:15.241479 INFO: quant_window   : 3
1 day, 20:22:15.241518 INFO: ==============================================
1 day, 20:22:15.242282 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:15.242326 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:15.242360 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 20:22:15.242383 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.19
1 day, 20:22:15.243006 INFO: Starting candidate selection
1 day, 20:22:18.334829 INFO: Starting candidate scoring
1 day, 20:22:18.571688 INFO: Finished candidate processing
1 day, 20:22:18.571822 INFO: Collecting candidate features
1 day, 20:22:18.585262 INFO: Collecting fragment features
1 day, 20:22:18.588874 INFO: Finished candidate scoring
1 day, 20:22:18.590936 INFO: performing precursor FDR with 47 features
1 day, 20:22:18.590983 INFO: Decoy channel: -1
1 day, 20:22:18.591007 INFO: Competetive: True
1 day, 20:22:18.593938 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:18.596336 INFO: Using random state 502199 for train-test-split
1 day, 20:22:18.606994 INFO: Test AUC: 0.750
1 day, 20:22:18.607053 INFO: Train AUC: 0.757
1 day, 20:22:18.607082 INFO: AUC difference: 0.95%
1 day, 20:22:18.823569 INFO: Resetting torch num_threads to 80
1 day, 20:22:18.824096 PROGRESS: === Extracted 3386 precursors and 37612 fragments ===
1 day, 20:22:18.824507 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:22:18.825985 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:18.826074 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:18.826130 PROGRESS: Target precursors: 577 (96.17%)
1 day, 20:22:18.826188 PROGRESS: Decoy precursors: 23 (3.83%)
1 day, 20:22:18.826235 PROGRESS: 
1 day, 20:22:18.826277 PROGRESS: Precursor Summary:
1 day, 20:22:18.827253 PROGRESS: Channel   0:	 0.050 FDR:   577; 0.010 FDR:   533; 0.001 FDR:     0
1 day, 20:22:18.828019 PROGRESS: 
1 day, 20:22:18.828076 PROGRESS: Protein Summary:
1 day, 20:22:18.829278 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:   484; 0.001 FDR:     0
1 day, 20:22:18.829373 PROGRESS: =========================================================================
1 day, 20:22:18.829526 INFO: Target number of precursors reached.
1 day, 20:22:18.836389 INFO: fragments_df: keeping 5000 of 37612 [sum(precursor_idx_mask)=16965 sum(mass_error_mask)=37612 stop_rank=5000
1 day, 20:22:18.840667 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:18.983551 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:19.128748 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:19.269760 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:19.947833 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:19.948260 INFO: Using score_cutoff 41.405161431884764 (fac=0.99, q=1)
1 day, 20:22:19.948564 INFO: Updating optimization_manager: fwhm_rt             : 2.894702672958374 -> 2.8507447242736816
1 day, 20:22:19.948643 INFO: Updating optimization_manager: fwhm_mobility       : 0.009028720669448376 -> 0.008683783002197742
1 day, 20:22:19.948695 INFO: Updating optimization_manager: score_cutoff        : 43.207262271881106 -> 41.405161431884764
1 day, 20:22:19.948757 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:19.949799 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:19.951135 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:19.951887 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:19.954052 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:19.954154 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:22:19.955838 INFO: Updating optimization_manager: rt_error            : 515.7000908443479 -> 67.21543845071736
1 day, 20:22:19.955933 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 67.2154.
1 day, 20:22:19.955996 INFO: ==============================================
1 day, 20:22:19.956060 INFO: Starting optimization step 2.
1 day, 20:22:19.956115 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:19.956167 INFO: Using classic extraction backend
1 day, 20:22:19.956269 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:19.956331 INFO: === Search parameters used ===
1 day, 20:22:19.956376 INFO: rt_error       : 67.21543845071736
1 day, 20:22:19.956419 INFO: mobility_error : 0.1
1 day, 20:22:19.956460 INFO: num_candidates : 3
1 day, 20:22:19.956499 INFO: ms1_error      : 7.5754825
1 day, 20:22:19.956539 INFO: ms2_error      : 17.494642
1 day, 20:22:19.956577 INFO: fwhm_rt        : 2.8507447242736816
1 day, 20:22:19.956623 INFO: quant_window   : 3
1 day, 20:22:19.956665 INFO: ==============================================
1 day, 20:22:19.957553 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:19.957601 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:19.957635 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 20:22:19.957657 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.03
1 day, 20:22:19.958363 INFO: Starting candidate selection
1 day, 20:22:20.696446 INFO: Starting candidate scoring
1 day, 20:22:20.907215 INFO: Finished candidate processing
1 day, 20:22:20.907318 INFO: Collecting candidate features
1 day, 20:22:20.920172 INFO: Collecting fragment features
1 day, 20:22:20.923779 INFO: Finished candidate scoring
1 day, 20:22:20.925781 INFO: performing precursor FDR with 47 features
1 day, 20:22:20.925830 INFO: Decoy channel: -1
1 day, 20:22:20.925863 INFO: Competetive: True
1 day, 20:22:20.928952 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:20.931083 INFO: Using random state 502199 for train-test-split
1 day, 20:22:20.941702 INFO: Test AUC: 0.761
1 day, 20:22:20.941763 INFO: Train AUC: 0.788
1 day, 20:22:20.941804 INFO: AUC difference: 3.51%
1 day, 20:22:21.160739 INFO: Resetting torch num_threads to 80
1 day, 20:22:21.161336 PROGRESS: === Extracted 3370 precursors and 36582 fragments ===
1 day, 20:22:21.161741 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:22:21.162336 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:21.162424 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:21.162482 PROGRESS: Target precursors: 591 (98.50%)
1 day, 20:22:21.162529 PROGRESS: Decoy precursors: 9 (1.50%)
1 day, 20:22:21.162573 PROGRESS: 
1 day, 20:22:21.162616 PROGRESS: Precursor Summary:
1 day, 20:22:21.163674 PROGRESS: Channel   0:	 0.050 FDR:   591; 0.010 FDR:   586; 0.001 FDR:   499
1 day, 20:22:21.163760 PROGRESS: 
1 day, 20:22:21.163818 PROGRESS: Protein Summary:
1 day, 20:22:21.165082 PROGRESS: Channel   0:	 0.050 FDR:   536; 0.010 FDR:   533; 0.001 FDR:   457
1 day, 20:22:21.165181 PROGRESS: =========================================================================
1 day, 20:22:21.165325 INFO: Target number of precursors reached.
1 day, 20:22:21.172402 INFO: fragments_df: keeping 5000 of 36582 [sum(precursor_idx_mask)=18352 sum(mass_error_mask)=36582 stop_rank=5000
1 day, 20:22:21.176704 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:21.315709 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:21.458435 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:21.598395 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:22.271376 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:22.271804 INFO: Using score_cutoff 38.74958469772339 (fac=0.99, q=1)
1 day, 20:22:22.272113 INFO: Updating optimization_manager: fwhm_rt             : 2.8507447242736816 -> 2.8138108253479004
1 day, 20:22:22.272193 INFO: Updating optimization_manager: fwhm_mobility       : 0.008683783002197742 -> 0.008341552689671516
1 day, 20:22:22.272245 INFO: Updating optimization_manager: score_cutoff        : 41.405161431884764 -> 38.74958469772339
1 day, 20:22:22.272297 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:22.273341 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:22.274713 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:22.275465 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:22.277668 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:22.277771 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:22:22.279537 INFO: Updating optimization_manager: rt_error            : 67.21543845071736 -> 23.844782530547167
1 day, 20:22:22.279635 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 23.8448.
1 day, 20:22:22.279698 INFO: ==============================================
1 day, 20:22:22.279763 INFO: Starting optimization step 3.
1 day, 20:22:22.279819 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:22.279876 INFO: Using classic extraction backend
1 day, 20:22:22.279979 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:22.280050 INFO: === Search parameters used ===
1 day, 20:22:22.280098 INFO: rt_error       : 23.844782530547167
1 day, 20:22:22.280140 INFO: mobility_error : 0.1
1 day, 20:22:22.280180 INFO: num_candidates : 3
1 day, 20:22:22.280218 INFO: ms1_error      : 7.5754825
1 day, 20:22:22.280257 INFO: ms2_error      : 17.494642
1 day, 20:22:22.280292 INFO: fwhm_rt        : 2.8138108253479004
1 day, 20:22:22.280330 INFO: quant_window   : 3
1 day, 20:22:22.280367 INFO: ==============================================
1 day, 20:22:22.281163 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:22.281212 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:22.281256 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 20:22:22.281279 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
1 day, 20:22:22.282257 INFO: Starting candidate selection
1 day, 20:22:22.851443 INFO: Starting candidate scoring
1 day, 20:22:23.068377 INFO: Finished candidate processing
1 day, 20:22:23.068476 INFO: Collecting candidate features
1 day, 20:22:23.081103 INFO: Collecting fragment features
1 day, 20:22:23.084707 INFO: Finished candidate scoring
1 day, 20:22:23.086607 INFO: performing precursor FDR with 47 features
1 day, 20:22:23.086655 INFO: Decoy channel: -1
1 day, 20:22:23.086680 INFO: Competetive: True
1 day, 20:22:23.089749 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:23.091934 INFO: Using random state 502199 for train-test-split
1 day, 20:22:23.103257 INFO: Test AUC: 0.798
1 day, 20:22:23.103320 INFO: Train AUC: 0.797
1 day, 20:22:23.103348 INFO: AUC difference: 0.14%
1 day, 20:22:23.318847 INFO: Resetting torch num_threads to 80
1 day, 20:22:23.319412 PROGRESS: === Extracted 3360 precursors and 36219 fragments ===
1 day, 20:22:23.319818 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:22:23.320410 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:23.320496 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:23.320552 PROGRESS: Target precursors: 590 (98.33%)
1 day, 20:22:23.320601 PROGRESS: Decoy precursors: 10 (1.67%)
1 day, 20:22:23.320645 PROGRESS: 
1 day, 20:22:23.320686 PROGRESS: Precursor Summary:
1 day, 20:22:23.321780 PROGRESS: Channel   0:	 0.050 FDR:   590; 0.010 FDR:   583; 0.001 FDR:   454
1 day, 20:22:23.321873 PROGRESS: 
1 day, 20:22:23.321927 PROGRESS: Protein Summary:
1 day, 20:22:23.323174 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:   530; 0.001 FDR:   423
1 day, 20:22:23.323260 PROGRESS: =========================================================================
1 day, 20:22:23.323397 INFO: Target number of precursors reached.
1 day, 20:22:23.330409 INFO: fragments_df: keeping 5000 of 36219 [sum(precursor_idx_mask)=18314 sum(mass_error_mask)=36219 stop_rank=5000
1 day, 20:22:23.336283 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:23.476293 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:23.611969 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:25.845143 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:26.468831 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:26.469269 INFO: Using score_cutoff 37.434831056213376 (fac=0.99, q=1)
1 day, 20:22:26.469576 INFO: Updating optimization_manager: fwhm_rt             : 2.8138108253479004 -> 2.832287073135376
1 day, 20:22:26.469657 INFO: Updating optimization_manager: fwhm_mobility       : 0.008341552689671516 -> 0.008262203074991703
1 day, 20:22:26.469709 INFO: Updating optimization_manager: score_cutoff        : 38.74958469772339 -> 37.434831056213376
1 day, 20:22:26.469763 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:26.470822 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:26.472170 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:26.472937 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:26.475047 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:26.475147 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 20:22:26.476965 INFO: Updating optimization_manager: rt_error            : 23.844782530547167 -> 16.58805351680339
1 day, 20:22:26.477072 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.5881.
1 day, 20:22:26.477138 INFO: ==============================================
1 day, 20:22:26.477203 INFO: Starting optimization step 4.
1 day, 20:22:26.477270 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:26.477325 INFO: Using classic extraction backend
1 day, 20:22:26.477456 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:26.477522 INFO: === Search parameters used ===
1 day, 20:22:26.477568 INFO: rt_error       : 16.58805351680339
1 day, 20:22:26.477613 INFO: mobility_error : 0.1
1 day, 20:22:26.477654 INFO: num_candidates : 3
1 day, 20:22:26.477692 INFO: ms1_error      : 7.5754825
1 day, 20:22:26.477732 INFO: ms2_error      : 17.494642
1 day, 20:22:26.477769 INFO: fwhm_rt        : 2.832287073135376
1 day, 20:22:26.477808 INFO: quant_window   : 3
1 day, 20:22:26.477847 INFO: ==============================================
1 day, 20:22:26.478660 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:26.478706 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:26.478740 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1 day, 20:22:26.478762 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
1 day, 20:22:26.479391 INFO: Starting candidate selection
1 day, 20:22:27.072341 INFO: Starting candidate scoring
1 day, 20:22:27.306179 INFO: Finished candidate processing
1 day, 20:22:27.306273 INFO: Collecting candidate features
1 day, 20:22:27.318694 INFO: Collecting fragment features
1 day, 20:22:27.322392 INFO: Finished candidate scoring
1 day, 20:22:27.324997 INFO: performing precursor FDR with 47 features
1 day, 20:22:27.325041 INFO: Decoy channel: -1
1 day, 20:22:27.325065 INFO: Competetive: True
1 day, 20:22:27.328325 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:27.330432 INFO: Using random state 502199 for train-test-split
1 day, 20:22:27.341135 INFO: Test AUC: 0.810
1 day, 20:22:27.341192 INFO: Train AUC: 0.801
1 day, 20:22:27.341221 INFO: AUC difference: 1.16%
1 day, 20:22:27.559094 INFO: Resetting torch num_threads to 80
1 day, 20:22:27.559935 PROGRESS: === Extracted 3362 precursors and 36114 fragments ===
1 day, 20:22:27.560344 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:22:27.560920 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:27.561039 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:27.561099 PROGRESS: Target precursors: 596 (99.33%)
1 day, 20:22:27.561148 PROGRESS: Decoy precursors: 4 (0.67%)
1 day, 20:22:27.561202 PROGRESS: 
1 day, 20:22:27.561248 PROGRESS: Precursor Summary:
1 day, 20:22:27.562307 PROGRESS: Channel   0:	 0.050 FDR:   596; 0.010 FDR:   596; 0.001 FDR:   449
1 day, 20:22:27.562395 PROGRESS: 
1 day, 20:22:27.562452 PROGRESS: Protein Summary:
1 day, 20:22:27.563739 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   541; 0.001 FDR:   417
1 day, 20:22:27.563827 PROGRESS: =========================================================================
1 day, 20:22:27.563965 INFO: Target number of precursors reached.
1 day, 20:22:27.571421 INFO: fragments_df: keeping 5000 of 36114 [sum(precursor_idx_mask)=18675 sum(mass_error_mask)=36114 stop_rank=5000
1 day, 20:22:27.577226 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:27.720347 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:27.868642 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:28.020296 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:28.716971 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:28.717822 INFO: Using score_cutoff 38.16458459472656 (fac=0.99, q=1)
1 day, 20:22:28.718260 INFO: Updating optimization_manager: fwhm_rt             : 2.832287073135376 -> 2.812016487121582
1 day, 20:22:28.718343 INFO: Updating optimization_manager: fwhm_mobility       : 0.008262203074991703 -> 0.008141936734318733
1 day, 20:22:28.718400 INFO: Updating optimization_manager: score_cutoff        : 37.434831056213376 -> 38.16458459472656
1 day, 20:22:28.718471 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:28.720172 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:28.721561 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:28.722337 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:28.724653 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:28.724772 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 20:22:28.726846 INFO: Updating optimization_manager: rt_error            : 16.58805351680339 -> 17.512822294774544
1 day, 20:22:28.726949 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 17.5128.
1 day, 20:22:28.727016 INFO: ==============================================
1 day, 20:22:28.727091 INFO: Starting optimization step 5.
1 day, 20:22:28.727157 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:28.727228 INFO: Using classic extraction backend
1 day, 20:22:28.727399 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:28.727471 INFO: === Search parameters used ===
1 day, 20:22:28.727518 INFO: rt_error       : 17.512822294774544
1 day, 20:22:28.727561 INFO: mobility_error : 0.1
1 day, 20:22:28.727604 INFO: num_candidates : 3
1 day, 20:22:28.727642 INFO: ms1_error      : 7.5754825
1 day, 20:22:28.727682 INFO: ms2_error      : 17.494642
1 day, 20:22:28.727720 INFO: fwhm_rt        : 2.812016487121582
1 day, 20:22:28.727758 INFO: quant_window   : 3
1 day, 20:22:28.727795 INFO: ==============================================
1 day, 20:22:28.731073 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:28.731126 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:28.731167 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 20:22:28.731191 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.78
1 day, 20:22:28.732023 INFO: Starting candidate selection
1 day, 20:22:29.258422 INFO: Starting candidate scoring
1 day, 20:22:29.458582 INFO: Finished candidate processing
1 day, 20:22:29.458839 INFO: Collecting candidate features
1 day, 20:22:29.472203 INFO: Collecting fragment features
1 day, 20:22:29.476303 INFO: Finished candidate scoring
1 day, 20:22:29.478783 INFO: performing precursor FDR with 47 features
1 day, 20:22:29.478832 INFO: Decoy channel: -1
1 day, 20:22:29.478858 INFO: Competetive: True
1 day, 20:22:29.483303 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:29.485646 INFO: Using random state 502199 for train-test-split
1 day, 20:22:29.497092 INFO: Test AUC: 0.810
1 day, 20:22:29.497154 INFO: Train AUC: 0.808
1 day, 20:22:29.497185 INFO: AUC difference: 0.29%
1 day, 20:22:29.715621 INFO: Resetting torch num_threads to 80
1 day, 20:22:29.716200 PROGRESS: === Extracted 3354 precursors and 36075 fragments ===
1 day, 20:22:29.716632 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:22:29.717243 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:29.717330 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:29.717385 PROGRESS: Target precursors: 594 (99.00%)
1 day, 20:22:29.717433 PROGRESS: Decoy precursors: 6 (1.00%)
1 day, 20:22:29.717477 PROGRESS: 
1 day, 20:22:29.717518 PROGRESS: Precursor Summary:
1 day, 20:22:29.718565 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:   594; 0.001 FDR:   452
1 day, 20:22:29.718655 PROGRESS: 
1 day, 20:22:29.718708 PROGRESS: Protein Summary:
1 day, 20:22:29.719966 PROGRESS: Channel   0:	 0.050 FDR:   539; 0.010 FDR:   539; 0.001 FDR:   421
1 day, 20:22:29.720054 PROGRESS: =========================================================================
1 day, 20:22:29.720193 INFO: Target number of precursors reached.
1 day, 20:22:29.727268 INFO: fragments_df: keeping 5000 of 36075 [sum(precursor_idx_mask)=18599 sum(mass_error_mask)=36075 stop_rank=5000
1 day, 20:22:29.732050 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:29.874017 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:30.015007 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:30.142364 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:30.758214 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:30.758651 INFO: Using score_cutoff 38.31532042579651 (fac=0.99, q=1)
1 day, 20:22:30.758974 INFO: Updating optimization_manager: fwhm_rt             : 2.812016487121582 -> 2.8106157779693604
1 day, 20:22:30.759053 INFO: Updating optimization_manager: fwhm_mobility       : 0.008141936734318733 -> 0.008135659620165825
1 day, 20:22:30.759108 INFO: Updating optimization_manager: score_cutoff        : 38.16458459472656 -> 38.31532042579651
1 day, 20:22:30.759161 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:30.760226 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:30.761584 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:30.762379 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:30.764440 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:30.764542 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 20:22:30.766384 INFO: Updating optimization_manager: rt_error            : 17.512822294774544 -> 17.701310455290695
1 day, 20:22:30.766487 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.7013.
1 day, 20:22:30.766555 INFO: ==============================================
1 day, 20:22:30.766621 INFO: Starting optimization step 6.
1 day, 20:22:30.766680 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:30.766734 INFO: Using classic extraction backend
1 day, 20:22:30.766840 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:30.766905 INFO: === Search parameters used ===
1 day, 20:22:30.766958 INFO: rt_error       : 17.701310455290695
1 day, 20:22:30.767003 INFO: mobility_error : 0.1
1 day, 20:22:30.767045 INFO: num_candidates : 3
1 day, 20:22:30.767085 INFO: ms1_error      : 7.5754825
1 day, 20:22:30.767128 INFO: ms2_error      : 17.494642
1 day, 20:22:30.767170 INFO: fwhm_rt        : 2.8106157779693604
1 day, 20:22:30.767210 INFO: quant_window   : 3
1 day, 20:22:30.767251 INFO: ==============================================
1 day, 20:22:30.768030 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:30.768079 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:30.768114 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 20:22:30.768137 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.77
1 day, 20:22:30.768793 INFO: Starting candidate selection
1 day, 20:22:31.311518 INFO: Starting candidate scoring
1 day, 20:22:31.517724 INFO: Finished candidate processing
1 day, 20:22:31.518367 INFO: Collecting candidate features
1 day, 20:22:31.532848 INFO: Collecting fragment features
1 day, 20:22:31.536485 INFO: Finished candidate scoring
1 day, 20:22:31.538678 INFO: performing precursor FDR with 47 features
1 day, 20:22:31.538723 INFO: Decoy channel: -1
1 day, 20:22:31.538747 INFO: Competetive: True
1 day, 20:22:31.541731 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:31.543818 INFO: Using random state 502199 for train-test-split
1 day, 20:22:31.554704 INFO: Test AUC: 0.830
1 day, 20:22:31.554762 INFO: Train AUC: 0.805
1 day, 20:22:31.554792 INFO: AUC difference: 3.05%
1 day, 20:22:31.770840 INFO: Resetting torch num_threads to 80
1 day, 20:22:31.771393 PROGRESS: === Extracted 3345 precursors and 35979 fragments ===
1 day, 20:22:31.771791 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:22:31.772382 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:31.772468 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:31.772524 PROGRESS: Target precursors: 592 (98.67%)
1 day, 20:22:31.772573 PROGRESS: Decoy precursors: 8 (1.33%)
1 day, 20:22:31.772625 PROGRESS: 
1 day, 20:22:31.772670 PROGRESS: Precursor Summary:
1 day, 20:22:31.773774 PROGRESS: Channel   0:	 0.050 FDR:   592; 0.010 FDR:   589; 0.001 FDR:   425
1 day, 20:22:31.773872 PROGRESS: 
1 day, 20:22:31.773926 PROGRESS: Protein Summary:
1 day, 20:22:31.775162 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   536; 0.001 FDR:   397
1 day, 20:22:31.775252 PROGRESS: =========================================================================
1 day, 20:22:31.775378 INFO: Target number of precursors reached.
1 day, 20:22:31.782236 INFO: fragments_df: keeping 5000 of 35979 [sum(precursor_idx_mask)=18423 sum(mass_error_mask)=35979 stop_rank=5000
1 day, 20:22:31.786496 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:31.927888 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:32.069257 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:32.218761 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:32.898287 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:32.898706 INFO: Using score_cutoff 38.28521410675049 (fac=0.99, q=1)
1 day, 20:22:32.899015 INFO: Updating optimization_manager: fwhm_rt             : 2.8106157779693604 -> 2.8080215454101562
1 day, 20:22:32.899092 INFO: Updating optimization_manager: fwhm_mobility       : 0.008135659620165825 -> 0.008137460798025131
1 day, 20:22:32.899143 INFO: Updating optimization_manager: score_cutoff        : 38.31532042579651 -> 38.28521410675049
1 day, 20:22:32.899193 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:32.900216 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:32.901566 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:32.902328 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:32.904417 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:32.904516 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 20:22:32.905492 INFO: Updating optimization_manager: rt_error            : 17.701310455290695 -> 16.58805351680339
1 day, 20:22:32.905615 INFO: Updating optimization_manager: classifier_version  : 7 -> 12
1 day, 20:22:32.905718 INFO: Updating optimization_manager: score_cutoff        : 38.28521410675049 -> 38.16458459472656
1 day, 20:22:32.905805 INFO: Updating optimization_manager: fwhm_rt             : 2.8080215454101562 -> 2.812016487121582
1 day, 20:22:32.905885 INFO: Updating optimization_manager: fwhm_mobility       : 0.008137460798025131 -> 0.008141936734318733
1 day, 20:22:32.905964 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 16.5881 found after 7 searches.
1 day, 20:22:32.906024 INFO: ==============================================
1 day, 20:22:32.906085 PROGRESS: Optimization finished for rt_error.
1 day, 20:22:32.909937 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:32.910751 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:32.912058 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:32.912832 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:32.938405 INFO: Starting optimization step 0.
1 day, 20:22:32.938542 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:32.938608 INFO: Using classic extraction backend
1 day, 20:22:32.938720 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:32.938787 INFO: === Search parameters used ===
1 day, 20:22:32.938835 INFO: rt_error       : 16.58805351680339
1 day, 20:22:32.938879 INFO: mobility_error : 0.1
1 day, 20:22:32.938921 INFO: num_candidates : 3
1 day, 20:22:32.938960 INFO: ms1_error      : 7.5754825
1 day, 20:22:32.938999 INFO: ms2_error      : 17.494642
1 day, 20:22:32.939044 INFO: fwhm_rt        : 2.812016487121582
1 day, 20:22:32.939086 INFO: quant_window   : 3
1 day, 20:22:32.939130 INFO: ==============================================
1 day, 20:22:32.939954 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:32.939999 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:32.940033 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 20:22:32.940054 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.78
1 day, 20:22:32.940718 INFO: Starting candidate selection
1 day, 20:22:33.452493 INFO: Starting candidate scoring
1 day, 20:22:33.641952 INFO: Finished candidate processing
1 day, 20:22:33.642140 INFO: Collecting candidate features
1 day, 20:22:33.661425 INFO: Collecting fragment features
1 day, 20:22:33.665394 INFO: Finished candidate scoring
1 day, 20:22:33.667531 INFO: performing precursor FDR with 47 features
1 day, 20:22:33.667576 INFO: Decoy channel: -1
1 day, 20:22:33.667601 INFO: Competetive: True
1 day, 20:22:33.670730 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:33.672949 INFO: Using random state 279242 for train-test-split
1 day, 20:22:33.683810 INFO: Test AUC: 0.796
1 day, 20:22:33.683871 INFO: Train AUC: 0.810
1 day, 20:22:33.683901 INFO: AUC difference: 1.75%
1 day, 20:22:33.899361 INFO: Resetting torch num_threads to 80
1 day, 20:22:33.899920 PROGRESS: === Extracted 3340 precursors and 35909 fragments ===
1 day, 20:22:33.900324 INFO: === FDR correction performed with classifier version 12 ===
1 day, 20:22:33.900885 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:33.900983 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:33.901042 PROGRESS: Target precursors: 594 (99.00%)
1 day, 20:22:33.901092 PROGRESS: Decoy precursors: 6 (1.00%)
1 day, 20:22:33.901137 PROGRESS: 
1 day, 20:22:33.901178 PROGRESS: Precursor Summary:
1 day, 20:22:33.902229 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:   594; 0.001 FDR:   525
1 day, 20:22:33.902318 PROGRESS: 
1 day, 20:22:33.902374 PROGRESS: Protein Summary:
1 day, 20:22:33.903618 PROGRESS: Channel   0:	 0.050 FDR:   539; 0.010 FDR:   539; 0.001 FDR:   480
1 day, 20:22:33.903707 PROGRESS: =========================================================================
1 day, 20:22:33.903837 INFO: Target number of precursors reached.
1 day, 20:22:33.910799 INFO: fragments_df: keeping 5000 of 35909 [sum(precursor_idx_mask)=18521 sum(mass_error_mask)=35909 stop_rank=5000
1 day, 20:22:33.915032 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:34.034195 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:34.153260 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:34.280348 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:34.892359 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:34.892771 INFO: Using score_cutoff 38.315320954513545 (fac=0.99, q=1)
1 day, 20:22:34.893147 INFO: Updating optimization_manager: fwhm_rt             : 2.812016487121582 -> 2.816441535949707
1 day, 20:22:34.893229 INFO: Updating optimization_manager: fwhm_mobility       : 0.008141936734318733 -> 0.008124709129333496
1 day, 20:22:34.893283 INFO: Updating optimization_manager: score_cutoff        : 38.16458459472656 -> 38.315320954513545
1 day, 20:22:34.893338 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:34.894346 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:34.895658 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:34.896405 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:34.898536 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:34.898633 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:22:34.899959 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06687816255142597
1 day, 20:22:34.900054 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0669.
1 day, 20:22:34.900127 INFO: ==============================================
1 day, 20:22:34.900192 INFO: Starting optimization step 1.
1 day, 20:22:34.900247 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:34.900298 INFO: Using classic extraction backend
1 day, 20:22:34.900407 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:34.900470 INFO: === Search parameters used ===
1 day, 20:22:34.900516 INFO: rt_error       : 16.58805351680339
1 day, 20:22:34.900558 INFO: mobility_error : 0.06687816255142597
1 day, 20:22:34.900601 INFO: num_candidates : 3
1 day, 20:22:34.900641 INFO: ms1_error      : 7.5754825
1 day, 20:22:34.900682 INFO: ms2_error      : 17.494642
1 day, 20:22:34.900720 INFO: fwhm_rt        : 2.816441535949707
1 day, 20:22:34.900759 INFO: quant_window   : 3
1 day, 20:22:34.900798 INFO: ==============================================
1 day, 20:22:34.901561 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:34.901609 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:34.901642 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 20:22:34.901666 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.77
1 day, 20:22:34.902311 INFO: Starting candidate selection
1 day, 20:22:35.401045 INFO: Starting candidate scoring
1 day, 20:22:35.609636 INFO: Finished candidate processing
1 day, 20:22:35.609738 INFO: Collecting candidate features
1 day, 20:22:35.618853 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3340)
1 day, 20:22:35.622087 INFO: Collecting fragment features
1 day, 20:22:35.625674 INFO: Finished candidate scoring
1 day, 20:22:35.627514 INFO: performing precursor FDR with 47 features
1 day, 20:22:35.627557 INFO: Decoy channel: -1
1 day, 20:22:35.627581 INFO: Competetive: True
1 day, 20:22:35.630356 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:35.631690 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 20:22:35.632761 INFO: Using random state 279242 for train-test-split
1 day, 20:22:35.643834 INFO: Test AUC: 0.812
1 day, 20:22:35.643893 INFO: Train AUC: 0.810
1 day, 20:22:35.643922 INFO: AUC difference: 0.34%
1 day, 20:22:35.857363 INFO: Resetting torch num_threads to 80
1 day, 20:22:35.857905 PROGRESS: === Extracted 3340 precursors and 35699 fragments ===
1 day, 20:22:35.858311 INFO: === FDR correction performed with classifier version 12 ===
1 day, 20:22:35.858867 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:35.858955 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:35.859012 PROGRESS: Target precursors: 591 (98.50%)
1 day, 20:22:35.859061 PROGRESS: Decoy precursors: 9 (1.50%)
1 day, 20:22:35.859107 PROGRESS: 
1 day, 20:22:35.859149 PROGRESS: Precursor Summary:
1 day, 20:22:35.860225 PROGRESS: Channel   0:	 0.050 FDR:   591; 0.010 FDR:   586; 0.001 FDR:   521
1 day, 20:22:35.860314 PROGRESS: 
1 day, 20:22:35.860368 PROGRESS: Protein Summary:
1 day, 20:22:35.861645 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   534; 0.001 FDR:   477
1 day, 20:22:35.861738 PROGRESS: =========================================================================
1 day, 20:22:35.861868 INFO: Target number of precursors reached.
1 day, 20:22:35.868688 INFO: fragments_df: keeping 5000 of 35699 [sum(precursor_idx_mask)=18289 sum(mass_error_mask)=35699 stop_rank=5000
1 day, 20:22:35.872888 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:35.993876 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:36.134461 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:36.277810 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:36.929566 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:36.929979 INFO: Using score_cutoff 37.46338457107544 (fac=0.99, q=1)
1 day, 20:22:36.930284 INFO: Updating optimization_manager: fwhm_rt             : 2.816441535949707 -> 2.813931941986084
1 day, 20:22:36.930367 INFO: Updating optimization_manager: fwhm_mobility       : 0.008124709129333496 -> 0.008135659620165825
1 day, 20:22:36.930419 INFO: Updating optimization_manager: score_cutoff        : 38.315320954513545 -> 37.46338457107544
1 day, 20:22:36.930470 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:36.931483 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:36.932789 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:36.933554 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:36.935569 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:36.935666 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:22:36.937090 INFO: Updating optimization_manager: mobility_error      : 0.06687816255142597 -> 0.05936866228317426
1 day, 20:22:36.937191 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0594.
1 day, 20:22:36.937255 INFO: ==============================================
1 day, 20:22:36.937319 INFO: Starting optimization step 2.
1 day, 20:22:36.937375 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:22:36.937428 INFO: Using classic extraction backend
1 day, 20:22:36.937528 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:22:36.937590 INFO: === Search parameters used ===
1 day, 20:22:36.937636 INFO: rt_error       : 16.58805351680339
1 day, 20:22:36.937678 INFO: mobility_error : 0.05936866228317426
1 day, 20:22:36.937718 INFO: num_candidates : 3
1 day, 20:22:36.937760 INFO: ms1_error      : 7.5754825
1 day, 20:22:36.937801 INFO: ms2_error      : 17.494642
1 day, 20:22:36.937839 INFO: fwhm_rt        : 2.813931941986084
1 day, 20:22:36.937879 INFO: quant_window   : 3
1 day, 20:22:36.937917 INFO: ==============================================
1 day, 20:22:36.938665 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:36.938712 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:36.938745 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 20:22:36.938766 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.77
1 day, 20:22:36.939407 INFO: Starting candidate selection
1 day, 20:22:37.416090 INFO: Starting candidate scoring
1 day, 20:22:37.611166 INFO: Finished candidate processing
1 day, 20:22:37.611265 INFO: Collecting candidate features
1 day, 20:22:37.624028 INFO: Collecting fragment features
1 day, 20:22:37.628364 INFO: Finished candidate scoring
1 day, 20:22:37.630507 INFO: performing precursor FDR with 47 features
1 day, 20:22:37.630563 INFO: Decoy channel: -1
1 day, 20:22:37.630588 INFO: Competetive: True
1 day, 20:22:37.633488 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:37.635572 INFO: Using random state 279242 for train-test-split
1 day, 20:22:37.646504 INFO: Test AUC: 0.846
1 day, 20:22:37.646564 INFO: Train AUC: 0.799
1 day, 20:22:37.646593 INFO: AUC difference: 5.91%
1 day, 20:22:37.646615 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:22:37.862228 INFO: Resetting torch num_threads to 80
1 day, 20:22:37.862792 PROGRESS: === Extracted 3339 precursors and 35537 fragments ===
1 day, 20:22:37.863200 INFO: === FDR correction performed with classifier version 12 ===
1 day, 20:22:37.863757 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:37.863843 PROGRESS: Total precursors accumulated: 600
1 day, 20:22:37.863908 PROGRESS: Target precursors: 593 (98.83%)
1 day, 20:22:37.863959 PROGRESS: Decoy precursors: 7 (1.17%)
1 day, 20:22:37.864004 PROGRESS: 
1 day, 20:22:37.864045 PROGRESS: Precursor Summary:
1 day, 20:22:37.865075 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   589; 0.001 FDR:   515
1 day, 20:22:37.865163 PROGRESS: 
1 day, 20:22:37.865224 PROGRESS: Protein Summary:
1 day, 20:22:37.866485 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   536; 0.001 FDR:   474
1 day, 20:22:37.866580 PROGRESS: =========================================================================
1 day, 20:22:37.866713 INFO: Target number of precursors reached.
1 day, 20:22:37.873558 INFO: fragments_df: keeping 5000 of 35537 [sum(precursor_idx_mask)=18367 sum(mass_error_mask)=35537 stop_rank=5000
1 day, 20:22:37.877795 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:37.996627 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:38.122656 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:38.244089 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:38.857648 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:22:38.858072 INFO: Using score_cutoff 37.38882164611816 (fac=0.99, q=1)
1 day, 20:22:38.858382 INFO: Updating optimization_manager: fwhm_rt             : 2.813931941986084 -> 2.8214282989501953
1 day, 20:22:38.858460 INFO: Updating optimization_manager: fwhm_mobility       : 0.008135659620165825 -> 0.008115558885037899
1 day, 20:22:38.858513 INFO: Updating optimization_manager: score_cutoff        : 37.46338457107544 -> 37.38882164611816
1 day, 20:22:38.858575 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:38.859612 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:38.860924 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:38.861701 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:38.863833 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:38.863929 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:22:38.864617 INFO: Updating optimization_manager: mobility_error      : 0.05936866228317426 -> 0.1
1 day, 20:22:38.864739 INFO: Updating optimization_manager: classifier_version  : 12 -> 15
1 day, 20:22:38.864832 INFO: Updating optimization_manager: score_cutoff        : 37.38882164611816 -> 38.315320954513545
1 day, 20:22:38.864918 INFO: Updating optimization_manager: fwhm_rt             : 2.8214282989501953 -> 2.816441535949707
1 day, 20:22:38.865017 INFO: Updating optimization_manager: fwhm_mobility       : 0.008115558885037899 -> 0.008124709129333496
1 day, 20:22:38.865100 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 20:22:38.865162 INFO: ==============================================
1 day, 20:22:38.865224 PROGRESS: Optimization finished for mobility_error.
1 day, 20:22:38.869225 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:38.870036 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:38.871324 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:38.872078 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:38.898558 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:22:38.898690 PROGRESS: ==============================================
1 day, 20:22:38.898764 PROGRESS: ms2_error      : 17.4946
1 day, 20:22:38.898825 PROGRESS: ms1_error      : 7.5755
1 day, 20:22:38.898874 PROGRESS: rt_error       : 16.5881
1 day, 20:22:38.898921 PROGRESS: mobility_error : 0.1000
1 day, 20:22:38.898962 PROGRESS: ==============================================
1 day, 20:22:38.899520 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:22:38.917929 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:22:39.000720 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:22:39.021368 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:22:39.235827 INFO: Using classic extraction backend
1 day, 20:22:39.236174 PROGRESS: Extracting batch of 146455 precursors
1 day, 20:22:39.236276 INFO: === Search parameters used ===
1 day, 20:22:39.237396 INFO: rt_error       : 16.58805351680339
1 day, 20:22:39.237458 INFO: mobility_error : 0.1
1 day, 20:22:39.237513 INFO: num_candidates : 3
1 day, 20:22:39.237565 INFO: ms1_error      : 7.5754825
1 day, 20:22:39.237616 INFO: ms2_error      : 17.494642
1 day, 20:22:39.237665 INFO: fwhm_rt        : 2.816441535949707
1 day, 20:22:39.237714 INFO: quant_window   : 3
1 day, 20:22:39.237771 INFO: ==============================================
1 day, 20:22:39.273678 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:39.273820 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:39.273870 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 20:22:39.273900 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.77
1 day, 20:22:39.274922 INFO: Starting candidate selection
1 day, 20:22:53.686699 INFO: Removed 114455 precursors with score below cutoff 38.315320954513545
1 day, 20:22:54.039875 INFO: Starting candidate scoring
1 day, 20:23:07.356622 INFO: Finished candidate processing
1 day, 20:23:07.356927 INFO: Collecting candidate features
1 day, 20:23:07.769637 INFO: Collecting fragment features
1 day, 20:23:07.948204 INFO: Finished candidate scoring
1 day, 20:23:08.086431 INFO: === Performing FDR correction with classifier version 15 ===
1 day, 20:23:08.087298 INFO: performing precursor FDR with 47 features
1 day, 20:23:08.087336 INFO: Decoy channel: -1
1 day, 20:23:08.087362 INFO: Competetive: True
1 day, 20:23:08.154844 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:23:08.182287 WARNING: FDR calculation for 175787 target and 122103 decoy PSMs
1 day, 20:23:08.182415 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 20:23:08.263482 INFO: Using random state 117784 for train-test-split
1 day, 20:23:13.193504 INFO: Test AUC: 0.855
1 day, 20:23:13.193626 INFO: Train AUC: 0.859
1 day, 20:23:13.193660 INFO: AUC difference: 0.43%
1 day, 20:23:13.518368 INFO: Resetting torch num_threads to 80
1 day, 20:23:13.528059 INFO: Removing fragments below FDR threshold
1 day, 20:23:13.583656 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:23:13.583888 PROGRESS: Total precursors accumulated: 73,145
1 day, 20:23:13.583955 PROGRESS: Target precursors: 72,524 (99.15%)
1 day, 20:23:13.584008 PROGRESS: Decoy precursors: 621 (0.85%)
1 day, 20:23:13.584056 PROGRESS: 
1 day, 20:23:13.584099 PROGRESS: Precursor Summary:
1 day, 20:23:13.615254 PROGRESS: Channel   0:	 0.050 FDR: 72,524; 0.010 FDR: 72,524; 0.001 FDR: 71,160
1 day, 20:23:13.615503 PROGRESS: 
1 day, 20:23:13.615565 PROGRESS: Protein Summary:
1 day, 20:23:13.655683 PROGRESS: Channel   0:	 0.050 FDR: 7,422; 0.010 FDR: 7,422; 0.001 FDR: 7,408
1 day, 20:23:13.655911 PROGRESS: =========================================================================
1 day, 20:23:13.659536 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/psm.parquet
1 day, 20:23:13.960204 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/frag.parquet
1 day, 20:23:14.227205 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 20:23:14.263232 PROGRESS: 
1 day, 20:23:14.263379 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
1 day, 20:23:14.263450 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/figures
1 day, 20:23:14.263616 INFO: Initializing TimingManager
1 day, 20:23:14.264125 INFO: Initializing RawFileManager
1 day, 20:23:14.264251 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:14.264315 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:14.264358 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:14.468645 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, 20:23:19.977887 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
1 day, 20:23:19.987426 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:20.002444 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:20.002911 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:20.003609 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:20.005114 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:20.020376 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:20.020802 INFO: Indexing quadrupole dimension
1 day, 20:23:20.608511 INFO: Transposing detector events
1 day, 20:23:30.860463 INFO: Finished transposing data
1 day, 20:23:30.902948 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 20:23:30.904404 INFO: RT (min)            : 0.0 - 70.0
1 day, 20:23:30.904522 INFO: RT duration (sec)   : 4199.8
1 day, 20:23:30.904579 INFO: RT duration (min)   : 70.0
1 day, 20:23:30.904630 INFO: Cycle len (scans)   : 9
1 day, 20:23:30.904676 INFO: Cycle len (sec)     : 0.97
1 day, 20:23:30.904722 INFO: Number of cycles    : 4347
1 day, 20:23:30.904769 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 20:23:30.904893 INFO: Creating DIA data object took: 16.640647888183594
1 day, 20:23:30.944487 INFO: Initializing CalibrationManager
1 day, 20:23:30.944769 INFO: Setting up calibration estimators ..
1 day, 20:23:30.944829 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 20:23:30.944914 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, 20:23:30.945017 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 20:23:30.945074 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, 20:23:30.945132 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, 20:23:30.945193 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, 20:23:30.945241 INFO: Done setting up calibration estimators.
1 day, 20:23:30.945361 INFO: Initializing OptimizationManager
1 day, 20:23:30.945465 INFO: initial parameter: ms1_error = 30
1 day, 20:23:30.945511 INFO: initial parameter: ms2_error = 30
1 day, 20:23:30.945560 INFO: initial parameter: rt_error = 2099.894844
1 day, 20:23:30.945602 INFO: initial parameter: mobility_error = 0.1
1 day, 20:23:30.945645 INFO: initial parameter: num_candidates = 1
1 day, 20:23:30.945685 INFO: initial parameter: fwhm_rt = 5
1 day, 20:23:30.945730 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 20:23:30.945770 INFO: initial parameter: score_cutoff = 0
1 day, 20:23:30.945809 INFO: initial parameter: classifier_version = -1
1 day, 20:23:30.945890 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 20:23:30.946207 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 20:23:30.946241 INFO: Initializing FDRManager
1 day, 20:23:30.946285 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 20:23:30.964801 PROGRESS: Initializing spectral library: 73,677 target precursors potentially observable (0 removed)
1 day, 20:23:30.978232 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 20:23:30.978576 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 2099.894844
1 day, 20:23:30.978692 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 20:23:30.978867 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 20:23:30.978959 PROGRESS: Starting initial search for precursors.
1 day, 20:23:30.979047 INFO: Starting optimization step 0.
1 day, 20:23:30.979110 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 20:23:30.979183 INFO: Using classic extraction backend
1 day, 20:23:30.979390 PROGRESS: Extracting batch of 399 precursors
1 day, 20:23:30.979462 INFO: === Search parameters used ===
1 day, 20:23:30.979511 INFO: rt_error       : 2099.894844
1 day, 20:23:30.979557 INFO: mobility_error : 0.1
1 day, 20:23:30.979599 INFO: num_candidates : 1
1 day, 20:23:30.979641 INFO: ms1_error      : 30
1 day, 20:23:30.979684 INFO: ms2_error      : 30
1 day, 20:23:30.979724 INFO: fwhm_rt        : 5
1 day, 20:23:30.979766 INFO: quant_window   : 3
1 day, 20:23:30.979805 INFO: ==============================================
1 day, 20:23:30.980603 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:23:30.980649 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:23:30.980684 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:23:30.980707 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:23:30.981653 INFO: Starting candidate selection
1 day, 20:23:35.222642 INFO: Starting candidate scoring
1 day, 20:23:35.314918 INFO: Finished candidate processing
1 day, 20:23:35.315044 INFO: Collecting candidate features
1 day, 20:23:35.324264 INFO: Collecting fragment features
1 day, 20:23:35.326397 INFO: Finished candidate scoring
1 day, 20:23:35.327205 INFO: performing precursor FDR with 47 features
1 day, 20:23:35.327248 INFO: Decoy channel: -1
1 day, 20:23:35.327273 INFO: Competetive: True
1 day, 20:23:35.328452 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:23:35.330995 INFO: Using random state 209287 for train-test-split
1 day, 20:23:35.339158 INFO: Test AUC: 0.463
1 day, 20:23:35.339217 INFO: Train AUC: 0.450
1 day, 20:23:35.339249 INFO: AUC difference: 2.83%
1 day, 20:23:35.562492 INFO: Resetting torch num_threads to 80
1 day, 20:23:35.562940 PROGRESS: === Extracted 399 precursors and 4570 fragments ===
1 day, 20:23:35.563359 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:23:35.564101 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:23:35.564191 PROGRESS: Total precursors accumulated: 200
1 day, 20:23:35.564250 PROGRESS: Target precursors: 139 (69.50%)
1 day, 20:23:35.564300 PROGRESS: Decoy precursors: 61 (30.50%)
1 day, 20:23:35.564344 PROGRESS: 
1 day, 20:23:35.564389 PROGRESS: Precursor Summary:
1 day, 20:23:35.565326 PROGRESS: Channel   0:	 0.050 FDR:   131; 0.010 FDR:   131; 0.001 FDR:   131
1 day, 20:23:35.565421 PROGRESS: 
1 day, 20:23:35.566347 PROGRESS: Protein Summary:
1 day, 20:23:35.567398 PROGRESS: Channel   0:	 0.050 FDR:   127; 0.010 FDR:   127; 0.001 FDR:   127
1 day, 20:23:35.567490 PROGRESS: =========================================================================
1 day, 20:23:35.567599 INFO: Target number of precursors not reached yet.
1 day, 20:23:35.570994 INFO: Starting optimization step 1.
