0:00:00.000026 INFO: Moved old log file ./alphadia_zenoswath8600/log.txt to alphadia_zenoswath8600/log.txt
0:00:00.000148 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/alphadia_zenoswath8600, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000182 INFO: User provided config file: config_alphadia_zenoswath8600.yaml.
0:00:00.000211 INFO: User provided config dict: {}.
0:00:00.013413 PROGRESS:           _      _         ___ ___   _   
0:00:00.013479 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.013507 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013533 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013558 PROGRESS:            |_|                           
0:00:00.013578 PROGRESS: 
0:00:00.013598 PROGRESS: version: 1.12.1
0:00:00.013626 INFO: hostname: thestral
0:00:00.013674 INFO: date: 2025-10-31 10:10:23
0:00:00.013695 INFO: ================ AlphaX Environment ===============
0:00:00.013717 INFO: alphatims       : 1.0.9
0:00:00.013737 INFO: alpharaw        : 0.4.7
0:00:00.013755 INFO: alphabase       : 1.7.1
0:00:00.013772 INFO: alphapeptdeep   : 1.3.2
0:00:00.013790 INFO: directlfq       : 0.3.1
0:00:00.013807 INFO: ===================================================
0:00:00.013824 INFO: ================= Pip Environment =================
0:00:00.077231 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
0:00:00.077336 INFO: ===================================================
0:00:00.077366 INFO: Running step 'library'
0:00:00.077487 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.088449 INFO: loading additional config provided via CLI
0:00:00.088511 INFO: loading additional config provided via CLI parameters
0:00:00.088884 INFO: Updating config with 'user defined'
0:00:00.089021 INFO: Updating config with 'user defined (cli)'
0:00:00.089058 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default_ng.yaml
0:00:00.089800 INFO: updating config with user defined values: [{'calibration': {'batch_size': 1000, 'optimization_lock_target': 1000, 'min_steps': 5}, 'optimization': {'rt_error': {'automatic_update_percentile_range': 0.999, 'automatic_update_factor': 1.5, 'maximal_decrease': 0.1, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.5}}}, {'version': 1, 'workflow_name': None, 'output_directory': None, 'library_path': None, 'raw_paths': ['/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff'], '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': True, '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': [395, 905], 'fragment_mz': [140, 1750], 'nce': 25.0, 'fragment_types': ['b', 'y'], 'max_fragment_charge': 2, 'instrument': 'SCIEX', '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': 'ng', 'target_ms1_tolerance': 0.0, 'target_ms2_tolerance': 0.0, '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': 'SCIEX'}}, {'raw_paths': ['/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff'], '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': 'alphadia_zenoswath8600/library'}]
0:00:00.090080 INFO: Updating config with 'ng_default'
0:00:00.090115 INFO: Updating config with 'user defined'
0:00:00.090223 INFO: Updating config with 'user defined (cli)'
0:00:00.090246 INFO: Updating config with 'multistep search'
0:00:00.090280 INFO: ├──version: 1
0:00:00.090304 INFO: ├──workflow_name: None
0:00:00.090326 INFO: [32;20m├──output_directory: alphadia_zenoswath8600/library [multistep search, default: None][0m
0:00:00.090347 INFO: ├──library_path: None
0:00:00.090365 INFO: ├──raw_paths:
0:00:00.090385 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff [user defined (cli), default: None][0m
0:00:00.090404 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff [user defined (cli), default: None][0m
0:00:00.090424 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff [user defined (cli), default: None][0m
0:00:00.090445 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff [user defined (cli), default: None][0m
0:00:00.090465 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff [user defined (cli), default: None][0m
0:00:00.090485 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff [user defined (cli), default: None][0m
0:00:00.090505 INFO: ├──fasta_paths:
0:00:00.090525 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.090545 INFO: ├──quant_directory: None
0:00:00.090564 INFO: ├──general
0:00:00.090584 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:00:00.090604 INFO: │   ├──transfer_step_enabled: False
0:00:00.090624 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.090644 INFO: │   ├──reuse_calibration: False
0:00:00.090662 INFO: │   ├──reuse_quant: False
0:00:00.090681 INFO: │   ├──astral_ms1: False
0:00:00.090699 INFO: │   ├──log_level: INFO
0:00:00.090720 INFO: │   ├──mmap_detector_events: False
0:00:00.090740 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.090759 INFO: │   ├──save_figures: True
0:00:00.090778 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.090797 INFO: │   ├──save_flat_library: False
0:00:00.090815 INFO: │   ├──input_library_type: base
0:00:00.090833 INFO: │   ├──save_mbr_library: True
0:00:00.090852 INFO: │   └──random_state: None
0:00:00.090871 INFO: ├──library_loading
0:00:00.090889 INFO: │   └──rt_heuristic: 180
0:00:00.090906 INFO: ├──library_prediction
0:00:00.090925 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.090945 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.090965 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.090983 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.091002 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.091023 INFO: │   ├──missed_cleavages: 1
0:00:00.091042 INFO: │   ├──precursor_len:
0:00:00.091063 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.091082 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.091100 INFO: │   ├──precursor_charge:
0:00:00.091118 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.091135 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.091151 INFO: │   ├──precursor_mz:
0:00:00.091168 INFO: │   │   [32;20m- 395 [user defined, default: 400][0m
0:00:00.091186 INFO: │   │   [32;20m- 905 [user defined, default: 1200][0m
0:00:00.091202 INFO: │   ├──fragment_mz:
0:00:00.091219 INFO: │   │   [32;20m- 140 [user defined, default: 200][0m
0:00:00.091236 INFO: │   │   [32;20m- 1750 [user defined, default: 2000][0m
0:00:00.091254 INFO: │   ├──nce: 25.0
0:00:00.091272 INFO: │   ├──fragment_types:
0:00:00.091292 INFO: │   │   - b
0:00:00.091310 INFO: │   │   - y
0:00:00.091328 INFO: │   ├──max_fragment_charge: 2
0:00:00.091347 INFO: │   [32;20m├──instrument: SCIEX [user defined, default: Lumos][0m
0:00:00.091364 INFO: │   ├──peptdeep_model_path: None
0:00:00.091383 INFO: │   └──peptdeep_model_type: generic
0:00:00.091400 INFO: ├──custom_modifications:
0:00:00.091419 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.091438 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.091457 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.091475 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.091494 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.091511 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.091531 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.091548 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.091568 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.091585 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.091604 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.091621 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.091640 INFO: │   ├──name: Label:13C(12)@K
0:00:00.091659 INFO: │   └──composition: C(12)
0:00:00.091677 INFO: ├──search
0:00:00.091695 INFO: │   [32;20m├──extraction_backend: ng [user defined, default: classic][0m
0:00:00.091715 INFO: │   [32;20m├──target_ms1_tolerance: 0.0 [user defined, default: 5][0m
0:00:00.091733 INFO: │   [32;20m├──target_ms2_tolerance: 0.0 [user defined, default: 10][0m
0:00:00.091751 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.091769 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.091788 INFO: │   ├──quant_window: 3
0:00:00.091805 INFO: │   ├──target_num_candidates: 3
0:00:00.091824 INFO: │   ├──channel_filter: 
0:00:00.091841 INFO: │   ├──exclude_shared_ions: True
0:00:00.091858 INFO: │   ├──compete_for_fragments: True
0:00:00.091875 INFO: │   ├──quant_all: True
0:00:00.091892 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.091909 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.091927 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.091946 INFO: │   ├──experimental_xic: True
0:00:00.091963 INFO: │   └──optimized_peak_group_score: False
0:00:00.091983 INFO: ├──calibration
0:00:00.092001 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.092021 INFO: │   ├──optimization_lock_target: 200
0:00:00.092038 INFO: │   ├──max_steps: 20
0:00:00.092056 INFO: │   ├──min_steps: 2
0:00:00.092073 INFO: │   ├──max_skips: 1
0:00:00.092092 INFO: │   ├──max_fragments: 5000
0:00:00.092109 INFO: │   └──min_correlation: 0.7
0:00:00.092127 INFO: ├──search_initial
0:00:00.092145 INFO: │   ├──initial_num_candidates: 1
0:00:00.092164 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.092181 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.092199 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.092222 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.092241 INFO: ├──selection_config
0:00:00.092262 INFO: │   ├──peak_len_rt: 10.0
0:00:00.092281 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.092302 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.092321 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.092339 INFO: │   ├──top_k_precursors: 3
0:00:00.092356 INFO: │   ├──kernel_size: 30
0:00:00.092374 INFO: │   ├──f_mobility: 1.0
0:00:00.092391 INFO: │   ├──f_rt: 0.99
0:00:00.092409 INFO: │   ├──center_fraction: 0.5
0:00:00.092426 INFO: │   ├──min_size_mobility: 8
0:00:00.092443 INFO: │   ├──min_size_rt: 3
0:00:00.092460 INFO: │   ├──max_size_mobility: 20
0:00:00.092479 INFO: │   ├──max_size_rt: 15
0:00:00.092497 INFO: │   ├──group_channels: False
0:00:00.092515 INFO: │   ├──use_weighted_score: True
0:00:00.092533 INFO: │   ├──join_close_candidates: False
0:00:00.092553 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.092572 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.092591 INFO: ├──scoring_config
0:00:00.092610 INFO: │   ├──score_grouped: False
0:00:00.092627 INFO: │   ├──top_k_isotopes: 3
0:00:00.092645 INFO: │   ├──reference_channel: -1
0:00:00.092662 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.092681 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.092697 INFO: ├──library_multiplexing
0:00:00.092715 INFO: │   ├──enabled: False
0:00:00.092732 INFO: │   ├──input_channel: 0
0:00:00.092750 INFO: │   └──multiplex_mapping:
0:00:00.092766 INFO: ├──multiplexing
0:00:00.092783 INFO: │   ├──enabled: False
0:00:00.092802 INFO: │   ├──target_channels: 4,8
0:00:00.092821 INFO: │   ├──decoy_channel: 12
0:00:00.092838 INFO: │   ├──reference_channel: 0
0:00:00.092856 INFO: │   └──competetive_scoring: True
0:00:00.092872 INFO: ├──fdr
0:00:00.092891 INFO: │   ├──fdr: 0.01
0:00:00.092909 INFO: │   ├──group_level: proteins
0:00:00.092926 INFO: │   ├──inference_strategy: heuristic
0:00:00.092944 INFO: │   ├──competetive_scoring: True
0:00:00.092961 INFO: │   ├──keep_decoys: False
0:00:00.092978 INFO: │   ├──channel_wise_fdr: False
0:00:00.092996 INFO: │   ├──enable_two_step_classifier: False
0:00:00.093014 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.093031 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.093048 INFO: ├──search_output
0:00:00.093065 INFO: │   ├──file_format: tsv
0:00:00.093082 INFO: │   ├──peptide_level_lfq: False
0:00:00.093099 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.093116 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.093134 INFO: │   ├──min_k_fragments: 12
0:00:00.093152 INFO: │   ├──min_correlation: 0.9
0:00:00.093170 INFO: │   ├──num_samples_quadratic: 50
0:00:00.093188 INFO: │   ├──min_nonnan: 3
0:00:00.093206 INFO: │   └──normalize_lfq: True
0:00:00.093225 INFO: ├──optimization
0:00:00.093242 INFO: │   ├──order_of_optimization: None
0:00:00.093260 INFO: │   ├──ms2_error
0:00:00.093280 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.093299 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.093317 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.093336 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.093354 INFO: │   │   ├──try_narrower_values: True
0:00:00.093372 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.093391 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.093410 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.093427 INFO: │   ├──ms1_error
0:00:00.093446 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.093474 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.093496 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.093515 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.093535 INFO: │   │   ├──try_narrower_values: False
0:00:00.093553 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.093572 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.093590 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.093608 INFO: │   ├──mobility_error
0:00:00.093626 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.093646 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.093663 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.093682 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.093700 INFO: │   │   ├──try_narrower_values: False
0:00:00.093719 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.093736 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.093755 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.093773 INFO: │   └──rt_error
0:00:00.093792 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.093809 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.093828 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.093846 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.093863 INFO: │       ├──try_narrower_values: True
0:00:00.093881 INFO: │       ├──maximal_decrease: 0.2
0:00:00.093899 INFO: │       ├──favour_narrower_optimum: True
0:00:00.093917 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.093934 INFO: ├──optimization_manager
0:00:00.093953 INFO: │   ├──fwhm_rt: 5
0:00:00.093971 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.093991 INFO: │   └──score_cutoff: 0
0:00:00.094008 INFO: ├──transfer_library
0:00:00.094027 INFO: │   ├──enabled: False
0:00:00.094044 INFO: │   ├──fragment_types:
0:00:00.094062 INFO: │   │   - b
0:00:00.094079 INFO: │   │   - y
0:00:00.094098 INFO: │   ├──max_charge: 2
0:00:00.094115 INFO: │   ├──top_k_samples: 3
0:00:00.094134 INFO: │   ├──norm_delta_max: True
0:00:00.094153 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.094172 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.094188 INFO: └──transfer_learning
0:00:00.094207 INFO:     ├──enabled: False
0:00:00.094224 INFO:     ├──batch_size: 2000
0:00:00.094243 INFO:     ├──max_lr: 0.0001
0:00:00.094260 INFO:     ├──train_fraction: 0.7
0:00:00.094278 INFO:     ├──validation_fraction: 0.2
0:00:00.094295 INFO:     ├──test_fraction: 0.1
0:00:00.094313 INFO:     ├──test_interval: 1
0:00:00.094331 INFO:     ├──lr_patience: 3
0:00:00.094350 INFO:     ├──epochs: 51
0:00:00.094367 INFO:     ├──warmup_epochs: 5
0:00:00.094386 INFO:     ├──nce: 25
0:00:00.094404 INFO:     [32;20m└──instrument: SCIEX [user defined, default: Lumos][0m
0:00:00.099417 INFO: Moved existing config file alphadia_zenoswath8600/library/frozen_config.yaml to alphadia_zenoswath8600/library/frozen_config.yaml
0:00:00.099616 INFO: Registering 7 custom modifications
0:00:00.127536 INFO: Searching 6 files:
0:00:00.127613 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff
0:00:00.127639 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff
0:00:00.127663 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff
0:00:00.127681 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff
0:00:00.127698 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff
0:00:00.127715 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff
0:00:00.127732 INFO: Using 1 fasta files:
0:00:00.127750 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:00:00.127776 INFO: Using library: None
0:00:00.127795 INFO: Saving output to: alphadia_zenoswath8600/library
0:00:00.127818 PROGRESS: Loading spectral library
0:00:00.127843 PROGRESS: No library provided. Building library from fasta files.
0:00:00.127872 INFO: Running FastaDigest
0:00:01.088544 INFO: Digesting fasta file
0:00:07.625960 INFO: Adding modifications
0:01:42.092841 INFO: Removing non-canonical amino acids
0:01:48.209043 INFO: Fasta library contains 5,696,279 precursors
0:01:48.209249 PROGRESS: Predicting library properties.
0:01:48.209314 INFO: Running PeptDeepPrediction
0:01:48.209400 INFO: Device set to cpu
0:01:49.118063 INFO: Loading PeptDeep models of type generic
0:01:49.880584 INFO: Predicting RT, MS2 and mobility
0:01:49.880781 INFO: Using multiprocessing with 80 processes ...
0:01:50.258447 INFO: Predicting rt,ms2,mobility ...
0:08:13.905764 INFO: Adding fragment mz information
0:08:14.233402 INFO: Adding fragment intensity information
0:08:14.563874 INFO: Adding precursor information
0:08:15.010380 INFO: Running PrecursorInitializer
0:08:15.114150 INFO: Running AnnotateFasta
0:08:15.285494 INFO: Dropping decoys from input library before annotation
0:08:42.470603 INFO: Running IsotopeGenerator
0:08:42.471819 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:12:18.192877 INFO: Running RTNormalization
0:12:18.193227 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:12:18.193345 INFO: Saving library to alphadia_zenoswath8600/library/speclib.hdf
0:12:52.447625 INFO: Running DecoyGenerator
0:14:38.981166 INFO: Running FlattenLibrary
0:15:15.710790 INFO: Running InitFlatColumns
0:15:15.970951 INFO: Running LogFlatLibraryStats
0:15:15.971100 INFO: ============ Library Stats ============
0:15:15.971139 INFO: Number of precursors: 11,362,281
0:15:17.510947 INFO: 	thereof targets:5,696,279
0:15:17.511096 INFO: 	thereof decoys: 5,666,002
0:15:17.586605 INFO: Number of elution groups: 5,696,279
0:15:17.586743 INFO: 	average size: 1.99
0:15:17.876737 INFO: Number of proteins: 117,993
0:15:17.904305 INFO: Number of channels: 1 ([0])
0:15:17.904485 INFO: Isotopes Distribution for 4 isotopes
0:15:17.904515 INFO: =======================================
0:15:17.913455 PROGRESS: Starting Search Workflows
0:15:17.913683 PROGRESS: 
0:15:17.913769 INFO: Quantification results path: alphadia_zenoswath8600/library/quant
0:15:17.913851 INFO: Creating folder alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/figures
0:15:17.914079 INFO: Initializing TimingManager
0:15:17.914949 INFO: Initializing RawFileManager
0:17:43.901970 INFO: Determining DIA cycle
0:17:44.112626 INFO: Found cycle with start 0.00 min and length 86.
0:17:44.345980 INFO: RT (min)            : 0.0 - 55.5
0:17:44.346081 INFO: RT duration (sec)   : 3327.2
0:17:44.346112 INFO: RT duration (min)   : 55.5
0:17:44.346136 INFO: Cycle len (scans)   : 86
0:17:44.346156 INFO: Cycle len (sec)     : 1.90
0:17:44.346176 INFO: Number of cycles    : 1747
0:17:44.346195 INFO: MS2 range (m/z)     : 399.5 - 903.5
0:17:44.346244 INFO: Creating DIA data object took: 146.43119430541992
0:17:45.509700 INFO: Creating DIA data NG object took: 1.1632914543151855
0:17:46.863558 INFO: Initializing CalibrationManager
0:17:46.863899 INFO: Setting up calibration estimators ..
0:17:46.863971 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:17:46.864066 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'}' ..
0:17:46.864209 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:17:46.864269 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:17:46.864327 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}}' ..
0:17:46.864391 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:17:46.864438 INFO: Done setting up calibration estimators.
0:17:46.864601 INFO: Initializing OptimizationManager
0:17:46.864764 INFO: initial parameter: ms1_error = 30
0:17:46.864818 INFO: initial parameter: ms2_error = 30
0:17:46.864865 INFO: initial parameter: rt_error = 1663.6044921875
0:17:46.864909 INFO: initial parameter: mobility_error = 0.1
0:17:46.864948 INFO: initial parameter: num_candidates = 1
0:17:46.864987 INFO: initial parameter: fwhm_rt = 5
0:17:46.865026 INFO: initial parameter: fwhm_mobility = 0.01
0:17:46.865067 INFO: initial parameter: score_cutoff = 0
0:17:46.865108 INFO: initial parameter: classifier_version = -1
0:17:46.865183 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
0:17:46.865905 INFO: FDRManager: loading saved state not requested, will be initialized.
0:17:46.865948 INFO: Initializing FDRManager
0:17:46.865992 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:17:48.202015 PROGRESS: Initializing spectral library: 5,608,555 target precursors potentially observable (87,724 removed)
0:17:49.488542 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:17:49.488896 INFO: Updating optimization_manager: rt_error            : 1663.6044921875 -> 1663.6044921875
0:17:49.489007 PROGRESS: Starting initial search for precursors.
0:17:49.489096 INFO: Starting optimization step 0.
0:17:49.489162 PROGRESS: === Extracting elution groups 0 to 200 ===
0:17:49.489223 INFO: Using ng extraction backend
0:17:49.489300 PROGRESS: Extracting batch of 394 precursors
0:17:49.491163 INFO: === Search parameters used ===
0:17:49.491255 INFO: rt_error       : 1663.6044921875
0:17:49.491305 INFO: mobility_error : 0.1
0:17:49.491349 INFO: num_candidates : 1
0:17:49.491393 INFO: ms1_error      : 30
0:17:49.491433 INFO: ms2_error      : 30
0:17:49.491471 INFO: fwhm_rt        : 5
0:17:49.491511 INFO: quant_window   : 3
0:17:49.491557 INFO: ==============================================
0:17:49.527419 INFO: performing precursor FDR with 40 features
0:17:49.527495 INFO: Decoy channel: -1
0:17:49.527520 INFO: Competetive: True
0:17:49.528474 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:49.531100 INFO: Using random state 395314 for train-test-split
0:17:49.549560 INFO: Test AUC: 0.487
0:17:49.549622 INFO: Train AUC: 0.521
0:17:49.549652 INFO: AUC difference: 6.51%
0:17:49.549676 WARNING: AUC difference > 5%. This may indicate overfitting.
0:17:49.812539 INFO: Resetting torch num_threads to 80
0:17:49.813893 PROGRESS: === Extracted 394 precursors and 2194 fragments ===
0:17:49.814234 INFO: === FDR correction performed with classifier version -1 ===
0:17:49.814662 PROGRESS: ============================= Precursor FDR =============================
0:17:49.814743 PROGRESS: Total precursors accumulated: 0
0:17:49.814802 PROGRESS: Target precursors: 0 (0.00%)
0:17:49.814851 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:49.814896 PROGRESS: 
0:17:49.814941 PROGRESS: Precursor Summary:
0:17:49.815048 PROGRESS: 
0:17:49.815108 PROGRESS: Protein Summary:
0:17:49.815180 PROGRESS: =========================================================================
0:17:49.815320 INFO: Target number of precursors not reached yet.
0:17:49.876298 INFO: Starting optimization step 1.
0:17:49.876509 PROGRESS: === Extracting elution groups 200 to 600 ===
0:17:49.876593 INFO: Using ng extraction backend
0:17:49.876657 PROGRESS: Extracting batch of 782 precursors
0:17:49.879067 INFO: === Search parameters used ===
0:17:49.879154 INFO: rt_error       : 1663.6044921875
0:17:49.879201 INFO: mobility_error : 0.1
0:17:49.879245 INFO: num_candidates : 1
0:17:49.879286 INFO: ms1_error      : 30
0:17:49.879331 INFO: ms2_error      : 30
0:17:49.879380 INFO: fwhm_rt        : 5
0:17:49.879421 INFO: quant_window   : 3
0:17:49.879461 INFO: ==============================================
0:17:49.909905 INFO: performing precursor FDR with 40 features
0:17:49.909980 INFO: Decoy channel: -1
0:17:49.910007 INFO: Competetive: True
0:17:49.912925 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:49.914493 INFO: Using random state 23244 for train-test-split
0:17:49.923504 INFO: Test AUC: 0.526
0:17:49.923568 INFO: Train AUC: 0.511
0:17:49.923598 INFO: AUC difference: 2.91%
0:17:50.132393 INFO: Resetting torch num_threads to 80
0:17:50.134544 PROGRESS: === Extracted 1174 precursors and 6630 fragments ===
0:17:50.134898 INFO: === FDR correction performed with classifier version -1 ===
0:17:50.135323 PROGRESS: ============================= Precursor FDR =============================
0:17:50.135407 PROGRESS: Total precursors accumulated: 0
0:17:50.135467 PROGRESS: Target precursors: 0 (0.00%)
0:17:50.135514 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:50.135560 PROGRESS: 
0:17:50.135601 PROGRESS: Precursor Summary:
0:17:50.135710 PROGRESS: 
0:17:50.135770 PROGRESS: Protein Summary:
0:17:50.135851 PROGRESS: =========================================================================
0:17:50.136032 INFO: Target number of precursors not reached yet.
0:17:50.199203 INFO: Starting optimization step 2.
0:17:50.199408 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:17:50.199492 INFO: Using ng extraction backend
0:17:50.199558 PROGRESS: Extracting batch of 1565 precursors
0:17:50.203713 INFO: === Search parameters used ===
0:17:50.203828 INFO: rt_error       : 1663.6044921875
0:17:50.203878 INFO: mobility_error : 0.1
0:17:50.203923 INFO: num_candidates : 1
0:17:50.203965 INFO: ms1_error      : 30
0:17:50.204004 INFO: ms2_error      : 30
0:17:50.204044 INFO: fwhm_rt        : 5
0:17:50.204083 INFO: quant_window   : 3
0:17:50.204125 INFO: ==============================================
0:17:50.243860 INFO: performing precursor FDR with 40 features
0:17:50.243944 INFO: Decoy channel: -1
0:17:50.243970 INFO: Competetive: True
0:17:50.247348 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:50.249219 INFO: Using random state 926472 for train-test-split
0:17:50.261914 INFO: Test AUC: 0.532
0:17:50.261983 INFO: Train AUC: 0.511
0:17:50.262014 INFO: AUC difference: 4.25%
0:17:50.472822 INFO: Resetting torch num_threads to 80
0:17:50.475427 PROGRESS: === Extracted 2734 precursors and 15555 fragments ===
0:17:50.475779 INFO: === FDR correction performed with classifier version -1 ===
0:17:50.476208 PROGRESS: ============================= Precursor FDR =============================
0:17:50.476292 PROGRESS: Total precursors accumulated: 0
0:17:50.476352 PROGRESS: Target precursors: 0 (0.00%)
0:17:50.476402 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:50.476447 PROGRESS: 
0:17:50.476498 PROGRESS: Precursor Summary:
0:17:50.476609 PROGRESS: 
0:17:50.476671 PROGRESS: Protein Summary:
0:17:50.476743 PROGRESS: =========================================================================
0:17:50.476936 INFO: Target number of precursors not reached yet.
0:17:50.542471 INFO: Starting optimization step 3.
0:17:50.542694 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:17:50.542779 INFO: Using ng extraction backend
0:17:50.542843 PROGRESS: Extracting batch of 3140 precursors
0:17:50.549372 INFO: === Search parameters used ===
0:17:50.549488 INFO: rt_error       : 1663.6044921875
0:17:50.549538 INFO: mobility_error : 0.1
0:17:50.549585 INFO: num_candidates : 1
0:17:50.549628 INFO: ms1_error      : 30
0:17:50.549676 INFO: ms2_error      : 30
0:17:50.549719 INFO: fwhm_rt        : 5
0:17:50.549759 INFO: quant_window   : 3
0:17:50.549798 INFO: ==============================================
0:17:50.604881 INFO: performing precursor FDR with 40 features
0:17:50.604985 INFO: Decoy channel: -1
0:17:50.605011 INFO: Competetive: True
0:17:50.609219 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:50.611554 INFO: Using random state 983952 for train-test-split
0:17:50.631982 INFO: Test AUC: 0.514
0:17:50.632062 INFO: Train AUC: 0.512
0:17:50.632091 INFO: AUC difference: 0.36%
0:17:50.843498 INFO: Resetting torch num_threads to 80
0:17:50.846838 PROGRESS: === Extracted 5868 precursors and 33640 fragments ===
0:17:50.847199 INFO: === FDR correction performed with classifier version -1 ===
0:17:50.847634 PROGRESS: ============================= Precursor FDR =============================
0:17:50.847721 PROGRESS: Total precursors accumulated: 0
0:17:50.847789 PROGRESS: Target precursors: 0 (0.00%)
0:17:50.847843 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:50.847888 PROGRESS: 
0:17:50.847931 PROGRESS: Precursor Summary:
0:17:50.848041 PROGRESS: 
0:17:50.848101 PROGRESS: Protein Summary:
0:17:50.848174 PROGRESS: =========================================================================
0:17:50.848399 INFO: Target number of precursors not reached yet.
0:17:50.918834 INFO: Starting optimization step 4.
0:17:50.919050 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:17:50.919135 INFO: Using ng extraction backend
0:17:50.919200 PROGRESS: Extracting batch of 6271 precursors
0:17:50.931252 INFO: === Search parameters used ===
0:17:50.931382 INFO: rt_error       : 1663.6044921875
0:17:50.931430 INFO: mobility_error : 0.1
0:17:50.931474 INFO: num_candidates : 1
0:17:50.931516 INFO: ms1_error      : 30
0:17:50.931555 INFO: ms2_error      : 30
0:17:50.931594 INFO: fwhm_rt        : 5
0:17:50.931632 INFO: quant_window   : 3
0:17:50.931670 INFO: ==============================================
0:17:51.024042 INFO: performing precursor FDR with 40 features
0:17:51.024940 INFO: Decoy channel: -1
0:17:51.024976 INFO: Competetive: True
0:17:51.031785 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:51.036707 INFO: Using random state 754497 for train-test-split
0:17:51.079402 INFO: Test AUC: 0.533
0:17:51.079525 INFO: Train AUC: 0.508
0:17:51.079558 INFO: AUC difference: 4.83%
0:17:51.290147 INFO: Resetting torch num_threads to 80
0:17:51.294521 PROGRESS: === Extracted 12129 precursors and 69806 fragments ===
0:17:51.294898 INFO: === FDR correction performed with classifier version -1 ===
0:17:51.295326 PROGRESS: ============================= Precursor FDR =============================
0:17:51.295408 PROGRESS: Total precursors accumulated: 0
0:17:51.295466 PROGRESS: Target precursors: 0 (0.00%)
0:17:51.295517 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:51.295564 PROGRESS: 
0:17:51.295608 PROGRESS: Precursor Summary:
0:17:51.295718 PROGRESS: 
0:17:51.295779 PROGRESS: Protein Summary:
0:17:51.295851 PROGRESS: =========================================================================
0:17:51.296128 INFO: Target number of precursors not reached yet.
0:17:51.373398 INFO: Starting optimization step 5.
0:17:51.373635 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:17:51.373729 INFO: Using ng extraction backend
0:17:51.373794 PROGRESS: Extracting batch of 12568 precursors
0:17:51.396422 INFO: === Search parameters used ===
0:17:51.396585 INFO: rt_error       : 1663.6044921875
0:17:51.396637 INFO: mobility_error : 0.1
0:17:51.396682 INFO: num_candidates : 1
0:17:51.396724 INFO: ms1_error      : 30
0:17:51.396766 INFO: ms2_error      : 30
0:17:51.396809 INFO: fwhm_rt        : 5
0:17:51.396861 INFO: quant_window   : 3
0:17:51.396905 INFO: ==============================================
0:17:51.546653 INFO: performing precursor FDR with 40 features
0:17:51.546770 INFO: Decoy channel: -1
0:17:51.546797 INFO: Competetive: True
0:17:51.556907 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:51.563390 INFO: Using random state 679290 for train-test-split
0:17:51.860460 INFO: Test AUC: 0.526
0:17:51.860588 INFO: Train AUC: 0.537
0:17:51.860620 INFO: AUC difference: 2.13%
0:17:52.100626 INFO: Resetting torch num_threads to 80
0:17:52.107017 PROGRESS: === Extracted 24680 precursors and 142036 fragments ===
0:17:52.107414 INFO: === FDR correction performed with classifier version -1 ===
0:17:52.107896 PROGRESS: ============================= Precursor FDR =============================
0:17:52.107994 PROGRESS: Total precursors accumulated: 43
0:17:52.108055 PROGRESS: Target precursors: 43 (100.00%)
0:17:52.108106 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:52.108152 PROGRESS: 
0:17:52.108195 PROGRESS: Precursor Summary:
0:17:52.109139 PROGRESS: Channel   0:	 0.050 FDR:    43; 0.010 FDR:    43; 0.001 FDR:    43
0:17:52.109224 PROGRESS: 
0:17:52.109278 PROGRESS: Protein Summary:
0:17:52.110355 PROGRESS: Channel   0:	 0.050 FDR:    43; 0.010 FDR:    43; 0.001 FDR:    43
0:17:52.110446 PROGRESS: =========================================================================
0:17:52.110861 INFO: Target number of precursors not reached yet.
0:17:52.207488 INFO: Starting optimization step 6.
0:17:52.207738 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:17:52.207826 INFO: Using ng extraction backend
0:17:52.207892 PROGRESS: Extracting batch of 25144 precursors
0:17:52.252278 INFO: === Search parameters used ===
0:17:52.252513 INFO: rt_error       : 1663.6044921875
0:17:52.252568 INFO: mobility_error : 0.1
0:17:52.252612 INFO: num_candidates : 1
0:17:52.252655 INFO: ms1_error      : 30
0:17:52.252696 INFO: ms2_error      : 30
0:17:52.252735 INFO: fwhm_rt        : 5
0:17:52.252775 INFO: quant_window   : 3
0:17:52.252816 INFO: ==============================================
0:17:52.608266 INFO: performing precursor FDR with 40 features
0:17:52.608399 INFO: Decoy channel: -1
0:17:52.608426 INFO: Competetive: True
0:17:52.626536 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:52.638280 INFO: Using random state 7346 for train-test-split
0:17:53.362165 INFO: Test AUC: 0.554
0:17:53.362275 INFO: Train AUC: 0.580
0:17:53.362305 INFO: AUC difference: 4.64%
0:17:53.934560 INFO: Resetting torch num_threads to 80
0:17:53.944720 PROGRESS: === Extracted 49786 precursors and 286377 fragments ===
0:17:53.945139 INFO: === FDR correction performed with classifier version -1 ===
0:17:53.945607 PROGRESS: ============================= Precursor FDR =============================
0:17:53.945694 PROGRESS: Total precursors accumulated: 0
0:17:53.945753 PROGRESS: Target precursors: 0 (0.00%)
0:17:53.945801 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:53.945845 PROGRESS: 
0:17:53.945889 PROGRESS: Precursor Summary:
0:17:53.946000 PROGRESS: 
0:17:53.946059 PROGRESS: Protein Summary:
0:17:53.946131 PROGRESS: =========================================================================
0:17:53.946799 INFO: Target number of precursors not reached yet.
0:17:54.100753 INFO: Starting optimization step 7.
0:17:54.101022 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:17:54.101123 INFO: Using ng extraction backend
0:17:54.101210 PROGRESS: Extracting batch of 50233 precursors
0:17:54.188131 INFO: === Search parameters used ===
0:17:54.188437 INFO: rt_error       : 1663.6044921875
0:17:54.188494 INFO: mobility_error : 0.1
0:17:54.188540 INFO: num_candidates : 1
0:17:54.188589 INFO: ms1_error      : 30
0:17:54.188631 INFO: ms2_error      : 30
0:17:54.188671 INFO: fwhm_rt        : 5
0:17:54.188709 INFO: quant_window   : 3
0:17:54.188747 INFO: ==============================================
0:17:54.700663 INFO: performing precursor FDR with 40 features
0:17:54.700784 INFO: Decoy channel: -1
0:17:54.700810 INFO: Competetive: True
0:17:54.737664 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:54.762453 INFO: Using random state 102244 for train-test-split
0:17:56.183762 INFO: Test AUC: 0.578
0:17:56.183894 INFO: Train AUC: 0.594
0:17:56.183926 INFO: AUC difference: 2.78%
0:17:56.438266 INFO: Resetting torch num_threads to 80
0:17:56.457240 PROGRESS: === Extracted 99934 precursors and 574989 fragments ===
0:17:56.457763 INFO: === FDR correction performed with classifier version -1 ===
0:17:56.458300 PROGRESS: ============================= Precursor FDR =============================
0:17:56.458397 PROGRESS: Total precursors accumulated: 223
0:17:56.458457 PROGRESS: Target precursors: 221 (99.10%)
0:17:56.458506 PROGRESS: Decoy precursors: 2 (0.90%)
0:17:56.458550 PROGRESS: 
0:17:56.458605 PROGRESS: Precursor Summary:
0:17:56.459538 PROGRESS: Channel   0:	 0.050 FDR:   221; 0.010 FDR:   221; 0.001 FDR:   192
0:17:56.459624 PROGRESS: 
0:17:56.459685 PROGRESS: Protein Summary:
0:17:56.460765 PROGRESS: Channel   0:	 0.050 FDR:   213; 0.010 FDR:   213; 0.001 FDR:   186
0:17:56.460851 PROGRESS: =========================================================================
0:17:56.462135 INFO: Target number of precursors reached.
0:17:56.505090 INFO: fragments_df: keeping 2190 of 574989 [sum(precursor_idx_mask)=2427 sum(mass_error_mask)=574989 stop_rank=2190
0:17:56.757133 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:56.895510 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:57.194706 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:17:57.195137 INFO: Using score_cutoff 14.771598060607909 (fac=0.99, q=1)
0:17:57.195511 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:17:57.195590 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:17:57.195645 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.771598060607909
0:17:57.195705 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:57.259877 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:57.410425 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:17:57.410708 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:17:57.410819 INFO: Starting optimization step 8.
0:17:57.410893 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:17:57.410971 INFO: Using ng extraction backend
0:17:57.411045 PROGRESS: Extracting batch of 100097 precursors
0:17:57.590175 INFO: === Search parameters used ===
0:17:57.590497 INFO: rt_error       : 1663.6044921875
0:17:57.590557 INFO: mobility_error : 0.1
0:17:57.590605 INFO: num_candidates : 3
0:17:57.590649 INFO: ms1_error      : 30
0:17:57.590692 INFO: ms2_error      : 30
0:17:57.590733 INFO: fwhm_rt        : 3.0
0:17:57.590773 INFO: quant_window   : 3
0:17:57.590814 INFO: ==============================================
0:17:59.720161 INFO: performing precursor FDR with 40 features
0:17:59.720286 INFO: Decoy channel: -1
0:17:59.720312 INFO: Competetive: True
0:17:59.821139 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:59.929251 INFO: Using random state 379259 for train-test-split
0:18:04.050282 INFO: Test AUC: 0.584
0:18:04.050533 INFO: Train AUC: 0.597
0:18:04.050570 INFO: AUC difference: 2.17%
0:18:04.372855 INFO: Resetting torch num_threads to 80
0:18:04.385043 PROGRESS: === Extracted 299805 precursors and 1684870 fragments ===
0:18:04.385528 INFO: === FDR correction performed with classifier version 7 ===
0:18:04.386014 PROGRESS: ============================= Precursor FDR =============================
0:18:04.386101 PROGRESS: Total precursors accumulated: 311
0:18:04.386161 PROGRESS: Target precursors: 308 (99.04%)
0:18:04.386210 PROGRESS: Decoy precursors: 3 (0.96%)
0:18:04.386257 PROGRESS: 
0:18:04.386304 PROGRESS: Precursor Summary:
0:18:04.387227 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   308; 0.001 FDR:   194
0:18:04.387315 PROGRESS: 
0:18:04.387370 PROGRESS: Protein Summary:
0:18:04.388462 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   296; 0.001 FDR:   190
0:18:04.388556 PROGRESS: =========================================================================
0:18:04.393778 INFO: Target number of precursors reached.
0:18:04.509943 INFO: fragments_df: keeping 4269 of 1684870 [sum(precursor_idx_mask)=7195 sum(mass_error_mask)=1684870 stop_rank=4269
0:18:04.742373 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:04.868556 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:05.465840 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:05.466280 INFO: Using score_cutoff 14.036366664218903 (fac=0.99, q=1)
0:18:05.466606 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:05.466685 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:05.466749 INFO: Updating optimization_manager: score_cutoff        : 14.771598060607909 -> 14.036366664218903
0:18:05.466814 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:05.603638 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:05.816770 INFO: === checking if optimization conditions were reached ===
0:18:05.817092 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:18:05.819725 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.842474631331681
0:18:05.819845 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 6.8425.
0:18:05.819912 INFO: ==============================================
0:18:05.819986 INFO: Starting optimization step 9.
0:18:05.820043 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:05.820129 INFO: Using ng extraction backend
0:18:05.820204 PROGRESS: Extracting batch of 100097 precursors
0:18:05.999791 INFO: === Search parameters used ===
0:18:06.000117 INFO: rt_error       : 1663.6044921875
0:18:06.000177 INFO: mobility_error : 0.1
0:18:06.000223 INFO: num_candidates : 3
0:18:06.000264 INFO: ms1_error      : 30
0:18:06.000306 INFO: ms2_error      : 6.842474631331681
0:18:06.000345 INFO: fwhm_rt        : 3.0
0:18:06.000383 INFO: quant_window   : 3
0:18:06.000423 INFO: ==============================================
0:18:07.491371 INFO: performing precursor FDR with 40 features
0:18:07.491503 INFO: Decoy channel: -1
0:18:07.491529 INFO: Competetive: True
0:18:07.568080 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:07.669030 INFO: Using random state 379259 for train-test-split
0:18:11.616757 INFO: Test AUC: 0.585
0:18:11.616887 INFO: Train AUC: 0.594
0:18:11.616917 INFO: AUC difference: 1.48%
0:18:11.932730 INFO: Resetting torch num_threads to 80
0:18:11.983640 PROGRESS: === Extracted 300279 precursors and 1822670 fragments ===
0:18:11.984078 INFO: === FDR correction performed with classifier version 7 ===
0:18:11.984553 PROGRESS: ============================= Precursor FDR =============================
0:18:11.984641 PROGRESS: Total precursors accumulated: 330
0:18:11.984699 PROGRESS: Target precursors: 327 (99.09%)
0:18:11.984747 PROGRESS: Decoy precursors: 3 (0.91%)
0:18:11.984791 PROGRESS: 
0:18:11.984834 PROGRESS: Precursor Summary:
0:18:11.985758 PROGRESS: Channel   0:	 0.050 FDR:   327; 0.010 FDR:   327; 0.001 FDR:   256
0:18:11.985845 PROGRESS: 
0:18:11.985899 PROGRESS: Protein Summary:
0:18:11.986999 PROGRESS: Channel   0:	 0.050 FDR:   313; 0.010 FDR:   313; 0.001 FDR:   244
0:18:11.987087 PROGRESS: =========================================================================
0:18:11.992167 INFO: Target number of precursors reached.
0:18:12.115654 INFO: fragments_df: keeping 4621 of 1822670 [sum(precursor_idx_mask)=8013 sum(mass_error_mask)=1822670 stop_rank=4621
0:18:12.452060 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:12.581444 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:13.198907 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:13.199385 INFO: Using score_cutoff 11.315423915290832 (fac=0.99, q=1)
0:18:13.199683 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:13.199759 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:13.199811 INFO: Updating optimization_manager: score_cutoff        : 14.036366664218903 -> 11.315423915290832
0:18:13.199869 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:13.260491 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:13.410537 INFO: === checking if optimization conditions were reached ===
0:18:13.410852 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:18:13.413894 INFO: Updating optimization_manager: ms2_error           : 6.842474631331681 -> 6.772889369333892
0:18:13.414033 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 6.7729.
0:18:13.414134 INFO: ==============================================
0:18:13.414226 INFO: Starting optimization step 10.
0:18:13.414301 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:13.414381 INFO: Using ng extraction backend
0:18:13.414452 PROGRESS: Extracting batch of 100097 precursors
0:18:13.594684 INFO: === Search parameters used ===
0:18:13.595014 INFO: rt_error       : 1663.6044921875
0:18:13.595073 INFO: mobility_error : 0.1
0:18:13.595120 INFO: num_candidates : 3
0:18:13.595163 INFO: ms1_error      : 30
0:18:13.595203 INFO: ms2_error      : 6.772889369333892
0:18:13.595243 INFO: fwhm_rt        : 3.0
0:18:13.595286 INFO: quant_window   : 3
0:18:13.595326 INFO: ==============================================
0:18:15.041323 INFO: performing precursor FDR with 40 features
0:18:15.043169 INFO: Decoy channel: -1
0:18:15.043200 INFO: Competetive: True
0:18:15.123452 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:15.225780 INFO: Using random state 379259 for train-test-split
0:18:19.180848 INFO: Test AUC: 0.583
0:18:19.180973 INFO: Train AUC: 0.593
0:18:19.181005 INFO: AUC difference: 1.66%
0:18:19.500904 INFO: Resetting torch num_threads to 80
0:18:19.514045 PROGRESS: === Extracted 300279 precursors and 1822373 fragments ===
0:18:19.514530 INFO: === FDR correction performed with classifier version 7 ===
0:18:19.515008 PROGRESS: ============================= Precursor FDR =============================
0:18:19.515095 PROGRESS: Total precursors accumulated: 349
0:18:19.515153 PROGRESS: Target precursors: 346 (99.14%)
0:18:19.515200 PROGRESS: Decoy precursors: 3 (0.86%)
0:18:19.515242 PROGRESS: 
0:18:19.515283 PROGRESS: Precursor Summary:
0:18:19.516212 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   346; 0.001 FDR:   231
0:18:19.516304 PROGRESS: 
0:18:19.516358 PROGRESS: Protein Summary:
0:18:19.517461 PROGRESS: Channel   0:	 0.050 FDR:   332; 0.010 FDR:   332; 0.001 FDR:   222
0:18:19.517557 PROGRESS: =========================================================================
0:18:19.523572 INFO: Target number of precursors reached.
0:18:19.649119 INFO: fragments_df: keeping 4877 of 1822373 [sum(precursor_idx_mask)=8472 sum(mass_error_mask)=1822373 stop_rank=4877
0:18:19.871598 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:20.067285 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:20.723824 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:20.724257 INFO: Using score_cutoff 11.658162367343902 (fac=0.99, q=1)
0:18:20.724586 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:20.724663 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:20.724718 INFO: Updating optimization_manager: score_cutoff        : 11.315423915290832 -> 11.658162367343902
0:18:20.724780 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:20.794294 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:20.971241 INFO: === checking if optimization conditions were reached ===
0:18:20.971559 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:18:20.972774 INFO: Updating optimization_manager: ms2_error           : 6.772889369333892 -> 6.772889369333892
0:18:20.972923 INFO: Updating optimization_manager: classifier_version  : 7 -> 10
0:18:20.973052 INFO: Updating optimization_manager: score_cutoff        : 11.658162367343902 -> 11.658162367343902
0:18:20.973167 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:20.973275 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:20.973379 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 6.7729 found after 3 searches.
0:18:20.973457 INFO: ==============================================
0:18:20.973562 PROGRESS: Optimization finished for ms2_error.
0:18:21.186399 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:21.253180 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:21.436874 INFO: Starting optimization step 0.
0:18:21.437107 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:21.437210 INFO: Using ng extraction backend
0:18:21.437292 PROGRESS: Extracting batch of 100097 precursors
0:18:21.618136 INFO: === Search parameters used ===
0:18:21.618439 INFO: rt_error       : 1663.6044921875
0:18:21.618509 INFO: mobility_error : 0.1
0:18:21.618557 INFO: num_candidates : 3
0:18:21.618602 INFO: ms1_error      : 30
0:18:21.618645 INFO: ms2_error      : 6.772889369333892
0:18:21.618687 INFO: fwhm_rt        : 3.0
0:18:21.618728 INFO: quant_window   : 3
0:18:21.618782 INFO: ==============================================
0:18:23.030722 INFO: performing precursor FDR with 40 features
0:18:23.030850 INFO: Decoy channel: -1
0:18:23.030876 INFO: Competetive: True
0:18:23.106519 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:23.205680 INFO: Using random state 545139 for train-test-split
0:18:27.231236 INFO: Test AUC: 0.587
0:18:27.231371 INFO: Train AUC: 0.602
0:18:27.231403 INFO: AUC difference: 2.42%
0:18:27.546602 INFO: Resetting torch num_threads to 80
0:18:27.558525 PROGRESS: === Extracted 300279 precursors and 1822212 fragments ===
0:18:27.558918 INFO: === FDR correction performed with classifier version 10 ===
0:18:27.559396 PROGRESS: ============================= Precursor FDR =============================
0:18:27.559484 PROGRESS: Total precursors accumulated: 314
0:18:27.559543 PROGRESS: Target precursors: 311 (99.04%)
0:18:27.559591 PROGRESS: Decoy precursors: 3 (0.96%)
0:18:27.559634 PROGRESS: 
0:18:27.559676 PROGRESS: Precursor Summary:
0:18:27.560575 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   311; 0.001 FDR:   262
0:18:27.560660 PROGRESS: 
0:18:27.560713 PROGRESS: Protein Summary:
0:18:27.561800 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   298; 0.001 FDR:   251
0:18:27.561888 PROGRESS: =========================================================================
0:18:27.566981 INFO: Target number of precursors reached.
0:18:27.694314 INFO: fragments_df: keeping 4436 of 1822212 [sum(precursor_idx_mask)=7628 sum(mass_error_mask)=1822212 stop_rank=4436
0:18:27.972016 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:28.177187 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:28.769998 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:28.770440 INFO: Using score_cutoff 11.656769528388978 (fac=0.99, q=1)
0:18:28.770734 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:28.770813 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:28.770867 INFO: Updating optimization_manager: score_cutoff        : 11.658162367343902 -> 11.656769528388978
0:18:28.770924 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:28.831220 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:28.977429 INFO: === checking if optimization conditions were reached ===
0:18:28.977736 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:18:28.980089 INFO: Updating optimization_manager: rt_error            : 1663.6044921875 -> 130.1416818357919
0:18:28.980204 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 130.1417.
0:18:28.980284 INFO: ==============================================
0:18:28.980366 INFO: Starting optimization step 1.
0:18:28.980434 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:28.980507 INFO: Using ng extraction backend
0:18:28.980576 PROGRESS: Extracting batch of 100097 precursors
0:18:29.156645 INFO: === Search parameters used ===
0:18:29.156956 INFO: rt_error       : 130.1416818357919
0:18:29.157011 INFO: mobility_error : 0.1
0:18:29.157058 INFO: num_candidates : 3
0:18:29.157100 INFO: ms1_error      : 30
0:18:29.157142 INFO: ms2_error      : 6.772889369333892
0:18:29.157195 INFO: fwhm_rt        : 3.0
0:18:29.157636 INFO: quant_window   : 3
0:18:29.157684 INFO: ==============================================
0:18:30.243871 INFO: performing precursor FDR with 40 features
0:18:30.243998 INFO: Decoy channel: -1
0:18:30.244024 INFO: Competetive: True
0:18:30.322498 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:30.423076 INFO: Using random state 545139 for train-test-split
0:18:34.574082 INFO: Test AUC: 0.582
0:18:34.574329 INFO: Train AUC: 0.598
0:18:34.574363 INFO: AUC difference: 2.70%
0:18:34.895313 INFO: Resetting torch num_threads to 80
0:18:34.909264 PROGRESS: === Extracted 300172 precursors and 1680436 fragments ===
0:18:34.909763 INFO: === FDR correction performed with classifier version 10 ===
0:18:34.910250 PROGRESS: ============================= Precursor FDR =============================
0:18:34.910342 PROGRESS: Total precursors accumulated: 383
0:18:34.910404 PROGRESS: Target precursors: 380 (99.22%)
0:18:34.910455 PROGRESS: Decoy precursors: 3 (0.78%)
0:18:34.910499 PROGRESS: 
0:18:34.910542 PROGRESS: Precursor Summary:
0:18:34.911489 PROGRESS: Channel   0:	 0.050 FDR:   380; 0.010 FDR:   380; 0.001 FDR:   258
0:18:34.911577 PROGRESS: 
0:18:34.911632 PROGRESS: Protein Summary:
0:18:34.912764 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   365; 0.001 FDR:   248
0:18:34.912853 PROGRESS: =========================================================================
0:18:34.918285 INFO: Target number of precursors reached.
0:18:35.036414 INFO: fragments_df: keeping 5000 of 1680436 [sum(precursor_idx_mask)=9086 sum(mass_error_mask)=1680436 stop_rank=5000
0:18:35.276760 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:35.432894 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:36.130999 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:36.131440 INFO: Using score_cutoff 11.559616157627104 (fac=0.99, q=1)
0:18:36.131753 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:36.131832 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:36.131885 INFO: Updating optimization_manager: score_cutoff        : 11.656769528388978 -> 11.559616157627104
0:18:36.131948 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:36.198304 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:36.351383 INFO: === checking if optimization conditions were reached ===
0:18:36.351709 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:18:36.354249 INFO: Updating optimization_manager: rt_error            : 130.1416818357919 -> 95.5041300881162
0:18:36.354378 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 95.5041.
0:18:36.354459 INFO: ==============================================
0:18:36.354546 INFO: Starting optimization step 2.
0:18:36.354615 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:36.354709 INFO: Using ng extraction backend
0:18:36.354800 PROGRESS: Extracting batch of 100097 precursors
0:18:36.535983 INFO: === Search parameters used ===
0:18:36.536284 INFO: rt_error       : 95.5041300881162
0:18:36.536347 INFO: mobility_error : 0.1
0:18:36.536396 INFO: num_candidates : 3
0:18:36.536453 INFO: ms1_error      : 30
0:18:36.536498 INFO: ms2_error      : 6.772889369333892
0:18:36.536541 INFO: fwhm_rt        : 3.0
0:18:36.536584 INFO: quant_window   : 3
0:18:36.536623 INFO: ==============================================
0:18:38.141334 INFO: performing precursor FDR with 40 features
0:18:38.141459 INFO: Decoy channel: -1
0:18:38.141492 INFO: Competetive: True
0:18:38.219471 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:38.326412 INFO: Using random state 545139 for train-test-split
0:18:42.318221 INFO: Test AUC: 0.585
0:18:42.318350 INFO: Train AUC: 0.597
0:18:42.318383 INFO: AUC difference: 2.08%
0:18:42.629449 INFO: Resetting torch num_threads to 80
0:18:42.641525 PROGRESS: === Extracted 300002 precursors and 1617558 fragments ===
0:18:42.642660 INFO: === FDR correction performed with classifier version 10 ===
0:18:42.643148 PROGRESS: ============================= Precursor FDR =============================
0:18:42.643235 PROGRESS: Total precursors accumulated: 367
0:18:42.643293 PROGRESS: Target precursors: 364 (99.18%)
0:18:42.643342 PROGRESS: Decoy precursors: 3 (0.82%)
0:18:42.643386 PROGRESS: 
0:18:42.643429 PROGRESS: Precursor Summary:
0:18:42.644377 PROGRESS: Channel   0:	 0.050 FDR:   364; 0.010 FDR:   364; 0.001 FDR:   313
0:18:42.644464 PROGRESS: 
0:18:42.644520 PROGRESS: Protein Summary:
0:18:42.645682 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   300
0:18:42.645772 PROGRESS: =========================================================================
0:18:42.650674 INFO: Target number of precursors reached.
0:18:42.760979 INFO: fragments_df: keeping 4830 of 1617558 [sum(precursor_idx_mask)=8508 sum(mass_error_mask)=1617558 stop_rank=4830
0:18:43.045410 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:43.171359 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:43.821041 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:43.821499 INFO: Using score_cutoff 12.580101075839996 (fac=0.99, q=1)
0:18:43.821795 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:43.821874 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:43.821929 INFO: Updating optimization_manager: score_cutoff        : 11.559616157627104 -> 12.580101075839996
0:18:43.821986 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:43.885827 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:44.033162 INFO: === checking if optimization conditions were reached ===
0:18:44.033484 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:18:44.035988 INFO: Updating optimization_manager: rt_error            : 95.5041300881162 -> 75.79357240310019
0:18:44.036101 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 75.7936.
0:18:44.036173 INFO: ==============================================
0:18:44.036245 INFO: Starting optimization step 3.
0:18:44.036305 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:44.036370 INFO: Using ng extraction backend
0:18:44.036432 PROGRESS: Extracting batch of 100097 precursors
0:18:44.229312 INFO: === Search parameters used ===
0:18:44.229827 INFO: rt_error       : 75.79357240310019
0:18:44.229905 INFO: mobility_error : 0.1
0:18:44.229957 INFO: num_candidates : 3
0:18:44.230002 INFO: ms1_error      : 30
0:18:44.230045 INFO: ms2_error      : 6.772889369333892
0:18:44.230087 INFO: fwhm_rt        : 3.0
0:18:44.230127 INFO: quant_window   : 3
0:18:44.230167 INFO: ==============================================
0:18:45.807560 INFO: performing precursor FDR with 40 features
0:18:45.807809 INFO: Decoy channel: -1
0:18:45.807842 INFO: Competetive: True
0:18:45.913788 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:46.046324 INFO: Using random state 545139 for train-test-split
0:18:50.738490 INFO: Test AUC: 0.581
0:18:50.738677 INFO: Train AUC: 0.598
0:18:50.738710 INFO: AUC difference: 2.71%
0:18:51.064806 INFO: Resetting torch num_threads to 80
0:18:51.081624 PROGRESS: === Extracted 299186 precursors and 1551477 fragments ===
0:18:51.082117 INFO: === FDR correction performed with classifier version 10 ===
0:18:51.082630 PROGRESS: ============================= Precursor FDR =============================
0:18:51.082723 PROGRESS: Total precursors accumulated: 339
0:18:51.082786 PROGRESS: Target precursors: 336 (99.12%)
0:18:51.082838 PROGRESS: Decoy precursors: 3 (0.88%)
0:18:51.082883 PROGRESS: 
0:18:51.082926 PROGRESS: Precursor Summary:
0:18:51.083915 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   336; 0.001 FDR:   319
0:18:51.084003 PROGRESS: 
0:18:51.084059 PROGRESS: Protein Summary:
0:18:51.085220 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   322; 0.001 FDR:   305
0:18:51.085319 PROGRESS: =========================================================================
0:18:51.092645 INFO: Target number of precursors reached.
0:18:51.196939 INFO: fragments_df: keeping 4454 of 1551477 [sum(precursor_idx_mask)=7777 sum(mass_error_mask)=1551477 stop_rank=4454
0:18:51.441200 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:51.563577 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:52.241044 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:52.241653 INFO: Using score_cutoff 13.045331917762757 (fac=0.99, q=1)
0:18:52.242074 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:52.242172 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:52.242245 INFO: Updating optimization_manager: score_cutoff        : 12.580101075839996 -> 13.045331917762757
0:18:52.242326 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:52.318150 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:52.487256 INFO: === checking if optimization conditions were reached ===
0:18:52.487569 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:18:52.490266 INFO: Updating optimization_manager: rt_error            : 75.79357240310019 -> 57.037096636001614
0:18:52.490396 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 57.0371.
0:18:52.490479 INFO: ==============================================
0:18:52.490569 INFO: Starting optimization step 4.
0:18:52.490640 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:52.490736 INFO: Using ng extraction backend
0:18:52.490831 PROGRESS: Extracting batch of 100097 precursors
0:18:52.687559 INFO: === Search parameters used ===
0:18:52.687921 INFO: rt_error       : 57.037096636001614
0:18:52.688004 INFO: mobility_error : 0.1
0:18:52.688078 INFO: num_candidates : 3
0:18:52.688142 INFO: ms1_error      : 30
0:18:52.688201 INFO: ms2_error      : 6.772889369333892
0:18:52.688261 INFO: fwhm_rt        : 3.0
0:18:52.688322 INFO: quant_window   : 3
0:18:52.688385 INFO: ==============================================
0:18:53.811918 INFO: performing precursor FDR with 40 features
0:18:53.812050 INFO: Decoy channel: -1
0:18:53.812077 INFO: Competetive: True
0:18:53.899245 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:54.000503 INFO: Using random state 545139 for train-test-split
0:18:58.259254 INFO: Test AUC: 0.587
0:18:58.259387 INFO: Train AUC: 0.597
0:18:58.259420 INFO: AUC difference: 1.64%
0:18:58.569289 INFO: Resetting torch num_threads to 80
0:18:58.582429 PROGRESS: === Extracted 281441 precursors and 1383799 fragments ===
0:18:58.582841 INFO: === FDR correction performed with classifier version 10 ===
0:18:58.583312 PROGRESS: ============================= Precursor FDR =============================
0:18:58.583398 PROGRESS: Total precursors accumulated: 333
0:18:58.583457 PROGRESS: Target precursors: 330 (99.10%)
0:18:58.583503 PROGRESS: Decoy precursors: 3 (0.90%)
0:18:58.583548 PROGRESS: 
0:18:58.583591 PROGRESS: Precursor Summary:
0:18:58.584520 PROGRESS: Channel   0:	 0.050 FDR:   330; 0.010 FDR:   330; 0.001 FDR:   265
0:18:58.584607 PROGRESS: 
0:18:58.584660 PROGRESS: Protein Summary:
0:18:58.585784 PROGRESS: Channel   0:	 0.050 FDR:   317; 0.010 FDR:   317; 0.001 FDR:   255
0:18:58.585873 PROGRESS: =========================================================================
0:18:58.591331 INFO: Target number of precursors reached.
0:18:58.684693 INFO: fragments_df: keeping 4043 of 1383799 [sum(precursor_idx_mask)=7046 sum(mass_error_mask)=1383799 stop_rank=4043
0:18:58.927067 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:59.047452 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:59.580149 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:59.580616 INFO: Using score_cutoff 11.775040952968597 (fac=0.99, q=1)
0:18:59.580905 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:59.580991 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:59.581043 INFO: Updating optimization_manager: score_cutoff        : 13.045331917762757 -> 11.775040952968597
0:18:59.581095 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:59.642033 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:59.795147 INFO: === checking if optimization conditions were reached ===
0:18:59.795485 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:18:59.798090 INFO: Updating optimization_manager: rt_error            : 57.037096636001614 -> 42.7801526019749
0:18:59.798229 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 42.7802.
0:18:59.798323 INFO: ==============================================
0:18:59.798417 INFO: Starting optimization step 5.
0:18:59.798499 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:59.798597 INFO: Using ng extraction backend
0:18:59.798682 PROGRESS: Extracting batch of 100097 precursors
0:18:59.973108 INFO: === Search parameters used ===
0:18:59.973416 INFO: rt_error       : 42.7801526019749
0:18:59.973476 INFO: mobility_error : 0.1
0:18:59.973526 INFO: num_candidates : 3
0:18:59.973567 INFO: ms1_error      : 30
0:18:59.973608 INFO: ms2_error      : 6.772889369333892
0:18:59.973647 INFO: fwhm_rt        : 3.0
0:18:59.973683 INFO: quant_window   : 3
0:18:59.973722 INFO: ==============================================
0:19:00.990368 INFO: performing precursor FDR with 40 features
0:19:00.990498 INFO: Decoy channel: -1
0:19:00.990524 INFO: Competetive: True
0:19:01.078851 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:01.181283 INFO: Using random state 545139 for train-test-split
0:19:06.325607 INFO: Test AUC: 0.586
0:19:06.325755 INFO: Train AUC: 0.597
0:19:06.325790 INFO: AUC difference: 1.71%
0:19:06.640377 INFO: Resetting torch num_threads to 80
0:19:06.658269 PROGRESS: === Extracted 281722 precursors and 1388728 fragments ===
0:19:06.658787 INFO: === FDR correction performed with classifier version 10 ===
0:19:06.659317 PROGRESS: ============================= Precursor FDR =============================
0:19:06.659415 PROGRESS: Total precursors accumulated: 340
0:19:06.659483 PROGRESS: Target precursors: 337 (99.12%)
0:19:06.659540 PROGRESS: Decoy precursors: 3 (0.88%)
0:19:06.659593 PROGRESS: 
0:19:06.659643 PROGRESS: Precursor Summary:
0:19:06.660644 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   337; 0.001 FDR:   278
0:19:06.660737 PROGRESS: 
0:19:06.660797 PROGRESS: Protein Summary:
0:19:06.663589 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   322; 0.001 FDR:   267
0:19:06.663767 PROGRESS: =========================================================================
0:19:06.670530 INFO: Target number of precursors reached.
0:19:06.766352 INFO: fragments_df: keeping 4135 of 1388728 [sum(precursor_idx_mask)=7190 sum(mass_error_mask)=1388728 stop_rank=4135
0:19:07.048436 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:07.173282 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:07.722881 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:07.723462 INFO: Using score_cutoff 11.878339224243163 (fac=0.99, q=1)
0:19:07.723833 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:07.723916 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:07.724000 INFO: Updating optimization_manager: score_cutoff        : 11.775040952968597 -> 11.878339224243163
0:19:07.724074 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:07.786839 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:07.950226 INFO: === checking if optimization conditions were reached ===
0:19:07.950550 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:19:07.953326 INFO: Updating optimization_manager: rt_error            : 42.7801526019749 -> 39.467558213841265
0:19:07.953476 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 39.4676.
0:19:07.953565 INFO: ==============================================
0:19:07.953671 INFO: Starting optimization step 6.
0:19:07.953749 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:19:07.953857 INFO: Using ng extraction backend
0:19:07.953959 PROGRESS: Extracting batch of 100097 precursors
0:19:08.134518 INFO: === Search parameters used ===
0:19:08.134834 INFO: rt_error       : 39.467558213841265
0:19:08.134897 INFO: mobility_error : 0.1
0:19:08.134952 INFO: num_candidates : 3
0:19:08.135007 INFO: ms1_error      : 30
0:19:08.135056 INFO: ms2_error      : 6.772889369333892
0:19:08.135105 INFO: fwhm_rt        : 3.0
0:19:08.135152 INFO: quant_window   : 3
0:19:08.135201 INFO: ==============================================
0:19:09.311855 INFO: performing precursor FDR with 40 features
0:19:09.311983 INFO: Decoy channel: -1
0:19:09.312009 INFO: Competetive: True
0:19:09.400738 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:09.499335 INFO: Using random state 545139 for train-test-split
0:19:14.047166 INFO: Test AUC: 0.582
0:19:14.047295 INFO: Train AUC: 0.595
0:19:14.047326 INFO: AUC difference: 2.16%
0:19:14.352595 INFO: Resetting torch num_threads to 80
0:19:14.366644 PROGRESS: === Extracted 281782 precursors and 1389909 fragments ===
0:19:14.367042 INFO: === FDR correction performed with classifier version 10 ===
0:19:14.367536 PROGRESS: ============================= Precursor FDR =============================
0:19:14.367623 PROGRESS: Total precursors accumulated: 342
0:19:14.367682 PROGRESS: Target precursors: 339 (99.12%)
0:19:14.367733 PROGRESS: Decoy precursors: 3 (0.88%)
0:19:14.367779 PROGRESS: 
0:19:14.367824 PROGRESS: Precursor Summary:
0:19:14.368754 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   339; 0.001 FDR:   272
0:19:14.368852 PROGRESS: 
0:19:14.368908 PROGRESS: Protein Summary:
0:19:14.370046 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   326; 0.001 FDR:   263
0:19:14.370133 PROGRESS: =========================================================================
0:19:14.376131 INFO: Target number of precursors reached.
0:19:14.468112 INFO: fragments_df: keeping 4140 of 1389909 [sum(precursor_idx_mask)=7240 sum(mass_error_mask)=1389909 stop_rank=4140
0:19:14.723361 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:14.852580 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:15.407271 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:15.407711 INFO: Using score_cutoff 11.382261661148071 (fac=0.99, q=1)
0:19:15.407996 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:15.408075 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:15.408129 INFO: Updating optimization_manager: score_cutoff        : 11.878339224243163 -> 11.382261661148071
0:19:15.408181 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:15.469460 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:15.622849 INFO: === checking if optimization conditions were reached ===
0:19:15.623152 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:19:15.625707 INFO: Updating optimization_manager: rt_error            : 39.467558213841265 -> 39.188372434687835
0:19:15.625826 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 39.1884.
0:19:15.625920 INFO: ==============================================
0:19:15.626004 INFO: Starting optimization step 7.
0:19:15.626075 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:19:15.626149 INFO: Using ng extraction backend
0:19:15.626219 PROGRESS: Extracting batch of 100097 precursors
0:19:15.800911 INFO: === Search parameters used ===
0:19:15.801225 INFO: rt_error       : 39.188372434687835
0:19:15.801282 INFO: mobility_error : 0.1
0:19:15.801331 INFO: num_candidates : 3
0:19:15.801390 INFO: ms1_error      : 30
0:19:15.801433 INFO: ms2_error      : 6.772889369333892
0:19:15.801487 INFO: fwhm_rt        : 3.0
0:19:15.801529 INFO: quant_window   : 3
0:19:15.801569 INFO: ==============================================
0:19:16.895890 INFO: performing precursor FDR with 40 features
0:19:16.896013 INFO: Decoy channel: -1
0:19:16.896039 INFO: Competetive: True
0:19:17.004991 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:17.127542 INFO: Using random state 545139 for train-test-split
0:19:21.998682 INFO: Test AUC: 0.584
0:19:21.998931 INFO: Train AUC: 0.597
0:19:21.998967 INFO: AUC difference: 2.11%
0:19:22.324185 INFO: Resetting torch num_threads to 80
0:19:22.338522 PROGRESS: === Extracted 281766 precursors and 1391298 fragments ===
0:19:22.339011 INFO: === FDR correction performed with classifier version 10 ===
0:19:22.339500 PROGRESS: ============================= Precursor FDR =============================
0:19:22.339586 PROGRESS: Total precursors accumulated: 332
0:19:22.339648 PROGRESS: Target precursors: 329 (99.10%)
0:19:22.339698 PROGRESS: Decoy precursors: 3 (0.90%)
0:19:22.339746 PROGRESS: 
0:19:22.339797 PROGRESS: Precursor Summary:
0:19:22.340743 PROGRESS: Channel   0:	 0.050 FDR:   329; 0.010 FDR:   329; 0.001 FDR:   271
0:19:22.340830 PROGRESS: 
0:19:22.340885 PROGRESS: Protein Summary:
0:19:22.342006 PROGRESS: Channel   0:	 0.050 FDR:   316; 0.010 FDR:   316; 0.001 FDR:   261
0:19:22.342097 PROGRESS: =========================================================================
0:19:22.347529 INFO: Target number of precursors reached.
0:19:22.447704 INFO: fragments_df: keeping 4050 of 1391298 [sum(precursor_idx_mask)=6983 sum(mass_error_mask)=1391298 stop_rank=4050
0:19:22.722093 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:22.848293 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:23.383284 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:23.383725 INFO: Using score_cutoff 12.1746178276062 (fac=0.99, q=1)
0:19:23.384053 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:23.384131 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:23.384186 INFO: Updating optimization_manager: score_cutoff        : 11.382261661148071 -> 12.1746178276062
0:19:23.384245 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:23.445288 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:23.599232 INFO: === checking if optimization conditions were reached ===
0:19:23.599626 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:19:23.601479 INFO: Updating optimization_manager: rt_error            : 39.188372434687835 -> 95.5041300881162
0:19:23.601644 INFO: Updating optimization_manager: classifier_version  : 10 -> 13
0:19:23.601759 INFO: Updating optimization_manager: score_cutoff        : 12.1746178276062 -> 12.580101075839996
0:19:23.601864 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:23.601966 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:23.602070 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 95.5041 found after 8 searches.
0:19:23.602147 INFO: ==============================================
0:19:23.602252 PROGRESS: Optimization finished for rt_error.
0:19:23.808726 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:23.870119 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:24.058822 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:19:24.059045 PROGRESS: ==============================================
0:19:24.059139 PROGRESS: ms2_error      : 6.7729
0:19:24.059209 PROGRESS: rt_error       : 95.5041
0:19:24.059267 PROGRESS: ==============================================
0:19:24.060298 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:31.037175 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:47.045673 INFO: Using ng extraction backend
0:19:47.046429 PROGRESS: Extracting batch of 11065368 precursors
0:20:02.079416 INFO: === Search parameters used ===
0:20:02.079712 INFO: rt_error       : 95.5041300881162
0:20:02.079783 INFO: mobility_error : 0.1
0:20:02.079837 INFO: num_candidates : 3
0:20:02.079881 INFO: ms1_error      : 30
0:20:02.079924 INFO: ms2_error      : 6.772889369333892
0:20:02.079964 INFO: fwhm_rt        : 3.0
0:20:02.080006 INFO: quant_window   : 3
0:20:02.080047 INFO: ==============================================
0:20:41.940184 INFO: Removed 17683446 precursors with score below cutoff 12.580101075839996
0:21:00.026774 INFO: performing precursor FDR with 40 features
0:21:00.026915 INFO: Decoy channel: -1
0:21:00.026946 INFO: Competetive: True
0:21:01.659807 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:08.036826 INFO: Using random state 677439 for train-test-split
0:25:08.131448 INFO: Test AUC: 0.604
0:25:08.131706 INFO: Train AUC: 0.605
0:25:08.131749 INFO: AUC difference: 0.13%
0:25:12.665375 INFO: Resetting torch num_threads to 80
0:25:14.291177 PROGRESS: ============================= Precursor FDR =============================
0:25:14.291471 PROGRESS: Total precursors accumulated: 55,432
0:25:14.291538 PROGRESS: Target precursors: 54,884 (99.01%)
0:25:14.291592 PROGRESS: Decoy precursors: 548 (0.99%)
0:25:14.291640 PROGRESS: 
0:25:14.291684 PROGRESS: Precursor Summary:
0:25:14.305099 PROGRESS: Channel   0:	 0.050 FDR: 54,884; 0.010 FDR: 54,884; 0.001 FDR: 36,126
0:25:14.305354 PROGRESS: 
0:25:14.305413 PROGRESS: Protein Summary:
0:25:14.325280 PROGRESS: Channel   0:	 0.050 FDR: 9,376; 0.010 FDR: 9,376; 0.001 FDR: 6,802
0:25:14.325533 PROGRESS: =========================================================================
0:25:14.416084 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/psm.parquet
0:25:14.548880 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/frag.parquet
0:25:14.725386 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
0:25:15.167087 PROGRESS: 
0:25:15.167249 INFO: Quantification results path: alphadia_zenoswath8600/library/quant
0:25:15.167327 INFO: Creating folder alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/figures
0:25:15.167499 INFO: Initializing TimingManager
0:25:15.168043 INFO: Initializing RawFileManager
0:27:39.038991 INFO: Determining DIA cycle
0:27:39.053949 INFO: Found cycle with start 0.00 min and length 86.
0:27:39.288260 INFO: RT (min)            : 0.0 - 55.4
0:27:39.288358 INFO: RT duration (sec)   : 3326.9
0:27:39.288389 INFO: RT duration (min)   : 55.4
0:27:39.288415 INFO: Cycle len (scans)   : 86
0:27:39.288436 INFO: Cycle len (sec)     : 1.90
0:27:39.288456 INFO: Number of cycles    : 1747
0:27:39.288475 INFO: MS2 range (m/z)     : 399.5 - 903.5
0:27:39.288534 INFO: Creating DIA data object took: 144.12039232254028
0:27:40.375839 INFO: Creating DIA data NG object took: 1.087155818939209
0:27:41.723924 INFO: Initializing CalibrationManager
0:27:41.724205 INFO: Setting up calibration estimators ..
0:27:41.724269 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:27:41.724369 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'}' ..
0:27:41.724499 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:27:41.724552 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:27:41.724608 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}}' ..
0:27:41.724661 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:27:41.724719 INFO: Done setting up calibration estimators.
0:27:41.724870 INFO: Initializing OptimizationManager
0:27:41.725038 INFO: initial parameter: ms1_error = 30
0:27:41.725090 INFO: initial parameter: ms2_error = 30
0:27:41.725139 INFO: initial parameter: rt_error = 1663.4844970703125
0:27:41.725183 INFO: initial parameter: mobility_error = 0.1
0:27:41.725225 INFO: initial parameter: num_candidates = 1
0:27:41.725265 INFO: initial parameter: fwhm_rt = 5
0:27:41.725305 INFO: initial parameter: fwhm_mobility = 0.01
0:27:41.725343 INFO: initial parameter: score_cutoff = 0
0:27:41.725383 INFO: initial parameter: classifier_version = -1
0:27:41.725454 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
0:27:41.725798 INFO: FDRManager: loading saved state not requested, will be initialized.
0:27:41.725835 INFO: Initializing FDRManager
0:27:41.725877 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:27:43.058023 PROGRESS: Initializing spectral library: 5,608,555 target precursors potentially observable (87,724 removed)
0:27:43.880835 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:27:43.881172 INFO: Updating optimization_manager: rt_error            : 1663.4844970703125 -> 1663.4844970703125
0:27:43.881275 PROGRESS: Starting initial search for precursors.
0:27:43.881362 INFO: Starting optimization step 0.
0:27:43.881427 PROGRESS: === Extracting elution groups 0 to 200 ===
0:27:43.881527 INFO: Using ng extraction backend
0:27:43.881608 PROGRESS: Extracting batch of 394 precursors
0:27:43.883678 INFO: === Search parameters used ===
0:27:43.883777 INFO: rt_error       : 1663.4844970703125
0:27:43.883827 INFO: mobility_error : 0.1
0:27:43.883872 INFO: num_candidates : 1
0:27:43.883913 INFO: ms1_error      : 30
0:27:43.883952 INFO: ms2_error      : 30
0:27:43.883990 INFO: fwhm_rt        : 5
0:27:43.884029 INFO: quant_window   : 3
0:27:43.884066 INFO: ==============================================
0:27:43.905535 INFO: performing precursor FDR with 40 features
0:27:43.905604 INFO: Decoy channel: -1
0:27:43.905630 INFO: Competetive: True
0:27:43.906577 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:43.909067 INFO: Using random state 31429 for train-test-split
0:27:43.916728 INFO: Test AUC: 0.576
0:27:43.916786 INFO: Train AUC: 0.466
0:27:43.916818 INFO: AUC difference: 23.62%
0:27:43.916842 WARNING: AUC difference > 5%. This may indicate overfitting.
0:27:44.138571 INFO: Resetting torch num_threads to 80
0:27:44.140204 PROGRESS: === Extracted 394 precursors and 2221 fragments ===
0:27:44.140604 INFO: === FDR correction performed with classifier version -1 ===
0:27:44.141068 PROGRESS: ============================= Precursor FDR =============================
0:27:44.141159 PROGRESS: Total precursors accumulated: 0
0:27:44.141225 PROGRESS: Target precursors: 0 (0.00%)
0:27:44.141282 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:44.141336 PROGRESS: 
0:27:44.141387 PROGRESS: Precursor Summary:
0:27:44.141522 PROGRESS: 
0:27:44.141600 PROGRESS: Protein Summary:
0:27:44.141683 PROGRESS: =========================================================================
0:27:44.141886 INFO: Target number of precursors not reached yet.
0:27:44.203781 INFO: Starting optimization step 1.
0:27:44.204050 PROGRESS: === Extracting elution groups 200 to 600 ===
0:27:44.204149 INFO: Using ng extraction backend
0:27:44.204221 PROGRESS: Extracting batch of 782 precursors
0:27:44.208341 INFO: === Search parameters used ===
0:27:44.208472 INFO: rt_error       : 1663.4844970703125
0:27:44.208527 INFO: mobility_error : 0.1
0:27:44.208577 INFO: num_candidates : 1
0:27:44.208626 INFO: ms1_error      : 30
0:27:44.208676 INFO: ms2_error      : 30
0:27:44.208722 INFO: fwhm_rt        : 5
0:27:44.208765 INFO: quant_window   : 3
0:27:44.208809 INFO: ==============================================
0:27:44.235567 INFO: performing precursor FDR with 40 features
0:27:44.235665 INFO: Decoy channel: -1
0:27:44.235691 INFO: Competetive: True
0:27:44.238972 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:44.240626 INFO: Using random state 827905 for train-test-split
0:27:44.249826 INFO: Test AUC: 0.550
0:27:44.249889 INFO: Train AUC: 0.487
0:27:44.249918 INFO: AUC difference: 13.06%
0:27:44.249942 WARNING: AUC difference > 5%. This may indicate overfitting.
0:27:44.471702 INFO: Resetting torch num_threads to 80
0:27:44.474292 PROGRESS: === Extracted 1175 precursors and 6627 fragments ===
0:27:44.474698 INFO: === FDR correction performed with classifier version -1 ===
0:27:44.475127 PROGRESS: ============================= Precursor FDR =============================
0:27:44.475213 PROGRESS: Total precursors accumulated: 0
0:27:44.475273 PROGRESS: Target precursors: 0 (0.00%)
0:27:44.475323 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:44.475370 PROGRESS: 
0:27:44.475415 PROGRESS: Precursor Summary:
0:27:44.475526 PROGRESS: 
0:27:44.475588 PROGRESS: Protein Summary:
0:27:44.475675 PROGRESS: =========================================================================
0:27:44.475916 INFO: Target number of precursors not reached yet.
0:27:44.540028 INFO: Starting optimization step 2.
0:27:44.540291 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:27:44.540381 INFO: Using ng extraction backend
0:27:44.540444 PROGRESS: Extracting batch of 1565 precursors
0:27:44.546689 INFO: === Search parameters used ===
0:27:44.546840 INFO: rt_error       : 1663.4844970703125
0:27:44.546892 INFO: mobility_error : 0.1
0:27:44.546938 INFO: num_candidates : 1
0:27:44.546979 INFO: ms1_error      : 30
0:27:44.547021 INFO: ms2_error      : 30
0:27:44.547061 INFO: fwhm_rt        : 5
0:27:44.547099 INFO: quant_window   : 3
0:27:44.547139 INFO: ==============================================
0:27:44.586960 INFO: performing precursor FDR with 40 features
0:27:44.587065 INFO: Decoy channel: -1
0:27:44.587091 INFO: Competetive: True
0:27:44.590791 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:44.592772 INFO: Using random state 857791 for train-test-split
0:27:44.605488 INFO: Test AUC: 0.513
0:27:44.605556 INFO: Train AUC: 0.500
0:27:44.605586 INFO: AUC difference: 2.53%
0:27:44.826911 INFO: Resetting torch num_threads to 80
0:27:44.830040 PROGRESS: === Extracted 2738 precursors and 15554 fragments ===
0:27:44.830452 INFO: === FDR correction performed with classifier version -1 ===
0:27:44.830888 PROGRESS: ============================= Precursor FDR =============================
0:27:44.830974 PROGRESS: Total precursors accumulated: 0
0:27:44.831034 PROGRESS: Target precursors: 0 (0.00%)
0:27:44.831083 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:44.831131 PROGRESS: 
0:27:44.831182 PROGRESS: Precursor Summary:
0:27:44.831299 PROGRESS: 
0:27:44.831362 PROGRESS: Protein Summary:
0:27:44.831432 PROGRESS: =========================================================================
0:27:44.831701 INFO: Target number of precursors not reached yet.
0:27:44.899283 INFO: Starting optimization step 3.
0:27:44.899561 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:27:44.899650 INFO: Using ng extraction backend
0:27:44.899716 PROGRESS: Extracting batch of 3140 precursors
0:27:44.908242 INFO: === Search parameters used ===
0:27:44.908391 INFO: rt_error       : 1663.4844970703125
0:27:44.908443 INFO: mobility_error : 0.1
0:27:44.908488 INFO: num_candidates : 1
0:27:44.908534 INFO: ms1_error      : 30
0:27:44.908577 INFO: ms2_error      : 30
0:27:44.908618 INFO: fwhm_rt        : 5
0:27:44.908657 INFO: quant_window   : 3
0:27:44.908696 INFO: ==============================================
0:27:44.965914 INFO: performing precursor FDR with 40 features
0:27:44.966041 INFO: Decoy channel: -1
0:27:44.966067 INFO: Competetive: True
0:27:44.970670 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:44.973263 INFO: Using random state 324512 for train-test-split
0:27:44.994832 INFO: Test AUC: 0.505
0:27:44.994931 INFO: Train AUC: 0.501
0:27:44.994975 INFO: AUC difference: 0.72%
0:27:45.219382 INFO: Resetting torch num_threads to 80
0:27:45.223513 PROGRESS: === Extracted 5873 precursors and 33590 fragments ===
0:27:45.223938 INFO: === FDR correction performed with classifier version -1 ===
0:27:45.224406 PROGRESS: ============================= Precursor FDR =============================
0:27:45.224501 PROGRESS: Total precursors accumulated: 1
0:27:45.224563 PROGRESS: Target precursors: 1 (100.00%)
0:27:45.224613 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:45.224660 PROGRESS: 
0:27:45.224704 PROGRESS: Precursor Summary:
0:27:45.225676 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:27:45.225770 PROGRESS: 
0:27:45.225827 PROGRESS: Protein Summary:
0:27:45.226851 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:27:45.226943 PROGRESS: =========================================================================
0:27:45.227252 INFO: Target number of precursors not reached yet.
0:27:45.301646 INFO: Starting optimization step 4.
0:27:45.301936 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:27:45.302022 INFO: Using ng extraction backend
0:27:45.302087 PROGRESS: Extracting batch of 6271 precursors
0:27:45.316131 INFO: === Search parameters used ===
0:27:45.316320 INFO: rt_error       : 1663.4844970703125
0:27:45.316373 INFO: mobility_error : 0.1
0:27:45.316417 INFO: num_candidates : 1
0:27:45.316460 INFO: ms1_error      : 30
0:27:45.316501 INFO: ms2_error      : 30
0:27:45.316542 INFO: fwhm_rt        : 5
0:27:45.316597 INFO: quant_window   : 3
0:27:45.316641 INFO: ==============================================
0:27:45.410044 INFO: performing precursor FDR with 40 features
0:27:45.410180 INFO: Decoy channel: -1
0:27:45.410206 INFO: Competetive: True
0:27:45.416801 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:45.420960 INFO: Using random state 908393 for train-test-split
0:27:45.462164 INFO: Test AUC: 0.491
0:27:45.462311 INFO: Train AUC: 0.500
0:27:45.462340 INFO: AUC difference: 1.85%
0:27:45.692167 INFO: Resetting torch num_threads to 80
0:27:45.697683 PROGRESS: === Extracted 12129 precursors and 69593 fragments ===
0:27:45.698122 INFO: === FDR correction performed with classifier version -1 ===
0:27:45.698607 PROGRESS: ============================= Precursor FDR =============================
0:27:45.698700 PROGRESS: Total precursors accumulated: 4
0:27:45.698761 PROGRESS: Target precursors: 4 (100.00%)
0:27:45.698808 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:45.698856 PROGRESS: 
0:27:45.698900 PROGRESS: Precursor Summary:
0:27:45.699836 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:27:45.699925 PROGRESS: 
0:27:45.699983 PROGRESS: Protein Summary:
0:27:45.701012 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:27:45.701100 PROGRESS: =========================================================================
0:27:45.701508 INFO: Target number of precursors not reached yet.