1 day, 20:23:35.571095 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 20:23:35.571164 INFO: Using classic extraction backend
1 day, 20:23:35.571271 PROGRESS: Extracting batch of 795 precursors
1 day, 20:23:35.571346 INFO: === Search parameters used ===
1 day, 20:23:35.571398 INFO: rt_error       : 2099.894844
1 day, 20:23:35.571442 INFO: mobility_error : 0.1
1 day, 20:23:35.571484 INFO: num_candidates : 1
1 day, 20:23:35.571524 INFO: ms1_error      : 30
1 day, 20:23:35.571564 INFO: ms2_error      : 30
1 day, 20:23:35.571603 INFO: fwhm_rt        : 5
1 day, 20:23:35.571642 INFO: quant_window   : 3
1 day, 20:23:35.571681 INFO: ==============================================
1 day, 20:23:35.572283 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:23:35.572325 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:23:35.572352 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:23:35.572373 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:23:35.573596 INFO: Starting candidate selection
1 day, 20:23:41.871855 INFO: Starting candidate scoring
1 day, 20:23:41.992441 INFO: Finished candidate processing
1 day, 20:23:41.992540 INFO: Collecting candidate features
1 day, 20:23:42.007706 INFO: Collecting fragment features
1 day, 20:23:42.011940 INFO: Finished candidate scoring
1 day, 20:23:42.015441 INFO: performing precursor FDR with 47 features
1 day, 20:23:42.015525 INFO: Decoy channel: -1
1 day, 20:23:42.015574 INFO: Competetive: True
1 day, 20:23:42.019993 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:23:42.022760 INFO: Using random state 337097 for train-test-split
1 day, 20:23:42.035639 INFO: Test AUC: 0.417
1 day, 20:23:42.035735 INFO: Train AUC: 0.494
1 day, 20:23:42.035786 INFO: AUC difference: 15.58%
1 day, 20:23:42.035822 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:23:42.251603 INFO: Resetting torch num_threads to 80
1 day, 20:23:42.252793 PROGRESS: === Extracted 1193 precursors and 13582 fragments ===
1 day, 20:23:42.253193 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:23:42.253757 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:23:42.253846 PROGRESS: Total precursors accumulated: 600
1 day, 20:23:42.253904 PROGRESS: Target precursors: 448 (74.67%)
1 day, 20:23:42.253962 PROGRESS: Decoy precursors: 152 (25.33%)
1 day, 20:23:42.254009 PROGRESS: 
1 day, 20:23:42.254051 PROGRESS: Precursor Summary:
1 day, 20:23:42.255033 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   410; 0.001 FDR:   410
1 day, 20:23:42.255123 PROGRESS: 
1 day, 20:23:42.255177 PROGRESS: Protein Summary:
1 day, 20:23:42.256324 PROGRESS: Channel   0:	 0.050 FDR:   381; 0.010 FDR:   381; 0.001 FDR:   381
1 day, 20:23:42.256415 PROGRESS: =========================================================================
1 day, 20:23:42.256573 INFO: Target number of precursors reached.
1 day, 20:23:42.260428 INFO: fragments_df: keeping 2671 of 13582 [sum(precursor_idx_mask)=4623 sum(mass_error_mask)=13582 stop_rank=2671
1 day, 20:23:42.265618 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:23:42.396871 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:23:42.533638 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:23:42.667455 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:23:43.023159 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 20:23:43.023582 INFO: Using score_cutoff 53.979062630081174 (fac=0.99, q=1)
1 day, 20:23:43.023916 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.647254467010498
1 day, 20:23:43.023999 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010883975774049759
1 day, 20:23:43.024053 INFO: Updating optimization_manager: score_cutoff        : 0 -> 53.979062630081174
1 day, 20:23:43.024117 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:23:43.025185 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:23:43.026519 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:23:43.027299 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:23:43.029608 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
1 day, 20:23:43.029705 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 20:23:43.029782 INFO: Starting optimization step 2.
1 day, 20:23:43.029840 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:23:43.029893 INFO: Using classic extraction backend
1 day, 20:23:43.029999 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:23:43.030062 INFO: === Search parameters used ===
1 day, 20:23:43.030111 INFO: rt_error       : 2099.894844
1 day, 20:23:43.030154 INFO: mobility_error : 0.1
1 day, 20:23:43.030195 INFO: num_candidates : 3
1 day, 20:23:43.030235 INFO: ms1_error      : 30
1 day, 20:23:43.030273 INFO: ms2_error      : 30
1 day, 20:23:43.030314 INFO: fwhm_rt        : 3.647254467010498
1 day, 20:23:43.030353 INFO: quant_window   : 3
1 day, 20:23:43.030393 INFO: ==============================================
1 day, 20:23:43.031236 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:23:43.031282 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:23:43.031316 INFO: FWHM in RT is 3.65 seconds, sigma is 0.80
1 day, 20:23:43.031340 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.05
1 day, 20:23:43.032003 INFO: Starting candidate selection
1 day, 20:23:53.112510 INFO: Starting candidate scoring
1 day, 20:23:53.470160 INFO: Finished candidate processing
1 day, 20:23:53.470272 INFO: Collecting candidate features
1 day, 20:23:53.484327 INFO: Collecting fragment features
1 day, 20:23:53.493231 INFO: Finished candidate scoring
1 day, 20:23:53.496398 INFO: performing precursor FDR with 47 features
1 day, 20:23:53.496504 INFO: Decoy channel: -1
1 day, 20:23:53.496570 INFO: Competetive: True
1 day, 20:23:53.503949 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:23:53.508068 INFO: Using random state 726051 for train-test-split
1 day, 20:23:53.528332 INFO: Test AUC: 0.511
1 day, 20:23:53.528422 INFO: Train AUC: 0.495
1 day, 20:23:53.528474 INFO: AUC difference: 3.14%
1 day, 20:23:53.751159 INFO: Resetting torch num_threads to 80
1 day, 20:23:53.751724 PROGRESS: === Extracted 3398 precursors and 38722 fragments ===
1 day, 20:23:53.752193 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:23:53.752763 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:23:53.752853 PROGRESS: Total precursors accumulated: 600
1 day, 20:23:53.752913 PROGRESS: Target precursors: 536 (89.33%)
1 day, 20:23:53.752978 PROGRESS: Decoy precursors: 64 (10.67%)
1 day, 20:23:53.753026 PROGRESS: 
1 day, 20:23:53.753071 PROGRESS: Precursor Summary:
1 day, 20:23:53.754084 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   516; 0.001 FDR:   516
1 day, 20:23:53.754173 PROGRESS: 
1 day, 20:23:53.754228 PROGRESS: Protein Summary:
1 day, 20:23:53.755435 PROGRESS: Channel   0:	 0.050 FDR:   473; 0.010 FDR:   473; 0.001 FDR:   473
1 day, 20:23:53.755524 PROGRESS: =========================================================================
1 day, 20:23:53.755797 INFO: Target number of precursors reached.
1 day, 20:23:53.762646 INFO: fragments_df: keeping 5000 of 38722 [sum(precursor_idx_mask)=16737 sum(mass_error_mask)=38722 stop_rank=5000
1 day, 20:23:53.767937 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:23:53.912473 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:23:54.057997 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:23:54.200084 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:23:54.861817 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:23:54.862387 INFO: Using score_cutoff 46.64963846969605 (fac=0.99, q=1)
1 day, 20:23:54.862811 INFO: Updating optimization_manager: fwhm_rt             : 3.647254467010498 -> 3.522406578063965
1 day, 20:23:54.862902 INFO: Updating optimization_manager: fwhm_mobility       : 0.010883975774049759 -> 0.010365212336182594
1 day, 20:23:54.862968 INFO: Updating optimization_manager: score_cutoff        : 53.979062630081174 -> 46.64963846969605
1 day, 20:23:54.863038 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:23:54.864333 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:23:54.865695 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:23:54.866464 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:23:54.868669 INFO: === checking if optimization conditions were reached ===
1 day, 20:23:54.870867 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.494642
1 day, 20:23:54.870974 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 20:23:54.871039 PROGRESS: ❌ ms2_error      : 17.4946 > 17.4946 or insufficient steps taken.
1 day, 20:23:54.872021 INFO: Updating optimization_manager: ms1_error           : 30 -> 11.844363326587226
1 day, 20:23:54.872124 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 20:23:54.872199 PROGRESS: ❌ ms1_error      : 11.8444 > 7.5755 or insufficient steps taken.
1 day, 20:23:54.872255 INFO: ==============================================
1 day, 20:23:54.872335 INFO: Starting optimization step 3.
1 day, 20:23:54.872397 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:23:54.872469 INFO: Using classic extraction backend
1 day, 20:23:54.872801 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:23:54.872880 INFO: === Search parameters used ===
1 day, 20:23:54.872950 INFO: rt_error       : 2099.894844
1 day, 20:23:54.872998 INFO: mobility_error : 0.1
1 day, 20:23:54.873041 INFO: num_candidates : 3
1 day, 20:23:54.873101 INFO: ms1_error      : 11.844363326587226
1 day, 20:23:54.873144 INFO: ms2_error      : 17.494642
1 day, 20:23:54.873185 INFO: fwhm_rt        : 3.522406578063965
1 day, 20:23:54.873225 INFO: quant_window   : 3
1 day, 20:23:54.873265 INFO: ==============================================
1 day, 20:23:54.875242 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:23:54.875292 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:23:54.875361 INFO: FWHM in RT is 3.52 seconds, sigma is 0.77
1 day, 20:23:54.875389 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.81
1 day, 20:23:54.876205 INFO: Starting candidate selection
1 day, 20:24:04.148279 INFO: Starting candidate scoring
1 day, 20:24:04.468122 INFO: Finished candidate processing
1 day, 20:24:04.468218 INFO: Collecting candidate features
1 day, 20:24:04.484875 INFO: Collecting fragment features
1 day, 20:24:04.491856 INFO: Finished candidate scoring
1 day, 20:24:04.493839 INFO: performing precursor FDR with 47 features
1 day, 20:24:04.493887 INFO: Decoy channel: -1
1 day, 20:24:04.493912 INFO: Competetive: True
1 day, 20:24:04.497307 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:24:04.499819 INFO: Using random state 95272 for train-test-split
1 day, 20:24:04.512207 INFO: Test AUC: 0.543
1 day, 20:24:04.512277 INFO: Train AUC: 0.510
1 day, 20:24:04.512308 INFO: AUC difference: 6.43%
1 day, 20:24:04.512330 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:24:04.737062 INFO: Resetting torch num_threads to 80
1 day, 20:24:04.737773 PROGRESS: === Extracted 3402 precursors and 37927 fragments ===
1 day, 20:24:04.738283 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:24:04.738941 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:24:04.739032 PROGRESS: Total precursors accumulated: 600
1 day, 20:24:04.739092 PROGRESS: Target precursors: 482 (80.33%)
1 day, 20:24:04.739142 PROGRESS: Decoy precursors: 118 (19.67%)
1 day, 20:24:04.739188 PROGRESS: 
1 day, 20:24:04.739230 PROGRESS: Precursor Summary:
1 day, 20:24:04.740254 PROGRESS: Channel   0:	 0.050 FDR:   421; 0.010 FDR:   421; 0.001 FDR:   421
1 day, 20:24:04.740343 PROGRESS: 
1 day, 20:24:04.740405 PROGRESS: Protein Summary:
1 day, 20:24:04.741605 PROGRESS: Channel   0:	 0.050 FDR:   392; 0.010 FDR:   392; 0.001 FDR:   392
1 day, 20:24:04.741698 PROGRESS: =========================================================================
1 day, 20:24:04.741859 INFO: Target number of precursors reached.
1 day, 20:24:04.748835 INFO: fragments_df: keeping 5000 of 37927 [sum(precursor_idx_mask)=13381 sum(mass_error_mask)=37927 stop_rank=5000
1 day, 20:24:04.755203 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:04.865094 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:04.983141 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:05.094662 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:05.761213 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:24:05.761909 INFO: Using score_cutoff 40.65477312469483 (fac=0.99, q=1)
1 day, 20:24:05.762270 INFO: Updating optimization_manager: fwhm_rt             : 3.522406578063965 -> 3.2743656635284424
1 day, 20:24:05.762361 INFO: Updating optimization_manager: fwhm_mobility       : 0.010365212336182594 -> 0.009284067898988724
1 day, 20:24:05.762431 INFO: Updating optimization_manager: score_cutoff        : 46.64963846969605 -> 40.65477312469483
1 day, 20:24:05.762501 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:05.763811 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:05.765516 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:05.766343 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:05.770196 INFO: === checking if optimization conditions were reached ===
1 day, 20:24:05.772384 INFO: Updating optimization_manager: ms2_error           : 17.494642 -> 17.494642
1 day, 20:24:05.772498 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
1 day, 20:24:05.772580 PROGRESS: ✅ ms2_error      : 17.4946 <= 17.4946
1 day, 20:24:05.773618 INFO: Updating optimization_manager: ms1_error           : 11.844363326587226 -> 7.5754825
1 day, 20:24:05.773727 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
1 day, 20:24:05.773804 PROGRESS: ✅ ms1_error      : 7.5755 <= 7.5755
1 day, 20:24:05.773871 INFO: ==============================================
1 day, 20:24:05.773952 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 20:24:05.779396 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:05.780333 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:05.781721 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:05.782537 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:05.784771 INFO: Starting optimization step 0.
1 day, 20:24:05.784877 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:24:05.784976 INFO: Using classic extraction backend
1 day, 20:24:05.785132 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:24:05.785779 INFO: === Search parameters used ===
1 day, 20:24:05.786007 INFO: rt_error       : 2099.894844
1 day, 20:24:05.786135 INFO: mobility_error : 0.1
1 day, 20:24:05.786246 INFO: num_candidates : 3
1 day, 20:24:05.786352 INFO: ms1_error      : 7.5754825
1 day, 20:24:05.786458 INFO: ms2_error      : 17.494642
1 day, 20:24:05.786557 INFO: fwhm_rt        : 3.2743656635284424
1 day, 20:24:05.786656 INFO: quant_window   : 3
1 day, 20:24:05.786772 INFO: ==============================================
1 day, 20:24:05.789788 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:24:05.789846 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:24:05.789890 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 20:24:05.789915 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.31
1 day, 20:24:05.790711 INFO: Starting candidate selection
1 day, 20:24:14.918906 INFO: Starting candidate scoring
1 day, 20:24:15.137033 INFO: Finished candidate processing
1 day, 20:24:15.138090 INFO: Collecting candidate features
1 day, 20:24:15.161319 INFO: Collecting fragment features
1 day, 20:24:15.170760 INFO: Finished candidate scoring
1 day, 20:24:15.173748 INFO: performing precursor FDR with 47 features
1 day, 20:24:15.173825 INFO: Decoy channel: -1
1 day, 20:24:15.173865 INFO: Competetive: True
1 day, 20:24:15.178535 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:24:15.181765 INFO: Using random state 821484 for train-test-split
1 day, 20:24:15.198849 INFO: Test AUC: 0.553
1 day, 20:24:15.198946 INFO: Train AUC: 0.511
1 day, 20:24:15.198996 INFO: AUC difference: 8.38%
1 day, 20:24:15.199034 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:24:15.425002 INFO: Resetting torch num_threads to 80
1 day, 20:24:15.425599 PROGRESS: === Extracted 3381 precursors and 37669 fragments ===
1 day, 20:24:15.426008 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:24:15.426593 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:24:15.426683 PROGRESS: Total precursors accumulated: 600
1 day, 20:24:15.426740 PROGRESS: Target precursors: 450 (75.00%)
1 day, 20:24:15.426791 PROGRESS: Decoy precursors: 150 (25.00%)
1 day, 20:24:15.426836 PROGRESS: 
1 day, 20:24:15.426880 PROGRESS: Precursor Summary:
1 day, 20:24:15.427848 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   348
1 day, 20:24:15.427942 PROGRESS: 
1 day, 20:24:15.427999 PROGRESS: Protein Summary:
1 day, 20:24:15.429168 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:   331; 0.001 FDR:   331
1 day, 20:24:15.429263 PROGRESS: =========================================================================
1 day, 20:24:15.429414 INFO: Target number of precursors reached.
1 day, 20:24:15.435035 INFO: fragments_df: keeping 4273 of 37669 [sum(precursor_idx_mask)=10886 sum(mass_error_mask)=37669 stop_rank=4273
1 day, 20:24:15.439381 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:15.551633 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:15.658509 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:15.784245 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:16.296491 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:24:16.296910 INFO: Using score_cutoff 39.367155016708374 (fac=0.99, q=1)
1 day, 20:24:16.297222 INFO: Updating optimization_manager: fwhm_rt             : 3.2743656635284424 -> 3.340178966522217
1 day, 20:24:16.297304 INFO: Updating optimization_manager: fwhm_mobility       : 0.009284067898988724 -> 0.009407581761479378
1 day, 20:24:16.297358 INFO: Updating optimization_manager: score_cutoff        : 40.65477312469483 -> 39.367155016708374
1 day, 20:24:16.297411 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:16.298486 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:16.299818 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:16.300581 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:16.302732 INFO: === checking if optimization conditions were reached ===
1 day, 20:24:16.302846 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:24:16.304337 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 1311.8300204337
1 day, 20:24:16.304436 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1311.8300.
1 day, 20:24:16.304500 INFO: ==============================================
1 day, 20:24:16.304564 INFO: Starting optimization step 1.
1 day, 20:24:16.304622 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:24:16.304674 INFO: Using classic extraction backend
1 day, 20:24:16.304781 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:24:16.304854 INFO: === Search parameters used ===
1 day, 20:24:16.304906 INFO: rt_error       : 1311.8300204337
1 day, 20:24:16.304961 INFO: mobility_error : 0.1
1 day, 20:24:16.305013 INFO: num_candidates : 3
1 day, 20:24:16.305054 INFO: ms1_error      : 7.5754825
1 day, 20:24:16.305094 INFO: ms2_error      : 17.494642
1 day, 20:24:16.305132 INFO: fwhm_rt        : 3.340178966522217
1 day, 20:24:16.305171 INFO: quant_window   : 3
1 day, 20:24:16.305210 INFO: ==============================================
1 day, 20:24:16.306136 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:24:16.306180 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:24:16.306215 INFO: FWHM in RT is 3.34 seconds, sigma is 0.73
1 day, 20:24:16.306238 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.36
1 day, 20:24:16.306908 INFO: Starting candidate selection
1 day, 20:24:22.474014 INFO: Starting candidate scoring
1 day, 20:24:22.701725 INFO: Finished candidate processing
1 day, 20:24:22.702356 INFO: Collecting candidate features
1 day, 20:24:22.717223 INFO: Collecting fragment features
1 day, 20:24:22.721914 INFO: Finished candidate scoring
1 day, 20:24:22.723858 INFO: performing precursor FDR with 47 features
1 day, 20:24:22.723904 INFO: Decoy channel: -1
1 day, 20:24:22.723928 INFO: Competetive: True
1 day, 20:24:22.727335 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:24:22.729550 INFO: Using random state 821484 for train-test-split
1 day, 20:24:22.740547 INFO: Test AUC: 0.522
1 day, 20:24:22.740608 INFO: Train AUC: 0.511
1 day, 20:24:22.740637 INFO: AUC difference: 2.01%
1 day, 20:24:22.962373 INFO: Resetting torch num_threads to 80
1 day, 20:24:22.962919 PROGRESS: === Extracted 3419 precursors and 38077 fragments ===
1 day, 20:24:22.963326 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:24:22.963913 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:24:22.964004 PROGRESS: Total precursors accumulated: 600
1 day, 20:24:22.964063 PROGRESS: Target precursors: 444 (74.00%)
1 day, 20:24:22.964115 PROGRESS: Decoy precursors: 156 (26.00%)
1 day, 20:24:22.964161 PROGRESS: 
1 day, 20:24:22.964206 PROGRESS: Precursor Summary:
1 day, 20:24:22.965181 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:   345; 0.001 FDR:   345
1 day, 20:24:22.965276 PROGRESS: 
1 day, 20:24:22.965333 PROGRESS: Protein Summary:
1 day, 20:24:22.966462 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   328; 0.001 FDR:   328
1 day, 20:24:22.966555 PROGRESS: =========================================================================
1 day, 20:24:22.966754 INFO: Target number of precursors reached.
1 day, 20:24:22.972459 INFO: fragments_df: keeping 4227 of 38077 [sum(precursor_idx_mask)=10874 sum(mass_error_mask)=38077 stop_rank=4227
1 day, 20:24:22.979302 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:23.083746 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:23.184471 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:23.289965 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:23.806008 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:24:23.806435 INFO: Using score_cutoff 38.99356291351318 (fac=0.99, q=1)
1 day, 20:24:23.806737 INFO: Updating optimization_manager: fwhm_rt             : 3.340178966522217 -> 3.378520965576172
1 day, 20:24:23.806817 INFO: Updating optimization_manager: fwhm_mobility       : 0.009407581761479378 -> 0.009389041922986507
1 day, 20:24:23.806870 INFO: Updating optimization_manager: score_cutoff        : 39.367155016708374 -> 38.99356291351318
1 day, 20:24:23.806923 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:23.807974 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:23.809329 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:23.810116 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:23.812917 INFO: === checking if optimization conditions were reached ===
1 day, 20:24:23.813035 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:24:23.814633 INFO: Updating optimization_manager: rt_error            : 1311.8300204337 -> 1041.4350676592924
1 day, 20:24:23.814733 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 1041.4351.
1 day, 20:24:23.814807 INFO: ==============================================
1 day, 20:24:23.814873 INFO: Starting optimization step 2.
1 day, 20:24:23.814929 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:24:23.814983 INFO: Using classic extraction backend
1 day, 20:24:23.815088 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:24:23.815152 INFO: === Search parameters used ===
1 day, 20:24:23.815198 INFO: rt_error       : 1041.4350676592924
1 day, 20:24:23.815241 INFO: mobility_error : 0.1
1 day, 20:24:23.815284 INFO: num_candidates : 3
1 day, 20:24:23.815323 INFO: ms1_error      : 7.5754825
1 day, 20:24:23.815364 INFO: ms2_error      : 17.494642
1 day, 20:24:23.815404 INFO: fwhm_rt        : 3.378520965576172
1 day, 20:24:23.815443 INFO: quant_window   : 3
1 day, 20:24:23.815482 INFO: ==============================================
1 day, 20:24:23.816317 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:24:23.816361 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:24:23.816396 INFO: FWHM in RT is 3.38 seconds, sigma is 0.74
1 day, 20:24:23.816417 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.36
1 day, 20:24:23.817776 INFO: Starting candidate selection
1 day, 20:24:29.567299 INFO: Starting candidate scoring
1 day, 20:24:29.777565 INFO: Finished candidate processing
1 day, 20:24:29.777663 INFO: Collecting candidate features
1 day, 20:24:29.790920 INFO: Collecting fragment features
1 day, 20:24:29.795432 INFO: Finished candidate scoring
1 day, 20:24:29.797304 INFO: performing precursor FDR with 47 features
1 day, 20:24:29.797349 INFO: Decoy channel: -1
1 day, 20:24:29.797374 INFO: Competetive: True
1 day, 20:24:29.800414 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:24:29.802457 INFO: Using random state 821484 for train-test-split
1 day, 20:24:29.812955 INFO: Test AUC: 0.514
1 day, 20:24:29.813017 INFO: Train AUC: 0.508
1 day, 20:24:29.813047 INFO: AUC difference: 1.22%
1 day, 20:24:30.031745 INFO: Resetting torch num_threads to 80
1 day, 20:24:30.032318 PROGRESS: === Extracted 3402 precursors and 37914 fragments ===
1 day, 20:24:30.032744 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:24:30.033328 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:24:30.033434 PROGRESS: Total precursors accumulated: 600
1 day, 20:24:30.033494 PROGRESS: Target precursors: 440 (73.33%)
1 day, 20:24:30.033542 PROGRESS: Decoy precursors: 160 (26.67%)
1 day, 20:24:30.033590 PROGRESS: 
1 day, 20:24:30.033640 PROGRESS: Precursor Summary:
1 day, 20:24:30.034600 PROGRESS: Channel   0:	 0.050 FDR:   344; 0.010 FDR:   344; 0.001 FDR:   344
1 day, 20:24:30.034690 PROGRESS: 
1 day, 20:24:30.034745 PROGRESS: Protein Summary:
1 day, 20:24:30.035871 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   324
1 day, 20:24:30.035964 PROGRESS: =========================================================================
1 day, 20:24:30.036383 INFO: Target number of precursors reached.
1 day, 20:24:30.042036 INFO: fragments_df: keeping 4230 of 37914 [sum(precursor_idx_mask)=10787 sum(mass_error_mask)=37914 stop_rank=4230
1 day, 20:24:30.047252 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:30.147540 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:30.252903 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:30.360116 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:30.871847 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:24:30.872287 INFO: Using score_cutoff 39.81981958580017 (fac=0.99, q=1)
1 day, 20:24:30.872597 INFO: Updating optimization_manager: fwhm_rt             : 3.378520965576172 -> 3.382279872894287
1 day, 20:24:30.872677 INFO: Updating optimization_manager: fwhm_mobility       : 0.009389041922986507 -> 0.009381113573908806
1 day, 20:24:30.872729 INFO: Updating optimization_manager: score_cutoff        : 38.99356291351318 -> 39.81981958580017
1 day, 20:24:30.872792 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:30.873878 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:30.875239 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:30.876007 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:30.878583 INFO: === checking if optimization conditions were reached ===
1 day, 20:24:30.878697 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:24:30.880418 INFO: Updating optimization_manager: rt_error            : 1041.4350676592924 -> 918.74845394622
1 day, 20:24:30.880517 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 918.7485.
1 day, 20:24:30.880585 INFO: ==============================================
1 day, 20:24:30.880652 INFO: Starting optimization step 3.
1 day, 20:24:30.880712 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:24:30.880769 INFO: Using classic extraction backend
1 day, 20:24:30.880926 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:24:30.881007 INFO: === Search parameters used ===
1 day, 20:24:30.881058 INFO: rt_error       : 918.74845394622
1 day, 20:24:30.881099 INFO: mobility_error : 0.1
1 day, 20:24:30.881138 INFO: num_candidates : 3
1 day, 20:24:30.881178 INFO: ms1_error      : 7.5754825
1 day, 20:24:30.881215 INFO: ms2_error      : 17.494642
1 day, 20:24:30.881254 INFO: fwhm_rt        : 3.382279872894287
1 day, 20:24:30.881293 INFO: quant_window   : 3
1 day, 20:24:30.881332 INFO: ==============================================
1 day, 20:24:30.882786 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:24:30.882832 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:24:30.882865 INFO: FWHM in RT is 3.38 seconds, sigma is 0.74
1 day, 20:24:30.882886 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.35
1 day, 20:24:30.883619 INFO: Starting candidate selection
1 day, 20:24:35.883586 INFO: Starting candidate scoring
1 day, 20:24:36.097262 INFO: Finished candidate processing
1 day, 20:24:36.097410 INFO: Collecting candidate features
1 day, 20:24:36.110996 INFO: Collecting fragment features
1 day, 20:24:36.116121 INFO: Finished candidate scoring
1 day, 20:24:36.118032 INFO: performing precursor FDR with 47 features
1 day, 20:24:36.118077 INFO: Decoy channel: -1
1 day, 20:24:36.118103 INFO: Competetive: True
1 day, 20:24:36.122436 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:24:36.125372 INFO: Using random state 821484 for train-test-split
1 day, 20:24:36.136995 INFO: Test AUC: 0.528
1 day, 20:24:36.137054 INFO: Train AUC: 0.504
1 day, 20:24:36.137084 INFO: AUC difference: 4.84%
1 day, 20:24:36.359157 INFO: Resetting torch num_threads to 80
1 day, 20:24:36.359735 PROGRESS: === Extracted 3397 precursors and 37835 fragments ===
1 day, 20:24:36.360213 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:24:36.360816 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:24:36.360905 PROGRESS: Total precursors accumulated: 600
1 day, 20:24:36.360973 PROGRESS: Target precursors: 438 (73.00%)
1 day, 20:24:36.361026 PROGRESS: Decoy precursors: 162 (27.00%)
1 day, 20:24:36.361072 PROGRESS: 
1 day, 20:24:36.361119 PROGRESS: Precursor Summary:
1 day, 20:24:36.362090 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   343; 0.001 FDR:   343
1 day, 20:24:36.362180 PROGRESS: 
1 day, 20:24:36.362243 PROGRESS: Protein Summary:
1 day, 20:24:36.363391 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   321; 0.001 FDR:   321
1 day, 20:24:36.363483 PROGRESS: =========================================================================
1 day, 20:24:36.363676 INFO: Target number of precursors reached.
1 day, 20:24:36.369279 INFO: fragments_df: keeping 4122 of 37835 [sum(precursor_idx_mask)=10678 sum(mass_error_mask)=37835 stop_rank=4122
1 day, 20:24:36.374338 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:36.498270 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:36.621130 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:36.747024 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:37.311034 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:24:37.311466 INFO: Using score_cutoff 40.86195913009644 (fac=0.99, q=1)
1 day, 20:24:37.311810 INFO: Updating optimization_manager: fwhm_rt             : 3.382279872894287 -> 3.4037065505981445
1 day, 20:24:37.311891 INFO: Updating optimization_manager: fwhm_mobility       : 0.009381113573908806 -> 0.00940483994781971
1 day, 20:24:37.311944 INFO: Updating optimization_manager: score_cutoff        : 39.81981958580017 -> 40.86195913009644
1 day, 20:24:37.312000 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:37.313061 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:37.314401 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:37.315171 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:37.317314 INFO: === checking if optimization conditions were reached ===
1 day, 20:24:37.317449 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 20:24:37.319385 INFO: Updating optimization_manager: rt_error            : 918.74845394622 -> 914.0938616824043
1 day, 20:24:37.319489 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 914.0939.
1 day, 20:24:37.319553 INFO: ==============================================
1 day, 20:24:37.319623 INFO: Starting optimization step 4.
1 day, 20:24:37.319680 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:24:37.319738 INFO: Using classic extraction backend
1 day, 20:24:37.319871 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:24:37.319938 INFO: === Search parameters used ===
1 day, 20:24:37.319986 INFO: rt_error       : 914.0938616824043
1 day, 20:24:37.320028 INFO: mobility_error : 0.1
1 day, 20:24:37.320076 INFO: num_candidates : 3
1 day, 20:24:37.320118 INFO: ms1_error      : 7.5754825
1 day, 20:24:37.320156 INFO: ms2_error      : 17.494642
1 day, 20:24:37.320193 INFO: fwhm_rt        : 3.4037065505981445
1 day, 20:24:37.320232 INFO: quant_window   : 3
1 day, 20:24:37.320270 INFO: ==============================================
1 day, 20:24:37.321309 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:24:37.321355 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:24:37.321399 INFO: FWHM in RT is 3.40 seconds, sigma is 0.75
1 day, 20:24:37.321423 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.36
1 day, 20:24:37.322136 INFO: Starting candidate selection
1 day, 20:24:42.133702 INFO: Starting candidate scoring
1 day, 20:24:42.359405 INFO: Finished candidate processing
1 day, 20:24:42.359546 INFO: Collecting candidate features
1 day, 20:24:42.373898 INFO: Collecting fragment features
1 day, 20:24:42.378668 INFO: Finished candidate scoring
1 day, 20:24:42.380548 INFO: performing precursor FDR with 47 features
1 day, 20:24:42.380592 INFO: Decoy channel: -1
1 day, 20:24:42.380616 INFO: Competetive: True
1 day, 20:24:42.383506 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:24:42.385557 INFO: Using random state 821484 for train-test-split
1 day, 20:24:42.396775 INFO: Test AUC: 0.496
1 day, 20:24:42.396846 INFO: Train AUC: 0.508
1 day, 20:24:42.396877 INFO: AUC difference: 2.42%
1 day, 20:24:42.613925 INFO: Resetting torch num_threads to 80
1 day, 20:24:42.614468 PROGRESS: === Extracted 3394 precursors and 37798 fragments ===
1 day, 20:24:42.614879 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:24:42.615457 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:24:42.615549 PROGRESS: Total precursors accumulated: 600
1 day, 20:24:42.615606 PROGRESS: Target precursors: 435 (72.50%)
1 day, 20:24:42.615656 PROGRESS: Decoy precursors: 165 (27.50%)
1 day, 20:24:42.615699 PROGRESS: 
1 day, 20:24:42.615744 PROGRESS: Precursor Summary:
1 day, 20:24:42.616688 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   337; 0.001 FDR:   337
1 day, 20:24:42.616776 PROGRESS: 
1 day, 20:24:42.616833 PROGRESS: Protein Summary:
1 day, 20:24:42.617962 PROGRESS: Channel   0:	 0.050 FDR:   317; 0.010 FDR:   317; 0.001 FDR:   317
1 day, 20:24:42.618058 PROGRESS: =========================================================================
1 day, 20:24:42.618199 INFO: Target number of precursors reached.
1 day, 20:24:42.623715 INFO: fragments_df: keeping 4066 of 37798 [sum(precursor_idx_mask)=10528 sum(mass_error_mask)=37798 stop_rank=4066
1 day, 20:24:42.628042 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:42.731131 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:42.834678 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:42.941100 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:43.422844 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:24:43.423266 INFO: Using score_cutoff 40.51846141204834 (fac=0.99, q=1)
1 day, 20:24:43.423568 INFO: Updating optimization_manager: fwhm_rt             : 3.4037065505981445 -> 3.4360437393188477
1 day, 20:24:43.423649 INFO: Updating optimization_manager: fwhm_mobility       : 0.00940483994781971 -> 0.00945995096117258
1 day, 20:24:43.423702 INFO: Updating optimization_manager: score_cutoff        : 40.86195913009644 -> 40.51846141204834
1 day, 20:24:43.423755 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:43.424804 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:43.426162 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:43.426937 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:43.429182 INFO: === checking if optimization conditions were reached ===
1 day, 20:24:43.429284 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 20:24:43.430235 INFO: Updating optimization_manager: rt_error            : 914.0938616824043 -> 914.0938616824043
1 day, 20:24:43.430356 INFO: Updating optimization_manager: classifier_version  : 3 -> 8
1 day, 20:24:43.430445 INFO: Updating optimization_manager: score_cutoff        : 40.51846141204834 -> 40.51846141204834
1 day, 20:24:43.430539 INFO: Updating optimization_manager: fwhm_rt             : 3.4360437393188477 -> 3.4360437393188477
1 day, 20:24:43.430621 INFO: Updating optimization_manager: fwhm_mobility       : 0.00945995096117258 -> 0.00945995096117258
1 day, 20:24:43.430701 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 914.0939 found after 5 searches.
1 day, 20:24:43.430760 INFO: ==============================================
1 day, 20:24:43.430822 PROGRESS: Optimization finished for rt_error.
1 day, 20:24:43.434792 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:43.435626 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:43.436970 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:43.437749 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:43.465101 INFO: Starting optimization step 0.
1 day, 20:24:43.465245 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:24:43.465322 INFO: Using classic extraction backend
1 day, 20:24:43.465435 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:24:43.465503 INFO: === Search parameters used ===
1 day, 20:24:43.465550 INFO: rt_error       : 914.0938616824043
1 day, 20:24:43.465592 INFO: mobility_error : 0.1
1 day, 20:24:43.465633 INFO: num_candidates : 3
1 day, 20:24:43.465675 INFO: ms1_error      : 7.5754825
1 day, 20:24:43.465714 INFO: ms2_error      : 17.494642
1 day, 20:24:43.465755 INFO: fwhm_rt        : 3.4360437393188477
1 day, 20:24:43.465800 INFO: quant_window   : 3
1 day, 20:24:43.465842 INFO: ==============================================
1 day, 20:24:43.466656 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:24:43.466701 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:24:43.466737 INFO: FWHM in RT is 3.44 seconds, sigma is 0.76
1 day, 20:24:43.466759 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.39
1 day, 20:24:43.467363 INFO: Starting candidate selection
1 day, 20:24:48.425283 INFO: Starting candidate scoring
1 day, 20:24:48.646428 INFO: Finished candidate processing
1 day, 20:24:48.646559 INFO: Collecting candidate features
1 day, 20:24:48.660705 INFO: Collecting fragment features
1 day, 20:24:48.664425 INFO: Finished candidate scoring
1 day, 20:24:48.666311 INFO: performing precursor FDR with 47 features
1 day, 20:24:48.666358 INFO: Decoy channel: -1
1 day, 20:24:48.666382 INFO: Competetive: True
1 day, 20:24:48.669399 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:24:48.671436 INFO: Using random state 481686 for train-test-split
1 day, 20:24:48.682160 INFO: Test AUC: 0.512
1 day, 20:24:48.682217 INFO: Train AUC: 0.498
1 day, 20:24:48.682247 INFO: AUC difference: 2.73%
1 day, 20:24:48.900438 INFO: Resetting torch num_threads to 80
1 day, 20:24:48.900989 PROGRESS: === Extracted 3396 precursors and 37837 fragments ===
1 day, 20:24:48.901397 INFO: === FDR correction performed with classifier version 8 ===
1 day, 20:24:48.901994 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:24:48.902085 PROGRESS: Total precursors accumulated: 600
1 day, 20:24:48.902144 PROGRESS: Target precursors: 434 (72.33%)
1 day, 20:24:48.902198 PROGRESS: Decoy precursors: 166 (27.67%)
1 day, 20:24:48.902242 PROGRESS: 
1 day, 20:24:48.902287 PROGRESS: Precursor Summary:
1 day, 20:24:48.903234 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   339; 0.001 FDR:   339
1 day, 20:24:48.903325 PROGRESS: 
1 day, 20:24:48.903380 PROGRESS: Protein Summary:
1 day, 20:24:48.904501 PROGRESS: Channel   0:	 0.050 FDR:   319; 0.010 FDR:   319; 0.001 FDR:   319
1 day, 20:24:48.904592 PROGRESS: =========================================================================
1 day, 20:24:48.904724 INFO: Target number of precursors reached.
1 day, 20:24:48.910268 INFO: fragments_df: keeping 4086 of 37837 [sum(precursor_idx_mask)=10644 sum(mass_error_mask)=37837 stop_rank=4086
1 day, 20:24:48.914518 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:49.014019 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:49.120519 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:49.225050 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:49.697279 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:24:49.697706 INFO: Using score_cutoff 39.79135206298828 (fac=0.99, q=1)
1 day, 20:24:49.698007 INFO: Updating optimization_manager: fwhm_rt             : 3.4360437393188477 -> 3.4514474868774414
1 day, 20:24:49.698088 INFO: Updating optimization_manager: fwhm_mobility       : 0.00945995096117258 -> 0.00940483994781971
1 day, 20:24:49.698144 INFO: Updating optimization_manager: score_cutoff        : 40.51846141204834 -> 39.79135206298828
1 day, 20:24:49.698198 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:49.699251 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:49.700601 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:49.701388 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:49.703602 INFO: === checking if optimization conditions were reached ===
1 day, 20:24:49.703699 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:24:49.705025 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06371492735372317
1 day, 20:24:49.705124 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0637.
1 day, 20:24:49.705188 INFO: ==============================================
1 day, 20:24:49.705255 INFO: Starting optimization step 1.
1 day, 20:24:49.705311 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:24:49.705366 INFO: Using classic extraction backend
1 day, 20:24:49.705472 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:24:49.705543 INFO: === Search parameters used ===
1 day, 20:24:49.705591 INFO: rt_error       : 914.0938616824043
1 day, 20:24:49.705634 INFO: mobility_error : 0.06371492735372317
1 day, 20:24:49.705674 INFO: num_candidates : 3
1 day, 20:24:49.705715 INFO: ms1_error      : 7.5754825
1 day, 20:24:49.705757 INFO: ms2_error      : 17.494642
1 day, 20:24:49.705798 INFO: fwhm_rt        : 3.4514474868774414
1 day, 20:24:49.705839 INFO: quant_window   : 3
1 day, 20:24:49.705878 INFO: ==============================================
1 day, 20:24:49.706640 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:24:49.706684 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:24:49.706718 INFO: FWHM in RT is 3.45 seconds, sigma is 0.76
1 day, 20:24:49.706741 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.36
1 day, 20:24:49.707395 INFO: Starting candidate selection
1 day, 20:24:53.671074 INFO: Starting candidate scoring
1 day, 20:24:53.884514 INFO: Finished candidate processing
1 day, 20:24:53.884613 INFO: Collecting candidate features
1 day, 20:24:53.897933 INFO: Collecting fragment features
1 day, 20:24:53.902453 INFO: Finished candidate scoring
1 day, 20:24:53.904574 INFO: performing precursor FDR with 47 features
1 day, 20:24:53.904624 INFO: Decoy channel: -1
1 day, 20:24:53.904650 INFO: Competetive: True
1 day, 20:24:53.907551 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:24:53.910139 INFO: Using random state 481686 for train-test-split
1 day, 20:24:53.920563 INFO: Test AUC: 0.541
1 day, 20:24:53.920621 INFO: Train AUC: 0.505
1 day, 20:24:53.920649 INFO: AUC difference: 7.16%
1 day, 20:24:53.920671 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:24:54.138942 INFO: Resetting torch num_threads to 80
1 day, 20:24:54.139514 PROGRESS: === Extracted 3402 precursors and 37701 fragments ===
1 day, 20:24:54.139918 INFO: === FDR correction performed with classifier version 8 ===
1 day, 20:24:54.140486 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:24:54.140577 PROGRESS: Total precursors accumulated: 600
1 day, 20:24:54.140634 PROGRESS: Target precursors: 430 (71.67%)
1 day, 20:24:54.140683 PROGRESS: Decoy precursors: 170 (28.33%)
1 day, 20:24:54.140728 PROGRESS: 
1 day, 20:24:54.140773 PROGRESS: Precursor Summary:
1 day, 20:24:54.142346 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:   331; 0.001 FDR:   331
1 day, 20:24:54.142573 PROGRESS: 
1 day, 20:24:54.142634 PROGRESS: Protein Summary:
1 day, 20:24:54.143816 PROGRESS: Channel   0:	 0.050 FDR:   315; 0.010 FDR:   315; 0.001 FDR:   315
1 day, 20:24:54.143909 PROGRESS: =========================================================================
1 day, 20:24:54.144116 INFO: Target number of precursors reached.
1 day, 20:24:54.150007 INFO: fragments_df: keeping 4009 of 37701 [sum(precursor_idx_mask)=10445 sum(mass_error_mask)=37701 stop_rank=4009
1 day, 20:24:54.154596 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:54.276899 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:54.404418 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:54.528846 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:55.069740 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:24:55.070172 INFO: Using score_cutoff 39.554094520568846 (fac=0.99, q=1)
1 day, 20:24:55.070471 INFO: Updating optimization_manager: fwhm_rt             : 3.4514474868774414 -> 3.4360437393188477
1 day, 20:24:55.070552 INFO: Updating optimization_manager: fwhm_mobility       : 0.00940483994781971 -> 0.00945188757032156
1 day, 20:24:55.070609 INFO: Updating optimization_manager: score_cutoff        : 39.79135206298828 -> 39.554094520568846
1 day, 20:24:55.070664 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:55.071732 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:55.073087 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:55.073874 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:55.076009 INFO: === checking if optimization conditions were reached ===
1 day, 20:24:55.076106 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:24:55.077503 INFO: Updating optimization_manager: mobility_error      : 0.06371492735372317 -> 0.0563962513336527
1 day, 20:24:55.077712 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0564.
1 day, 20:24:55.077780 INFO: ==============================================
1 day, 20:24:55.077845 INFO: Starting optimization step 2.
1 day, 20:24:55.077901 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:24:55.077956 INFO: Using classic extraction backend
1 day, 20:24:55.078063 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:24:55.078129 INFO: === Search parameters used ===
1 day, 20:24:55.078178 INFO: rt_error       : 914.0938616824043
1 day, 20:24:55.078219 INFO: mobility_error : 0.0563962513336527
1 day, 20:24:55.078260 INFO: num_candidates : 3
1 day, 20:24:55.078300 INFO: ms1_error      : 7.5754825
1 day, 20:24:55.078340 INFO: ms2_error      : 17.494642
1 day, 20:24:55.078379 INFO: fwhm_rt        : 3.4360437393188477
1 day, 20:24:55.078418 INFO: quant_window   : 3
1 day, 20:24:55.078456 INFO: ==============================================
1 day, 20:24:55.079221 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:24:55.079265 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:24:55.079300 INFO: FWHM in RT is 3.44 seconds, sigma is 0.76
1 day, 20:24:55.079322 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.38
1 day, 20:24:55.081006 INFO: Starting candidate selection
1 day, 20:24:58.431558 INFO: Starting candidate scoring
1 day, 20:24:58.656917 INFO: Finished candidate processing
1 day, 20:24:58.657122 INFO: Collecting candidate features
1 day, 20:24:58.672457 INFO: Collecting fragment features
1 day, 20:24:58.677564 INFO: Finished candidate scoring
1 day, 20:24:58.679375 INFO: performing precursor FDR with 47 features
1 day, 20:24:58.679418 INFO: Decoy channel: -1
1 day, 20:24:58.679442 INFO: Competetive: True
1 day, 20:24:58.682379 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:24:58.684377 INFO: Using random state 481686 for train-test-split
1 day, 20:24:58.695118 INFO: Test AUC: 0.507
1 day, 20:24:58.695175 INFO: Train AUC: 0.517
1 day, 20:24:58.695204 INFO: AUC difference: 2.04%
1 day, 20:24:58.919596 INFO: Resetting torch num_threads to 80
1 day, 20:24:58.920137 PROGRESS: === Extracted 3390 precursors and 37445 fragments ===
1 day, 20:24:58.920544 INFO: === FDR correction performed with classifier version 8 ===
1 day, 20:24:58.921136 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:24:58.921225 PROGRESS: Total precursors accumulated: 600
1 day, 20:24:58.921290 PROGRESS: Target precursors: 437 (72.83%)
1 day, 20:24:58.921339 PROGRESS: Decoy precursors: 163 (27.17%)
1 day, 20:24:58.921389 PROGRESS: 
1 day, 20:24:58.921433 PROGRESS: Precursor Summary:
1 day, 20:24:58.922381 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   326; 0.001 FDR:   326
1 day, 20:24:58.922472 PROGRESS: 
1 day, 20:24:58.922527 PROGRESS: Protein Summary:
1 day, 20:24:58.923637 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   312; 0.001 FDR:   312
1 day, 20:24:58.923725 PROGRESS: =========================================================================
1 day, 20:24:58.923869 INFO: Target number of precursors reached.
1 day, 20:24:58.929258 INFO: fragments_df: keeping 3896 of 37445 [sum(precursor_idx_mask)=10192 sum(mass_error_mask)=37445 stop_rank=3896
1 day, 20:24:58.934449 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:59.029639 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:59.135874 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:59.240171 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:59.701980 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:24:59.702413 INFO: Using score_cutoff 38.71271178245544 (fac=0.99, q=1)
1 day, 20:24:59.702719 INFO: Updating optimization_manager: fwhm_rt             : 3.4360437393188477 -> 3.372483730316162
1 day, 20:24:59.702797 INFO: Updating optimization_manager: fwhm_mobility       : 0.00945188757032156 -> 0.009421738795936108
1 day, 20:24:59.702849 INFO: Updating optimization_manager: score_cutoff        : 39.554094520568846 -> 38.71271178245544
1 day, 20:24:59.702901 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:59.703968 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:59.705318 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:59.706096 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:59.708349 INFO: === checking if optimization conditions were reached ===
1 day, 20:24:59.708451 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:24:59.709136 INFO: Updating optimization_manager: mobility_error      : 0.0563962513336527 -> 0.1
1 day, 20:24:59.709257 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1 day, 20:24:59.709348 INFO: Updating optimization_manager: score_cutoff        : 38.71271178245544 -> 39.79135206298828
1 day, 20:24:59.709430 INFO: Updating optimization_manager: fwhm_rt             : 3.372483730316162 -> 3.4514474868774414
1 day, 20:24:59.709509 INFO: Updating optimization_manager: fwhm_mobility       : 0.009421738795936108 -> 0.00940483994781971
1 day, 20:24:59.709586 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 20:24:59.709643 INFO: ==============================================
1 day, 20:24:59.709706 PROGRESS: Optimization finished for mobility_error.
1 day, 20:24:59.713717 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:59.714549 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:59.715867 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:59.716637 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:24:59.740915 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:24:59.741080 PROGRESS: ==============================================
1 day, 20:24:59.741168 PROGRESS: ms2_error      : 17.4946
1 day, 20:24:59.741237 PROGRESS: ms1_error      : 7.5755
1 day, 20:24:59.741301 PROGRESS: rt_error       : 914.0939
1 day, 20:24:59.741349 PROGRESS: mobility_error : 0.1000
1 day, 20:24:59.741391 PROGRESS: ==============================================
1 day, 20:24:59.742078 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:24:59.761829 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:24:59.856081 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:24:59.878251 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:25:00.108401 INFO: Using classic extraction backend
1 day, 20:25:00.108858 PROGRESS: Extracting batch of 146455 precursors
1 day, 20:25:00.108967 INFO: === Search parameters used ===
1 day, 20:25:00.109027 INFO: rt_error       : 914.0938616824043
1 day, 20:25:00.109080 INFO: mobility_error : 0.1
1 day, 20:25:00.109126 INFO: num_candidates : 3
1 day, 20:25:00.109170 INFO: ms1_error      : 7.5754825
1 day, 20:25:00.109212 INFO: ms2_error      : 17.494642
1 day, 20:25:00.109255 INFO: fwhm_rt        : 3.4514474868774414
1 day, 20:25:00.109298 INFO: quant_window   : 3
1 day, 20:25:00.109339 INFO: ==============================================
1 day, 20:25:00.145454 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:25:00.145630 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:25:00.145680 INFO: FWHM in RT is 3.45 seconds, sigma is 0.76
1 day, 20:25:00.145704 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.36
1 day, 20:25:00.146472 INFO: Starting candidate selection
1 day, 20:31:42.143199 INFO: Removed 23808 precursors with score below cutoff 39.79135206298828
1 day, 20:31:42.486396 INFO: Starting candidate scoring
1 day, 20:31:59.151693 INFO: Finished candidate processing
1 day, 20:31:59.151869 INFO: Collecting candidate features
1 day, 20:31:59.688977 INFO: Collecting fragment features
1 day, 20:31:59.943441 INFO: Finished candidate scoring
1 day, 20:32:00.229989 INFO: === Performing FDR correction with classifier version 9 ===
1 day, 20:32:00.231122 INFO: performing precursor FDR with 47 features
1 day, 20:32:00.231176 INFO: Decoy channel: -1
1 day, 20:32:00.231214 INFO: Competetive: True
1 day, 20:32:00.326134 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:32:00.489155 INFO: Using random state 998891 for train-test-split
1 day, 20:32:06.979830 INFO: Test AUC: 0.733
1 day, 20:32:06.979960 INFO: Train AUC: 0.734
1 day, 20:32:06.979992 INFO: AUC difference: 0.11%
1 day, 20:32:07.271599 INFO: Resetting torch num_threads to 80
1 day, 20:32:07.285747 INFO: Removing fragments below FDR threshold
1 day, 20:32:07.363196 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:32:07.363429 PROGRESS: Total precursors accumulated: 67,775
1 day, 20:32:07.363495 PROGRESS: Target precursors: 67,104 (99.01%)
1 day, 20:32:07.363549 PROGRESS: Decoy precursors: 671 (0.99%)
1 day, 20:32:07.363596 PROGRESS: 
1 day, 20:32:07.363639 PROGRESS: Precursor Summary:
1 day, 20:32:07.391869 PROGRESS: Channel   0:	 0.050 FDR: 67,104; 0.010 FDR: 67,104; 0.001 FDR: 62,635
1 day, 20:32:07.392107 PROGRESS: 
1 day, 20:32:07.392175 PROGRESS: Protein Summary:
1 day, 20:32:07.428781 PROGRESS: Channel   0:	 0.050 FDR: 7,375; 0.010 FDR: 7,375; 0.001 FDR: 7,300
1 day, 20:32:07.429016 PROGRESS: =========================================================================
1 day, 20:32:07.432928 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/psm.parquet
1 day, 20:32:07.716754 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/frag.parquet
1 day, 20:32:07.972586 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 20:32:08.010597 PROGRESS: 
1 day, 20:32:08.010742 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
1 day, 20:32:08.010814 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/figures
1 day, 20:32:08.010984 INFO: Initializing TimingManager
1 day, 20:32:08.011448 INFO: Initializing RawFileManager
1 day, 20:32:08.011554 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:08.011618 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:08.011662 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:08.212715 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, 20:32:13.638592 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
1 day, 20:32:13.639978 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:13.642812 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:13.643027 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:13.643414 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:13.644786 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:13.658741 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:13.658955 INFO: Indexing quadrupole dimension
1 day, 20:32:14.142479 INFO: Transposing detector events
1 day, 20:32:22.783794 INFO: Finished transposing data
1 day, 20:32:22.810473 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 20:32:22.818977 INFO: RT (min)            : 0.0 - 70.0
1 day, 20:32:22.819031 INFO: RT duration (sec)   : 4199.8
1 day, 20:32:22.819057 INFO: RT duration (min)   : 70.0
1 day, 20:32:22.819079 INFO: Cycle len (scans)   : 9
1 day, 20:32:22.819098 INFO: Cycle len (sec)     : 0.97
1 day, 20:32:22.819116 INFO: Number of cycles    : 4347
1 day, 20:32:22.819136 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 20:32:22.819182 INFO: Creating DIA data object took: 14.8076331615448
1 day, 20:32:22.856571 INFO: Initializing CalibrationManager
1 day, 20:32:22.856858 INFO: Setting up calibration estimators ..
1 day, 20:32:22.856919 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 20:32:22.857027 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, 20:32:22.857121 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 20:32:22.857179 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, 20:32:22.857232 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, 20:32:22.857293 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, 20:32:22.857341 INFO: Done setting up calibration estimators.
1 day, 20:32:22.857461 INFO: Initializing OptimizationManager
1 day, 20:32:22.857551 INFO: initial parameter: ms1_error = 30
1 day, 20:32:22.857597 INFO: initial parameter: ms2_error = 30
1 day, 20:32:22.857641 INFO: initial parameter: rt_error = 2099.8992935
1 day, 20:32:22.857683 INFO: initial parameter: mobility_error = 0.1
1 day, 20:32:22.857723 INFO: initial parameter: num_candidates = 1
1 day, 20:32:22.857763 INFO: initial parameter: fwhm_rt = 5
1 day, 20:32:22.857802 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 20:32:22.857848 INFO: initial parameter: score_cutoff = 0
1 day, 20:32:22.857888 INFO: initial parameter: classifier_version = -1
1 day, 20:32:22.857963 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 20:32:22.858259 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 20:32:22.858296 INFO: Initializing FDRManager
1 day, 20:32:22.858335 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 20:32:22.877721 PROGRESS: Initializing spectral library: 73,677 target precursors potentially observable (0 removed)
1 day, 20:32:22.891384 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 20:32:22.891790 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 2099.8992935
1 day, 20:32:22.891917 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 20:32:22.892094 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 20:32:22.892186 PROGRESS: Starting initial search for precursors.
1 day, 20:32:22.892279 INFO: Starting optimization step 0.
1 day, 20:32:22.892344 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 20:32:22.892426 INFO: Using classic extraction backend
1 day, 20:32:22.892756 PROGRESS: Extracting batch of 399 precursors
1 day, 20:32:22.892838 INFO: === Search parameters used ===
1 day, 20:32:22.892893 INFO: rt_error       : 2099.8992935
1 day, 20:32:22.892949 INFO: mobility_error : 0.1
1 day, 20:32:22.893001 INFO: num_candidates : 1
1 day, 20:32:22.893044 INFO: ms1_error      : 30
1 day, 20:32:22.893096 INFO: ms2_error      : 30
1 day, 20:32:22.893142 INFO: fwhm_rt        : 5
1 day, 20:32:22.893193 INFO: quant_window   : 3
1 day, 20:32:22.893234 INFO: ==============================================
1 day, 20:32:22.894459 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:32:22.894505 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:32:22.894565 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:32:22.894588 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:32:22.902560 INFO: Starting candidate selection
1 day, 20:32:26.800918 INFO: Starting candidate scoring
1 day, 20:32:26.883921 INFO: Finished candidate processing
1 day, 20:32:26.884029 INFO: Collecting candidate features
1 day, 20:32:26.893263 INFO: Collecting fragment features
1 day, 20:32:26.895633 INFO: Finished candidate scoring
1 day, 20:32:26.896340 INFO: performing precursor FDR with 47 features
1 day, 20:32:26.896383 INFO: Decoy channel: -1
1 day, 20:32:26.896408 INFO: Competetive: True
1 day, 20:32:26.897578 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:32:26.900089 INFO: Using random state 838300 for train-test-split
1 day, 20:32:26.908053 INFO: Test AUC: 0.469
1 day, 20:32:26.908111 INFO: Train AUC: 0.451
1 day, 20:32:26.908143 INFO: AUC difference: 3.96%
1 day, 20:32:27.135268 INFO: Resetting torch num_threads to 80
1 day, 20:32:27.135722 PROGRESS: === Extracted 399 precursors and 4576 fragments ===
1 day, 20:32:27.136145 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:32:27.136688 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:32:27.136776 PROGRESS: Total precursors accumulated: 200
1 day, 20:32:27.136836 PROGRESS: Target precursors: 149 (74.50%)
1 day, 20:32:27.136888 PROGRESS: Decoy precursors: 51 (25.50%)
1 day, 20:32:27.136934 PROGRESS: 
1 day, 20:32:27.136988 PROGRESS: Precursor Summary:
1 day, 20:32:27.137834 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
1 day, 20:32:27.137920 PROGRESS: 
1 day, 20:32:27.137982 PROGRESS: Protein Summary:
1 day, 20:32:27.138920 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
1 day, 20:32:27.139005 PROGRESS: =========================================================================
1 day, 20:32:27.139108 INFO: Target number of precursors not reached yet.
1 day, 20:32:27.142402 INFO: Starting optimization step 1.
1 day, 20:32:27.142507 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 20:32:27.142576 INFO: Using classic extraction backend
1 day, 20:32:27.142684 PROGRESS: Extracting batch of 795 precursors
1 day, 20:32:27.142750 INFO: === Search parameters used ===
1 day, 20:32:27.142801 INFO: rt_error       : 2099.8992935
1 day, 20:32:27.142844 INFO: mobility_error : 0.1
1 day, 20:32:27.142885 INFO: num_candidates : 1
1 day, 20:32:27.142926 INFO: ms1_error      : 30
1 day, 20:32:27.142965 INFO: ms2_error      : 30
1 day, 20:32:27.143005 INFO: fwhm_rt        : 5
1 day, 20:32:27.143044 INFO: quant_window   : 3
1 day, 20:32:27.143083 INFO: ==============================================
1 day, 20:32:27.143694 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:32:27.143738 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:32:27.143766 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:32:27.143787 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:32:27.144452 INFO: Starting candidate selection
1 day, 20:32:33.562686 INFO: Starting candidate scoring
1 day, 20:32:33.683997 INFO: Finished candidate processing
1 day, 20:32:33.684199 INFO: Collecting candidate features
1 day, 20:32:33.694057 INFO: Collecting fragment features
1 day, 20:32:33.696860 INFO: Finished candidate scoring
1 day, 20:32:33.698967 INFO: performing precursor FDR with 47 features
1 day, 20:32:33.699017 INFO: Decoy channel: -1
1 day, 20:32:33.699044 INFO: Competetive: True
1 day, 20:32:33.702057 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:32:33.703761 INFO: Using random state 390065 for train-test-split
1 day, 20:32:33.711979 INFO: Test AUC: 0.418
1 day, 20:32:33.712038 INFO: Train AUC: 0.449
1 day, 20:32:33.712068 INFO: AUC difference: 6.89%
1 day, 20:32:33.712090 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:32:33.928244 INFO: Resetting torch num_threads to 80
1 day, 20:32:33.929416 PROGRESS: === Extracted 1193 precursors and 13612 fragments ===
1 day, 20:32:33.929810 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:32:33.930371 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:32:33.930460 PROGRESS: Total precursors accumulated: 600
1 day, 20:32:33.930521 PROGRESS: Target precursors: 444 (74.00%)
1 day, 20:32:33.930579 PROGRESS: Decoy precursors: 156 (26.00%)
1 day, 20:32:33.930629 PROGRESS: 
1 day, 20:32:33.930676 PROGRESS: Precursor Summary:
1 day, 20:32:33.931559 PROGRESS: Channel   0:	 0.050 FDR:    39; 0.010 FDR:    39; 0.001 FDR:    39
1 day, 20:32:33.931647 PROGRESS: 
1 day, 20:32:33.931704 PROGRESS: Protein Summary:
1 day, 20:32:33.932667 PROGRESS: Channel   0:	 0.050 FDR:    39; 0.010 FDR:    39; 0.001 FDR:    39
1 day, 20:32:33.932755 PROGRESS: =========================================================================
1 day, 20:32:33.932889 INFO: Target number of precursors not reached yet.
1 day, 20:32:33.937052 INFO: Starting optimization step 2.
1 day, 20:32:33.937155 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 20:32:33.937226 INFO: Using classic extraction backend
1 day, 20:32:33.937332 PROGRESS: Extracting batch of 1588 precursors
1 day, 20:32:33.937401 INFO: === Search parameters used ===
1 day, 20:32:33.937451 INFO: rt_error       : 2099.8992935
1 day, 20:32:33.937496 INFO: mobility_error : 0.1
1 day, 20:32:33.937540 INFO: num_candidates : 1
1 day, 20:32:33.937580 INFO: ms1_error      : 30
1 day, 20:32:33.937622 INFO: ms2_error      : 30
1 day, 20:32:33.937663 INFO: fwhm_rt        : 5
1 day, 20:32:33.937703 INFO: quant_window   : 3
1 day, 20:32:33.937742 INFO: ==============================================
1 day, 20:32:33.938413 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:32:33.938458 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:32:33.938486 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:32:33.938510 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:32:33.939106 INFO: Starting candidate selection
1 day, 20:32:46.224188 INFO: Starting candidate scoring
1 day, 20:32:46.456727 INFO: Finished candidate processing
1 day, 20:32:46.456879 INFO: Collecting candidate features
1 day, 20:32:46.481807 INFO: Collecting fragment features
1 day, 20:32:46.491076 INFO: Finished candidate scoring
1 day, 20:32:46.497646 INFO: performing precursor FDR with 47 features
1 day, 20:32:46.497762 INFO: Decoy channel: -1
1 day, 20:32:46.497824 INFO: Competetive: True
1 day, 20:32:46.504888 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:32:46.509844 INFO: Using random state 514016 for train-test-split
1 day, 20:32:46.526924 INFO: Test AUC: 0.444
1 day, 20:32:46.527015 INFO: Train AUC: 0.440
1 day, 20:32:46.527065 INFO: AUC difference: 0.84%
1 day, 20:32:46.740736 INFO: Resetting torch num_threads to 80
1 day, 20:32:46.742411 PROGRESS: === Extracted 2780 precursors and 31571 fragments ===
1 day, 20:32:46.742816 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:32:46.743690 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:32:46.743785 PROGRESS: Total precursors accumulated: 1,400
1 day, 20:32:46.743843 PROGRESS: Target precursors: 1,015 (72.50%)
1 day, 20:32:46.743892 PROGRESS: Decoy precursors: 385 (27.50%)
1 day, 20:32:46.743937 PROGRESS: 
1 day, 20:32:46.743979 PROGRESS: Precursor Summary:
1 day, 20:32:46.744889 PROGRESS: Channel   0:	 0.050 FDR:    89; 0.010 FDR:    89; 0.001 FDR:    89
1 day, 20:32:46.744989 PROGRESS: 
1 day, 20:32:46.745048 PROGRESS: Protein Summary:
1 day, 20:32:46.746047 PROGRESS: Channel   0:	 0.050 FDR:    88; 0.010 FDR:    88; 0.001 FDR:    88
1 day, 20:32:46.746138 PROGRESS: =========================================================================
1 day, 20:32:46.746305 INFO: Target number of precursors not reached yet.
1 day, 20:32:46.752120 INFO: Starting optimization step 3.
1 day, 20:32:46.752229 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 20:32:46.752299 INFO: Using classic extraction backend
1 day, 20:32:46.752406 PROGRESS: Extracting batch of 3184 precursors
1 day, 20:32:46.752476 INFO: === Search parameters used ===
1 day, 20:32:46.752525 INFO: rt_error       : 2099.8992935
1 day, 20:32:46.752575 INFO: mobility_error : 0.1
1 day, 20:32:46.752627 INFO: num_candidates : 1
1 day, 20:32:46.752671 INFO: ms1_error      : 30
1 day, 20:32:46.752711 INFO: ms2_error      : 30
1 day, 20:32:46.752752 INFO: fwhm_rt        : 5
1 day, 20:32:46.752790 INFO: quant_window   : 3
1 day, 20:32:46.752828 INFO: ==============================================
1 day, 20:32:46.753724 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:32:46.753770 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:32:46.753797 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:32:46.753817 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:32:46.760466 INFO: Starting candidate selection
1 day, 20:33:07.878331 INFO: Starting candidate scoring
1 day, 20:33:08.220665 INFO: Finished candidate processing
1 day, 20:33:08.220779 INFO: Collecting candidate features
1 day, 20:33:08.234725 INFO: Collecting fragment features
1 day, 20:33:08.240167 INFO: Finished candidate scoring
1 day, 20:33:08.245781 INFO: performing precursor FDR with 47 features
1 day, 20:33:08.245833 INFO: Decoy channel: -1
1 day, 20:33:08.245857 INFO: Competetive: True
1 day, 20:33:08.250493 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:33:08.253779 INFO: Using random state 337548 for train-test-split
1 day, 20:33:08.276466 INFO: Test AUC: 0.443
1 day, 20:33:08.276550 INFO: Train AUC: 0.449
1 day, 20:33:08.276582 INFO: AUC difference: 1.21%
1 day, 20:33:08.489053 INFO: Resetting torch num_threads to 80
1 day, 20:33:08.491104 PROGRESS: === Extracted 5960 precursors and 67734 fragments ===
1 day, 20:33:08.491572 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:33:08.492515 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:33:08.492607 PROGRESS: Total precursors accumulated: 2,999
1 day, 20:33:08.492667 PROGRESS: Target precursors: 2,201 (73.39%)
1 day, 20:33:08.492717 PROGRESS: Decoy precursors: 798 (26.61%)
1 day, 20:33:08.492760 PROGRESS: 
1 day, 20:33:08.492803 PROGRESS: Precursor Summary:
1 day, 20:33:08.493758 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 20:33:08.493850 PROGRESS: 
1 day, 20:33:08.493905 PROGRESS: Protein Summary:
1 day, 20:33:08.494962 PROGRESS: Channel   0:	 0.050 FDR:   196; 0.010 FDR:   196; 0.001 FDR:   196
1 day, 20:33:08.495052 PROGRESS: =========================================================================
1 day, 20:33:08.495255 INFO: Target number of precursors reached.
1 day, 20:33:08.501590 INFO: fragments_df: keeping 740 of 67734 [sum(precursor_idx_mask)=2260 sum(mass_error_mask)=67734 stop_rank=740
1 day, 20:33:08.514517 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:33:08.628675 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:33:08.747969 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:33:08.869092 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:33:09.013935 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 20:33:09.014354 INFO: Using score_cutoff 49.95409282264709 (fac=0.99, q=1)
1 day, 20:33:09.014714 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.661266326904297
1 day, 20:33:09.014796 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010327601805329323
1 day, 20:33:09.014851 INFO: Updating optimization_manager: score_cutoff        : 0 -> 49.95409282264709
1 day, 20:33:09.014913 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:33:09.016544 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:33:09.021372 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:33:09.022701 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:33:09.031458 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
1 day, 20:33:09.031575 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 20:33:09.031661 INFO: Starting optimization step 4.
1 day, 20:33:09.031722 PROGRESS: === Extracting elution groups 0 to 3000 ===
1 day, 20:33:09.031782 INFO: Using classic extraction backend
1 day, 20:33:09.031936 PROGRESS: Extracting batch of 5966 precursors
1 day, 20:33:09.032012 INFO: === Search parameters used ===
1 day, 20:33:09.032062 INFO: rt_error       : 2099.8992935
1 day, 20:33:09.032105 INFO: mobility_error : 0.1
1 day, 20:33:09.032147 INFO: num_candidates : 3
1 day, 20:33:09.032189 INFO: ms1_error      : 30
1 day, 20:33:09.032230 INFO: ms2_error      : 30
1 day, 20:33:09.032269 INFO: fwhm_rt        : 3.661266326904297
1 day, 20:33:09.032310 INFO: quant_window   : 3
1 day, 20:33:09.032351 INFO: ==============================================
1 day, 20:33:09.034103 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:33:09.034150 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:33:09.034192 INFO: FWHM in RT is 3.66 seconds, sigma is 0.80
1 day, 20:33:09.034216 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.79
1 day, 20:33:09.034866 INFO: Starting candidate selection
1 day, 20:33:49.403713 INFO: Starting candidate scoring
1 day, 20:33:51.043877 INFO: Finished candidate processing
1 day, 20:33:51.044048 INFO: Collecting candidate features
1 day, 20:33:51.107310 INFO: Collecting fragment features
1 day, 20:33:51.125730 INFO: Finished candidate scoring
1 day, 20:33:51.132806 INFO: performing precursor FDR with 47 features
1 day, 20:33:51.132889 INFO: Decoy channel: -1
1 day, 20:33:51.132914 INFO: Competetive: True
1 day, 20:33:51.138891 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:33:51.143740 INFO: Using random state 519847 for train-test-split
1 day, 20:33:51.268508 INFO: Test AUC: 0.675
1 day, 20:33:51.268602 INFO: Train AUC: 0.669
1 day, 20:33:51.268633 INFO: AUC difference: 0.90%
1 day, 20:33:51.500486 INFO: Resetting torch num_threads to 80
1 day, 20:33:51.501296 PROGRESS: === Extracted 16952 precursors and 192709 fragments ===
1 day, 20:33:51.501786 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:33:51.502629 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:33:51.502719 PROGRESS: Total precursors accumulated: 3,000
1 day, 20:33:51.502779 PROGRESS: Target precursors: 2,611 (87.03%)
1 day, 20:33:51.502828 PROGRESS: Decoy precursors: 389 (12.97%)
1 day, 20:33:51.502873 PROGRESS: 
1 day, 20:33:51.502918 PROGRESS: Precursor Summary:
1 day, 20:33:51.504081 PROGRESS: Channel   0:	 0.050 FDR: 1,871; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:33:51.504175 PROGRESS: 
1 day, 20:33:51.504231 PROGRESS: Protein Summary:
1 day, 20:33:51.505537 PROGRESS: Channel   0:	 0.050 FDR: 1,432; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:33:51.505640 PROGRESS: =========================================================================
1 day, 20:33:51.505948 INFO: Target number of precursors not reached yet.
1 day, 20:33:51.517357 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:33:51.519145 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:33:51.524256 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:33:51.525673 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:33:51.535603 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:33:51.535755 INFO: Starting optimization step 5.
1 day, 20:33:51.535822 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 20:33:51.535892 INFO: Using classic extraction backend
1 day, 20:33:51.536048 PROGRESS: Extracting batch of 6376 precursors
1 day, 20:33:51.536120 INFO: === Search parameters used ===
1 day, 20:33:51.536171 INFO: rt_error       : 2099.8992935
1 day, 20:33:51.536215 INFO: mobility_error : 0.1
1 day, 20:33:51.536255 INFO: num_candidates : 3
1 day, 20:33:51.536295 INFO: ms1_error      : 30
1 day, 20:33:51.536334 INFO: ms2_error      : 30
1 day, 20:33:51.536373 INFO: fwhm_rt        : 3.661266326904297
1 day, 20:33:51.536412 INFO: quant_window   : 3
1 day, 20:33:51.536449 INFO: ==============================================
1 day, 20:33:51.538023 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:33:51.538071 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:33:51.538113 INFO: FWHM in RT is 3.66 seconds, sigma is 0.80
1 day, 20:33:51.538135 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.79
1 day, 20:33:51.538917 INFO: Starting candidate selection
1 day, 20:34:35.605886 INFO: Starting candidate scoring
1 day, 20:34:37.384186 INFO: Finished candidate processing
1 day, 20:34:37.384303 INFO: Collecting candidate features
1 day, 20:34:37.416001 INFO: Collecting fragment features
1 day, 20:34:37.428622 INFO: Finished candidate scoring
1 day, 20:34:37.443411 INFO: performing precursor FDR with 47 features
1 day, 20:34:37.443532 INFO: Decoy channel: -1
1 day, 20:34:37.443558 INFO: Competetive: True
1 day, 20:34:37.455840 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:37.464307 INFO: Using random state 519847 for train-test-split
1 day, 20:34:37.884047 INFO: Test AUC: 0.709
1 day, 20:34:37.884160 INFO: Train AUC: 0.706
1 day, 20:34:37.884192 INFO: AUC difference: 0.44%
1 day, 20:34:38.121990 INFO: Resetting torch num_threads to 80
1 day, 20:34:38.126886 PROGRESS: === Extracted 35046 precursors and 399205 fragments ===
1 day, 20:34:38.127534 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:34:38.128783 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:38.128878 PROGRESS: Total precursors accumulated: 6,199
1 day, 20:34:38.128957 PROGRESS: Target precursors: 5,578 (89.98%)
1 day, 20:34:38.129011 PROGRESS: Decoy precursors: 621 (10.02%)
1 day, 20:34:38.129056 PROGRESS: 
1 day, 20:34:38.129097 PROGRESS: Precursor Summary:
1 day, 20:34:38.130943 PROGRESS: Channel   0:	 0.050 FDR: 5,032; 0.010 FDR: 3,719; 0.001 FDR: 1,521
1 day, 20:34:38.131038 PROGRESS: 
1 day, 20:34:38.131093 PROGRESS: Protein Summary:
1 day, 20:34:38.133747 PROGRESS: Channel   0:	 0.050 FDR: 2,997; 0.010 FDR: 2,355; 0.001 FDR: 1,132
1 day, 20:34:38.133845 PROGRESS: =========================================================================
1 day, 20:34:38.134145 INFO: Target number of precursors reached.
1 day, 20:34:38.199429 INFO: fragments_df: keeping 5000 of 399205 [sum(precursor_idx_mask)=121105 sum(mass_error_mask)=399205 stop_rank=5000
1 day, 20:34:38.207768 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:34:38.633238 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:34:41.676634 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:34:42.097166 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:34:42.714687 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:34:42.715168 INFO: Using score_cutoff 52.15966039352417 (fac=0.99, q=1)
1 day, 20:34:42.715578 INFO: Updating optimization_manager: fwhm_rt             : 3.661266326904297 -> 3.0796749591827393
1 day, 20:34:42.715667 INFO: Updating optimization_manager: fwhm_mobility       : 0.010327601805329323 -> 0.010509118437767029
1 day, 20:34:42.715726 INFO: Updating optimization_manager: score_cutoff        : 49.95409282264709 -> 52.15966039352417
1 day, 20:34:42.715784 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:34:42.716851 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:34:42.718224 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:34:42.718996 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:34:42.721365 INFO: === checking if optimization conditions were reached ===
1 day, 20:34:42.723004 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.494642
1 day, 20:34:42.723109 INFO: Updating optimization_manager: classifier_version  : 3 -> 5
1 day, 20:34:42.723179 PROGRESS: ❌ ms2_error      : 17.4946 > 17.4946 or insufficient steps taken.
1 day, 20:34:42.724616 INFO: Updating optimization_manager: ms1_error           : 30 -> 7.5754825
1 day, 20:34:42.724716 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
1 day, 20:34:42.724785 PROGRESS: ❌ ms1_error      : 7.5755 > 7.5755 or insufficient steps taken.
1 day, 20:34:42.724844 INFO: ==============================================
1 day, 20:34:42.724916 INFO: Starting optimization step 6.
1 day, 20:34:42.724990 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:34:42.725051 INFO: Using classic extraction backend
1 day, 20:34:42.725192 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:34:42.725268 INFO: === Search parameters used ===
1 day, 20:34:42.725328 INFO: rt_error       : 2099.8992935
1 day, 20:34:42.725374 INFO: mobility_error : 0.1
1 day, 20:34:42.725418 INFO: num_candidates : 3
1 day, 20:34:42.725462 INFO: ms1_error      : 7.5754825
1 day, 20:34:42.725505 INFO: ms2_error      : 17.494642
1 day, 20:34:42.725549 INFO: fwhm_rt        : 3.0796749591827393
1 day, 20:34:42.725591 INFO: quant_window   : 3
1 day, 20:34:42.725634 INFO: ==============================================
1 day, 20:34:42.726658 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:34:42.726707 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:34:42.726747 INFO: FWHM in RT is 3.08 seconds, sigma is 0.68
1 day, 20:34:42.726772 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.87
1 day, 20:34:42.727454 INFO: Starting candidate selection
1 day, 20:34:51.630782 INFO: Starting candidate scoring
1 day, 20:34:51.852965 INFO: Finished candidate processing
1 day, 20:34:51.853756 INFO: Collecting candidate features
1 day, 20:34:51.868078 INFO: Collecting fragment features
1 day, 20:34:51.872321 INFO: Finished candidate scoring
1 day, 20:34:51.875748 INFO: performing precursor FDR with 47 features
1 day, 20:34:51.875796 INFO: Decoy channel: -1
1 day, 20:34:51.875820 INFO: Competetive: True
1 day, 20:34:51.879495 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:51.882112 INFO: Using random state 32924 for train-test-split
1 day, 20:34:51.893634 INFO: Test AUC: 0.738
1 day, 20:34:51.893693 INFO: Train AUC: 0.723
1 day, 20:34:51.893724 INFO: AUC difference: 2.06%
1 day, 20:34:52.109379 INFO: Resetting torch num_threads to 80
1 day, 20:34:52.109938 PROGRESS: === Extracted 3394 precursors and 37839 fragments ===
1 day, 20:34:52.110345 INFO: === FDR correction performed with classifier version 5 ===
1 day, 20:34:52.110948 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:52.111038 PROGRESS: Total precursors accumulated: 600
1 day, 20:34:52.111097 PROGRESS: Target precursors: 567 (94.50%)
1 day, 20:34:52.111146 PROGRESS: Decoy precursors: 33 (5.50%)
1 day, 20:34:52.111190 PROGRESS: 
1 day, 20:34:52.111234 PROGRESS: Precursor Summary:
1 day, 20:34:52.112296 PROGRESS: Channel   0:	 0.050 FDR:   563; 0.010 FDR:   515; 0.001 FDR:   344
1 day, 20:34:52.112396 PROGRESS: 
1 day, 20:34:52.112452 PROGRESS: Protein Summary:
1 day, 20:34:52.113705 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   470; 0.001 FDR:   327
1 day, 20:34:52.113803 PROGRESS: =========================================================================
1 day, 20:34:52.114110 INFO: Target number of precursors reached.
1 day, 20:34:52.120888 INFO: fragments_df: keeping 5000 of 37839 [sum(precursor_idx_mask)=16547 sum(mass_error_mask)=37839 stop_rank=5000
1 day, 20:34:52.125288 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:34:52.267799 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:34:52.408468 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:34:52.552936 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:34:53.237595 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:34:53.238024 INFO: Using score_cutoff 42.65696874160766 (fac=0.99, q=1)
1 day, 20:34:53.238335 INFO: Updating optimization_manager: fwhm_rt             : 3.0796749591827393 -> 2.806854248046875
1 day, 20:34:53.238417 INFO: Updating optimization_manager: fwhm_mobility       : 0.010509118437767029 -> 0.008838995359838009
1 day, 20:34:53.238471 INFO: Updating optimization_manager: score_cutoff        : 52.15966039352417 -> 42.65696874160766
1 day, 20:34:53.238523 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:34:53.239592 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:34:53.240937 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:34:53.241750 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:34:53.243909 INFO: === checking if optimization conditions were reached ===
1 day, 20:34:53.245559 INFO: Updating optimization_manager: ms2_error           : 17.494642 -> 17.494642
1 day, 20:34:53.245658 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
1 day, 20:34:53.245731 PROGRESS: ✅ ms2_error      : 17.4946 <= 17.4946
1 day, 20:34:53.246705 INFO: Updating optimization_manager: ms1_error           : 7.5754825 -> 7.5754825
1 day, 20:34:53.246804 INFO: Updating optimization_manager: classifier_version  : 6 -> 6
1 day, 20:34:53.246863 PROGRESS: ✅ ms1_error      : 7.5755 <= 7.5755
1 day, 20:34:53.246918 INFO: ==============================================
1 day, 20:34:53.246980 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 20:34:53.250977 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:34:53.251811 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:34:53.253149 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:34:53.253936 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:34:53.256098 INFO: Starting optimization step 0.
1 day, 20:34:53.256193 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:34:53.256258 INFO: Using classic extraction backend
1 day, 20:34:53.256365 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:34:53.256433 INFO: === Search parameters used ===
1 day, 20:34:53.256483 INFO: rt_error       : 2099.8992935
1 day, 20:34:53.256526 INFO: mobility_error : 0.1
1 day, 20:34:53.256568 INFO: num_candidates : 3
1 day, 20:34:53.256613 INFO: ms1_error      : 7.5754825
1 day, 20:34:53.256655 INFO: ms2_error      : 17.494642
1 day, 20:34:53.256696 INFO: fwhm_rt        : 2.806854248046875
1 day, 20:34:53.256742 INFO: quant_window   : 3
1 day, 20:34:53.256782 INFO: ==============================================
1 day, 20:34:53.257511 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:34:53.257557 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:34:53.257591 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 20:34:53.257613 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.10
1 day, 20:34:53.258286 INFO: Starting candidate selection
1 day, 20:35:01.930949 INFO: Starting candidate scoring
1 day, 20:35:02.185904 INFO: Finished candidate processing
1 day, 20:35:02.186095 INFO: Collecting candidate features
1 day, 20:35:02.199979 INFO: Collecting fragment features
1 day, 20:35:02.203666 INFO: Finished candidate scoring
1 day, 20:35:02.206560 INFO: performing precursor FDR with 47 features
1 day, 20:35:02.206608 INFO: Decoy channel: -1
1 day, 20:35:02.206633 INFO: Competetive: True
1 day, 20:35:02.209758 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:02.212215 INFO: Using random state 498866 for train-test-split
1 day, 20:35:02.223191 INFO: Test AUC: 0.709
1 day, 20:35:02.223252 INFO: Train AUC: 0.736
1 day, 20:35:02.223281 INFO: AUC difference: 3.56%
1 day, 20:35:02.437395 INFO: Resetting torch num_threads to 80
1 day, 20:35:02.437960 PROGRESS: === Extracted 3377 precursors and 37589 fragments ===
1 day, 20:35:02.438369 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:35:02.438949 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:02.439040 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:02.439097 PROGRESS: Target precursors: 566 (94.33%)
1 day, 20:35:02.439147 PROGRESS: Decoy precursors: 34 (5.67%)
1 day, 20:35:02.439191 PROGRESS: 
1 day, 20:35:02.439236 PROGRESS: Precursor Summary:
1 day, 20:35:02.440283 PROGRESS: Channel   0:	 0.050 FDR:   556; 0.010 FDR:   513; 0.001 FDR:   329
1 day, 20:35:02.440379 PROGRESS: 
1 day, 20:35:02.440433 PROGRESS: Protein Summary:
1 day, 20:35:02.441682 PROGRESS: Channel   0:	 0.050 FDR:   507; 0.010 FDR:   468; 0.001 FDR:   314
1 day, 20:35:02.441781 PROGRESS: =========================================================================
1 day, 20:35:02.441922 INFO: Target number of precursors reached.
1 day, 20:35:02.448645 INFO: fragments_df: keeping 5000 of 37589 [sum(precursor_idx_mask)=16336 sum(mass_error_mask)=37589 stop_rank=5000
1 day, 20:35:02.452938 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:02.582693 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:02.700836 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:02.823353 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:03.443412 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:03.443854 INFO: Using score_cutoff 42.799974993896484 (fac=0.99, q=1)
1 day, 20:35:03.444169 INFO: Updating optimization_manager: fwhm_rt             : 2.806854248046875 -> 2.78090500831604
1 day, 20:35:03.444253 INFO: Updating optimization_manager: fwhm_mobility       : 0.008838995359838009 -> 0.008772498928010464
1 day, 20:35:03.444314 INFO: Updating optimization_manager: score_cutoff        : 42.65696874160766 -> 42.799974993896484
1 day, 20:35:03.444368 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:03.445502 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:03.446866 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:03.447655 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:03.449869 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:03.449973 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:35:03.451603 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 278.0552527051108
1 day, 20:35:03.451705 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 278.0553.
1 day, 20:35:03.451771 INFO: ==============================================
1 day, 20:35:03.451834 INFO: Starting optimization step 1.
1 day, 20:35:03.451889 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:35:03.451940 INFO: Using classic extraction backend
1 day, 20:35:03.452042 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:35:03.452112 INFO: === Search parameters used ===
1 day, 20:35:03.452159 INFO: rt_error       : 278.0552527051108
1 day, 20:35:03.452201 INFO: mobility_error : 0.1
1 day, 20:35:03.452240 INFO: num_candidates : 3
1 day, 20:35:03.452281 INFO: ms1_error      : 7.5754825
1 day, 20:35:03.452320 INFO: ms2_error      : 17.494642
1 day, 20:35:03.452360 INFO: fwhm_rt        : 2.78090500831604
1 day, 20:35:03.452401 INFO: quant_window   : 3
1 day, 20:35:03.452445 INFO: ==============================================
1 day, 20:35:03.453333 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:03.453381 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:03.453415 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1 day, 20:35:03.453435 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.07
1 day, 20:35:03.454083 INFO: Starting candidate selection
1 day, 20:35:05.304450 INFO: Starting candidate scoring
1 day, 20:35:05.508678 INFO: Finished candidate processing
1 day, 20:35:05.508787 INFO: Collecting candidate features
1 day, 20:35:05.521927 INFO: Collecting fragment features
1 day, 20:35:05.525739 INFO: Finished candidate scoring
1 day, 20:35:05.528462 INFO: performing precursor FDR with 47 features
1 day, 20:35:05.528506 INFO: Decoy channel: -1
1 day, 20:35:05.528531 INFO: Competetive: True
1 day, 20:35:05.531711 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:05.533945 INFO: Using random state 498866 for train-test-split
1 day, 20:35:05.545078 INFO: Test AUC: 0.749
1 day, 20:35:05.545139 INFO: Train AUC: 0.746
1 day, 20:35:05.545168 INFO: AUC difference: 0.47%
1 day, 20:35:05.762156 INFO: Resetting torch num_threads to 80
1 day, 20:35:05.762753 PROGRESS: === Extracted 3382 precursors and 37243 fragments ===
1 day, 20:35:05.763159 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:35:05.763751 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:05.763840 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:05.763896 PROGRESS: Target precursors: 579 (96.50%)
1 day, 20:35:05.763944 PROGRESS: Decoy precursors: 21 (3.50%)
1 day, 20:35:05.763987 PROGRESS: 
1 day, 20:35:05.764031 PROGRESS: Precursor Summary:
1 day, 20:35:05.765254 PROGRESS: Channel   0:	 0.050 FDR:   579; 0.010 FDR:   548; 0.001 FDR:   346
1 day, 20:35:05.765360 PROGRESS: 
1 day, 20:35:05.765415 PROGRESS: Protein Summary:
1 day, 20:35:05.766663 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   500; 0.001 FDR:   328
1 day, 20:35:05.766764 PROGRESS: =========================================================================
1 day, 20:35:05.766906 INFO: Target number of precursors reached.
1 day, 20:35:05.774063 INFO: fragments_df: keeping 5000 of 37243 [sum(precursor_idx_mask)=17373 sum(mass_error_mask)=37243 stop_rank=5000
1 day, 20:35:05.778432 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:05.909255 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:06.034015 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:06.159672 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:06.780211 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:06.780780 INFO: Using score_cutoff 42.96260110473633 (fac=0.99, q=1)
1 day, 20:35:06.781105 INFO: Updating optimization_manager: fwhm_rt             : 2.78090500831604 -> 2.780507802963257
1 day, 20:35:06.781190 INFO: Updating optimization_manager: fwhm_mobility       : 0.008772498928010464 -> 0.008696263656020164
1 day, 20:35:06.781245 INFO: Updating optimization_manager: score_cutoff        : 42.799974993896484 -> 42.96260110473633
1 day, 20:35:06.781298 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:06.782362 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:06.783756 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:06.784535 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:06.786610 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:06.786715 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:35:06.788437 INFO: Updating optimization_manager: rt_error            : 278.0552527051108 -> 39.36188173647363
1 day, 20:35:06.788548 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 39.3619.
1 day, 20:35:06.788613 INFO: ==============================================
1 day, 20:35:06.788679 INFO: Starting optimization step 2.
1 day, 20:35:06.788736 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:35:06.788790 INFO: Using classic extraction backend
1 day, 20:35:06.788895 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:35:06.788968 INFO: === Search parameters used ===
1 day, 20:35:06.789019 INFO: rt_error       : 39.36188173647363
1 day, 20:35:06.789063 INFO: mobility_error : 0.1
1 day, 20:35:06.789104 INFO: num_candidates : 3
1 day, 20:35:06.789145 INFO: ms1_error      : 7.5754825
1 day, 20:35:06.789186 INFO: ms2_error      : 17.494642
1 day, 20:35:06.789226 INFO: fwhm_rt        : 2.780507802963257
1 day, 20:35:06.789265 INFO: quant_window   : 3
1 day, 20:35:06.789304 INFO: ==============================================
1 day, 20:35:06.790095 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:06.790140 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:06.790174 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1 day, 20:35:06.790199 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.03
1 day, 20:35:06.790843 INFO: Starting candidate selection
1 day, 20:35:07.445433 INFO: Starting candidate scoring
1 day, 20:35:07.667023 INFO: Finished candidate processing
1 day, 20:35:07.667121 INFO: Collecting candidate features
1 day, 20:35:07.679714 INFO: Collecting fragment features
1 day, 20:35:07.683409 INFO: Finished candidate scoring
1 day, 20:35:07.685771 INFO: performing precursor FDR with 47 features
1 day, 20:35:07.685819 INFO: Decoy channel: -1
1 day, 20:35:07.685844 INFO: Competetive: True
1 day, 20:35:07.689002 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:07.691050 INFO: Using random state 498866 for train-test-split
1 day, 20:35:07.701482 INFO: Test AUC: 0.764
1 day, 20:35:07.701548 INFO: Train AUC: 0.776
1 day, 20:35:07.701578 INFO: AUC difference: 1.54%
1 day, 20:35:07.921088 INFO: Resetting torch num_threads to 80
1 day, 20:35:07.921682 PROGRESS: === Extracted 3384 precursors and 36720 fragments ===
1 day, 20:35:07.922111 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:35:07.922727 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:07.922824 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:07.922882 PROGRESS: Target precursors: 586 (97.67%)
1 day, 20:35:07.922941 PROGRESS: Decoy precursors: 14 (2.33%)
1 day, 20:35:07.922989 PROGRESS: 
1 day, 20:35:07.923034 PROGRESS: Precursor Summary:
1 day, 20:35:07.924152 PROGRESS: Channel   0:	 0.050 FDR:   586; 0.010 FDR:   572; 0.001 FDR:   495
1 day, 20:35:07.924245 PROGRESS: 
1 day, 20:35:07.924301 PROGRESS: Protein Summary:
1 day, 20:35:07.925596 PROGRESS: Channel   0:	 0.050 FDR:   531; 0.010 FDR:   519; 0.001 FDR:   457
1 day, 20:35:07.925690 PROGRESS: =========================================================================
1 day, 20:35:07.925825 INFO: Target number of precursors reached.
1 day, 20:35:07.932966 INFO: fragments_df: keeping 5000 of 36720 [sum(precursor_idx_mask)=17874 sum(mass_error_mask)=36720 stop_rank=5000
1 day, 20:35:07.937390 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:08.055968 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:08.180096 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:08.308012 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:08.928996 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:08.929433 INFO: Using score_cutoff 40.89605299530029 (fac=0.99, q=1)
1 day, 20:35:08.929750 INFO: Updating optimization_manager: fwhm_rt             : 2.780507802963257 -> 2.751291275024414
1 day, 20:35:08.929830 INFO: Updating optimization_manager: fwhm_mobility       : 0.008696263656020164 -> 0.008670469745993614
1 day, 20:35:08.929886 INFO: Updating optimization_manager: score_cutoff        : 42.96260110473633 -> 40.89605299530029
1 day, 20:35:08.929944 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:08.931018 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:08.932385 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:08.933173 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:08.935292 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:08.935397 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:35:08.937250 INFO: Updating optimization_manager: rt_error            : 39.36188173647363 -> 16.56018427395254
1 day, 20:35:08.937354 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 16.5602.
1 day, 20:35:08.937417 INFO: ==============================================
1 day, 20:35:08.937485 INFO: Starting optimization step 3.
1 day, 20:35:08.937543 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:35:08.937596 INFO: Using classic extraction backend
1 day, 20:35:08.937699 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:35:08.937766 INFO: === Search parameters used ===
1 day, 20:35:08.937814 INFO: rt_error       : 16.56018427395254
1 day, 20:35:08.937857 INFO: mobility_error : 0.1
1 day, 20:35:08.937898 INFO: num_candidates : 3
1 day, 20:35:08.937939 INFO: ms1_error      : 7.5754825
1 day, 20:35:08.937978 INFO: ms2_error      : 17.494642
1 day, 20:35:08.938016 INFO: fwhm_rt        : 2.751291275024414
1 day, 20:35:08.938053 INFO: quant_window   : 3
1 day, 20:35:08.938448 INFO: ==============================================
1 day, 20:35:08.939421 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:08.939468 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:08.939502 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 20:35:08.939524 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.02
1 day, 20:35:08.940731 INFO: Starting candidate selection
1 day, 20:35:09.492307 INFO: Starting candidate scoring
1 day, 20:35:09.679460 INFO: Finished candidate processing
1 day, 20:35:09.679562 INFO: Collecting candidate features
1 day, 20:35:09.692763 INFO: Collecting fragment features
1 day, 20:35:09.696589 INFO: Finished candidate scoring
1 day, 20:35:09.698913 INFO: performing precursor FDR with 47 features
1 day, 20:35:09.698968 INFO: Decoy channel: -1
1 day, 20:35:09.699002 INFO: Competetive: True
1 day, 20:35:09.702858 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:09.704922 INFO: Using random state 498866 for train-test-split
1 day, 20:35:09.715928 INFO: Test AUC: 0.762
1 day, 20:35:09.715991 INFO: Train AUC: 0.777
1 day, 20:35:09.716031 INFO: AUC difference: 1.97%
1 day, 20:35:09.938796 INFO: Resetting torch num_threads to 80
1 day, 20:35:09.939381 PROGRESS: === Extracted 3364 precursors and 36228 fragments ===
1 day, 20:35:09.939796 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:35:09.940381 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:09.940472 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:09.940532 PROGRESS: Target precursors: 593 (98.83%)
1 day, 20:35:09.940583 PROGRESS: Decoy precursors: 7 (1.17%)
1 day, 20:35:09.940631 PROGRESS: 
1 day, 20:35:09.940676 PROGRESS: Precursor Summary:
1 day, 20:35:09.941786 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   590; 0.001 FDR:   532
1 day, 20:35:09.941884 PROGRESS: 
1 day, 20:35:09.941940 PROGRESS: Protein Summary:
1 day, 20:35:09.943207 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   535; 0.001 FDR:   486
1 day, 20:35:09.943304 PROGRESS: =========================================================================
1 day, 20:35:09.943457 INFO: Target number of precursors reached.