0:27:45.786404 INFO: Starting optimization step 5.
0:27:45.786704 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:27:45.786793 INFO: Using ng extraction backend
0:27:45.786858 PROGRESS: Extracting batch of 12568 precursors
0:27:45.812000 INFO: === Search parameters used ===
0:27:45.812270 INFO: rt_error       : 1663.4844970703125
0:27:45.812326 INFO: mobility_error : 0.1
0:27:45.812371 INFO: num_candidates : 1
0:27:45.812415 INFO: ms1_error      : 30
0:27:45.812457 INFO: ms2_error      : 30
0:27:45.812499 INFO: fwhm_rt        : 5
0:27:45.812539 INFO: quant_window   : 3
0:27:45.812582 INFO: ==============================================
0:27:45.970475 INFO: performing precursor FDR with 40 features
0:27:45.970628 INFO: Decoy channel: -1
0:27:45.970659 INFO: Competetive: True
0:27:45.982682 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:45.990121 INFO: Using random state 715881 for train-test-split
0:27:46.258201 INFO: Test AUC: 0.500
0:27:46.258358 INFO: Train AUC: 0.520
0:27:46.258388 INFO: AUC difference: 3.76%
0:27:46.476599 INFO: Resetting torch num_threads to 80
0:27:46.484674 PROGRESS: === Extracted 24680 precursors and 141894 fragments ===
0:27:46.485109 INFO: === FDR correction performed with classifier version -1 ===
0:27:46.485613 PROGRESS: ============================= Precursor FDR =============================
0:27:46.485708 PROGRESS: Total precursors accumulated: 59
0:27:46.485768 PROGRESS: Target precursors: 59 (100.00%)
0:27:46.485817 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:46.485865 PROGRESS: 
0:27:46.485914 PROGRESS: Precursor Summary:
0:27:46.486886 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
0:27:46.486977 PROGRESS: 
0:27:46.487035 PROGRESS: Protein Summary:
0:27:46.488099 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
0:27:46.488188 PROGRESS: =========================================================================
0:27:46.488735 INFO: Target number of precursors not reached yet.
0:27:46.595865 INFO: Starting optimization step 6.
0:27:46.596190 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:27:46.596278 INFO: Using ng extraction backend
0:27:46.596345 PROGRESS: Extracting batch of 25144 precursors
0:27:46.644017 INFO: === Search parameters used ===
0:27:46.644387 INFO: rt_error       : 1663.4844970703125
0:27:46.644441 INFO: mobility_error : 0.1
0:27:46.644486 INFO: num_candidates : 1
0:27:46.644529 INFO: ms1_error      : 30
0:27:46.644568 INFO: ms2_error      : 30
0:27:46.644608 INFO: fwhm_rt        : 5
0:27:46.644646 INFO: quant_window   : 3
0:27:46.644686 INFO: ==============================================
0:27:46.914871 INFO: performing precursor FDR with 40 features
0:27:46.915031 INFO: Decoy channel: -1
0:27:46.915060 INFO: Competetive: True
0:27:46.943406 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:46.961828 INFO: Using random state 188604 for train-test-split
0:27:47.710167 INFO: Test AUC: 0.559
0:27:47.710321 INFO: Train AUC: 0.564
0:27:47.710351 INFO: AUC difference: 0.81%
0:27:47.964032 INFO: Resetting torch num_threads to 80
0:27:47.977058 PROGRESS: === Extracted 49781 precursors and 285907 fragments ===
0:27:47.977586 INFO: === FDR correction performed with classifier version -1 ===
0:27:47.978069 PROGRESS: ============================= Precursor FDR =============================
0:27:47.978161 PROGRESS: Total precursors accumulated: 116
0:27:47.978223 PROGRESS: Target precursors: 115 (99.14%)
0:27:47.978273 PROGRESS: Decoy precursors: 1 (0.86%)
0:27:47.978322 PROGRESS: 
0:27:47.978365 PROGRESS: Precursor Summary:
0:27:47.979251 PROGRESS: Channel   0:	 0.050 FDR:   115; 0.010 FDR:   115; 0.001 FDR:    90
0:27:47.979352 PROGRESS: 
0:27:47.979411 PROGRESS: Protein Summary:
0:27:47.980413 PROGRESS: Channel   0:	 0.050 FDR:   114; 0.010 FDR:   114; 0.001 FDR:    89
0:27:47.980504 PROGRESS: =========================================================================
0:27:47.981434 INFO: Target number of precursors not reached yet.
0:27:48.136773 INFO: Starting optimization step 7.
0:27:48.137110 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:27:48.137204 INFO: Using ng extraction backend
0:27:48.137271 PROGRESS: Extracting batch of 50233 precursors
0:27:48.228587 INFO: === Search parameters used ===
0:27:48.229013 INFO: rt_error       : 1663.4844970703125
0:27:48.229069 INFO: mobility_error : 0.1
0:27:48.229118 INFO: num_candidates : 1
0:27:48.229162 INFO: ms1_error      : 30
0:27:48.229206 INFO: ms2_error      : 30
0:27:48.229254 INFO: fwhm_rt        : 5
0:27:48.229301 INFO: quant_window   : 3
0:27:48.229343 INFO: ==============================================
0:27:48.678210 INFO: performing precursor FDR with 40 features
0:27:48.678370 INFO: Decoy channel: -1
0:27:48.678398 INFO: Competetive: True
0:27:48.729741 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:48.768102 INFO: Using random state 158623 for train-test-split
0:27:50.542960 INFO: Test AUC: 0.582
0:27:50.543104 INFO: Train AUC: 0.590
0:27:50.543138 INFO: AUC difference: 1.36%
0:27:50.798887 INFO: Resetting torch num_threads to 80
0:27:50.823881 PROGRESS: === Extracted 99927 precursors and 574109 fragments ===
0:27:50.824573 INFO: === FDR correction performed with classifier version -1 ===
0:27:50.825164 PROGRESS: ============================= Precursor FDR =============================
0:27:50.825269 PROGRESS: Total precursors accumulated: 224
0:27:50.825331 PROGRESS: Target precursors: 222 (99.11%)
0:27:50.825384 PROGRESS: Decoy precursors: 2 (0.89%)
0:27:50.825432 PROGRESS: 
0:27:50.825493 PROGRESS: Precursor Summary:
0:27:50.826435 PROGRESS: Channel   0:	 0.050 FDR:   222; 0.010 FDR:   222; 0.001 FDR:     0
0:27:50.826529 PROGRESS: 
0:27:50.826586 PROGRESS: Protein Summary:
0:27:50.827618 PROGRESS: Channel   0:	 0.050 FDR:   213; 0.010 FDR:   213; 0.001 FDR:     0
0:27:50.827711 PROGRESS: =========================================================================
0:27:50.829859 INFO: Target number of precursors reached.
0:27:50.874217 INFO: fragments_df: keeping 2207 of 574109 [sum(precursor_idx_mask)=2425 sum(mass_error_mask)=574109 stop_rank=2207
0:27:51.136406 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:51.233155 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:51.483897 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:27:51.484433 INFO: Using score_cutoff 14.426588419532777 (fac=0.99, q=1)
0:27:51.484789 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:27:51.484871 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:27:51.484926 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.426588419532777
0:27:51.484991 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:51.548899 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:51.691754 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:27:51.692058 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:27:51.692154 INFO: Starting optimization step 8.
0:27:51.692218 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:27:51.692288 INFO: Using ng extraction backend
0:27:51.692351 PROGRESS: Extracting batch of 100097 precursors
0:27:51.876006 INFO: === Search parameters used ===
0:27:51.876397 INFO: rt_error       : 1663.4844970703125
0:27:51.876451 INFO: mobility_error : 0.1
0:27:51.876500 INFO: num_candidates : 3
0:27:51.876545 INFO: ms1_error      : 30
0:27:51.876587 INFO: ms2_error      : 30
0:27:51.876628 INFO: fwhm_rt        : 3.0
0:27:51.876668 INFO: quant_window   : 3
0:27:51.876709 INFO: ==============================================
0:27:53.371825 INFO: performing precursor FDR with 40 features
0:27:53.371972 INFO: Decoy channel: -1
0:27:53.372000 INFO: Competetive: True
0:27:53.476835 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:53.602745 INFO: Using random state 10730 for train-test-split
0:27:59.368702 INFO: Test AUC: 0.589
0:27:59.368866 INFO: Train AUC: 0.596
0:27:59.368899 INFO: AUC difference: 1.21%
0:27:59.688309 INFO: Resetting torch num_threads to 80
0:27:59.702397 PROGRESS: === Extracted 299829 precursors and 1682488 fragments ===
0:27:59.702878 INFO: === FDR correction performed with classifier version 7 ===
0:27:59.703368 PROGRESS: ============================= Precursor FDR =============================
0:27:59.703460 PROGRESS: Total precursors accumulated: 264
0:27:59.703520 PROGRESS: Target precursors: 262 (99.24%)
0:27:59.703576 PROGRESS: Decoy precursors: 2 (0.76%)
0:27:59.703623 PROGRESS: 
0:27:59.703665 PROGRESS: Precursor Summary:
0:27:59.704601 PROGRESS: Channel   0:	 0.050 FDR:   262; 0.010 FDR:   262; 0.001 FDR:   228
0:27:59.704692 PROGRESS: 
0:27:59.704750 PROGRESS: Protein Summary:
0:27:59.705867 PROGRESS: Channel   0:	 0.050 FDR:   251; 0.010 FDR:   251; 0.001 FDR:   219
0:27:59.705960 PROGRESS: =========================================================================
0:27:59.712402 INFO: Target number of precursors reached.
0:27:59.823649 INFO: fragments_df: keeping 3769 of 1682488 [sum(precursor_idx_mask)=6250 sum(mass_error_mask)=1682488 stop_rank=3769
0:28:00.109013 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:00.217653 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:00.702626 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:00.703146 INFO: Using score_cutoff 14.44327596616745 (fac=0.99, q=1)
0:28:00.703468 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:00.703554 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:00.703615 INFO: Updating optimization_manager: score_cutoff        : 14.426588419532777 -> 14.44327596616745
0:28:00.703676 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:00.765623 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:00.910290 INFO: === checking if optimization conditions were reached ===
0:28:00.910699 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:28:00.913252 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.029147298221573
0:28:00.913368 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.0291.
0:28:00.913444 INFO: ==============================================
0:28:00.913536 INFO: Starting optimization step 9.
0:28:00.913605 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:28:00.913679 INFO: Using ng extraction backend
0:28:00.913745 PROGRESS: Extracting batch of 100097 precursors
0:28:01.097143 INFO: === Search parameters used ===
0:28:01.097543 INFO: rt_error       : 1663.4844970703125
0:28:01.097618 INFO: mobility_error : 0.1
0:28:01.097681 INFO: num_candidates : 3
0:28:01.097742 INFO: ms1_error      : 30
0:28:01.097798 INFO: ms2_error      : 7.029147298221573
0:28:01.097852 INFO: fwhm_rt        : 3.0
0:28:01.097902 INFO: quant_window   : 3
0:28:01.097950 INFO: ==============================================
0:28:02.550033 INFO: performing precursor FDR with 40 features
0:28:02.550190 INFO: Decoy channel: -1
0:28:02.550219 INFO: Competetive: True
0:28:02.656968 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:02.784681 INFO: Using random state 10730 for train-test-split
0:28:08.245770 INFO: Test AUC: 0.587
0:28:08.245942 INFO: Train AUC: 0.594
0:28:08.245972 INFO: AUC difference: 1.16%
0:28:09.464256 INFO: Resetting torch num_threads to 80
0:28:09.478947 PROGRESS: === Extracted 300278 precursors and 1822693 fragments ===
0:28:09.479414 INFO: === FDR correction performed with classifier version 7 ===
0:28:09.479938 PROGRESS: ============================= Precursor FDR =============================
0:28:09.480038 PROGRESS: Total precursors accumulated: 321
0:28:09.480098 PROGRESS: Target precursors: 318 (99.07%)
0:28:09.480147 PROGRESS: Decoy precursors: 3 (0.93%)
0:28:09.480194 PROGRESS: 
0:28:09.480238 PROGRESS: Precursor Summary:
0:28:09.481209 PROGRESS: Channel   0:	 0.050 FDR:   318; 0.010 FDR:   318; 0.001 FDR:   274
0:28:09.481301 PROGRESS: 
0:28:09.481358 PROGRESS: Protein Summary:
0:28:09.482502 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   305; 0.001 FDR:   263
0:28:09.482595 PROGRESS: =========================================================================
0:28:09.489220 INFO: Target number of precursors reached.
0:28:09.611303 INFO: fragments_df: keeping 4573 of 1822693 [sum(precursor_idx_mask)=7848 sum(mass_error_mask)=1822693 stop_rank=4573
0:28:10.119301 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:10.240443 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:10.788954 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:10.789494 INFO: Using score_cutoff 14.33506617794037 (fac=0.99, q=1)
0:28:10.789807 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:10.789891 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:10.789946 INFO: Updating optimization_manager: score_cutoff        : 14.44327596616745 -> 14.33506617794037
0:28:10.790009 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:10.851605 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:11.004680 INFO: === checking if optimization conditions were reached ===
0:28:11.005000 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:28:11.007779 INFO: Updating optimization_manager: ms2_error           : 7.029147298221573 -> 6.952074823324619
0:28:11.007917 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 6.9521.
0:28:11.007989 INFO: ==============================================
0:28:11.008061 INFO: Starting optimization step 10.
0:28:11.008123 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:28:11.008191 INFO: Using ng extraction backend
0:28:11.008252 PROGRESS: Extracting batch of 100097 precursors
0:28:11.187585 INFO: === Search parameters used ===
0:28:11.187995 INFO: rt_error       : 1663.4844970703125
0:28:11.188059 INFO: mobility_error : 0.1
0:28:11.188108 INFO: num_candidates : 3
0:28:11.188160 INFO: ms1_error      : 30
0:28:11.188204 INFO: ms2_error      : 6.952074823324619
0:28:11.188246 INFO: fwhm_rt        : 3.0
0:28:11.188287 INFO: quant_window   : 3
0:28:11.188327 INFO: ==============================================
0:28:12.630448 INFO: performing precursor FDR with 40 features
0:28:12.630606 INFO: Decoy channel: -1
0:28:12.630633 INFO: Competetive: True
0:28:12.738038 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:12.865499 INFO: Using random state 10730 for train-test-split
0:28:18.375956 INFO: Test AUC: 0.584
0:28:18.376120 INFO: Train AUC: 0.594
0:28:18.376151 INFO: AUC difference: 1.68%
0:28:18.697058 INFO: Resetting torch num_threads to 80
0:28:18.712100 PROGRESS: === Extracted 300279 precursors and 1822345 fragments ===
0:28:18.712575 INFO: === FDR correction performed with classifier version 7 ===
0:28:18.713090 PROGRESS: ============================= Precursor FDR =============================
0:28:18.713180 PROGRESS: Total precursors accumulated: 348
0:28:18.713240 PROGRESS: Target precursors: 345 (99.14%)
0:28:18.713288 PROGRESS: Decoy precursors: 3 (0.86%)
0:28:18.713335 PROGRESS: 
0:28:18.713379 PROGRESS: Precursor Summary:
0:28:18.714360 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:   345; 0.001 FDR:   270
0:28:18.714453 PROGRESS: 
0:28:18.714509 PROGRESS: Protein Summary:
0:28:18.715679 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   328; 0.001 FDR:   260
0:28:18.715773 PROGRESS: =========================================================================
0:28:18.722341 INFO: Target number of precursors reached.
0:28:18.845933 INFO: fragments_df: keeping 4872 of 1822345 [sum(precursor_idx_mask)=8458 sum(mass_error_mask)=1822345 stop_rank=4872
0:28:19.109404 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:19.225004 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:19.817895 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:19.818415 INFO: Using score_cutoff 13.971662622070312 (fac=0.99, q=1)
0:28:19.818726 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:19.818808 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:19.818871 INFO: Updating optimization_manager: score_cutoff        : 14.33506617794037 -> 13.971662622070312
0:28:19.818930 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:19.879717 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:20.025588 INFO: === checking if optimization conditions were reached ===
0:28:20.025909 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:28:20.026965 INFO: Updating optimization_manager: ms2_error           : 6.952074823324619 -> 6.952074823324619
0:28:20.027098 INFO: Updating optimization_manager: classifier_version  : 7 -> 10
0:28:20.027204 INFO: Updating optimization_manager: score_cutoff        : 13.971662622070312 -> 13.971662622070312
0:28:20.027309 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:20.027396 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:20.027479 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 6.9521 found after 3 searches.
0:28:20.027544 INFO: ==============================================
0:28:20.027616 PROGRESS: Optimization finished for ms2_error.
0:28:20.282260 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:20.343487 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:20.514546 INFO: Starting optimization step 0.
0:28:20.514817 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:28:20.514900 INFO: Using ng extraction backend
0:28:20.514965 PROGRESS: Extracting batch of 100097 precursors
0:28:20.694828 INFO: === Search parameters used ===
0:28:20.695203 INFO: rt_error       : 1663.4844970703125
0:28:20.695262 INFO: mobility_error : 0.1
0:28:20.695311 INFO: num_candidates : 3
0:28:20.695358 INFO: ms1_error      : 30
0:28:20.695406 INFO: ms2_error      : 6.952074823324619
0:28:20.695448 INFO: fwhm_rt        : 3.0
0:28:20.695489 INFO: quant_window   : 3
0:28:20.695531 INFO: ==============================================
0:28:22.147637 INFO: performing precursor FDR with 40 features
0:28:22.147789 INFO: Decoy channel: -1
0:28:22.147815 INFO: Competetive: True
0:28:22.255490 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:22.382783 INFO: Using random state 79617 for train-test-split
0:28:27.885434 INFO: Test AUC: 0.589
0:28:27.885612 INFO: Train AUC: 0.599
0:28:27.885646 INFO: AUC difference: 1.69%
0:28:28.203606 INFO: Resetting torch num_threads to 80
0:28:28.218805 PROGRESS: === Extracted 300279 precursors and 1821253 fragments ===
0:28:28.219279 INFO: === FDR correction performed with classifier version 10 ===
0:28:28.219787 PROGRESS: ============================= Precursor FDR =============================
0:28:28.219881 PROGRESS: Total precursors accumulated: 361
0:28:28.219941 PROGRESS: Target precursors: 358 (99.17%)
0:28:28.219990 PROGRESS: Decoy precursors: 3 (0.83%)
0:28:28.220038 PROGRESS: 
0:28:28.220081 PROGRESS: Precursor Summary:
0:28:28.221026 PROGRESS: Channel   0:	 0.050 FDR:   358; 0.010 FDR:   358; 0.001 FDR:   285
0:28:28.221117 PROGRESS: 
0:28:28.221173 PROGRESS: Protein Summary:
0:28:28.222316 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   339; 0.001 FDR:   274
0:28:28.222418 PROGRESS: =========================================================================
0:28:28.229044 INFO: Target number of precursors reached.
0:28:28.350641 INFO: fragments_df: keeping 4955 of 1821253 [sum(precursor_idx_mask)=8755 sum(mass_error_mask)=1821253 stop_rank=4955
0:28:28.611648 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:28.732929 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:29.338022 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:29.338551 INFO: Using score_cutoff 12.719357714080811 (fac=0.99, q=1)
0:28:29.338868 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:29.338949 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:29.339003 INFO: Updating optimization_manager: score_cutoff        : 13.971662622070312 -> 12.719357714080811
0:28:29.339056 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:29.400060 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:29.553206 INFO: === checking if optimization conditions were reached ===
0:28:29.553492 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:28:29.555615 INFO: Updating optimization_manager: rt_error            : 1663.4844970703125 -> 176.55639524370366
0:28:29.555722 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 176.5564.
0:28:29.555790 INFO: ==============================================
0:28:29.555861 INFO: Starting optimization step 1.
0:28:29.555935 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:28:29.556006 INFO: Using ng extraction backend
0:28:29.556070 PROGRESS: Extracting batch of 100097 precursors
0:28:29.733429 INFO: === Search parameters used ===
0:28:29.733824 INFO: rt_error       : 176.55639524370366
0:28:29.733880 INFO: mobility_error : 0.1
0:28:29.733928 INFO: num_candidates : 3
0:28:29.733974 INFO: ms1_error      : 30
0:28:29.734018 INFO: ms2_error      : 6.952074823324619
0:28:29.734060 INFO: fwhm_rt        : 3.0
0:28:29.734102 INFO: quant_window   : 3
0:28:29.734147 INFO: ==============================================
0:28:31.105911 INFO: performing precursor FDR with 40 features
0:28:31.106067 INFO: Decoy channel: -1
0:28:31.106094 INFO: Competetive: True
0:28:31.213930 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:31.341284 INFO: Using random state 79617 for train-test-split
0:28:36.876943 INFO: Test AUC: 0.586
0:28:36.877115 INFO: Train AUC: 0.598
0:28:36.877149 INFO: AUC difference: 2.00%
0:28:37.196933 INFO: Resetting torch num_threads to 80
0:28:37.210497 PROGRESS: === Extracted 300217 precursors and 1715835 fragments ===
0:28:37.210971 INFO: === FDR correction performed with classifier version 10 ===
0:28:37.211515 PROGRESS: ============================= Precursor FDR =============================
0:28:37.211614 PROGRESS: Total precursors accumulated: 415
0:28:37.211678 PROGRESS: Target precursors: 411 (99.04%)
0:28:37.211727 PROGRESS: Decoy precursors: 4 (0.96%)
0:28:37.211775 PROGRESS: 
0:28:37.211820 PROGRESS: Precursor Summary:
0:28:37.212786 PROGRESS: Channel   0:	 0.050 FDR:   411; 0.010 FDR:   411; 0.001 FDR:   363
0:28:37.212879 PROGRESS: 
0:28:37.212934 PROGRESS: Protein Summary:
0:28:37.214112 PROGRESS: Channel   0:	 0.050 FDR:   388; 0.010 FDR:   388; 0.001 FDR:   344
0:28:37.214205 PROGRESS: =========================================================================
0:28:37.220632 INFO: Target number of precursors reached.
0:28:37.335766 INFO: fragments_df: keeping 5000 of 1715835 [sum(precursor_idx_mask)=9923 sum(mass_error_mask)=1715835 stop_rank=5000
0:28:37.499450 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:37.611511 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:38.229047 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:38.229576 INFO: Using score_cutoff 12.701750247001648 (fac=0.99, q=1)
0:28:38.229895 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:38.229980 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:38.230034 INFO: Updating optimization_manager: score_cutoff        : 12.719357714080811 -> 12.701750247001648
0:28:38.230089 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:38.260816 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:38.330035 INFO: === checking if optimization conditions were reached ===
0:28:38.330348 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:28:38.332559 INFO: Updating optimization_manager: rt_error            : 176.55639524370366 -> 116.10870804417104
0:28:38.332664 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 116.1087.
0:28:38.332733 INFO: ==============================================
0:28:38.332822 INFO: Starting optimization step 2.
0:28:38.332884 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:28:38.332948 INFO: Using ng extraction backend
0:28:38.333009 PROGRESS: Extracting batch of 49864 precursors
0:28:38.421016 INFO: === Search parameters used ===
0:28:38.421478 INFO: rt_error       : 116.10870804417104
0:28:38.421537 INFO: mobility_error : 0.1
0:28:38.421585 INFO: num_candidates : 3
0:28:38.421632 INFO: ms1_error      : 30
0:28:38.421677 INFO: ms2_error      : 6.952074823324619
0:28:38.421721 INFO: fwhm_rt        : 3.0
0:28:38.421762 INFO: quant_window   : 3
0:28:38.421803 INFO: ==============================================
0:28:39.081874 INFO: performing precursor FDR with 40 features
0:28:39.082035 INFO: Decoy channel: -1
0:28:39.082063 INFO: Competetive: True
0:28:39.138451 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:39.193392 INFO: Using random state 79617 for train-test-split
0:28:41.732891 INFO: Test AUC: 0.578
0:28:41.733048 INFO: Train AUC: 0.602
0:28:41.733080 INFO: AUC difference: 4.03%
0:28:42.004073 INFO: Resetting torch num_threads to 80
0:28:42.011330 PROGRESS: === Extracted 149525 precursors and 822116 fragments ===
0:28:42.011740 INFO: === FDR correction performed with classifier version 10 ===
0:28:42.012205 PROGRESS: ============================= Precursor FDR =============================
0:28:42.012294 PROGRESS: Total precursors accumulated: 207
0:28:42.012353 PROGRESS: Target precursors: 205 (99.03%)
0:28:42.012402 PROGRESS: Decoy precursors: 2 (0.97%)
0:28:42.012449 PROGRESS: 
0:28:42.012493 PROGRESS: Precursor Summary:
0:28:42.013382 PROGRESS: Channel   0:	 0.050 FDR:   205; 0.010 FDR:   205; 0.001 FDR:   177
0:28:42.013487 PROGRESS: 
0:28:42.013547 PROGRESS: Protein Summary:
0:28:42.014589 PROGRESS: Channel   0:	 0.050 FDR:   201; 0.010 FDR:   201; 0.001 FDR:   173
0:28:42.014680 PROGRESS: =========================================================================
0:28:42.017203 INFO: Target number of precursors reached.
0:28:42.073221 INFO: fragments_df: keeping 2649 of 822116 [sum(precursor_idx_mask)=4809 sum(mass_error_mask)=822116 stop_rank=2649
0:28:42.228596 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:42.328849 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:42.624623 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:42.625133 INFO: Using score_cutoff 12.015364629364013 (fac=0.99, q=1)
0:28:42.625442 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:42.625547 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:42.625609 INFO: Updating optimization_manager: score_cutoff        : 12.701750247001648 -> 12.015364629364013
0:28:42.625673 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:42.656839 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:42.727276 INFO: === checking if optimization conditions were reached ===
0:28:42.727641 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:28:42.729887 INFO: Updating optimization_manager: rt_error            : 116.10870804417104 -> 74.5971843803895
0:28:42.729998 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 74.5972.
0:28:42.730087 INFO: ==============================================
0:28:42.730161 INFO: Starting optimization step 3.
0:28:42.730222 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:28:42.730285 INFO: Using ng extraction backend
0:28:42.730346 PROGRESS: Extracting batch of 49864 precursors
0:28:42.818314 INFO: === Search parameters used ===
0:28:42.818751 INFO: rt_error       : 74.5971843803895
0:28:42.818808 INFO: mobility_error : 0.1
0:28:42.818855 INFO: num_candidates : 3
0:28:42.818902 INFO: ms1_error      : 30
0:28:42.818947 INFO: ms2_error      : 6.952074823324619
0:28:42.818989 INFO: fwhm_rt        : 3.0
0:28:42.819028 INFO: quant_window   : 3
0:28:42.819070 INFO: ==============================================
0:28:43.446931 INFO: performing precursor FDR with 40 features
0:28:43.447091 INFO: Decoy channel: -1
0:28:43.447119 INFO: Competetive: True
0:28:43.502906 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:43.557365 INFO: Using random state 79617 for train-test-split
0:28:46.097890 INFO: Test AUC: 0.583
0:28:46.098061 INFO: Train AUC: 0.601
0:28:46.098092 INFO: AUC difference: 2.92%
0:28:46.371587 INFO: Resetting torch num_threads to 80
0:28:46.380067 PROGRESS: === Extracted 148985 precursors and 770766 fragments ===
0:28:46.380489 INFO: === FDR correction performed with classifier version 10 ===
0:28:46.380944 PROGRESS: ============================= Precursor FDR =============================
0:28:46.381042 PROGRESS: Total precursors accumulated: 186
0:28:46.381103 PROGRESS: Target precursors: 185 (99.46%)
0:28:46.381152 PROGRESS: Decoy precursors: 1 (0.54%)
0:28:46.381200 PROGRESS: 
0:28:46.381251 PROGRESS: Precursor Summary:
0:28:46.382147 PROGRESS: Channel   0:	 0.050 FDR:   185; 0.010 FDR:   185; 0.001 FDR:   178
0:28:46.382242 PROGRESS: 
0:28:46.382297 PROGRESS: Protein Summary:
0:28:46.383312 PROGRESS: Channel   0:	 0.050 FDR:   182; 0.010 FDR:   182; 0.001 FDR:   175
0:28:46.383404 PROGRESS: =========================================================================
0:28:46.386211 INFO: Target number of precursors not reached yet.
0:28:46.577068 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:46.609134 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:46.679412 INFO: === skipping optimization until target number of precursors are found ===
0:28:46.679725 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:28:46.679821 INFO: Starting optimization step 4.
0:28:46.679891 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:28:46.679959 INFO: Using ng extraction backend
0:28:46.680026 PROGRESS: Extracting batch of 50233 precursors
0:28:46.768965 INFO: === Search parameters used ===
0:28:46.769395 INFO: rt_error       : 74.5971843803895
0:28:46.769450 INFO: mobility_error : 0.1
0:28:46.769515 INFO: num_candidates : 3
0:28:46.769565 INFO: ms1_error      : 30
0:28:46.769612 INFO: ms2_error      : 6.952074823324619
0:28:46.769673 INFO: fwhm_rt        : 3.0
0:28:46.769719 INFO: quant_window   : 3
0:28:46.769761 INFO: ==============================================
0:28:47.492289 INFO: performing precursor FDR with 40 features
0:28:47.492447 INFO: Decoy channel: -1
0:28:47.492476 INFO: Competetive: True
0:28:47.648571 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:47.789837 INFO: Using random state 79617 for train-test-split
0:28:52.558261 INFO: Test AUC: 0.584
0:28:52.558428 INFO: Train AUC: 0.597
0:28:52.558462 INFO: AUC difference: 2.21%
0:28:52.880156 INFO: Resetting torch num_threads to 80
0:28:52.941710 PROGRESS: === Extracted 299005 precursors and 1546806 fragments ===
0:28:52.942533 INFO: === FDR correction performed with classifier version 10 ===
0:28:52.943235 PROGRESS: ============================= Precursor FDR =============================
0:28:52.943331 PROGRESS: Total precursors accumulated: 374
0:28:52.943394 PROGRESS: Target precursors: 371 (99.20%)
0:28:52.943446 PROGRESS: Decoy precursors: 3 (0.80%)
0:28:52.943494 PROGRESS: 
0:28:52.943538 PROGRESS: Precursor Summary:
0:28:52.944519 PROGRESS: Channel   0:	 0.050 FDR:   371; 0.010 FDR:   371; 0.001 FDR:   261
0:28:52.944619 PROGRESS: 
0:28:52.944678 PROGRESS: Protein Summary:
0:28:52.945837 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   352; 0.001 FDR:   250
0:28:52.945934 PROGRESS: =========================================================================
0:28:52.951241 INFO: Target number of precursors reached.
0:28:53.070310 INFO: fragments_df: keeping 4829 of 1546806 [sum(precursor_idx_mask)=8505 sum(mass_error_mask)=1546806 stop_rank=4829
0:28:53.561577 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:53.670313 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:54.260662 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:54.261174 INFO: Using score_cutoff 13.364513202667236 (fac=0.99, q=1)
0:28:54.261493 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:54.261579 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:54.261636 INFO: Updating optimization_manager: score_cutoff        : 12.015364629364013 -> 13.364513202667236
0:28:54.261693 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:54.322503 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:54.474080 INFO: === checking if optimization conditions were reached ===
0:28:54.474393 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:28:54.476771 INFO: Updating optimization_manager: rt_error            : 74.5971843803895 -> 59.28162425876302
0:28:54.476884 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 59.2816.
0:28:54.476953 INFO: ==============================================
0:28:54.477027 INFO: Starting optimization step 5.
0:28:54.477087 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:28:54.477151 INFO: Using ng extraction backend
0:28:54.477212 PROGRESS: Extracting batch of 100097 precursors
0:28:54.658124 INFO: === Search parameters used ===
0:28:54.658896 INFO: rt_error       : 59.28162425876302
0:28:54.658959 INFO: mobility_error : 0.1
0:28:54.659008 INFO: num_candidates : 3
0:28:54.659070 INFO: ms1_error      : 30
0:28:54.659116 INFO: ms2_error      : 6.952074823324619
0:28:54.659157 INFO: fwhm_rt        : 3.0
0:28:54.659195 INFO: quant_window   : 3
0:28:54.659234 INFO: ==============================================
0:28:55.790814 INFO: performing precursor FDR with 40 features
0:28:55.790955 INFO: Decoy channel: -1
0:28:55.790982 INFO: Competetive: True
0:28:55.892988 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:56.012858 INFO: Using random state 79617 for train-test-split
0:29:01.068332 INFO: Test AUC: 0.583
0:29:01.068493 INFO: Train AUC: 0.595
0:29:01.068526 INFO: AUC difference: 2.13%
0:29:01.380062 INFO: Resetting torch num_threads to 80
0:29:01.394425 PROGRESS: === Extracted 286765 precursors and 1419271 fragments ===
0:29:01.394886 INFO: === FDR correction performed with classifier version 10 ===
0:29:01.395414 PROGRESS: ============================= Precursor FDR =============================
0:29:01.395510 PROGRESS: Total precursors accumulated: 358
0:29:01.395570 PROGRESS: Target precursors: 355 (99.16%)
0:29:01.395618 PROGRESS: Decoy precursors: 3 (0.84%)
0:29:01.395665 PROGRESS: 
0:29:01.395709 PROGRESS: Precursor Summary:
0:29:01.396663 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   304
0:29:01.396755 PROGRESS: 
0:29:01.396813 PROGRESS: Protein Summary:
0:29:01.397951 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   337; 0.001 FDR:   291
0:29:01.398046 PROGRESS: =========================================================================
0:29:01.404194 INFO: Target number of precursors reached.
0:29:01.497604 INFO: fragments_df: keeping 4403 of 1419271 [sum(precursor_idx_mask)=7634 sum(mass_error_mask)=1419271 stop_rank=4403
0:29:01.749402 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:29:01.856183 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:29:02.376573 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:29:02.377088 INFO: Using score_cutoff 13.988817922782896 (fac=0.99, q=1)
0:29:02.377402 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:29:02.377498 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:29:02.377558 INFO: Updating optimization_manager: score_cutoff        : 13.364513202667236 -> 13.988817922782896
0:29:02.377616 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:02.439699 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:02.599971 INFO: === checking if optimization conditions were reached ===
0:29:02.600279 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:29:02.602637 INFO: Updating optimization_manager: rt_error            : 59.28162425876302 -> 41.02621715743802
0:29:02.602748 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 41.0262.
0:29:02.602816 INFO: ==============================================
0:29:02.602889 INFO: Starting optimization step 6.
0:29:02.602949 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:29:02.603014 INFO: Using ng extraction backend
0:29:02.603077 PROGRESS: Extracting batch of 100097 precursors
0:29:02.783103 INFO: === Search parameters used ===
0:29:02.783553 INFO: rt_error       : 41.02621715743802
0:29:02.783624 INFO: mobility_error : 0.1
0:29:02.783675 INFO: num_candidates : 3
0:29:02.783721 INFO: ms1_error      : 30
0:29:02.783767 INFO: ms2_error      : 6.952074823324619
0:29:02.783810 INFO: fwhm_rt        : 3.0
0:29:02.783850 INFO: quant_window   : 3
0:29:02.783890 INFO: ==============================================
0:29:03.885149 INFO: performing precursor FDR with 40 features
0:29:03.885303 INFO: Decoy channel: -1
0:29:03.885338 INFO: Competetive: True
0:29:03.990381 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:04.122352 INFO: Using random state 79617 for train-test-split
0:29:08.183263 INFO: Test AUC: 0.580
0:29:08.183393 INFO: Train AUC: 0.597
0:29:08.183424 INFO: AUC difference: 2.86%
0:29:08.505535 INFO: Resetting torch num_threads to 80
0:29:08.521111 PROGRESS: === Extracted 281604 precursors and 1388241 fragments ===
0:29:08.521579 INFO: === FDR correction performed with classifier version 10 ===
0:29:08.522072 PROGRESS: ============================= Precursor FDR =============================
0:29:08.522161 PROGRESS: Total precursors accumulated: 367
0:29:08.522219 PROGRESS: Target precursors: 364 (99.18%)
0:29:08.522268 PROGRESS: Decoy precursors: 3 (0.82%)
0:29:08.522314 PROGRESS: 
0:29:08.522358 PROGRESS: Precursor Summary:
0:29:08.523293 PROGRESS: Channel   0:	 0.050 FDR:   364; 0.010 FDR:   364; 0.001 FDR:   305
0:29:08.523386 PROGRESS: 
0:29:08.523441 PROGRESS: Protein Summary:
0:29:08.524580 PROGRESS: Channel   0:	 0.050 FDR:   347; 0.010 FDR:   347; 0.001 FDR:   292
0:29:08.524670 PROGRESS: =========================================================================
0:29:08.531946 INFO: Target number of precursors reached.
0:29:08.628126 INFO: fragments_df: keeping 4405 of 1388241 [sum(precursor_idx_mask)=7689 sum(mass_error_mask)=1388241 stop_rank=4405
0:29:08.873518 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:29:08.983983 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:29:09.521770 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:29:09.522296 INFO: Using score_cutoff 12.151495039272309 (fac=0.99, q=1)
0:29:09.522615 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:29:09.522700 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:29:09.522758 INFO: Updating optimization_manager: score_cutoff        : 13.988817922782896 -> 12.151495039272309
0:29:09.522814 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:09.584662 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:09.758842 INFO: === checking if optimization conditions were reached ===
0:29:09.759355 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:29:09.762080 INFO: Updating optimization_manager: rt_error            : 41.02621715743802 -> 39.26189939032689
0:29:09.762196 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 39.2619.
0:29:09.762266 INFO: ==============================================
0:29:09.762340 INFO: Starting optimization step 7.
0:29:09.762398 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:29:09.762460 INFO: Using ng extraction backend
0:29:09.762525 PROGRESS: Extracting batch of 100097 precursors
0:29:09.945296 INFO: === Search parameters used ===
0:29:09.945708 INFO: rt_error       : 39.26189939032689
0:29:09.945771 INFO: mobility_error : 0.1
0:29:09.945822 INFO: num_candidates : 3
0:29:09.945867 INFO: ms1_error      : 30
0:29:09.945910 INFO: ms2_error      : 6.952074823324619
0:29:09.945951 INFO: fwhm_rt        : 3.0
0:29:09.945995 INFO: quant_window   : 3
0:29:09.946035 INFO: ==============================================
0:29:11.046072 INFO: performing precursor FDR with 40 features
0:29:11.046222 INFO: Decoy channel: -1
0:29:11.046249 INFO: Competetive: True
0:29:11.148705 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:11.259218 INFO: Using random state 79617 for train-test-split
0:29:15.525473 INFO: Test AUC: 0.582
0:29:15.525600 INFO: Train AUC: 0.597
0:29:15.525632 INFO: AUC difference: 2.51%
0:29:15.834394 INFO: Resetting torch num_threads to 80
0:29:15.845457 PROGRESS: === Extracted 281612 precursors and 1388232 fragments ===
0:29:15.845860 INFO: === FDR correction performed with classifier version 10 ===
0:29:15.846321 PROGRESS: ============================= Precursor FDR =============================
0:29:15.846407 PROGRESS: Total precursors accumulated: 308
0:29:15.846466 PROGRESS: Target precursors: 305 (99.03%)
0:29:15.846513 PROGRESS: Decoy precursors: 3 (0.97%)
0:29:15.846559 PROGRESS: 
0:29:15.846602 PROGRESS: Precursor Summary:
0:29:15.847516 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   305; 0.001 FDR:   239
0:29:15.847605 PROGRESS: 
0:29:15.847660 PROGRESS: Protein Summary:
0:29:15.848729 PROGRESS: Channel   0:	 0.050 FDR:   292; 0.010 FDR:   292; 0.001 FDR:   230
0:29:15.848819 PROGRESS: =========================================================================
0:29:15.853506 INFO: Target number of precursors reached.
0:29:15.941875 INFO: fragments_df: keeping 3835 of 1388232 [sum(precursor_idx_mask)=6502 sum(mass_error_mask)=1388232 stop_rank=3835
0:29:16.190032 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:29:16.350780 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:29:16.848168 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:29:16.848615 INFO: Using score_cutoff 12.299440481185913 (fac=0.99, q=1)
0:29:16.848908 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:29:16.848990 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:29:16.849046 INFO: Updating optimization_manager: score_cutoff        : 12.151495039272309 -> 12.299440481185913
0:29:16.849102 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:16.909698 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:17.065935 INFO: === checking if optimization conditions were reached ===
0:29:17.066236 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:29:17.067556 INFO: Updating optimization_manager: rt_error            : 39.26189939032689 -> 74.5971843803895
0:29:17.067708 INFO: Updating optimization_manager: classifier_version  : 10 -> 15
0:29:17.067827 INFO: Updating optimization_manager: score_cutoff        : 12.299440481185913 -> 13.364513202667236
0:29:17.067933 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:29:17.068036 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:29:17.068162 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 74.5972 found after 7 searches.
0:29:17.068245 INFO: ==============================================
0:29:17.068330 PROGRESS: Optimization finished for rt_error.