1 day, 20:35:09.950538 INFO: fragments_df: keeping 5000 of 36228 [sum(precursor_idx_mask)=18367 sum(mass_error_mask)=36228 stop_rank=5000
1 day, 20:35:09.955710 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:10.077029 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:10.198177 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:10.318191 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:10.939404 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:10.939835 INFO: Using score_cutoff 38.74918491210937 (fac=0.99, q=1)
1 day, 20:35:10.940149 INFO: Updating optimization_manager: fwhm_rt             : 2.751291275024414 -> 2.7563889026641846
1 day, 20:35:10.940232 INFO: Updating optimization_manager: fwhm_mobility       : 0.008670469745993614 -> 0.008559593930840492
1 day, 20:35:10.940287 INFO: Updating optimization_manager: score_cutoff        : 40.89605299530029 -> 38.74918491210937
1 day, 20:35:10.940340 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:10.941396 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:10.942745 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:10.943528 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:10.945651 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:10.945756 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 20:35:10.947577 INFO: Updating optimization_manager: rt_error            : 16.56018427395254 -> 15.61705158604194
1 day, 20:35:10.947680 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 15.6171.
1 day, 20:35:10.947745 INFO: ==============================================
1 day, 20:35:10.947809 INFO: Starting optimization step 4.
1 day, 20:35:10.947870 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:35:10.947924 INFO: Using classic extraction backend
1 day, 20:35:10.948026 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:35:10.948090 INFO: === Search parameters used ===
1 day, 20:35:10.948146 INFO: rt_error       : 15.61705158604194
1 day, 20:35:10.948191 INFO: mobility_error : 0.1
1 day, 20:35:10.948235 INFO: num_candidates : 3
1 day, 20:35:10.948277 INFO: ms1_error      : 7.5754825
1 day, 20:35:10.948325 INFO: ms2_error      : 17.494642
1 day, 20:35:10.948367 INFO: fwhm_rt        : 2.7563889026641846
1 day, 20:35:10.948407 INFO: quant_window   : 3
1 day, 20:35:10.948448 INFO: ==============================================
1 day, 20:35:10.949264 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:10.949311 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:10.949344 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 20:35:10.949366 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.97
1 day, 20:35:10.950142 INFO: Starting candidate selection
1 day, 20:35:11.516477 INFO: Starting candidate scoring
1 day, 20:35:11.731478 INFO: Finished candidate processing
1 day, 20:35:11.731573 INFO: Collecting candidate features
1 day, 20:35:11.744562 INFO: Collecting fragment features
1 day, 20:35:11.748323 INFO: Finished candidate scoring
1 day, 20:35:11.750431 INFO: performing precursor FDR with 47 features
1 day, 20:35:11.750478 INFO: Decoy channel: -1
1 day, 20:35:11.750504 INFO: Competetive: True
1 day, 20:35:11.753477 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:11.755512 INFO: Using random state 498866 for train-test-split
1 day, 20:35:11.766783 INFO: Test AUC: 0.801
1 day, 20:35:11.766843 INFO: Train AUC: 0.768
1 day, 20:35:11.766874 INFO: AUC difference: 4.27%
1 day, 20:35:11.986221 INFO: Resetting torch num_threads to 80
1 day, 20:35:11.986795 PROGRESS: === Extracted 3361 precursors and 35965 fragments ===
1 day, 20:35:11.987205 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:35:11.987771 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:11.987859 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:11.987919 PROGRESS: Target precursors: 594 (99.00%)
1 day, 20:35:11.987969 PROGRESS: Decoy precursors: 6 (1.00%)
1 day, 20:35:11.988017 PROGRESS: 
1 day, 20:35:11.988063 PROGRESS: Precursor Summary:
1 day, 20:35:11.989130 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:   591; 0.001 FDR:   515
1 day, 20:35:11.989224 PROGRESS: 
1 day, 20:35:11.989281 PROGRESS: Protein Summary:
1 day, 20:35:11.990532 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   535; 0.001 FDR:   472
1 day, 20:35:11.990622 PROGRESS: =========================================================================
1 day, 20:35:11.990779 INFO: Target number of precursors reached.
1 day, 20:35:11.997724 INFO: fragments_df: keeping 5000 of 35965 [sum(precursor_idx_mask)=18312 sum(mass_error_mask)=35965 stop_rank=5000
1 day, 20:35:12.002572 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:12.125810 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:12.250561 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:12.369522 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:12.988373 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:12.988801 INFO: Using score_cutoff 36.96820518493652 (fac=0.99, q=1)
1 day, 20:35:12.989125 INFO: Updating optimization_manager: fwhm_rt             : 2.7563889026641846 -> 2.7681097984313965
1 day, 20:35:12.989208 INFO: Updating optimization_manager: fwhm_mobility       : 0.008559593930840492 -> 0.008461957797408104
1 day, 20:35:12.989265 INFO: Updating optimization_manager: score_cutoff        : 38.74918491210937 -> 36.96820518493652
1 day, 20:35:12.989322 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:12.990407 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:12.991753 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:12.992528 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:12.994631 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:12.994736 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 20:35:12.996582 INFO: Updating optimization_manager: rt_error            : 15.61705158604194 -> 13.500294699262021
1 day, 20:35:12.996684 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 13.5003.
1 day, 20:35:12.996916 INFO: ==============================================
1 day, 20:35:12.997016 INFO: Starting optimization step 5.
1 day, 20:35:12.997092 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:35:12.997159 INFO: Using classic extraction backend
1 day, 20:35:12.997283 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:35:12.997359 INFO: === Search parameters used ===
1 day, 20:35:12.997408 INFO: rt_error       : 13.500294699262021
1 day, 20:35:12.997453 INFO: mobility_error : 0.1
1 day, 20:35:12.997496 INFO: num_candidates : 3
1 day, 20:35:12.997536 INFO: ms1_error      : 7.5754825
1 day, 20:35:12.997577 INFO: ms2_error      : 17.494642
1 day, 20:35:12.997618 INFO: fwhm_rt        : 2.7681097984313965
1 day, 20:35:12.997658 INFO: quant_window   : 3
1 day, 20:35:12.997696 INFO: ==============================================
1 day, 20:35:12.998480 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:12.998526 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:12.998559 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 20:35:12.998581 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 20:35:12.999245 INFO: Starting candidate selection
1 day, 20:35:13.512617 INFO: Starting candidate scoring
1 day, 20:35:13.715020 INFO: Finished candidate processing
1 day, 20:35:13.715159 INFO: Collecting candidate features
1 day, 20:35:13.730154 INFO: Collecting fragment features
1 day, 20:35:13.733827 INFO: Finished candidate scoring
1 day, 20:35:13.735862 INFO: performing precursor FDR with 47 features
1 day, 20:35:13.735906 INFO: Decoy channel: -1
1 day, 20:35:13.735934 INFO: Competetive: True
1 day, 20:35:13.738935 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:13.741333 INFO: Using random state 498866 for train-test-split
1 day, 20:35:13.752380 INFO: Test AUC: 0.783
1 day, 20:35:13.752439 INFO: Train AUC: 0.773
1 day, 20:35:13.752468 INFO: AUC difference: 1.36%
1 day, 20:35:13.971291 INFO: Resetting torch num_threads to 80
1 day, 20:35:13.971845 PROGRESS: === Extracted 3353 precursors and 35800 fragments ===
1 day, 20:35:13.972259 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:35:13.972821 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:13.972913 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:13.972985 PROGRESS: Target precursors: 594 (99.00%)
1 day, 20:35:13.973038 PROGRESS: Decoy precursors: 6 (1.00%)
1 day, 20:35:13.973086 PROGRESS: 
1 day, 20:35:13.973139 PROGRESS: Precursor Summary:
1 day, 20:35:13.974198 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:   591; 0.001 FDR:   509
1 day, 20:35:13.974291 PROGRESS: 
1 day, 20:35:13.974351 PROGRESS: Protein Summary:
1 day, 20:35:13.975621 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   534; 0.001 FDR:   468
1 day, 20:35:13.975714 PROGRESS: =========================================================================
1 day, 20:35:13.975864 INFO: Target number of precursors reached.
1 day, 20:35:13.982663 INFO: fragments_df: keeping 5000 of 35800 [sum(precursor_idx_mask)=18298 sum(mass_error_mask)=35800 stop_rank=5000
1 day, 20:35:13.986982 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:14.110913 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:14.232012 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:14.351546 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:14.971900 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:14.972325 INFO: Using score_cutoff 36.21162620544433 (fac=0.99, q=1)
1 day, 20:35:14.972643 INFO: Updating optimization_manager: fwhm_rt             : 2.7681097984313965 -> 2.7681097984313965
1 day, 20:35:14.972731 INFO: Updating optimization_manager: fwhm_mobility       : 0.008461957797408104 -> 0.008467677049338818
1 day, 20:35:14.972786 INFO: Updating optimization_manager: score_cutoff        : 36.96820518493652 -> 36.21162620544433
1 day, 20:35:14.972839 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:14.973889 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:14.975236 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:14.975996 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:14.978125 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:14.978232 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 20:35:14.980017 INFO: Updating optimization_manager: rt_error            : 13.500294699262021 -> 12.977056332513865
1 day, 20:35:14.980118 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 12.9771.
1 day, 20:35:14.980183 INFO: ==============================================
1 day, 20:35:14.980247 INFO: Starting optimization step 6.
1 day, 20:35:14.980306 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:35:14.980357 INFO: Using classic extraction backend
1 day, 20:35:14.980493 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:35:14.980559 INFO: === Search parameters used ===
1 day, 20:35:14.980606 INFO: rt_error       : 12.977056332513865
1 day, 20:35:14.980649 INFO: mobility_error : 0.1
1 day, 20:35:14.980692 INFO: num_candidates : 3
1 day, 20:35:14.980733 INFO: ms1_error      : 7.5754825
1 day, 20:35:14.980773 INFO: ms2_error      : 17.494642
1 day, 20:35:14.980820 INFO: fwhm_rt        : 2.7681097984313965
1 day, 20:35:14.980861 INFO: quant_window   : 3
1 day, 20:35:14.980900 INFO: ==============================================
1 day, 20:35:14.981706 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:14.981754 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:14.981787 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 20:35:14.981810 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 20:35:14.982487 INFO: Starting candidate selection
1 day, 20:35:15.485129 INFO: Starting candidate scoring
1 day, 20:35:15.709074 INFO: Finished candidate processing
1 day, 20:35:15.709234 INFO: Collecting candidate features
1 day, 20:35:15.737258 INFO: Collecting fragment features
1 day, 20:35:15.745348 INFO: Finished candidate scoring
1 day, 20:35:15.748314 INFO: performing precursor FDR with 47 features
1 day, 20:35:15.748411 INFO: Decoy channel: -1
1 day, 20:35:15.748467 INFO: Competetive: True
1 day, 20:35:15.754568 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:15.758691 INFO: Using random state 498866 for train-test-split
1 day, 20:35:15.775250 INFO: Test AUC: 0.796
1 day, 20:35:15.775345 INFO: Train AUC: 0.778
1 day, 20:35:15.775398 INFO: AUC difference: 2.23%
1 day, 20:35:15.998435 INFO: Resetting torch num_threads to 80
1 day, 20:35:15.998990 PROGRESS: === Extracted 3354 precursors and 35801 fragments ===
1 day, 20:35:15.999400 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:35:15.999949 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:16.000037 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:16.000095 PROGRESS: Target precursors: 594 (99.00%)
1 day, 20:35:16.000144 PROGRESS: Decoy precursors: 6 (1.00%)
1 day, 20:35:16.000189 PROGRESS: 
1 day, 20:35:16.000232 PROGRESS: Precursor Summary:
1 day, 20:35:16.001304 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:   593; 0.001 FDR:   553
1 day, 20:35:16.001399 PROGRESS: 
1 day, 20:35:16.001453 PROGRESS: Protein Summary:
1 day, 20:35:16.002706 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   536; 0.001 FDR:   505
1 day, 20:35:16.002799 PROGRESS: =========================================================================
1 day, 20:35:16.002984 INFO: Target number of precursors reached.
1 day, 20:35:16.009880 INFO: fragments_df: keeping 5000 of 35801 [sum(precursor_idx_mask)=18321 sum(mass_error_mask)=35801 stop_rank=5000
1 day, 20:35:16.014200 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:16.133980 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:16.260762 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:16.379248 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:16.989377 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:16.989816 INFO: Using score_cutoff 36.46922409667969 (fac=0.99, q=1)
1 day, 20:35:16.990124 INFO: Updating optimization_manager: fwhm_rt             : 2.7681097984313965 -> 2.765390634536743
1 day, 20:35:16.990202 INFO: Updating optimization_manager: fwhm_mobility       : 0.008467677049338818 -> 0.008539236150681973
1 day, 20:35:16.990257 INFO: Updating optimization_manager: score_cutoff        : 36.21162620544433 -> 36.46922409667969
1 day, 20:35:16.990309 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:16.991345 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:16.992672 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:16.993448 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:16.995564 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:16.995668 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 20:35:16.996576 INFO: Updating optimization_manager: rt_error            : 12.977056332513865 -> 12.977056332513865
1 day, 20:35:16.996702 INFO: Updating optimization_manager: classifier_version  : 6 -> 13
1 day, 20:35:16.996797 INFO: Updating optimization_manager: score_cutoff        : 36.46922409667969 -> 36.46922409667969
1 day, 20:35:16.996885 INFO: Updating optimization_manager: fwhm_rt             : 2.765390634536743 -> 2.765390634536743
1 day, 20:35:16.996977 INFO: Updating optimization_manager: fwhm_mobility       : 0.008539236150681973 -> 0.008539236150681973
1 day, 20:35:16.997064 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 12.9771 found after 7 searches.
1 day, 20:35:16.997127 INFO: ==============================================
1 day, 20:35:16.997189 PROGRESS: Optimization finished for rt_error.
1 day, 20:35:17.001064 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:17.001916 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:17.003217 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:17.003968 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:17.028842 INFO: Starting optimization step 0.
1 day, 20:35:17.028991 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:35:17.029059 INFO: Using classic extraction backend
1 day, 20:35:17.029174 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:35:17.029243 INFO: === Search parameters used ===
1 day, 20:35:17.029291 INFO: rt_error       : 12.977056332513865
1 day, 20:35:17.029335 INFO: mobility_error : 0.1
1 day, 20:35:17.029377 INFO: num_candidates : 3
1 day, 20:35:17.029418 INFO: ms1_error      : 7.5754825
1 day, 20:35:17.029457 INFO: ms2_error      : 17.494642
1 day, 20:35:17.029496 INFO: fwhm_rt        : 2.765390634536743
1 day, 20:35:17.029537 INFO: quant_window   : 3
1 day, 20:35:17.029576 INFO: ==============================================
1 day, 20:35:17.030414 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:17.030461 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:17.030495 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 20:35:17.030519 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.96
1 day, 20:35:17.031174 INFO: Starting candidate selection
1 day, 20:35:17.527815 INFO: Starting candidate scoring
1 day, 20:35:17.742151 INFO: Finished candidate processing
1 day, 20:35:17.742248 INFO: Collecting candidate features
1 day, 20:35:17.754300 INFO: Collecting fragment features
1 day, 20:35:17.757801 INFO: Finished candidate scoring
1 day, 20:35:17.759560 INFO: performing precursor FDR with 47 features
1 day, 20:35:17.759607 INFO: Decoy channel: -1
1 day, 20:35:17.759632 INFO: Competetive: True
1 day, 20:35:17.762456 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:17.764434 INFO: Using random state 166422 for train-test-split
1 day, 20:35:17.775277 INFO: Test AUC: 0.797
1 day, 20:35:17.775338 INFO: Train AUC: 0.781
1 day, 20:35:17.775368 INFO: AUC difference: 2.07%
1 day, 20:35:17.997046 INFO: Resetting torch num_threads to 80
1 day, 20:35:17.997603 PROGRESS: === Extracted 3349 precursors and 35746 fragments ===
1 day, 20:35:17.998007 INFO: === FDR correction performed with classifier version 13 ===
1 day, 20:35:17.998588 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:17.998676 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:17.998755 PROGRESS: Target precursors: 595 (99.17%)
1 day, 20:35:17.998809 PROGRESS: Decoy precursors: 5 (0.83%)
1 day, 20:35:17.998853 PROGRESS: 
1 day, 20:35:17.998896 PROGRESS: Precursor Summary:
1 day, 20:35:17.999939 PROGRESS: Channel   0:	 0.050 FDR:   595; 0.010 FDR:   595; 0.001 FDR:   554
1 day, 20:35:18.000029 PROGRESS: 
1 day, 20:35:18.000082 PROGRESS: Protein Summary:
1 day, 20:35:18.001359 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   538; 0.001 FDR:   506
1 day, 20:35:18.001452 PROGRESS: =========================================================================
1 day, 20:35:18.001584 INFO: Target number of precursors reached.
1 day, 20:35:18.008410 INFO: fragments_df: keeping 5000 of 35746 [sum(precursor_idx_mask)=18329 sum(mass_error_mask)=35746 stop_rank=5000
1 day, 20:35:18.012634 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:18.154638 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:18.301316 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:18.443177 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:19.063351 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:19.063784 INFO: Using score_cutoff 37.02618391799927 (fac=0.99, q=1)
1 day, 20:35:19.064090 INFO: Updating optimization_manager: fwhm_rt             : 2.765390634536743 -> 2.761733055114746
1 day, 20:35:19.064167 INFO: Updating optimization_manager: fwhm_mobility       : 0.008539236150681973 -> 0.008469853550195694
1 day, 20:35:19.064228 INFO: Updating optimization_manager: score_cutoff        : 36.46922409667969 -> 37.02618391799927
1 day, 20:35:19.064281 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:19.065349 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:19.066658 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:19.067412 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:19.069488 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:19.069585 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:35:19.070915 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07096139806910133
1 day, 20:35:19.071010 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0710.
1 day, 20:35:19.071072 INFO: ==============================================
1 day, 20:35:19.071136 INFO: Starting optimization step 1.
1 day, 20:35:19.071195 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:35:19.071248 INFO: Using classic extraction backend
1 day, 20:35:19.071351 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:35:19.071414 INFO: === Search parameters used ===
1 day, 20:35:19.071740 INFO: rt_error       : 12.977056332513865
1 day, 20:35:19.071783 INFO: mobility_error : 0.07096139806910133
1 day, 20:35:19.071824 INFO: num_candidates : 3
1 day, 20:35:19.071865 INFO: ms1_error      : 7.5754825
1 day, 20:35:19.071904 INFO: ms2_error      : 17.494642
1 day, 20:35:19.071962 INFO: fwhm_rt        : 2.761733055114746
1 day, 20:35:19.072002 INFO: quant_window   : 3
1 day, 20:35:19.072039 INFO: ==============================================
1 day, 20:35:19.072797 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:19.072841 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:19.072873 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 20:35:19.072894 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 20:35:19.073576 INFO: Starting candidate selection
1 day, 20:35:19.573845 INFO: Starting candidate scoring
1 day, 20:35:19.758813 INFO: Finished candidate processing
1 day, 20:35:19.759001 INFO: Collecting candidate features
1 day, 20:35:19.773284 INFO: Collecting fragment features
1 day, 20:35:19.777144 INFO: Finished candidate scoring
1 day, 20:35:19.779015 INFO: performing precursor FDR with 47 features
1 day, 20:35:19.779059 INFO: Decoy channel: -1
1 day, 20:35:19.779084 INFO: Competetive: True
1 day, 20:35:19.782059 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:19.784223 INFO: Using random state 166422 for train-test-split
1 day, 20:35:19.795127 INFO: Test AUC: 0.782
1 day, 20:35:19.795185 INFO: Train AUC: 0.785
1 day, 20:35:19.795213 INFO: AUC difference: 0.35%
1 day, 20:35:20.015616 INFO: Resetting torch num_threads to 80
1 day, 20:35:20.016160 PROGRESS: === Extracted 3339 precursors and 35436 fragments ===
1 day, 20:35:20.016570 INFO: === FDR correction performed with classifier version 13 ===
1 day, 20:35:20.017140 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:20.017232 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:20.017289 PROGRESS: Target precursors: 592 (98.67%)
1 day, 20:35:20.017338 PROGRESS: Decoy precursors: 8 (1.33%)
1 day, 20:35:20.017382 PROGRESS: 
1 day, 20:35:20.017426 PROGRESS: Precursor Summary:
1 day, 20:35:20.018466 PROGRESS: Channel   0:	 0.050 FDR:   592; 0.010 FDR:   586; 0.001 FDR:   532
1 day, 20:35:20.018556 PROGRESS: 
1 day, 20:35:20.018610 PROGRESS: Protein Summary:
1 day, 20:35:20.019866 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   533; 0.001 FDR:   488
1 day, 20:35:20.019956 PROGRESS: =========================================================================
1 day, 20:35:20.020121 INFO: Target number of precursors reached.
1 day, 20:35:20.026871 INFO: fragments_df: keeping 5000 of 35436 [sum(precursor_idx_mask)=18045 sum(mass_error_mask)=35436 stop_rank=5000
1 day, 20:35:20.031147 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:20.177876 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:20.322764 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:20.465601 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:21.140676 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:21.141123 INFO: Using score_cutoff 38.55063149642944 (fac=0.99, q=1)
1 day, 20:35:21.141437 INFO: Updating optimization_manager: fwhm_rt             : 2.761733055114746 -> 2.758025646209717
1 day, 20:35:21.141516 INFO: Updating optimization_manager: fwhm_mobility       : 0.008469853550195694 -> 0.008482375182211399
1 day, 20:35:21.141569 INFO: Updating optimization_manager: score_cutoff        : 37.02618391799927 -> 38.55063149642944
1 day, 20:35:21.141624 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:21.142655 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:21.143976 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:21.144727 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:21.146945 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:21.147050 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:35:21.148498 INFO: Updating optimization_manager: mobility_error      : 0.07096139806910133 -> 0.059171658515434655
1 day, 20:35:21.148595 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0592.
1 day, 20:35:21.148659 INFO: ==============================================
1 day, 20:35:21.148725 INFO: Starting optimization step 2.
1 day, 20:35:21.148780 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:35:21.148836 INFO: Using classic extraction backend
1 day, 20:35:21.148969 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:35:21.149040 INFO: === Search parameters used ===
1 day, 20:35:21.149088 INFO: rt_error       : 12.977056332513865
1 day, 20:35:21.149130 INFO: mobility_error : 0.059171658515434655
1 day, 20:35:21.149169 INFO: num_candidates : 3
1 day, 20:35:21.149208 INFO: ms1_error      : 7.5754825
1 day, 20:35:21.149246 INFO: ms2_error      : 17.494642
1 day, 20:35:21.149283 INFO: fwhm_rt        : 2.758025646209717
1 day, 20:35:21.149321 INFO: quant_window   : 3
1 day, 20:35:21.149359 INFO: ==============================================
1 day, 20:35:21.150741 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:21.150786 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:21.150818 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 20:35:21.150839 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 20:35:21.152148 INFO: Starting candidate selection
1 day, 20:35:21.639841 INFO: Starting candidate scoring
1 day, 20:35:21.848043 INFO: Finished candidate processing
1 day, 20:35:21.848145 INFO: Collecting candidate features
1 day, 20:35:21.858137 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3349)
1 day, 20:35:21.861281 INFO: Collecting fragment features
1 day, 20:35:21.864785 INFO: Finished candidate scoring
1 day, 20:35:21.866658 INFO: performing precursor FDR with 47 features
1 day, 20:35:21.866702 INFO: Decoy channel: -1
1 day, 20:35:21.866727 INFO: Competetive: True
1 day, 20:35:21.869863 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:21.871119 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 20:35:21.872218 INFO: Using random state 166422 for train-test-split
1 day, 20:35:21.883063 INFO: Test AUC: 0.756
1 day, 20:35:21.883126 INFO: Train AUC: 0.788
1 day, 20:35:21.883156 INFO: AUC difference: 4.06%
1 day, 20:35:22.102036 INFO: Resetting torch num_threads to 80
1 day, 20:35:22.103220 PROGRESS: === Extracted 3349 precursors and 35379 fragments ===
1 day, 20:35:22.103643 INFO: === FDR correction performed with classifier version 13 ===
1 day, 20:35:22.104200 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:22.104289 PROGRESS: Total precursors accumulated: 600
1 day, 20:35:22.104347 PROGRESS: Target precursors: 593 (98.83%)
1 day, 20:35:22.104395 PROGRESS: Decoy precursors: 7 (1.17%)
1 day, 20:35:22.104439 PROGRESS: 
1 day, 20:35:22.104481 PROGRESS: Precursor Summary:
1 day, 20:35:22.105538 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   584; 0.001 FDR:   540
1 day, 20:35:22.105629 PROGRESS: 
1 day, 20:35:22.105685 PROGRESS: Protein Summary:
1 day, 20:35:22.106949 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   531; 0.001 FDR:   496
1 day, 20:35:22.107050 PROGRESS: =========================================================================
1 day, 20:35:22.107227 INFO: Target number of precursors reached.
1 day, 20:35:22.113992 INFO: fragments_df: keeping 5000 of 35379 [sum(precursor_idx_mask)=17981 sum(mass_error_mask)=35379 stop_rank=5000
1 day, 20:35:22.118979 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:22.264311 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:22.408686 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:22.530166 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:23.145490 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:35:23.146330 INFO: Using score_cutoff 35.97563894348145 (fac=0.99, q=1)
1 day, 20:35:23.146723 INFO: Updating optimization_manager: fwhm_rt             : 2.758025646209717 -> 2.755237102508545
1 day, 20:35:23.146802 INFO: Updating optimization_manager: fwhm_mobility       : 0.008482375182211399 -> 0.008439784869551659
1 day, 20:35:23.146856 INFO: Updating optimization_manager: score_cutoff        : 38.55063149642944 -> 35.97563894348145
1 day, 20:35:23.146915 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:23.148470 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:23.149824 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:23.150589 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:23.152881 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:23.152989 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:35:23.153858 INFO: Updating optimization_manager: mobility_error      : 0.059171658515434655 -> 0.1
1 day, 20:35:23.153980 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
1 day, 20:35:23.154073 INFO: Updating optimization_manager: score_cutoff        : 35.97563894348145 -> 37.02618391799927
1 day, 20:35:23.154158 INFO: Updating optimization_manager: fwhm_rt             : 2.755237102508545 -> 2.761733055114746
1 day, 20:35:23.154242 INFO: Updating optimization_manager: fwhm_mobility       : 0.008439784869551659 -> 0.008469853550195694
1 day, 20:35:23.154327 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 20:35:23.154387 INFO: ==============================================
1 day, 20:35:23.154456 PROGRESS: Optimization finished for mobility_error.
1 day, 20:35:23.159268 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:23.160081 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:23.161386 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:23.162140 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:23.190014 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:35:23.190144 PROGRESS: ==============================================
1 day, 20:35:23.190217 PROGRESS: ms2_error      : 17.4946
1 day, 20:35:23.190275 PROGRESS: ms1_error      : 7.5755
1 day, 20:35:23.190330 PROGRESS: rt_error       : 12.9771
1 day, 20:35:23.190376 PROGRESS: mobility_error : 0.1000
1 day, 20:35:23.190420 PROGRESS: ==============================================
1 day, 20:35:23.191245 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:35:23.209982 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:35:23.291118 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:35:23.311077 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:35:23.531071 INFO: Using classic extraction backend
1 day, 20:35:23.531629 PROGRESS: Extracting batch of 146455 precursors
1 day, 20:35:23.531744 INFO: === Search parameters used ===
1 day, 20:35:23.531811 INFO: rt_error       : 12.977056332513865
1 day, 20:35:23.531868 INFO: mobility_error : 0.1
1 day, 20:35:23.531921 INFO: num_candidates : 3
1 day, 20:35:23.531973 INFO: ms1_error      : 7.5754825
1 day, 20:35:23.532023 INFO: ms2_error      : 17.494642
1 day, 20:35:23.532074 INFO: fwhm_rt        : 2.761733055114746
1 day, 20:35:23.532123 INFO: quant_window   : 3
1 day, 20:35:23.532175 INFO: ==============================================
1 day, 20:35:23.567990 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:23.568125 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:23.568182 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 20:35:23.568206 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 20:35:23.569021 INFO: Starting candidate selection
1 day, 20:35:34.960917 INFO: Removed 121573 precursors with score below cutoff 37.02618391799927
1 day, 20:35:35.297695 INFO: Starting candidate scoring
1 day, 20:35:48.391618 INFO: Finished candidate processing
1 day, 20:35:48.391783 INFO: Collecting candidate features
1 day, 20:35:48.791020 INFO: Collecting fragment features
1 day, 20:35:48.994247 INFO: Finished candidate scoring
1 day, 20:35:49.260185 INFO: === Performing FDR correction with classifier version 14 ===
1 day, 20:35:49.260964 INFO: performing precursor FDR with 47 features
1 day, 20:35:49.261000 INFO: Decoy channel: -1
1 day, 20:35:49.261024 INFO: Competetive: True
1 day, 20:35:49.327362 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:49.354748 WARNING: FDR calculation for 171734 target and 119050 decoy PSMs
1 day, 20:35:49.354885 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 20:35:49.433384 INFO: Using random state 857456 for train-test-split
1 day, 20:35:54.063978 INFO: Test AUC: 0.865
1 day, 20:35:54.064100 INFO: Train AUC: 0.869
1 day, 20:35:54.064135 INFO: AUC difference: 0.48%
1 day, 20:35:54.376333 INFO: Resetting torch num_threads to 80
1 day, 20:35:54.390120 INFO: Removing fragments below FDR threshold
1 day, 20:35:54.444505 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:54.444739 PROGRESS: Total precursors accumulated: 72,132
1 day, 20:35:54.444801 PROGRESS: Target precursors: 71,418 (99.01%)
1 day, 20:35:54.444866 PROGRESS: Decoy precursors: 714 (0.99%)
1 day, 20:35:54.444915 PROGRESS: 
1 day, 20:35:54.444968 PROGRESS: Precursor Summary:
1 day, 20:35:54.475138 PROGRESS: Channel   0:	 0.050 FDR: 71,418; 0.010 FDR: 71,418; 0.001 FDR: 69,168
1 day, 20:35:54.475391 PROGRESS: 
1 day, 20:35:54.475455 PROGRESS: Protein Summary:
1 day, 20:35:54.515129 PROGRESS: Channel   0:	 0.050 FDR: 7,419; 0.010 FDR: 7,419; 0.001 FDR: 7,402
1 day, 20:35:54.515363 PROGRESS: =========================================================================
1 day, 20:35:54.518680 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/psm.parquet
1 day, 20:35:54.814960 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/frag.parquet
1 day, 20:35:55.077320 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 20:35:55.110707 PROGRESS: 
1 day, 20:35:55.110845 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
1 day, 20:35:55.110912 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/figures
1 day, 20:35:55.111073 INFO: Initializing TimingManager
1 day, 20:35:55.111530 INFO: Initializing RawFileManager
1 day, 20:35:55.111634 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:35:55.111683 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:35:55.111720 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:35:55.309751 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, 20:36:03.177756 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
1 day, 20:36:03.180279 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:36:03.184551 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:36:03.185484 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:36:03.185988 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:36:03.187291 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:36:03.205379 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:36:03.205862 INFO: Indexing quadrupole dimension
1 day, 20:36:03.679298 INFO: Transposing detector events
1 day, 20:36:12.266995 INFO: Finished transposing data
1 day, 20:36:12.305763 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:36:12.306802 INFO: RT (min)            : 0.0 - 70.0
1 day, 20:36:12.306902 INFO: RT duration (sec)   : 4199.8
1 day, 20:36:12.306958 INFO: RT duration (min)   : 70.0
1 day, 20:36:12.307010 INFO: Cycle len (scans)   : 9
1 day, 20:36:12.307059 INFO: Cycle len (sec)     : 0.97
1 day, 20:36:12.307102 INFO: Number of cycles    : 4347
1 day, 20:36:12.307147 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 20:36:12.307240 INFO: Creating DIA data object took: 17.19559597969055
1 day, 20:36:12.349264 INFO: Initializing CalibrationManager
1 day, 20:36:12.349524 INFO: Setting up calibration estimators ..
1 day, 20:36:12.349587 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 20:36:12.349666 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, 20:36:12.349752 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 20:36:12.349808 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, 20:36:12.349861 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, 20:36:12.349922 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, 20:36:12.349969 INFO: Done setting up calibration estimators.
1 day, 20:36:12.350088 INFO: Initializing OptimizationManager
1 day, 20:36:12.350177 INFO: initial parameter: ms1_error = 30
1 day, 20:36:12.350221 INFO: initial parameter: ms2_error = 30
1 day, 20:36:12.350265 INFO: initial parameter: rt_error = 2099.891532
1 day, 20:36:12.350307 INFO: initial parameter: mobility_error = 0.1
1 day, 20:36:12.350347 INFO: initial parameter: num_candidates = 1
1 day, 20:36:12.350386 INFO: initial parameter: fwhm_rt = 5
1 day, 20:36:12.350427 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 20:36:12.350468 INFO: initial parameter: score_cutoff = 0
1 day, 20:36:12.350506 INFO: initial parameter: classifier_version = -1
1 day, 20:36:12.350580 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:36:12.350828 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 20:36:12.350859 INFO: Initializing FDRManager
1 day, 20:36:12.350897 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 20:36:12.368919 PROGRESS: Initializing spectral library: 73,677 target precursors potentially observable (0 removed)
1 day, 20:36:12.381374 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 20:36:12.381751 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 2099.891532
1 day, 20:36:12.381866 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 20:36:12.382037 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 20:36:12.382127 PROGRESS: Starting initial search for precursors.
1 day, 20:36:12.382205 INFO: Starting optimization step 0.
1 day, 20:36:12.382269 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 20:36:12.382336 INFO: Using classic extraction backend
1 day, 20:36:12.382531 PROGRESS: Extracting batch of 399 precursors
1 day, 20:36:12.382604 INFO: === Search parameters used ===
1 day, 20:36:12.382651 INFO: rt_error       : 2099.891532
1 day, 20:36:12.382693 INFO: mobility_error : 0.1
1 day, 20:36:12.382732 INFO: num_candidates : 1
1 day, 20:36:12.382771 INFO: ms1_error      : 30
1 day, 20:36:12.382812 INFO: ms2_error      : 30
1 day, 20:36:12.382849 INFO: fwhm_rt        : 5
1 day, 20:36:12.382888 INFO: quant_window   : 3
1 day, 20:36:12.382929 INFO: ==============================================
1 day, 20:36:12.383666 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:36:12.383710 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:36:12.383744 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:36:12.383765 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:36:12.384636 INFO: Starting candidate selection
1 day, 20:36:16.592530 INFO: Starting candidate scoring
1 day, 20:36:16.678709 INFO: Finished candidate processing
1 day, 20:36:16.678817 INFO: Collecting candidate features
1 day, 20:36:16.687927 INFO: Collecting fragment features
1 day, 20:36:16.689986 INFO: Finished candidate scoring
1 day, 20:36:16.690747 INFO: performing precursor FDR with 47 features
1 day, 20:36:16.690789 INFO: Decoy channel: -1
1 day, 20:36:16.690813 INFO: Competetive: True
1 day, 20:36:16.691980 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:36:16.694466 INFO: Using random state 523516 for train-test-split
1 day, 20:36:16.704038 INFO: Test AUC: 0.500
1 day, 20:36:16.704124 INFO: Train AUC: 0.500
1 day, 20:36:16.704179 INFO: AUC difference: 0.00%
1 day, 20:36:16.928857 INFO: Resetting torch num_threads to 80
1 day, 20:36:16.929319 PROGRESS: === Extracted 399 precursors and 4572 fragments ===
1 day, 20:36:16.929741 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:36:16.930303 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:36:16.930394 PROGRESS: Total precursors accumulated: 200
1 day, 20:36:16.930453 PROGRESS: Target precursors: 200 (100.00%)
1 day, 20:36:16.930502 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 20:36:16.930546 PROGRESS: 
1 day, 20:36:16.930590 PROGRESS: Precursor Summary:
1 day, 20:36:16.931554 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 20:36:16.931640 PROGRESS: 
1 day, 20:36:16.931694 PROGRESS: Protein Summary:
1 day, 20:36:16.932809 PROGRESS: Channel   0:	 0.050 FDR:   193; 0.010 FDR:   193; 0.001 FDR:   193
1 day, 20:36:16.932901 PROGRESS: =========================================================================
1 day, 20:36:16.933013 INFO: Target number of precursors reached.
1 day, 20:36:16.934894 INFO: fragments_df: keeping 1289 of 4572 [sum(precursor_idx_mask)=2287 sum(mass_error_mask)=4572 stop_rank=1289
1 day, 20:36:16.937773 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:36:17.035689 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:36:17.134604 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:36:17.230580 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:36:17.394310 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 20:36:17.394742 INFO: Using score_cutoff 49.534370724105834 (fac=0.99, q=1)
1 day, 20:36:17.395067 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.233485460281372
1 day, 20:36:17.395158 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010237797163426876
1 day, 20:36:17.395213 INFO: Updating optimization_manager: score_cutoff        : 0 -> 49.534370724105834
1 day, 20:36:17.395268 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:36:17.396217 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:36:17.397122 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:36:17.397800 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:36:17.398907 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 20:36:17.399005 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 20:36:17.399079 INFO: Starting optimization step 1.
1 day, 20:36:17.399137 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 20:36:17.399193 INFO: Using classic extraction backend
1 day, 20:36:17.399294 PROGRESS: Extracting batch of 399 precursors
1 day, 20:36:17.399354 INFO: === Search parameters used ===
1 day, 20:36:17.399400 INFO: rt_error       : 2099.891532
1 day, 20:36:17.399441 INFO: mobility_error : 0.1
1 day, 20:36:17.399479 INFO: num_candidates : 3
1 day, 20:36:17.399519 INFO: ms1_error      : 30
1 day, 20:36:17.399559 INFO: ms2_error      : 30
1 day, 20:36:17.399596 INFO: fwhm_rt        : 3.233485460281372
1 day, 20:36:17.399635 INFO: quant_window   : 3
1 day, 20:36:17.399673 INFO: ==============================================
1 day, 20:36:17.400311 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:36:17.400355 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:36:17.400395 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
1 day, 20:36:17.400421 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.75
1 day, 20:36:17.401065 INFO: Starting candidate selection
1 day, 20:36:21.711029 INFO: Starting candidate scoring
1 day, 20:36:21.856670 INFO: Finished candidate processing
1 day, 20:36:21.856770 INFO: Collecting candidate features
1 day, 20:36:21.866994 INFO: Collecting fragment features
1 day, 20:36:21.870565 INFO: Finished candidate scoring
1 day, 20:36:21.871445 INFO: performing precursor FDR with 47 features
1 day, 20:36:21.871487 INFO: Decoy channel: -1
1 day, 20:36:21.871511 INFO: Competetive: True
1 day, 20:36:21.873983 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:36:21.875667 INFO: Using random state 191519 for train-test-split
1 day, 20:36:21.882918 INFO: Test AUC: 0.500
1 day, 20:36:21.882977 INFO: Train AUC: 0.500
1 day, 20:36:21.883007 INFO: AUC difference: 0.00%
1 day, 20:36:22.112411 INFO: Resetting torch num_threads to 80
1 day, 20:36:22.112869 PROGRESS: === Extracted 1139 precursors and 13015 fragments ===
1 day, 20:36:22.113292 INFO: === FDR correction performed with classifier version 0 ===
1 day, 20:36:22.113846 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:36:22.113938 PROGRESS: Total precursors accumulated: 200
1 day, 20:36:22.113997 PROGRESS: Target precursors: 200 (100.00%)
1 day, 20:36:22.114048 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 20:36:22.114093 PROGRESS: 
1 day, 20:36:22.114137 PROGRESS: Precursor Summary:
1 day, 20:36:22.115086 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1 day, 20:36:22.115176 PROGRESS: 
1 day, 20:36:22.115232 PROGRESS: Protein Summary:
1 day, 20:36:22.116326 PROGRESS: Channel   0:	 0.050 FDR:   193; 0.010 FDR:   193; 0.001 FDR:   193
1 day, 20:36:22.116416 PROGRESS: =========================================================================
1 day, 20:36:22.116558 INFO: Target number of precursors reached.
1 day, 20:36:22.119676 INFO: fragments_df: keeping 2488 of 13015 [sum(precursor_idx_mask)=6556 sum(mass_error_mask)=13015 stop_rank=2488
1 day, 20:36:22.122604 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:36:22.235257 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:36:22.349412 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:36:22.465913 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:36:22.803223 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:36:22.803652 INFO: Using score_cutoff 50.11087411766052 (fac=0.99, q=1)
1 day, 20:36:22.803949 INFO: Updating optimization_manager: fwhm_rt             : 3.233485460281372 -> 3.1455864906311035
1 day, 20:36:22.804037 INFO: Updating optimization_manager: fwhm_mobility       : 0.010237797163426876 -> 0.010118741542100906
1 day, 20:36:22.804090 INFO: Updating optimization_manager: score_cutoff        : 49.534370724105834 -> 50.11087411766052
1 day, 20:36:22.804141 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:36:22.805120 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:36:22.806014 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:36:22.806701 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:36:22.807816 INFO: === checking if optimization conditions were reached ===
1 day, 20:36:22.809081 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.494642
1 day, 20:36:22.809179 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
1 day, 20:36:22.809240 PROGRESS: ❌ ms2_error      : 17.4946 > 17.4946 or insufficient steps taken.
1 day, 20:36:22.810141 INFO: Updating optimization_manager: ms1_error           : 30 -> 9.826846534238971
1 day, 20:36:22.810235 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
1 day, 20:36:22.810297 PROGRESS: ❌ ms1_error      : 9.8268 > 7.5755 or insufficient steps taken.
1 day, 20:36:22.810351 INFO: ==============================================
1 day, 20:36:22.810413 INFO: Starting optimization step 2.
1 day, 20:36:22.810467 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 20:36:22.810518 INFO: Using classic extraction backend
1 day, 20:36:22.810618 PROGRESS: Extracting batch of 399 precursors
1 day, 20:36:22.810678 INFO: === Search parameters used ===
1 day, 20:36:22.810723 INFO: rt_error       : 2099.891532
1 day, 20:36:22.810765 INFO: mobility_error : 0.1
1 day, 20:36:22.810805 INFO: num_candidates : 3
1 day, 20:36:22.810844 INFO: ms1_error      : 9.826846534238971
1 day, 20:36:22.810884 INFO: ms2_error      : 17.494642
1 day, 20:36:22.810923 INFO: fwhm_rt        : 3.1455864906311035
1 day, 20:36:22.810967 INFO: quant_window   : 3
1 day, 20:36:22.811008 INFO: ==============================================
1 day, 20:36:22.811648 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:36:22.811692 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:36:22.811723 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
1 day, 20:36:22.811744 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.69
1 day, 20:36:22.812436 INFO: Starting candidate selection
1 day, 20:36:26.851802 INFO: Starting candidate scoring
1 day, 20:36:26.977043 INFO: Finished candidate processing
1 day, 20:36:26.977177 INFO: Collecting candidate features
1 day, 20:36:26.995494 INFO: Collecting fragment features
1 day, 20:36:27.003796 INFO: Finished candidate scoring
1 day, 20:36:27.005370 INFO: performing precursor FDR with 47 features
1 day, 20:36:27.005468 INFO: Decoy channel: -1
1 day, 20:36:27.005524 INFO: Competetive: True
1 day, 20:36:27.010535 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:36:27.013140 INFO: Using random state 642700 for train-test-split
1 day, 20:36:27.024404 INFO: Test AUC: 0.500
1 day, 20:36:27.024490 INFO: Train AUC: 0.497
1 day, 20:36:27.024540 INFO: AUC difference: 0.65%
1 day, 20:36:27.232251 INFO: Resetting torch num_threads to 80
1 day, 20:36:27.232692 PROGRESS: === Extracted 1134 precursors and 12713 fragments ===
1 day, 20:36:27.233110 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:36:27.233658 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:36:27.233753 PROGRESS: Total precursors accumulated: 200
1 day, 20:36:27.233815 PROGRESS: Target precursors: 197 (98.50%)
1 day, 20:36:27.233866 PROGRESS: Decoy precursors: 3 (1.50%)
1 day, 20:36:27.233911 PROGRESS: 
1 day, 20:36:27.233955 PROGRESS: Precursor Summary:
1 day, 20:36:27.234798 PROGRESS: Channel   0:	 0.050 FDR:   197; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:36:27.234884 PROGRESS: 
1 day, 20:36:27.234937 PROGRESS: Protein Summary:
1 day, 20:36:27.235883 PROGRESS: Channel   0:	 0.050 FDR:   190; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:36:27.235972 PROGRESS: =========================================================================
1 day, 20:36:27.236106 INFO: Target number of precursors not reached yet.
1 day, 20:36:27.240186 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:36:27.241104 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:36:27.242203 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:36:27.242928 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:36:27.244517 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:36:27.244637 INFO: Starting optimization step 3.
1 day, 20:36:27.244703 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 20:36:27.244762 INFO: Using classic extraction backend
1 day, 20:36:27.244865 PROGRESS: Extracting batch of 795 precursors
1 day, 20:36:27.244931 INFO: === Search parameters used ===
1 day, 20:36:27.244992 INFO: rt_error       : 2099.891532
1 day, 20:36:27.245035 INFO: mobility_error : 0.1
1 day, 20:36:27.245077 INFO: num_candidates : 3
1 day, 20:36:27.245117 INFO: ms1_error      : 9.826846534238971
1 day, 20:36:27.245158 INFO: ms2_error      : 17.494642
1 day, 20:36:27.245197 INFO: fwhm_rt        : 3.1455864906311035
1 day, 20:36:27.245234 INFO: quant_window   : 3
1 day, 20:36:27.245274 INFO: ==============================================
1 day, 20:36:27.245888 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:36:27.245931 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:36:27.245966 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
1 day, 20:36:27.245988 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.69
1 day, 20:36:27.246675 INFO: Starting candidate selection
1 day, 20:36:33.764157 INFO: Starting candidate scoring
1 day, 20:36:33.952247 INFO: Finished candidate processing
1 day, 20:36:33.952383 INFO: Collecting candidate features
1 day, 20:36:33.964978 INFO: Collecting fragment features
1 day, 20:36:33.969096 INFO: Finished candidate scoring
1 day, 20:36:33.971779 INFO: performing precursor FDR with 47 features
1 day, 20:36:33.971826 INFO: Decoy channel: -1
1 day, 20:36:33.971851 INFO: Competetive: True
1 day, 20:36:33.975318 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:36:33.977558 INFO: Using random state 642700 for train-test-split
1 day, 20:36:33.987398 INFO: Test AUC: 0.495
1 day, 20:36:33.987455 INFO: Train AUC: 0.499
1 day, 20:36:33.987484 INFO: AUC difference: 0.70%
1 day, 20:36:34.195861 INFO: Resetting torch num_threads to 80
1 day, 20:36:34.197275 PROGRESS: === Extracted 3376 precursors and 37525 fragments ===
1 day, 20:36:34.197685 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:36:34.198262 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:36:34.198352 PROGRESS: Total precursors accumulated: 600
1 day, 20:36:34.198410 PROGRESS: Target precursors: 592 (98.67%)
1 day, 20:36:34.198461 PROGRESS: Decoy precursors: 8 (1.33%)
1 day, 20:36:34.198513 PROGRESS: 
1 day, 20:36:34.198557 PROGRESS: Precursor Summary:
1 day, 20:36:34.199470 PROGRESS: Channel   0:	 0.050 FDR:   592; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 20:36:34.199562 PROGRESS: 
1 day, 20:36:34.199622 PROGRESS: Protein Summary:
1 day, 20:36:34.200661 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 20:36:34.200754 PROGRESS: =========================================================================
1 day, 20:36:34.201410 INFO: Target number of precursors not reached yet.
1 day, 20:36:34.205773 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:36:34.206777 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:36:34.208287 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:36:34.209116 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:36:34.212533 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:36:34.212652 INFO: Starting optimization step 4.
1 day, 20:36:34.212718 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 20:36:34.212780 INFO: Using classic extraction backend
1 day, 20:36:34.212885 PROGRESS: Extracting batch of 1588 precursors
1 day, 20:36:34.212962 INFO: === Search parameters used ===
1 day, 20:36:34.213016 INFO: rt_error       : 2099.891532
1 day, 20:36:34.213062 INFO: mobility_error : 0.1
1 day, 20:36:34.213104 INFO: num_candidates : 3
1 day, 20:36:34.213145 INFO: ms1_error      : 9.826846534238971
1 day, 20:36:34.213186 INFO: ms2_error      : 17.494642
1 day, 20:36:34.213235 INFO: fwhm_rt        : 3.1455864906311035
1 day, 20:36:34.213277 INFO: quant_window   : 3
1 day, 20:36:34.213316 INFO: ==============================================
1 day, 20:36:34.214040 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:36:34.214084 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:36:34.214118 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
1 day, 20:36:34.214142 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.69
1 day, 20:36:34.214813 INFO: Starting candidate selection
1 day, 20:36:45.932084 INFO: Starting candidate scoring
1 day, 20:36:46.227226 INFO: Finished candidate processing
1 day, 20:36:46.227478 INFO: Collecting candidate features
1 day, 20:36:46.243144 INFO: Collecting fragment features
1 day, 20:36:46.248060 INFO: Finished candidate scoring
1 day, 20:36:46.253856 INFO: performing precursor FDR with 47 features
1 day, 20:36:46.253911 INFO: Decoy channel: -1
1 day, 20:36:46.253937 INFO: Competetive: True
1 day, 20:36:46.258830 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:36:46.261945 INFO: Using random state 642700 for train-test-split
1 day, 20:36:46.279207 INFO: Test AUC: 0.500
1 day, 20:36:46.279283 INFO: Train AUC: 0.500
1 day, 20:36:46.279314 INFO: AUC difference: 0.06%
1 day, 20:36:46.501643 INFO: Resetting torch num_threads to 80
1 day, 20:36:46.503680 PROGRESS: === Extracted 7863 precursors and 87134 fragments ===
1 day, 20:36:46.504149 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:36:46.504777 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:36:46.504868 PROGRESS: Total precursors accumulated: 1,400
1 day, 20:36:46.504930 PROGRESS: Target precursors: 1,385 (98.93%)
1 day, 20:36:46.505007 PROGRESS: Decoy precursors: 15 (1.07%)
1 day, 20:36:46.505069 PROGRESS: 
1 day, 20:36:46.505126 PROGRESS: Precursor Summary:
1 day, 20:36:46.506118 PROGRESS: Channel   0:	 0.050 FDR: 1,385; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:36:46.506210 PROGRESS: 
1 day, 20:36:46.506266 PROGRESS: Protein Summary:
1 day, 20:36:46.507454 PROGRESS: Channel   0:	 0.050 FDR: 1,145; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:36:46.507545 PROGRESS: =========================================================================
1 day, 20:36:46.507719 INFO: Target number of precursors not reached yet.
1 day, 20:36:46.516574 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:36:46.517941 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:36:46.520331 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:36:46.521350 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:36:46.526739 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:36:46.526883 INFO: Starting optimization step 5.
1 day, 20:36:46.526950 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 20:36:46.527017 INFO: Using classic extraction backend
1 day, 20:36:46.527167 PROGRESS: Extracting batch of 3184 precursors
1 day, 20:36:46.527245 INFO: === Search parameters used ===
1 day, 20:36:46.527295 INFO: rt_error       : 2099.891532
1 day, 20:36:46.527340 INFO: mobility_error : 0.1
1 day, 20:36:46.527383 INFO: num_candidates : 3
1 day, 20:36:46.527423 INFO: ms1_error      : 9.826846534238971
1 day, 20:36:46.527463 INFO: ms2_error      : 17.494642
1 day, 20:36:46.527505 INFO: fwhm_rt        : 3.1455864906311035
1 day, 20:36:46.527545 INFO: quant_window   : 3
1 day, 20:36:46.527585 INFO: ==============================================
1 day, 20:36:46.528655 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:36:46.528703 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:36:46.528745 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
1 day, 20:36:46.528769 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.69
1 day, 20:36:46.529540 INFO: Starting candidate selection
1 day, 20:37:07.155885 INFO: Starting candidate scoring
1 day, 20:37:07.658231 INFO: Finished candidate processing
1 day, 20:37:07.658340 INFO: Collecting candidate features
1 day, 20:37:07.685600 INFO: Collecting fragment features
1 day, 20:37:07.694607 INFO: Finished candidate scoring
1 day, 20:37:07.702926 INFO: performing precursor FDR with 47 features
1 day, 20:37:07.703005 INFO: Decoy channel: -1
1 day, 20:37:07.703031 INFO: Competetive: True
1 day, 20:37:07.708980 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:37:07.713547 INFO: Using random state 642700 for train-test-split
1 day, 20:37:07.863082 INFO: Test AUC: 0.683
1 day, 20:37:07.863183 INFO: Train AUC: 0.671
1 day, 20:37:07.863213 INFO: AUC difference: 1.85%
1 day, 20:37:08.086027 INFO: Resetting torch num_threads to 80
1 day, 20:37:08.089163 PROGRESS: === Extracted 16897 precursors and 187519 fragments ===
1 day, 20:37:08.089613 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:37:08.090442 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:37:08.090537 PROGRESS: Total precursors accumulated: 3,000
1 day, 20:37:08.090596 PROGRESS: Target precursors: 2,513 (83.77%)
1 day, 20:37:08.090648 PROGRESS: Decoy precursors: 487 (16.23%)
1 day, 20:37:08.090704 PROGRESS: 
1 day, 20:37:08.090749 PROGRESS: Precursor Summary:
1 day, 20:37:08.091573 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:37:08.091659 PROGRESS: 
1 day, 20:37:08.091712 PROGRESS: Protein Summary:
1 day, 20:37:08.092609 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 20:37:08.092695 PROGRESS: =========================================================================
1 day, 20:37:08.093095 INFO: Target number of precursors not reached yet.
1 day, 20:37:08.102511 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:37:08.104086 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:37:08.108445 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:37:08.109838 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:37:08.118646 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:37:08.118785 INFO: Starting optimization step 6.
1 day, 20:37:08.118851 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 20:37:08.118913 INFO: Using classic extraction backend
1 day, 20:37:08.119023 PROGRESS: Extracting batch of 6376 precursors
1 day, 20:37:08.119093 INFO: === Search parameters used ===
1 day, 20:37:08.119141 INFO: rt_error       : 2099.891532
1 day, 20:37:08.119184 INFO: mobility_error : 0.1
1 day, 20:37:08.119226 INFO: num_candidates : 3
1 day, 20:37:08.119280 INFO: ms1_error      : 9.826846534238971
1 day, 20:37:08.119323 INFO: ms2_error      : 17.494642
1 day, 20:37:08.119370 INFO: fwhm_rt        : 3.1455864906311035
1 day, 20:37:08.119410 INFO: quant_window   : 3
1 day, 20:37:08.119450 INFO: ==============================================
1 day, 20:37:08.120847 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:37:08.120892 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:37:08.120928 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
1 day, 20:37:08.120961 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.69
1 day, 20:37:08.121604 INFO: Starting candidate selection
1 day, 20:37:47.164925 INFO: Starting candidate scoring
1 day, 20:37:48.136728 INFO: Finished candidate processing
1 day, 20:37:48.136896 INFO: Collecting candidate features
1 day, 20:37:48.200450 INFO: Collecting fragment features
1 day, 20:37:48.219570 INFO: Finished candidate scoring
1 day, 20:37:48.239602 INFO: performing precursor FDR with 47 features
1 day, 20:37:48.239720 INFO: Decoy channel: -1
1 day, 20:37:48.239745 INFO: Competetive: True
1 day, 20:37:48.251715 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:37:48.260463 INFO: Using random state 642700 for train-test-split
1 day, 20:37:48.680604 INFO: Test AUC: 0.735
1 day, 20:37:48.680715 INFO: Train AUC: 0.737
1 day, 20:37:48.680746 INFO: AUC difference: 0.22%
1 day, 20:37:48.920634 INFO: Resetting torch num_threads to 80
1 day, 20:37:48.925615 PROGRESS: === Extracted 34977 precursors and 389208 fragments ===
1 day, 20:37:48.926163 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:37:48.927386 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:37:48.927482 PROGRESS: Total precursors accumulated: 6,199
1 day, 20:37:48.927543 PROGRESS: Target precursors: 5,803 (93.61%)
1 day, 20:37:48.927593 PROGRESS: Decoy precursors: 396 (6.39%)
1 day, 20:37:48.927641 PROGRESS: 
1 day, 20:37:48.927684 PROGRESS: Precursor Summary:
1 day, 20:37:48.930017 PROGRESS: Channel   0:	 0.050 FDR: 5,674; 0.010 FDR: 4,380; 0.001 FDR: 1,407
1 day, 20:37:48.930121 PROGRESS: 
1 day, 20:37:48.930177 PROGRESS: Protein Summary:
1 day, 20:37:48.932983 PROGRESS: Channel   0:	 0.050 FDR: 3,274; 0.010 FDR: 2,689; 0.001 FDR: 1,074
1 day, 20:37:48.933079 PROGRESS: =========================================================================
1 day, 20:37:48.933581 INFO: Target number of precursors reached.
1 day, 20:37:49.004503 INFO: fragments_df: keeping 5000 of 389208 [sum(precursor_idx_mask)=138972 sum(mass_error_mask)=389208 stop_rank=5000
1 day, 20:37:49.013992 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:37:49.528724 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:37:50.058956 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:37:50.577456 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:37:51.189494 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:37:51.189952 INFO: Using score_cutoff 46.479556391143795 (fac=0.99, q=1)
1 day, 20:37:51.190398 INFO: Updating optimization_manager: fwhm_rt             : 3.1455864906311035 -> 2.9500670433044434
1 day, 20:37:51.190483 INFO: Updating optimization_manager: fwhm_mobility       : 0.010118741542100906 -> 0.009236378595232964
1 day, 20:37:51.190537 INFO: Updating optimization_manager: score_cutoff        : 50.11087411766052 -> 46.479556391143795
1 day, 20:37:51.190594 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:37:51.191603 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:37:51.192921 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:37:51.193692 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:37:51.195837 INFO: === checking if optimization conditions were reached ===
1 day, 20:37:51.197395 INFO: Updating optimization_manager: ms2_error           : 17.494642 -> 17.494642
1 day, 20:37:51.197494 INFO: Updating optimization_manager: classifier_version  : 1 -> 6
1 day, 20:37:51.197565 PROGRESS: ✅ ms2_error      : 17.4946 <= 17.4946
1 day, 20:37:51.199020 INFO: Updating optimization_manager: ms1_error           : 9.826846534238971 -> 7.5754825
1 day, 20:37:51.199116 INFO: Updating optimization_manager: classifier_version  : 6 -> 6
1 day, 20:37:51.199177 PROGRESS: ✅ ms1_error      : 7.5755 <= 7.5755
1 day, 20:37:51.199237 INFO: ==============================================
1 day, 20:37:51.199311 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 20:37:51.203186 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:37:51.203983 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:37:51.205288 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:37:51.206028 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:37:51.208136 INFO: Starting optimization step 0.
1 day, 20:37:51.208231 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:37:51.208298 INFO: Using classic extraction backend
1 day, 20:37:51.208454 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:37:51.208523 INFO: === Search parameters used ===
1 day, 20:37:51.208572 INFO: rt_error       : 2099.891532
1 day, 20:37:51.208614 INFO: mobility_error : 0.1
1 day, 20:37:51.208655 INFO: num_candidates : 3
1 day, 20:37:51.208694 INFO: ms1_error      : 7.5754825
1 day, 20:37:51.208733 INFO: ms2_error      : 17.494642
1 day, 20:37:51.208771 INFO: fwhm_rt        : 2.9500670433044434
1 day, 20:37:51.208809 INFO: quant_window   : 3
1 day, 20:37:51.208850 INFO: ==============================================
1 day, 20:37:51.209652 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:37:51.209698 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:37:51.209739 INFO: FWHM in RT is 2.95 seconds, sigma is 0.65
1 day, 20:37:51.209761 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.28
1 day, 20:37:51.210405 INFO: Starting candidate selection
1 day, 20:38:00.077493 INFO: Starting candidate scoring
1 day, 20:38:00.292254 INFO: Finished candidate processing
1 day, 20:38:00.292384 INFO: Collecting candidate features
1 day, 20:38:00.306313 INFO: Collecting fragment features
1 day, 20:38:00.310152 INFO: Finished candidate scoring
1 day, 20:38:00.311995 INFO: performing precursor FDR with 47 features
1 day, 20:38:00.312039 INFO: Decoy channel: -1
1 day, 20:38:00.312064 INFO: Competetive: True
1 day, 20:38:00.315290 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:00.317632 INFO: Using random state 819915 for train-test-split
1 day, 20:38:00.328893 INFO: Test AUC: 0.725
1 day, 20:38:00.328960 INFO: Train AUC: 0.738
1 day, 20:38:00.328992 INFO: AUC difference: 1.82%
1 day, 20:38:00.545056 INFO: Resetting torch num_threads to 80
1 day, 20:38:00.545562 PROGRESS: === Extracted 3402 precursors and 37800 fragments ===
1 day, 20:38:00.545974 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:38:00.546552 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:00.546642 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:00.546699 PROGRESS: Target precursors: 567 (94.50%)
1 day, 20:38:00.546747 PROGRESS: Decoy precursors: 33 (5.50%)
1 day, 20:38:00.546790 PROGRESS: 
1 day, 20:38:00.546833 PROGRESS: Precursor Summary:
1 day, 20:38:00.547838 PROGRESS: Channel   0:	 0.050 FDR:   562; 0.010 FDR:   510; 0.001 FDR:   336
1 day, 20:38:00.547930 PROGRESS: 
1 day, 20:38:00.547985 PROGRESS: Protein Summary:
1 day, 20:38:00.549191 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   462; 0.001 FDR:   318
1 day, 20:38:00.549285 PROGRESS: =========================================================================
1 day, 20:38:00.549582 INFO: Target number of precursors reached.
1 day, 20:38:00.556187 INFO: fragments_df: keeping 5000 of 37800 [sum(precursor_idx_mask)=16217 sum(mass_error_mask)=37800 stop_rank=5000
1 day, 20:38:00.560453 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:00.672446 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:00.790702 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:00.909821 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:01.538755 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:01.539178 INFO: Using score_cutoff 42.600857512664795 (fac=0.99, q=1)
1 day, 20:38:01.539480 INFO: Updating optimization_manager: fwhm_rt             : 2.9500670433044434 -> 2.9295096397399902
1 day, 20:38:01.539565 INFO: Updating optimization_manager: fwhm_mobility       : 0.009236378595232964 -> 0.008878725580871105
1 day, 20:38:01.539618 INFO: Updating optimization_manager: score_cutoff        : 46.479556391143795 -> 42.600857512664795
1 day, 20:38:01.539670 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:01.540698 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:01.542022 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:01.542778 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:01.544834 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:01.544950 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:38:01.546542 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 194.125969405871
1 day, 20:38:01.546639 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 194.1260.
1 day, 20:38:01.546702 INFO: ==============================================
1 day, 20:38:01.546767 INFO: Starting optimization step 1.
1 day, 20:38:01.546819 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:38:01.546873 INFO: Using classic extraction backend
1 day, 20:38:01.546969 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:38:01.547031 INFO: === Search parameters used ===
1 day, 20:38:01.547078 INFO: rt_error       : 194.125969405871
1 day, 20:38:01.547117 INFO: mobility_error : 0.1
1 day, 20:38:01.547158 INFO: num_candidates : 3
1 day, 20:38:01.547205 INFO: ms1_error      : 7.5754825
1 day, 20:38:01.547246 INFO: ms2_error      : 17.494642
1 day, 20:38:01.547283 INFO: fwhm_rt        : 2.9295096397399902
1 day, 20:38:01.547321 INFO: quant_window   : 3
1 day, 20:38:01.547359 INFO: ==============================================
1 day, 20:38:01.548127 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:01.548173 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:01.548205 INFO: FWHM in RT is 2.93 seconds, sigma is 0.64
1 day, 20:38:01.548226 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 20:38:01.548869 INFO: Starting candidate selection
1 day, 20:38:03.024684 INFO: Starting candidate scoring
1 day, 20:38:03.217963 INFO: Finished candidate processing
1 day, 20:38:03.218060 INFO: Collecting candidate features
1 day, 20:38:03.231546 INFO: Collecting fragment features
1 day, 20:38:03.241199 INFO: Finished candidate scoring
1 day, 20:38:03.244020 INFO: performing precursor FDR with 47 features
1 day, 20:38:03.244125 INFO: Decoy channel: -1
1 day, 20:38:03.244190 INFO: Competetive: True
1 day, 20:38:03.249947 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:03.253126 INFO: Using random state 819915 for train-test-split
1 day, 20:38:03.269523 INFO: Test AUC: 0.758
1 day, 20:38:03.269614 INFO: Train AUC: 0.762
1 day, 20:38:03.269662 INFO: AUC difference: 0.46%
1 day, 20:38:03.490396 INFO: Resetting torch num_threads to 80
1 day, 20:38:03.490922 PROGRESS: === Extracted 3380 precursors and 37015 fragments ===
1 day, 20:38:03.491334 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:38:03.491913 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:03.492002 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:03.492828 PROGRESS: Target precursors: 576 (96.00%)
1 day, 20:38:03.492883 PROGRESS: Decoy precursors: 24 (4.00%)
1 day, 20:38:03.492929 PROGRESS: 
1 day, 20:38:03.492994 PROGRESS: Precursor Summary:
1 day, 20:38:03.494039 PROGRESS: Channel   0:	 0.050 FDR:   576; 0.010 FDR:   526; 0.001 FDR:   450
1 day, 20:38:03.494130 PROGRESS: 
1 day, 20:38:03.494185 PROGRESS: Protein Summary:
1 day, 20:38:03.495432 PROGRESS: Channel   0:	 0.050 FDR:   523; 0.010 FDR:   477; 0.001 FDR:   412
1 day, 20:38:03.495527 PROGRESS: =========================================================================
1 day, 20:38:03.495654 INFO: Target number of precursors reached.
1 day, 20:38:03.502203 INFO: fragments_df: keeping 5000 of 37015 [sum(precursor_idx_mask)=16588 sum(mass_error_mask)=37015 stop_rank=5000
1 day, 20:38:03.506456 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:03.618072 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:03.737810 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:03.858875 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:04.491589 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:04.492012 INFO: Using score_cutoff 41.566209926605225 (fac=0.99, q=1)
1 day, 20:38:04.492322 INFO: Updating optimization_manager: fwhm_rt             : 2.9295096397399902 -> 2.863511562347412
1 day, 20:38:04.492405 INFO: Updating optimization_manager: fwhm_mobility       : 0.008878725580871105 -> 0.0087879728525877
1 day, 20:38:04.492459 INFO: Updating optimization_manager: score_cutoff        : 42.600857512664795 -> 41.566209926605225
1 day, 20:38:04.492510 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:04.493543 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:04.494866 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:04.495631 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:04.498156 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:04.498257 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:38:04.499945 INFO: Updating optimization_manager: rt_error            : 194.125969405871 -> 37.0839524736676
1 day, 20:38:04.500044 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 37.0840.
1 day, 20:38:04.500108 INFO: ==============================================
1 day, 20:38:04.500174 INFO: Starting optimization step 2.
1 day, 20:38:04.500240 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:38:04.500297 INFO: Using classic extraction backend
1 day, 20:38:04.500398 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:38:04.500462 INFO: === Search parameters used ===
1 day, 20:38:04.500514 INFO: rt_error       : 37.0839524736676
1 day, 20:38:04.500556 INFO: mobility_error : 0.1
1 day, 20:38:04.500601 INFO: num_candidates : 3
1 day, 20:38:04.500643 INFO: ms1_error      : 7.5754825
1 day, 20:38:04.500684 INFO: ms2_error      : 17.494642
1 day, 20:38:04.500723 INFO: fwhm_rt        : 2.863511562347412
1 day, 20:38:04.500762 INFO: quant_window   : 3
1 day, 20:38:04.500802 INFO: ==============================================
1 day, 20:38:04.501689 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:04.501736 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:04.501770 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:38:04.501794 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.08
1 day, 20:38:04.502709 INFO: Starting candidate selection
1 day, 20:38:05.087655 INFO: Starting candidate scoring
1 day, 20:38:05.284822 INFO: Finished candidate processing
1 day, 20:38:05.285620 INFO: Collecting candidate features
1 day, 20:38:05.299213 INFO: Collecting fragment features
1 day, 20:38:05.302857 INFO: Finished candidate scoring
1 day, 20:38:05.304605 INFO: performing precursor FDR with 47 features
1 day, 20:38:05.304664 INFO: Decoy channel: -1
1 day, 20:38:05.304692 INFO: Competetive: True
1 day, 20:38:05.307690 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:05.310204 INFO: Using random state 819915 for train-test-split
1 day, 20:38:05.320758 INFO: Test AUC: 0.789
1 day, 20:38:05.320819 INFO: Train AUC: 0.784
1 day, 20:38:05.320853 INFO: AUC difference: 0.63%
1 day, 20:38:05.538000 INFO: Resetting torch num_threads to 80
1 day, 20:38:05.538556 PROGRESS: === Extracted 3355 precursors and 36179 fragments ===
1 day, 20:38:05.538971 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:38:05.539548 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:05.539640 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:05.539703 PROGRESS: Target precursors: 587 (97.83%)
1 day, 20:38:05.539759 PROGRESS: Decoy precursors: 13 (2.17%)
1 day, 20:38:05.539809 PROGRESS: 
1 day, 20:38:05.539856 PROGRESS: Precursor Summary:
1 day, 20:38:05.540938 PROGRESS: Channel   0:	 0.050 FDR:   587; 0.010 FDR:   579; 0.001 FDR:   519
1 day, 20:38:05.541111 PROGRESS: 
1 day, 20:38:05.541174 PROGRESS: Protein Summary:
1 day, 20:38:05.542447 PROGRESS: Channel   0:	 0.050 FDR:   530; 0.010 FDR:   525; 0.001 FDR:   469
1 day, 20:38:05.542546 PROGRESS: =========================================================================
1 day, 20:38:05.542674 INFO: Target number of precursors reached.
1 day, 20:38:05.549513 INFO: fragments_df: keeping 5000 of 36179 [sum(precursor_idx_mask)=18151 sum(mass_error_mask)=36179 stop_rank=5000
1 day, 20:38:05.553688 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:05.670190 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:05.791549 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:05.914120 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:06.542401 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:06.542834 INFO: Using score_cutoff 38.16364128799439 (fac=0.99, q=1)
1 day, 20:38:06.543146 INFO: Updating optimization_manager: fwhm_rt             : 2.863511562347412 -> 2.820862293243408
1 day, 20:38:06.543231 INFO: Updating optimization_manager: fwhm_mobility       : 0.0087879728525877 -> 0.008525155484676361
1 day, 20:38:06.543294 INFO: Updating optimization_manager: score_cutoff        : 41.566209926605225 -> 38.16364128799439
1 day, 20:38:06.543353 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:06.544405 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:06.545741 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:06.546513 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:06.548593 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:06.548699 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:38:06.550482 INFO: Updating optimization_manager: rt_error            : 37.0839524736676 -> 17.008883634046768
1 day, 20:38:06.550593 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 17.0089.
1 day, 20:38:06.550663 INFO: ==============================================
1 day, 20:38:06.550737 INFO: Starting optimization step 3.
1 day, 20:38:06.550800 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:38:06.550859 INFO: Using classic extraction backend
1 day, 20:38:06.550969 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:38:06.551042 INFO: === Search parameters used ===
1 day, 20:38:06.551096 INFO: rt_error       : 17.008883634046768
1 day, 20:38:06.551145 INFO: mobility_error : 0.1
1 day, 20:38:06.551194 INFO: num_candidates : 3
1 day, 20:38:06.551241 INFO: ms1_error      : 7.5754825
1 day, 20:38:06.551286 INFO: ms2_error      : 17.494642
1 day, 20:38:06.551332 INFO: fwhm_rt        : 2.820862293243408
1 day, 20:38:06.551393 INFO: quant_window   : 3
1 day, 20:38:06.551440 INFO: ==============================================
1 day, 20:38:06.552317 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:06.552369 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:06.552405 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 20:38:06.552429 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
1 day, 20:38:06.553232 INFO: Starting candidate selection
1 day, 20:38:07.088692 INFO: Starting candidate scoring
1 day, 20:38:07.300183 INFO: Finished candidate processing
1 day, 20:38:07.300375 INFO: Collecting candidate features
1 day, 20:38:07.312101 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3348)
1 day, 20:38:07.315326 INFO: Collecting fragment features
1 day, 20:38:07.319000 INFO: Finished candidate scoring
1 day, 20:38:07.320794 INFO: performing precursor FDR with 47 features
1 day, 20:38:07.320840 INFO: Decoy channel: -1
1 day, 20:38:07.320865 INFO: Competetive: True
1 day, 20:38:07.324140 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:07.325463 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 20:38:07.326736 INFO: Using random state 819915 for train-test-split
1 day, 20:38:07.337301 INFO: Test AUC: 0.785
1 day, 20:38:07.337357 INFO: Train AUC: 0.802
1 day, 20:38:07.337386 INFO: AUC difference: 2.09%
1 day, 20:38:07.555647 INFO: Resetting torch num_threads to 80
1 day, 20:38:07.556184 PROGRESS: === Extracted 3348 precursors and 35858 fragments ===
1 day, 20:38:07.556591 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:38:07.557166 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:07.557264 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:07.557323 PROGRESS: Target precursors: 592 (98.67%)
1 day, 20:38:07.557372 PROGRESS: Decoy precursors: 8 (1.33%)
1 day, 20:38:07.557415 PROGRESS: 
1 day, 20:38:07.557464 PROGRESS: Precursor Summary:
1 day, 20:38:07.558496 PROGRESS: Channel   0:	 0.050 FDR:   592; 0.010 FDR:   580; 0.001 FDR:   525
1 day, 20:38:07.558588 PROGRESS: 
1 day, 20:38:07.558643 PROGRESS: Protein Summary:
1 day, 20:38:07.559895 PROGRESS: Channel   0:	 0.050 FDR:   536; 0.010 FDR:   527; 0.001 FDR:   475
1 day, 20:38:07.559990 PROGRESS: =========================================================================
1 day, 20:38:07.560115 INFO: Target number of precursors reached.
1 day, 20:38:07.566824 INFO: fragments_df: keeping 5000 of 35858 [sum(precursor_idx_mask)=18004 sum(mass_error_mask)=35858 stop_rank=5000
1 day, 20:38:07.571065 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:07.688586 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:07.811095 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:07.934404 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:08.557880 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:08.558306 INFO: Using score_cutoff 37.36710312080383 (fac=0.99, q=1)
1 day, 20:38:08.558623 INFO: Updating optimization_manager: fwhm_rt             : 2.820862293243408 -> 2.846208095550537
1 day, 20:38:08.558717 INFO: Updating optimization_manager: fwhm_mobility       : 0.008525155484676361 -> 0.008504994213581085
1 day, 20:38:08.558780 INFO: Updating optimization_manager: score_cutoff        : 38.16364128799439 -> 37.36710312080383
1 day, 20:38:08.558841 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:08.559891 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:08.561217 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:08.561975 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:08.564421 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:08.564530 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 20:38:08.566345 INFO: Updating optimization_manager: rt_error            : 17.008883634046768 -> 15.453399585598428
1 day, 20:38:08.566452 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 15.4534.
1 day, 20:38:08.566521 INFO: ==============================================
1 day, 20:38:08.566592 INFO: Starting optimization step 4.
1 day, 20:38:08.566653 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:38:08.566714 INFO: Using classic extraction backend
1 day, 20:38:08.566823 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:38:08.566893 INFO: === Search parameters used ===
1 day, 20:38:08.566945 INFO: rt_error       : 15.453399585598428
1 day, 20:38:08.566993 INFO: mobility_error : 0.1
1 day, 20:38:08.567040 INFO: num_candidates : 3
1 day, 20:38:08.567085 INFO: ms1_error      : 7.5754825
1 day, 20:38:08.567137 INFO: ms2_error      : 17.494642
1 day, 20:38:08.567183 INFO: fwhm_rt        : 2.846208095550537
1 day, 20:38:08.567227 INFO: quant_window   : 3
1 day, 20:38:08.567274 INFO: ==============================================
1 day, 20:38:08.568078 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:08.568124 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:08.568161 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 20:38:08.568186 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.94
1 day, 20:38:08.568922 INFO: Starting candidate selection
1 day, 20:38:09.082450 INFO: Starting candidate scoring
1 day, 20:38:09.306953 INFO: Finished candidate processing
1 day, 20:38:09.307142 INFO: Collecting candidate features
1 day, 20:38:09.321755 INFO: Collecting fragment features
1 day, 20:38:09.325387 INFO: Finished candidate scoring
1 day, 20:38:09.327129 INFO: performing precursor FDR with 47 features
1 day, 20:38:09.327173 INFO: Decoy channel: -1
1 day, 20:38:09.327196 INFO: Competetive: True
1 day, 20:38:09.329950 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:09.332245 INFO: Using random state 819915 for train-test-split
1 day, 20:38:09.342430 INFO: Test AUC: 0.836
1 day, 20:38:09.342490 INFO: Train AUC: 0.800
1 day, 20:38:09.342519 INFO: AUC difference: 4.49%
1 day, 20:38:09.560215 INFO: Resetting torch num_threads to 80
1 day, 20:38:09.560739 PROGRESS: === Extracted 3347 precursors and 35628 fragments ===
1 day, 20:38:09.561157 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:38:09.561716 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:09.561804 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:09.561860 PROGRESS: Target precursors: 590 (98.33%)
1 day, 20:38:09.561907 PROGRESS: Decoy precursors: 10 (1.67%)
1 day, 20:38:09.561950 PROGRESS: 
1 day, 20:38:09.561993 PROGRESS: Precursor Summary:
1 day, 20:38:09.563028 PROGRESS: Channel   0:	 0.050 FDR:   590; 0.010 FDR:   578; 0.001 FDR:   556
1 day, 20:38:09.563121 PROGRESS: 
1 day, 20:38:09.563174 PROGRESS: Protein Summary:
1 day, 20:38:09.564426 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:   524; 0.001 FDR:   505
1 day, 20:38:09.564517 PROGRESS: =========================================================================
1 day, 20:38:09.564637 INFO: Target number of precursors reached.
1 day, 20:38:09.571351 INFO: fragments_df: keeping 5000 of 35628 [sum(precursor_idx_mask)=17847 sum(mass_error_mask)=35628 stop_rank=5000
1 day, 20:38:09.575612 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:09.693073 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:09.811496 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:09.937592 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:10.620158 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:10.620581 INFO: Using score_cutoff 35.48765203514099 (fac=0.99, q=1)
1 day, 20:38:10.620892 INFO: Updating optimization_manager: fwhm_rt             : 2.846208095550537 -> 2.826964855194092
1 day, 20:38:10.620990 INFO: Updating optimization_manager: fwhm_mobility       : 0.008504994213581085 -> 0.008466949686408043
1 day, 20:38:10.621048 INFO: Updating optimization_manager: score_cutoff        : 37.36710312080383 -> 35.48765203514099
1 day, 20:38:10.621105 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:10.622135 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:10.623440 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:10.624190 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:10.626220 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:10.626324 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 20:38:10.628077 INFO: Updating optimization_manager: rt_error            : 15.453399585598428 -> 11.813011012742345
1 day, 20:38:10.628176 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 11.8130.
1 day, 20:38:10.628241 INFO: ==============================================
1 day, 20:38:10.628307 INFO: Starting optimization step 5.
1 day, 20:38:10.628364 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:38:10.628427 INFO: Using classic extraction backend
1 day, 20:38:10.628531 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:38:10.628594 INFO: === Search parameters used ===
1 day, 20:38:10.628643 INFO: rt_error       : 11.813011012742345
1 day, 20:38:10.628685 INFO: mobility_error : 0.1
1 day, 20:38:10.628727 INFO: num_candidates : 3
1 day, 20:38:10.628768 INFO: ms1_error      : 7.5754825
1 day, 20:38:10.628808 INFO: ms2_error      : 17.494642
1 day, 20:38:10.628849 INFO: fwhm_rt        : 2.826964855194092
1 day, 20:38:10.628888 INFO: quant_window   : 3
1 day, 20:38:10.628926 INFO: ==============================================
1 day, 20:38:10.629771 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:10.629817 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:10.629851 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1 day, 20:38:10.629878 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 20:38:10.630557 INFO: Starting candidate selection
1 day, 20:38:11.139799 INFO: Starting candidate scoring
1 day, 20:38:11.318790 INFO: Finished candidate processing
1 day, 20:38:11.318926 INFO: Collecting candidate features
1 day, 20:38:11.329626 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3341)
1 day, 20:38:11.332866 INFO: Collecting fragment features
1 day, 20:38:11.336468 INFO: Finished candidate scoring
1 day, 20:38:11.338363 INFO: performing precursor FDR with 47 features
1 day, 20:38:11.338409 INFO: Decoy channel: -1
1 day, 20:38:11.338435 INFO: Competetive: True
1 day, 20:38:11.341408 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:11.342655 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 20:38:11.343743 INFO: Using random state 819915 for train-test-split
1 day, 20:38:11.354981 INFO: Test AUC: 0.799
1 day, 20:38:11.355040 INFO: Train AUC: 0.806
1 day, 20:38:11.355068 INFO: AUC difference: 0.90%
1 day, 20:38:11.566711 INFO: Resetting torch num_threads to 80
1 day, 20:38:11.567238 PROGRESS: === Extracted 3341 precursors and 35540 fragments ===
1 day, 20:38:11.567640 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:38:11.568190 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:11.568278 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:11.568333 PROGRESS: Target precursors: 590 (98.33%)
1 day, 20:38:11.568381 PROGRESS: Decoy precursors: 10 (1.67%)
1 day, 20:38:11.568425 PROGRESS: 
1 day, 20:38:11.568467 PROGRESS: Precursor Summary:
1 day, 20:38:11.569521 PROGRESS: Channel   0:	 0.050 FDR:   590; 0.010 FDR:   583; 0.001 FDR:   550
1 day, 20:38:11.569614 PROGRESS: 
1 day, 20:38:11.569675 PROGRESS: Protein Summary:
1 day, 20:38:11.570947 PROGRESS: Channel   0:	 0.050 FDR:   534; 0.010 FDR:   528; 0.001 FDR:   499
1 day, 20:38:11.571043 PROGRESS: =========================================================================
1 day, 20:38:11.571174 INFO: Target number of precursors reached.
1 day, 20:38:11.577823 INFO: fragments_df: keeping 5000 of 35540 [sum(precursor_idx_mask)=18052 sum(mass_error_mask)=35540 stop_rank=5000
1 day, 20:38:11.582076 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:11.698385 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:11.819486 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:11.939536 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:12.577675 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:12.578106 INFO: Using score_cutoff 32.535513494110106 (fac=0.99, q=1)
1 day, 20:38:12.578419 INFO: Updating optimization_manager: fwhm_rt             : 2.826964855194092 -> 2.849644660949707
1 day, 20:38:12.578499 INFO: Updating optimization_manager: fwhm_mobility       : 0.008466949686408043 -> 0.008489420637488365
1 day, 20:38:12.578551 INFO: Updating optimization_manager: score_cutoff        : 35.48765203514099 -> 32.535513494110106
1 day, 20:38:12.578603 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:12.579630 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:12.580936 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:12.581706 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:12.583831 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:12.583939 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 20:38:12.585722 INFO: Updating optimization_manager: rt_error            : 11.813011012742345 -> 11.323221813268585
1 day, 20:38:12.585823 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 11.3232.
1 day, 20:38:12.585887 INFO: ==============================================
1 day, 20:38:12.585954 INFO: Starting optimization step 6.
1 day, 20:38:12.586010 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:38:12.586065 INFO: Using classic extraction backend
1 day, 20:38:12.586167 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:38:12.586232 INFO: === Search parameters used ===
1 day, 20:38:12.586280 INFO: rt_error       : 11.323221813268585
1 day, 20:38:12.586322 INFO: mobility_error : 0.1
1 day, 20:38:12.586362 INFO: num_candidates : 3
1 day, 20:38:12.586402 INFO: ms1_error      : 7.5754825
1 day, 20:38:12.586440 INFO: ms2_error      : 17.494642
1 day, 20:38:12.586479 INFO: fwhm_rt        : 2.849644660949707
1 day, 20:38:12.586519 INFO: quant_window   : 3
1 day, 20:38:12.586560 INFO: ==============================================
1 day, 20:38:12.587411 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:12.587454 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:12.587487 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 20:38:12.587509 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.94
1 day, 20:38:12.588692 INFO: Starting candidate selection
1 day, 20:38:13.080759 INFO: Starting candidate scoring
1 day, 20:38:13.259869 INFO: Finished candidate processing
1 day, 20:38:13.260004 INFO: Collecting candidate features
1 day, 20:38:13.270185 WARNING: intensity_correlation has 2 NaNs ( 0.06 % out of 3352)
1 day, 20:38:13.273499 INFO: Collecting fragment features
1 day, 20:38:13.277165 INFO: Finished candidate scoring
1 day, 20:38:13.278927 INFO: performing precursor FDR with 47 features
1 day, 20:38:13.278972 INFO: Decoy channel: -1
1 day, 20:38:13.278997 INFO: Competetive: True
1 day, 20:38:13.281983 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:13.283242 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 20:38:13.284207 INFO: Using random state 819915 for train-test-split
1 day, 20:38:13.295914 INFO: Test AUC: 0.797
1 day, 20:38:13.295975 INFO: Train AUC: 0.799
1 day, 20:38:13.296003 INFO: AUC difference: 0.31%
1 day, 20:38:13.510443 INFO: Resetting torch num_threads to 80
1 day, 20:38:13.510971 PROGRESS: === Extracted 3352 precursors and 35568 fragments ===
1 day, 20:38:13.511380 INFO: === FDR correction performed with classifier version 6 ===
1 day, 20:38:13.511944 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:13.512043 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:13.512104 PROGRESS: Target precursors: 585 (97.50%)
1 day, 20:38:13.512155 PROGRESS: Decoy precursors: 15 (2.50%)
1 day, 20:38:13.512202 PROGRESS: 
1 day, 20:38:13.512247 PROGRESS: Precursor Summary:
1 day, 20:38:13.513287 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   562; 0.001 FDR:   517
1 day, 20:38:13.513383 PROGRESS: 
1 day, 20:38:13.513440 PROGRESS: Protein Summary:
1 day, 20:38:13.514673 PROGRESS: Channel   0:	 0.050 FDR:   530; 0.010 FDR:   509; 0.001 FDR:   468
1 day, 20:38:13.514765 PROGRESS: =========================================================================
1 day, 20:38:13.514898 INFO: Target number of precursors reached.
1 day, 20:38:13.521369 INFO: fragments_df: keeping 5000 of 35568 [sum(precursor_idx_mask)=17359 sum(mass_error_mask)=35568 stop_rank=5000
1 day, 20:38:13.526349 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:13.642297 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:13.762564 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:13.882612 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:14.522535 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:14.522969 INFO: Using score_cutoff 33.72452462768555 (fac=0.99, q=1)
1 day, 20:38:14.523278 INFO: Updating optimization_manager: fwhm_rt             : 2.849644660949707 -> 2.8248281478881836
1 day, 20:38:14.523359 INFO: Updating optimization_manager: fwhm_mobility       : 0.008489420637488365 -> 0.008574625477194786
1 day, 20:38:14.523423 INFO: Updating optimization_manager: score_cutoff        : 32.535513494110106 -> 33.72452462768555
1 day, 20:38:14.523477 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:14.524505 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:14.525836 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:14.526596 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:14.528703 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:14.528802 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 20:38:14.529741 INFO: Updating optimization_manager: rt_error            : 11.323221813268585 -> 11.323221813268585
1 day, 20:38:14.529866 INFO: Updating optimization_manager: classifier_version  : 6 -> 13
1 day, 20:38:14.529960 INFO: Updating optimization_manager: score_cutoff        : 33.72452462768555 -> 33.72452462768555
1 day, 20:38:14.530049 INFO: Updating optimization_manager: fwhm_rt             : 2.8248281478881836 -> 2.8248281478881836
1 day, 20:38:14.530132 INFO: Updating optimization_manager: fwhm_mobility       : 0.008574625477194786 -> 0.008574625477194786
1 day, 20:38:14.530215 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 11.3232 found after 7 searches.
1 day, 20:38:14.530274 INFO: ==============================================
1 day, 20:38:14.530336 PROGRESS: Optimization finished for rt_error.
1 day, 20:38:14.534340 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:14.535146 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:14.536442 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:14.537224 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:14.562475 INFO: Starting optimization step 0.
1 day, 20:38:14.562617 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:38:14.562686 INFO: Using classic extraction backend
1 day, 20:38:14.562796 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:38:14.562865 INFO: === Search parameters used ===
1 day, 20:38:14.562915 INFO: rt_error       : 11.323221813268585
1 day, 20:38:14.562959 INFO: mobility_error : 0.1
1 day, 20:38:14.563002 INFO: num_candidates : 3
1 day, 20:38:14.563043 INFO: ms1_error      : 7.5754825
1 day, 20:38:14.563084 INFO: ms2_error      : 17.494642
1 day, 20:38:14.563123 INFO: fwhm_rt        : 2.8248281478881836
1 day, 20:38:14.563162 INFO: quant_window   : 3
1 day, 20:38:14.563201 INFO: ==============================================
1 day, 20:38:14.564113 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:14.564159 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:14.564193 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 20:38:14.564216 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
1 day, 20:38:14.565177 INFO: Starting candidate selection
1 day, 20:38:15.040996 INFO: Starting candidate scoring
1 day, 20:38:15.265608 INFO: Finished candidate processing
1 day, 20:38:15.266552 INFO: Collecting candidate features
1 day, 20:38:15.281640 INFO: Collecting fragment features
1 day, 20:38:15.286087 INFO: Finished candidate scoring
1 day, 20:38:15.287843 INFO: performing precursor FDR with 47 features
1 day, 20:38:15.287888 INFO: Decoy channel: -1
1 day, 20:38:15.287913 INFO: Competetive: True
1 day, 20:38:15.290782 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:15.292744 INFO: Using random state 110394 for train-test-split
1 day, 20:38:15.303284 INFO: Test AUC: 0.787
1 day, 20:38:15.303340 INFO: Train AUC: 0.796
1 day, 20:38:15.303369 INFO: AUC difference: 1.12%
1 day, 20:38:15.515602 INFO: Resetting torch num_threads to 80
1 day, 20:38:15.516151 PROGRESS: === Extracted 3360 precursors and 35618 fragments ===
1 day, 20:38:15.516561 INFO: === FDR correction performed with classifier version 13 ===
1 day, 20:38:15.517145 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:15.517236 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:15.517293 PROGRESS: Target precursors: 583 (97.17%)
1 day, 20:38:15.517342 PROGRESS: Decoy precursors: 17 (2.83%)
1 day, 20:38:15.517387 PROGRESS: 
1 day, 20:38:15.517431 PROGRESS: Precursor Summary:
1 day, 20:38:15.518452 PROGRESS: Channel   0:	 0.050 FDR:   583; 0.010 FDR:   558; 0.001 FDR:   524
1 day, 20:38:15.518543 PROGRESS: 
1 day, 20:38:15.518598 PROGRESS: Protein Summary:
1 day, 20:38:15.519859 PROGRESS: Channel   0:	 0.050 FDR:   529; 0.010 FDR:   507; 0.001 FDR:   477
1 day, 20:38:15.519953 PROGRESS: =========================================================================
1 day, 20:38:15.520083 INFO: Target number of precursors reached.
1 day, 20:38:15.526688 INFO: fragments_df: keeping 5000 of 35618 [sum(precursor_idx_mask)=17272 sum(mass_error_mask)=35618 stop_rank=5000
1 day, 20:38:15.530915 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:15.646896 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:15.766560 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:15.892839 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:16.535061 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:16.535513 INFO: Using score_cutoff 35.398559437179564 (fac=0.99, q=1)
1 day, 20:38:16.535821 INFO: Updating optimization_manager: fwhm_rt             : 2.8248281478881836 -> 2.8432135581970215
1 day, 20:38:16.535903 INFO: Updating optimization_manager: fwhm_mobility       : 0.008574625477194786 -> 0.008608466945588589
1 day, 20:38:16.535958 INFO: Updating optimization_manager: score_cutoff        : 33.72452462768555 -> 35.398559437179564
1 day, 20:38:16.536021 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:16.537066 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:16.538378 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:16.539137 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:16.542198 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:16.542301 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:38:16.543648 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06873997089021633
1 day, 20:38:16.543746 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0687.
1 day, 20:38:16.543809 INFO: ==============================================
1 day, 20:38:16.543874 INFO: Starting optimization step 1.
1 day, 20:38:16.543930 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:38:16.543987 INFO: Using classic extraction backend
1 day, 20:38:16.544090 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:38:16.544154 INFO: === Search parameters used ===
1 day, 20:38:16.544200 INFO: rt_error       : 11.323221813268585
1 day, 20:38:16.544242 INFO: mobility_error : 0.06873997089021633
1 day, 20:38:16.544284 INFO: num_candidates : 3
1 day, 20:38:16.544326 INFO: ms1_error      : 7.5754825
1 day, 20:38:16.544367 INFO: ms2_error      : 17.494642
1 day, 20:38:16.544408 INFO: fwhm_rt        : 2.8432135581970215
1 day, 20:38:16.544450 INFO: quant_window   : 3
1 day, 20:38:16.544490 INFO: ==============================================
1 day, 20:38:16.545315 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:16.545361 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:16.545395 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
1 day, 20:38:16.545416 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 20:38:16.546232 INFO: Starting candidate selection
1 day, 20:38:17.038520 INFO: Starting candidate scoring
1 day, 20:38:17.254363 INFO: Finished candidate processing
1 day, 20:38:17.254557 INFO: Collecting candidate features
1 day, 20:38:17.269306 INFO: Collecting fragment features
1 day, 20:38:17.273242 INFO: Finished candidate scoring
1 day, 20:38:17.275043 INFO: performing precursor FDR with 47 features
1 day, 20:38:17.275088 INFO: Decoy channel: -1
1 day, 20:38:17.275115 INFO: Competetive: True
1 day, 20:38:17.277898 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:17.279883 INFO: Using random state 110394 for train-test-split
1 day, 20:38:17.290891 INFO: Test AUC: 0.791
1 day, 20:38:17.290953 INFO: Train AUC: 0.802
1 day, 20:38:17.290982 INFO: AUC difference: 1.33%
1 day, 20:38:17.501616 INFO: Resetting torch num_threads to 80
1 day, 20:38:17.502141 PROGRESS: === Extracted 3352 precursors and 35304 fragments ===
1 day, 20:38:17.502553 INFO: === FDR correction performed with classifier version 13 ===
1 day, 20:38:17.503102 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:17.503188 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:17.503244 PROGRESS: Target precursors: 584 (97.33%)
1 day, 20:38:17.503293 PROGRESS: Decoy precursors: 16 (2.67%)
1 day, 20:38:17.503336 PROGRESS: 
1 day, 20:38:17.503379 PROGRESS: Precursor Summary:
1 day, 20:38:17.504412 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   557; 0.001 FDR:   521
1 day, 20:38:17.504503 PROGRESS: 
1 day, 20:38:17.504557 PROGRESS: Protein Summary:
1 day, 20:38:17.505798 PROGRESS: Channel   0:	 0.050 FDR:   530; 0.010 FDR:   506; 0.001 FDR:   473
1 day, 20:38:17.505889 PROGRESS: =========================================================================
1 day, 20:38:17.506013 INFO: Target number of precursors reached.