0:29:17.318647 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:17.379876 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:17.570784 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:29:17.571035 PROGRESS: ==============================================
0:29:17.571144 PROGRESS: ms2_error      : 6.9521
0:29:17.571225 PROGRESS: rt_error       : 74.5972
0:29:17.571296 PROGRESS: ==============================================
0:29:17.571974 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:24.539532 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:40.578579 INFO: Using ng extraction backend
0:29:40.578975 PROGRESS: Extracting batch of 11065368 precursors
0:29:56.020519 INFO: === Search parameters used ===
0:29:56.020798 INFO: rt_error       : 74.5971843803895
0:29:56.020866 INFO: mobility_error : 0.1
0:29:56.020915 INFO: num_candidates : 3
0:29:56.020962 INFO: ms1_error      : 30
0:29:56.021006 INFO: ms2_error      : 6.952074823324619
0:29:56.021059 INFO: fwhm_rt        : 3.0
0:29:56.021108 INFO: quant_window   : 3
0:29:56.021150 INFO: ==============================================
0:30:19.401162 INFO: Removed 20938743 precursors with score below cutoff 13.364513202667236
0:30:33.802837 INFO: performing precursor FDR with 40 features
0:30:33.802971 INFO: Decoy channel: -1
0:30:33.802999 INFO: Competetive: True
0:30:35.129159 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:39.965684 INFO: Using random state 13757 for train-test-split
0:34:18.213669 INFO: Test AUC: 0.604
0:34:18.214126 INFO: Train AUC: 0.605
0:34:18.214168 INFO: AUC difference: 0.17%
0:34:22.852698 INFO: Resetting torch num_threads to 80
0:34:25.103401 PROGRESS: ============================= Precursor FDR =============================
0:34:25.103701 PROGRESS: Total precursors accumulated: 50,912
0:34:25.103769 PROGRESS: Target precursors: 50,408 (99.01%)
0:34:25.103824 PROGRESS: Decoy precursors: 504 (0.99%)
0:34:25.103872 PROGRESS: 
0:34:25.103919 PROGRESS: Precursor Summary:
0:34:25.117886 PROGRESS: Channel   0:	 0.050 FDR: 50,408; 0.010 FDR: 50,408; 0.001 FDR: 33,161
0:34:25.118175 PROGRESS: 
0:34:25.118236 PROGRESS: Protein Summary:
0:34:25.139491 PROGRESS: Channel   0:	 0.050 FDR: 8,781; 0.010 FDR: 8,781; 0.001 FDR: 6,532
0:34:25.139763 PROGRESS: =========================================================================
0:34:25.236032 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/psm.parquet
0:34:25.365317 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/frag.parquet
0:34:25.537329 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
0:34:26.112417 PROGRESS: 
0:34:26.112600 INFO: Quantification results path: alphadia_zenoswath8600/library/quant
0:34:26.112686 INFO: Creating folder alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/figures
0:34:26.112863 INFO: Initializing TimingManager
0:34:26.113562 INFO: Initializing RawFileManager
0:36:49.034475 INFO: Determining DIA cycle
0:36:49.049452 INFO: Found cycle with start 0.00 min and length 86.
0:36:49.282374 INFO: RT (min)            : 0.0 - 55.5
0:36:49.282477 INFO: RT duration (sec)   : 3327.1
0:36:49.282506 INFO: RT duration (min)   : 55.5
0:36:49.282531 INFO: Cycle len (scans)   : 86
0:36:49.282550 INFO: Cycle len (sec)     : 1.90
0:36:49.282569 INFO: Number of cycles    : 1747
0:36:49.282587 INFO: MS2 range (m/z)     : 399.5 - 903.5
0:36:49.282646 INFO: Creating DIA data object took: 143.16898226737976
0:36:50.320745 INFO: Creating DIA data NG object took: 1.037935495376587
0:36:51.698797 INFO: Initializing CalibrationManager
0:36:51.699099 INFO: Setting up calibration estimators ..
0:36:51.699162 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:36:51.699265 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'}' ..
0:36:51.699409 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:36:51.699464 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:36:51.699521 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}}' ..
0:36:51.699577 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:36:51.699624 INFO: Done setting up calibration estimators.
0:36:51.699780 INFO: Initializing OptimizationManager
0:36:51.699964 INFO: initial parameter: ms1_error = 30
0:36:51.700018 INFO: initial parameter: ms2_error = 30
0:36:51.700067 INFO: initial parameter: rt_error = 1663.596435546875
0:36:51.700110 INFO: initial parameter: mobility_error = 0.1
0:36:51.700156 INFO: initial parameter: num_candidates = 1
0:36:51.700198 INFO: initial parameter: fwhm_rt = 5
0:36:51.700552 INFO: initial parameter: fwhm_mobility = 0.01
0:36:51.700597 INFO: initial parameter: score_cutoff = 0
0:36:51.700639 INFO: initial parameter: classifier_version = -1
0:36:51.700717 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
0:36:51.701083 INFO: FDRManager: loading saved state not requested, will be initialized.
0:36:51.701120 INFO: Initializing FDRManager
0:36:51.701164 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:36:53.076568 PROGRESS: Initializing spectral library: 5,608,555 target precursors potentially observable (87,724 removed)
0:36:53.924352 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:36:53.924720 INFO: Updating optimization_manager: rt_error            : 1663.596435546875 -> 1663.596435546875
0:36:53.924833 PROGRESS: Starting initial search for precursors.
0:36:53.924927 INFO: Starting optimization step 0.
0:36:53.924991 PROGRESS: === Extracting elution groups 0 to 200 ===
0:36:53.925056 INFO: Using ng extraction backend
0:36:53.925132 PROGRESS: Extracting batch of 394 precursors
0:36:53.927527 INFO: === Search parameters used ===
0:36:53.927649 INFO: rt_error       : 1663.596435546875
0:36:53.927702 INFO: mobility_error : 0.1
0:36:53.927746 INFO: num_candidates : 1
0:36:53.927792 INFO: ms1_error      : 30
0:36:53.927833 INFO: ms2_error      : 30
0:36:53.927873 INFO: fwhm_rt        : 5
0:36:53.927911 INFO: quant_window   : 3
0:36:53.927951 INFO: ==============================================
0:36:53.948230 INFO: performing precursor FDR with 40 features
0:36:53.948305 INFO: Decoy channel: -1
0:36:53.948334 INFO: Competetive: True
0:36:53.949373 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:53.952038 INFO: Using random state 833452 for train-test-split
0:36:53.960018 INFO: Test AUC: 0.524
0:36:53.960075 INFO: Train AUC: 0.477
0:36:53.960107 INFO: AUC difference: 9.79%
0:36:53.960132 WARNING: AUC difference > 5%. This may indicate overfitting.
0:36:54.181618 INFO: Resetting torch num_threads to 80
0:36:54.183059 PROGRESS: === Extracted 393 precursors and 2236 fragments ===
0:36:54.183430 INFO: === FDR correction performed with classifier version -1 ===
0:36:54.183863 PROGRESS: ============================= Precursor FDR =============================
0:36:54.183950 PROGRESS: Total precursors accumulated: 0
0:36:54.184011 PROGRESS: Target precursors: 0 (0.00%)
0:36:54.184062 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:54.184108 PROGRESS: 
0:36:54.184154 PROGRESS: Precursor Summary:
0:36:54.184267 PROGRESS: 
0:36:54.184332 PROGRESS: Protein Summary:
0:36:54.184408 PROGRESS: =========================================================================
0:36:54.184591 INFO: Target number of precursors not reached yet.
0:36:54.245785 INFO: Starting optimization step 1.
0:36:54.246014 PROGRESS: === Extracting elution groups 200 to 600 ===
0:36:54.246104 INFO: Using ng extraction backend
0:36:54.246169 PROGRESS: Extracting batch of 782 precursors
0:36:54.250054 INFO: === Search parameters used ===
0:36:54.250196 INFO: rt_error       : 1663.596435546875
0:36:54.250249 INFO: mobility_error : 0.1
0:36:54.250295 INFO: num_candidates : 1
0:36:54.250338 INFO: ms1_error      : 30
0:36:54.250381 INFO: ms2_error      : 30
0:36:54.250422 INFO: fwhm_rt        : 5
0:36:54.250462 INFO: quant_window   : 3
0:36:54.250502 INFO: ==============================================
0:36:54.277011 INFO: performing precursor FDR with 40 features
0:36:54.277091 INFO: Decoy channel: -1
0:36:54.277118 INFO: Competetive: True
0:36:54.280227 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:54.281822 INFO: Using random state 132119 for train-test-split
0:36:54.290319 INFO: Test AUC: 0.371
0:36:54.290380 INFO: Train AUC: 0.531
0:36:54.290410 INFO: AUC difference: 30.18%
0:36:54.290434 WARNING: AUC difference > 5%. This may indicate overfitting.
0:36:54.507493 INFO: Resetting torch num_threads to 80
0:36:54.509843 PROGRESS: === Extracted 1171 precursors and 6660 fragments ===
0:36:54.510235 INFO: === FDR correction performed with classifier version -1 ===
0:36:54.510665 PROGRESS: ============================= Precursor FDR =============================
0:36:54.510752 PROGRESS: Total precursors accumulated: 0
0:36:54.510812 PROGRESS: Target precursors: 0 (0.00%)
0:36:54.510862 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:54.510909 PROGRESS: 
0:36:54.510956 PROGRESS: Precursor Summary:
0:36:54.511066 PROGRESS: 
0:36:54.511130 PROGRESS: Protein Summary:
0:36:54.511216 PROGRESS: =========================================================================
0:36:54.511431 INFO: Target number of precursors not reached yet.
0:36:54.574471 INFO: Starting optimization step 2.
0:36:54.574699 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:36:54.574785 INFO: Using ng extraction backend
0:36:54.574852 PROGRESS: Extracting batch of 1565 precursors
0:36:54.579660 INFO: === Search parameters used ===
0:36:54.579788 INFO: rt_error       : 1663.596435546875
0:36:54.579841 INFO: mobility_error : 0.1
0:36:54.579886 INFO: num_candidates : 1
0:36:54.579928 INFO: ms1_error      : 30
0:36:54.579973 INFO: ms2_error      : 30
0:36:54.580016 INFO: fwhm_rt        : 5
0:36:54.580055 INFO: quant_window   : 3
0:36:54.580097 INFO: ==============================================
0:36:54.615923 INFO: performing precursor FDR with 40 features
0:36:54.616010 INFO: Decoy channel: -1
0:36:54.616037 INFO: Competetive: True
0:36:54.619627 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:54.621565 INFO: Using random state 275794 for train-test-split
0:36:54.633378 INFO: Test AUC: 0.491
0:36:54.633440 INFO: Train AUC: 0.510
0:36:54.633480 INFO: AUC difference: 3.68%
0:36:54.852005 INFO: Resetting torch num_threads to 80
0:36:54.854840 PROGRESS: === Extracted 2731 precursors and 15562 fragments ===
0:36:54.855219 INFO: === FDR correction performed with classifier version -1 ===
0:36:54.855647 PROGRESS: ============================= Precursor FDR =============================
0:36:54.855734 PROGRESS: Total precursors accumulated: 0
0:36:54.855796 PROGRESS: Target precursors: 0 (0.00%)
0:36:54.855847 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:54.855894 PROGRESS: 
0:36:54.855947 PROGRESS: Precursor Summary:
0:36:54.856060 PROGRESS: 
0:36:54.856122 PROGRESS: Protein Summary:
0:36:54.856196 PROGRESS: =========================================================================
0:36:54.856422 INFO: Target number of precursors not reached yet.
0:36:54.922337 INFO: Starting optimization step 3.
0:36:54.922576 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:36:54.922666 INFO: Using ng extraction backend
0:36:54.922732 PROGRESS: Extracting batch of 3140 precursors
0:36:54.930475 INFO: === Search parameters used ===
0:36:54.930639 INFO: rt_error       : 1663.596435546875
0:36:54.930692 INFO: mobility_error : 0.1
0:36:54.930736 INFO: num_candidates : 1
0:36:54.930780 INFO: ms1_error      : 30
0:36:54.930822 INFO: ms2_error      : 30
0:36:54.930866 INFO: fwhm_rt        : 5
0:36:54.930905 INFO: quant_window   : 3
0:36:54.930945 INFO: ==============================================
0:36:54.987031 INFO: performing precursor FDR with 40 features
0:36:54.987146 INFO: Decoy channel: -1
0:36:54.987173 INFO: Competetive: True
0:36:54.991542 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:54.994020 INFO: Using random state 626074 for train-test-split
0:36:55.012569 INFO: Test AUC: 0.486
0:36:55.012670 INFO: Train AUC: 0.505
0:36:55.012700 INFO: AUC difference: 3.75%
0:36:55.287190 INFO: Resetting torch num_threads to 80
0:36:55.291386 PROGRESS: === Extracted 5864 precursors and 33589 fragments ===
0:36:55.291862 INFO: === FDR correction performed with classifier version -1 ===
0:36:55.292352 PROGRESS: ============================= Precursor FDR =============================
0:36:55.292450 PROGRESS: Total precursors accumulated: 1
0:36:55.292513 PROGRESS: Target precursors: 1 (100.00%)
0:36:55.292564 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:55.292618 PROGRESS: 
0:36:55.292665 PROGRESS: Precursor Summary:
0:36:55.293639 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:36:55.293732 PROGRESS: 
0:36:55.293793 PROGRESS: Protein Summary:
0:36:55.294849 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:36:55.294940 PROGRESS: =========================================================================
0:36:55.295227 INFO: Target number of precursors not reached yet.
0:36:55.365458 INFO: Starting optimization step 4.
0:36:55.365718 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:36:55.365807 INFO: Using ng extraction backend
0:36:55.365870 PROGRESS: Extracting batch of 6271 precursors
0:36:55.379511 INFO: === Search parameters used ===
0:36:55.379774 INFO: rt_error       : 1663.596435546875
0:36:55.379829 INFO: mobility_error : 0.1
0:36:55.379875 INFO: num_candidates : 1
0:36:55.379922 INFO: ms1_error      : 30
0:36:55.379965 INFO: ms2_error      : 30
0:36:55.380006 INFO: fwhm_rt        : 5
0:36:55.380058 INFO: quant_window   : 3
0:36:55.380103 INFO: ==============================================
0:36:55.472501 INFO: performing precursor FDR with 40 features
0:36:55.472621 INFO: Decoy channel: -1
0:36:55.472647 INFO: Competetive: True
0:36:55.478921 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:55.482749 INFO: Using random state 73233 for train-test-split
0:36:55.523624 INFO: Test AUC: 0.477
0:36:55.523743 INFO: Train AUC: 0.503
0:36:55.523773 INFO: AUC difference: 5.04%
0:36:55.523799 WARNING: AUC difference > 5%. This may indicate overfitting.
0:36:55.751541 INFO: Resetting torch num_threads to 80
0:36:55.756358 PROGRESS: === Extracted 12121 precursors and 69774 fragments ===
0:36:55.756771 INFO: === FDR correction performed with classifier version -1 ===
0:36:55.757236 PROGRESS: ============================= Precursor FDR =============================
0:36:55.757322 PROGRESS: Total precursors accumulated: 2
0:36:55.757382 PROGRESS: Target precursors: 2 (100.00%)
0:36:55.757431 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:55.757488 PROGRESS: 
0:36:55.757536 PROGRESS: Precursor Summary:
0:36:55.758456 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:36:55.758545 PROGRESS: 
0:36:55.758602 PROGRESS: Protein Summary:
0:36:55.759625 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:36:55.759713 PROGRESS: =========================================================================
0:36:55.760060 INFO: Target number of precursors not reached yet.
0:36:55.837492 INFO: Starting optimization step 5.
0:36:55.837752 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:36:55.837839 INFO: Using ng extraction backend
0:36:55.837903 PROGRESS: Extracting batch of 12568 precursors
0:36:55.862157 INFO: === Search parameters used ===
0:36:55.862381 INFO: rt_error       : 1663.596435546875
0:36:55.862436 INFO: mobility_error : 0.1
0:36:55.862482 INFO: num_candidates : 1
0:36:55.862525 INFO: ms1_error      : 30
0:36:55.862567 INFO: ms2_error      : 30
0:36:55.862607 INFO: fwhm_rt        : 5
0:36:55.862647 INFO: quant_window   : 3
0:36:55.862687 INFO: ==============================================
0:36:56.010741 INFO: performing precursor FDR with 40 features
0:36:56.010885 INFO: Decoy channel: -1
0:36:56.010911 INFO: Competetive: True
0:36:56.021425 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:56.028392 INFO: Using random state 778365 for train-test-split
0:36:56.315635 INFO: Test AUC: 0.500
0:36:56.315765 INFO: Train AUC: 0.500
0:36:56.315805 INFO: AUC difference: 0.02%
0:36:56.560779 INFO: Resetting torch num_threads to 80
0:36:56.567494 PROGRESS: === Extracted 24675 precursors and 142075 fragments ===
0:36:56.568004 INFO: === FDR correction performed with classifier version -1 ===
0:36:56.568470 PROGRESS: ============================= Precursor FDR =============================
0:36:56.568560 PROGRESS: Total precursors accumulated: 0
0:36:56.568621 PROGRESS: Target precursors: 0 (0.00%)
0:36:56.569930 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:56.569990 PROGRESS: 
0:36:56.570035 PROGRESS: Precursor Summary:
0:36:56.570158 PROGRESS: 
0:36:56.570219 PROGRESS: Protein Summary:
0:36:56.570292 PROGRESS: =========================================================================
0:36:56.570776 INFO: Target number of precursors not reached yet.
0:36:56.663991 INFO: Starting optimization step 6.
0:36:56.664291 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:36:56.664393 INFO: Using ng extraction backend
0:36:56.664461 PROGRESS: Extracting batch of 25144 precursors
0:36:56.710543 INFO: === Search parameters used ===
0:36:56.710844 INFO: rt_error       : 1663.596435546875
0:36:56.710899 INFO: mobility_error : 0.1
0:36:56.710945 INFO: num_candidates : 1
0:36:56.710990 INFO: ms1_error      : 30
0:36:56.711036 INFO: ms2_error      : 30
0:36:56.711082 INFO: fwhm_rt        : 5
0:36:56.711125 INFO: quant_window   : 3
0:36:56.711166 INFO: ==============================================
0:36:56.957785 INFO: performing precursor FDR with 40 features
0:36:56.957925 INFO: Decoy channel: -1
0:36:56.957952 INFO: Competetive: True
0:36:56.977275 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:56.990562 INFO: Using random state 584566 for train-test-split
0:36:57.604298 INFO: Test AUC: 0.546
0:36:57.604429 INFO: Train AUC: 0.564
0:36:57.604461 INFO: AUC difference: 3.18%
0:36:57.840486 INFO: Resetting torch num_threads to 80
0:36:57.851063 PROGRESS: === Extracted 49778 precursors and 286563 fragments ===
0:36:57.851662 INFO: === FDR correction performed with classifier version -1 ===
0:36:57.852157 PROGRESS: ============================= Precursor FDR =============================
0:36:57.852245 PROGRESS: Total precursors accumulated: 107
0:36:57.852305 PROGRESS: Target precursors: 106 (99.07%)
0:36:57.852353 PROGRESS: Decoy precursors: 1 (0.93%)
0:36:57.852397 PROGRESS: 
0:36:57.852440 PROGRESS: Precursor Summary:
0:36:57.853327 PROGRESS: Channel   0:	 0.050 FDR:   106; 0.010 FDR:   106; 0.001 FDR:    85
0:36:57.853413 PROGRESS: 
0:36:57.853479 PROGRESS: Protein Summary:
0:36:57.854493 PROGRESS: Channel   0:	 0.050 FDR:   105; 0.010 FDR:   105; 0.001 FDR:    84
0:36:57.854579 PROGRESS: =========================================================================
0:36:57.855313 INFO: Target number of precursors not reached yet.
0:36:57.981836 INFO: Starting optimization step 7.
0:36:57.982154 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:36:57.982244 INFO: Using ng extraction backend
0:36:57.982308 PROGRESS: Extracting batch of 50233 precursors
0:36:58.070061 INFO: === Search parameters used ===
0:36:58.070390 INFO: rt_error       : 1663.596435546875
0:36:58.070445 INFO: mobility_error : 0.1
0:36:58.070490 INFO: num_candidates : 1
0:36:58.070534 INFO: ms1_error      : 30
0:36:58.070579 INFO: ms2_error      : 30
0:36:58.070622 INFO: fwhm_rt        : 5
0:36:58.070662 INFO: quant_window   : 3
0:36:58.070704 INFO: ==============================================
0:36:58.525818 INFO: performing precursor FDR with 40 features
0:36:58.525964 INFO: Decoy channel: -1
0:36:58.525992 INFO: Competetive: True
0:36:58.567734 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:58.597681 INFO: Using random state 798418 for train-test-split
0:36:59.926772 INFO: Test AUC: 0.574
0:36:59.926906 INFO: Train AUC: 0.588
0:36:59.926936 INFO: AUC difference: 2.36%
0:37:00.180273 INFO: Resetting torch num_threads to 80
0:37:00.201450 PROGRESS: === Extracted 99941 precursors and 575105 fragments ===
0:37:00.202163 INFO: === FDR correction performed with classifier version -1 ===
0:37:00.202736 PROGRESS: ============================= Precursor FDR =============================
0:37:00.202830 PROGRESS: Total precursors accumulated: 253
0:37:00.202898 PROGRESS: Target precursors: 251 (99.21%)
0:37:00.202960 PROGRESS: Decoy precursors: 2 (0.79%)
0:37:00.203010 PROGRESS: 
0:37:00.203054 PROGRESS: Precursor Summary:
0:37:00.204009 PROGRESS: Channel   0:	 0.050 FDR:   251; 0.010 FDR:   251; 0.001 FDR:   214
0:37:00.204104 PROGRESS: 
0:37:00.204161 PROGRESS: Protein Summary:
0:37:00.205245 PROGRESS: Channel   0:	 0.050 FDR:   242; 0.010 FDR:   242; 0.001 FDR:   206
0:37:00.205341 PROGRESS: =========================================================================
0:37:00.206975 INFO: Target number of precursors reached.
0:37:00.250840 INFO: fragments_df: keeping 2431 of 575105 [sum(precursor_idx_mask)=2697 sum(mass_error_mask)=575105 stop_rank=2431
0:37:00.448809 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:00.565398 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:00.888227 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:37:00.888689 INFO: Using score_cutoff 15.974305930137634 (fac=0.99, q=1)
0:37:00.889005 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:37:00.889086 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:37:00.889142 INFO: Updating optimization_manager: score_cutoff        : 0 -> 15.974305930137634
0:37:00.889200 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:00.956235 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:01.100549 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:37:01.100861 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:37:01.100975 INFO: Starting optimization step 8.
0:37:01.101052 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:37:01.101130 INFO: Using ng extraction backend
0:37:01.101204 PROGRESS: Extracting batch of 100097 precursors
0:37:01.278704 INFO: === Search parameters used ===
0:37:01.279053 INFO: rt_error       : 1663.596435546875
0:37:01.279109 INFO: mobility_error : 0.1
0:37:01.279156 INFO: num_candidates : 3
0:37:01.279201 INFO: ms1_error      : 30
0:37:01.279243 INFO: ms2_error      : 30
0:37:01.279285 INFO: fwhm_rt        : 3.0
0:37:01.279327 INFO: quant_window   : 3
0:37:01.279369 INFO: ==============================================
0:37:02.742799 INFO: performing precursor FDR with 40 features
0:37:02.742932 INFO: Decoy channel: -1
0:37:02.742962 INFO: Competetive: True
0:37:02.829276 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:02.938478 INFO: Using random state 680649 for train-test-split
0:37:07.592965 INFO: Test AUC: 0.589
0:37:07.593104 INFO: Train AUC: 0.597
0:37:07.593135 INFO: AUC difference: 1.40%
0:37:07.915569 INFO: Resetting torch num_threads to 80
0:37:07.926908 PROGRESS: === Extracted 299853 precursors and 1684505 fragments ===
0:37:07.927325 INFO: === FDR correction performed with classifier version 7 ===
0:37:07.927783 PROGRESS: ============================= Precursor FDR =============================
0:37:07.927872 PROGRESS: Total precursors accumulated: 267
0:37:07.927932 PROGRESS: Target precursors: 265 (99.25%)
0:37:07.927980 PROGRESS: Decoy precursors: 2 (0.75%)
0:37:07.928027 PROGRESS: 
0:37:07.928079 PROGRESS: Precursor Summary:
0:37:07.928985 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:   265; 0.001 FDR:   235
0:37:07.929075 PROGRESS: 
0:37:07.929131 PROGRESS: Protein Summary:
0:37:07.930205 PROGRESS: Channel   0:	 0.050 FDR:   254; 0.010 FDR:   254; 0.001 FDR:   225
0:37:07.930298 PROGRESS: =========================================================================
0:37:07.935019 INFO: Target number of precursors reached.
0:37:08.043365 INFO: fragments_df: keeping 3702 of 1684505 [sum(precursor_idx_mask)=6133 sum(mass_error_mask)=1684505 stop_rank=3702
0:37:08.244970 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:08.370729 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:08.862433 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:08.862897 INFO: Using score_cutoff 11.770421656036376 (fac=0.99, q=1)
0:37:08.863199 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:08.863279 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:08.863335 INFO: Updating optimization_manager: score_cutoff        : 15.974305930137634 -> 11.770421656036376
0:37:08.863397 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:08.924592 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:09.082089 INFO: === checking if optimization conditions were reached ===
0:37:09.082446 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:37:09.085402 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.821063393969928
0:37:09.085685 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 6.8211.
0:37:09.085887 INFO: ==============================================
0:37:09.086090 INFO: Starting optimization step 9.
0:37:09.086280 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:37:09.086477 INFO: Using ng extraction backend
0:37:09.086663 PROGRESS: Extracting batch of 100097 precursors
0:37:09.264191 INFO: === Search parameters used ===
0:37:09.264548 INFO: rt_error       : 1663.596435546875
0:37:09.264600 INFO: mobility_error : 0.1
0:37:09.264645 INFO: num_candidates : 3
0:37:09.264684 INFO: ms1_error      : 30
0:37:09.264723 INFO: ms2_error      : 6.821063393969928
0:37:09.264761 INFO: fwhm_rt        : 3.0
0:37:09.264801 INFO: quant_window   : 3
0:37:09.264840 INFO: ==============================================
0:37:10.739147 INFO: performing precursor FDR with 40 features
0:37:10.739282 INFO: Decoy channel: -1
0:37:10.739308 INFO: Competetive: True
0:37:10.844691 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:11.006070 INFO: Using random state 680649 for train-test-split
0:37:15.560664 INFO: Test AUC: 0.580
0:37:15.560793 INFO: Train AUC: 0.597
0:37:15.560824 INFO: AUC difference: 2.81%
0:37:15.873141 INFO: Resetting torch num_threads to 80
0:37:15.885182 PROGRESS: === Extracted 300279 precursors and 1823142 fragments ===
0:37:15.885609 INFO: === FDR correction performed with classifier version 7 ===
0:37:15.886073 PROGRESS: ============================= Precursor FDR =============================
0:37:15.886160 PROGRESS: Total precursors accumulated: 327
0:37:15.886219 PROGRESS: Target precursors: 324 (99.08%)
0:37:15.886277 PROGRESS: Decoy precursors: 3 (0.92%)
0:37:15.886325 PROGRESS: 
0:37:15.886369 PROGRESS: Precursor Summary:
0:37:15.887289 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   215
0:37:15.887377 PROGRESS: 
0:37:15.887431 PROGRESS: Protein Summary:
0:37:15.888508 PROGRESS: Channel   0:	 0.050 FDR:   309; 0.010 FDR:   309; 0.001 FDR:   206
0:37:15.888597 PROGRESS: =========================================================================
0:37:15.893401 INFO: Target number of precursors reached.
0:37:16.012116 INFO: fragments_df: keeping 4616 of 1823142 [sum(precursor_idx_mask)=7972 sum(mass_error_mask)=1823142 stop_rank=4616
0:37:16.214881 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:16.342695 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:16.988119 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:16.988579 INFO: Using score_cutoff 13.175479403400422 (fac=0.99, q=1)
0:37:16.988878 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:16.988958 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:16.989013 INFO: Updating optimization_manager: score_cutoff        : 11.770421656036376 -> 13.175479403400422
0:37:16.989069 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:17.049736 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:17.185405 INFO: === checking if optimization conditions were reached ===
0:37:17.185720 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:37:17.188369 INFO: Updating optimization_manager: ms2_error           : 6.821063393969928 -> 6.8279296177876505
0:37:17.188490 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 6.8279.
0:37:17.188560 INFO: ==============================================
0:37:17.188642 INFO: Starting optimization step 10.
0:37:17.188703 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:37:17.188768 INFO: Using ng extraction backend
0:37:17.188827 PROGRESS: Extracting batch of 100097 precursors
0:37:17.366021 INFO: === Search parameters used ===
0:37:17.366383 INFO: rt_error       : 1663.596435546875
0:37:17.366444 INFO: mobility_error : 0.1
0:37:17.366493 INFO: num_candidates : 3
0:37:17.366538 INFO: ms1_error      : 30
0:37:17.366583 INFO: ms2_error      : 6.8279296177876505
0:37:17.366629 INFO: fwhm_rt        : 3.0
0:37:17.366672 INFO: quant_window   : 3
0:37:17.366715 INFO: ==============================================
0:37:18.737184 INFO: performing precursor FDR with 40 features
0:37:18.737317 INFO: Decoy channel: -1
0:37:18.737344 INFO: Competetive: True
0:37:18.820566 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:18.931789 INFO: Using random state 680649 for train-test-split
0:37:23.501890 INFO: Test AUC: 0.582
0:37:23.502030 INFO: Train AUC: 0.596
0:37:23.502063 INFO: AUC difference: 2.36%
0:37:23.818645 INFO: Resetting torch num_threads to 80
0:37:23.830923 PROGRESS: === Extracted 300279 precursors and 1823083 fragments ===
0:37:23.831367 INFO: === FDR correction performed with classifier version 7 ===
0:37:23.831836 PROGRESS: ============================= Precursor FDR =============================
0:37:23.831922 PROGRESS: Total precursors accumulated: 326
0:37:23.831988 PROGRESS: Target precursors: 323 (99.08%)
0:37:23.832038 PROGRESS: Decoy precursors: 3 (0.92%)
0:37:23.832083 PROGRESS: 
0:37:23.832128 PROGRESS: Precursor Summary:
0:37:23.833051 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   323; 0.001 FDR:   246
0:37:23.833137 PROGRESS: 
0:37:23.833190 PROGRESS: Protein Summary:
0:37:23.834289 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   308; 0.001 FDR:   235
0:37:23.834380 PROGRESS: =========================================================================
0:37:23.839405 INFO: Target number of precursors reached.
0:37:23.962035 INFO: fragments_df: keeping 4554 of 1823083 [sum(precursor_idx_mask)=7909 sum(mass_error_mask)=1823083 stop_rank=4554
0:37:24.168640 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:24.468896 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:25.083364 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:25.083833 INFO: Using score_cutoff 13.026226406478882 (fac=0.99, q=1)
0:37:25.084139 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:25.084219 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:25.084275 INFO: Updating optimization_manager: score_cutoff        : 13.175479403400422 -> 13.026226406478882
0:37:25.084331 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:25.180370 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:25.355575 INFO: === checking if optimization conditions were reached ===
0:37:25.355904 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:37:25.357016 INFO: Updating optimization_manager: ms2_error           : 6.8279296177876505 -> 6.821063393969928
0:37:25.357163 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
0:37:25.357277 INFO: Updating optimization_manager: score_cutoff        : 13.026226406478882 -> 13.175479403400422
0:37:25.357379 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:25.357488 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:25.357597 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 6.8211 found after 3 searches.
0:37:25.357674 INFO: ==============================================
0:37:25.357760 PROGRESS: Optimization finished for ms2_error.
0:37:25.567985 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:25.629118 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:26.774507 INFO: Starting optimization step 0.
0:37:26.774737 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:37:26.774817 INFO: Using ng extraction backend
0:37:26.774881 PROGRESS: Extracting batch of 100097 precursors
0:37:26.949250 INFO: === Search parameters used ===
0:37:26.949614 INFO: rt_error       : 1663.596435546875
0:37:26.949673 INFO: mobility_error : 0.1
0:37:26.949732 INFO: num_candidates : 3
0:37:26.949779 INFO: ms1_error      : 30
0:37:26.949822 INFO: ms2_error      : 6.821063393969928
0:37:26.949862 INFO: fwhm_rt        : 3.0
0:37:26.949903 INFO: quant_window   : 3
0:37:26.949944 INFO: ==============================================
0:37:28.311947 INFO: performing precursor FDR with 40 features
0:37:28.312076 INFO: Decoy channel: -1
0:37:28.312104 INFO: Competetive: True
0:37:28.396489 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:28.506067 INFO: Using random state 196176 for train-test-split
0:37:33.419599 INFO: Test AUC: 0.590
0:37:33.419736 INFO: Train AUC: 0.602
0:37:33.419773 INFO: AUC difference: 2.04%
0:37:33.734642 INFO: Resetting torch num_threads to 80
0:37:33.747079 PROGRESS: === Extracted 300279 precursors and 1822331 fragments ===
0:37:33.747537 INFO: === FDR correction performed with classifier version 9 ===
0:37:33.748051 PROGRESS: ============================= Precursor FDR =============================
0:37:33.748155 PROGRESS: Total precursors accumulated: 355
0:37:33.748232 PROGRESS: Target precursors: 352 (99.15%)
0:37:33.748295 PROGRESS: Decoy precursors: 3 (0.85%)
0:37:33.748355 PROGRESS: 
0:37:33.748411 PROGRESS: Precursor Summary:
0:37:33.749431 PROGRESS: Channel   0:	 0.050 FDR:   352; 0.010 FDR:   352; 0.001 FDR:   258
0:37:33.749550 PROGRESS: 
0:37:33.749624 PROGRESS: Protein Summary:
0:37:33.750813 PROGRESS: Channel   0:	 0.050 FDR:   334; 0.010 FDR:   334; 0.001 FDR:   247
0:37:33.750912 PROGRESS: =========================================================================
0:37:33.755903 INFO: Target number of precursors reached.
0:37:33.876064 INFO: fragments_df: keeping 4887 of 1822331 [sum(precursor_idx_mask)=8584 sum(mass_error_mask)=1822331 stop_rank=4887
0:37:34.078683 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:34.207634 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:34.873263 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:34.873772 INFO: Using score_cutoff 12.50420403728485 (fac=0.99, q=1)
0:37:34.874102 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:34.874193 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:34.874263 INFO: Updating optimization_manager: score_cutoff        : 13.175479403400422 -> 12.50420403728485
0:37:34.874333 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:34.934203 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:35.081716 INFO: === checking if optimization conditions were reached ===
0:37:35.082037 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:37:35.084430 INFO: Updating optimization_manager: rt_error            : 1663.596435546875 -> 270.54733955280864
0:37:35.084556 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 270.5473.
0:37:35.084642 INFO: ==============================================
0:37:35.084730 INFO: Starting optimization step 1.
0:37:35.084803 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:37:35.084882 INFO: Using ng extraction backend
0:37:35.084957 PROGRESS: Extracting batch of 100097 precursors
0:37:35.263218 INFO: === Search parameters used ===
0:37:35.263592 INFO: rt_error       : 270.54733955280864
0:37:35.263667 INFO: mobility_error : 0.1
0:37:35.263728 INFO: num_candidates : 3
0:37:35.263785 INFO: ms1_error      : 30
0:37:35.263840 INFO: ms2_error      : 6.821063393969928
0:37:35.263893 INFO: fwhm_rt        : 3.0
0:37:35.263944 INFO: quant_window   : 3
0:37:35.263996 INFO: ==============================================
0:37:36.370424 INFO: performing precursor FDR with 40 features
0:37:36.370570 INFO: Decoy channel: -1
0:37:36.370597 INFO: Competetive: True
0:37:36.454066 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:36.563637 INFO: Using random state 196176 for train-test-split
0:37:41.240702 INFO: Test AUC: 0.585
0:37:41.240843 INFO: Train AUC: 0.599
0:37:41.240875 INFO: AUC difference: 2.28%
0:37:41.557494 INFO: Resetting torch num_threads to 80
0:37:41.568548 PROGRESS: === Extracted 300244 precursors and 1756701 fragments ===
0:37:41.568977 INFO: === FDR correction performed with classifier version 9 ===
0:37:41.569448 PROGRESS: ============================= Precursor FDR =============================
0:37:41.569548 PROGRESS: Total precursors accumulated: 407
0:37:41.569606 PROGRESS: Target precursors: 403 (99.02%)
0:37:41.569655 PROGRESS: Decoy precursors: 4 (0.98%)
0:37:41.569699 PROGRESS: 
0:37:41.569743 PROGRESS: Precursor Summary:
0:37:41.570700 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   403; 0.001 FDR:   318
0:37:41.570790 PROGRESS: 
0:37:41.570848 PROGRESS: Protein Summary:
0:37:41.571993 PROGRESS: Channel   0:	 0.050 FDR:   382; 0.010 FDR:   382; 0.001 FDR:   304
0:37:41.572080 PROGRESS: =========================================================================
0:37:41.576998 INFO: Target number of precursors reached.
0:37:41.691371 INFO: fragments_df: keeping 5000 of 1756701 [sum(precursor_idx_mask)=9690 sum(mass_error_mask)=1756701 stop_rank=5000
0:37:41.827101 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:41.958413 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:42.642308 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:42.642772 INFO: Using score_cutoff 10.687820756149293 (fac=0.99, q=1)
0:37:42.643074 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:42.643155 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:42.643211 INFO: Updating optimization_manager: score_cutoff        : 12.50420403728485 -> 10.687820756149293
0:37:42.643266 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:42.673707 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:42.740607 INFO: === checking if optimization conditions were reached ===
0:37:42.740996 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:37:42.743581 INFO: Updating optimization_manager: rt_error            : 270.54733955280864 -> 217.49164608066607
0:37:42.743759 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 217.4916.
0:37:42.743856 INFO: ==============================================
0:37:42.743954 INFO: Starting optimization step 2.
0:37:42.744038 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:37:42.744130 INFO: Using ng extraction backend
0:37:42.744240 PROGRESS: Extracting batch of 49864 precursors
0:37:42.836535 INFO: === Search parameters used ===
0:37:42.836919 INFO: rt_error       : 217.49164608066607
0:37:42.836976 INFO: mobility_error : 0.1
0:37:42.837023 INFO: num_candidates : 3
0:37:42.837068 INFO: ms1_error      : 30
0:37:42.837109 INFO: ms2_error      : 6.821063393969928
0:37:42.837150 INFO: fwhm_rt        : 3.0
0:37:42.837190 INFO: quant_window   : 3
0:37:42.837231 INFO: ==============================================
0:37:43.457106 INFO: performing precursor FDR with 40 features
0:37:43.457236 INFO: Decoy channel: -1
0:37:43.457261 INFO: Competetive: True
0:37:43.500173 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:43.544128 INFO: Using random state 196176 for train-test-split
0:37:45.682043 INFO: Test AUC: 0.587
0:37:45.682178 INFO: Train AUC: 0.603
0:37:45.682209 INFO: AUC difference: 2.75%
0:37:45.947347 INFO: Resetting torch num_threads to 80
0:37:45.954260 PROGRESS: === Extracted 149579 precursors and 866876 fragments ===
0:37:45.954643 INFO: === FDR correction performed with classifier version 9 ===
0:37:45.955077 PROGRESS: ============================= Precursor FDR =============================
0:37:45.955170 PROGRESS: Total precursors accumulated: 159
0:37:45.955228 PROGRESS: Target precursors: 158 (99.37%)
0:37:45.955277 PROGRESS: Decoy precursors: 1 (0.63%)
0:37:45.955322 PROGRESS: 
0:37:45.955364 PROGRESS: Precursor Summary:
0:37:45.956232 PROGRESS: Channel   0:	 0.050 FDR:   158; 0.010 FDR:   158; 0.001 FDR:   132
0:37:45.956317 PROGRESS: 
0:37:45.956369 PROGRESS: Protein Summary:
0:37:45.957375 PROGRESS: Channel   0:	 0.050 FDR:   154; 0.010 FDR:   154; 0.001 FDR:   130
0:37:45.957474 PROGRESS: =========================================================================
0:37:45.959748 INFO: Target number of precursors not reached yet.
0:37:46.086643 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:46.117989 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:46.201734 INFO: === skipping optimization until target number of precursors are found ===
0:37:46.202089 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:37:46.202214 INFO: Starting optimization step 3.
0:37:46.202292 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:37:46.202370 INFO: Using ng extraction backend
0:37:46.202442 PROGRESS: Extracting batch of 50233 precursors
0:37:46.297302 INFO: === Search parameters used ===
0:37:46.297689 INFO: rt_error       : 217.49164608066607
0:37:46.297747 INFO: mobility_error : 0.1
0:37:46.297794 INFO: num_candidates : 3
0:37:46.297837 INFO: ms1_error      : 30
0:37:46.297879 INFO: ms2_error      : 6.821063393969928
0:37:46.297920 INFO: fwhm_rt        : 3.0
0:37:46.297959 INFO: quant_window   : 3
0:37:46.297999 INFO: ==============================================
0:37:47.012876 INFO: performing precursor FDR with 40 features
0:37:47.013012 INFO: Decoy channel: -1
0:37:47.013040 INFO: Competetive: True
0:37:47.128563 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:47.236579 INFO: Using random state 196176 for train-test-split
0:37:51.935480 INFO: Test AUC: 0.588
0:37:51.935623 INFO: Train AUC: 0.598
0:37:51.935655 INFO: AUC difference: 1.77%
0:37:52.252452 INFO: Resetting torch num_threads to 80
0:37:52.303279 PROGRESS: === Extracted 300222 precursors and 1738709 fragments ===
0:37:52.304018 INFO: === FDR correction performed with classifier version 9 ===
0:37:52.304642 PROGRESS: ============================= Precursor FDR =============================
0:37:52.304731 PROGRESS: Total precursors accumulated: 380
0:37:52.304793 PROGRESS: Target precursors: 377 (99.21%)
0:37:52.304842 PROGRESS: Decoy precursors: 3 (0.79%)
0:37:52.304890 PROGRESS: 
0:37:52.304935 PROGRESS: Precursor Summary:
0:37:52.305923 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   377; 0.001 FDR:   315
0:37:52.306016 PROGRESS: 
0:37:52.306074 PROGRESS: Protein Summary:
0:37:52.307215 PROGRESS: Channel   0:	 0.050 FDR:   360; 0.010 FDR:   360; 0.001 FDR:   301
0:37:52.307305 PROGRESS: =========================================================================
0:37:52.311507 INFO: Target number of precursors reached.
0:37:52.438459 INFO: fragments_df: keeping 5000 of 1738709 [sum(precursor_idx_mask)=9108 sum(mass_error_mask)=1738709 stop_rank=5000
0:37:52.638364 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:52.772869 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:53.452333 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:53.452789 INFO: Using score_cutoff 11.50283293876648 (fac=0.99, q=1)
0:37:53.453086 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:53.453166 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:53.453228 INFO: Updating optimization_manager: score_cutoff        : 10.687820756149293 -> 11.50283293876648
0:37:53.453285 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:53.513539 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:53.661847 INFO: === checking if optimization conditions were reached ===
0:37:53.662340 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:37:53.665097 INFO: Updating optimization_manager: rt_error            : 217.49164608066607 -> 166.78655774993675
0:37:53.665347 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 166.7866.
0:37:53.665554 INFO: ==============================================
0:37:53.665758 INFO: Starting optimization step 4.
0:37:53.665942 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:37:53.666130 INFO: Using ng extraction backend
0:37:53.666314 PROGRESS: Extracting batch of 100097 precursors
0:37:53.851877 INFO: === Search parameters used ===
0:37:53.852225 INFO: rt_error       : 166.78655774993675
0:37:53.852281 INFO: mobility_error : 0.1
0:37:53.852326 INFO: num_candidates : 3
0:37:53.852368 INFO: ms1_error      : 30
0:37:53.852408 INFO: ms2_error      : 6.821063393969928
0:37:53.852447 INFO: fwhm_rt        : 3.0
0:37:53.852487 INFO: quant_window   : 3
0:37:53.852527 INFO: ==============================================
0:37:55.046941 INFO: performing precursor FDR with 40 features
0:37:55.047065 INFO: Decoy channel: -1
0:37:55.047091 INFO: Competetive: True
0:37:55.132029 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:55.241696 INFO: Using random state 196176 for train-test-split
0:37:59.635087 INFO: Test AUC: 0.583
0:37:59.635230 INFO: Train AUC: 0.597
0:37:59.635261 INFO: AUC difference: 2.37%
0:37:59.954313 INFO: Resetting torch num_threads to 80
0:37:59.967237 PROGRESS: === Extracted 300196 precursors and 1705891 fragments ===
0:37:59.967662 INFO: === FDR correction performed with classifier version 9 ===
0:37:59.968128 PROGRESS: ============================= Precursor FDR =============================
0:37:59.968212 PROGRESS: Total precursors accumulated: 380
0:37:59.968270 PROGRESS: Target precursors: 377 (99.21%)
0:37:59.968318 PROGRESS: Decoy precursors: 3 (0.79%)
0:37:59.968361 PROGRESS: 
0:37:59.968404 PROGRESS: Precursor Summary:
0:37:59.969312 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   377; 0.001 FDR:   287
0:37:59.969400 PROGRESS: 
0:37:59.969454 PROGRESS: Protein Summary:
0:37:59.970576 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   361; 0.001 FDR:   275
0:37:59.970667 PROGRESS: =========================================================================
0:37:59.975738 INFO: Target number of precursors reached.
0:38:00.092807 INFO: fragments_df: keeping 5000 of 1705891 [sum(precursor_idx_mask)=9087 sum(mass_error_mask)=1705891 stop_rank=5000
0:38:00.295467 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:00.424206 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:01.105910 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:38:01.106401 INFO: Using score_cutoff 13.866880534744263 (fac=0.99, q=1)
0:38:01.106731 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:38:01.106845 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:38:01.106920 INFO: Updating optimization_manager: score_cutoff        : 11.50283293876648 -> 13.866880534744263
0:38:01.106992 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:01.168350 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:01.319922 INFO: === checking if optimization conditions were reached ===
0:38:01.320256 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:38:01.323006 INFO: Updating optimization_manager: rt_error            : 166.78655774993675 -> 119.80219761574857
0:38:01.323277 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 119.8022.
0:38:01.323488 INFO: ==============================================
0:38:01.323704 INFO: Starting optimization step 5.
0:38:01.323908 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:38:01.324113 INFO: Using ng extraction backend
0:38:01.324315 PROGRESS: Extracting batch of 100097 precursors
0:38:01.506468 INFO: === Search parameters used ===
0:38:01.506976 INFO: rt_error       : 119.80219761574857
0:38:01.507137 INFO: mobility_error : 0.1
0:38:01.507283 INFO: num_candidates : 3
0:38:01.507426 INFO: ms1_error      : 30
0:38:01.507566 INFO: ms2_error      : 6.821063393969928
0:38:01.507713 INFO: fwhm_rt        : 3.0
0:38:01.507852 INFO: quant_window   : 3
0:38:01.507988 INFO: ==============================================
0:38:02.662895 INFO: performing precursor FDR with 40 features
0:38:02.663032 INFO: Decoy channel: -1
0:38:02.663059 INFO: Competetive: True
0:38:02.748145 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:02.856411 INFO: Using random state 196176 for train-test-split
0:38:07.237664 INFO: Test AUC: 0.583
0:38:07.237801 INFO: Train AUC: 0.598
0:38:07.237833 INFO: AUC difference: 2.42%
0:38:07.556805 INFO: Resetting torch num_threads to 80
0:38:07.569833 PROGRESS: === Extracted 300132 precursors and 1661432 fragments ===
0:38:07.570269 INFO: === FDR correction performed with classifier version 9 ===
0:38:07.570754 PROGRESS: ============================= Precursor FDR =============================
0:38:07.570850 PROGRESS: Total precursors accumulated: 375
0:38:07.570909 PROGRESS: Target precursors: 372 (99.20%)
0:38:07.570960 PROGRESS: Decoy precursors: 3 (0.80%)
0:38:07.571007 PROGRESS: 
0:38:07.571050 PROGRESS: Precursor Summary:
0:38:07.572002 PROGRESS: Channel   0:	 0.050 FDR:   372; 0.010 FDR:   372; 0.001 FDR:   329
0:38:07.572092 PROGRESS: 
0:38:07.572146 PROGRESS: Protein Summary:
0:38:07.573276 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   353; 0.001 FDR:   314
0:38:07.573367 PROGRESS: =========================================================================
0:38:07.578579 INFO: Target number of precursors reached.
0:38:07.694336 INFO: fragments_df: keeping 5000 of 1661432 [sum(precursor_idx_mask)=8917 sum(mass_error_mask)=1661432 stop_rank=5000
0:38:07.896869 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:08.023854 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:08.703753 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:38:08.704232 INFO: Using score_cutoff 12.742721351909637 (fac=0.99, q=1)
0:38:08.704531 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:38:08.704608 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:38:08.704661 INFO: Updating optimization_manager: score_cutoff        : 13.866880534744263 -> 12.742721351909637
0:38:08.704718 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:08.765538 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:08.924133 INFO: === checking if optimization conditions were reached ===
0:38:08.924452 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:38:08.926761 INFO: Updating optimization_manager: rt_error            : 119.80219761574857 -> 74.95323887192691
0:38:08.926874 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 74.9532.
0:38:08.926942 INFO: ==============================================
0:38:08.927013 INFO: Starting optimization step 6.
0:38:08.927073 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:38:08.927135 INFO: Using ng extraction backend
0:38:08.927196 PROGRESS: Extracting batch of 100097 precursors
0:38:09.108997 INFO: === Search parameters used ===
0:38:09.109399 INFO: rt_error       : 74.95323887192691
0:38:09.109476 INFO: mobility_error : 0.1
0:38:09.109530 INFO: num_candidates : 3
0:38:09.109575 INFO: ms1_error      : 30
0:38:09.109648 INFO: ms2_error      : 6.821063393969928
0:38:09.109693 INFO: fwhm_rt        : 3.0
0:38:09.109736 INFO: quant_window   : 3
0:38:09.109775 INFO: ==============================================
0:38:10.299228 INFO: performing precursor FDR with 40 features
0:38:10.299358 INFO: Decoy channel: -1
0:38:10.299385 INFO: Competetive: True
0:38:10.383361 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:10.495792 INFO: Using random state 196176 for train-test-split
0:38:14.926409 INFO: Test AUC: 0.583
0:38:14.926546 INFO: Train AUC: 0.598
0:38:14.926576 INFO: AUC difference: 2.42%
0:38:15.241739 INFO: Resetting torch num_threads to 80
0:38:15.254887 PROGRESS: === Extracted 299053 precursors and 1547326 fragments ===
0:38:15.255323 INFO: === FDR correction performed with classifier version 9 ===
0:38:15.255794 PROGRESS: ============================= Precursor FDR =============================
0:38:15.255881 PROGRESS: Total precursors accumulated: 331
0:38:15.255941 PROGRESS: Target precursors: 328 (99.09%)
0:38:15.255992 PROGRESS: Decoy precursors: 3 (0.91%)
0:38:15.256039 PROGRESS: 
0:38:15.256083 PROGRESS: Precursor Summary:
0:38:15.257064 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   328; 0.001 FDR:   261
0:38:15.257154 PROGRESS: 
0:38:15.257211 PROGRESS: Protein Summary:
0:38:15.258392 PROGRESS: Channel   0:	 0.050 FDR:   313; 0.010 FDR:   313; 0.001 FDR:   250
0:38:15.258486 PROGRESS: =========================================================================
0:38:15.264551 INFO: Target number of precursors reached.
0:38:15.368794 INFO: fragments_df: keeping 4371 of 1547326 [sum(precursor_idx_mask)=7556 sum(mass_error_mask)=1547326 stop_rank=4371
0:38:15.577893 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:15.980663 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:16.576045 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:38:16.576534 INFO: Using score_cutoff 13.418647964572905 (fac=0.99, q=1)
0:38:16.576839 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:38:16.576920 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:38:16.576975 INFO: Updating optimization_manager: score_cutoff        : 12.742721351909637 -> 13.418647964572905
0:38:16.577031 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:16.679356 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:16.852351 INFO: === checking if optimization conditions were reached ===
0:38:16.853473 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:38:16.856181 INFO: Updating optimization_manager: rt_error            : 74.95323887192691 -> 58.556970689498144
0:38:16.856305 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 58.5570.
0:38:16.856390 INFO: ==============================================
0:38:16.856477 INFO: Starting optimization step 7.
0:38:16.856549 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:38:16.856626 INFO: Using ng extraction backend
0:38:16.856703 PROGRESS: Extracting batch of 100097 precursors
0:38:17.038971 INFO: === Search parameters used ===
0:38:17.039306 INFO: rt_error       : 58.556970689498144
0:38:17.039378 INFO: mobility_error : 0.1
0:38:17.039427 INFO: num_candidates : 3
0:38:17.039471 INFO: ms1_error      : 30
0:38:17.039512 INFO: ms2_error      : 6.821063393969928
0:38:17.039551 INFO: fwhm_rt        : 3.0
0:38:17.039590 INFO: quant_window   : 3
0:38:17.039628 INFO: ==============================================
0:38:18.115111 INFO: performing precursor FDR with 40 features
0:38:18.115243 INFO: Decoy channel: -1
0:38:18.115268 INFO: Competetive: True
0:38:18.197596 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:18.301169 INFO: Using random state 196176 for train-test-split
0:38:23.027441 INFO: Test AUC: 0.584
0:38:23.027612 INFO: Train AUC: 0.594
0:38:23.027649 INFO: AUC difference: 1.64%
0:38:23.339731 INFO: Resetting torch num_threads to 80
0:38:23.353297 PROGRESS: === Extracted 285316 precursors and 1412219 fragments ===
0:38:23.353734 INFO: === FDR correction performed with classifier version 9 ===
0:38:23.354194 PROGRESS: ============================= Precursor FDR =============================
0:38:23.354284 PROGRESS: Total precursors accumulated: 253
0:38:23.354343 PROGRESS: Target precursors: 251 (99.21%)
0:38:23.354393 PROGRESS: Decoy precursors: 2 (0.79%)
0:38:23.354439 PROGRESS: 
0:38:23.354493 PROGRESS: Precursor Summary:
0:38:23.355391 PROGRESS: Channel   0:	 0.050 FDR:   251; 0.010 FDR:   251; 0.001 FDR:   235
0:38:23.355479 PROGRESS: 
0:38:23.355534 PROGRESS: Protein Summary:
0:38:23.356574 PROGRESS: Channel   0:	 0.050 FDR:   240; 0.010 FDR:   240; 0.001 FDR:   225
0:38:23.356662 PROGRESS: =========================================================================
0:38:23.362966 INFO: Target number of precursors reached.
0:38:23.457491 INFO: fragments_df: keeping 3332 of 1412219 [sum(precursor_idx_mask)=5466 sum(mass_error_mask)=1412219 stop_rank=3332
0:38:23.820656 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:23.936908 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:24.356835 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:38:24.357317 INFO: Using score_cutoff 15.128241119384766 (fac=0.99, q=1)
0:38:24.357623 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:38:24.357707 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:38:24.357764 INFO: Updating optimization_manager: score_cutoff        : 13.418647964572905 -> 15.128241119384766
0:38:24.357820 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:24.420052 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:24.581665 INFO: === checking if optimization conditions were reached ===
0:38:24.582076 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:38:24.583572 INFO: Updating optimization_manager: rt_error            : 58.556970689498144 -> 119.80219761574857
0:38:24.583730 INFO: Updating optimization_manager: classifier_version  : 9 -> 16
0:38:24.583862 INFO: Updating optimization_manager: score_cutoff        : 15.128241119384766 -> 12.742721351909637
0:38:24.583963 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:38:24.584059 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:38:24.584162 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 119.8022 found after 7 searches.
0:38:24.584239 INFO: ==============================================
0:38:24.584341 PROGRESS: Optimization finished for rt_error.
0:38:24.851755 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:24.914335 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:25.099552 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:38:25.099807 PROGRESS: ==============================================
0:38:25.099879 PROGRESS: ms2_error      : 6.8211
0:38:25.099936 PROGRESS: rt_error       : 119.8022
0:38:25.099985 PROGRESS: ==============================================
0:38:25.100642 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:32.192802 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:49.327463 INFO: Using ng extraction backend
0:38:49.327855 PROGRESS: Extracting batch of 11065368 precursors
0:39:04.679656 INFO: === Search parameters used ===
0:39:04.679966 INFO: rt_error       : 119.80219761574857
0:39:04.680029 INFO: mobility_error : 0.1
0:39:04.680081 INFO: num_candidates : 3
0:39:04.680124 INFO: ms1_error      : 30
0:39:04.680168 INFO: ms2_error      : 6.821063393969928
0:39:04.680211 INFO: fwhm_rt        : 3.0
0:39:04.680251 INFO: quant_window   : 3
0:39:04.680289 INFO: ==============================================
0:39:29.277077 INFO: Removed 16276201 precursors with score below cutoff 12.742721351909637
0:39:44.040312 INFO: performing precursor FDR with 40 features
0:39:44.040455 INFO: Decoy channel: -1
0:39:44.040485 INFO: Competetive: True
0:39:45.960827 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:53.059134 INFO: Using random state 458496 for train-test-split
0:44:07.809934 INFO: Test AUC: 0.604
0:44:07.810203 INFO: Train AUC: 0.606
0:44:07.810248 INFO: AUC difference: 0.22%
0:44:12.312755 INFO: Resetting torch num_threads to 80
0:44:14.044121 PROGRESS: ============================= Precursor FDR =============================
0:44:14.044489 PROGRESS: Total precursors accumulated: 55,229
0:44:14.044565 PROGRESS: Target precursors: 54,683 (99.01%)
0:44:14.044623 PROGRESS: Decoy precursors: 546 (0.99%)
0:44:14.044672 PROGRESS: 
0:44:14.044716 PROGRESS: Precursor Summary:
0:44:14.058251 PROGRESS: Channel   0:	 0.050 FDR: 54,683; 0.010 FDR: 54,683; 0.001 FDR: 35,059
0:44:14.058537 PROGRESS: 
0:44:14.058598 PROGRESS: Protein Summary:
0:44:14.080280 PROGRESS: Channel   0:	 0.050 FDR: 9,370; 0.010 FDR: 9,370; 0.001 FDR: 6,716
0:44:14.080529 PROGRESS: =========================================================================
0:44:14.193795 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/psm.parquet
0:44:14.315558 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/frag.parquet
0:44:14.492467 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
0:44:14.952421 PROGRESS: 
0:44:14.952611 INFO: Quantification results path: alphadia_zenoswath8600/library/quant
0:44:14.952695 INFO: Creating folder alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/figures
0:44:14.952916 INFO: Initializing TimingManager
0:44:14.953694 INFO: Initializing RawFileManager
0:46:37.570250 INFO: Determining DIA cycle
0:46:37.585104 INFO: Found cycle with start 0.00 min and length 86.
0:46:37.820697 INFO: RT (min)            : 0.0 - 55.4
0:46:37.820798 INFO: RT duration (sec)   : 3325.7
0:46:37.820829 INFO: RT duration (min)   : 55.4
0:46:37.820856 INFO: Cycle len (scans)   : 86
0:46:37.820875 INFO: Cycle len (sec)     : 1.90
0:46:37.820895 INFO: Number of cycles    : 1747
0:46:37.820913 INFO: MS2 range (m/z)     : 399.5 - 903.5
0:46:37.820942 INFO: Creating DIA data object took: 142.86715126037598
0:46:39.114232 INFO: Creating DIA data NG object took: 1.2931628227233887
0:46:40.298469 INFO: Initializing CalibrationManager
0:46:40.298763 INFO: Setting up calibration estimators ..
0:46:40.298833 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:46:40.298934 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'}' ..
0:46:40.299107 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:46:40.299165 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:46:40.299217 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}}' ..
0:46:40.299280 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:46:40.299333 INFO: Done setting up calibration estimators.
0:46:40.299500 INFO: Initializing OptimizationManager
0:46:40.299678 INFO: initial parameter: ms1_error = 30
0:46:40.299736 INFO: initial parameter: ms2_error = 30
0:46:40.299784 INFO: initial parameter: rt_error = 1662.873046875
0:46:40.299828 INFO: initial parameter: mobility_error = 0.1
0:46:40.299871 INFO: initial parameter: num_candidates = 1
0:46:40.299911 INFO: initial parameter: fwhm_rt = 5
0:46:40.299953 INFO: initial parameter: fwhm_mobility = 0.01
0:46:40.299992 INFO: initial parameter: score_cutoff = 0
0:46:40.300033 INFO: initial parameter: classifier_version = -1
0:46:40.300111 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
0:46:40.300443 INFO: FDRManager: loading saved state not requested, will be initialized.
0:46:40.300484 INFO: Initializing FDRManager
0:46:40.300526 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:46:41.665372 PROGRESS: Initializing spectral library: 5,608,555 target precursors potentially observable (87,724 removed)
0:46:42.522044 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:46:42.522398 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 1662.873046875
0:46:42.522512 PROGRESS: Starting initial search for precursors.
0:46:42.522608 INFO: Starting optimization step 0.
0:46:42.522683 PROGRESS: === Extracting elution groups 0 to 200 ===
0:46:42.522762 INFO: Using ng extraction backend
0:46:42.522846 PROGRESS: Extracting batch of 394 precursors
0:46:42.525207 INFO: === Search parameters used ===
0:46:42.525354 INFO: rt_error       : 1662.873046875
0:46:42.525406 INFO: mobility_error : 0.1
0:46:42.525450 INFO: num_candidates : 1
0:46:42.525506 INFO: ms1_error      : 30
0:46:42.525550 INFO: ms2_error      : 30
0:46:42.525590 INFO: fwhm_rt        : 5
0:46:42.525630 INFO: quant_window   : 3
0:46:42.525670 INFO: ==============================================
0:46:42.550762 INFO: performing precursor FDR with 40 features
0:46:42.550838 INFO: Decoy channel: -1
0:46:42.550866 INFO: Competetive: True
0:46:42.551850 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:42.554174 INFO: Using random state 840331 for train-test-split
0:46:42.561433 INFO: Test AUC: 0.334
0:46:42.561499 INFO: Train AUC: 0.515
0:46:42.561530 INFO: AUC difference: 35.17%
0:46:42.561553 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:42.779092 INFO: Resetting torch num_threads to 80
0:46:42.780510 PROGRESS: === Extracted 394 precursors and 2191 fragments ===
0:46:42.780875 INFO: === FDR correction performed with classifier version -1 ===
0:46:42.781321 PROGRESS: ============================= Precursor FDR =============================
0:46:42.781406 PROGRESS: Total precursors accumulated: 0
0:46:42.781475 PROGRESS: Target precursors: 0 (0.00%)
0:46:42.781530 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:42.781579 PROGRESS: 
0:46:42.781627 PROGRESS: Precursor Summary:
0:46:42.781737 PROGRESS: 
0:46:42.781799 PROGRESS: Protein Summary:
0:46:42.781872 PROGRESS: =========================================================================
0:46:42.782060 INFO: Target number of precursors not reached yet.
0:46:42.844308 INFO: Starting optimization step 1.
0:46:42.844524 PROGRESS: === Extracting elution groups 200 to 600 ===
0:46:42.844611 INFO: Using ng extraction backend
0:46:42.844674 PROGRESS: Extracting batch of 782 precursors
0:46:42.848533 INFO: === Search parameters used ===
0:46:42.848714 INFO: rt_error       : 1662.873046875
0:46:42.848768 INFO: mobility_error : 0.1
0:46:42.848814 INFO: num_candidates : 1
0:46:42.848860 INFO: ms1_error      : 30
0:46:42.848904 INFO: ms2_error      : 30
0:46:42.848946 INFO: fwhm_rt        : 5
0:46:42.848991 INFO: quant_window   : 3
0:46:42.849039 INFO: ==============================================
0:46:42.875305 INFO: performing precursor FDR with 40 features
0:46:42.875384 INFO: Decoy channel: -1
0:46:42.875410 INFO: Competetive: True
0:46:42.878478 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:42.880092 INFO: Using random state 919594 for train-test-split
0:46:42.888523 INFO: Test AUC: 0.466
0:46:42.888584 INFO: Train AUC: 0.510
0:46:42.888613 INFO: AUC difference: 8.61%
0:46:42.888635 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:44.235029 INFO: Resetting torch num_threads to 80
0:46:44.237437 PROGRESS: === Extracted 1175 precursors and 6551 fragments ===
0:46:44.237803 INFO: === FDR correction performed with classifier version -1 ===
0:46:44.238233 PROGRESS: ============================= Precursor FDR =============================
0:46:44.238319 PROGRESS: Total precursors accumulated: 0
0:46:44.238380 PROGRESS: Target precursors: 0 (0.00%)
0:46:44.238431 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:44.238480 PROGRESS: 
0:46:44.238525 PROGRESS: Precursor Summary:
0:46:44.238634 PROGRESS: 
0:46:44.238695 PROGRESS: Protein Summary:
0:46:44.238775 PROGRESS: =========================================================================
0:46:44.238997 INFO: Target number of precursors not reached yet.
0:46:44.302475 INFO: Starting optimization step 2.
0:46:44.302681 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:46:44.302764 INFO: Using ng extraction backend
0:46:44.302824 PROGRESS: Extracting batch of 1565 precursors
0:46:44.308418 INFO: === Search parameters used ===
0:46:44.308541 INFO: rt_error       : 1662.873046875
0:46:44.308591 INFO: mobility_error : 0.1
0:46:44.308635 INFO: num_candidates : 1
0:46:44.308680 INFO: ms1_error      : 30
0:46:44.308723 INFO: ms2_error      : 30
0:46:44.308764 INFO: fwhm_rt        : 5
0:46:44.308804 INFO: quant_window   : 3
0:46:44.308843 INFO: ==============================================
0:46:44.347730 INFO: performing precursor FDR with 40 features
0:46:44.347824 INFO: Decoy channel: -1
0:46:44.347850 INFO: Competetive: True
0:46:44.351529 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:44.353601 INFO: Using random state 739293 for train-test-split
0:46:44.365644 INFO: Test AUC: 0.534
0:46:44.365713 INFO: Train AUC: 0.495
0:46:44.365742 INFO: AUC difference: 7.73%
0:46:44.365765 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:44.581606 INFO: Resetting torch num_threads to 80
0:46:44.584539 PROGRESS: === Extracted 2736 precursors and 15483 fragments ===
0:46:44.584892 INFO: === FDR correction performed with classifier version -1 ===
0:46:44.585347 PROGRESS: ============================= Precursor FDR =============================
0:46:44.585436 PROGRESS: Total precursors accumulated: 1
0:46:44.585509 PROGRESS: Target precursors: 1 (100.00%)
0:46:44.585563 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:44.585610 PROGRESS: 
0:46:44.585662 PROGRESS: Precursor Summary:
0:46:44.586647 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:46:44.586738 PROGRESS: 
0:46:44.586796 PROGRESS: Protein Summary:
0:46:44.587874 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:46:44.587969 PROGRESS: =========================================================================
0:46:44.589672 INFO: Target number of precursors not reached yet.
0:46:44.658850 INFO: Starting optimization step 3.
0:46:44.659073 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:46:44.659159 INFO: Using ng extraction backend
0:46:44.659220 PROGRESS: Extracting batch of 3140 precursors
0:46:44.667250 INFO: === Search parameters used ===
0:46:44.667395 INFO: rt_error       : 1662.873046875
0:46:44.667448 INFO: mobility_error : 0.1
0:46:44.667493 INFO: num_candidates : 1
0:46:44.667534 INFO: ms1_error      : 30
0:46:44.667574 INFO: ms2_error      : 30
0:46:44.667615 INFO: fwhm_rt        : 5
0:46:44.667659 INFO: quant_window   : 3
0:46:44.667699 INFO: ==============================================
0:46:44.723444 INFO: performing precursor FDR with 40 features
0:46:44.723549 INFO: Decoy channel: -1
0:46:44.723575 INFO: Competetive: True
0:46:44.727900 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:44.730585 INFO: Using random state 449096 for train-test-split
0:46:44.749710 INFO: Test AUC: 0.506
0:46:44.749797 INFO: Train AUC: 0.499
0:46:44.749827 INFO: AUC difference: 1.25%
0:46:44.970846 INFO: Resetting torch num_threads to 80
0:46:44.977861 PROGRESS: === Extracted 5873 precursors and 33566 fragments ===
0:46:44.978262 INFO: === FDR correction performed with classifier version -1 ===
0:46:44.978711 PROGRESS: ============================= Precursor FDR =============================
0:46:44.978797 PROGRESS: Total precursors accumulated: 0
0:46:44.978856 PROGRESS: Target precursors: 0 (0.00%)
0:46:44.978904 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:44.978951 PROGRESS: 
0:46:44.978996 PROGRESS: Precursor Summary:
0:46:44.979107 PROGRESS: 
0:46:44.979170 PROGRESS: Protein Summary:
0:46:44.979242 PROGRESS: =========================================================================
0:46:44.979583 INFO: Target number of precursors not reached yet.
0:46:45.058404 INFO: Starting optimization step 4.
0:46:45.058633 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:46:45.058728 INFO: Using ng extraction backend
0:46:45.058791 PROGRESS: Extracting batch of 6271 precursors
0:46:45.072082 INFO: === Search parameters used ===
0:46:45.072251 INFO: rt_error       : 1662.873046875
0:46:45.072305 INFO: mobility_error : 0.1
0:46:45.072348 INFO: num_candidates : 1
0:46:45.072390 INFO: ms1_error      : 30
0:46:45.072433 INFO: ms2_error      : 30
0:46:45.072478 INFO: fwhm_rt        : 5
0:46:45.072526 INFO: quant_window   : 3
0:46:45.072568 INFO: ==============================================
0:46:45.167668 INFO: performing precursor FDR with 40 features
0:46:45.167780 INFO: Decoy channel: -1
0:46:45.167807 INFO: Competetive: True
0:46:45.175166 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:45.179911 INFO: Using random state 260646 for train-test-split
0:46:45.217023 INFO: Test AUC: 0.517
0:46:45.217126 INFO: Train AUC: 0.491
0:46:45.217156 INFO: AUC difference: 5.31%
0:46:45.217178 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:45.441773 INFO: Resetting torch num_threads to 80
0:46:45.446420 PROGRESS: === Extracted 12128 precursors and 69617 fragments ===
0:46:45.446810 INFO: === FDR correction performed with classifier version -1 ===
0:46:45.447251 PROGRESS: ============================= Precursor FDR =============================
0:46:45.447342 PROGRESS: Total precursors accumulated: 0
0:46:45.447403 PROGRESS: Target precursors: 0 (0.00%)
0:46:45.447452 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:45.447500 PROGRESS: 
0:46:45.447546 PROGRESS: Precursor Summary:
0:46:45.447656 PROGRESS: 
0:46:45.447719 PROGRESS: Protein Summary:
0:46:45.447789 PROGRESS: =========================================================================
0:46:45.448098 INFO: Target number of precursors not reached yet.
0:46:45.540255 INFO: Starting optimization step 5.
0:46:45.540489 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:46:45.540572 INFO: Using ng extraction backend
0:46:45.540634 PROGRESS: Extracting batch of 12568 precursors
0:46:45.565166 INFO: === Search parameters used ===
0:46:45.565359 INFO: rt_error       : 1662.873046875
0:46:45.565413 INFO: mobility_error : 0.1
0:46:45.565459 INFO: num_candidates : 1
0:46:45.565526 INFO: ms1_error      : 30
0:46:45.565572 INFO: ms2_error      : 30
0:46:45.565614 INFO: fwhm_rt        : 5
0:46:45.565654 INFO: quant_window   : 3
0:46:45.565695 INFO: ==============================================
0:46:45.713193 INFO: performing precursor FDR with 40 features
0:46:45.713323 INFO: Decoy channel: -1
0:46:45.713350 INFO: Competetive: True
0:46:45.724336 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:45.731075 INFO: Using random state 758980 for train-test-split
0:46:45.917927 INFO: Test AUC: 0.512
0:46:45.918056 INFO: Train AUC: 0.509
0:46:45.918087 INFO: AUC difference: 0.68%
0:46:46.154412 INFO: Resetting torch num_threads to 80
0:46:46.161360 PROGRESS: === Extracted 24681 precursors and 142074 fragments ===
0:46:46.161821 INFO: === FDR correction performed with classifier version -1 ===
0:46:46.162380 PROGRESS: ============================= Precursor FDR =============================
0:46:46.162470 PROGRESS: Total precursors accumulated: 2
0:46:46.162530 PROGRESS: Target precursors: 2 (100.00%)
0:46:46.162581 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:46.162628 PROGRESS: 
0:46:46.162673 PROGRESS: Precursor Summary:
0:46:46.163587 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:46:46.163682 PROGRESS: 
0:46:46.163739 PROGRESS: Protein Summary:
0:46:46.164760 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:46:46.164850 PROGRESS: =========================================================================
0:46:46.165346 INFO: Target number of precursors not reached yet.
0:46:46.278075 INFO: Starting optimization step 6.
0:46:46.278347 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:46:46.278825 INFO: Using ng extraction backend
0:46:46.278897 PROGRESS: Extracting batch of 25144 precursors
0:46:46.324667 INFO: === Search parameters used ===
0:46:46.324969 INFO: rt_error       : 1662.873046875
0:46:46.325022 INFO: mobility_error : 0.1
0:46:46.325068 INFO: num_candidates : 1
0:46:46.325115 INFO: ms1_error      : 30
0:46:46.325158 INFO: ms2_error      : 30
0:46:46.325200 INFO: fwhm_rt        : 5
0:46:46.325240 INFO: quant_window   : 3
0:46:46.325282 INFO: ==============================================
0:46:46.576266 INFO: performing precursor FDR with 40 features
0:46:46.576398 INFO: Decoy channel: -1
0:46:46.576424 INFO: Competetive: True
0:46:46.597609 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:46.610484 INFO: Using random state 494139 for train-test-split
0:46:47.212511 INFO: Test AUC: 0.550
0:46:47.212621 INFO: Train AUC: 0.564
0:46:47.212651 INFO: AUC difference: 2.45%
0:46:47.456605 INFO: Resetting torch num_threads to 80
0:46:47.476352 PROGRESS: === Extracted 49783 precursors and 286458 fragments ===
0:46:47.476835 INFO: === FDR correction performed with classifier version -1 ===
0:46:47.477310 PROGRESS: ============================= Precursor FDR =============================
0:46:47.477397 PROGRESS: Total precursors accumulated: 0
0:46:47.477462 PROGRESS: Target precursors: 0 (0.00%)
0:46:47.477525 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:47.477573 PROGRESS: 
0:46:47.477618 PROGRESS: Precursor Summary:
0:46:47.477731 PROGRESS: 
0:46:47.477793 PROGRESS: Protein Summary:
0:46:47.477865 PROGRESS: =========================================================================
0:46:47.478874 INFO: Target number of precursors not reached yet.
0:46:47.639751 INFO: Starting optimization step 7.
0:46:47.640026 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:46:47.640119 INFO: Using ng extraction backend
0:46:47.640185 PROGRESS: Extracting batch of 50233 precursors
0:46:47.733818 INFO: === Search parameters used ===
0:46:47.734249 INFO: rt_error       : 1662.873046875
0:46:47.734309 INFO: mobility_error : 0.1
0:46:47.734356 INFO: num_candidates : 1
0:46:47.734403 INFO: ms1_error      : 30
0:46:47.734448 INFO: ms2_error      : 30
0:46:47.734490 INFO: fwhm_rt        : 5
0:46:47.734530 INFO: quant_window   : 3
0:46:47.734571 INFO: ==============================================
0:46:48.190737 INFO: performing precursor FDR with 40 features
0:46:48.190869 INFO: Decoy channel: -1
0:46:48.190896 INFO: Competetive: True
0:46:48.236057 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:48.263066 INFO: Using random state 99874 for train-test-split
0:46:49.656020 INFO: Test AUC: 0.576
0:46:49.656142 INFO: Train AUC: 0.591
0:46:49.656174 INFO: AUC difference: 2.58%
0:46:49.910782 INFO: Resetting torch num_threads to 80
0:46:49.933649 PROGRESS: === Extracted 99921 precursors and 574317 fragments ===
0:46:49.934224 INFO: === FDR correction performed with classifier version -1 ===
0:46:49.934780 PROGRESS: ============================= Precursor FDR =============================
0:46:49.934878 PROGRESS: Total precursors accumulated: 255
0:46:49.934939 PROGRESS: Target precursors: 253 (99.22%)
0:46:49.934988 PROGRESS: Decoy precursors: 2 (0.78%)
0:46:49.935032 PROGRESS: 
0:46:49.935074 PROGRESS: Precursor Summary:
0:46:49.936016 PROGRESS: Channel   0:	 0.050 FDR:   253; 0.010 FDR:   253; 0.001 FDR:     0
0:46:49.936105 PROGRESS: 
0:46:49.936160 PROGRESS: Protein Summary:
0:46:49.937206 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:   243; 0.001 FDR:     0
0:46:49.937292 PROGRESS: =========================================================================
0:46:49.939471 INFO: Target number of precursors reached.
0:46:49.981620 INFO: fragments_df: keeping 2478 of 574317 [sum(precursor_idx_mask)=2732 sum(mass_error_mask)=574317 stop_rank=2478
0:46:50.185943 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:50.340282 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:50.681084 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:46:50.681811 INFO: Using score_cutoff 13.781623439025878 (fac=0.99, q=1)
0:46:50.682192 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:46:50.682277 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:46:50.682333 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.781623439025878
0:46:50.682391 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:50.751365 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:50.904238 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:46:50.904674 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:46:50.904790 INFO: Starting optimization step 8.
0:46:50.904886 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:46:50.904994 INFO: Using ng extraction backend
0:46:50.905092 PROGRESS: Extracting batch of 100097 precursors
0:46:51.089162 INFO: === Search parameters used ===
0:46:51.089581 INFO: rt_error       : 1662.873046875
0:46:51.089640 INFO: mobility_error : 0.1
0:46:51.089690 INFO: num_candidates : 3
0:46:51.089737 INFO: ms1_error      : 30
0:46:51.089781 INFO: ms2_error      : 30
0:46:51.089825 INFO: fwhm_rt        : 3.0
0:46:51.089868 INFO: quant_window   : 3
0:46:51.089913 INFO: ==============================================
0:46:52.713558 INFO: performing precursor FDR with 40 features
0:46:52.713744 INFO: Decoy channel: -1
0:46:52.713773 INFO: Competetive: True
0:46:52.801401 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:52.915677 INFO: Using random state 286463 for train-test-split
0:46:57.348450 INFO: Test AUC: 0.585
0:46:57.348579 INFO: Train AUC: 0.596
0:46:57.348612 INFO: AUC difference: 1.85%
0:46:57.680255 INFO: Resetting torch num_threads to 80
0:46:57.702736 PROGRESS: === Extracted 299819 precursors and 1681768 fragments ===
0:46:57.703281 INFO: === FDR correction performed with classifier version 7 ===
0:46:57.703850 PROGRESS: ============================= Precursor FDR =============================
0:46:57.703949 PROGRESS: Total precursors accumulated: 244
0:46:57.704015 PROGRESS: Target precursors: 242 (99.18%)
0:46:57.704069 PROGRESS: Decoy precursors: 2 (0.82%)
0:46:57.704122 PROGRESS: 
0:46:57.704175 PROGRESS: Precursor Summary:
0:46:57.705237 PROGRESS: Channel   0:	 0.050 FDR:   242; 0.010 FDR:   242; 0.001 FDR:     0
0:46:57.705337 PROGRESS: 
0:46:57.705409 PROGRESS: Protein Summary:
0:46:57.706722 PROGRESS: Channel   0:	 0.050 FDR:   230; 0.010 FDR:   230; 0.001 FDR:     0
0:46:57.706824 PROGRESS: =========================================================================
0:46:57.719196 INFO: Target number of precursors reached.
0:46:57.841061 INFO: fragments_df: keeping 3469 of 1681768 [sum(precursor_idx_mask)=5714 sum(mass_error_mask)=1681768 stop_rank=3469
0:46:58.049494 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:58.157294 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:58.614198 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:58.614767 INFO: Using score_cutoff 17.296142340660094 (fac=0.99, q=1)
0:46:58.615104 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:58.615185 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:58.615242 INFO: Updating optimization_manager: score_cutoff        : 13.781623439025878 -> 17.296142340660094
0:46:58.615308 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:58.676152 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:58.832713 INFO: === checking if optimization conditions were reached ===
0:46:58.833109 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:46:58.835898 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.836823014739446
0:46:58.836025 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 6.8368.
0:46:58.836104 INFO: ==============================================
0:46:58.836201 INFO: Starting optimization step 9.
0:46:58.836275 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:46:58.836368 INFO: Using ng extraction backend
0:46:58.836446 PROGRESS: Extracting batch of 100097 precursors
0:46:59.014068 INFO: === Search parameters used ===
0:46:59.014407 INFO: rt_error       : 1662.873046875
0:46:59.014463 INFO: mobility_error : 0.1
0:46:59.014510 INFO: num_candidates : 3
0:46:59.014554 INFO: ms1_error      : 30
0:46:59.014597 INFO: ms2_error      : 6.836823014739446
0:46:59.014639 INFO: fwhm_rt        : 3.0
0:46:59.014679 INFO: quant_window   : 3
0:46:59.014725 INFO: ==============================================
0:47:00.998993 INFO: performing precursor FDR with 40 features
0:47:00.999119 INFO: Decoy channel: -1
0:47:00.999146 INFO: Competetive: True
0:47:01.119021 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:01.287171 INFO: Using random state 286463 for train-test-split
0:47:05.397225 INFO: Test AUC: 0.583
0:47:05.397366 INFO: Train AUC: 0.594
0:47:05.397397 INFO: AUC difference: 1.92%
0:47:05.712134 INFO: Resetting torch num_threads to 80
0:47:05.725162 PROGRESS: === Extracted 300279 precursors and 1819792 fragments ===
0:47:05.725584 INFO: === FDR correction performed with classifier version 7 ===
0:47:05.726056 PROGRESS: ============================= Precursor FDR =============================
0:47:05.726144 PROGRESS: Total precursors accumulated: 321
0:47:05.726204 PROGRESS: Target precursors: 318 (99.07%)
0:47:05.726254 PROGRESS: Decoy precursors: 3 (0.93%)
0:47:05.726301 PROGRESS: 
0:47:05.726346 PROGRESS: Precursor Summary:
0:47:05.727274 PROGRESS: Channel   0:	 0.050 FDR:   318; 0.010 FDR:   318; 0.001 FDR:   216
0:47:05.727362 PROGRESS: 
0:47:05.727417 PROGRESS: Protein Summary:
0:47:05.728502 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   303; 0.001 FDR:   208
0:47:05.728594 PROGRESS: =========================================================================
0:47:05.733361 INFO: Target number of precursors reached.
0:47:05.854883 INFO: fragments_df: keeping 4550 of 1819792 [sum(precursor_idx_mask)=7796 sum(mass_error_mask)=1819792 stop_rank=4550
0:47:06.062495 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:06.185766 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:06.790698 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:06.791139 INFO: Using score_cutoff 11.516263003063202 (fac=0.99, q=1)
0:47:06.791430 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:06.791510 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:06.791565 INFO: Updating optimization_manager: score_cutoff        : 17.296142340660094 -> 11.516263003063202
0:47:06.791619 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:06.852058 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:07.009216 INFO: === checking if optimization conditions were reached ===
0:47:07.009621 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:47:07.012621 INFO: Updating optimization_manager: ms2_error           : 6.836823014739446 -> 6.834620391558377
0:47:07.012773 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 6.8346.
0:47:07.012884 INFO: ==============================================
0:47:07.012980 INFO: Starting optimization step 10.
0:47:07.013061 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:47:07.013147 INFO: Using ng extraction backend
0:47:07.013233 PROGRESS: Extracting batch of 100097 precursors
0:47:07.189018 INFO: === Search parameters used ===
0:47:07.189346 INFO: rt_error       : 1662.873046875
0:47:07.189401 INFO: mobility_error : 0.1
0:47:07.189448 INFO: num_candidates : 3
0:47:07.189501 INFO: ms1_error      : 30
0:47:07.189543 INFO: ms2_error      : 6.834620391558377
0:47:07.189586 INFO: fwhm_rt        : 3.0
0:47:07.189626 INFO: quant_window   : 3
0:47:07.189664 INFO: ==============================================
0:47:08.607567 INFO: performing precursor FDR with 40 features
0:47:08.607691 INFO: Decoy channel: -1
0:47:08.607729 INFO: Competetive: True
0:47:08.690772 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:08.796352 INFO: Using random state 286463 for train-test-split
0:47:13.268902 INFO: Test AUC: 0.580
0:47:13.269033 INFO: Train AUC: 0.594
0:47:13.269065 INFO: AUC difference: 2.28%
0:47:13.588326 INFO: Resetting torch num_threads to 80
0:47:13.601332 PROGRESS: === Extracted 300279 precursors and 1819694 fragments ===
0:47:13.601758 INFO: === FDR correction performed with classifier version 7 ===
0:47:13.602226 PROGRESS: ============================= Precursor FDR =============================
0:47:13.602315 PROGRESS: Total precursors accumulated: 298
0:47:13.602375 PROGRESS: Target precursors: 296 (99.33%)
0:47:13.602426 PROGRESS: Decoy precursors: 2 (0.67%)
0:47:13.602485 PROGRESS: 
0:47:13.602535 PROGRESS: Precursor Summary:
0:47:13.603456 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   296; 0.001 FDR:   245
0:47:13.603544 PROGRESS: 
0:47:13.603599 PROGRESS: Protein Summary:
0:47:13.604692 PROGRESS: Channel   0:	 0.050 FDR:   281; 0.010 FDR:   281; 0.001 FDR:   236
0:47:13.604781 PROGRESS: =========================================================================
0:47:13.609508 INFO: Target number of precursors reached.