1 day, 20:38:17.512449 INFO: fragments_df: keeping 5000 of 35304 [sum(precursor_idx_mask)=17157 sum(mass_error_mask)=35304 stop_rank=5000
1 day, 20:38:17.516575 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:20.481769 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:20.602483 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:20.723490 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:21.341393 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:21.341836 INFO: Using score_cutoff 35.47741724395752 (fac=0.99, q=1)
1 day, 20:38:21.342273 INFO: Updating optimization_manager: fwhm_rt             : 2.8432135581970215 -> 2.8332841396331787
1 day, 20:38:21.342359 INFO: Updating optimization_manager: fwhm_mobility       : 0.008608466945588589 -> 0.008507073856890202
1 day, 20:38:21.342420 INFO: Updating optimization_manager: score_cutoff        : 35.398559437179564 -> 35.47741724395752
1 day, 20:38:21.342478 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:21.343561 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:21.344934 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:21.345736 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:21.347843 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:21.347950 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:38:21.349418 INFO: Updating optimization_manager: mobility_error      : 0.06873997089021633 -> 0.05993643009803202
1 day, 20:38:21.349526 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0599.
1 day, 20:38:21.349596 INFO: ==============================================
1 day, 20:38:21.349666 INFO: Starting optimization step 2.
1 day, 20:38:21.349731 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:38:21.349792 INFO: Using classic extraction backend
1 day, 20:38:21.349931 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:38:21.350003 INFO: === Search parameters used ===
1 day, 20:38:21.350054 INFO: rt_error       : 11.323221813268585
1 day, 20:38:21.350105 INFO: mobility_error : 0.05993643009803202
1 day, 20:38:21.350157 INFO: num_candidates : 3
1 day, 20:38:21.350206 INFO: ms1_error      : 7.5754825
1 day, 20:38:21.350250 INFO: ms2_error      : 17.494642
1 day, 20:38:21.350295 INFO: fwhm_rt        : 2.8332841396331787
1 day, 20:38:21.350341 INFO: quant_window   : 3
1 day, 20:38:21.350385 INFO: ==============================================
1 day, 20:38:21.351210 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:21.351258 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:21.351296 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1 day, 20:38:21.351323 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
1 day, 20:38:21.351983 INFO: Starting candidate selection
1 day, 20:38:21.859456 INFO: Starting candidate scoring
1 day, 20:38:22.058444 INFO: Finished candidate processing
1 day, 20:38:22.058580 INFO: Collecting candidate features
1 day, 20:38:22.068222 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3341)
1 day, 20:38:22.071572 INFO: Collecting fragment features
1 day, 20:38:22.075306 INFO: Finished candidate scoring
1 day, 20:38:22.079023 INFO: performing precursor FDR with 47 features
1 day, 20:38:22.079070 INFO: Decoy channel: -1
1 day, 20:38:22.079095 INFO: Competetive: True
1 day, 20:38:22.082364 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:22.083714 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 20:38:22.084703 INFO: Using random state 110394 for train-test-split
1 day, 20:38:22.095923 INFO: Test AUC: 0.773
1 day, 20:38:22.095985 INFO: Train AUC: 0.808
1 day, 20:38:22.096014 INFO: AUC difference: 4.29%
1 day, 20:38:22.313853 INFO: Resetting torch num_threads to 80
1 day, 20:38:22.314435 PROGRESS: === Extracted 3341 precursors and 35049 fragments ===
1 day, 20:38:22.314847 INFO: === FDR correction performed with classifier version 13 ===
1 day, 20:38:22.315540 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:22.315632 PROGRESS: Total precursors accumulated: 600
1 day, 20:38:22.315690 PROGRESS: Target precursors: 584 (97.33%)
1 day, 20:38:22.315739 PROGRESS: Decoy precursors: 16 (2.67%)
1 day, 20:38:22.315783 PROGRESS: 
1 day, 20:38:22.315825 PROGRESS: Precursor Summary:
1 day, 20:38:22.316926 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   560; 0.001 FDR:   514
1 day, 20:38:22.317035 PROGRESS: 
1 day, 20:38:22.317092 PROGRESS: Protein Summary:
1 day, 20:38:22.318380 PROGRESS: Channel   0:	 0.050 FDR:   530; 0.010 FDR:   509; 0.001 FDR:   467
1 day, 20:38:22.318476 PROGRESS: =========================================================================
1 day, 20:38:22.318603 INFO: Target number of precursors reached.
1 day, 20:38:22.325330 INFO: fragments_df: keeping 5000 of 35049 [sum(precursor_idx_mask)=17249 sum(mass_error_mask)=35049 stop_rank=5000
1 day, 20:38:22.329703 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:22.471519 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:22.592602 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:22.713184 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:23.335108 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:38:23.335531 INFO: Using score_cutoff 33.85308799209595 (fac=0.99, q=1)
1 day, 20:38:23.335841 INFO: Updating optimization_manager: fwhm_rt             : 2.8332841396331787 -> 2.838191032409668
1 day, 20:38:23.335925 INFO: Updating optimization_manager: fwhm_mobility       : 0.008507073856890202 -> 0.008432616479694843
1 day, 20:38:23.335979 INFO: Updating optimization_manager: score_cutoff        : 35.47741724395752 -> 33.85308799209595
1 day, 20:38:23.336033 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:23.337103 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:23.338439 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:23.339216 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:23.341322 INFO: === checking if optimization conditions were reached ===
1 day, 20:38:23.341428 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:38:23.342090 INFO: Updating optimization_manager: mobility_error      : 0.05993643009803202 -> 0.05993643009803202
1 day, 20:38:23.342210 INFO: Updating optimization_manager: classifier_version  : 13 -> 16
1 day, 20:38:23.342301 INFO: Updating optimization_manager: score_cutoff        : 33.85308799209595 -> 33.85308799209595
1 day, 20:38:23.342394 INFO: Updating optimization_manager: fwhm_rt             : 2.838191032409668 -> 2.838191032409668
1 day, 20:38:23.342479 INFO: Updating optimization_manager: fwhm_mobility       : 0.008432616479694843 -> 0.008432616479694843
1 day, 20:38:23.342561 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0599 found after 3 searches.
1 day, 20:38:23.342621 INFO: ==============================================
1 day, 20:38:23.342684 PROGRESS: Optimization finished for mobility_error.
1 day, 20:38:23.346623 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:23.347451 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:23.348763 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:23.349547 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:23.374921 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:38:23.375050 PROGRESS: ==============================================
1 day, 20:38:23.375144 PROGRESS: ms2_error      : 17.4946
1 day, 20:38:23.375203 PROGRESS: ms1_error      : 7.5755
1 day, 20:38:23.375254 PROGRESS: rt_error       : 11.3232
1 day, 20:38:23.375462 PROGRESS: mobility_error : 0.0599
1 day, 20:38:23.375510 PROGRESS: ==============================================
1 day, 20:38:23.376004 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:38:23.392604 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:38:23.473650 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:38:23.494209 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:38:23.710543 INFO: Using classic extraction backend
1 day, 20:38:23.710949 PROGRESS: Extracting batch of 146455 precursors
1 day, 20:38:23.711051 INFO: === Search parameters used ===
1 day, 20:38:23.711115 INFO: rt_error       : 11.323221813268585
1 day, 20:38:23.711170 INFO: mobility_error : 0.05993643009803202
1 day, 20:38:23.711225 INFO: num_candidates : 3
1 day, 20:38:23.711277 INFO: ms1_error      : 7.5754825
1 day, 20:38:23.711327 INFO: ms2_error      : 17.494642
1 day, 20:38:23.711378 INFO: fwhm_rt        : 2.838191032409668
1 day, 20:38:23.711429 INFO: quant_window   : 3
1 day, 20:38:23.711479 INFO: ==============================================
1 day, 20:38:23.741663 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:38:23.741804 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:38:23.741853 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
1 day, 20:38:23.741882 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.91
1 day, 20:38:23.746361 INFO: Starting candidate selection
1 day, 20:38:32.717980 INFO: Removed 100624 precursors with score below cutoff 33.85308799209595
1 day, 20:38:33.078835 INFO: Starting candidate scoring
1 day, 20:38:46.413445 INFO: Finished candidate processing
1 day, 20:38:46.413558 INFO: Collecting candidate features
1 day, 20:38:46.790849 INFO: Collecting fragment features
1 day, 20:38:46.972420 INFO: Finished candidate scoring
1 day, 20:38:47.110835 INFO: === Performing FDR correction with classifier version 16 ===
1 day, 20:38:47.113120 INFO: performing precursor FDR with 47 features
1 day, 20:38:47.113158 INFO: Decoy channel: -1
1 day, 20:38:47.113183 INFO: Competetive: True
1 day, 20:38:47.181174 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:38:47.208222 WARNING: FDR calculation for 178258 target and 131777 decoy PSMs
1 day, 20:38:47.208357 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 20:38:47.291677 INFO: Using random state 120703 for train-test-split
1 day, 20:38:52.397464 INFO: Test AUC: 0.863
1 day, 20:38:52.397585 INFO: Train AUC: 0.866
1 day, 20:38:52.397618 INFO: AUC difference: 0.40%
1 day, 20:38:52.719127 INFO: Resetting torch num_threads to 80
1 day, 20:38:52.732681 INFO: Removing fragments below FDR threshold
1 day, 20:38:52.788385 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:38:52.788645 PROGRESS: Total precursors accumulated: 70,599
1 day, 20:38:52.788712 PROGRESS: Target precursors: 69,900 (99.01%)
1 day, 20:38:52.788763 PROGRESS: Decoy precursors: 699 (0.99%)
1 day, 20:38:52.788809 PROGRESS: 
1 day, 20:38:52.788856 PROGRESS: Precursor Summary:
1 day, 20:38:52.818745 PROGRESS: Channel   0:	 0.050 FDR: 69,900; 0.010 FDR: 69,900; 0.001 FDR: 67,805
1 day, 20:38:52.819189 PROGRESS: 
1 day, 20:38:52.819266 PROGRESS: Protein Summary:
1 day, 20:38:52.857579 PROGRESS: Channel   0:	 0.050 FDR: 7,421; 0.010 FDR: 7,421; 0.001 FDR: 7,403
1 day, 20:38:52.857819 PROGRESS: =========================================================================
1 day, 20:38:52.861207 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/psm.parquet
1 day, 20:38:53.153114 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/frag.parquet
1 day, 20:38:53.409978 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:38:53.441770 PROGRESS: 
1 day, 20:38:53.441914 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
1 day, 20:38:53.441980 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/figures
1 day, 20:38:53.442153 INFO: Initializing TimingManager
1 day, 20:38:53.442801 INFO: Initializing RawFileManager
1 day, 20:38:53.442903 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:38:53.442953 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:38:53.442990 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:38:53.654087 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, 20:39:00.167802 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
1 day, 20:39:00.169096 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:39:00.171022 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:39:00.171233 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:39:00.171607 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:39:00.173077 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:39:00.187932 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:39:00.188102 INFO: Indexing quadrupole dimension
1 day, 20:39:00.632848 INFO: Transposing detector events
1 day, 20:39:09.121259 INFO: Finished transposing data
1 day, 20:39:09.156277 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:39:09.157007 INFO: RT (min)            : 0.0 - 70.0
1 day, 20:39:09.157103 INFO: RT duration (sec)   : 4199.9
1 day, 20:39:09.157159 INFO: RT duration (min)   : 70.0
1 day, 20:39:09.157210 INFO: Cycle len (scans)   : 9
1 day, 20:39:09.157257 INFO: Cycle len (sec)     : 0.97
1 day, 20:39:09.157301 INFO: Number of cycles    : 4347
1 day, 20:39:09.157346 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 20:39:09.157401 INFO: Creating DIA data object took: 15.714506149291992
1 day, 20:39:09.179641 INFO: Initializing CalibrationManager
1 day, 20:39:09.179994 INFO: Setting up calibration estimators ..
1 day, 20:39:09.180090 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 20:39:09.180205 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, 20:39:09.180318 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 20:39:09.180405 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, 20:39:09.180490 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, 20:39:09.180577 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, 20:39:09.180654 INFO: Done setting up calibration estimators.
1 day, 20:39:09.180810 INFO: Initializing OptimizationManager
1 day, 20:39:09.180971 INFO: initial parameter: ms1_error = 30
1 day, 20:39:09.181055 INFO: initial parameter: ms2_error = 30
1 day, 20:39:09.181131 INFO: initial parameter: rt_error = 2099.9331315
1 day, 20:39:09.181205 INFO: initial parameter: mobility_error = 0.1
1 day, 20:39:09.181275 INFO: initial parameter: num_candidates = 1
1 day, 20:39:09.181342 INFO: initial parameter: fwhm_rt = 5
1 day, 20:39:09.181409 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 20:39:09.181475 INFO: initial parameter: score_cutoff = 0
1 day, 20:39:09.181541 INFO: initial parameter: classifier_version = -1
1 day, 20:39:09.181649 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:39:09.181881 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 20:39:09.181931 INFO: Initializing FDRManager
1 day, 20:39:09.181979 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 20:39:09.205161 PROGRESS: Initializing spectral library: 73,677 target precursors potentially observable (0 removed)
1 day, 20:39:09.216664 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 20:39:09.217037 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 2099.9331315
1 day, 20:39:09.217140 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 20:39:09.217304 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 20:39:09.217391 PROGRESS: Starting initial search for precursors.
1 day, 20:39:09.217468 INFO: Starting optimization step 0.
1 day, 20:39:09.217527 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 20:39:09.217593 INFO: Using classic extraction backend
1 day, 20:39:09.217710 PROGRESS: Extracting batch of 399 precursors
1 day, 20:39:09.217776 INFO: === Search parameters used ===
1 day, 20:39:09.217822 INFO: rt_error       : 2099.9331315
1 day, 20:39:09.217868 INFO: mobility_error : 0.1
1 day, 20:39:09.217908 INFO: num_candidates : 1
1 day, 20:39:09.217950 INFO: ms1_error      : 30
1 day, 20:39:09.217990 INFO: ms2_error      : 30
1 day, 20:39:09.218030 INFO: fwhm_rt        : 5
1 day, 20:39:09.218069 INFO: quant_window   : 3
1 day, 20:39:09.218108 INFO: ==============================================
1 day, 20:39:09.218821 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:39:09.218864 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:39:09.218899 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:39:09.218920 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:39:09.219809 INFO: Starting candidate selection
1 day, 20:39:13.761043 INFO: Starting candidate scoring
1 day, 20:39:13.833501 INFO: Finished candidate processing
1 day, 20:39:13.834314 INFO: Collecting candidate features
1 day, 20:39:13.843505 INFO: Collecting fragment features
1 day, 20:39:13.845669 INFO: Finished candidate scoring
1 day, 20:39:13.846527 INFO: performing precursor FDR with 47 features
1 day, 20:39:13.846571 INFO: Decoy channel: -1
1 day, 20:39:13.846596 INFO: Competetive: True
1 day, 20:39:13.847760 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:39:13.849896 INFO: Using random state 639367 for train-test-split
1 day, 20:39:13.857020 INFO: Test AUC: 0.480
1 day, 20:39:13.857078 INFO: Train AUC: 0.482
1 day, 20:39:13.857108 INFO: AUC difference: 0.51%
1 day, 20:39:14.076313 INFO: Resetting torch num_threads to 80
1 day, 20:39:14.076784 PROGRESS: === Extracted 399 precursors and 4570 fragments ===
1 day, 20:39:14.077210 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:39:14.077742 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:39:14.077832 PROGRESS: Total precursors accumulated: 200
1 day, 20:39:14.077890 PROGRESS: Target precursors: 164 (82.00%)
1 day, 20:39:14.077942 PROGRESS: Decoy precursors: 36 (18.00%)
1 day, 20:39:14.077986 PROGRESS: 
1 day, 20:39:14.078027 PROGRESS: Precursor Summary:
1 day, 20:39:14.078933 PROGRESS: Channel   0:	 0.050 FDR:   156; 0.010 FDR:   156; 0.001 FDR:   156
1 day, 20:39:14.079022 PROGRESS: 
1 day, 20:39:14.079086 PROGRESS: Protein Summary:
1 day, 20:39:14.080110 PROGRESS: Channel   0:	 0.050 FDR:   151; 0.010 FDR:   151; 0.001 FDR:   151
1 day, 20:39:14.080199 PROGRESS: =========================================================================
1 day, 20:39:14.080294 INFO: Target number of precursors not reached yet.
1 day, 20:39:14.083596 INFO: Starting optimization step 1.
1 day, 20:39:14.083702 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 20:39:14.083770 INFO: Using classic extraction backend
1 day, 20:39:14.083877 PROGRESS: Extracting batch of 795 precursors
1 day, 20:39:14.083943 INFO: === Search parameters used ===
1 day, 20:39:14.083990 INFO: rt_error       : 2099.9331315
1 day, 20:39:14.084034 INFO: mobility_error : 0.1
1 day, 20:39:14.084075 INFO: num_candidates : 1
1 day, 20:39:14.084117 INFO: ms1_error      : 30
1 day, 20:39:14.084158 INFO: ms2_error      : 30
1 day, 20:39:14.084197 INFO: fwhm_rt        : 5
1 day, 20:39:14.084237 INFO: quant_window   : 3
1 day, 20:39:14.084276 INFO: ==============================================
1 day, 20:39:14.084901 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:39:14.084953 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:39:14.084981 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:39:14.085003 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:39:14.086789 INFO: Starting candidate selection
1 day, 20:39:20.712568 INFO: Starting candidate scoring
1 day, 20:39:20.832562 INFO: Finished candidate processing
1 day, 20:39:20.832657 INFO: Collecting candidate features
1 day, 20:39:20.842069 INFO: Collecting fragment features
1 day, 20:39:20.844659 INFO: Finished candidate scoring
1 day, 20:39:20.847115 INFO: performing precursor FDR with 47 features
1 day, 20:39:20.847165 INFO: Decoy channel: -1
1 day, 20:39:20.847190 INFO: Competetive: True
1 day, 20:39:20.850183 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:39:20.851959 INFO: Using random state 775848 for train-test-split
1 day, 20:39:20.860187 INFO: Test AUC: 0.456
1 day, 20:39:20.860243 INFO: Train AUC: 0.491
1 day, 20:39:20.860274 INFO: AUC difference: 6.99%
1 day, 20:39:20.860299 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:39:21.070246 INFO: Resetting torch num_threads to 80
1 day, 20:39:21.071507 PROGRESS: === Extracted 1193 precursors and 13594 fragments ===
1 day, 20:39:21.071914 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:39:21.072527 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:39:21.072617 PROGRESS: Total precursors accumulated: 600
1 day, 20:39:21.072679 PROGRESS: Target precursors: 492 (82.00%)
1 day, 20:39:21.072737 PROGRESS: Decoy precursors: 108 (18.00%)
1 day, 20:39:21.072788 PROGRESS: 
1 day, 20:39:21.072833 PROGRESS: Precursor Summary:
1 day, 20:39:21.073886 PROGRESS: Channel   0:	 0.050 FDR:   467; 0.010 FDR:   467; 0.001 FDR:   467
1 day, 20:39:21.073982 PROGRESS: 
1 day, 20:39:21.074041 PROGRESS: Protein Summary:
1 day, 20:39:21.075233 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   430; 0.001 FDR:   430
1 day, 20:39:21.075326 PROGRESS: =========================================================================
1 day, 20:39:21.075465 INFO: Target number of precursors reached.
1 day, 20:39:21.078857 INFO: fragments_df: keeping 3014 of 13594 [sum(precursor_idx_mask)=5291 sum(mass_error_mask)=13594 stop_rank=3014
1 day, 20:39:21.083272 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:21.201533 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:21.317549 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:21.433550 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:39:21.765820 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 20:39:21.766264 INFO: Using score_cutoff 47.97224899749756 (fac=0.99, q=1)
1 day, 20:39:21.766590 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.4446871280670166
1 day, 20:39:21.766670 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010783446952700615
1 day, 20:39:21.766723 INFO: Updating optimization_manager: score_cutoff        : 0 -> 47.97224899749756
1 day, 20:39:21.766787 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:21.767868 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:21.769277 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:21.770076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:39:21.772267 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
1 day, 20:39:21.772362 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 20:39:21.772438 INFO: Starting optimization step 2.
1 day, 20:39:21.772500 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:39:21.772557 INFO: Using classic extraction backend
1 day, 20:39:21.772660 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:39:21.772721 INFO: === Search parameters used ===
1 day, 20:39:21.772767 INFO: rt_error       : 2099.9331315
1 day, 20:39:21.772808 INFO: mobility_error : 0.1
1 day, 20:39:21.772848 INFO: num_candidates : 3
1 day, 20:39:21.772888 INFO: ms1_error      : 30
1 day, 20:39:21.772928 INFO: ms2_error      : 30
1 day, 20:39:21.772977 INFO: fwhm_rt        : 3.4446871280670166
1 day, 20:39:21.773020 INFO: quant_window   : 3
1 day, 20:39:21.773061 INFO: ==============================================
1 day, 20:39:21.773962 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:39:21.774006 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:39:21.774040 INFO: FWHM in RT is 3.44 seconds, sigma is 0.76
1 day, 20:39:21.774061 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.00
1 day, 20:39:21.774762 INFO: Starting candidate selection
1 day, 20:39:31.338320 INFO: Starting candidate scoring
1 day, 20:39:31.681573 INFO: Finished candidate processing
1 day, 20:39:31.682271 INFO: Collecting candidate features
1 day, 20:39:31.694826 INFO: Collecting fragment features
1 day, 20:39:31.698565 INFO: Finished candidate scoring
1 day, 20:39:31.701322 INFO: performing precursor FDR with 47 features
1 day, 20:39:31.701368 INFO: Decoy channel: -1
1 day, 20:39:31.701391 INFO: Competetive: True
1 day, 20:39:31.704763 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:39:31.706975 INFO: Using random state 484272 for train-test-split
1 day, 20:39:31.717217 INFO: Test AUC: 0.481
1 day, 20:39:31.717274 INFO: Train AUC: 0.502
1 day, 20:39:31.717303 INFO: AUC difference: 4.09%
1 day, 20:39:31.936066 INFO: Resetting torch num_threads to 80
1 day, 20:39:31.936637 PROGRESS: === Extracted 3412 precursors and 38861 fragments ===
1 day, 20:39:31.937061 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:39:31.937717 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:39:31.937807 PROGRESS: Total precursors accumulated: 600
1 day, 20:39:31.937870 PROGRESS: Target precursors: 567 (94.50%)
1 day, 20:39:31.937922 PROGRESS: Decoy precursors: 33 (5.50%)
1 day, 20:39:31.937968 PROGRESS: 
1 day, 20:39:31.938012 PROGRESS: Precursor Summary:
1 day, 20:39:31.939085 PROGRESS: Channel   0:	 0.050 FDR:   556; 0.010 FDR:   555; 0.001 FDR:   555
1 day, 20:39:31.939180 PROGRESS: 
1 day, 20:39:31.939236 PROGRESS: Protein Summary:
1 day, 20:39:31.940474 PROGRESS: Channel   0:	 0.050 FDR:   505; 0.010 FDR:   504; 0.001 FDR:   504
1 day, 20:39:31.940570 PROGRESS: =========================================================================
1 day, 20:39:31.940740 INFO: Target number of precursors reached.
1 day, 20:39:31.947959 INFO: fragments_df: keeping 5000 of 38861 [sum(precursor_idx_mask)=18094 sum(mass_error_mask)=38861 stop_rank=5000
1 day, 20:39:31.952546 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:32.085708 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:32.203161 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:32.322908 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:39:32.933452 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:39:32.933891 INFO: Using score_cutoff 47.74091625823974 (fac=0.99, q=1)
1 day, 20:39:32.934201 INFO: Updating optimization_manager: fwhm_rt             : 3.4446871280670166 -> 3.3753528594970703
1 day, 20:39:32.934290 INFO: Updating optimization_manager: fwhm_mobility       : 0.010783446952700615 -> 0.01014096848666668
1 day, 20:39:32.934346 INFO: Updating optimization_manager: score_cutoff        : 47.97224899749756 -> 47.74091625823974
1 day, 20:39:32.934398 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:32.935460 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:32.936807 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:32.937586 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:39:32.939772 INFO: === checking if optimization conditions were reached ===
1 day, 20:39:32.941433 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.494642
1 day, 20:39:32.941535 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 20:39:32.941596 PROGRESS: ❌ ms2_error      : 17.4946 > 17.4946 or insufficient steps taken.
1 day, 20:39:32.942551 INFO: Updating optimization_manager: ms1_error           : 30 -> 11.909770455953797
1 day, 20:39:32.942646 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 20:39:32.942705 PROGRESS: ❌ ms1_error      : 11.9098 > 7.5755 or insufficient steps taken.
1 day, 20:39:32.942757 INFO: ==============================================
1 day, 20:39:32.942815 INFO: Starting optimization step 3.
1 day, 20:39:32.942867 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:39:32.942915 INFO: Using classic extraction backend
1 day, 20:39:32.943052 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:39:32.943116 INFO: === Search parameters used ===
1 day, 20:39:32.943348 INFO: rt_error       : 2099.9331315
1 day, 20:39:32.943398 INFO: mobility_error : 0.1
1 day, 20:39:32.943440 INFO: num_candidates : 3
1 day, 20:39:32.943480 INFO: ms1_error      : 11.909770455953797
1 day, 20:39:32.943523 INFO: ms2_error      : 17.494642
1 day, 20:39:32.943564 INFO: fwhm_rt        : 3.3753528594970703
1 day, 20:39:32.943602 INFO: quant_window   : 3
1 day, 20:39:32.943641 INFO: ==============================================
1 day, 20:39:32.944458 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:39:32.944502 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:39:32.944536 INFO: FWHM in RT is 3.38 seconds, sigma is 0.74
1 day, 20:39:32.944557 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.70
1 day, 20:39:32.945717 INFO: Starting candidate selection
1 day, 20:39:41.419463 INFO: Starting candidate scoring
1 day, 20:39:41.629972 INFO: Finished candidate processing
1 day, 20:39:41.630075 INFO: Collecting candidate features
1 day, 20:39:41.644744 INFO: Collecting fragment features
1 day, 20:39:41.649306 INFO: Finished candidate scoring
1 day, 20:39:41.652190 INFO: performing precursor FDR with 47 features
1 day, 20:39:41.652243 INFO: Decoy channel: -1
1 day, 20:39:41.652268 INFO: Competetive: True
1 day, 20:39:41.655555 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:39:41.657711 INFO: Using random state 227613 for train-test-split
1 day, 20:39:41.668546 INFO: Test AUC: 0.535
1 day, 20:39:41.668605 INFO: Train AUC: 0.494
1 day, 20:39:41.668635 INFO: AUC difference: 8.26%
1 day, 20:39:41.668658 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:39:41.888057 INFO: Resetting torch num_threads to 80
1 day, 20:39:41.888729 PROGRESS: === Extracted 3406 precursors and 37888 fragments ===
1 day, 20:39:41.889244 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:39:41.890436 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:39:41.890561 PROGRESS: Total precursors accumulated: 600
1 day, 20:39:41.890621 PROGRESS: Target precursors: 492 (82.00%)
1 day, 20:39:41.890671 PROGRESS: Decoy precursors: 108 (18.00%)
1 day, 20:39:41.890715 PROGRESS: 
1 day, 20:39:41.890764 PROGRESS: Precursor Summary:
1 day, 20:39:41.891866 PROGRESS: Channel   0:	 0.050 FDR:   450; 0.010 FDR:   450; 0.001 FDR:   450
1 day, 20:39:41.891961 PROGRESS: 
1 day, 20:39:41.892017 PROGRESS: Protein Summary:
1 day, 20:39:41.893226 PROGRESS: Channel   0:	 0.050 FDR:   416; 0.010 FDR:   416; 0.001 FDR:   416
1 day, 20:39:41.893319 PROGRESS: =========================================================================
1 day, 20:39:41.893568 INFO: Target number of precursors reached.
1 day, 20:39:41.900335 INFO: fragments_df: keeping 5000 of 37888 [sum(precursor_idx_mask)=14257 sum(mass_error_mask)=37888 stop_rank=5000
1 day, 20:39:41.905755 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:42.045595 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:42.184353 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:42.319939 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:39:43.004932 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:39:43.005514 INFO: Using score_cutoff 39.684505713272095 (fac=0.99, q=1)
1 day, 20:39:43.005915 INFO: Updating optimization_manager: fwhm_rt             : 3.3753528594970703 -> 3.200900077819824
1 day, 20:39:43.005997 INFO: Updating optimization_manager: fwhm_mobility       : 0.01014096848666668 -> 0.008872045204043388
1 day, 20:39:43.006052 INFO: Updating optimization_manager: score_cutoff        : 47.74091625823974 -> 39.684505713272095
1 day, 20:39:43.006115 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:43.007280 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:43.008684 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:43.009469 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:39:43.011829 INFO: === checking if optimization conditions were reached ===
1 day, 20:39:43.013532 INFO: Updating optimization_manager: ms2_error           : 17.494642 -> 17.494642
1 day, 20:39:43.013644 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
1 day, 20:39:43.013711 PROGRESS: ✅ ms2_error      : 17.4946 <= 17.4946
1 day, 20:39:43.014974 INFO: Updating optimization_manager: ms1_error           : 11.909770455953797 -> 7.5754825
1 day, 20:39:43.015069 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
1 day, 20:39:43.015129 PROGRESS: ✅ ms1_error      : 7.5755 <= 7.5755
1 day, 20:39:43.015184 INFO: ==============================================
1 day, 20:39:43.015256 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 20:39:43.019602 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:43.020436 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:43.021774 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:43.022552 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:39:43.024740 INFO: Starting optimization step 0.
1 day, 20:39:43.024843 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:39:43.024921 INFO: Using classic extraction backend
1 day, 20:39:43.025117 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:39:43.025198 INFO: === Search parameters used ===
1 day, 20:39:43.025250 INFO: rt_error       : 2099.9331315
1 day, 20:39:43.025295 INFO: mobility_error : 0.1
1 day, 20:39:43.025340 INFO: num_candidates : 3
1 day, 20:39:43.025394 INFO: ms1_error      : 7.5754825
1 day, 20:39:43.025435 INFO: ms2_error      : 17.494642
1 day, 20:39:43.025473 INFO: fwhm_rt        : 3.200900077819824
1 day, 20:39:43.025514 INFO: quant_window   : 3
1 day, 20:39:43.025558 INFO: ==============================================
1 day, 20:39:43.026522 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:39:43.026568 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:39:43.026608 INFO: FWHM in RT is 3.20 seconds, sigma is 0.70
1 day, 20:39:43.026631 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 20:39:43.027393 INFO: Starting candidate selection
1 day, 20:39:51.980409 INFO: Starting candidate scoring
1 day, 20:39:52.204292 INFO: Finished candidate processing
1 day, 20:39:52.204400 INFO: Collecting candidate features
1 day, 20:39:52.217129 INFO: Collecting fragment features
1 day, 20:39:52.220989 INFO: Finished candidate scoring
1 day, 20:39:52.223337 INFO: performing precursor FDR with 47 features
1 day, 20:39:52.223382 INFO: Decoy channel: -1
1 day, 20:39:52.223406 INFO: Competetive: True
1 day, 20:39:52.226999 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:39:52.229319 INFO: Using random state 40552 for train-test-split
1 day, 20:39:52.240524 INFO: Test AUC: 0.497
1 day, 20:39:52.240580 INFO: Train AUC: 0.506
1 day, 20:39:52.240613 INFO: AUC difference: 1.86%
1 day, 20:39:52.463839 INFO: Resetting torch num_threads to 80
1 day, 20:39:52.464402 PROGRESS: === Extracted 3398 precursors and 37704 fragments ===
1 day, 20:39:52.464833 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:39:52.465522 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:39:52.465626 PROGRESS: Total precursors accumulated: 600
1 day, 20:39:52.465685 PROGRESS: Target precursors: 451 (75.17%)
1 day, 20:39:52.465736 PROGRESS: Decoy precursors: 149 (24.83%)
1 day, 20:39:52.465782 PROGRESS: 
1 day, 20:39:52.465826 PROGRESS: Precursor Summary:
1 day, 20:39:52.466831 PROGRESS: Channel   0:	 0.050 FDR:   376; 0.010 FDR:   376; 0.001 FDR:   376
1 day, 20:39:52.466925 PROGRESS: 
1 day, 20:39:52.466979 PROGRESS: Protein Summary:
1 day, 20:39:52.468151 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   350; 0.001 FDR:   350
1 day, 20:39:52.468247 PROGRESS: =========================================================================
1 day, 20:39:52.468392 INFO: Target number of precursors reached.
1 day, 20:39:52.474533 INFO: fragments_df: keeping 4482 of 37704 [sum(precursor_idx_mask)=11863 sum(mass_error_mask)=37704 stop_rank=4482
1 day, 20:39:52.478872 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:52.600543 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:52.729053 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:52.854814 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:39:53.390168 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:39:53.390595 INFO: Using score_cutoff 41.5844704914093 (fac=0.99, q=1)
1 day, 20:39:53.390913 INFO: Updating optimization_manager: fwhm_rt             : 3.200900077819824 -> 3.2570853233337402
1 day, 20:39:53.390995 INFO: Updating optimization_manager: fwhm_mobility       : 0.008872045204043388 -> 0.009064490906894207
1 day, 20:39:53.391049 INFO: Updating optimization_manager: score_cutoff        : 39.684505713272095 -> 41.5844704914093
1 day, 20:39:53.391103 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:53.392161 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:53.393550 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:53.394324 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:39:53.396535 INFO: === checking if optimization conditions were reached ===
1 day, 20:39:53.396646 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:39:53.398187 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 1128.9642073238783
1 day, 20:39:53.398288 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1128.9642.
1 day, 20:39:53.398351 INFO: ==============================================
1 day, 20:39:53.398415 INFO: Starting optimization step 1.
1 day, 20:39:53.398469 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:39:53.398523 INFO: Using classic extraction backend
1 day, 20:39:53.398628 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:39:53.398690 INFO: === Search parameters used ===
1 day, 20:39:53.398744 INFO: rt_error       : 1128.9642073238783
1 day, 20:39:53.398789 INFO: mobility_error : 0.1
1 day, 20:39:53.398830 INFO: num_candidates : 3
1 day, 20:39:53.398870 INFO: ms1_error      : 7.5754825
1 day, 20:39:53.398911 INFO: ms2_error      : 17.494642
1 day, 20:39:53.398955 INFO: fwhm_rt        : 3.2570853233337402
1 day, 20:39:53.398995 INFO: quant_window   : 3
1 day, 20:39:53.399034 INFO: ==============================================
1 day, 20:39:53.399816 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:39:53.399861 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:39:53.399895 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
1 day, 20:39:53.399918 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.20
1 day, 20:39:53.400583 INFO: Starting candidate selection
1 day, 20:39:59.120113 INFO: Starting candidate scoring
1 day, 20:39:59.344332 INFO: Finished candidate processing
1 day, 20:39:59.344471 INFO: Collecting candidate features
1 day, 20:39:59.359514 INFO: Collecting fragment features
1 day, 20:39:59.363198 INFO: Finished candidate scoring
1 day, 20:39:59.365762 INFO: performing precursor FDR with 47 features
1 day, 20:39:59.365812 INFO: Decoy channel: -1
1 day, 20:39:59.365837 INFO: Competetive: True
1 day, 20:39:59.368924 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:39:59.371091 INFO: Using random state 40552 for train-test-split
1 day, 20:39:59.382731 INFO: Test AUC: 0.479
1 day, 20:39:59.382801 INFO: Train AUC: 0.508
1 day, 20:39:59.382831 INFO: AUC difference: 5.74%
1 day, 20:39:59.382853 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:39:59.607857 INFO: Resetting torch num_threads to 80
1 day, 20:39:59.608405 PROGRESS: === Extracted 3398 precursors and 37787 fragments ===
1 day, 20:39:59.608809 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:39:59.609407 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:39:59.609509 PROGRESS: Total precursors accumulated: 600
1 day, 20:39:59.609567 PROGRESS: Target precursors: 451 (75.17%)
1 day, 20:39:59.609618 PROGRESS: Decoy precursors: 149 (24.83%)
1 day, 20:39:59.609663 PROGRESS: 
1 day, 20:39:59.609708 PROGRESS: Precursor Summary:
1 day, 20:39:59.610738 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   377; 0.001 FDR:   377
1 day, 20:39:59.610835 PROGRESS: 
1 day, 20:39:59.610890 PROGRESS: Protein Summary:
1 day, 20:39:59.612072 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   352; 0.001 FDR:   352
1 day, 20:39:59.612167 PROGRESS: =========================================================================
1 day, 20:39:59.612312 INFO: Target number of precursors reached.
1 day, 20:39:59.618337 INFO: fragments_df: keeping 4488 of 37787 [sum(precursor_idx_mask)=11901 sum(mass_error_mask)=37787 stop_rank=4488
1 day, 20:39:59.622599 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:39:59.727132 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:39:59.833816 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:39:59.941805 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:00.483849 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:40:00.484272 INFO: Using score_cutoff 40.264524508666995 (fac=0.99, q=1)
1 day, 20:40:00.484586 INFO: Updating optimization_manager: fwhm_rt             : 3.2570853233337402 -> 3.2650227546691895
1 day, 20:40:00.484668 INFO: Updating optimization_manager: fwhm_mobility       : 0.009064490906894207 -> 0.009035764262080193
1 day, 20:40:00.484721 INFO: Updating optimization_manager: score_cutoff        : 41.5844704914093 -> 40.264524508666995
1 day, 20:40:00.484774 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:00.485840 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:00.487219 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:00.487993 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:00.490202 INFO: === checking if optimization conditions were reached ===
1 day, 20:40:00.490305 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:40:00.491889 INFO: Updating optimization_manager: rt_error            : 1128.9642073238783 -> 845.901463425512
1 day, 20:40:00.491988 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 845.9015.
1 day, 20:40:00.492066 INFO: ==============================================
1 day, 20:40:00.492133 INFO: Starting optimization step 2.
1 day, 20:40:00.492191 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:40:00.492243 INFO: Using classic extraction backend
1 day, 20:40:00.492348 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:40:00.492418 INFO: === Search parameters used ===
1 day, 20:40:00.492465 INFO: rt_error       : 845.901463425512
1 day, 20:40:00.492507 INFO: mobility_error : 0.1
1 day, 20:40:00.492549 INFO: num_candidates : 3
1 day, 20:40:00.492589 INFO: ms1_error      : 7.5754825
1 day, 20:40:00.492628 INFO: ms2_error      : 17.494642
1 day, 20:40:00.492666 INFO: fwhm_rt        : 3.2650227546691895
1 day, 20:40:00.492704 INFO: quant_window   : 3
1 day, 20:40:00.492741 INFO: ==============================================
1 day, 20:40:00.493533 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:40:00.493580 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:40:00.493613 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 20:40:00.493634 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.19
1 day, 20:40:00.494327 INFO: Starting candidate selection
1 day, 20:40:05.030498 INFO: Starting candidate scoring
1 day, 20:40:05.236727 INFO: Finished candidate processing
1 day, 20:40:05.236825 INFO: Collecting candidate features
1 day, 20:40:05.249451 INFO: Collecting fragment features
1 day, 20:40:05.252995 INFO: Finished candidate scoring
1 day, 20:40:05.255202 INFO: performing precursor FDR with 47 features
1 day, 20:40:05.255248 INFO: Decoy channel: -1
1 day, 20:40:05.255277 INFO: Competetive: True
1 day, 20:40:05.260977 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:40:05.264517 INFO: Using random state 40552 for train-test-split
1 day, 20:40:05.281444 INFO: Test AUC: 0.493
1 day, 20:40:05.281540 INFO: Train AUC: 0.508
1 day, 20:40:05.281589 INFO: AUC difference: 3.07%
1 day, 20:40:05.511552 INFO: Resetting torch num_threads to 80
1 day, 20:40:05.512108 PROGRESS: === Extracted 3391 precursors and 37707 fragments ===
1 day, 20:40:05.512520 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:40:05.513177 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:40:05.513272 PROGRESS: Total precursors accumulated: 600
1 day, 20:40:05.513331 PROGRESS: Target precursors: 449 (74.83%)
1 day, 20:40:05.513385 PROGRESS: Decoy precursors: 151 (25.17%)
1 day, 20:40:05.513432 PROGRESS: 
1 day, 20:40:05.513485 PROGRESS: Precursor Summary:
1 day, 20:40:05.514500 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   378; 0.001 FDR:   378
1 day, 20:40:05.514596 PROGRESS: 
1 day, 20:40:05.514652 PROGRESS: Protein Summary:
1 day, 20:40:05.515826 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   355
1 day, 20:40:05.515929 PROGRESS: =========================================================================
1 day, 20:40:05.516070 INFO: Target number of precursors reached.
1 day, 20:40:05.522008 INFO: fragments_df: keeping 4538 of 37707 [sum(precursor_idx_mask)=11928 sum(mass_error_mask)=37707 stop_rank=4538
1 day, 20:40:05.526280 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:05.634448 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:05.748473 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:05.854835 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:06.398089 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:40:06.398520 INFO: Using score_cutoff 39.46056768608093 (fac=0.99, q=1)
1 day, 20:40:06.398825 INFO: Updating optimization_manager: fwhm_rt             : 3.2650227546691895 -> 3.2735676765441895
1 day, 20:40:06.398907 INFO: Updating optimization_manager: fwhm_mobility       : 0.009035764262080193 -> 0.008965249173343182
1 day, 20:40:06.398961 INFO: Updating optimization_manager: score_cutoff        : 40.264524508666995 -> 39.46056768608093
1 day, 20:40:06.399015 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:06.400071 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:06.401470 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:06.402252 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:06.404443 INFO: === checking if optimization conditions were reached ===
1 day, 20:40:06.404546 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:40:06.407024 INFO: Updating optimization_manager: rt_error            : 845.901463425512 -> 840.1646624487639
1 day, 20:40:06.407246 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 840.1647.
1 day, 20:40:06.407319 INFO: ==============================================
1 day, 20:40:06.407388 INFO: Starting optimization step 3.
1 day, 20:40:06.407445 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:40:06.407502 INFO: Using classic extraction backend
1 day, 20:40:06.407611 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:40:06.407679 INFO: === Search parameters used ===
1 day, 20:40:06.407727 INFO: rt_error       : 840.1646624487639
1 day, 20:40:06.407772 INFO: mobility_error : 0.1
1 day, 20:40:06.407814 INFO: num_candidates : 3
1 day, 20:40:06.407865 INFO: ms1_error      : 7.5754825
1 day, 20:40:06.407907 INFO: ms2_error      : 17.494642
1 day, 20:40:06.407948 INFO: fwhm_rt        : 3.2735676765441895
1 day, 20:40:06.407990 INFO: quant_window   : 3
1 day, 20:40:06.408028 INFO: ==============================================
1 day, 20:40:06.409203 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:40:06.409251 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:40:06.409285 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 20:40:06.409306 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.16
1 day, 20:40:06.410066 INFO: Starting candidate selection
1 day, 20:40:10.899891 INFO: Starting candidate scoring
1 day, 20:40:11.104321 INFO: Finished candidate processing
1 day, 20:40:11.105099 INFO: Collecting candidate features
1 day, 20:40:11.117953 INFO: Collecting fragment features
1 day, 20:40:11.121655 INFO: Finished candidate scoring
1 day, 20:40:11.123752 INFO: performing precursor FDR with 47 features
1 day, 20:40:11.123803 INFO: Decoy channel: -1
1 day, 20:40:11.123828 INFO: Competetive: True
1 day, 20:40:11.127398 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:40:11.129435 INFO: Using random state 40552 for train-test-split
1 day, 20:40:11.139890 INFO: Test AUC: 0.488
1 day, 20:40:11.139957 INFO: Train AUC: 0.508
1 day, 20:40:11.139986 INFO: AUC difference: 3.93%
1 day, 20:40:11.365114 INFO: Resetting torch num_threads to 80
1 day, 20:40:11.365663 PROGRESS: === Extracted 3394 precursors and 37735 fragments ===
1 day, 20:40:11.366069 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:40:11.366688 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:40:11.366778 PROGRESS: Total precursors accumulated: 600
1 day, 20:40:11.366836 PROGRESS: Target precursors: 439 (73.17%)
1 day, 20:40:11.366887 PROGRESS: Decoy precursors: 161 (26.83%)
1 day, 20:40:11.366932 PROGRESS: 
1 day, 20:40:11.366976 PROGRESS: Precursor Summary:
1 day, 20:40:11.367957 PROGRESS: Channel   0:	 0.050 FDR:   379; 0.010 FDR:   379; 0.001 FDR:   379
1 day, 20:40:11.368052 PROGRESS: 
1 day, 20:40:11.368108 PROGRESS: Protein Summary:
1 day, 20:40:11.369299 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   355
1 day, 20:40:11.369395 PROGRESS: =========================================================================
1 day, 20:40:11.369535 INFO: Target number of precursors reached.
1 day, 20:40:11.375583 INFO: fragments_df: keeping 4511 of 37735 [sum(precursor_idx_mask)=11925 sum(mass_error_mask)=37735 stop_rank=4511
1 day, 20:40:11.379853 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:11.484597 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:11.596114 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:11.702797 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:12.243064 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:40:12.243487 INFO: Using score_cutoff 38.86175821151733 (fac=0.99, q=1)
1 day, 20:40:12.243800 INFO: Updating optimization_manager: fwhm_rt             : 3.2735676765441895 -> 3.272610664367676
1 day, 20:40:12.243887 INFO: Updating optimization_manager: fwhm_mobility       : 0.008965249173343182 -> 0.008829683065414429
1 day, 20:40:12.243942 INFO: Updating optimization_manager: score_cutoff        : 39.46056768608093 -> 38.86175821151733
1 day, 20:40:12.243997 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:12.245080 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:12.246476 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:12.247258 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:12.249489 INFO: === checking if optimization conditions were reached ===
1 day, 20:40:12.249593 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 20:40:12.250552 INFO: Updating optimization_manager: rt_error            : 840.1646624487639 -> 840.1646624487639
1 day, 20:40:12.250672 INFO: Updating optimization_manager: classifier_version  : 3 -> 7
1 day, 20:40:12.250764 INFO: Updating optimization_manager: score_cutoff        : 38.86175821151733 -> 38.86175821151733
1 day, 20:40:12.250849 INFO: Updating optimization_manager: fwhm_rt             : 3.272610664367676 -> 3.272610664367676
1 day, 20:40:12.250930 INFO: Updating optimization_manager: fwhm_mobility       : 0.008829683065414429 -> 0.008829683065414429
1 day, 20:40:12.251009 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 840.1647 found after 4 searches.
1 day, 20:40:12.251070 INFO: ==============================================
1 day, 20:40:12.251132 PROGRESS: Optimization finished for rt_error.
1 day, 20:40:12.255006 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:12.255834 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:12.257167 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:12.257940 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:12.286194 INFO: Starting optimization step 0.