0:47:13.731186 INFO: fragments_df: keeping 4297 of 1819694 [sum(precursor_idx_mask)=7327 sum(mass_error_mask)=1819694 stop_rank=4297
0:47:13.938624 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:14.066099 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:14.586905 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:14.587351 INFO: Using score_cutoff 11.814880424022673 (fac=0.99, q=1)
0:47:14.587640 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:14.587720 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:14.587775 INFO: Updating optimization_manager: score_cutoff        : 11.516263003063202 -> 11.814880424022673
0:47:14.587828 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:14.654073 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:14.811536 INFO: === checking if optimization conditions were reached ===
0:47:14.811898 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:47:14.813074 INFO: Updating optimization_manager: ms2_error           : 6.834620391558377 -> 6.836823014739446
0:47:14.813222 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
0:47:14.813334 INFO: Updating optimization_manager: score_cutoff        : 11.814880424022673 -> 11.516263003063202
0:47:14.813436 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:14.813552 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:14.813655 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 6.8368 found after 3 searches.
0:47:14.813731 INFO: ==============================================
0:47:14.813815 PROGRESS: Optimization finished for ms2_error.
0:47:15.025344 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:15.086933 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:15.306900 INFO: Starting optimization step 0.
0:47:15.307158 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:47:15.307252 INFO: Using ng extraction backend
0:47:15.307328 PROGRESS: Extracting batch of 100097 precursors
0:47:15.482198 INFO: === Search parameters used ===
0:47:15.482523 INFO: rt_error       : 1662.873046875
0:47:15.482581 INFO: mobility_error : 0.1
0:47:15.482630 INFO: num_candidates : 3
0:47:15.482676 INFO: ms1_error      : 30
0:47:15.482719 INFO: ms2_error      : 6.836823014739446
0:47:15.482774 INFO: fwhm_rt        : 3.0
0:47:15.482818 INFO: quant_window   : 3
0:47:15.482859 INFO: ==============================================
0:47:16.871448 INFO: performing precursor FDR with 40 features
0:47:16.871576 INFO: Decoy channel: -1
0:47:16.871603 INFO: Competetive: True
0:47:16.954827 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:17.062515 INFO: Using random state 449273 for train-test-split
0:47:21.642597 INFO: Test AUC: 0.588
0:47:21.642747 INFO: Train AUC: 0.599
0:47:21.642782 INFO: AUC difference: 1.82%
0:47:21.971164 INFO: Resetting torch num_threads to 80
0:47:21.982847 PROGRESS: === Extracted 300279 precursors and 1820659 fragments ===
0:47:21.983242 INFO: === FDR correction performed with classifier version 9 ===
0:47:21.983709 PROGRESS: ============================= Precursor FDR =============================
0:47:21.983798 PROGRESS: Total precursors accumulated: 237
0:47:21.983857 PROGRESS: Target precursors: 235 (99.16%)
0:47:21.983907 PROGRESS: Decoy precursors: 2 (0.84%)
0:47:21.983951 PROGRESS: 
0:47:21.983994 PROGRESS: Precursor Summary:
0:47:21.984875 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:   235; 0.001 FDR:   131
0:47:21.984962 PROGRESS: 
0:47:21.985016 PROGRESS: Protein Summary:
0:47:21.986062 PROGRESS: Channel   0:	 0.050 FDR:   226; 0.010 FDR:   226; 0.001 FDR:   130
0:47:21.986155 PROGRESS: =========================================================================
0:47:21.991009 INFO: Target number of precursors reached.
0:47:22.108125 INFO: fragments_df: keeping 3509 of 1820659 [sum(precursor_idx_mask)=5914 sum(mass_error_mask)=1820659 stop_rank=3509
0:47:22.313969 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:22.426472 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:22.907747 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:22.908265 INFO: Using score_cutoff 16.011373998641968 (fac=0.99, q=1)
0:47:22.908603 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:22.908700 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:22.908763 INFO: Updating optimization_manager: score_cutoff        : 11.516263003063202 -> 16.011373998641968
0:47:22.908829 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:22.973650 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:23.114291 INFO: === checking if optimization conditions were reached ===
0:47:23.114612 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:47:23.116529 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 68.21582671817131
0:47:23.116636 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 68.2158.
0:47:23.116706 INFO: ==============================================
0:47:23.116775 INFO: Starting optimization step 1.
0:47:23.116834 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:47:23.116897 INFO: Using ng extraction backend
0:47:23.116954 PROGRESS: Extracting batch of 100097 precursors
0:47:23.293650 INFO: === Search parameters used ===
0:47:23.294044 INFO: rt_error       : 68.21582671817131
0:47:23.294111 INFO: mobility_error : 0.1
0:47:23.294184 INFO: num_candidates : 3
0:47:23.294243 INFO: ms1_error      : 30
0:47:23.294297 INFO: ms2_error      : 6.836823014739446
0:47:23.294349 INFO: fwhm_rt        : 3.0
0:47:23.294400 INFO: quant_window   : 3
0:47:23.294452 INFO: ==============================================
0:47:24.484180 INFO: performing precursor FDR with 40 features
0:47:24.484342 INFO: Decoy channel: -1
0:47:24.484375 INFO: Competetive: True
0:47:24.578178 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:24.686329 INFO: Using random state 449273 for train-test-split
0:47:29.341521 INFO: Test AUC: 0.584
0:47:29.341672 INFO: Train AUC: 0.596
0:47:29.341706 INFO: AUC difference: 2.02%
0:47:29.662708 INFO: Resetting torch num_threads to 80
0:47:29.676123 PROGRESS: === Extracted 297143 precursors and 1514339 fragments ===
0:47:29.676519 INFO: === FDR correction performed with classifier version 9 ===
0:47:29.676987 PROGRESS: ============================= Precursor FDR =============================
0:47:29.677074 PROGRESS: Total precursors accumulated: 393
0:47:29.677133 PROGRESS: Target precursors: 390 (99.24%)
0:47:29.677192 PROGRESS: Decoy precursors: 3 (0.76%)
0:47:29.677238 PROGRESS: 
0:47:29.677282 PROGRESS: Precursor Summary:
0:47:29.678226 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   390; 0.001 FDR:   322
0:47:29.678317 PROGRESS: 
0:47:29.678370 PROGRESS: Protein Summary:
0:47:29.679500 PROGRESS: Channel   0:	 0.050 FDR:   374; 0.010 FDR:   374; 0.001 FDR:   309
0:47:29.679593 PROGRESS: =========================================================================
0:47:29.684697 INFO: Target number of precursors reached.
0:47:29.788736 INFO: fragments_df: keeping 4803 of 1514339 [sum(precursor_idx_mask)=8614 sum(mass_error_mask)=1514339 stop_rank=4803
0:47:29.993901 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:30.118650 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:30.792144 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:30.792579 INFO: Using score_cutoff 6.98098559103012 (fac=0.99, q=1)
0:47:30.792869 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:30.792948 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:30.793003 INFO: Updating optimization_manager: score_cutoff        : 16.011373998641968 -> 6.98098559103012
0:47:30.793059 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:30.853196 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:31.027453 INFO: === checking if optimization conditions were reached ===
0:47:31.027803 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:47:31.030276 INFO: Updating optimization_manager: rt_error            : 68.21582671817131 -> 51.05307177671688
0:47:31.030400 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 51.0531.
0:47:31.030480 INFO: ==============================================
0:47:31.030563 INFO: Starting optimization step 2.
0:47:31.030631 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:47:31.030702 INFO: Using ng extraction backend
0:47:31.030772 PROGRESS: Extracting batch of 100097 precursors
0:47:31.208598 INFO: === Search parameters used ===
0:47:31.208922 INFO: rt_error       : 51.05307177671688
0:47:31.208999 INFO: mobility_error : 0.1
0:47:31.209051 INFO: num_candidates : 3
0:47:31.209095 INFO: ms1_error      : 30
0:47:31.209137 INFO: ms2_error      : 6.836823014739446
0:47:31.209183 INFO: fwhm_rt        : 3.0
0:47:31.209225 INFO: quant_window   : 3
0:47:31.209268 INFO: ==============================================
0:47:32.320350 INFO: performing precursor FDR with 40 features
0:47:32.320477 INFO: Decoy channel: -1
0:47:32.320505 INFO: Competetive: True
0:47:32.401671 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:32.529211 INFO: Using random state 449273 for train-test-split
0:47:37.417238 INFO: Test AUC: 0.583
0:47:37.417727 INFO: Train AUC: 0.596
0:47:37.417767 INFO: AUC difference: 2.18%
0:47:37.725571 INFO: Resetting torch num_threads to 80
0:47:37.738212 PROGRESS: === Extracted 281566 precursors and 1389766 fragments ===
0:47:37.738619 INFO: === FDR correction performed with classifier version 9 ===
0:47:37.739103 PROGRESS: ============================= Precursor FDR =============================
0:47:37.739192 PROGRESS: Total precursors accumulated: 336
0:47:37.739252 PROGRESS: Target precursors: 333 (99.11%)
0:47:37.739305 PROGRESS: Decoy precursors: 3 (0.89%)
0:47:37.739352 PROGRESS: 
0:47:37.739396 PROGRESS: Precursor Summary:
0:47:37.740354 PROGRESS: Channel   0:	 0.050 FDR:   333; 0.010 FDR:   333; 0.001 FDR:   313
0:47:37.740445 PROGRESS: 
0:47:37.740500 PROGRESS: Protein Summary:
0:47:37.741648 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   321; 0.001 FDR:   301
0:47:37.741741 PROGRESS: =========================================================================
0:47:37.746754 INFO: Target number of precursors reached.
0:47:37.838344 INFO: fragments_df: keeping 4024 of 1389766 [sum(precursor_idx_mask)=6940 sum(mass_error_mask)=1389766 stop_rank=4024
0:47:38.048174 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:38.246577 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:38.804374 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:38.804821 INFO: Using score_cutoff 11.430128567504884 (fac=0.99, q=1)
0:47:38.805109 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:38.805188 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:38.805244 INFO: Updating optimization_manager: score_cutoff        : 6.98098559103012 -> 11.430128567504884
0:47:38.805297 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:38.895311 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:39.075159 INFO: === checking if optimization conditions were reached ===
0:47:39.075546 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:47:39.078278 INFO: Updating optimization_manager: rt_error            : 51.05307177671688 -> 39.035646265860024
0:47:39.078405 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 39.0356.
0:47:39.078483 INFO: ==============================================
0:47:39.078562 INFO: Starting optimization step 3.
0:47:39.078629 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:47:39.078701 INFO: Using ng extraction backend
0:47:39.078772 PROGRESS: Extracting batch of 100097 precursors
0:47:39.259842 INFO: === Search parameters used ===
0:47:39.260250 INFO: rt_error       : 39.035646265860024
0:47:39.260310 INFO: mobility_error : 0.1
0:47:39.260361 INFO: num_candidates : 3
0:47:39.260406 INFO: ms1_error      : 30
0:47:39.260449 INFO: ms2_error      : 6.836823014739446
0:47:39.260490 INFO: fwhm_rt        : 3.0
0:47:39.260530 INFO: quant_window   : 3
0:47:39.260569 INFO: ==============================================
0:47:40.349937 INFO: performing precursor FDR with 40 features
0:47:40.350089 INFO: Decoy channel: -1
0:47:40.350116 INFO: Competetive: True
0:47:40.443125 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:40.560771 INFO: Using random state 449273 for train-test-split
0:47:45.723152 INFO: Test AUC: 0.585
0:47:45.723316 INFO: Train AUC: 0.594
0:47:45.723348 INFO: AUC difference: 1.58%
0:47:46.042573 INFO: Resetting torch num_threads to 80
0:47:46.055601 PROGRESS: === Extracted 281781 precursors and 1391770 fragments ===
0:47:46.056058 INFO: === FDR correction performed with classifier version 9 ===
0:47:46.056544 PROGRESS: ============================= Precursor FDR =============================
0:47:46.056632 PROGRESS: Total precursors accumulated: 339
0:47:46.056691 PROGRESS: Target precursors: 336 (99.12%)
0:47:46.056740 PROGRESS: Decoy precursors: 3 (0.88%)
0:47:46.056786 PROGRESS: 
0:47:46.056830 PROGRESS: Precursor Summary:
0:47:46.057785 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   336; 0.001 FDR:   296
0:47:46.057876 PROGRESS: 
0:47:46.057931 PROGRESS: Protein Summary:
0:47:46.059062 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   323; 0.001 FDR:   284
0:47:46.059161 PROGRESS: =========================================================================
0:47:46.064743 INFO: Target number of precursors reached.
0:47:46.158630 INFO: fragments_df: keeping 4054 of 1391770 [sum(precursor_idx_mask)=7044 sum(mass_error_mask)=1391770 stop_rank=4054
0:47:46.423798 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:46.537541 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:47.018878 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:47.019384 INFO: Using score_cutoff 11.43681011581421 (fac=0.99, q=1)
0:47:47.019699 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:47.019778 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:47.019833 INFO: Updating optimization_manager: score_cutoff        : 11.430128567504884 -> 11.43681011581421
0:47:47.019890 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:47.081798 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:47.242666 INFO: === checking if optimization conditions were reached ===
0:47:47.243093 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:47:47.245854 INFO: Updating optimization_manager: rt_error            : 39.035646265860024 -> 38.47558466724426
0:47:47.245973 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 38.4756.
0:47:47.246051 INFO: ==============================================
0:47:47.246133 INFO: Starting optimization step 4.
0:47:47.246202 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:47:47.246295 INFO: Using ng extraction backend
0:47:47.246368 PROGRESS: Extracting batch of 100097 precursors
0:47:47.425531 INFO: === Search parameters used ===
0:47:47.426232 INFO: rt_error       : 38.47558466724426
0:47:47.426296 INFO: mobility_error : 0.1
0:47:47.426344 INFO: num_candidates : 3
0:47:47.426389 INFO: ms1_error      : 30
0:47:47.426431 INFO: ms2_error      : 6.836823014739446
0:47:47.426472 INFO: fwhm_rt        : 3.0
0:47:47.426513 INFO: quant_window   : 3
0:47:47.426552 INFO: ==============================================
0:47:48.508929 INFO: performing precursor FDR with 40 features
0:47:48.509090 INFO: Decoy channel: -1
0:47:48.509118 INFO: Competetive: True
0:47:48.600751 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:48.710614 INFO: Using random state 449273 for train-test-split
0:47:53.862095 INFO: Test AUC: 0.587
0:47:53.862263 INFO: Train AUC: 0.594
0:47:53.862296 INFO: AUC difference: 1.26%
0:47:54.176279 INFO: Resetting torch num_threads to 80
0:47:54.189447 PROGRESS: === Extracted 281764 precursors and 1392340 fragments ===
0:47:54.189917 INFO: === FDR correction performed with classifier version 9 ===
0:47:54.190418 PROGRESS: ============================= Precursor FDR =============================
0:47:54.190508 PROGRESS: Total precursors accumulated: 349
0:47:54.190570 PROGRESS: Target precursors: 346 (99.14%)
0:47:54.190619 PROGRESS: Decoy precursors: 3 (0.86%)
0:47:54.190667 PROGRESS: 
0:47:54.190712 PROGRESS: Precursor Summary:
0:47:54.191663 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   346; 0.001 FDR:   307
0:47:54.191754 PROGRESS: 
0:47:54.191818 PROGRESS: Protein Summary:
0:47:54.192945 PROGRESS: Channel   0:	 0.050 FDR:   333; 0.010 FDR:   333; 0.001 FDR:   295
0:47:54.193033 PROGRESS: =========================================================================
0:47:54.198584 INFO: Target number of precursors reached.
0:47:54.296359 INFO: fragments_df: keeping 4175 of 1392340 [sum(precursor_idx_mask)=7282 sum(mass_error_mask)=1392340 stop_rank=4175
0:47:54.562484 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:54.674958 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:55.168054 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:55.168569 INFO: Using score_cutoff 11.692502491950988 (fac=0.99, q=1)
0:47:55.168885 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:55.168966 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:55.169021 INFO: Updating optimization_manager: score_cutoff        : 11.43681011581421 -> 11.692502491950988
0:47:55.169078 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:55.230416 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:55.377947 INFO: === checking if optimization conditions were reached ===
0:47:55.378332 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:47:55.379616 INFO: Updating optimization_manager: rt_error            : 38.47558466724426 -> 68.21582671817131
0:47:55.379748 INFO: Updating optimization_manager: classifier_version  : 9 -> 12
0:47:55.379843 INFO: Updating optimization_manager: score_cutoff        : 11.692502491950988 -> 6.98098559103012
0:47:55.379947 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:55.380044 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:55.380129 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 68.2158 found after 5 searches.
0:47:55.380192 INFO: ==============================================
0:47:55.380263 PROGRESS: Optimization finished for rt_error.
0:47:55.638655 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:55.700180 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:55.876427 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:47:55.876687 PROGRESS: ==============================================
0:47:55.876756 PROGRESS: ms2_error      : 6.8368
0:47:55.876811 PROGRESS: rt_error       : 68.2158
0:47:55.876857 PROGRESS: ==============================================
0:47:55.877541 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:48:02.939610 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:48:18.647964 INFO: Using ng extraction backend
0:48:18.648400 PROGRESS: Extracting batch of 11065368 precursors
0:48:34.565305 INFO: === Search parameters used ===
0:48:34.565633 INFO: rt_error       : 68.21582671817131
0:48:34.565698 INFO: mobility_error : 0.1
0:48:34.565748 INFO: num_candidates : 3
0:48:34.565804 INFO: ms1_error      : 30
0:48:34.565849 INFO: ms2_error      : 6.836823014739446
0:48:34.565894 INFO: fwhm_rt        : 3.0
0:48:34.565939 INFO: quant_window   : 3
0:48:34.565980 INFO: ==============================================
0:48:55.328462 INFO: Removed 8895700 precursors with score below cutoff 6.98098559103012
0:49:15.241262 INFO: performing precursor FDR with 40 features
0:49:15.241539 INFO: Decoy channel: -1
0:49:15.241574 INFO: Competetive: True
0:49:17.804255 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:27.382010 INFO: Using random state 179486 for train-test-split
0:55:54.710157 INFO: Test AUC: 0.607
0:55:54.710312 INFO: Train AUC: 0.608
0:55:54.710356 INFO: AUC difference: 0.12%
0:56:00.270306 INFO: Resetting torch num_threads to 80
0:56:02.176996 PROGRESS: ============================= Precursor FDR =============================
0:56:02.177285 PROGRESS: Total precursors accumulated: 49,314
0:56:02.177356 PROGRESS: Target precursors: 48,826 (99.01%)
0:56:02.177412 PROGRESS: Decoy precursors: 488 (0.99%)
0:56:02.177472 PROGRESS: 
0:56:02.177523 PROGRESS: Precursor Summary:
0:56:02.189108 PROGRESS: Channel   0:	 0.050 FDR: 48,826; 0.010 FDR: 48,826; 0.001 FDR: 32,065
0:56:02.189351 PROGRESS: 
0:56:02.189411 PROGRESS: Protein Summary:
0:56:02.207041 PROGRESS: Channel   0:	 0.050 FDR: 8,803; 0.010 FDR: 8,803; 0.001 FDR: 6,489
0:56:02.207274 PROGRESS: =========================================================================
0:56:02.430722 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/psm.parquet
0:56:02.536470 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/frag.parquet
0:56:02.701694 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
0:56:03.146291 PROGRESS: 
0:56:03.146455 INFO: Quantification results path: alphadia_zenoswath8600/library/quant
0:56:03.146521 INFO: Creating folder alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/figures
0:56:03.146698 INFO: Initializing TimingManager
0:56:03.147316 INFO: Initializing RawFileManager
0:58:30.913774 INFO: Determining DIA cycle
0:58:30.928602 INFO: Found cycle with start 0.00 min and length 86.
0:58:31.176145 INFO: RT (min)            : 0.0 - 55.4
0:58:31.176243 INFO: RT duration (sec)   : 3325.7
0:58:31.176274 INFO: RT duration (min)   : 55.4
0:58:31.176301 INFO: Cycle len (scans)   : 86
0:58:31.176323 INFO: Cycle len (sec)     : 1.90
0:58:31.176343 INFO: Number of cycles    : 1747
0:58:31.176363 INFO: MS2 range (m/z)     : 399.5 - 903.5
0:58:31.176405 INFO: Creating DIA data object took: 148.0289945602417
0:58:32.326692 INFO: Creating DIA data NG object took: 1.1501600742340088
0:58:33.732833 INFO: Initializing CalibrationManager
0:58:33.733111 INFO: Setting up calibration estimators ..
0:58:33.733170 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:58:33.733235 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'}' ..
0:58:33.733306 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:58:33.733356 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:58:33.733407 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}}' ..
0:58:33.733455 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:58:33.733510 INFO: Done setting up calibration estimators.
0:58:33.733667 INFO: Initializing OptimizationManager
0:58:33.733829 INFO: initial parameter: ms1_error = 30
0:58:33.733881 INFO: initial parameter: ms2_error = 30
0:58:33.733927 INFO: initial parameter: rt_error = 1662.873046875
0:58:33.733969 INFO: initial parameter: mobility_error = 0.1
0:58:33.734008 INFO: initial parameter: num_candidates = 1
0:58:33.734047 INFO: initial parameter: fwhm_rt = 5
0:58:33.734087 INFO: initial parameter: fwhm_mobility = 0.01
0:58:33.734126 INFO: initial parameter: score_cutoff = 0
0:58:33.734165 INFO: initial parameter: classifier_version = -1
0:58:33.734229 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
0:58:33.734449 INFO: FDRManager: loading saved state not requested, will be initialized.
0:58:33.734485 INFO: Initializing FDRManager
0:58:33.734516 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:58:35.131484 PROGRESS: Initializing spectral library: 5,608,555 target precursors potentially observable (87,724 removed)
0:58:35.973899 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:58:35.974235 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 1662.873046875
0:58:35.974326 PROGRESS: Starting initial search for precursors.
0:58:35.974405 INFO: Starting optimization step 0.
0:58:35.974464 PROGRESS: === Extracting elution groups 0 to 200 ===
0:58:35.974516 INFO: Using ng extraction backend
0:58:35.974568 PROGRESS: Extracting batch of 394 precursors
0:58:35.976582 INFO: === Search parameters used ===
0:58:35.976671 INFO: rt_error       : 1662.873046875
0:58:35.976721 INFO: mobility_error : 0.1
0:58:35.976766 INFO: num_candidates : 1
0:58:35.976807 INFO: ms1_error      : 30
0:58:35.976851 INFO: ms2_error      : 30
0:58:35.976891 INFO: fwhm_rt        : 5
0:58:35.976930 INFO: quant_window   : 3
0:58:35.976969 INFO: ==============================================
0:58:36.004351 INFO: performing precursor FDR with 40 features
0:58:36.004415 INFO: Decoy channel: -1
0:58:36.004441 INFO: Competetive: True
0:58:36.005395 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:36.007477 INFO: Using random state 993963 for train-test-split
0:58:36.014263 INFO: Test AUC: 0.519
0:58:36.014321 INFO: Train AUC: 0.512
0:58:36.014350 INFO: AUC difference: 1.37%
0:58:36.224046 INFO: Resetting torch num_threads to 80
0:58:36.225371 PROGRESS: === Extracted 393 precursors and 2208 fragments ===
0:58:36.225724 INFO: === FDR correction performed with classifier version -1 ===
0:58:36.226174 PROGRESS: ============================= Precursor FDR =============================
0:58:36.226263 PROGRESS: Total precursors accumulated: 1
0:58:36.226325 PROGRESS: Target precursors: 1 (100.00%)
0:58:36.226377 PROGRESS: Decoy precursors: 0 (0.00%)
0:58:36.227624 PROGRESS: 
0:58:36.227676 PROGRESS: Precursor Summary:
0:58:36.228615 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:58:36.228703 PROGRESS: 
0:58:36.228760 PROGRESS: Protein Summary:
0:58:36.229798 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:58:36.229889 PROGRESS: =========================================================================
0:58:36.230062 INFO: Target number of precursors not reached yet.
0:58:36.290793 INFO: Starting optimization step 1.
0:58:36.290953 PROGRESS: === Extracting elution groups 200 to 600 ===
0:58:36.291030 INFO: Using ng extraction backend
0:58:36.291091 PROGRESS: Extracting batch of 782 precursors
0:58:36.294290 INFO: === Search parameters used ===
0:58:36.294388 INFO: rt_error       : 1662.873046875
0:58:36.294438 INFO: mobility_error : 0.1
0:58:36.294482 INFO: num_candidates : 1
0:58:36.294524 INFO: ms1_error      : 30
0:58:36.294564 INFO: ms2_error      : 30
0:58:36.294603 INFO: fwhm_rt        : 5
0:58:36.294643 INFO: quant_window   : 3
0:58:36.294682 INFO: ==============================================
0:58:36.331448 INFO: performing precursor FDR with 40 features
0:58:36.331531 INFO: Decoy channel: -1
0:58:36.331564 INFO: Competetive: True
0:58:36.334595 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:36.336210 INFO: Using random state 338862 for train-test-split
0:58:36.344533 INFO: Test AUC: 0.526
0:58:36.344592 INFO: Train AUC: 0.502
0:58:36.344629 INFO: AUC difference: 4.79%
0:58:36.565523 INFO: Resetting torch num_threads to 80
0:58:36.567958 PROGRESS: === Extracted 1174 precursors and 6610 fragments ===
0:58:36.568375 INFO: === FDR correction performed with classifier version -1 ===
0:58:36.568876 PROGRESS: ============================= Precursor FDR =============================
0:58:36.568979 PROGRESS: Total precursors accumulated: 0
0:58:36.569057 PROGRESS: Target precursors: 0 (0.00%)
0:58:36.569120 PROGRESS: Decoy precursors: 0 (0.00%)
0:58:36.569177 PROGRESS: 
0:58:36.569231 PROGRESS: Precursor Summary:
0:58:36.569379 PROGRESS: 
0:58:36.569453 PROGRESS: Protein Summary:
0:58:36.569560 PROGRESS: =========================================================================
0:58:36.569827 INFO: Target number of precursors not reached yet.
0:58:36.632852 INFO: Starting optimization step 2.
0:58:36.633099 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:58:36.633203 INFO: Using ng extraction backend
0:58:36.633279 PROGRESS: Extracting batch of 1565 precursors
0:58:36.637784 INFO: === Search parameters used ===
0:58:36.637905 INFO: rt_error       : 1662.873046875
0:58:36.637973 INFO: mobility_error : 0.1
0:58:36.638031 INFO: num_candidates : 1
0:58:36.638086 INFO: ms1_error      : 30
0:58:36.638139 INFO: ms2_error      : 30
0:58:36.638191 INFO: fwhm_rt        : 5
0:58:36.638242 INFO: quant_window   : 3
0:58:36.638291 INFO: ==============================================
0:58:36.695657 INFO: performing precursor FDR with 40 features
0:58:36.695757 INFO: Decoy channel: -1
0:58:36.695786 INFO: Competetive: True
0:58:36.700621 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:36.702669 INFO: Using random state 17284 for train-test-split
0:58:36.714716 INFO: Test AUC: 0.508
0:58:36.714794 INFO: Train AUC: 0.508
0:58:36.714826 INFO: AUC difference: 0.05%
0:58:36.943407 INFO: Resetting torch num_threads to 80
0:58:36.946486 PROGRESS: === Extracted 2736 precursors and 15540 fragments ===
0:58:36.946881 INFO: === FDR correction performed with classifier version -1 ===
0:58:36.947367 PROGRESS: ============================= Precursor FDR =============================
0:58:36.947459 PROGRESS: Total precursors accumulated: 3
0:58:36.948068 PROGRESS: Target precursors: 3 (100.00%)
0:58:36.948134 PROGRESS: Decoy precursors: 0 (0.00%)
0:58:36.948186 PROGRESS: 
0:58:36.948237 PROGRESS: Precursor Summary:
0:58:36.949191 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:58:36.949280 PROGRESS: 
0:58:36.949340 PROGRESS: Protein Summary:
0:58:36.950416 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:58:36.950521 PROGRESS: =========================================================================
0:58:36.950772 INFO: Target number of precursors not reached yet.
0:58:37.017930 INFO: Starting optimization step 3.
0:58:37.018203 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:58:37.018301 INFO: Using ng extraction backend
0:58:37.018370 PROGRESS: Extracting batch of 3140 precursors
0:58:37.026404 INFO: === Search parameters used ===
0:58:37.026660 INFO: rt_error       : 1662.873046875
0:58:37.026719 INFO: mobility_error : 0.1
0:58:37.026771 INFO: num_candidates : 1
0:58:37.026820 INFO: ms1_error      : 30
0:58:37.026868 INFO: ms2_error      : 30
0:58:37.026915 INFO: fwhm_rt        : 5
0:58:37.026959 INFO: quant_window   : 3
0:58:37.027024 INFO: ==============================================
0:58:37.088420 INFO: performing precursor FDR with 40 features
0:58:37.088558 INFO: Decoy channel: -1
0:58:37.088588 INFO: Competetive: True
0:58:37.093746 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:37.096746 INFO: Using random state 812773 for train-test-split
0:58:37.122507 INFO: Test AUC: 0.519
0:58:37.122649 INFO: Train AUC: 0.499
0:58:37.122680 INFO: AUC difference: 3.95%
0:58:37.368617 INFO: Resetting torch num_threads to 80
0:58:37.374116 PROGRESS: === Extracted 5873 precursors and 33587 fragments ===
0:58:37.374638 INFO: === FDR correction performed with classifier version -1 ===
0:58:37.375149 PROGRESS: ============================= Precursor FDR =============================
0:58:37.375239 PROGRESS: Total precursors accumulated: 4
0:58:37.375298 PROGRESS: Target precursors: 4 (100.00%)
0:58:37.375347 PROGRESS: Decoy precursors: 0 (0.00%)
0:58:37.375393 PROGRESS: 
0:58:37.375436 PROGRESS: Precursor Summary:
0:58:37.376378 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:58:37.376466 PROGRESS: 
0:58:37.376521 PROGRESS: Protein Summary:
0:58:37.377573 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:58:37.377662 PROGRESS: =========================================================================
0:58:37.377958 INFO: Target number of precursors not reached yet.
0:58:37.448304 INFO: Starting optimization step 4.
0:58:37.448580 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:58:37.448664 INFO: Using ng extraction backend
0:58:37.448730 PROGRESS: Extracting batch of 6271 precursors
0:58:37.462240 INFO: === Search parameters used ===
0:58:37.462573 INFO: rt_error       : 1662.873046875
0:58:37.462645 INFO: mobility_error : 0.1
0:58:37.462692 INFO: num_candidates : 1
0:58:37.462734 INFO: ms1_error      : 30
0:58:37.462775 INFO: ms2_error      : 30
0:58:37.462816 INFO: fwhm_rt        : 5
0:58:37.462855 INFO: quant_window   : 3
0:58:37.462893 INFO: ==============================================
0:58:37.550292 INFO: performing precursor FDR with 40 features
0:58:37.550416 INFO: Decoy channel: -1
0:58:37.550442 INFO: Competetive: True
0:58:37.556500 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:37.560124 INFO: Using random state 729390 for train-test-split
0:58:37.596106 INFO: Test AUC: 0.488
0:58:37.596226 INFO: Train AUC: 0.506
0:58:37.596257 INFO: AUC difference: 3.58%
0:58:37.819697 INFO: Resetting torch num_threads to 80
0:58:37.824163 PROGRESS: === Extracted 12130 precursors and 69770 fragments ===
0:58:37.824533 INFO: === FDR correction performed with classifier version -1 ===
0:58:37.824991 PROGRESS: ============================= Precursor FDR =============================
0:58:37.825079 PROGRESS: Total precursors accumulated: 1
0:58:37.825139 PROGRESS: Target precursors: 1 (100.00%)
0:58:37.825186 PROGRESS: Decoy precursors: 0 (0.00%)
0:58:37.825230 PROGRESS: 
0:58:37.825275 PROGRESS: Precursor Summary:
0:58:37.826193 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:58:37.826283 PROGRESS: 
0:58:37.826339 PROGRESS: Protein Summary:
0:58:37.827344 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:58:37.827441 PROGRESS: =========================================================================
0:58:37.827770 INFO: Target number of precursors not reached yet.
0:58:37.905951 INFO: Starting optimization step 5.
0:58:37.906198 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:58:37.906283 INFO: Using ng extraction backend
0:58:37.906344 PROGRESS: Extracting batch of 12568 precursors
0:58:37.929632 INFO: === Search parameters used ===
0:58:37.929816 INFO: rt_error       : 1662.873046875
0:58:37.929870 INFO: mobility_error : 0.1
0:58:37.929915 INFO: num_candidates : 1
0:58:37.929958 INFO: ms1_error      : 30
0:58:37.930003 INFO: ms2_error      : 30
0:58:37.930046 INFO: fwhm_rt        : 5
0:58:37.930089 INFO: quant_window   : 3
0:58:37.930129 INFO: ==============================================
0:58:38.076429 INFO: performing precursor FDR with 40 features
0:58:38.076552 INFO: Decoy channel: -1
0:58:38.076579 INFO: Competetive: True
0:58:38.087742 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:38.093966 INFO: Using random state 453327 for train-test-split
0:58:38.343866 INFO: Test AUC: 0.497
0:58:38.344009 INFO: Train AUC: 0.497
0:58:38.344045 INFO: AUC difference: 0.13%
0:58:38.582729 INFO: Resetting torch num_threads to 80
0:58:38.588869 PROGRESS: === Extracted 24677 precursors and 141951 fragments ===
0:58:38.589250 INFO: === FDR correction performed with classifier version -1 ===
0:58:38.589729 PROGRESS: ============================= Precursor FDR =============================
0:58:38.589822 PROGRESS: Total precursors accumulated: 1
0:58:38.589882 PROGRESS: Target precursors: 1 (100.00%)
0:58:38.589932 PROGRESS: Decoy precursors: 0 (0.00%)
0:58:38.589980 PROGRESS: 
0:58:38.590026 PROGRESS: Precursor Summary:
0:58:38.590935 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:58:38.591032 PROGRESS: 
0:58:38.591090 PROGRESS: Protein Summary:
0:58:38.592099 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:58:38.592191 PROGRESS: =========================================================================
0:58:38.592630 INFO: Target number of precursors not reached yet.
0:58:38.686389 INFO: Starting optimization step 6.
0:58:38.686670 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:58:38.686756 INFO: Using ng extraction backend
0:58:38.686824 PROGRESS: Extracting batch of 25144 precursors
0:58:38.731787 INFO: === Search parameters used ===
0:58:38.732145 INFO: rt_error       : 1662.873046875
0:58:38.732208 INFO: mobility_error : 0.1
0:58:38.732263 INFO: num_candidates : 1
0:58:38.732316 INFO: ms1_error      : 30
0:58:38.732368 INFO: ms2_error      : 30
0:58:38.732418 INFO: fwhm_rt        : 5
0:58:38.732468 INFO: quant_window   : 3
0:58:38.732516 INFO: ==============================================
0:58:38.979781 INFO: performing precursor FDR with 40 features
0:58:38.979903 INFO: Decoy channel: -1
0:58:38.979930 INFO: Competetive: True
0:58:38.998562 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:39.017381 INFO: Using random state 749429 for train-test-split
0:58:39.663219 INFO: Test AUC: 0.557
0:58:39.663342 INFO: Train AUC: 0.554
0:58:39.663372 INFO: AUC difference: 0.49%
0:58:39.893816 INFO: Resetting torch num_threads to 80
0:58:39.903646 PROGRESS: === Extracted 49793 precursors and 286397 fragments ===
0:58:39.904121 INFO: === FDR correction performed with classifier version -1 ===
0:58:39.904625 PROGRESS: ============================= Precursor FDR =============================
0:58:39.904714 PROGRESS: Total precursors accumulated: 2
0:58:39.904783 PROGRESS: Target precursors: 2 (100.00%)
0:58:39.904839 PROGRESS: Decoy precursors: 0 (0.00%)
0:58:39.904885 PROGRESS: 
0:58:39.904930 PROGRESS: Precursor Summary:
0:58:39.905872 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:58:39.905962 PROGRESS: 
0:58:39.906020 PROGRESS: Protein Summary:
0:58:39.907034 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:58:39.907131 PROGRESS: =========================================================================
0:58:39.907837 INFO: Target number of precursors not reached yet.
0:58:40.043869 INFO: Starting optimization step 7.
0:58:40.044891 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:58:40.044997 INFO: Using ng extraction backend
0:58:40.045077 PROGRESS: Extracting batch of 50233 precursors
0:58:40.133326 INFO: === Search parameters used ===
0:58:40.134179 INFO: rt_error       : 1662.873046875
0:58:40.134242 INFO: mobility_error : 0.1
0:58:40.134290 INFO: num_candidates : 1
0:58:40.134335 INFO: ms1_error      : 30
0:58:40.134377 INFO: ms2_error      : 30
0:58:40.134419 INFO: fwhm_rt        : 5
0:58:40.134461 INFO: quant_window   : 3
0:58:40.134514 INFO: ==============================================
0:58:40.574179 INFO: performing precursor FDR with 40 features
0:58:40.574301 INFO: Decoy channel: -1
0:58:40.574328 INFO: Competetive: True
0:58:40.614979 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:40.642297 INFO: Using random state 916808 for train-test-split
0:58:42.065094 INFO: Test AUC: 0.573
0:58:42.065221 INFO: Train AUC: 0.584
0:58:42.065253 INFO: AUC difference: 1.99%
0:58:42.341499 INFO: Resetting torch num_threads to 80
0:58:42.359772 PROGRESS: === Extracted 99946 precursors and 573869 fragments ===
0:58:42.360349 INFO: === FDR correction performed with classifier version -1 ===
0:58:42.360873 PROGRESS: ============================= Precursor FDR =============================
0:58:42.360964 PROGRESS: Total precursors accumulated: 241
0:58:42.361024 PROGRESS: Target precursors: 239 (99.17%)
0:58:42.361073 PROGRESS: Decoy precursors: 2 (0.83%)
0:58:42.361121 PROGRESS: 
0:58:42.361166 PROGRESS: Precursor Summary:
0:58:42.362109 PROGRESS: Channel   0:	 0.050 FDR:   239; 0.010 FDR:   239; 0.001 FDR:   220
0:58:42.362199 PROGRESS: 
0:58:42.362254 PROGRESS: Protein Summary:
0:58:42.363337 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:   213
0:58:42.363426 PROGRESS: =========================================================================
0:58:42.365060 INFO: Target number of precursors reached.
0:58:42.408785 INFO: fragments_df: keeping 2389 of 573869 [sum(precursor_idx_mask)=2635 sum(mass_error_mask)=573869 stop_rank=2389
0:58:42.606976 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:58:42.719953 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:58:43.033808 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:58:43.034241 INFO: Using score_cutoff 16.54161366920471 (fac=0.99, q=1)
0:58:43.034536 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:58:43.034616 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:58:43.034671 INFO: Updating optimization_manager: score_cutoff        : 0 -> 16.54161366920471
0:58:43.034728 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:58:43.098221 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:43.251392 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:58:43.251772 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:58:43.251874 INFO: Starting optimization step 8.
0:58:43.251942 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:58:43.252014 INFO: Using ng extraction backend
0:58:43.252081 PROGRESS: Extracting batch of 100097 precursors
0:58:43.430107 INFO: === Search parameters used ===
0:58:43.430510 INFO: rt_error       : 1662.873046875
0:58:43.430567 INFO: mobility_error : 0.1
0:58:43.430613 INFO: num_candidates : 3
0:58:43.430655 INFO: ms1_error      : 30
0:58:43.430697 INFO: ms2_error      : 30
0:58:43.430739 INFO: fwhm_rt        : 3.0
0:58:43.430787 INFO: quant_window   : 3
0:58:43.430832 INFO: ==============================================
0:58:44.975930 INFO: performing precursor FDR with 40 features
0:58:44.976092 INFO: Decoy channel: -1
0:58:44.976119 INFO: Competetive: True
0:58:45.096224 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:45.241918 INFO: Using random state 408151 for train-test-split
0:58:50.683220 INFO: Test AUC: 0.589
0:58:50.683384 INFO: Train AUC: 0.593
0:58:50.683416 INFO: AUC difference: 0.67%
0:58:51.010749 INFO: Resetting torch num_threads to 80
0:58:51.025828 PROGRESS: === Extracted 299813 precursors and 1681134 fragments ===
0:58:51.026309 INFO: === FDR correction performed with classifier version 7 ===
0:58:51.026808 PROGRESS: ============================= Precursor FDR =============================
0:58:51.026901 PROGRESS: Total precursors accumulated: 292
0:58:51.026962 PROGRESS: Target precursors: 290 (99.32%)
0:58:51.027013 PROGRESS: Decoy precursors: 2 (0.68%)
0:58:51.027061 PROGRESS: 
0:58:51.027107 PROGRESS: Precursor Summary:
0:58:51.028065 PROGRESS: Channel   0:	 0.050 FDR:   290; 0.010 FDR:   290; 0.001 FDR:   253
0:58:51.028157 PROGRESS: 
0:58:51.028212 PROGRESS: Protein Summary:
0:58:51.029327 PROGRESS: Channel   0:	 0.050 FDR:   278; 0.010 FDR:   278; 0.001 FDR:   242
0:58:51.029420 PROGRESS: =========================================================================
0:58:51.036362 INFO: Target number of precursors reached.
0:58:51.148443 INFO: fragments_df: keeping 4018 of 1681134 [sum(precursor_idx_mask)=6806 sum(mass_error_mask)=1681134 stop_rank=4018
0:58:51.419401 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:58:51.516428 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:58:51.981364 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:58:51.981905 INFO: Using score_cutoff 13.29438438205719 (fac=0.99, q=1)
0:58:51.982224 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:58:51.982306 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:58:51.982371 INFO: Updating optimization_manager: score_cutoff        : 16.54161366920471 -> 13.29438438205719
0:58:51.982431 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:58:52.044179 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:52.190490 INFO: === checking if optimization conditions were reached ===
0:58:52.190957 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:58:52.193486 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.046289431072226
0:58:52.193597 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.0463.
0:58:52.193664 INFO: ==============================================
0:58:52.193735 INFO: Starting optimization step 9.
0:58:52.193795 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:58:52.193860 INFO: Using ng extraction backend
0:58:52.193922 PROGRESS: Extracting batch of 100097 precursors
0:58:52.374608 INFO: === Search parameters used ===
0:58:52.375629 INFO: rt_error       : 1662.873046875
0:58:52.375690 INFO: mobility_error : 0.1
0:58:52.375737 INFO: num_candidates : 3
0:58:52.375781 INFO: ms1_error      : 30
0:58:52.375823 INFO: ms2_error      : 7.046289431072226
0:58:52.375865 INFO: fwhm_rt        : 3.0
0:58:52.375904 INFO: quant_window   : 3
0:58:52.375958 INFO: ==============================================
0:58:53.839165 INFO: performing precursor FDR with 40 features
0:58:53.839343 INFO: Decoy channel: -1
0:58:53.839369 INFO: Competetive: True
0:58:53.944762 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:54.062927 INFO: Using random state 408151 for train-test-split
0:58:59.623633 INFO: Test AUC: 0.583
0:58:59.623801 INFO: Train AUC: 0.594
0:58:59.623832 INFO: AUC difference: 1.84%
0:58:59.955698 INFO: Resetting torch num_threads to 80
0:58:59.968125 PROGRESS: === Extracted 300276 precursors and 1819722 fragments ===
0:58:59.968601 INFO: === FDR correction performed with classifier version 7 ===
0:58:59.969088 PROGRESS: ============================= Precursor FDR =============================
0:58:59.969180 PROGRESS: Total precursors accumulated: 260
0:58:59.969241 PROGRESS: Target precursors: 258 (99.23%)
0:58:59.969292 PROGRESS: Decoy precursors: 2 (0.77%)
0:58:59.969352 PROGRESS: 
0:58:59.969403 PROGRESS: Precursor Summary:
0:58:59.970321 PROGRESS: Channel   0:	 0.050 FDR:   258; 0.010 FDR:   258; 0.001 FDR:   209
0:58:59.970415 PROGRESS: 
0:58:59.970472 PROGRESS: Protein Summary:
0:58:59.971543 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   246; 0.001 FDR:   201
0:58:59.971634 PROGRESS: =========================================================================
0:58:59.977243 INFO: Target number of precursors reached.
0:59:00.096906 INFO: fragments_df: keeping 3813 of 1819722 [sum(precursor_idx_mask)=6477 sum(mass_error_mask)=1819722 stop_rank=3813
0:59:00.427635 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:00.525714 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:00.965355 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:00.965872 INFO: Using score_cutoff 13.326489666938782 (fac=0.99, q=1)
0:59:00.966194 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:00.966279 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:00.966335 INFO: Updating optimization_manager: score_cutoff        : 13.29438438205719 -> 13.326489666938782
0:59:00.966396 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:01.028976 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:01.179532 INFO: === checking if optimization conditions were reached ===
0:59:01.179934 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:59:01.182611 INFO: Updating optimization_manager: ms2_error           : 7.046289431072226 -> 6.868495574807184
0:59:01.182724 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 6.8685.
0:59:01.182794 INFO: ==============================================
0:59:01.182870 INFO: Starting optimization step 10.
0:59:01.182932 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:59:01.182998 INFO: Using ng extraction backend
0:59:01.183060 PROGRESS: Extracting batch of 100097 precursors
0:59:01.360466 INFO: === Search parameters used ===
0:59:01.360870 INFO: rt_error       : 1662.873046875
0:59:01.360927 INFO: mobility_error : 0.1
0:59:01.360973 INFO: num_candidates : 3
0:59:01.361017 INFO: ms1_error      : 30
0:59:01.361058 INFO: ms2_error      : 6.868495574807184
0:59:01.361116 INFO: fwhm_rt        : 3.0
0:59:01.361158 INFO: quant_window   : 3
0:59:01.361199 INFO: ==============================================
0:59:02.839018 INFO: performing precursor FDR with 40 features
0:59:02.839169 INFO: Decoy channel: -1
0:59:02.839196 INFO: Competetive: True
0:59:02.933269 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:03.047840 INFO: Using random state 408151 for train-test-split
0:59:08.583015 INFO: Test AUC: 0.584
0:59:08.583282 INFO: Train AUC: 0.596
0:59:08.583324 INFO: AUC difference: 1.89%
0:59:08.910897 INFO: Resetting torch num_threads to 80
0:59:08.924437 PROGRESS: === Extracted 300279 precursors and 1817408 fragments ===
0:59:08.924983 INFO: === FDR correction performed with classifier version 7 ===
0:59:08.925510 PROGRESS: ============================= Precursor FDR =============================
0:59:08.925610 PROGRESS: Total precursors accumulated: 319
0:59:08.925674 PROGRESS: Target precursors: 316 (99.06%)
0:59:08.925724 PROGRESS: Decoy precursors: 3 (0.94%)
0:59:08.925771 PROGRESS: 
0:59:08.925815 PROGRESS: Precursor Summary:
0:59:08.926790 PROGRESS: Channel   0:	 0.050 FDR:   316; 0.010 FDR:   316; 0.001 FDR:   266
0:59:08.926883 PROGRESS: 
0:59:08.926938 PROGRESS: Protein Summary:
0:59:08.928081 PROGRESS: Channel   0:	 0.050 FDR:   302; 0.010 FDR:   302; 0.001 FDR:   253
0:59:08.928171 PROGRESS: =========================================================================
0:59:08.933930 INFO: Target number of precursors reached.
0:59:09.059667 INFO: fragments_df: keeping 4416 of 1817408 [sum(precursor_idx_mask)=7684 sum(mass_error_mask)=1817408 stop_rank=4416
0:59:09.281885 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:09.406318 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:09.961004 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:09.961486 INFO: Using score_cutoff 12.091531049251556 (fac=0.99, q=1)
0:59:09.961822 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:09.961904 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:09.961960 INFO: Updating optimization_manager: score_cutoff        : 13.326489666938782 -> 12.091531049251556
0:59:09.962022 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:10.025429 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:10.170160 INFO: === checking if optimization conditions were reached ===
0:59:10.170559 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:59:10.171663 INFO: Updating optimization_manager: ms2_error           : 6.868495574807184 -> 6.868495574807184
0:59:10.171792 INFO: Updating optimization_manager: classifier_version  : 7 -> 10
0:59:10.171889 INFO: Updating optimization_manager: score_cutoff        : 12.091531049251556 -> 12.091531049251556
0:59:10.171975 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:10.172063 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:10.172146 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 6.8685 found after 3 searches.
0:59:10.172211 INFO: ==============================================
0:59:10.172303 PROGRESS: Optimization finished for ms2_error.
0:59:10.426756 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:10.488084 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:10.674066 INFO: Starting optimization step 0.
0:59:10.674466 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:59:10.674606 INFO: Using ng extraction backend
0:59:10.674720 PROGRESS: Extracting batch of 100097 precursors
0:59:10.858883 INFO: === Search parameters used ===
0:59:10.859266 INFO: rt_error       : 1662.873046875
0:59:10.859324 INFO: mobility_error : 0.1
0:59:10.859371 INFO: num_candidates : 3
0:59:10.859415 INFO: ms1_error      : 30
0:59:10.859458 INFO: ms2_error      : 6.868495574807184
0:59:10.859502 INFO: fwhm_rt        : 3.0
0:59:10.859544 INFO: quant_window   : 3
0:59:10.859583 INFO: ==============================================
0:59:12.312287 INFO: performing precursor FDR with 40 features
0:59:12.312436 INFO: Decoy channel: -1
0:59:12.312463 INFO: Competetive: True
0:59:12.406220 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:12.521333 INFO: Using random state 260293 for train-test-split
0:59:17.938639 INFO: Test AUC: 0.588
0:59:17.938797 INFO: Train AUC: 0.600
0:59:17.938829 INFO: AUC difference: 1.99%
0:59:18.255231 INFO: Resetting torch num_threads to 80
0:59:18.268364 PROGRESS: === Extracted 300279 precursors and 1818095 fragments ===
0:59:18.268803 INFO: === FDR correction performed with classifier version 10 ===
0:59:18.269315 PROGRESS: ============================= Precursor FDR =============================
0:59:18.269411 PROGRESS: Total precursors accumulated: 312
0:59:18.269481 PROGRESS: Target precursors: 309 (99.04%)
0:59:18.269536 PROGRESS: Decoy precursors: 3 (0.96%)
0:59:18.269584 PROGRESS: 
0:59:18.269628 PROGRESS: Precursor Summary:
0:59:18.270580 PROGRESS: Channel   0:	 0.050 FDR:   309; 0.010 FDR:   309; 0.001 FDR:   221
0:59:18.270680 PROGRESS: 
0:59:18.270737 PROGRESS: Protein Summary:
0:59:18.271834 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   296; 0.001 FDR:   212
0:59:18.271926 PROGRESS: =========================================================================
0:59:18.277628 INFO: Target number of precursors reached.
0:59:18.396652 INFO: fragments_df: keeping 4413 of 1818095 [sum(precursor_idx_mask)=7670 sum(mass_error_mask)=1818095 stop_rank=4413
0:59:18.657702 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:18.761461 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:19.283483 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:19.283990 INFO: Using score_cutoff 14.168945832824706 (fac=0.99, q=1)
0:59:19.284304 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:19.284385 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:19.284441 INFO: Updating optimization_manager: score_cutoff        : 12.091531049251556 -> 14.168945832824706
0:59:19.284495 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:19.346067 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:19.494035 INFO: === checking if optimization conditions were reached ===
0:59:19.494417 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:59:19.496498 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 108.58214548707679
0:59:19.497224 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 108.5821.
0:59:19.497298 INFO: ==============================================
0:59:19.497370 INFO: Starting optimization step 1.
0:59:19.497430 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:59:19.497506 INFO: Using ng extraction backend
0:59:19.497568 PROGRESS: Extracting batch of 100097 precursors
0:59:19.673898 INFO: === Search parameters used ===
0:59:19.674273 INFO: rt_error       : 108.58214548707679
0:59:19.674333 INFO: mobility_error : 0.1
0:59:19.674383 INFO: num_candidates : 3
0:59:19.674429 INFO: ms1_error      : 30
0:59:19.674471 INFO: ms2_error      : 6.868495574807184
0:59:19.674513 INFO: fwhm_rt        : 3.0
0:59:19.674554 INFO: quant_window   : 3
0:59:19.674593 INFO: ==============================================
0:59:20.836838 INFO: performing precursor FDR with 40 features
0:59:20.836981 INFO: Decoy channel: -1
0:59:20.837008 INFO: Competetive: True
0:59:20.929539 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:21.044564 INFO: Using random state 260293 for train-test-split
0:59:26.647415 INFO: Test AUC: 0.583
0:59:26.647564 INFO: Train AUC: 0.598
0:59:26.647597 INFO: AUC difference: 2.57%
0:59:26.972439 INFO: Resetting torch num_threads to 80
0:59:26.986985 PROGRESS: === Extracted 300097 precursors and 1641318 fragments ===
0:59:26.987415 INFO: === FDR correction performed with classifier version 10 ===
0:59:26.987897 PROGRESS: ============================= Precursor FDR =============================
0:59:26.987982 PROGRESS: Total precursors accumulated: 380
0:59:26.988039 PROGRESS: Target precursors: 377 (99.21%)
0:59:26.988086 PROGRESS: Decoy precursors: 3 (0.79%)
0:59:26.988136 PROGRESS: 
0:59:26.988179 PROGRESS: Precursor Summary:
0:59:26.989093 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   377; 0.001 FDR:   291
0:59:26.989177 PROGRESS: 
0:59:26.989228 PROGRESS: Protein Summary:
0:59:26.990336 PROGRESS: Channel   0:	 0.050 FDR:   360; 0.010 FDR:   360; 0.001 FDR:   278
0:59:26.990424 PROGRESS: =========================================================================
0:59:26.996587 INFO: Target number of precursors reached.
0:59:27.109758 INFO: fragments_df: keeping 4989 of 1641318 [sum(precursor_idx_mask)=8900 sum(mass_error_mask)=1641318 stop_rank=4989
0:59:27.410033 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:27.518098 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:28.132951 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:28.133455 INFO: Using score_cutoff 13.504989279556275 (fac=0.99, q=1)
0:59:28.133780 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:28.133857 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:28.133911 INFO: Updating optimization_manager: score_cutoff        : 14.168945832824706 -> 13.504989279556275
0:59:28.133971 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:28.195277 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:28.344016 INFO: === checking if optimization conditions were reached ===
0:59:28.344368 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:59:28.346583 INFO: Updating optimization_manager: rt_error            : 108.58214548707679 -> 76.52942523183964
0:59:28.346686 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 76.5294.
0:59:28.346752 INFO: ==============================================
0:59:28.346825 INFO: Starting optimization step 2.
0:59:28.346882 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:59:28.346944 INFO: Using ng extraction backend
0:59:28.347002 PROGRESS: Extracting batch of 100097 precursors
0:59:28.522621 INFO: === Search parameters used ===
0:59:28.522995 INFO: rt_error       : 76.52942523183964
0:59:28.523048 INFO: mobility_error : 0.1
0:59:28.523091 INFO: num_candidates : 3
0:59:28.523131 INFO: ms1_error      : 30
0:59:28.523170 INFO: ms2_error      : 6.868495574807184
0:59:28.523220 INFO: fwhm_rt        : 3.0
0:59:28.523260 INFO: quant_window   : 3
0:59:28.523298 INFO: ==============================================
0:59:29.672048 INFO: performing precursor FDR with 40 features
0:59:29.672187 INFO: Decoy channel: -1
0:59:29.672213 INFO: Competetive: True
0:59:29.766071 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:29.881067 INFO: Using random state 260293 for train-test-split
0:59:35.247129 INFO: Test AUC: 0.588
0:59:35.247283 INFO: Train AUC: 0.596
0:59:35.247314 INFO: AUC difference: 1.33%
0:59:35.563326 INFO: Resetting torch num_threads to 80
0:59:35.576990 PROGRESS: === Extracted 299268 precursors and 1551894 fragments ===
0:59:35.577461 INFO: === FDR correction performed with classifier version 10 ===
0:59:35.577971 PROGRESS: ============================= Precursor FDR =============================
0:59:35.578063 PROGRESS: Total precursors accumulated: 311
0:59:35.578121 PROGRESS: Target precursors: 308 (99.04%)
0:59:35.578179 PROGRESS: Decoy precursors: 3 (0.96%)
0:59:35.578228 PROGRESS: 
0:59:35.578269 PROGRESS: Precursor Summary:
0:59:35.579194 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   308; 0.001 FDR:   231
0:59:35.579279 PROGRESS: 
0:59:35.579332 PROGRESS: Protein Summary:
0:59:35.580395 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   296; 0.001 FDR:   221
0:59:35.580482 PROGRESS: =========================================================================
0:59:35.586351 INFO: Target number of precursors reached.
0:59:35.688053 INFO: fragments_df: keeping 4175 of 1551894 [sum(precursor_idx_mask)=7175 sum(mass_error_mask)=1551894 stop_rank=4175
0:59:35.971805 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:36.071605 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:36.562374 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:36.562867 INFO: Using score_cutoff 14.168068087005615 (fac=0.99, q=1)
0:59:36.563173 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:36.563250 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:36.563303 INFO: Updating optimization_manager: score_cutoff        : 13.504989279556275 -> 14.168068087005615
0:59:36.563357 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:36.625382 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:36.775298 INFO: === checking if optimization conditions were reached ===
0:59:36.775661 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:59:36.777933 INFO: Updating optimization_manager: rt_error            : 76.52942523183964 -> 58.09521872680166
0:59:36.778048 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 58.0952.
0:59:36.778115 INFO: ==============================================
0:59:36.778185 INFO: Starting optimization step 3.
0:59:36.778241 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:59:36.778301 INFO: Using ng extraction backend
0:59:36.778372 PROGRESS: Extracting batch of 100097 precursors
0:59:36.955305 INFO: === Search parameters used ===
0:59:36.955957 INFO: rt_error       : 58.09521872680166
0:59:36.956161 INFO: mobility_error : 0.1
0:59:36.956375 INFO: num_candidates : 3
0:59:36.956578 INFO: ms1_error      : 30
0:59:36.956760 INFO: ms2_error      : 6.868495574807184
0:59:36.956944 INFO: fwhm_rt        : 3.0
0:59:36.957130 INFO: quant_window   : 3
0:59:36.957317 INFO: ==============================================
0:59:38.289474 INFO: performing precursor FDR with 40 features
0:59:38.289636 INFO: Decoy channel: -1
0:59:38.289669 INFO: Competetive: True
0:59:38.394349 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:38.514358 INFO: Using random state 260293 for train-test-split
0:59:43.153049 INFO: Test AUC: 0.584
0:59:43.153188 INFO: Train AUC: 0.597
0:59:43.153220 INFO: AUC difference: 2.16%
0:59:43.466111 INFO: Resetting torch num_threads to 80
0:59:43.482050 PROGRESS: === Extracted 284102 precursors and 1397999 fragments ===
0:59:43.482614 INFO: === FDR correction performed with classifier version 10 ===
0:59:43.483147 PROGRESS: ============================= Precursor FDR =============================
0:59:43.483256 PROGRESS: Total precursors accumulated: 283
0:59:43.483318 PROGRESS: Target precursors: 281 (99.29%)
0:59:43.483369 PROGRESS: Decoy precursors: 2 (0.71%)
0:59:43.483416 PROGRESS: 
0:59:43.483462 PROGRESS: Precursor Summary:
0:59:43.484379 PROGRESS: Channel   0:	 0.050 FDR:   281; 0.010 FDR:   281; 0.001 FDR:   203
0:59:43.484470 PROGRESS: 
0:59:43.484525 PROGRESS: Protein Summary:
0:59:43.485605 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:   196
0:59:43.485703 PROGRESS: =========================================================================
0:59:43.491575 INFO: Target number of precursors reached.
0:59:43.582635 INFO: fragments_df: keeping 3629 of 1397999 [sum(precursor_idx_mask)=6102 sum(mass_error_mask)=1397999 stop_rank=3629
0:59:43.827846 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:43.945269 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:44.424125 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:44.424591 INFO: Using score_cutoff 13.578793910980224 (fac=0.99, q=1)
0:59:44.424887 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:44.424968 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:44.425024 INFO: Updating optimization_manager: score_cutoff        : 14.168068087005615 -> 13.578793910980224
0:59:44.425080 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:44.486847 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:44.648937 INFO: === checking if optimization conditions were reached ===
0:59:44.649315 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:59:44.651890 INFO: Updating optimization_manager: rt_error            : 58.09521872680166 -> 44.739486276293306
0:59:44.652016 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 44.7395.
0:59:44.652098 INFO: ==============================================
0:59:44.652179 INFO: Starting optimization step 4.
0:59:44.652249 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:59:44.652320 INFO: Using ng extraction backend
0:59:44.652396 PROGRESS: Extracting batch of 100097 precursors
0:59:44.832307 INFO: === Search parameters used ===
0:59:44.832663 INFO: rt_error       : 44.739486276293306
0:59:44.832724 INFO: mobility_error : 0.1
0:59:44.832774 INFO: num_candidates : 3
0:59:44.832820 INFO: ms1_error      : 30
0:59:44.832862 INFO: ms2_error      : 6.868495574807184
0:59:44.832903 INFO: fwhm_rt        : 3.0
0:59:44.832943 INFO: quant_window   : 3
0:59:44.832982 INFO: ==============================================
0:59:45.865186 INFO: performing precursor FDR with 40 features
0:59:45.865321 INFO: Decoy channel: -1
0:59:45.865347 INFO: Competetive: True
0:59:45.954237 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:46.060169 INFO: Using random state 260293 for train-test-split
0:59:50.835606 INFO: Test AUC: 0.589
0:59:50.835746 INFO: Train AUC: 0.597
0:59:50.835777 INFO: AUC difference: 1.39%
0:59:51.142834 INFO: Resetting torch num_threads to 80
0:59:51.155764 PROGRESS: === Extracted 281643 precursors and 1386428 fragments ===
0:59:51.156179 INFO: === FDR correction performed with classifier version 10 ===
0:59:51.156677 PROGRESS: ============================= Precursor FDR =============================
0:59:51.156770 PROGRESS: Total precursors accumulated: 287
0:59:51.156830 PROGRESS: Target precursors: 285 (99.30%)
0:59:51.156881 PROGRESS: Decoy precursors: 2 (0.70%)
0:59:51.156928 PROGRESS: 
0:59:51.156971 PROGRESS: Precursor Summary:
0:59:51.157880 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   285; 0.001 FDR:   181
0:59:51.157974 PROGRESS: 
0:59:51.158029 PROGRESS: Protein Summary:
0:59:51.159091 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   274; 0.001 FDR:   176
0:59:51.159183 PROGRESS: =========================================================================
0:59:51.164753 INFO: Target number of precursors reached.
0:59:51.256578 INFO: fragments_df: keeping 3620 of 1386428 [sum(precursor_idx_mask)=6088 sum(mass_error_mask)=1386428 stop_rank=3620
0:59:51.502650 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:51.605577 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:52.015875 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:52.016341 INFO: Using score_cutoff 13.987411365509033 (fac=0.99, q=1)
0:59:52.016637 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:52.016717 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:52.016780 INFO: Updating optimization_manager: score_cutoff        : 13.578793910980224 -> 13.987411365509033
0:59:52.016836 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:52.079066 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:52.238622 INFO: === checking if optimization conditions were reached ===
0:59:52.238993 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:59:52.241580 INFO: Updating optimization_manager: rt_error            : 44.739486276293306 -> 38.85974189403125
0:59:52.241699 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 38.8597.
0:59:52.241779 INFO: ==============================================
0:59:52.241860 INFO: Starting optimization step 5.
0:59:52.241930 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:59:52.242001 INFO: Using ng extraction backend
0:59:52.242072 PROGRESS: Extracting batch of 100097 precursors
0:59:52.421411 INFO: === Search parameters used ===
0:59:52.421742 INFO: rt_error       : 38.85974189403125
0:59:52.421803 INFO: mobility_error : 0.1
0:59:52.421855 INFO: num_candidates : 3
0:59:52.421900 INFO: ms1_error      : 30
0:59:52.421942 INFO: ms2_error      : 6.868495574807184
0:59:52.421982 INFO: fwhm_rt        : 3.0
0:59:52.422022 INFO: quant_window   : 3
0:59:52.422074 INFO: ==============================================
0:59:53.450357 INFO: performing precursor FDR with 40 features
0:59:53.450491 INFO: Decoy channel: -1
0:59:53.450517 INFO: Competetive: True
0:59:53.536474 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:53.648511 INFO: Using random state 260293 for train-test-split
0:59:58.202300 INFO: Test AUC: 0.583
0:59:58.202440 INFO: Train AUC: 0.597
0:59:58.202472 INFO: AUC difference: 2.28%
0:59:58.512787 INFO: Resetting torch num_threads to 80
0:59:58.525942 PROGRESS: === Extracted 281721 precursors and 1389629 fragments ===
0:59:58.526362 INFO: === FDR correction performed with classifier version 10 ===
0:59:58.526846 PROGRESS: ============================= Precursor FDR =============================
0:59:58.526939 PROGRESS: Total precursors accumulated: 289
0:59:58.526999 PROGRESS: Target precursors: 287 (99.31%)
0:59:58.527057 PROGRESS: Decoy precursors: 2 (0.69%)
0:59:58.527104 PROGRESS: 
0:59:58.527149 PROGRESS: Precursor Summary:
0:59:58.528072 PROGRESS: Channel   0:	 0.050 FDR:   287; 0.010 FDR:   287; 0.001 FDR:   174
0:59:58.528163 PROGRESS: 
0:59:58.528217 PROGRESS: Protein Summary:
0:59:58.529276 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   273; 0.001 FDR:   168
0:59:58.529368 PROGRESS: =========================================================================
0:59:58.535071 INFO: Target number of precursors reached.
0:59:58.625621 INFO: fragments_df: keeping 3664 of 1389629 [sum(precursor_idx_mask)=6169 sum(mass_error_mask)=1389629 stop_rank=3664
0:59:58.871017 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:58.970134 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:59.385521 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:59.385986 INFO: Using score_cutoff 13.988354086875916 (fac=0.99, q=1)
0:59:59.386288 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:59.386367 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:59.386421 INFO: Updating optimization_manager: score_cutoff        : 13.987411365509033 -> 13.988354086875916
0:59:59.386472 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:59.448643 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:59.605620 INFO: === checking if optimization conditions were reached ===
0:59:59.606003 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:59:59.608568 INFO: Updating optimization_manager: rt_error            : 38.85974189403125 -> 37.84441941915539
0:59:59.608689 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 37.8444.
0:59:59.608768 INFO: ==============================================
0:59:59.608847 INFO: Starting optimization step 6.
0:59:59.608914 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:59:59.608984 INFO: Using ng extraction backend
0:59:59.609054 PROGRESS: Extracting batch of 100097 precursors
0:59:59.786065 INFO: === Search parameters used ===
0:59:59.786386 INFO: rt_error       : 37.84441941915539
0:59:59.786442 INFO: mobility_error : 0.1
0:59:59.786489 INFO: num_candidates : 3
0:59:59.786537 INFO: ms1_error      : 30
0:59:59.786579 INFO: ms2_error      : 6.868495574807184
0:59:59.786630 INFO: fwhm_rt        : 3.0
0:59:59.786672 INFO: quant_window   : 3
0:59:59.786711 INFO: ==============================================
1:00:00.842376 INFO: performing precursor FDR with 40 features
1:00:00.842518 INFO: Decoy channel: -1
1:00:00.842545 INFO: Competetive: True
1:00:00.929396 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:01.037024 INFO: Using random state 260293 for train-test-split
1:00:05.727603 INFO: Test AUC: 0.585
1:00:05.727741 INFO: Train AUC: 0.598
1:00:05.727773 INFO: AUC difference: 2.30%
1:00:06.035699 INFO: Resetting torch num_threads to 80
1:00:06.048995 PROGRESS: === Extracted 281719 precursors and 1390871 fragments ===
1:00:06.049407 INFO: === FDR correction performed with classifier version 10 ===
1:00:06.049888 PROGRESS: ============================= Precursor FDR =============================
1:00:06.049982 PROGRESS: Total precursors accumulated: 310
1:00:06.050041 PROGRESS: Target precursors: 307 (99.03%)
1:00:06.050090 PROGRESS: Decoy precursors: 3 (0.97%)
1:00:06.050140 PROGRESS: 
1:00:06.050184 PROGRESS: Precursor Summary:
1:00:06.051088 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   307; 0.001 FDR:   206
1:00:06.051185 PROGRESS: 
1:00:06.051241 PROGRESS: Protein Summary:
1:00:06.052302 PROGRESS: Channel   0:	 0.050 FDR:   293; 0.010 FDR:   293; 0.001 FDR:   198
1:00:06.052390 PROGRESS: =========================================================================
1:00:06.058225 INFO: Target number of precursors reached.
1:00:06.150215 INFO: fragments_df: keeping 3839 of 1390871 [sum(precursor_idx_mask)=6522 sum(mass_error_mask)=1390871 stop_rank=3839
1:00:06.437904 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:00:07.792032 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:00:08.235443 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:00:08.235919 INFO: Using score_cutoff 14.002442035675049 (fac=0.99, q=1)
1:00:08.236216 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:00:08.236298 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:00:08.236355 INFO: Updating optimization_manager: score_cutoff        : 13.988354086875916 -> 14.002442035675049
1:00:08.236412 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:00:08.298797 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:00:08.455503 INFO: === checking if optimization conditions were reached ===
1:00:08.455884 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:00:08.457313 INFO: Updating optimization_manager: rt_error            : 37.84441941915539 -> 108.58214548707679
1:00:08.457476 INFO: Updating optimization_manager: classifier_version  : 10 -> 12
1:00:08.457596 INFO: Updating optimization_manager: score_cutoff        : 14.002442035675049 -> 13.504989279556275
1:00:08.457702 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:00:08.457802 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:00:08.457902 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 108.5821 found after 7 searches.
1:00:08.457979 INFO: ==============================================
1:00:08.458065 PROGRESS: Optimization finished for rt_error.
1:00:08.706861 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:00:08.768769 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:00:08.959209 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:00:08.959467 PROGRESS: ==============================================
1:00:08.959545 PROGRESS: ms2_error      : 6.8685
1:00:08.959608 PROGRESS: rt_error       : 108.5821
1:00:08.959664 PROGRESS: ==============================================
1:00:08.960319 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:00:16.034310 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:00:32.108936 INFO: Using ng extraction backend
1:00:32.109325 PROGRESS: Extracting batch of 11065368 precursors
1:00:47.257929 INFO: === Search parameters used ===
1:00:47.258206 INFO: rt_error       : 108.58214548707679
1:00:47.258266 INFO: mobility_error : 0.1
1:00:47.258316 INFO: num_candidates : 3
1:00:47.258361 INFO: ms1_error      : 30
1:00:47.258403 INFO: ms2_error      : 6.868495574807184
1:00:47.258448 INFO: fwhm_rt        : 3.0
1:00:47.258492 INFO: quant_window   : 3
1:00:47.258537 INFO: ==============================================
1:01:09.232268 INFO: Removed 18128480 precursors with score below cutoff 13.504989279556275
1:01:26.892524 INFO: performing precursor FDR with 40 features
1:01:26.892671 INFO: Decoy channel: -1
1:01:26.892699 INFO: Competetive: True
1:01:28.515232 INFO: Setting torch num_threads to 2 for FDR classification task
1:01:34.759202 INFO: Using random state 681858 for train-test-split
1:06:19.354968 INFO: Test AUC: 0.605
1:06:19.355382 INFO: Train AUC: 0.605
1:06:19.355425 INFO: AUC difference: 0.11%
1:06:23.753267 INFO: Resetting torch num_threads to 80
1:06:26.166555 PROGRESS: ============================= Precursor FDR =============================
1:06:26.166924 PROGRESS: Total precursors accumulated: 55,805
1:06:26.167010 PROGRESS: Target precursors: 55,253 (99.01%)
1:06:26.167067 PROGRESS: Decoy precursors: 552 (0.99%)
1:06:26.167116 PROGRESS: 
1:06:26.167163 PROGRESS: Precursor Summary:
1:06:26.181084 PROGRESS: Channel   0:	 0.050 FDR: 55,253; 0.010 FDR: 55,253; 0.001 FDR: 37,255
1:06:26.181386 PROGRESS: 
1:06:26.181448 PROGRESS: Protein Summary:
1:06:26.202575 PROGRESS: Channel   0:	 0.050 FDR: 9,632; 0.010 FDR: 9,632; 0.001 FDR: 6,862
1:06:26.202873 PROGRESS: =========================================================================
1:06:26.310862 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/psm.parquet
1:06:26.430558 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/frag.parquet
1:06:26.613093 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
1:06:27.213681 PROGRESS: 
1:06:27.213943 INFO: Quantification results path: alphadia_zenoswath8600/library/quant
1:06:27.214046 INFO: Creating folder alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/figures
1:06:27.214270 INFO: Initializing TimingManager
1:06:27.215137 INFO: Initializing RawFileManager
1:08:51.847700 INFO: Determining DIA cycle
1:08:51.862776 INFO: Found cycle with start 0.00 min and length 86.
1:08:52.104798 INFO: RT (min)            : 0.0 - 55.4
1:08:52.104908 INFO: RT duration (sec)   : 3325.6
1:08:52.104943 INFO: RT duration (min)   : 55.4
1:08:52.104970 INFO: Cycle len (scans)   : 86
1:08:52.104990 INFO: Cycle len (sec)     : 1.90
1:08:52.105010 INFO: Number of cycles    : 1747
1:08:52.105030 INFO: MS2 range (m/z)     : 399.5 - 903.5
1:08:52.105109 INFO: Creating DIA data object took: 144.88985967636108
1:08:53.260437 INFO: Creating DIA data NG object took: 1.1551566123962402
1:08:54.612035 INFO: Initializing CalibrationManager
1:08:54.612337 INFO: Setting up calibration estimators ..
1:08:54.612400 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:08:54.612519 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'}' ..
1:08:54.612628 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:08:54.612681 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:08:54.612743 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}}' ..
1:08:54.612798 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:08:54.612843 INFO: Done setting up calibration estimators.
1:08:54.612991 INFO: Initializing OptimizationManager
1:08:54.613541 INFO: initial parameter: ms1_error = 30
1:08:54.613600 INFO: initial parameter: ms2_error = 30
1:08:54.613646 INFO: initial parameter: rt_error = 1662.8485107421875
1:08:54.613690 INFO: initial parameter: mobility_error = 0.1
1:08:54.613732 INFO: initial parameter: num_candidates = 1
1:08:54.613771 INFO: initial parameter: fwhm_rt = 5
1:08:54.613811 INFO: initial parameter: fwhm_mobility = 0.01
1:08:54.613851 INFO: initial parameter: score_cutoff = 0
1:08:54.613892 INFO: initial parameter: classifier_version = -1
1:08:54.613965 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
1:08:54.614419 INFO: FDRManager: loading saved state not requested, will be initialized.
1:08:54.614460 INFO: Initializing FDRManager
1:08:54.614501 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:08:56.183380 PROGRESS: Initializing spectral library: 5,608,555 target precursors potentially observable (87,724 removed)
1:08:57.111989 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:08:57.112376 INFO: Updating optimization_manager: rt_error            : 1662.8485107421875 -> 1662.8485107421875
1:08:57.112485 PROGRESS: Starting initial search for precursors.
1:08:57.112579 INFO: Starting optimization step 0.
1:08:57.112647 PROGRESS: === Extracting elution groups 0 to 200 ===
1:08:57.112713 INFO: Using ng extraction backend
1:08:57.112791 PROGRESS: Extracting batch of 394 precursors
1:08:57.115056 INFO: === Search parameters used ===
1:08:57.115162 INFO: rt_error       : 1662.8485107421875
1:08:57.115214 INFO: mobility_error : 0.1
1:08:57.115263 INFO: num_candidates : 1
1:08:57.115305 INFO: ms1_error      : 30
1:08:57.115345 INFO: ms2_error      : 30
1:08:57.115387 INFO: fwhm_rt        : 5
1:08:57.115428 INFO: quant_window   : 3
1:08:57.115468 INFO: ==============================================
1:08:57.153421 INFO: performing precursor FDR with 40 features
1:08:57.153512 INFO: Decoy channel: -1
1:08:57.153538 INFO: Competetive: True
1:08:57.154692 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:57.157635 INFO: Using random state 690050 for train-test-split
1:08:57.166610 INFO: Test AUC: 0.453
1:08:57.166672 INFO: Train AUC: 0.443
1:08:57.166702 INFO: AUC difference: 2.24%
1:08:57.392439 INFO: Resetting torch num_threads to 80
1:08:57.394093 PROGRESS: === Extracted 393 precursors and 2227 fragments ===
1:08:57.394469 INFO: === FDR correction performed with classifier version -1 ===
1:08:57.394909 PROGRESS: ============================= Precursor FDR =============================
1:08:57.394995 PROGRESS: Total precursors accumulated: 0
1:08:57.395056 PROGRESS: Target precursors: 0 (0.00%)
1:08:57.395106 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:57.395152 PROGRESS: 
1:08:57.395198 PROGRESS: Precursor Summary:
1:08:57.395314 PROGRESS: 
1:08:57.395379 PROGRESS: Protein Summary:
1:08:57.395482 PROGRESS: =========================================================================
1:08:57.395691 INFO: Target number of precursors not reached yet.
1:08:57.457139 INFO: Starting optimization step 1.
1:08:57.457388 PROGRESS: === Extracting elution groups 200 to 600 ===
1:08:57.457491 INFO: Using ng extraction backend
1:08:57.457559 PROGRESS: Extracting batch of 782 precursors
1:08:57.460594 INFO: === Search parameters used ===
1:08:57.460715 INFO: rt_error       : 1662.8485107421875
1:08:57.460767 INFO: mobility_error : 0.1
1:08:57.460811 INFO: num_candidates : 1
1:08:57.460857 INFO: ms1_error      : 30
1:08:57.460900 INFO: ms2_error      : 30
1:08:57.460940 INFO: fwhm_rt        : 5
1:08:57.460979 INFO: quant_window   : 3
1:08:57.461019 INFO: ==============================================
1:08:57.491345 INFO: performing precursor FDR with 40 features
1:08:57.491425 INFO: Decoy channel: -1
1:08:57.491452 INFO: Competetive: True
1:08:57.494791 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:57.496467 INFO: Using random state 120789 for train-test-split
1:08:57.505342 INFO: Test AUC: 0.430
1:08:57.505399 INFO: Train AUC: 0.483
1:08:57.505428 INFO: AUC difference: 10.93%
1:08:57.505451 WARNING: AUC difference > 5%. This may indicate overfitting.
1:08:57.723711 INFO: Resetting torch num_threads to 80
1:08:57.726278 PROGRESS: === Extracted 1171 precursors and 6606 fragments ===
1:08:57.726669 INFO: === FDR correction performed with classifier version -1 ===
1:08:57.727100 PROGRESS: ============================= Precursor FDR =============================
1:08:57.727187 PROGRESS: Total precursors accumulated: 0
1:08:57.727245 PROGRESS: Target precursors: 0 (0.00%)
1:08:57.727293 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:57.727340 PROGRESS: 
1:08:57.727382 PROGRESS: Precursor Summary:
1:08:57.727497 PROGRESS: 
1:08:57.727560 PROGRESS: Protein Summary:
1:08:57.727641 PROGRESS: =========================================================================
1:08:57.727875 INFO: Target number of precursors not reached yet.
1:08:57.791393 INFO: Starting optimization step 2.
1:08:57.791630 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:08:57.791716 INFO: Using ng extraction backend
1:08:57.791781 PROGRESS: Extracting batch of 1565 precursors
1:08:57.796267 INFO: === Search parameters used ===
1:08:57.796394 INFO: rt_error       : 1662.8485107421875
1:08:57.796444 INFO: mobility_error : 0.1
1:08:57.796489 INFO: num_candidates : 1
1:08:57.796530 INFO: ms1_error      : 30
1:08:57.796573 INFO: ms2_error      : 30
1:08:57.796615 INFO: fwhm_rt        : 5
1:08:57.796664 INFO: quant_window   : 3
1:08:57.796704 INFO: ==============================================
1:08:57.836669 INFO: performing precursor FDR with 40 features
1:08:57.836764 INFO: Decoy channel: -1
1:08:57.836791 INFO: Competetive: True
1:08:57.840544 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:57.842603 INFO: Using random state 362774 for train-test-split
1:08:57.854541 INFO: Test AUC: 0.459
1:08:57.854608 INFO: Train AUC: 0.483
1:08:57.854638 INFO: AUC difference: 5.09%
1:08:57.854661 WARNING: AUC difference > 5%. This may indicate overfitting.
1:08:58.074131 INFO: Resetting torch num_threads to 80
1:08:58.077226 PROGRESS: === Extracted 2730 precursors and 15516 fragments ===
1:08:58.077615 INFO: === FDR correction performed with classifier version -1 ===
1:08:58.078055 PROGRESS: ============================= Precursor FDR =============================
1:08:58.078141 PROGRESS: Total precursors accumulated: 0
1:08:58.078201 PROGRESS: Target precursors: 0 (0.00%)
1:08:58.078251 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:58.078298 PROGRESS: 
1:08:58.078348 PROGRESS: Precursor Summary:
1:08:58.078467 PROGRESS: 
1:08:58.078531 PROGRESS: Protein Summary:
1:08:58.078607 PROGRESS: =========================================================================
1:08:58.078861 INFO: Target number of precursors not reached yet.
1:08:58.144734 INFO: Starting optimization step 3.
1:08:58.144997 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:08:58.145088 INFO: Using ng extraction backend
1:08:58.145156 PROGRESS: Extracting batch of 3140 precursors
1:08:58.152440 INFO: === Search parameters used ===
1:08:58.152614 INFO: rt_error       : 1662.8485107421875
1:08:58.152666 INFO: mobility_error : 0.1
1:08:58.152711 INFO: num_candidates : 1
1:08:58.152754 INFO: ms1_error      : 30
1:08:58.152794 INFO: ms2_error      : 30
1:08:58.152834 INFO: fwhm_rt        : 5
1:08:58.152874 INFO: quant_window   : 3
1:08:58.152915 INFO: ==============================================
1:08:58.212298 INFO: performing precursor FDR with 40 features
1:08:58.212421 INFO: Decoy channel: -1
1:08:58.212448 INFO: Competetive: True
1:08:58.217269 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:58.219957 INFO: Using random state 576359 for train-test-split
1:08:58.241584 INFO: Test AUC: 0.489
1:08:58.241692 INFO: Train AUC: 0.481
1:08:58.241723 INFO: AUC difference: 1.67%
1:08:58.467417 INFO: Resetting torch num_threads to 80
1:08:58.471579 PROGRESS: === Extracted 5867 precursors and 33570 fragments ===
1:08:58.472015 INFO: === FDR correction performed with classifier version -1 ===
1:08:58.472456 PROGRESS: ============================= Precursor FDR =============================
1:08:58.472550 PROGRESS: Total precursors accumulated: 0
1:08:58.472612 PROGRESS: Target precursors: 0 (0.00%)
1:08:58.472662 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:58.472708 PROGRESS: 
1:08:58.472752 PROGRESS: Precursor Summary:
1:08:58.472866 PROGRESS: 
1:08:58.472929 PROGRESS: Protein Summary:
1:08:58.473002 PROGRESS: =========================================================================
1:08:58.473298 INFO: Target number of precursors not reached yet.
1:08:58.544061 INFO: Starting optimization step 4.
1:08:58.544328 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:08:58.544418 INFO: Using ng extraction backend
1:08:58.544487 PROGRESS: Extracting batch of 6271 precursors
1:08:58.557168 INFO: === Search parameters used ===
1:08:58.557358 INFO: rt_error       : 1662.8485107421875
1:08:58.557411 INFO: mobility_error : 0.1
1:08:58.557456 INFO: num_candidates : 1
1:08:58.557517 INFO: ms1_error      : 30
1:08:58.557560 INFO: ms2_error      : 30
1:08:58.557601 INFO: fwhm_rt        : 5
1:08:58.557640 INFO: quant_window   : 3
1:08:58.557681 INFO: ==============================================
1:08:58.647760 INFO: performing precursor FDR with 40 features
1:08:58.647891 INFO: Decoy channel: -1
1:08:58.647920 INFO: Competetive: True
1:08:58.654743 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:58.658822 INFO: Using random state 53724 for train-test-split
1:08:58.700247 INFO: Test AUC: 0.472
1:08:58.700372 INFO: Train AUC: 0.482
1:08:58.700404 INFO: AUC difference: 2.15%
1:08:58.925862 INFO: Resetting torch num_threads to 80
1:08:58.931384 PROGRESS: === Extracted 12129 precursors and 69689 fragments ===
1:08:58.931842 INFO: === FDR correction performed with classifier version -1 ===
1:08:58.932292 PROGRESS: ============================= Precursor FDR =============================
1:08:58.932378 PROGRESS: Total precursors accumulated: 0
1:08:58.932439 PROGRESS: Target precursors: 0 (0.00%)
1:08:58.932491 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:58.932537 PROGRESS: 
1:08:58.932585 PROGRESS: Precursor Summary:
1:08:58.932706 PROGRESS: 
1:08:58.932772 PROGRESS: Protein Summary:
1:08:58.932847 PROGRESS: =========================================================================
1:08:58.933228 INFO: Target number of precursors not reached yet.