1 day, 20:40:12.286327 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:40:12.286396 INFO: Using classic extraction backend
1 day, 20:40:12.286514 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:40:12.286583 INFO: === Search parameters used ===
1 day, 20:40:12.286632 INFO: rt_error       : 840.1646624487639
1 day, 20:40:12.286675 INFO: mobility_error : 0.1
1 day, 20:40:12.286718 INFO: num_candidates : 3
1 day, 20:40:12.286760 INFO: ms1_error      : 7.5754825
1 day, 20:40:12.286800 INFO: ms2_error      : 17.494642
1 day, 20:40:12.286840 INFO: fwhm_rt        : 3.272610664367676
1 day, 20:40:12.286883 INFO: quant_window   : 3
1 day, 20:40:12.286922 INFO: ==============================================
1 day, 20:40:12.287701 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:40:12.287746 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:40:12.287780 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 20:40:12.287802 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.10
1 day, 20:40:12.288436 INFO: Starting candidate selection
1 day, 20:40:16.483286 INFO: Starting candidate scoring
1 day, 20:40:16.698368 INFO: Finished candidate processing
1 day, 20:40:16.698514 INFO: Collecting candidate features
1 day, 20:40:16.713453 INFO: Collecting fragment features
1 day, 20:40:16.717467 INFO: Finished candidate scoring
1 day, 20:40:16.719782 INFO: performing precursor FDR with 47 features
1 day, 20:40:16.719830 INFO: Decoy channel: -1
1 day, 20:40:16.719855 INFO: Competetive: True
1 day, 20:40:16.724272 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:40:16.726741 INFO: Using random state 104571 for train-test-split
1 day, 20:40:16.739337 INFO: Test AUC: 0.465
1 day, 20:40:16.739403 INFO: Train AUC: 0.513
1 day, 20:40:16.739434 INFO: AUC difference: 9.26%
1 day, 20:40:16.739457 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:40:16.987049 INFO: Resetting torch num_threads to 80
1 day, 20:40:16.987820 PROGRESS: === Extracted 3390 precursors and 37670 fragments ===
1 day, 20:40:16.988338 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:40:16.989231 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:40:16.989331 PROGRESS: Total precursors accumulated: 600
1 day, 20:40:16.989399 PROGRESS: Target precursors: 448 (74.67%)
1 day, 20:40:16.989454 PROGRESS: Decoy precursors: 152 (25.33%)
1 day, 20:40:16.989502 PROGRESS: 
1 day, 20:40:16.989547 PROGRESS: Precursor Summary:
1 day, 20:40:16.990646 PROGRESS: Channel   0:	 0.050 FDR:   376; 0.010 FDR:   376; 0.001 FDR:   376
1 day, 20:40:16.990744 PROGRESS: 
1 day, 20:40:16.990802 PROGRESS: Protein Summary:
1 day, 20:40:16.991974 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   352; 0.001 FDR:   352
1 day, 20:40:16.992068 PROGRESS: =========================================================================
1 day, 20:40:16.992277 INFO: Target number of precursors reached.
1 day, 20:40:16.999290 INFO: fragments_df: keeping 4504 of 37670 [sum(precursor_idx_mask)=11770 sum(mass_error_mask)=37670 stop_rank=4504
1 day, 20:40:17.005376 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:17.133265 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:17.273383 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:17.402687 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:17.952270 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:40:17.952696 INFO: Using score_cutoff 38.759967756271365 (fac=0.99, q=1)
1 day, 20:40:17.953008 INFO: Updating optimization_manager: fwhm_rt             : 3.272610664367676 -> 3.3319544792175293
1 day, 20:40:17.953090 INFO: Updating optimization_manager: fwhm_mobility       : 0.008829683065414429 -> 0.008830053731799126
1 day, 20:40:17.953144 INFO: Updating optimization_manager: score_cutoff        : 38.86175821151733 -> 38.759967756271365
1 day, 20:40:17.953205 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:17.954274 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:17.955676 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:17.956451 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:17.958675 INFO: === checking if optimization conditions were reached ===
1 day, 20:40:17.958776 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:40:17.960063 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07549984317266395
1 day, 20:40:17.960161 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0755.
1 day, 20:40:17.960222 INFO: ==============================================
1 day, 20:40:17.960289 INFO: Starting optimization step 1.
1 day, 20:40:17.960345 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:40:17.960400 INFO: Using classic extraction backend
1 day, 20:40:17.960500 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:40:17.960562 INFO: === Search parameters used ===
1 day, 20:40:17.960613 INFO: rt_error       : 840.1646624487639
1 day, 20:40:17.960654 INFO: mobility_error : 0.07549984317266395
1 day, 20:40:17.960698 INFO: num_candidates : 3
1 day, 20:40:17.960742 INFO: ms1_error      : 7.5754825
1 day, 20:40:17.960785 INFO: ms2_error      : 17.494642
1 day, 20:40:17.960825 INFO: fwhm_rt        : 3.3319544792175293
1 day, 20:40:17.960870 INFO: quant_window   : 3
1 day, 20:40:17.960910 INFO: ==============================================
1 day, 20:40:17.961718 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:40:17.961763 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:40:17.961795 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
1 day, 20:40:17.961817 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.10
1 day, 20:40:17.962533 INFO: Starting candidate selection
1 day, 20:40:22.128612 INFO: Starting candidate scoring
1 day, 20:40:22.336213 INFO: Finished candidate processing
1 day, 20:40:22.336963 INFO: Collecting candidate features
1 day, 20:40:22.349557 INFO: Collecting fragment features
1 day, 20:40:22.353158 INFO: Finished candidate scoring
1 day, 20:40:22.355291 INFO: performing precursor FDR with 47 features
1 day, 20:40:22.355334 INFO: Decoy channel: -1
1 day, 20:40:22.355357 INFO: Competetive: True
1 day, 20:40:22.358599 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:40:22.360667 INFO: Using random state 104571 for train-test-split
1 day, 20:40:22.372281 INFO: Test AUC: 0.526
1 day, 20:40:22.372339 INFO: Train AUC: 0.506
1 day, 20:40:22.372369 INFO: AUC difference: 3.92%
1 day, 20:40:22.596620 INFO: Resetting torch num_threads to 80
1 day, 20:40:22.597192 PROGRESS: === Extracted 3394 precursors and 37620 fragments ===
1 day, 20:40:22.597608 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:40:22.598180 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:40:22.598271 PROGRESS: Total precursors accumulated: 600
1 day, 20:40:22.598328 PROGRESS: Target precursors: 448 (74.67%)
1 day, 20:40:22.598378 PROGRESS: Decoy precursors: 152 (25.33%)
1 day, 20:40:22.598425 PROGRESS: 
1 day, 20:40:22.598469 PROGRESS: Precursor Summary:
1 day, 20:40:22.599466 PROGRESS: Channel   0:	 0.050 FDR:   370; 0.010 FDR:   370; 0.001 FDR:   370
1 day, 20:40:22.599559 PROGRESS: 
1 day, 20:40:22.599614 PROGRESS: Protein Summary:
1 day, 20:40:22.600772 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   348
1 day, 20:40:22.600864 PROGRESS: =========================================================================
1 day, 20:40:22.601047 INFO: Target number of precursors reached.
1 day, 20:40:22.606974 INFO: fragments_df: keeping 4445 of 37620 [sum(precursor_idx_mask)=11644 sum(mass_error_mask)=37620 stop_rank=4445
1 day, 20:40:22.611487 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:22.721152 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:22.834555 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:22.945804 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:23.494262 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:40:23.494692 INFO: Using score_cutoff 38.857774517440795 (fac=0.99, q=1)
1 day, 20:40:23.494999 INFO: Updating optimization_manager: fwhm_rt             : 3.3319544792175293 -> 3.349724292755127
1 day, 20:40:23.495080 INFO: Updating optimization_manager: fwhm_mobility       : 0.008830053731799126 -> 0.008822152391076088
1 day, 20:40:23.495132 INFO: Updating optimization_manager: score_cutoff        : 38.759967756271365 -> 38.857774517440795
1 day, 20:40:23.495184 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:23.496248 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:23.497623 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:23.498410 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:23.500630 INFO: === checking if optimization conditions were reached ===
1 day, 20:40:23.500730 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:40:23.502172 INFO: Updating optimization_manager: mobility_error      : 0.07549984317266395 -> 0.07185048166958545
1 day, 20:40:23.502271 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0719.
1 day, 20:40:23.502337 INFO: ==============================================
1 day, 20:40:23.502402 INFO: Starting optimization step 2.
1 day, 20:40:23.502458 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:40:23.502511 INFO: Using classic extraction backend
1 day, 20:40:23.502644 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:40:23.502723 INFO: === Search parameters used ===
1 day, 20:40:23.502773 INFO: rt_error       : 840.1646624487639
1 day, 20:40:23.502815 INFO: mobility_error : 0.07185048166958545
1 day, 20:40:23.502857 INFO: num_candidates : 3
1 day, 20:40:23.502897 INFO: ms1_error      : 7.5754825
1 day, 20:40:23.502937 INFO: ms2_error      : 17.494642
1 day, 20:40:23.502975 INFO: fwhm_rt        : 3.349724292755127
1 day, 20:40:23.503014 INFO: quant_window   : 3
1 day, 20:40:23.503054 INFO: ==============================================
1 day, 20:40:23.503960 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:40:23.504005 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:40:23.504039 INFO: FWHM in RT is 3.35 seconds, sigma is 0.74
1 day, 20:40:23.504061 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.09
1 day, 20:40:23.504753 INFO: Starting candidate selection
1 day, 20:40:27.489610 INFO: Starting candidate scoring
1 day, 20:40:27.701886 INFO: Finished candidate processing
1 day, 20:40:27.702037 INFO: Collecting candidate features
1 day, 20:40:27.733392 INFO: Collecting fragment features
1 day, 20:40:27.742449 INFO: Finished candidate scoring
1 day, 20:40:27.745801 INFO: performing precursor FDR with 47 features
1 day, 20:40:27.745900 INFO: Decoy channel: -1
1 day, 20:40:27.745956 INFO: Competetive: True
1 day, 20:40:27.752309 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:40:27.755635 INFO: Using random state 104571 for train-test-split
1 day, 20:40:27.773085 INFO: Test AUC: 0.463
1 day, 20:40:27.773180 INFO: Train AUC: 0.512
1 day, 20:40:27.773229 INFO: AUC difference: 9.53%
1 day, 20:40:27.773265 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:40:28.001878 INFO: Resetting torch num_threads to 80
1 day, 20:40:28.002748 PROGRESS: === Extracted 3381 precursors and 37403 fragments ===
1 day, 20:40:28.003170 INFO: === FDR correction performed with classifier version 7 ===
1 day, 20:40:28.003789 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:40:28.003882 PROGRESS: Total precursors accumulated: 600
1 day, 20:40:28.003939 PROGRESS: Target precursors: 439 (73.17%)
1 day, 20:40:28.004000 PROGRESS: Decoy precursors: 161 (26.83%)
1 day, 20:40:28.004049 PROGRESS: 
1 day, 20:40:28.004094 PROGRESS: Precursor Summary:
1 day, 20:40:28.005094 PROGRESS: Channel   0:	 0.050 FDR:   359; 0.010 FDR:   359; 0.001 FDR:   359
1 day, 20:40:28.005192 PROGRESS: 
1 day, 20:40:28.005251 PROGRESS: Protein Summary:
1 day, 20:40:28.006407 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   338; 0.001 FDR:   338
1 day, 20:40:28.006500 PROGRESS: =========================================================================
1 day, 20:40:28.006745 INFO: Target number of precursors reached.
1 day, 20:40:28.012669 INFO: fragments_df: keeping 4318 of 37403 [sum(precursor_idx_mask)=11261 sum(mass_error_mask)=37403 stop_rank=4318
1 day, 20:40:28.017824 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:28.144779 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:28.274846 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:28.401962 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:28.980779 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:40:28.981581 INFO: Using score_cutoff 38.707916809844974 (fac=0.99, q=1)
1 day, 20:40:28.982006 INFO: Updating optimization_manager: fwhm_rt             : 3.349724292755127 -> 3.3369221687316895
1 day, 20:40:28.982087 INFO: Updating optimization_manager: fwhm_mobility       : 0.008822152391076088 -> 0.008829683065414429
1 day, 20:40:28.982141 INFO: Updating optimization_manager: score_cutoff        : 38.857774517440795 -> 38.707916809844974
1 day, 20:40:28.982212 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:28.983829 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:28.985220 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:28.986004 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:28.988186 INFO: === checking if optimization conditions were reached ===
1 day, 20:40:28.988301 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:40:28.989219 INFO: Updating optimization_manager: mobility_error      : 0.07185048166958545 -> 0.1
1 day, 20:40:28.989353 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1 day, 20:40:28.989446 INFO: Updating optimization_manager: score_cutoff        : 38.707916809844974 -> 38.759967756271365
1 day, 20:40:28.989533 INFO: Updating optimization_manager: fwhm_rt             : 3.3369221687316895 -> 3.3319544792175293
1 day, 20:40:28.989615 INFO: Updating optimization_manager: fwhm_mobility       : 0.008829683065414429 -> 0.008830053731799126
1 day, 20:40:28.989697 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 20:40:28.989757 INFO: ==============================================
1 day, 20:40:28.989828 PROGRESS: Optimization finished for mobility_error.
1 day, 20:40:28.994210 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:28.995045 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:28.996352 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:28.997133 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:29.025113 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:40:29.025261 PROGRESS: ==============================================
1 day, 20:40:29.025332 PROGRESS: ms2_error      : 17.4946
1 day, 20:40:29.025392 PROGRESS: ms1_error      : 7.5755
1 day, 20:40:29.025445 PROGRESS: rt_error       : 840.1647
1 day, 20:40:29.025491 PROGRESS: mobility_error : 0.1000
1 day, 20:40:29.025534 PROGRESS: ==============================================
1 day, 20:40:29.026274 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:40:29.046021 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:40:29.128678 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:40:29.150251 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:40:29.375560 INFO: Using classic extraction backend
1 day, 20:40:29.376061 PROGRESS: Extracting batch of 146455 precursors
1 day, 20:40:29.376181 INFO: === Search parameters used ===
1 day, 20:40:29.376245 INFO: rt_error       : 840.1646624487639
1 day, 20:40:29.376300 INFO: mobility_error : 0.1
1 day, 20:40:29.376352 INFO: num_candidates : 3
1 day, 20:40:29.376403 INFO: ms1_error      : 7.5754825
1 day, 20:40:29.376453 INFO: ms2_error      : 17.494642
1 day, 20:40:29.376503 INFO: fwhm_rt        : 3.3319544792175293
1 day, 20:40:29.376549 INFO: quant_window   : 3
1 day, 20:40:29.376598 INFO: ==============================================
1 day, 20:40:29.412681 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:40:29.412802 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:40:29.412854 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
1 day, 20:40:29.412879 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.10
1 day, 20:40:29.413643 INFO: Starting candidate selection
1 day, 20:47:48.842398 INFO: Removed 20271 precursors with score below cutoff 38.759967756271365
1 day, 20:47:49.180098 INFO: Starting candidate scoring
1 day, 20:48:05.270790 INFO: Finished candidate processing
1 day, 20:48:05.271787 INFO: Collecting candidate features
1 day, 20:48:05.841931 INFO: Collecting fragment features
1 day, 20:48:06.099828 INFO: Finished candidate scoring
1 day, 20:48:06.372673 INFO: === Performing FDR correction with classifier version 8 ===
1 day, 20:48:06.376150 INFO: performing precursor FDR with 47 features
1 day, 20:48:06.376241 INFO: Decoy channel: -1
1 day, 20:48:06.376270 INFO: Competetive: True
1 day, 20:48:06.481283 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:48:06.645219 INFO: Using random state 650907 for train-test-split
1 day, 20:48:14.926339 INFO: Test AUC: 0.757
1 day, 20:48:14.926504 INFO: Train AUC: 0.760
1 day, 20:48:14.926543 INFO: AUC difference: 0.38%
1 day, 20:48:15.352015 INFO: Resetting torch num_threads to 80
1 day, 20:48:15.369039 INFO: Removing fragments below FDR threshold
1 day, 20:48:15.448785 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:48:15.449140 PROGRESS: Total precursors accumulated: 67,847
1 day, 20:48:15.449212 PROGRESS: Target precursors: 67,176 (99.01%)
1 day, 20:48:15.449267 PROGRESS: Decoy precursors: 671 (0.99%)
1 day, 20:48:15.449329 PROGRESS: 
1 day, 20:48:15.449375 PROGRESS: Precursor Summary:
1 day, 20:48:15.484397 PROGRESS: Channel   0:	 0.050 FDR: 67,176; 0.010 FDR: 67,176; 0.001 FDR: 62,308
1 day, 20:48:15.484720 PROGRESS: 
1 day, 20:48:15.484785 PROGRESS: Protein Summary:
1 day, 20:48:15.527498 PROGRESS: Channel   0:	 0.050 FDR: 7,366; 0.010 FDR: 7,366; 0.001 FDR: 7,288
1 day, 20:48:15.527812 PROGRESS: =========================================================================
1 day, 20:48:15.533049 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/psm.parquet
1 day, 20:48:15.832832 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/frag.parquet
1 day, 20:48:16.089964 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:48:16.142999 PROGRESS: 
1 day, 20:48:16.143236 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
1 day, 20:48:16.143329 INFO: Creating folder run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/figures
1 day, 20:48:16.143579 INFO: Initializing TimingManager
1 day, 20:48:16.144348 INFO: Initializing RawFileManager
1 day, 20:48:16.144497 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:16.144584 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:16.144651 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:16.373366 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, 20:48:24.187458 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
1 day, 20:48:24.190781 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:24.201084 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:24.201514 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:24.202101 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:24.203790 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:24.221143 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:24.221518 INFO: Indexing quadrupole dimension
1 day, 20:48:24.710991 INFO: Transposing detector events
1 day, 20:48:38.498724 INFO: Finished transposing data
1 day, 20:48:38.536388 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:48:38.539157 INFO: RT (min)            : 0.0 - 70.0
1 day, 20:48:38.539259 INFO: RT duration (sec)   : 4199.8
1 day, 20:48:38.539317 INFO: RT duration (min)   : 70.0
1 day, 20:48:38.539367 INFO: Cycle len (scans)   : 9
1 day, 20:48:38.539417 INFO: Cycle len (sec)     : 0.97
1 day, 20:48:38.539462 INFO: Number of cycles    : 4347
1 day, 20:48:38.539509 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 20:48:38.539649 INFO: Creating DIA data object took: 22.395148038864136
1 day, 20:48:38.592507 INFO: Initializing CalibrationManager
1 day, 20:48:38.592900 INFO: Setting up calibration estimators ..
1 day, 20:48:38.593029 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 20:48:38.593147 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, 20:48:38.593261 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 20:48:38.593323 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, 20:48:38.593384 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, 20:48:38.593460 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, 20:48:38.593509 INFO: Done setting up calibration estimators.
1 day, 20:48:38.593646 INFO: Initializing OptimizationManager
1 day, 20:48:38.593743 INFO: initial parameter: ms1_error = 30
1 day, 20:48:38.593791 INFO: initial parameter: ms2_error = 30
1 day, 20:48:38.593835 INFO: initial parameter: rt_error = 2099.9231665
1 day, 20:48:38.593878 INFO: initial parameter: mobility_error = 0.1
1 day, 20:48:38.593920 INFO: initial parameter: num_candidates = 1
1 day, 20:48:38.593960 INFO: initial parameter: fwhm_rt = 5
1 day, 20:48:38.594002 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 20:48:38.594043 INFO: initial parameter: score_cutoff = 0
1 day, 20:48:38.594090 INFO: initial parameter: classifier_version = -1
1 day, 20:48:38.594178 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:48:38.594616 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 20:48:38.594654 INFO: Initializing FDRManager
1 day, 20:48:38.594704 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 20:48:38.618811 PROGRESS: Initializing spectral library: 73,677 target precursors potentially observable (0 removed)
1 day, 20:48:38.633285 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 20:48:38.633712 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 2099.9231665
1 day, 20:48:38.633850 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 20:48:38.634026 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 20:48:38.634124 PROGRESS: Starting initial search for precursors.
1 day, 20:48:38.634204 INFO: Starting optimization step 0.
1 day, 20:48:38.634265 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 20:48:38.634345 INFO: Using classic extraction backend
1 day, 20:48:38.634615 PROGRESS: Extracting batch of 399 precursors
1 day, 20:48:38.634704 INFO: === Search parameters used ===
1 day, 20:48:38.634756 INFO: rt_error       : 2099.9231665
1 day, 20:48:38.634801 INFO: mobility_error : 0.1
1 day, 20:48:38.634842 INFO: num_candidates : 1
1 day, 20:48:38.634881 INFO: ms1_error      : 30
1 day, 20:48:38.634921 INFO: ms2_error      : 30
1 day, 20:48:38.634962 INFO: fwhm_rt        : 5
1 day, 20:48:38.635000 INFO: quant_window   : 3
1 day, 20:48:38.635037 INFO: ==============================================
1 day, 20:48:38.636203 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:48:38.636249 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:48:38.636286 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:48:38.636307 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:48:38.641201 INFO: Starting candidate selection
1 day, 20:48:43.102284 INFO: Starting candidate scoring
1 day, 20:48:43.202691 INFO: Finished candidate processing
1 day, 20:48:43.202980 INFO: Collecting candidate features
1 day, 20:48:43.213246 INFO: Collecting fragment features
1 day, 20:48:43.215617 INFO: Finished candidate scoring
1 day, 20:48:43.216529 INFO: performing precursor FDR with 47 features
1 day, 20:48:43.216574 INFO: Decoy channel: -1
1 day, 20:48:43.216603 INFO: Competetive: True
1 day, 20:48:43.217853 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:48:43.220935 INFO: Using random state 866050 for train-test-split
1 day, 20:48:43.234846 INFO: Test AUC: 0.487
1 day, 20:48:43.234946 INFO: Train AUC: 0.494
1 day, 20:48:43.234997 INFO: AUC difference: 1.55%
1 day, 20:48:43.466798 INFO: Resetting torch num_threads to 80
1 day, 20:48:43.467293 PROGRESS: === Extracted 399 precursors and 4566 fragments ===
1 day, 20:48:43.467729 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:48:43.468262 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:48:43.468354 PROGRESS: Total precursors accumulated: 200
1 day, 20:48:43.468412 PROGRESS: Target precursors: 191 (95.50%)
1 day, 20:48:43.468462 PROGRESS: Decoy precursors: 9 (4.50%)
1 day, 20:48:43.468508 PROGRESS: 
1 day, 20:48:43.468552 PROGRESS: Precursor Summary:
1 day, 20:48:43.469491 PROGRESS: Channel   0:	 0.050 FDR:   191; 0.010 FDR:   190; 0.001 FDR:   190
1 day, 20:48:43.469581 PROGRESS: 
1 day, 20:48:43.469641 PROGRESS: Protein Summary:
1 day, 20:48:43.470731 PROGRESS: Channel   0:	 0.050 FDR:   184; 0.010 FDR:   183; 0.001 FDR:   183
1 day, 20:48:43.470829 PROGRESS: =========================================================================
1 day, 20:48:43.470943 INFO: Target number of precursors not reached yet.
1 day, 20:48:43.474579 INFO: Starting optimization step 1.
1 day, 20:48:43.474692 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 20:48:43.474762 INFO: Using classic extraction backend
1 day, 20:48:43.474880 PROGRESS: Extracting batch of 795 precursors
1 day, 20:48:43.474950 INFO: === Search parameters used ===
1 day, 20:48:43.474999 INFO: rt_error       : 2099.9231665
1 day, 20:48:43.475044 INFO: mobility_error : 0.1
1 day, 20:48:43.475091 INFO: num_candidates : 1
1 day, 20:48:43.475145 INFO: ms1_error      : 30
1 day, 20:48:43.475201 INFO: ms2_error      : 30
1 day, 20:48:43.475253 INFO: fwhm_rt        : 5
1 day, 20:48:43.475307 INFO: quant_window   : 3
1 day, 20:48:43.475357 INFO: ==============================================
1 day, 20:48:43.476040 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:48:43.476086 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:48:43.476116 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:48:43.476137 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:48:43.476847 INFO: Starting candidate selection
1 day, 20:48:49.876889 INFO: Starting candidate scoring
1 day, 20:48:50.001175 INFO: Finished candidate processing
1 day, 20:48:50.001293 INFO: Collecting candidate features
1 day, 20:48:50.012473 INFO: Collecting fragment features
1 day, 20:48:50.014968 INFO: Finished candidate scoring
1 day, 20:48:50.017142 INFO: performing precursor FDR with 47 features
1 day, 20:48:50.017197 INFO: Decoy channel: -1
1 day, 20:48:50.017223 INFO: Competetive: True
1 day, 20:48:50.021031 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:48:50.022874 INFO: Using random state 165475 for train-test-split
1 day, 20:48:50.030817 INFO: Test AUC: 0.500
1 day, 20:48:50.030881 INFO: Train AUC: 0.507
1 day, 20:48:50.030912 INFO: AUC difference: 1.46%
1 day, 20:48:50.249828 INFO: Resetting torch num_threads to 80
1 day, 20:48:50.251279 PROGRESS: === Extracted 1193 precursors and 13592 fragments ===
1 day, 20:48:50.252355 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:48:50.252963 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:48:50.253053 PROGRESS: Total precursors accumulated: 600
1 day, 20:48:50.253112 PROGRESS: Target precursors: 582 (97.00%)
1 day, 20:48:50.253171 PROGRESS: Decoy precursors: 18 (3.00%)
1 day, 20:48:50.253220 PROGRESS: 
1 day, 20:48:50.253265 PROGRESS: Precursor Summary:
1 day, 20:48:50.254358 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   579; 0.001 FDR:   579
1 day, 20:48:50.254452 PROGRESS: 
1 day, 20:48:50.254510 PROGRESS: Protein Summary:
1 day, 20:48:50.255820 PROGRESS: Channel   0:	 0.050 FDR:   528; 0.010 FDR:   525; 0.001 FDR:   525
1 day, 20:48:50.255914 PROGRESS: =========================================================================
1 day, 20:48:50.256074 INFO: Target number of precursors reached.
1 day, 20:48:50.259798 INFO: fragments_df: keeping 3859 of 13592 [sum(precursor_idx_mask)=6585 sum(mass_error_mask)=13592 stop_rank=3859
1 day, 20:48:50.264641 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:48:50.389092 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:48:50.514304 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:48:50.639000 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:48:51.081225 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 20:48:51.081737 INFO: Using score_cutoff 49.504209947204586 (fac=0.99, q=1)
1 day, 20:48:51.082102 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.2974021434783936
1 day, 20:48:51.082183 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.01031171903014183
1 day, 20:48:51.082240 INFO: Updating optimization_manager: score_cutoff        : 0 -> 49.504209947204586
1 day, 20:48:51.082518 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:48:51.083752 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:48:51.085148 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:48:51.085915 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:48:51.088289 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
1 day, 20:48:51.088384 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 20:48:51.088463 INFO: Starting optimization step 2.
1 day, 20:48:51.088522 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:48:51.088577 INFO: Using classic extraction backend
1 day, 20:48:51.088696 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:48:51.088760 INFO: === Search parameters used ===
1 day, 20:48:51.088807 INFO: rt_error       : 2099.9231665
1 day, 20:48:51.088850 INFO: mobility_error : 0.1
1 day, 20:48:51.088891 INFO: num_candidates : 3
1 day, 20:48:51.088931 INFO: ms1_error      : 30
1 day, 20:48:51.088980 INFO: ms2_error      : 30
1 day, 20:48:51.089020 INFO: fwhm_rt        : 3.2974021434783936
1 day, 20:48:51.089060 INFO: quant_window   : 3
1 day, 20:48:51.089098 INFO: ==============================================
1 day, 20:48:51.089995 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:48:51.090041 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:48:51.090074 INFO: FWHM in RT is 3.30 seconds, sigma is 0.72
1 day, 20:48:51.090101 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.78
1 day, 20:48:51.090827 INFO: Starting candidate selection
1 day, 20:49:00.895188 INFO: Starting candidate scoring
1 day, 20:49:01.250515 INFO: Finished candidate processing
1 day, 20:49:01.250634 INFO: Collecting candidate features
1 day, 20:49:01.264614 INFO: Collecting fragment features
1 day, 20:49:01.269234 INFO: Finished candidate scoring
1 day, 20:49:01.271315 INFO: performing precursor FDR with 47 features
1 day, 20:49:01.271366 INFO: Decoy channel: -1
1 day, 20:49:01.271392 INFO: Competetive: True
1 day, 20:49:01.274945 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:49:01.277121 INFO: Using random state 476306 for train-test-split
1 day, 20:49:01.288955 INFO: Test AUC: 0.500
1 day, 20:49:01.289021 INFO: Train AUC: 0.501
1 day, 20:49:01.289052 INFO: AUC difference: 0.18%
1 day, 20:49:01.506791 INFO: Resetting torch num_threads to 80
1 day, 20:49:01.507369 PROGRESS: === Extracted 3411 precursors and 38810 fragments ===
1 day, 20:49:01.507798 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:49:01.508459 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:49:01.508555 PROGRESS: Total precursors accumulated: 600
1 day, 20:49:01.508614 PROGRESS: Target precursors: 595 (99.17%)
1 day, 20:49:01.508665 PROGRESS: Decoy precursors: 5 (0.83%)
1 day, 20:49:01.508710 PROGRESS: 
1 day, 20:49:01.508756 PROGRESS: Precursor Summary:
1 day, 20:49:01.509815 PROGRESS: Channel   0:	 0.050 FDR:   595; 0.010 FDR:   595; 0.001 FDR:   595
1 day, 20:49:01.509911 PROGRESS: 
1 day, 20:49:01.509967 PROGRESS: Protein Summary:
1 day, 20:49:01.511259 PROGRESS: Channel   0:	 0.050 FDR:   539; 0.010 FDR:   539; 0.001 FDR:   539
1 day, 20:49:01.511354 PROGRESS: =========================================================================
1 day, 20:49:01.511497 INFO: Target number of precursors reached.
1 day, 20:49:01.518955 INFO: fragments_df: keeping 5000 of 38810 [sum(precursor_idx_mask)=19427 sum(mass_error_mask)=38810 stop_rank=5000
1 day, 20:49:01.523787 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:01.646135 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:01.770609 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:01.890068 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:02.503023 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:49:02.503491 INFO: Using score_cutoff 49.06854378204346 (fac=0.99, q=1)
1 day, 20:49:02.503829 INFO: Updating optimization_manager: fwhm_rt             : 3.2974021434783936 -> 3.233872175216675
1 day, 20:49:02.503923 INFO: Updating optimization_manager: fwhm_mobility       : 0.01031171903014183 -> 0.010094226337969303
1 day, 20:49:02.503978 INFO: Updating optimization_manager: score_cutoff        : 49.504209947204586 -> 49.06854378204346
1 day, 20:49:02.504030 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:02.505126 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:02.506478 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:02.507236 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:02.509357 INFO: === checking if optimization conditions were reached ===
1 day, 20:49:02.510932 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.494642
1 day, 20:49:02.511042 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 20:49:02.511103 PROGRESS: ❌ ms2_error      : 17.4946 > 17.4946 or insufficient steps taken.
1 day, 20:49:02.512068 INFO: Updating optimization_manager: ms1_error           : 30 -> 10.58178927776165
1 day, 20:49:02.512164 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 20:49:02.512223 PROGRESS: ❌ ms1_error      : 10.5818 > 7.5755 or insufficient steps taken.
1 day, 20:49:02.512276 INFO: ==============================================
1 day, 20:49:02.512340 INFO: Starting optimization step 3.
1 day, 20:49:02.512395 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:49:02.512450 INFO: Using classic extraction backend
1 day, 20:49:02.512562 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:49:02.512623 INFO: === Search parameters used ===
1 day, 20:49:02.512676 INFO: rt_error       : 2099.9231665
1 day, 20:49:02.512719 INFO: mobility_error : 0.1
1 day, 20:49:02.512759 INFO: num_candidates : 3
1 day, 20:49:02.512798 INFO: ms1_error      : 10.58178927776165
1 day, 20:49:02.512837 INFO: ms2_error      : 17.494642
1 day, 20:49:02.512874 INFO: fwhm_rt        : 3.233872175216675
1 day, 20:49:02.512912 INFO: quant_window   : 3
1 day, 20:49:02.512960 INFO: ==============================================
1 day, 20:49:02.513765 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:49:02.513809 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:49:02.513845 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
1 day, 20:49:02.513866 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.68
1 day, 20:49:02.514565 INFO: Starting candidate selection
1 day, 20:49:12.098648 INFO: Starting candidate scoring
1 day, 20:49:12.308752 INFO: Finished candidate processing
1 day, 20:49:12.308866 INFO: Collecting candidate features
1 day, 20:49:12.323043 INFO: Collecting fragment features
1 day, 20:49:12.327303 INFO: Finished candidate scoring
1 day, 20:49:12.329480 INFO: performing precursor FDR with 47 features
1 day, 20:49:12.329531 INFO: Decoy channel: -1
1 day, 20:49:12.329556 INFO: Competetive: True
1 day, 20:49:12.332884 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:49:12.335060 INFO: Using random state 740215 for train-test-split
1 day, 20:49:12.346045 INFO: Test AUC: 0.491
1 day, 20:49:12.346111 INFO: Train AUC: 0.505
1 day, 20:49:12.346140 INFO: AUC difference: 2.85%
1 day, 20:49:12.562864 INFO: Resetting torch num_threads to 80
1 day, 20:49:12.563432 PROGRESS: === Extracted 3390 precursors and 37729 fragments ===
1 day, 20:49:12.563860 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:49:12.564589 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:49:12.564681 PROGRESS: Total precursors accumulated: 600
1 day, 20:49:12.564743 PROGRESS: Target precursors: 579 (96.50%)
1 day, 20:49:12.564795 PROGRESS: Decoy precursors: 21 (3.50%)
1 day, 20:49:12.564840 PROGRESS: 
1 day, 20:49:12.564885 PROGRESS: Precursor Summary:
1 day, 20:49:12.565935 PROGRESS: Channel   0:	 0.050 FDR:   579; 0.010 FDR:   572; 0.001 FDR:   572
1 day, 20:49:12.566049 PROGRESS: 
1 day, 20:49:12.566107 PROGRESS: Protein Summary:
1 day, 20:49:12.567374 PROGRESS: Channel   0:	 0.050 FDR:   527; 0.010 FDR:   520; 0.001 FDR:   520
1 day, 20:49:12.567467 PROGRESS: =========================================================================
1 day, 20:49:12.567612 INFO: Target number of precursors reached.
1 day, 20:49:12.574704 INFO: fragments_df: keeping 5000 of 37729 [sum(precursor_idx_mask)=18306 sum(mass_error_mask)=37729 stop_rank=5000
1 day, 20:49:12.579455 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:12.700572 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:12.822861 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:12.943735 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:13.555371 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:49:13.555839 INFO: Using score_cutoff 39.82896435127258 (fac=0.99, q=1)
1 day, 20:49:13.556157 INFO: Updating optimization_manager: fwhm_rt             : 3.233872175216675 -> 2.9949703216552734
1 day, 20:49:13.556238 INFO: Updating optimization_manager: fwhm_mobility       : 0.010094226337969303 -> 0.00884279329329729
1 day, 20:49:13.556291 INFO: Updating optimization_manager: score_cutoff        : 49.06854378204346 -> 39.82896435127258
1 day, 20:49:13.556345 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:13.557452 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:13.558784 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:13.559543 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:13.561669 INFO: === checking if optimization conditions were reached ===
1 day, 20:49:13.563229 INFO: Updating optimization_manager: ms2_error           : 17.494642 -> 17.494642
1 day, 20:49:13.563330 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
1 day, 20:49:13.563394 PROGRESS: ✅ ms2_error      : 17.4946 <= 17.4946
1 day, 20:49:13.564366 INFO: Updating optimization_manager: ms1_error           : 10.58178927776165 -> 7.5754825
1 day, 20:49:13.564460 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
1 day, 20:49:13.564519 PROGRESS: ✅ ms1_error      : 7.5755 <= 7.5755
1 day, 20:49:13.564572 INFO: ==============================================
1 day, 20:49:13.564638 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 20:49:13.569064 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:13.569884 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:13.571185 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:13.571947 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:13.574087 INFO: Starting optimization step 0.
1 day, 20:49:13.574193 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:49:13.574258 INFO: Using classic extraction backend
1 day, 20:49:13.574378 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:49:13.574449 INFO: === Search parameters used ===
1 day, 20:49:13.574500 INFO: rt_error       : 2099.9231665
1 day, 20:49:13.574545 INFO: mobility_error : 0.1
1 day, 20:49:13.574587 INFO: num_candidates : 3
1 day, 20:49:13.574629 INFO: ms1_error      : 7.5754825
1 day, 20:49:13.574668 INFO: ms2_error      : 17.494642
1 day, 20:49:13.574708 INFO: fwhm_rt        : 2.9949703216552734
1 day, 20:49:13.574748 INFO: quant_window   : 3
1 day, 20:49:13.574800 INFO: ==============================================
1 day, 20:49:13.575510 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:49:13.575556 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:49:13.575590 INFO: FWHM in RT is 2.99 seconds, sigma is 0.66
1 day, 20:49:13.575611 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.10
1 day, 20:49:13.576300 INFO: Starting candidate selection
1 day, 20:49:22.185230 INFO: Starting candidate scoring
1 day, 20:49:22.394427 INFO: Finished candidate processing
1 day, 20:49:22.394543 INFO: Collecting candidate features
1 day, 20:49:22.409003 INFO: Collecting fragment features
1 day, 20:49:22.412770 INFO: Finished candidate scoring
1 day, 20:49:22.414947 INFO: performing precursor FDR with 47 features
1 day, 20:49:22.414997 INFO: Decoy channel: -1
1 day, 20:49:22.415022 INFO: Competetive: True
1 day, 20:49:22.418187 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:49:22.420247 INFO: Using random state 815013 for train-test-split
1 day, 20:49:22.430594 INFO: Test AUC: 0.515
1 day, 20:49:22.430655 INFO: Train AUC: 0.507
1 day, 20:49:22.430686 INFO: AUC difference: 1.42%
1 day, 20:49:22.644268 INFO: Resetting torch num_threads to 80
1 day, 20:49:22.644824 PROGRESS: === Extracted 3390 precursors and 37733 fragments ===
1 day, 20:49:22.645279 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:49:22.645877 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:49:22.645969 PROGRESS: Total precursors accumulated: 600
1 day, 20:49:22.646028 PROGRESS: Target precursors: 555 (92.50%)
1 day, 20:49:22.646078 PROGRESS: Decoy precursors: 45 (7.50%)
1 day, 20:49:22.646123 PROGRESS: 
1 day, 20:49:22.646168 PROGRESS: Precursor Summary:
1 day, 20:49:22.647191 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   541; 0.001 FDR:   541
1 day, 20:49:22.647284 PROGRESS: 
1 day, 20:49:22.647338 PROGRESS: Protein Summary:
1 day, 20:49:22.648589 PROGRESS: Channel   0:	 0.050 FDR:   491; 0.010 FDR:   491; 0.001 FDR:   491
1 day, 20:49:22.648689 PROGRESS: =========================================================================
1 day, 20:49:22.648841 INFO: Target number of precursors reached.
1 day, 20:49:22.655825 INFO: fragments_df: keeping 5000 of 37733 [sum(precursor_idx_mask)=17324 sum(mass_error_mask)=37733 stop_rank=5000
1 day, 20:49:22.660567 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:22.776466 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:22.896773 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:23.015393 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:23.631519 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:49:23.632024 INFO: Using score_cutoff 38.922062393188476 (fac=0.99, q=1)
1 day, 20:49:23.632369 INFO: Updating optimization_manager: fwhm_rt             : 2.9949703216552734 -> 3.0280303955078125
1 day, 20:49:23.632454 INFO: Updating optimization_manager: fwhm_mobility       : 0.00884279329329729 -> 0.008922403678297997
1 day, 20:49:23.632507 INFO: Updating optimization_manager: score_cutoff        : 39.82896435127258 -> 38.922062393188476
1 day, 20:49:23.632562 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:23.633685 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:23.635019 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:23.635784 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:23.637948 INFO: === checking if optimization conditions were reached ===
1 day, 20:49:23.638071 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:49:23.639739 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 917.9843149014104
1 day, 20:49:23.639850 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 917.9843.
1 day, 20:49:23.639917 INFO: ==============================================
1 day, 20:49:23.639983 INFO: Starting optimization step 1.
1 day, 20:49:23.640044 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:49:23.640100 INFO: Using classic extraction backend
1 day, 20:49:23.640217 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:49:23.640283 INFO: === Search parameters used ===
1 day, 20:49:23.640350 INFO: rt_error       : 917.9843149014104
1 day, 20:49:23.640397 INFO: mobility_error : 0.1
1 day, 20:49:23.640439 INFO: num_candidates : 3
1 day, 20:49:23.640481 INFO: ms1_error      : 7.5754825
1 day, 20:49:23.640521 INFO: ms2_error      : 17.494642
1 day, 20:49:23.640559 INFO: fwhm_rt        : 3.0280303955078125
1 day, 20:49:23.640600 INFO: quant_window   : 3
1 day, 20:49:23.640639 INFO: ==============================================
1 day, 20:49:23.641511 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:49:23.641557 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:49:23.641592 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 20:49:23.641616 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
1 day, 20:49:23.642440 INFO: Starting candidate selection
1 day, 20:49:29.003806 INFO: Starting candidate scoring
1 day, 20:49:29.203897 INFO: Finished candidate processing
1 day, 20:49:29.204015 INFO: Collecting candidate features
1 day, 20:49:29.217663 INFO: Collecting fragment features
1 day, 20:49:29.222037 INFO: Finished candidate scoring
1 day, 20:49:29.224046 INFO: performing precursor FDR with 47 features
1 day, 20:49:29.224091 INFO: Decoy channel: -1
1 day, 20:49:29.224115 INFO: Competetive: True
1 day, 20:49:29.227445 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:49:29.230031 INFO: Using random state 815013 for train-test-split
1 day, 20:49:29.240793 INFO: Test AUC: 0.522
1 day, 20:49:29.240857 INFO: Train AUC: 0.502
1 day, 20:49:29.240887 INFO: AUC difference: 3.88%
1 day, 20:49:29.457919 INFO: Resetting torch num_threads to 80
1 day, 20:49:29.458504 PROGRESS: === Extracted 3394 precursors and 37760 fragments ===
1 day, 20:49:29.458936 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:49:29.459530 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:49:29.459619 PROGRESS: Total precursors accumulated: 600
1 day, 20:49:29.459675 PROGRESS: Target precursors: 559 (93.17%)
1 day, 20:49:29.459725 PROGRESS: Decoy precursors: 41 (6.83%)
1 day, 20:49:29.459769 PROGRESS: 
1 day, 20:49:29.459816 PROGRESS: Precursor Summary:
1 day, 20:49:29.460873 PROGRESS: Channel   0:	 0.050 FDR:   545; 0.010 FDR:   545; 0.001 FDR:   545
1 day, 20:49:29.460979 PROGRESS: 
1 day, 20:49:29.461037 PROGRESS: Protein Summary:
1 day, 20:49:29.462276 PROGRESS: Channel   0:	 0.050 FDR:   494; 0.010 FDR:   494; 0.001 FDR:   494
1 day, 20:49:29.462368 PROGRESS: =========================================================================
1 day, 20:49:29.462560 INFO: Target number of precursors reached.
1 day, 20:49:29.469627 INFO: fragments_df: keeping 5000 of 37760 [sum(precursor_idx_mask)=17418 sum(mass_error_mask)=37760 stop_rank=5000
1 day, 20:49:29.474874 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:29.591093 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:29.708476 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:29.831014 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:30.445481 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:49:30.445965 INFO: Using score_cutoff 38.51797921600342 (fac=0.99, q=1)
1 day, 20:49:30.446285 INFO: Updating optimization_manager: fwhm_rt             : 3.0280303955078125 -> 3.0268325805664062
1 day, 20:49:30.446371 INFO: Updating optimization_manager: fwhm_mobility       : 0.008922403678297997 -> 0.008928842842578888
1 day, 20:49:30.446425 INFO: Updating optimization_manager: score_cutoff        : 38.922062393188476 -> 38.51797921600342
1 day, 20:49:30.446476 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:30.447591 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:30.448914 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:30.449695 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:30.451844 INFO: === checking if optimization conditions were reached ===
1 day, 20:49:30.451950 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:49:30.453745 INFO: Updating optimization_manager: rt_error            : 917.9843149014104 -> 809.4415254153689
1 day, 20:49:30.453847 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 809.4415.
1 day, 20:49:30.453921 INFO: ==============================================
1 day, 20:49:30.453987 INFO: Starting optimization step 2.
1 day, 20:49:30.454046 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:49:30.454100 INFO: Using classic extraction backend
1 day, 20:49:30.454213 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:49:30.454276 INFO: === Search parameters used ===
1 day, 20:49:30.454323 INFO: rt_error       : 809.4415254153689
1 day, 20:49:30.454364 INFO: mobility_error : 0.1
1 day, 20:49:30.454407 INFO: num_candidates : 3
1 day, 20:49:30.454446 INFO: ms1_error      : 7.5754825
1 day, 20:49:30.454484 INFO: ms2_error      : 17.494642
1 day, 20:49:30.454520 INFO: fwhm_rt        : 3.0268325805664062
1 day, 20:49:30.454558 INFO: quant_window   : 3
1 day, 20:49:30.454596 INFO: ==============================================
1 day, 20:49:30.455377 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:49:30.455422 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:49:30.455455 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 20:49:30.455477 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
1 day, 20:49:30.456189 INFO: Starting candidate selection
1 day, 20:49:35.643295 INFO: Starting candidate scoring
1 day, 20:49:35.860628 INFO: Finished candidate processing
1 day, 20:49:35.860776 INFO: Collecting candidate features
1 day, 20:49:35.875379 INFO: Collecting fragment features
1 day, 20:49:35.879315 INFO: Finished candidate scoring
1 day, 20:49:35.881434 INFO: performing precursor FDR with 47 features
1 day, 20:49:35.881482 INFO: Decoy channel: -1
1 day, 20:49:35.881507 INFO: Competetive: True
1 day, 20:49:35.885385 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:49:35.887492 INFO: Using random state 815013 for train-test-split
1 day, 20:49:35.898821 INFO: Test AUC: 0.506
1 day, 20:49:35.898896 INFO: Train AUC: 0.502
1 day, 20:49:35.898926 INFO: AUC difference: 0.86%
1 day, 20:49:36.121252 INFO: Resetting torch num_threads to 80
1 day, 20:49:36.121833 PROGRESS: === Extracted 3402 precursors and 37813 fragments ===
1 day, 20:49:36.122267 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:49:36.122832 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:49:36.122923 PROGRESS: Total precursors accumulated: 600
1 day, 20:49:36.122983 PROGRESS: Target precursors: 552 (92.00%)
1 day, 20:49:36.123034 PROGRESS: Decoy precursors: 48 (8.00%)
1 day, 20:49:36.123079 PROGRESS: 
1 day, 20:49:36.123133 PROGRESS: Precursor Summary:
1 day, 20:49:36.124158 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   538; 0.001 FDR:   538
1 day, 20:49:36.124248 PROGRESS: 
1 day, 20:49:36.124304 PROGRESS: Protein Summary:
1 day, 20:49:36.125557 PROGRESS: Channel   0:	 0.050 FDR:   488; 0.010 FDR:   488; 0.001 FDR:   488
1 day, 20:49:36.125651 PROGRESS: =========================================================================
1 day, 20:49:36.125834 INFO: Target number of precursors reached.
1 day, 20:49:36.132643 INFO: fragments_df: keeping 5000 of 37813 [sum(precursor_idx_mask)=17198 sum(mass_error_mask)=37813 stop_rank=5000
1 day, 20:49:36.139280 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:36.259148 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:36.388382 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:36.506121 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:37.142851 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:49:37.143319 INFO: Using score_cutoff 38.83206787948608 (fac=0.99, q=1)
1 day, 20:49:37.143637 INFO: Updating optimization_manager: fwhm_rt             : 3.0268325805664062 -> 3.0411176681518555
1 day, 20:49:37.143719 INFO: Updating optimization_manager: fwhm_mobility       : 0.008928842842578888 -> 0.008950423449277878
1 day, 20:49:37.143775 INFO: Updating optimization_manager: score_cutoff        : 38.51797921600342 -> 38.83206787948608
1 day, 20:49:37.143828 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:37.144921 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:37.146278 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:37.147050 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:37.149347 INFO: === checking if optimization conditions were reached ===
1 day, 20:49:37.149452 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:49:37.151238 INFO: Updating optimization_manager: rt_error            : 809.4415254153689 -> 743.5523558578888
1 day, 20:49:37.151340 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 743.5524.
1 day, 20:49:37.151407 INFO: ==============================================
1 day, 20:49:37.151473 INFO: Starting optimization step 3.
1 day, 20:49:37.151532 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:49:37.151588 INFO: Using classic extraction backend
1 day, 20:49:37.151704 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:49:37.151769 INFO: === Search parameters used ===
1 day, 20:49:37.151815 INFO: rt_error       : 743.5523558578888
1 day, 20:49:37.151860 INFO: mobility_error : 0.1
1 day, 20:49:37.151902 INFO: num_candidates : 3
1 day, 20:49:37.151942 INFO: ms1_error      : 7.5754825
1 day, 20:49:37.151983 INFO: ms2_error      : 17.494642
1 day, 20:49:37.152021 INFO: fwhm_rt        : 3.0411176681518555
1 day, 20:49:37.152060 INFO: quant_window   : 3
1 day, 20:49:37.152098 INFO: ==============================================
1 day, 20:49:37.153101 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:49:37.153147 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:49:37.153183 INFO: FWHM in RT is 3.04 seconds, sigma is 0.67
1 day, 20:49:37.153208 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.15
1 day, 20:49:37.154245 INFO: Starting candidate selection
1 day, 20:49:41.780658 INFO: Starting candidate scoring
1 day, 20:49:41.986048 INFO: Finished candidate processing
1 day, 20:49:41.986165 INFO: Collecting candidate features
1 day, 20:49:41.999475 INFO: Collecting fragment features
1 day, 20:49:42.003292 INFO: Finished candidate scoring
1 day, 20:49:42.005467 INFO: performing precursor FDR with 47 features
1 day, 20:49:42.005520 INFO: Decoy channel: -1
1 day, 20:49:42.005545 INFO: Competetive: True
1 day, 20:49:42.008572 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:49:42.010674 INFO: Using random state 815013 for train-test-split
1 day, 20:49:42.020744 INFO: Test AUC: 0.505
1 day, 20:49:42.020815 INFO: Train AUC: 0.505
1 day, 20:49:42.020845 INFO: AUC difference: 0.11%
1 day, 20:49:42.238970 INFO: Resetting torch num_threads to 80
1 day, 20:49:42.239557 PROGRESS: === Extracted 3400 precursors and 37812 fragments ===
1 day, 20:49:42.240018 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:49:42.240602 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:49:42.240692 PROGRESS: Total precursors accumulated: 600
1 day, 20:49:42.240754 PROGRESS: Target precursors: 556 (92.67%)
1 day, 20:49:42.240805 PROGRESS: Decoy precursors: 44 (7.33%)
1 day, 20:49:42.240853 PROGRESS: 
1 day, 20:49:42.240903 PROGRESS: Precursor Summary:
1 day, 20:49:42.241942 PROGRESS: Channel   0:	 0.050 FDR:   539; 0.010 FDR:   539; 0.001 FDR:   539
1 day, 20:49:42.242038 PROGRESS: 
1 day, 20:49:42.242095 PROGRESS: Protein Summary:
1 day, 20:49:42.243354 PROGRESS: Channel   0:	 0.050 FDR:   491; 0.010 FDR:   491; 0.001 FDR:   491
1 day, 20:49:42.243444 PROGRESS: =========================================================================
1 day, 20:49:42.243602 INFO: Target number of precursors reached.
1 day, 20:49:42.250570 INFO: fragments_df: keeping 5000 of 37812 [sum(precursor_idx_mask)=17237 sum(mass_error_mask)=37812 stop_rank=5000
1 day, 20:49:42.255027 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:42.374517 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:42.503667 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:42.624749 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:43.266357 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:49:43.266819 INFO: Using score_cutoff 38.571477978515624 (fac=0.99, q=1)
1 day, 20:49:43.267150 INFO: Updating optimization_manager: fwhm_rt             : 3.0411176681518555 -> 3.0280303955078125
1 day, 20:49:43.267231 INFO: Updating optimization_manager: fwhm_mobility       : 0.008950423449277878 -> 0.008959644474089146
1 day, 20:49:43.267287 INFO: Updating optimization_manager: score_cutoff        : 38.83206787948608 -> 38.571477978515624
1 day, 20:49:43.267343 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:43.268451 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:43.269794 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:43.270563 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:43.273089 INFO: === checking if optimization conditions were reached ===
1 day, 20:49:43.273198 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 20:49:43.275014 INFO: Updating optimization_manager: rt_error            : 743.5523558578888 -> 699.3390942612896
1 day, 20:49:43.275117 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 699.3391.
1 day, 20:49:43.275184 INFO: ==============================================
1 day, 20:49:43.275254 INFO: Starting optimization step 4.
1 day, 20:49:43.275314 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:49:43.275371 INFO: Using classic extraction backend
1 day, 20:49:43.275602 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:49:43.275680 INFO: === Search parameters used ===
1 day, 20:49:43.275731 INFO: rt_error       : 699.3390942612896
1 day, 20:49:43.275773 INFO: mobility_error : 0.1
1 day, 20:49:43.275822 INFO: num_candidates : 3
1 day, 20:49:43.275865 INFO: ms1_error      : 7.5754825
1 day, 20:49:43.275907 INFO: ms2_error      : 17.494642
1 day, 20:49:43.275945 INFO: fwhm_rt        : 3.0280303955078125
1 day, 20:49:43.275985 INFO: quant_window   : 3
1 day, 20:49:43.276023 INFO: ==============================================
1 day, 20:49:43.276834 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:49:43.276881 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:49:43.276915 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 20:49:43.276937 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.16
1 day, 20:49:43.277665 INFO: Starting candidate selection
1 day, 20:49:47.802145 INFO: Starting candidate scoring
1 day, 20:49:48.016512 INFO: Finished candidate processing
1 day, 20:49:48.016638 INFO: Collecting candidate features
1 day, 20:49:48.030700 INFO: Collecting fragment features
1 day, 20:49:48.035523 INFO: Finished candidate scoring
1 day, 20:49:48.037671 INFO: performing precursor FDR with 47 features
1 day, 20:49:48.037717 INFO: Decoy channel: -1
1 day, 20:49:48.037741 INFO: Competetive: True
1 day, 20:49:48.041299 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:49:48.043317 INFO: Using random state 815013 for train-test-split
1 day, 20:49:48.053769 INFO: Test AUC: 0.490
1 day, 20:49:48.053842 INFO: Train AUC: 0.504
1 day, 20:49:48.053885 INFO: AUC difference: 2.72%
1 day, 20:49:48.272726 INFO: Resetting torch num_threads to 80
1 day, 20:49:48.273912 PROGRESS: === Extracted 3404 precursors and 37836 fragments ===
1 day, 20:49:48.274365 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:49:48.275012 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:49:48.275104 PROGRESS: Total precursors accumulated: 600
1 day, 20:49:48.275162 PROGRESS: Target precursors: 555 (92.50%)
1 day, 20:49:48.275213 PROGRESS: Decoy precursors: 45 (7.50%)
1 day, 20:49:48.275259 PROGRESS: 
1 day, 20:49:48.275304 PROGRESS: Precursor Summary:
1 day, 20:49:48.276349 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   537; 0.001 FDR:   537
1 day, 20:49:48.276442 PROGRESS: 
1 day, 20:49:48.276499 PROGRESS: Protein Summary:
1 day, 20:49:48.277757 PROGRESS: Channel   0:	 0.050 FDR:   486; 0.010 FDR:   486; 0.001 FDR:   486
1 day, 20:49:48.277854 PROGRESS: =========================================================================
1 day, 20:49:48.278078 INFO: Target number of precursors reached.
1 day, 20:49:48.285107 INFO: fragments_df: keeping 5000 of 37836 [sum(precursor_idx_mask)=17153 sum(mass_error_mask)=37836 stop_rank=5000
1 day, 20:49:48.292149 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:48.411447 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:48.540333 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:48.663482 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:49.297630 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:49:49.298503 INFO: Using score_cutoff 38.7098225326538 (fac=0.99, q=1)
1 day, 20:49:49.298973 INFO: Updating optimization_manager: fwhm_rt             : 3.0280303955078125 -> 3.004621744155884
1 day, 20:49:49.299057 INFO: Updating optimization_manager: fwhm_mobility       : 0.008959644474089146 -> 0.008925243280827999
1 day, 20:49:49.299112 INFO: Updating optimization_manager: score_cutoff        : 38.571477978515624 -> 38.7098225326538
1 day, 20:49:49.299203 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:49.301049 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:49.302420 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:49.303206 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:49.305926 INFO: === checking if optimization conditions were reached ===
1 day, 20:49:49.306105 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 20:49:49.308388 INFO: Updating optimization_manager: rt_error            : 699.3390942612896 -> 687.1901938790633
1 day, 20:49:49.308495 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 687.1902.
1 day, 20:49:49.308568 INFO: ==============================================
1 day, 20:49:49.308668 INFO: Starting optimization step 5.
1 day, 20:49:49.308758 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:49:49.308862 INFO: Using classic extraction backend
1 day, 20:49:49.309150 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:49:49.309244 INFO: === Search parameters used ===
1 day, 20:49:49.309296 INFO: rt_error       : 687.1901938790633
1 day, 20:49:49.309341 INFO: mobility_error : 0.1
1 day, 20:49:49.309384 INFO: num_candidates : 3
1 day, 20:49:49.309426 INFO: ms1_error      : 7.5754825
1 day, 20:49:49.309466 INFO: ms2_error      : 17.494642
1 day, 20:49:49.309504 INFO: fwhm_rt        : 3.004621744155884
1 day, 20:49:49.309544 INFO: quant_window   : 3
1 day, 20:49:49.309582 INFO: ==============================================
1 day, 20:49:49.312382 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:49:49.312436 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:49:49.312500 INFO: FWHM in RT is 3.00 seconds, sigma is 0.66
1 day, 20:49:49.312531 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
1 day, 20:49:49.313391 INFO: Starting candidate selection
1 day, 20:49:53.816656 INFO: Starting candidate scoring
1 day, 20:49:54.028459 INFO: Finished candidate processing
1 day, 20:49:54.028576 INFO: Collecting candidate features
1 day, 20:49:54.042793 INFO: Collecting fragment features
1 day, 20:49:54.047713 INFO: Finished candidate scoring
1 day, 20:49:54.050014 INFO: performing precursor FDR with 47 features
1 day, 20:49:54.050062 INFO: Decoy channel: -1
1 day, 20:49:54.050087 INFO: Competetive: True
1 day, 20:49:54.053746 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:49:54.055993 INFO: Using random state 815013 for train-test-split
1 day, 20:49:54.068147 INFO: Test AUC: 0.481
1 day, 20:49:54.068214 INFO: Train AUC: 0.506
1 day, 20:49:54.068248 INFO: AUC difference: 5.02%
1 day, 20:49:54.068275 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 20:49:54.287908 INFO: Resetting torch num_threads to 80
1 day, 20:49:54.288467 PROGRESS: === Extracted 3401 precursors and 37809 fragments ===
1 day, 20:49:54.288977 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:49:54.289578 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:49:54.289670 PROGRESS: Total precursors accumulated: 600
1 day, 20:49:54.289728 PROGRESS: Target precursors: 555 (92.50%)
1 day, 20:49:54.289779 PROGRESS: Decoy precursors: 45 (7.50%)
1 day, 20:49:54.289824 PROGRESS: 
1 day, 20:49:54.289869 PROGRESS: Precursor Summary:
1 day, 20:49:54.291114 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   538; 0.001 FDR:   538
1 day, 20:49:54.291219 PROGRESS: 
1 day, 20:49:54.291277 PROGRESS: Protein Summary:
1 day, 20:49:54.292537 PROGRESS: Channel   0:	 0.050 FDR:   486; 0.010 FDR:   486; 0.001 FDR:   486
1 day, 20:49:54.292638 PROGRESS: =========================================================================
1 day, 20:49:54.293002 INFO: Target number of precursors reached.
1 day, 20:49:54.300476 INFO: fragments_df: keeping 5000 of 37809 [sum(precursor_idx_mask)=17233 sum(mass_error_mask)=37809 stop_rank=5000
1 day, 20:49:54.305593 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:54.429015 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:54.554550 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:54.675158 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:55.321826 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:49:55.322282 INFO: Using score_cutoff 38.6898599899292 (fac=0.99, q=1)
1 day, 20:49:55.322624 INFO: Updating optimization_manager: fwhm_rt             : 3.004621744155884 -> 3.020007610321045
1 day, 20:49:55.322708 INFO: Updating optimization_manager: fwhm_mobility       : 0.008925243280827999 -> 0.008950423449277878
1 day, 20:49:55.322764 INFO: Updating optimization_manager: score_cutoff        : 38.7098225326538 -> 38.6898599899292
1 day, 20:49:55.322819 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:55.323920 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:55.325260 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:55.326022 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:55.328593 INFO: === checking if optimization conditions were reached ===
1 day, 20:49:55.328699 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 20:49:55.329754 INFO: Updating optimization_manager: rt_error            : 687.1901938790633 -> 687.1901938790633
1 day, 20:49:55.329877 INFO: Updating optimization_manager: classifier_version  : 3 -> 9
1 day, 20:49:55.329968 INFO: Updating optimization_manager: score_cutoff        : 38.6898599899292 -> 38.6898599899292
1 day, 20:49:55.330051 INFO: Updating optimization_manager: fwhm_rt             : 3.020007610321045 -> 3.020007610321045
1 day, 20:49:55.330150 INFO: Updating optimization_manager: fwhm_mobility       : 0.008950423449277878 -> 0.008950423449277878
1 day, 20:49:55.330236 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 687.1902 found after 6 searches.
1 day, 20:49:55.330296 INFO: ==============================================
1 day, 20:49:55.330359 PROGRESS: Optimization finished for rt_error.
1 day, 20:49:55.334486 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:49:55.335313 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:49:55.336612 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:49:55.337382 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:49:55.365015 INFO: Starting optimization step 0.
1 day, 20:49:55.365180 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:49:55.365248 INFO: Using classic extraction backend
1 day, 20:49:55.365368 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:49:55.365441 INFO: === Search parameters used ===
1 day, 20:49:55.365500 INFO: rt_error       : 687.1901938790633
1 day, 20:49:55.365544 INFO: mobility_error : 0.1
1 day, 20:49:55.365590 INFO: num_candidates : 3
1 day, 20:49:55.365632 INFO: ms1_error      : 7.5754825
1 day, 20:49:55.365673 INFO: ms2_error      : 17.494642
1 day, 20:49:55.365711 INFO: fwhm_rt        : 3.020007610321045
1 day, 20:49:55.365749 INFO: quant_window   : 3
1 day, 20:49:55.365789 INFO: ==============================================
1 day, 20:49:55.366703 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:49:55.366748 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:49:55.366783 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
1 day, 20:49:55.366804 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.15
1 day, 20:49:55.367509 INFO: Starting candidate selection
1 day, 20:49:59.456758 INFO: Starting candidate scoring
1 day, 20:49:59.663610 INFO: Finished candidate processing
1 day, 20:49:59.663782 INFO: Collecting candidate features
1 day, 20:49:59.693377 INFO: Collecting fragment features
1 day, 20:49:59.701641 INFO: Finished candidate scoring
1 day, 20:49:59.704644 INFO: performing precursor FDR with 47 features
1 day, 20:49:59.704748 INFO: Decoy channel: -1
1 day, 20:49:59.704807 INFO: Competetive: True
1 day, 20:49:59.710965 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:49:59.715088 INFO: Using random state 937323 for train-test-split
1 day, 20:49:59.732009 INFO: Test AUC: 0.481
1 day, 20:49:59.732113 INFO: Train AUC: 0.507
1 day, 20:49:59.732163 INFO: AUC difference: 4.96%
1 day, 20:49:59.952024 INFO: Resetting torch num_threads to 80
1 day, 20:49:59.952677 PROGRESS: === Extracted 3401 precursors and 37822 fragments ===
1 day, 20:49:59.953176 INFO: === FDR correction performed with classifier version 9 ===
1 day, 20:49:59.953797 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:49:59.953884 PROGRESS: Total precursors accumulated: 600
1 day, 20:49:59.953942 PROGRESS: Target precursors: 546 (91.00%)
1 day, 20:49:59.953991 PROGRESS: Decoy precursors: 54 (9.00%)
1 day, 20:49:59.954036 PROGRESS: 
1 day, 20:49:59.954079 PROGRESS: Precursor Summary:
1 day, 20:49:59.955149 PROGRESS: Channel   0:	 0.050 FDR:   533; 0.010 FDR:   533; 0.001 FDR:   533
1 day, 20:49:59.955240 PROGRESS: 
1 day, 20:49:59.955293 PROGRESS: Protein Summary:
1 day, 20:49:59.956527 PROGRESS: Channel   0:	 0.050 FDR:   482; 0.010 FDR:   482; 0.001 FDR:   482
1 day, 20:49:59.956620 PROGRESS: =========================================================================
1 day, 20:49:59.956763 INFO: Target number of precursors reached.
1 day, 20:49:59.963851 INFO: fragments_df: keeping 5000 of 37822 [sum(precursor_idx_mask)=17056 sum(mass_error_mask)=37822 stop_rank=5000
1 day, 20:49:59.968748 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:50:00.107151 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:50:00.253196 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:50:00.393999 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:50:01.093608 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:50:01.094124 INFO: Using score_cutoff 38.58184415588379 (fac=0.99, q=1)
1 day, 20:50:01.094460 INFO: Updating optimization_manager: fwhm_rt             : 3.020007610321045 -> 3.0280303955078125
1 day, 20:50:01.094538 INFO: Updating optimization_manager: fwhm_mobility       : 0.008950423449277878 -> 0.008996542543172836
1 day, 20:50:01.094591 INFO: Updating optimization_manager: score_cutoff        : 38.6898599899292 -> 38.58184415588379
1 day, 20:50:01.094643 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:50:01.095855 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:50:01.097197 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:50:01.097965 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:50:01.100132 INFO: === checking if optimization conditions were reached ===
1 day, 20:50:01.100236 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:50:01.101683 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.08066918256020489
1 day, 20:50:01.101790 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0807.
1 day, 20:50:01.101854 INFO: ==============================================
1 day, 20:50:01.101919 INFO: Starting optimization step 1.
1 day, 20:50:01.101977 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:50:01.102033 INFO: Using classic extraction backend
1 day, 20:50:01.102153 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:50:01.102217 INFO: === Search parameters used ===
1 day, 20:50:01.102262 INFO: rt_error       : 687.1901938790633
1 day, 20:50:01.102304 INFO: mobility_error : 0.08066918256020489
1 day, 20:50:01.102344 INFO: num_candidates : 3
1 day, 20:50:01.102383 INFO: ms1_error      : 7.5754825
1 day, 20:50:01.102422 INFO: ms2_error      : 17.494642
1 day, 20:50:01.102458 INFO: fwhm_rt        : 3.0280303955078125
1 day, 20:50:01.102497 INFO: quant_window   : 3
1 day, 20:50:01.102535 INFO: ==============================================
1 day, 20:50:01.103373 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:50:01.103418 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:50:01.103452 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 20:50:01.103473 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.17
1 day, 20:50:01.104228 INFO: Starting candidate selection
1 day, 20:50:05.258002 INFO: Starting candidate scoring
1 day, 20:50:05.473998 INFO: Finished candidate processing
1 day, 20:50:05.474113 INFO: Collecting candidate features
1 day, 20:50:05.486944 INFO: Collecting fragment features
1 day, 20:50:05.490912 INFO: Finished candidate scoring
1 day, 20:50:05.493160 INFO: performing precursor FDR with 47 features
1 day, 20:50:05.493218 INFO: Decoy channel: -1
1 day, 20:50:05.493243 INFO: Competetive: True
1 day, 20:50:05.496330 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:50:05.498408 INFO: Using random state 937323 for train-test-split
1 day, 20:50:05.509953 INFO: Test AUC: 0.510
1 day, 20:50:05.510019 INFO: Train AUC: 0.502
1 day, 20:50:05.510049 INFO: AUC difference: 1.66%
1 day, 20:50:05.728209 INFO: Resetting torch num_threads to 80
1 day, 20:50:05.728806 PROGRESS: === Extracted 3400 precursors and 37744 fragments ===
1 day, 20:50:05.729260 INFO: === FDR correction performed with classifier version 9 ===
1 day, 20:50:05.729877 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:50:05.729969 PROGRESS: Total precursors accumulated: 600
1 day, 20:50:05.730032 PROGRESS: Target precursors: 541 (90.17%)
1 day, 20:50:05.730093 PROGRESS: Decoy precursors: 59 (9.83%)
1 day, 20:50:05.730149 PROGRESS: 
1 day, 20:50:05.730199 PROGRESS: Precursor Summary:
1 day, 20:50:05.731233 PROGRESS: Channel   0:	 0.050 FDR:   527; 0.010 FDR:   527; 0.001 FDR:   527
1 day, 20:50:05.731324 PROGRESS: 
1 day, 20:50:05.731381 PROGRESS: Protein Summary:
1 day, 20:50:05.732625 PROGRESS: Channel   0:	 0.050 FDR:   479; 0.010 FDR:   479; 0.001 FDR:   479
1 day, 20:50:05.732718 PROGRESS: =========================================================================
1 day, 20:50:05.732877 INFO: Target number of precursors reached.
1 day, 20:50:05.739928 INFO: fragments_df: keeping 5000 of 37744 [sum(precursor_idx_mask)=16901 sum(mass_error_mask)=37744 stop_rank=5000
1 day, 20:50:05.744356 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:50:05.860223 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:50:05.985712 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:50:06.111142 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:50:06.737216 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:50:06.737677 INFO: Using score_cutoff 37.153815607452394 (fac=0.99, q=1)
1 day, 20:50:06.737987 INFO: Updating optimization_manager: fwhm_rt             : 3.0280303955078125 -> 3.040296792984009
1 day, 20:50:06.738067 INFO: Updating optimization_manager: fwhm_mobility       : 0.008996542543172836 -> 0.008996542543172836
1 day, 20:50:06.738121 INFO: Updating optimization_manager: score_cutoff        : 38.58184415588379 -> 37.153815607452394
1 day, 20:50:06.738173 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:50:06.739265 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:50:06.740577 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:50:06.741353 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:50:06.743489 INFO: === checking if optimization conditions were reached ===
1 day, 20:50:06.743591 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:50:06.745032 INFO: Updating optimization_manager: mobility_error      : 0.08066918256020489 -> 0.07045796629604156
1 day, 20:50:06.745133 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0705.
1 day, 20:50:06.745199 INFO: ==============================================
1 day, 20:50:06.745265 INFO: Starting optimization step 2.
1 day, 20:50:06.745323 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 20:50:06.745378 INFO: Using classic extraction backend
1 day, 20:50:06.745484 PROGRESS: Extracting batch of 1194 precursors
1 day, 20:50:06.745548 INFO: === Search parameters used ===
1 day, 20:50:06.745596 INFO: rt_error       : 687.1901938790633
1 day, 20:50:06.745638 INFO: mobility_error : 0.07045796629604156
1 day, 20:50:06.745680 INFO: num_candidates : 3
1 day, 20:50:06.745721 INFO: ms1_error      : 7.5754825
1 day, 20:50:06.745761 INFO: ms2_error      : 17.494642
1 day, 20:50:06.745801 INFO: fwhm_rt        : 3.040296792984009
1 day, 20:50:06.745842 INFO: quant_window   : 3
1 day, 20:50:06.745881 INFO: ==============================================
1 day, 20:50:06.746655 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:50:06.746700 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:50:06.746733 INFO: FWHM in RT is 3.04 seconds, sigma is 0.67
1 day, 20:50:06.746755 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.17
1 day, 20:50:06.747481 INFO: Starting candidate selection
1 day, 20:50:09.966277 INFO: Starting candidate scoring
1 day, 20:50:10.181407 INFO: Finished candidate processing
1 day, 20:50:10.181519 INFO: Collecting candidate features
1 day, 20:50:10.193882 INFO: Collecting fragment features
1 day, 20:50:10.197594 INFO: Finished candidate scoring
1 day, 20:50:10.199435 INFO: performing precursor FDR with 47 features
1 day, 20:50:10.199494 INFO: Decoy channel: -1
1 day, 20:50:10.199518 INFO: Competetive: True
1 day, 20:50:10.202392 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:50:10.204391 INFO: Using random state 937323 for train-test-split
1 day, 20:50:10.215411 INFO: Test AUC: 0.499
1 day, 20:50:10.215481 INFO: Train AUC: 0.509
1 day, 20:50:10.215511 INFO: AUC difference: 1.95%
1 day, 20:50:10.432704 INFO: Resetting torch num_threads to 80
1 day, 20:50:10.433306 PROGRESS: === Extracted 3405 precursors and 37693 fragments ===
1 day, 20:50:10.434144 INFO: === FDR correction performed with classifier version 9 ===
1 day, 20:50:10.435107 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:50:10.435205 PROGRESS: Total precursors accumulated: 600
1 day, 20:50:10.435266 PROGRESS: Target precursors: 548 (91.33%)
1 day, 20:50:10.435318 PROGRESS: Decoy precursors: 52 (8.67%)
1 day, 20:50:10.435362 PROGRESS: 
1 day, 20:50:10.435407 PROGRESS: Precursor Summary:
1 day, 20:50:10.436459 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   525; 0.001 FDR:   525
1 day, 20:50:10.436551 PROGRESS: 
1 day, 20:50:10.436606 PROGRESS: Protein Summary:
1 day, 20:50:10.437857 PROGRESS: Channel   0:	 0.050 FDR:   478; 0.010 FDR:   478; 0.001 FDR:   478
1 day, 20:50:10.437951 PROGRESS: =========================================================================
1 day, 20:50:10.438115 INFO: Target number of precursors reached.
1 day, 20:50:10.445359 INFO: fragments_df: keeping 5000 of 37693 [sum(precursor_idx_mask)=16801 sum(mass_error_mask)=37693 stop_rank=5000
1 day, 20:50:10.451100 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:50:10.572709 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:50:10.696298 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:50:10.814850 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:50:11.432371 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 20:50:11.432833 INFO: Using score_cutoff 37.65688722839355 (fac=0.99, q=1)
1 day, 20:50:11.433155 INFO: Updating optimization_manager: fwhm_rt             : 3.040296792984009 -> 3.0280303955078125
1 day, 20:50:11.433238 INFO: Updating optimization_manager: fwhm_mobility       : 0.008996542543172836 -> 0.008988329209387302
1 day, 20:50:11.433292 INFO: Updating optimization_manager: score_cutoff        : 37.153815607452394 -> 37.65688722839355
1 day, 20:50:11.433345 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:50:11.434442 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:50:11.435767 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:50:11.436527 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:50:11.438693 INFO: === checking if optimization conditions were reached ===
1 day, 20:50:11.438797 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:50:11.439498 INFO: Updating optimization_manager: mobility_error      : 0.07045796629604156 -> 0.1
1 day, 20:50:11.439615 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1 day, 20:50:11.439707 INFO: Updating optimization_manager: score_cutoff        : 37.65688722839355 -> 38.58184415588379
1 day, 20:50:11.439791 INFO: Updating optimization_manager: fwhm_rt             : 3.0280303955078125 -> 3.0280303955078125
1 day, 20:50:11.439873 INFO: Updating optimization_manager: fwhm_mobility       : 0.008988329209387302 -> 0.008996542543172836
1 day, 20:50:11.439954 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 20:50:11.440013 INFO: ==============================================
1 day, 20:50:11.440076 PROGRESS: Optimization finished for mobility_error.
1 day, 20:50:11.444234 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:50:11.445065 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:50:11.446371 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:50:11.447136 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:50:11.473589 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:50:11.473749 PROGRESS: ==============================================
1 day, 20:50:11.473836 PROGRESS: ms2_error      : 17.4946
1 day, 20:50:11.473917 PROGRESS: ms1_error      : 7.5755
1 day, 20:50:11.473971 PROGRESS: rt_error       : 687.1902
1 day, 20:50:11.474017 PROGRESS: mobility_error : 0.1000
1 day, 20:50:11.474060 PROGRESS: ==============================================
1 day, 20:50:11.474771 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 20:50:11.494245 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 20:50:11.581256 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 20:50:11.600798 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 20:50:11.830401 INFO: Using classic extraction backend
1 day, 20:50:11.830763 PROGRESS: Extracting batch of 146455 precursors
1 day, 20:50:11.830853 INFO: === Search parameters used ===
1 day, 20:50:11.830907 INFO: rt_error       : 687.1901938790633
1 day, 20:50:11.830954 INFO: mobility_error : 0.1
1 day, 20:50:11.831012 INFO: num_candidates : 3
1 day, 20:50:11.831058 INFO: ms1_error      : 7.5754825
1 day, 20:50:11.831100 INFO: ms2_error      : 17.494642
1 day, 20:50:11.831141 INFO: fwhm_rt        : 3.0280303955078125
1 day, 20:50:11.831182 INFO: quant_window   : 3
1 day, 20:50:11.831221 INFO: ==============================================
1 day, 20:50:11.864037 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:50:11.864192 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:50:11.864237 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 20:50:11.864262 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.17
1 day, 20:50:11.865046 INFO: Starting candidate selection
1 day, 20:55:45.770895 INFO: Removed 21029 precursors with score below cutoff 38.58184415588379
1 day, 20:55:46.110823 INFO: Starting candidate scoring
1 day, 20:56:01.485171 INFO: Finished candidate processing
1 day, 20:56:01.485603 INFO: Collecting candidate features
1 day, 20:56:02.018559 INFO: Collecting fragment features
1 day, 20:56:02.263993 INFO: Finished candidate scoring
1 day, 20:56:02.444538 INFO: === Performing FDR correction with classifier version 10 ===
1 day, 20:56:02.445727 INFO: performing precursor FDR with 47 features
1 day, 20:56:02.445767 INFO: Decoy channel: -1
1 day, 20:56:02.445795 INFO: Competetive: True
1 day, 20:56:02.545202 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:56:02.704758 INFO: Using random state 252838 for train-test-split
1 day, 20:56:10.736180 INFO: Test AUC: 0.755
1 day, 20:56:10.736342 INFO: Train AUC: 0.757
1 day, 20:56:10.736382 INFO: AUC difference: 0.19%
1 day, 20:56:11.088252 INFO: Resetting torch num_threads to 80
1 day, 20:56:11.102909 INFO: Removing fragments below FDR threshold
1 day, 20:56:11.178447 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:56:11.178739 PROGRESS: Total precursors accumulated: 68,550
1 day, 20:56:11.178812 PROGRESS: Target precursors: 67,872 (99.01%)
1 day, 20:56:11.178872 PROGRESS: Decoy precursors: 678 (0.99%)
1 day, 20:56:11.178924 PROGRESS: 
1 day, 20:56:11.178975 PROGRESS: Precursor Summary:
1 day, 20:56:11.207788 PROGRESS: Channel   0:	 0.050 FDR: 67,872; 0.010 FDR: 67,872; 0.001 FDR: 65,454
1 day, 20:56:11.208089 PROGRESS: 
1 day, 20:56:11.208163 PROGRESS: Protein Summary:
1 day, 20:56:11.244881 PROGRESS: Channel   0:	 0.050 FDR: 7,370; 0.010 FDR: 7,370; 0.001 FDR: 7,325
1 day, 20:56:11.245170 PROGRESS: =========================================================================
1 day, 20:56:11.249216 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/psm.parquet
1 day, 20:56:11.556554 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/frag.parquet
1 day, 20:56:11.820603 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:56:13.182792 PROGRESS: Processing search outputs
1 day, 20:56:13.182921 PROGRESS: Performing protein grouping and FDR
1 day, 20:56:13.182961 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 20:56:13.246534 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 20:56:13.312537 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 20:56:13.367180 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:56:13.420178 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:56:13.471865 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:56:13.523797 INFO: Building combined output
1 day, 20:56:13.563158 INFO: Performing protein inference
1 day, 20:56:14.020380 INFO: Inference strategy: library. Using library grouping for protein inference
1 day, 20:56:14.022685 INFO: Performing protein FDR
1 day, 20:56:21.358531 INFO: Normalizing q-values using 7,424 targets and 2,317 decoys
1 day, 20:56:21.360801 INFO: Test AUC: 1.000
1 day, 20:56:21.360850 INFO: Train AUC: 1.000
1 day, 20:56:21.360881 INFO: AUC difference: 0.01%
1 day, 20:56:22.020652 PROGRESS: ================ Protein FDR =================
1 day, 20:56:22.020816 PROGRESS: Unique protein groups in output
1 day, 20:56:22.020847 PROGRESS:   1% protein FDR: 7,424
1 day, 20:56:22.020868 PROGRESS: 
1 day, 20:56:22.020886 PROGRESS: Unique precursor in output
1 day, 20:56:22.020905 PROGRESS:   1% protein FDR: 73,574
1 day, 20:56:22.020922 PROGRESS: ================================================
1 day, 20:56:22.084551 PROGRESS: Building search statistics
1 day, 20:56:22.193504 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
1 day, 20:56:22.193743 INFO: Initializing OptimizationManager
1 day, 20:56:22.194032 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
1 day, 20:56:22.194115 INFO: Initializing CalibrationManager
1 day, 20:56:22.194325 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
1 day, 20:56:22.194398 INFO: Initializing RawFileManager
1 day, 20:56:22.223458 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
1 day, 20:56:22.223670 INFO: Initializing OptimizationManager
1 day, 20:56:22.223913 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
1 day, 20:56:22.223987 INFO: Initializing CalibrationManager
1 day, 20:56:22.224186 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
1 day, 20:56:22.224256 INFO: Initializing RawFileManager
1 day, 20:56:22.253397 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
1 day, 20:56:22.253619 INFO: Initializing OptimizationManager
1 day, 20:56:22.253849 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
1 day, 20:56:22.253928 INFO: Initializing CalibrationManager
1 day, 20:56:22.254136 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
1 day, 20:56:22.254231 INFO: Initializing RawFileManager
1 day, 20:56:22.283558 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
1 day, 20:56:22.283775 INFO: Initializing OptimizationManager
1 day, 20:56:22.284011 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
1 day, 20:56:22.284089 INFO: Initializing CalibrationManager
1 day, 20:56:22.284294 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
1 day, 20:56:22.284363 INFO: Initializing RawFileManager
1 day, 20:56:22.312492 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
1 day, 20:56:22.312708 INFO: Initializing OptimizationManager
1 day, 20:56:22.312936 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
1 day, 20:56:22.313030 INFO: Initializing CalibrationManager
1 day, 20:56:22.313231 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
1 day, 20:56:22.313681 INFO: Initializing RawFileManager
1 day, 20:56:22.343517 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
1 day, 20:56:22.343737 INFO: Initializing OptimizationManager
1 day, 20:56:22.343967 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
1 day, 20:56:22.344048 INFO: Initializing CalibrationManager
1 day, 20:56:22.344463 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
1 day, 20:56:22.344542 INFO: Initializing RawFileManager
1 day, 20:56:22.346940 INFO: Writing stat output to disk
1 day, 20:56:22.347003 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/stat.tsv to disk
1 day, 20:56:22.353772 PROGRESS: Building internal statistics
1 day, 20:56:22.354123 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
1 day, 20:56:22.354172 INFO: Initializing TimingManager
1 day, 20:56:22.354569 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
1 day, 20:56:22.354611 INFO: Initializing TimingManager
1 day, 20:56:22.354796 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
1 day, 20:56:22.354834 INFO: Initializing TimingManager
1 day, 20:56:22.355010 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
1 day, 20:56:22.355046 INFO: Initializing TimingManager
1 day, 20:56:22.355213 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
1 day, 20:56:22.355251 INFO: Initializing TimingManager
1 day, 20:56:22.355421 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
1 day, 20:56:22.355469 INFO: Initializing TimingManager
1 day, 20:56:22.355893 INFO: Writing internal output to disk
1 day, 20:56:22.355942 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/internal.tsv to disk
1 day, 20:56:22.356511 PROGRESS: Performing label free quantification
1 day, 20:56:22.436764 INFO: Accumulating fragment data
1 day, 20:56:22.437182 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 20:56:22.490917 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 20:56:23.540405 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 20:56:24.496966 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:56:25.467474 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:56:26.479983 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:56:27.649872 PROGRESS: Performing label free quantification on the precursor level
1 day, 20:56:27.650189 INFO: Filtering fragments by quality
1 day, 20:56:27.865870 INFO: Performing label-free quantification using directLFQ
1 day, 20:56:28.744768 INFO: 73574 lfq-groups total
1 day, 20:58:10.003541 INFO: using 80 processes
1 day, 20:58:10.247590 INFO: lfq-object 0
1 day, 20:58:10.372928 INFO: lfq-object 100
1 day, 20:58:10.397789 INFO: lfq-object 300
1 day, 20:58:10.437069 INFO: lfq-object 500
1 day, 20:58:10.488723 INFO: lfq-object 700
1 day, 20:58:10.498249 INFO: lfq-object 200
1 day, 20:58:10.556403 INFO: lfq-object 400
1 day, 20:58:10.563234 INFO: lfq-object 600
1 day, 20:58:10.616750 INFO: lfq-object 1000
1 day, 20:58:10.620483 INFO: lfq-object 800
1 day, 20:58:10.645915 INFO: lfq-object 1200
1 day, 20:58:10.688095 INFO: lfq-object 1400
1 day, 20:58:10.740225 INFO: lfq-object 1100
1 day, 20:58:10.745608 INFO: lfq-object 900
1 day, 20:58:10.769224 INFO: lfq-object 1300
1 day, 20:58:10.817170 INFO: lfq-object 1500
1 day, 20:58:10.875719 INFO: lfq-object 1700
1 day, 20:58:10.951673 INFO: lfq-object 1600
1 day, 20:58:10.991421 INFO: lfq-object 1900
1 day, 20:58:11.001716 INFO: lfq-object 1800
1 day, 20:58:11.114453 INFO: lfq-object 2000
1 day, 20:58:11.301288 INFO: lfq-object 2100
1 day, 20:58:11.417358 INFO: lfq-object 2300
1 day, 20:58:11.428562 INFO: lfq-object 2200
1 day, 20:58:11.546438 INFO: lfq-object 2400
1 day, 20:58:11.592938 INFO: lfq-object 2600
1 day, 20:58:11.618249 INFO: lfq-object 2800
1 day, 20:58:11.670417 INFO: lfq-object 2500
1 day, 20:58:11.714557 INFO: lfq-object 2700
1 day, 20:58:11.742790 INFO: lfq-object 2900
1 day, 20:58:15.772579 INFO: lfq-object 3000
1 day, 20:58:15.896026 INFO: lfq-object 3100
1 day, 20:58:16.018366 INFO: lfq-object 3200
1 day, 20:58:16.069139 INFO: lfq-object 3300
1 day, 20:58:16.113894 INFO: lfq-object 3500
1 day, 20:58:16.164070 INFO: lfq-object 3700
1 day, 20:58:16.197026 INFO: lfq-object 3400
1 day, 20:58:16.241402 INFO: lfq-object 3600
1 day, 20:58:16.297577 INFO: lfq-object 3800
1 day, 20:58:16.305577 INFO: lfq-object 4000
1 day, 20:58:16.364822 INFO: lfq-object 4200
1 day, 20:58:16.391430 INFO: lfq-object 4400
1 day, 20:58:16.420935 INFO: lfq-object 3900
1 day, 20:58:16.431403 INFO: lfq-object 4100
1 day, 20:58:16.436892 INFO: lfq-object 4600
1 day, 20:58:16.494734 INFO: lfq-object 4300
1 day, 20:58:16.514330 INFO: lfq-object 4500
1 day, 20:58:16.563274 INFO: lfq-object 4700
1 day, 20:58:16.612975 INFO: lfq-object 4900
1 day, 20:58:16.677732 INFO: lfq-object 5100
1 day, 20:58:16.688218 INFO: lfq-object 4800
1 day, 20:58:16.736521 INFO: lfq-object 5000
1 day, 20:58:16.739188 INFO: lfq-object 5300
1 day, 20:58:16.802994 INFO: lfq-object 5200
1 day, 20:58:16.862590 INFO: lfq-object 5400
1 day, 20:58:16.978193 INFO: lfq-object 5600
1 day, 20:58:16.986989 INFO: lfq-object 5500
1 day, 20:58:17.103718 INFO: lfq-object 5700
1 day, 20:58:17.170611 INFO: lfq-object 5800
1 day, 20:58:17.297150 INFO: lfq-object 5900
1 day, 20:58:17.302061 INFO: lfq-object 6000
1 day, 20:58:17.427126 INFO: lfq-object 6100
1 day, 20:58:17.523012 INFO: lfq-object 6300
1 day, 20:58:17.548991 INFO: lfq-object 6200
1 day, 20:58:17.557652 INFO: lfq-object 6500
1 day, 20:58:17.583360 INFO: lfq-object 6700
1 day, 20:58:17.647367 INFO: lfq-object 6400
1 day, 20:58:17.650385 INFO: lfq-object 6900
1 day, 20:58:17.680880 INFO: lfq-object 6600
1 day, 20:58:17.746107 INFO: lfq-object 6800
1 day, 20:58:17.799397 INFO: lfq-object 7200
1 day, 20:58:17.811795 INFO: lfq-object 7000
1 day, 20:58:17.855434 INFO: lfq-object 7400
1 day, 20:58:17.891813 INFO: lfq-object 7600
1 day, 20:58:17.923341 INFO: lfq-object 7300
1 day, 20:58:17.936779 INFO: lfq-object 7100
1 day, 20:58:17.982255 INFO: lfq-object 7500
1 day, 20:58:18.015243 INFO: lfq-object 7700
1 day, 20:58:18.098908 INFO: lfq-object 7900
1 day, 20:58:18.137466 INFO: lfq-object 7800
1 day, 20:58:18.177710 INFO: lfq-object 8100
1 day, 20:58:18.224321 INFO: lfq-object 8000
1 day, 20:58:18.235666 INFO: lfq-object 8300
1 day, 20:58:18.300694 INFO: lfq-object 8200
1 day, 20:58:18.361033 INFO: lfq-object 8400
1 day, 20:58:18.414248 INFO: lfq-object 8600
1 day, 20:58:18.473630 INFO: lfq-object 8800
1 day, 20:58:18.483168 INFO: lfq-object 8500
1 day, 20:58:18.538268 INFO: lfq-object 8700
1 day, 20:58:18.570484 INFO: lfq-object 9000
1 day, 20:58:18.602225 INFO: lfq-object 8900
1 day, 20:58:18.628297 INFO: lfq-object 9200
1 day, 20:58:18.694130 INFO: lfq-object 9100
1 day, 20:58:18.757051 INFO: lfq-object 9300
1 day, 20:58:18.809280 INFO: lfq-object 9500
1 day, 20:58:18.863873 INFO: lfq-object 9700
1 day, 20:58:18.880407 INFO: lfq-object 9400
1 day, 20:58:18.922405 INFO: lfq-object 9900
1 day, 20:58:18.934288 INFO: lfq-object 9600
1 day, 20:58:18.988040 INFO: lfq-object 9800
1 day, 20:58:19.047145 INFO: lfq-object 10000
1 day, 20:58:19.101341 INFO: lfq-object 10200
1 day, 20:58:19.160169 INFO: lfq-object 10400
1 day, 20:58:19.168383 INFO: lfq-object 10100
1 day, 20:58:19.205167 INFO: lfq-object 10600
1 day, 20:58:19.227247 INFO: lfq-object 10300
1 day, 20:58:19.286556 INFO: lfq-object 10500
1 day, 20:58:19.331181 INFO: lfq-object 10700
1 day, 20:58:19.383172 INFO: lfq-object 10900
1 day, 20:58:19.442987 INFO: lfq-object 11100
1 day, 20:58:19.456474 INFO: lfq-object 10800
1 day, 20:58:19.490115 INFO: lfq-object 11300
1 day, 20:58:19.510943 INFO: lfq-object 11000
1 day, 20:58:19.537737 INFO: lfq-object 11500
1 day, 20:58:19.568242 INFO: lfq-object 11200
1 day, 20:58:19.616291 INFO: lfq-object 11400
1 day, 20:58:19.661073 INFO: lfq-object 11600
1 day, 20:58:19.725771 INFO: lfq-object 11800
1 day, 20:58:19.781985 INFO: lfq-object 12000
1 day, 20:58:19.784724 INFO: lfq-object 11700
1 day, 20:58:19.848291 INFO: lfq-object 12200
1 day, 20:58:19.850550 INFO: lfq-object 11900
1 day, 20:58:19.906038 INFO: lfq-object 12100
1 day, 20:58:19.973294 INFO: lfq-object 12300
1 day, 20:58:20.096834 INFO: lfq-object 12400
1 day, 20:58:20.151713 INFO: lfq-object 12500
1 day, 20:58:20.214167 INFO: lfq-object 12700
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1 day, 20:59:01.219041 INFO: lfq-object 73300
1 day, 20:59:01.333721 INFO: lfq-object 73500
1 day, 20:59:07.738848 INFO: Writing precursor output to disk
1 day, 20:59:07.739021 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/precursor.matrix.tsv to disk
1 day, 20:59:08.129538 PROGRESS: Performing label free quantification on the pg level
1 day, 20:59:08.129650 INFO: Filtering fragments by quality
1 day, 20:59:08.349755 INFO: Performing label-free quantification using directLFQ
1 day, 20:59:08.784433 INFO: 7424 lfq-groups total
1 day, 21:00:37.974435 INFO: using 80 processes
1 day, 21:00:38.078196 INFO: lfq-object 0
1 day, 21:00:38.318039 INFO: lfq-object 600
1 day, 21:00:38.456987 INFO: lfq-object 200
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1 day, 21:00:40.943873 INFO: lfq-object 5500
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1 day, 21:00:41.066899 INFO: lfq-object 5700
1 day, 21:00:41.069665 INFO: lfq-object 5300
1 day, 21:00:41.195241 INFO: lfq-object 6000
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1 day, 21:00:41.431990 INFO: lfq-object 6400
1 day, 21:00:41.433163 INFO: lfq-object 6600
1 day, 21:00:41.471540 INFO: lfq-object 6300
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1 day, 21:00:46.506013 INFO: Writing pg output to disk
1 day, 21:00:46.506210 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/pg.matrix.tsv to disk
1 day, 21:00:46.704526 INFO: Writing psm output to disk
1 day, 21:00:46.704698 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/precursors.tsv to disk
1 day, 21:01:10.584517 PROGRESS: Building MBR spectral library
1 day, 21:01:10.673201 INFO: Running MbrLibraryBuilder
1 day, 21:01:10.879169 INFO: MBR spectral library contains 73,574 precursors, 7,424 proteins
1 day, 21:01:10.879327 INFO: Writing MBR spectral library to disk
1 day, 21:01:11.453726 PROGRESS: =================== Search Finished ===================