1:08:59.013183 INFO: Starting optimization step 5.
1:08:59.013485 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:08:59.013583 INFO: Using ng extraction backend
1:08:59.013655 PROGRESS: Extracting batch of 12568 precursors
1:08:59.037820 INFO: === Search parameters used ===
1:08:59.038048 INFO: rt_error       : 1662.8485107421875
1:08:59.038104 INFO: mobility_error : 0.1
1:08:59.038153 INFO: num_candidates : 1
1:08:59.038200 INFO: ms1_error      : 30
1:08:59.038244 INFO: ms2_error      : 30
1:08:59.038297 INFO: fwhm_rt        : 5
1:08:59.038343 INFO: quant_window   : 3
1:08:59.038387 INFO: ==============================================
1:08:59.201376 INFO: performing precursor FDR with 40 features
1:08:59.201540 INFO: Decoy channel: -1
1:08:59.201572 INFO: Competetive: True
1:08:59.217221 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:59.226979 INFO: Using random state 923258 for train-test-split
1:08:59.514147 INFO: Test AUC: 0.506
1:08:59.514284 INFO: Train AUC: 0.504
1:08:59.514314 INFO: AUC difference: 0.56%
1:08:59.748538 INFO: Resetting torch num_threads to 80
1:08:59.758955 PROGRESS: === Extracted 24672 precursors and 141874 fragments ===
1:08:59.759651 INFO: === FDR correction performed with classifier version -1 ===
1:08:59.760292 PROGRESS: ============================= Precursor FDR =============================
1:08:59.760384 PROGRESS: Total precursors accumulated: 1
1:08:59.760443 PROGRESS: Target precursors: 1 (100.00%)
1:08:59.760496 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:59.760543 PROGRESS: 
1:08:59.760588 PROGRESS: Precursor Summary:
1:08:59.761556 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:08:59.761646 PROGRESS: 
1:08:59.761702 PROGRESS: Protein Summary:
1:08:59.762747 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:08:59.762831 PROGRESS: =========================================================================
1:08:59.763557 INFO: Target number of precursors not reached yet.
1:08:59.863286 INFO: Starting optimization step 6.
1:08:59.863602 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:08:59.863699 INFO: Using ng extraction backend
1:08:59.863768 PROGRESS: Extracting batch of 25144 precursors
1:08:59.911074 INFO: === Search parameters used ===
1:08:59.911546 INFO: rt_error       : 1662.8485107421875
1:08:59.911599 INFO: mobility_error : 0.1
1:08:59.911645 INFO: num_candidates : 1
1:08:59.911687 INFO: ms1_error      : 30
1:08:59.911727 INFO: ms2_error      : 30
1:08:59.911767 INFO: fwhm_rt        : 5
1:08:59.911804 INFO: quant_window   : 3
1:08:59.911843 INFO: ==============================================
1:09:00.174910 INFO: performing precursor FDR with 40 features
1:09:00.175065 INFO: Decoy channel: -1
1:09:00.175094 INFO: Competetive: True
1:09:00.199511 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:00.214624 INFO: Using random state 253448 for train-test-split
1:09:00.926448 INFO: Test AUC: 0.544
1:09:00.926591 INFO: Train AUC: 0.550
1:09:00.926622 INFO: AUC difference: 1.15%
1:09:01.165539 INFO: Resetting torch num_threads to 80
1:09:01.178616 PROGRESS: === Extracted 49781 precursors and 286451 fragments ===
1:09:01.179254 INFO: === FDR correction performed with classifier version -1 ===
1:09:01.179855 PROGRESS: ============================= Precursor FDR =============================
1:09:01.179947 PROGRESS: Total precursors accumulated: 80
1:09:01.180008 PROGRESS: Target precursors: 80 (100.00%)
1:09:01.180059 PROGRESS: Decoy precursors: 0 (0.00%)
1:09:01.180105 PROGRESS: 
1:09:01.180149 PROGRESS: Precursor Summary:
1:09:01.181106 PROGRESS: Channel   0:	 0.050 FDR:    80; 0.010 FDR:    80; 0.001 FDR:    80
1:09:01.181192 PROGRESS: 
1:09:01.181247 PROGRESS: Protein Summary:
1:09:01.182332 PROGRESS: Channel   0:	 0.050 FDR:    79; 0.010 FDR:    79; 0.001 FDR:    79
1:09:01.182422 PROGRESS: =========================================================================
1:09:01.183366 INFO: Target number of precursors not reached yet.
1:09:01.320177 INFO: Starting optimization step 7.
1:09:01.320497 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:09:01.320590 INFO: Using ng extraction backend
1:09:01.320658 PROGRESS: Extracting batch of 50233 precursors
1:09:01.409678 INFO: === Search parameters used ===
1:09:01.410092 INFO: rt_error       : 1662.8485107421875
1:09:01.410146 INFO: mobility_error : 0.1
1:09:01.410193 INFO: num_candidates : 1
1:09:01.410236 INFO: ms1_error      : 30
1:09:01.410279 INFO: ms2_error      : 30
1:09:01.410320 INFO: fwhm_rt        : 5
1:09:01.410362 INFO: quant_window   : 3
1:09:01.410402 INFO: ==============================================
1:09:01.936518 INFO: performing precursor FDR with 40 features
1:09:01.936665 INFO: Decoy channel: -1
1:09:01.936692 INFO: Competetive: True
1:09:01.990817 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:02.024418 INFO: Using random state 852924 for train-test-split
1:09:03.811988 INFO: Test AUC: 0.583
1:09:03.812119 INFO: Train AUC: 0.584
1:09:03.812150 INFO: AUC difference: 0.09%
1:09:04.073925 INFO: Resetting torch num_threads to 80
1:09:04.102751 PROGRESS: === Extracted 99935 precursors and 574371 fragments ===
1:09:04.103531 INFO: === FDR correction performed with classifier version -1 ===
1:09:04.104178 PROGRESS: ============================= Precursor FDR =============================
1:09:04.104272 PROGRESS: Total precursors accumulated: 228
1:09:04.104333 PROGRESS: Target precursors: 226 (99.12%)
1:09:04.104385 PROGRESS: Decoy precursors: 2 (0.88%)
1:09:04.104430 PROGRESS: 
1:09:04.104474 PROGRESS: Precursor Summary:
1:09:04.105413 PROGRESS: Channel   0:	 0.050 FDR:   226; 0.010 FDR:   226; 0.001 FDR:     0
1:09:04.105508 PROGRESS: 
1:09:04.105564 PROGRESS: Protein Summary:
1:09:04.106634 PROGRESS: Channel   0:	 0.050 FDR:   217; 0.010 FDR:   217; 0.001 FDR:     0
1:09:04.106724 PROGRESS: =========================================================================
1:09:04.109350 INFO: Target number of precursors reached.
1:09:04.152850 INFO: fragments_df: keeping 2239 of 574371 [sum(precursor_idx_mask)=2479 sum(mass_error_mask)=574371 stop_rank=2239
1:09:04.378203 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:04.486005 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:04.787287 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:09:04.787828 INFO: Using score_cutoff 11.342170143127442 (fac=0.99, q=1)
1:09:04.788155 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:09:04.788232 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:09:04.788284 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.342170143127442
1:09:04.788342 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:04.937201 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:05.115593 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:09:05.116178 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:09:05.116419 INFO: Starting optimization step 8.
1:09:05.116631 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:09:05.116858 INFO: Using ng extraction backend
1:09:05.117056 PROGRESS: Extracting batch of 100097 precursors
1:09:05.294977 INFO: === Search parameters used ===
1:09:05.295354 INFO: rt_error       : 1662.8485107421875
1:09:05.295408 INFO: mobility_error : 0.1
1:09:05.295453 INFO: num_candidates : 3
1:09:05.295494 INFO: ms1_error      : 30
1:09:05.295532 INFO: ms2_error      : 30
1:09:05.295572 INFO: fwhm_rt        : 3.0
1:09:05.295611 INFO: quant_window   : 3
1:09:05.295648 INFO: ==============================================
1:09:06.933411 INFO: performing precursor FDR with 40 features
1:09:06.933553 INFO: Decoy channel: -1
1:09:06.933583 INFO: Competetive: True
1:09:07.048722 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:07.172837 INFO: Using random state 266969 for train-test-split
1:09:12.275788 INFO: Test AUC: 0.580
1:09:12.275928 INFO: Train AUC: 0.595
1:09:12.275960 INFO: AUC difference: 2.65%
1:09:12.594730 INFO: Resetting torch num_threads to 80
1:09:12.605437 PROGRESS: === Extracted 299811 precursors and 1681375 fragments ===
1:09:12.605829 INFO: === FDR correction performed with classifier version 7 ===
1:09:12.606275 PROGRESS: ============================= Precursor FDR =============================
1:09:12.606362 PROGRESS: Total precursors accumulated: 250
1:09:12.606421 PROGRESS: Target precursors: 248 (99.20%)
1:09:12.606471 PROGRESS: Decoy precursors: 2 (0.80%)
1:09:12.606515 PROGRESS: 
1:09:12.606560 PROGRESS: Precursor Summary:
1:09:12.607423 PROGRESS: Channel   0:	 0.050 FDR:   248; 0.010 FDR:   248; 0.001 FDR:   202
1:09:12.607510 PROGRESS: 
1:09:12.607573 PROGRESS: Protein Summary:
1:09:12.608610 PROGRESS: Channel   0:	 0.050 FDR:   236; 0.010 FDR:   236; 0.001 FDR:   197
1:09:12.608701 PROGRESS: =========================================================================
1:09:12.613271 INFO: Target number of precursors reached.
1:09:12.724030 INFO: fragments_df: keeping 3597 of 1681375 [sum(precursor_idx_mask)=5943 sum(mass_error_mask)=1681375 stop_rank=3597
1:09:12.966486 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:13.082065 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:13.539792 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:13.540233 INFO: Using score_cutoff 14.255079125976563 (fac=0.99, q=1)
1:09:13.540526 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:13.540605 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:13.540659 INFO: Updating optimization_manager: score_cutoff        : 11.342170143127442 -> 14.255079125976563
1:09:13.540718 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:13.602014 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:13.763930 INFO: === checking if optimization conditions were reached ===
1:09:13.764386 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
1:09:13.767087 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.745636996191881
1:09:13.767225 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 6.7456.
1:09:13.767320 INFO: ==============================================
1:09:13.767402 INFO: Starting optimization step 9.
1:09:13.767473 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:09:13.767544 INFO: Using ng extraction backend
1:09:13.767614 PROGRESS: Extracting batch of 100097 precursors
1:09:13.946051 INFO: === Search parameters used ===
1:09:13.946401 INFO: rt_error       : 1662.8485107421875
1:09:13.946459 INFO: mobility_error : 0.1
1:09:13.946507 INFO: num_candidates : 3
1:09:13.946553 INFO: ms1_error      : 30
1:09:13.946597 INFO: ms2_error      : 6.745636996191881
1:09:13.946640 INFO: fwhm_rt        : 3.0
1:09:13.946681 INFO: quant_window   : 3
1:09:13.946722 INFO: ==============================================
1:09:15.401976 INFO: performing precursor FDR with 40 features
1:09:15.402107 INFO: Decoy channel: -1
1:09:15.402148 INFO: Competetive: True
1:09:15.482699 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:15.616216 INFO: Using random state 266969 for train-test-split
1:09:20.896485 INFO: Test AUC: 0.587
1:09:20.896621 INFO: Train AUC: 0.593
1:09:20.896652 INFO: AUC difference: 0.98%
1:09:21.210760 INFO: Resetting torch num_threads to 80
1:09:21.222100 PROGRESS: === Extracted 300279 precursors and 1818443 fragments ===
1:09:21.222509 INFO: === FDR correction performed with classifier version 7 ===
1:09:21.222965 PROGRESS: ============================= Precursor FDR =============================
1:09:21.223057 PROGRESS: Total precursors accumulated: 315
1:09:21.223118 PROGRESS: Target precursors: 312 (99.05%)
1:09:21.223170 PROGRESS: Decoy precursors: 3 (0.95%)
1:09:21.223217 PROGRESS: 
1:09:21.223260 PROGRESS: Precursor Summary:
1:09:21.224177 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   312; 0.001 FDR:   305
1:09:21.224266 PROGRESS: 
1:09:21.224320 PROGRESS: Protein Summary:
1:09:21.225406 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   298; 0.001 FDR:   291
1:09:21.225507 PROGRESS: =========================================================================
1:09:21.230027 INFO: Target number of precursors reached.
1:09:21.346240 INFO: fragments_df: keeping 4452 of 1818443 [sum(precursor_idx_mask)=7691 sum(mass_error_mask)=1818443 stop_rank=4452
1:09:21.592119 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:21.694016 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:22.217509 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:22.217965 INFO: Using score_cutoff 12.115887202262877 (fac=0.99, q=1)
1:09:22.218254 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:22.218333 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:22.218388 INFO: Updating optimization_manager: score_cutoff        : 14.255079125976563 -> 12.115887202262877
1:09:22.218440 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:22.279648 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:22.428058 INFO: === checking if optimization conditions were reached ===
1:09:22.428418 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
1:09:22.430899 INFO: Updating optimization_manager: ms2_error           : 6.745636996191881 -> 6.777928779112163
1:09:22.431069 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 6.7779.
1:09:22.431149 INFO: ==============================================
1:09:22.431229 INFO: Starting optimization step 10.
1:09:22.431298 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:09:22.431368 INFO: Using ng extraction backend
1:09:22.431437 PROGRESS: Extracting batch of 100097 precursors
1:09:22.609584 INFO: === Search parameters used ===
1:09:22.609974 INFO: rt_error       : 1662.8485107421875
1:09:22.610059 INFO: mobility_error : 0.1
1:09:22.610132 INFO: num_candidates : 3
1:09:22.610201 INFO: ms1_error      : 30
1:09:22.610271 INFO: ms2_error      : 6.777928779112163
1:09:22.610339 INFO: fwhm_rt        : 3.0
1:09:22.610407 INFO: quant_window   : 3
1:09:22.610477 INFO: ==============================================
1:09:24.462727 INFO: performing precursor FDR with 40 features
1:09:24.462885 INFO: Decoy channel: -1
1:09:24.462912 INFO: Competetive: True
1:09:24.576190 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:24.708846 INFO: Using random state 266969 for train-test-split
1:09:28.785173 INFO: Test AUC: 0.586
1:09:28.785322 INFO: Train AUC: 0.595
1:09:28.785356 INFO: AUC difference: 1.50%
1:09:29.106575 INFO: Resetting torch num_threads to 80
1:09:29.119547 PROGRESS: === Extracted 300279 precursors and 1819390 fragments ===
1:09:29.120015 INFO: === FDR correction performed with classifier version 7 ===
1:09:29.120507 PROGRESS: ============================= Precursor FDR =============================
1:09:29.120596 PROGRESS: Total precursors accumulated: 330
1:09:29.120669 PROGRESS: Target precursors: 327 (99.09%)
1:09:29.120720 PROGRESS: Decoy precursors: 3 (0.91%)
1:09:29.120774 PROGRESS: 
1:09:29.120822 PROGRESS: Precursor Summary:
1:09:29.121753 PROGRESS: Channel   0:	 0.050 FDR:   327; 0.010 FDR:   327; 0.001 FDR:   297
1:09:29.121844 PROGRESS: 
1:09:29.121912 PROGRESS: Protein Summary:
1:09:29.123009 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   312; 0.001 FDR:   282
1:09:29.123096 PROGRESS: =========================================================================
1:09:29.129813 INFO: Target number of precursors reached.
1:09:29.250516 INFO: fragments_df: keeping 4598 of 1819390 [sum(precursor_idx_mask)=7983 sum(mass_error_mask)=1819390 stop_rank=4598
1:09:29.509619 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:29.688181 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:30.261833 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:30.262380 INFO: Using score_cutoff 9.51459311027527 (fac=0.99, q=1)
1:09:30.262697 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:30.262778 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:30.262835 INFO: Updating optimization_manager: score_cutoff        : 12.115887202262877 -> 9.51459311027527
1:09:30.262896 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:30.355163 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:30.505934 INFO: === checking if optimization conditions were reached ===
1:09:30.506501 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
1:09:30.507976 INFO: Updating optimization_manager: ms2_error           : 6.777928779112163 -> 6.777928779112163
1:09:30.508147 INFO: Updating optimization_manager: classifier_version  : 7 -> 10
1:09:30.508281 INFO: Updating optimization_manager: score_cutoff        : 9.51459311027527 -> 9.51459311027527
1:09:30.508402 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:30.508522 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:30.508643 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 6.7779 found after 3 searches.
1:09:30.508743 INFO: ==============================================
1:09:30.508872 PROGRESS: Optimization finished for ms2_error.
1:09:30.757604 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:30.821274 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:31.013061 INFO: Starting optimization step 0.
1:09:31.013397 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:09:31.013578 INFO: Using ng extraction backend
1:09:31.013924 PROGRESS: Extracting batch of 100097 precursors
1:09:31.193857 INFO: === Search parameters used ===
1:09:31.194241 INFO: rt_error       : 1662.8485107421875
1:09:31.194298 INFO: mobility_error : 0.1
1:09:31.194345 INFO: num_candidates : 3
1:09:31.194388 INFO: ms1_error      : 30
1:09:31.194441 INFO: ms2_error      : 6.777928779112163
1:09:31.194483 INFO: fwhm_rt        : 3.0
1:09:31.194522 INFO: quant_window   : 3
1:09:31.194560 INFO: ==============================================
1:09:32.704839 INFO: performing precursor FDR with 40 features
1:09:32.704970 INFO: Decoy channel: -1
1:09:32.704996 INFO: Competetive: True
1:09:32.786258 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:32.896986 INFO: Using random state 121843 for train-test-split
1:09:38.165722 INFO: Test AUC: 0.587
1:09:38.165940 INFO: Train AUC: 0.599
1:09:38.165974 INFO: AUC difference: 1.88%
1:09:38.554592 INFO: Resetting torch num_threads to 80
1:09:38.572402 PROGRESS: === Extracted 300279 precursors and 1820236 fragments ===
1:09:38.573899 INFO: === FDR correction performed with classifier version 10 ===
1:09:38.574448 PROGRESS: ============================= Precursor FDR =============================
1:09:38.574541 PROGRESS: Total precursors accumulated: 284
1:09:38.574600 PROGRESS: Target precursors: 282 (99.30%)
1:09:38.574662 PROGRESS: Decoy precursors: 2 (0.70%)
1:09:38.574707 PROGRESS: 
1:09:38.574750 PROGRESS: Precursor Summary:
1:09:38.575741 PROGRESS: Channel   0:	 0.050 FDR:   282; 0.010 FDR:   282; 0.001 FDR:   246
1:09:38.575833 PROGRESS: 
1:09:38.575886 PROGRESS: Protein Summary:
1:09:38.576998 PROGRESS: Channel   0:	 0.050 FDR:   269; 0.010 FDR:   269; 0.001 FDR:   238
1:09:38.577091 PROGRESS: =========================================================================
1:09:38.586804 INFO: Target number of precursors reached.
1:09:38.719765 INFO: fragments_df: keeping 3976 of 1820236 [sum(precursor_idx_mask)=6858 sum(mass_error_mask)=1820236 stop_rank=3976
1:09:38.969671 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:39.099374 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:39.627174 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:39.627689 INFO: Using score_cutoff 10.00087634124756 (fac=0.99, q=1)
1:09:39.628021 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:39.628101 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:39.628156 INFO: Updating optimization_manager: score_cutoff        : 9.51459311027527 -> 10.00087634124756
1:09:39.628216 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:39.694904 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:39.845313 INFO: === checking if optimization conditions were reached ===
1:09:39.845740 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:09:39.848248 INFO: Updating optimization_manager: rt_error            : 1662.8485107421875 -> 322.2088218905434
1:09:39.848370 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 322.2088.
1:09:39.848450 INFO: ==============================================
1:09:39.848532 INFO: Starting optimization step 1.
1:09:39.848602 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:09:39.848683 INFO: Using ng extraction backend
1:09:39.848764 PROGRESS: Extracting batch of 100097 precursors
1:09:40.027541 INFO: === Search parameters used ===
1:09:40.027907 INFO: rt_error       : 322.2088218905434
1:09:40.027966 INFO: mobility_error : 0.1
1:09:40.028029 INFO: num_candidates : 3
1:09:40.028075 INFO: ms1_error      : 30
1:09:40.028118 INFO: ms2_error      : 6.777928779112163
1:09:40.028162 INFO: fwhm_rt        : 3.0
1:09:40.028207 INFO: quant_window   : 3
1:09:40.028247 INFO: ==============================================
1:09:41.224149 INFO: performing precursor FDR with 40 features
1:09:41.224304 INFO: Decoy channel: -1
1:09:41.224332 INFO: Competetive: True
1:09:41.351229 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:41.516486 INFO: Using random state 121843 for train-test-split
1:09:46.872109 INFO: Test AUC: 0.592
1:09:46.872265 INFO: Train AUC: 0.598
1:09:46.872296 INFO: AUC difference: 1.01%
1:09:47.191648 INFO: Resetting torch num_threads to 80
1:09:47.206938 PROGRESS: === Extracted 300247 precursors and 1781165 fragments ===
1:09:47.207407 INFO: === FDR correction performed with classifier version 10 ===
1:09:47.207874 PROGRESS: ============================= Precursor FDR =============================
1:09:47.207962 PROGRESS: Total precursors accumulated: 356
1:09:47.208025 PROGRESS: Target precursors: 353 (99.16%)
1:09:47.208076 PROGRESS: Decoy precursors: 3 (0.84%)
1:09:47.208123 PROGRESS: 
1:09:47.208169 PROGRESS: Precursor Summary:
1:09:47.209098 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   353; 0.001 FDR:   288
1:09:47.209186 PROGRESS: 
1:09:47.209241 PROGRESS: Protein Summary:
1:09:47.210353 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   338; 0.001 FDR:   274
1:09:47.210446 PROGRESS: =========================================================================
1:09:47.227898 INFO: Target number of precursors reached.
1:09:47.347883 INFO: fragments_df: keeping 4867 of 1781165 [sum(precursor_idx_mask)=8578 sum(mass_error_mask)=1781165 stop_rank=4867
1:09:47.579630 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:47.703826 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:48.366210 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:48.366729 INFO: Using score_cutoff 8.838004789352416 (fac=0.99, q=1)
1:09:48.367038 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:48.367116 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:48.367170 INFO: Updating optimization_manager: score_cutoff        : 10.00087634124756 -> 8.838004789352416
1:09:48.367228 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:48.434420 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:48.586105 INFO: === checking if optimization conditions were reached ===
1:09:48.586656 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:09:48.589411 INFO: Updating optimization_manager: rt_error            : 322.2088218905434 -> 194.17791013910403
1:09:48.589670 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 194.1779.
1:09:48.589871 INFO: ==============================================
1:09:48.590074 INFO: Starting optimization step 2.
1:09:48.590265 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:09:48.590466 INFO: Using ng extraction backend
1:09:48.590657 PROGRESS: Extracting batch of 100097 precursors
1:09:48.769634 INFO: === Search parameters used ===
1:09:48.770023 INFO: rt_error       : 194.17791013910403
1:09:48.770082 INFO: mobility_error : 0.1
1:09:48.770128 INFO: num_candidates : 3
1:09:48.770174 INFO: ms1_error      : 30
1:09:48.770218 INFO: ms2_error      : 6.777928779112163
1:09:48.770259 INFO: fwhm_rt        : 3.0
1:09:48.770302 INFO: quant_window   : 3
1:09:48.770345 INFO: ==============================================
1:09:49.938502 INFO: performing precursor FDR with 40 features
1:09:49.938652 INFO: Decoy channel: -1
1:09:49.938679 INFO: Competetive: True
1:09:50.043187 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:50.173893 INFO: Using random state 121843 for train-test-split
1:09:55.431271 INFO: Test AUC: 0.588
1:09:55.431422 INFO: Train AUC: 0.595
1:09:55.431453 INFO: AUC difference: 1.20%
1:09:55.755838 INFO: Resetting torch num_threads to 80
1:09:55.771039 PROGRESS: === Extracted 300224 precursors and 1725734 fragments ===
1:09:55.771494 INFO: === FDR correction performed with classifier version 10 ===
1:09:55.772001 PROGRESS: ============================= Precursor FDR =============================
1:09:55.772091 PROGRESS: Total precursors accumulated: 361
1:09:55.772151 PROGRESS: Target precursors: 358 (99.17%)
1:09:55.772200 PROGRESS: Decoy precursors: 3 (0.83%)
1:09:55.772249 PROGRESS: 
1:09:55.772293 PROGRESS: Precursor Summary:
1:09:55.773227 PROGRESS: Channel   0:	 0.050 FDR:   358; 0.010 FDR:   358; 0.001 FDR:   326
1:09:55.773322 PROGRESS: 
1:09:55.773377 PROGRESS: Protein Summary:
1:09:55.774497 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   342; 0.001 FDR:   311
1:09:55.774590 PROGRESS: =========================================================================
1:09:55.780811 INFO: Target number of precursors reached.
1:09:55.898387 INFO: fragments_df: keeping 4932 of 1725734 [sum(precursor_idx_mask)=8683 sum(mass_error_mask)=1725734 stop_rank=4932
1:09:56.143445 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:56.411155 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:57.220459 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:57.221023 INFO: Using score_cutoff 11.742974802589416 (fac=0.99, q=1)
1:09:57.221346 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:57.221423 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:57.221483 INFO: Updating optimization_manager: score_cutoff        : 8.838004789352416 -> 11.742974802589416
1:09:57.221541 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:57.340570 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:57.548300 INFO: === checking if optimization conditions were reached ===
1:09:57.548713 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:09:57.551552 INFO: Updating optimization_manager: rt_error            : 194.17791013910403 -> 132.00577264117825
1:09:57.551681 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 132.0058.
1:09:57.551761 INFO: ==============================================
1:09:57.551841 INFO: Starting optimization step 3.
1:09:57.551905 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:09:57.551978 INFO: Using ng extraction backend
1:09:57.552059 PROGRESS: Extracting batch of 100097 precursors
1:09:57.745533 INFO: === Search parameters used ===
1:09:57.745903 INFO: rt_error       : 132.00577264117825
1:09:57.745960 INFO: mobility_error : 0.1
1:09:57.746007 INFO: num_candidates : 3
1:09:57.746051 INFO: ms1_error      : 30
1:09:57.746091 INFO: ms2_error      : 6.777928779112163
1:09:57.746132 INFO: fwhm_rt        : 3.0
1:09:57.746171 INFO: quant_window   : 3
1:09:57.746210 INFO: ==============================================
1:09:59.025781 INFO: performing precursor FDR with 40 features
1:09:59.025937 INFO: Decoy channel: -1
1:09:59.025965 INFO: Competetive: True
1:09:59.131530 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:59.258684 INFO: Using random state 121843 for train-test-split
1:10:04.446124 INFO: Test AUC: 0.581
1:10:04.446279 INFO: Train AUC: 0.595
1:10:04.446312 INFO: AUC difference: 2.40%
1:10:04.767498 INFO: Resetting torch num_threads to 80
1:10:04.785407 PROGRESS: === Extracted 300149 precursors and 1674082 fragments ===
1:10:04.785956 INFO: === FDR correction performed with classifier version 10 ===
1:10:04.786454 PROGRESS: ============================= Precursor FDR =============================
1:10:04.786545 PROGRESS: Total precursors accumulated: 375
1:10:04.786603 PROGRESS: Target precursors: 372 (99.20%)
1:10:04.786651 PROGRESS: Decoy precursors: 3 (0.80%)
1:10:04.786697 PROGRESS: 
1:10:04.786744 PROGRESS: Precursor Summary:
1:10:04.787700 PROGRESS: Channel   0:	 0.050 FDR:   372; 0.010 FDR:   372; 0.001 FDR:   317
1:10:04.787792 PROGRESS: 
1:10:04.787847 PROGRESS: Protein Summary:
1:10:04.789001 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   303
1:10:04.789104 PROGRESS: =========================================================================
1:10:04.797963 INFO: Target number of precursors reached.
1:10:04.910582 INFO: fragments_df: keeping 5000 of 1674082 [sum(precursor_idx_mask)=8844 sum(mass_error_mask)=1674082 stop_rank=5000
1:10:05.148220 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:05.274369 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:05.956058 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:05.956585 INFO: Using score_cutoff 9.794734684181215 (fac=0.99, q=1)
1:10:05.956909 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:05.956991 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:05.957048 INFO: Updating optimization_manager: score_cutoff        : 11.742974802589416 -> 9.794734684181215
1:10:05.957107 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:06.040093 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:06.197985 INFO: === checking if optimization conditions were reached ===
1:10:06.198783 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:10:06.201741 INFO: Updating optimization_manager: rt_error            : 132.00577264117825 -> 102.93185371157638
1:10:06.202069 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 102.9319.
1:10:06.202324 INFO: ==============================================
1:10:06.202585 INFO: Starting optimization step 4.
1:10:06.202975 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:10:06.203226 INFO: Using ng extraction backend
1:10:06.203468 PROGRESS: Extracting batch of 100097 precursors
1:10:06.384948 INFO: === Search parameters used ===
1:10:06.385329 INFO: rt_error       : 102.93185371157638
1:10:06.385400 INFO: mobility_error : 0.1
1:10:06.385485 INFO: num_candidates : 3
1:10:06.385546 INFO: ms1_error      : 30
1:10:06.385605 INFO: ms2_error      : 6.777928779112163
1:10:06.385662 INFO: fwhm_rt        : 3.0
1:10:06.385718 INFO: quant_window   : 3
1:10:06.385774 INFO: ==============================================
1:10:07.534546 INFO: performing precursor FDR with 40 features
1:10:07.534703 INFO: Decoy channel: -1
1:10:07.534729 INFO: Competetive: True
1:10:07.638042 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:07.764107 INFO: Using random state 121843 for train-test-split
1:10:12.685981 INFO: Test AUC: 0.582
1:10:12.686140 INFO: Train AUC: 0.593
1:10:12.686172 INFO: AUC difference: 1.87%
1:10:13.007517 INFO: Resetting torch num_threads to 80
1:10:13.022887 PROGRESS: === Extracted 300071 precursors and 1634325 fragments ===
1:10:13.023343 INFO: === FDR correction performed with classifier version 10 ===
1:10:13.023808 PROGRESS: ============================= Precursor FDR =============================
1:10:13.023893 PROGRESS: Total precursors accumulated: 375
1:10:13.023952 PROGRESS: Target precursors: 372 (99.20%)
1:10:13.024000 PROGRESS: Decoy precursors: 3 (0.80%)
1:10:13.024045 PROGRESS: 
1:10:13.024087 PROGRESS: Precursor Summary:
1:10:13.025012 PROGRESS: Channel   0:	 0.050 FDR:   372; 0.010 FDR:   372; 0.001 FDR:   353
1:10:13.025098 PROGRESS: 
1:10:13.025161 PROGRESS: Protein Summary:
1:10:13.026396 PROGRESS: Channel   0:	 0.050 FDR:   356; 0.010 FDR:   356; 0.001 FDR:   337
1:10:13.026486 PROGRESS: =========================================================================
1:10:13.033179 INFO: Target number of precursors reached.
1:10:13.147100 INFO: fragments_df: keeping 4975 of 1634325 [sum(precursor_idx_mask)=8747 sum(mass_error_mask)=1634325 stop_rank=4975
1:10:13.376017 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:13.485397 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:14.106642 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:14.107153 INFO: Using score_cutoff 10.509505505275726 (fac=0.99, q=1)
1:10:14.107463 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:14.107547 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:14.107601 INFO: Updating optimization_manager: score_cutoff        : 9.794734684181215 -> 10.509505505275726
1:10:14.107656 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:14.180731 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:14.332645 INFO: === checking if optimization conditions were reached ===
1:10:14.332986 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:10:14.335150 INFO: Updating optimization_manager: rt_error            : 102.93185371157638 -> 71.7184496686549
1:10:14.335264 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 71.7184.
1:10:14.335351 INFO: ==============================================
1:10:14.335424 INFO: Starting optimization step 5.
1:10:14.335486 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:10:14.335548 INFO: Using ng extraction backend
1:10:14.335608 PROGRESS: Extracting batch of 100097 precursors
1:10:14.511574 INFO: === Search parameters used ===
1:10:14.511913 INFO: rt_error       : 71.7184496686549
1:10:14.511974 INFO: mobility_error : 0.1
1:10:14.512025 INFO: num_candidates : 3
1:10:14.512071 INFO: ms1_error      : 30
1:10:14.512117 INFO: ms2_error      : 6.777928779112163
1:10:14.512158 INFO: fwhm_rt        : 3.0
1:10:14.512202 INFO: quant_window   : 3
1:10:14.512243 INFO: ==============================================
1:10:15.621221 INFO: performing precursor FDR with 40 features
1:10:15.621363 INFO: Decoy channel: -1
1:10:15.621388 INFO: Competetive: True
1:10:15.702564 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:15.809586 INFO: Using random state 121843 for train-test-split
1:10:21.205338 INFO: Test AUC: 0.585
1:10:21.205484 INFO: Train AUC: 0.594
1:10:21.205515 INFO: AUC difference: 1.48%
1:10:21.522034 INFO: Resetting torch num_threads to 80
1:10:21.534124 PROGRESS: === Extracted 298417 precursors and 1533822 fragments ===
1:10:21.534544 INFO: === FDR correction performed with classifier version 10 ===
1:10:21.535031 PROGRESS: ============================= Precursor FDR =============================
1:10:21.535120 PROGRESS: Total precursors accumulated: 344
1:10:21.535178 PROGRESS: Target precursors: 341 (99.13%)
1:10:21.535229 PROGRESS: Decoy precursors: 3 (0.87%)
1:10:21.535273 PROGRESS: 
1:10:21.535318 PROGRESS: Precursor Summary:
1:10:21.536246 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   341; 0.001 FDR:   326
1:10:21.536334 PROGRESS: 
1:10:21.536388 PROGRESS: Protein Summary:
1:10:21.537523 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   328; 0.001 FDR:   313
1:10:21.537628 PROGRESS: =========================================================================
1:10:21.542222 INFO: Target number of precursors reached.
1:10:21.644593 INFO: fragments_df: keeping 4406 of 1533822 [sum(precursor_idx_mask)=7724 sum(mass_error_mask)=1533822 stop_rank=4406
1:10:21.888423 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:22.097876 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:24.364830 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:24.365289 INFO: Using score_cutoff 11.04085316848755 (fac=0.99, q=1)
1:10:24.365595 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:24.365677 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:24.365731 INFO: Updating optimization_manager: score_cutoff        : 10.509505505275726 -> 11.04085316848755
1:10:24.365784 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:24.446176 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:24.597445 INFO: === checking if optimization conditions were reached ===
1:10:24.598046 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:10:24.600701 INFO: Updating optimization_manager: rt_error            : 71.7184496686549 -> 53.888000787815955
1:10:24.600971 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 53.8880.
1:10:24.601170 INFO: ==============================================
1:10:24.601373 INFO: Starting optimization step 6.
1:10:24.601576 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:10:24.601804 INFO: Using ng extraction backend
1:10:24.601999 PROGRESS: Extracting batch of 100097 precursors
1:10:24.780977 INFO: === Search parameters used ===
1:10:24.781355 INFO: rt_error       : 53.888000787815955
1:10:24.781413 INFO: mobility_error : 0.1
1:10:24.781460 INFO: num_candidates : 3
1:10:24.781532 INFO: ms1_error      : 30
1:10:24.781578 INFO: ms2_error      : 6.777928779112163
1:10:24.781620 INFO: fwhm_rt        : 3.0
1:10:24.781659 INFO: quant_window   : 3
1:10:24.781697 INFO: ==============================================
1:10:25.824673 INFO: performing precursor FDR with 40 features
1:10:25.824811 INFO: Decoy channel: -1
1:10:25.824837 INFO: Competetive: True
1:10:25.903430 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:26.004343 INFO: Using random state 121843 for train-test-split
1:10:31.213108 INFO: Test AUC: 0.585
1:10:31.213253 INFO: Train AUC: 0.594
1:10:31.213284 INFO: AUC difference: 1.43%
1:10:31.529244 INFO: Resetting torch num_threads to 80
1:10:31.540774 PROGRESS: === Extracted 281679 precursors and 1385483 fragments ===
1:10:31.541193 INFO: === FDR correction performed with classifier version 10 ===
1:10:31.541702 PROGRESS: ============================= Precursor FDR =============================
1:10:31.541821 PROGRESS: Total precursors accumulated: 345
1:10:31.541893 PROGRESS: Target precursors: 342 (99.13%)
1:10:31.541960 PROGRESS: Decoy precursors: 3 (0.87%)
1:10:31.542027 PROGRESS: 
1:10:31.542088 PROGRESS: Precursor Summary:
1:10:31.543083 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   342; 0.001 FDR:   302
1:10:31.543184 PROGRESS: 
1:10:31.543252 PROGRESS: Protein Summary:
1:10:31.544407 PROGRESS: Channel   0:	 0.050 FDR:   330; 0.010 FDR:   330; 0.001 FDR:   290
1:10:31.544506 PROGRESS: =========================================================================
1:10:31.549017 INFO: Target number of precursors reached.
1:10:31.639523 INFO: fragments_df: keeping 4129 of 1385483 [sum(precursor_idx_mask)=7143 sum(mass_error_mask)=1385483 stop_rank=4129
1:10:31.882508 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:32.021275 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:32.570397 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:32.570840 INFO: Using score_cutoff 8.725469963550568 (fac=0.99, q=1)
1:10:32.571135 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:32.571213 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:32.571267 INFO: Updating optimization_manager: score_cutoff        : 11.04085316848755 -> 8.725469963550568
1:10:32.571321 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:32.631634 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:32.791001 INFO: === checking if optimization conditions were reached ===
1:10:32.791392 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:10:32.793998 INFO: Updating optimization_manager: rt_error            : 53.888000787815955 -> 40.385009227377054
1:10:32.794121 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 40.3850.
1:10:32.794201 INFO: ==============================================
1:10:32.794282 INFO: Starting optimization step 7.
1:10:32.794351 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:10:32.794421 INFO: Using ng extraction backend
1:10:32.794490 PROGRESS: Extracting batch of 100097 precursors
1:10:32.971274 INFO: === Search parameters used ===
1:10:32.971644 INFO: rt_error       : 40.385009227377054
1:10:32.971704 INFO: mobility_error : 0.1
1:10:32.971751 INFO: num_candidates : 3
1:10:32.971792 INFO: ms1_error      : 30
1:10:32.971831 INFO: ms2_error      : 6.777928779112163
1:10:32.971871 INFO: fwhm_rt        : 3.0
1:10:32.971913 INFO: quant_window   : 3
1:10:32.971951 INFO: ==============================================
1:10:33.991795 INFO: performing precursor FDR with 40 features
1:10:33.991935 INFO: Decoy channel: -1
1:10:33.991960 INFO: Competetive: True
1:10:34.068350 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:34.167173 INFO: Using random state 121843 for train-test-split
1:10:39.021461 INFO: Test AUC: 0.583
1:10:39.021613 INFO: Train AUC: 0.594
1:10:39.021644 INFO: AUC difference: 1.91%
1:10:39.338034 INFO: Resetting torch num_threads to 80
1:10:39.351876 PROGRESS: === Extracted 281765 precursors and 1390807 fragments ===
1:10:39.352344 INFO: === FDR correction performed with classifier version 10 ===
1:10:39.352874 PROGRESS: ============================= Precursor FDR =============================
1:10:39.352986 PROGRESS: Total precursors accumulated: 349
1:10:39.354894 PROGRESS: Target precursors: 346 (99.14%)
1:10:39.354986 PROGRESS: Decoy precursors: 3 (0.86%)
1:10:39.355051 PROGRESS: 
1:10:39.355113 PROGRESS: Precursor Summary:
1:10:39.356510 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   346; 0.001 FDR:   294
1:10:39.356801 PROGRESS: 
1:10:39.356891 PROGRESS: Protein Summary:
1:10:39.358571 PROGRESS: Channel   0:	 0.050 FDR:   333; 0.010 FDR:   333; 0.001 FDR:   283
1:10:39.358673 PROGRESS: =========================================================================
1:10:39.364967 INFO: Target number of precursors reached.
1:10:39.459600 INFO: fragments_df: keeping 4211 of 1390807 [sum(precursor_idx_mask)=7251 sum(mass_error_mask)=1390807 stop_rank=4211
1:10:39.703753 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:39.821011 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:40.315116 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:40.315573 INFO: Using score_cutoff 10.317410160541534 (fac=0.99, q=1)
1:10:40.315870 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:40.315952 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:40.316007 INFO: Updating optimization_manager: score_cutoff        : 8.725469963550568 -> 10.317410160541534
1:10:40.316063 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:40.376896 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:40.534444 INFO: === checking if optimization conditions were reached ===
1:10:40.534849 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1:10:40.537369 INFO: Updating optimization_manager: rt_error            : 40.385009227377054 -> 39.65023128624826
1:10:40.537505 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 39.6502.
1:10:40.537585 INFO: ==============================================
1:10:40.537666 INFO: Starting optimization step 8.
1:10:40.537737 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:10:40.537807 INFO: Using ng extraction backend
1:10:40.537877 PROGRESS: Extracting batch of 100097 precursors
1:10:40.712874 INFO: === Search parameters used ===
1:10:40.713238 INFO: rt_error       : 39.65023128624826
1:10:40.713294 INFO: mobility_error : 0.1
1:10:40.713344 INFO: num_candidates : 3
1:10:40.713389 INFO: ms1_error      : 30
1:10:40.713430 INFO: ms2_error      : 6.777928779112163
1:10:40.713484 INFO: fwhm_rt        : 3.0
1:10:40.713526 INFO: quant_window   : 3
1:10:40.713565 INFO: ==============================================
1:10:41.733869 INFO: performing precursor FDR with 40 features
1:10:41.734004 INFO: Decoy channel: -1
1:10:41.734030 INFO: Competetive: True
1:10:41.810202 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:41.910347 INFO: Using random state 121843 for train-test-split
1:10:46.869019 INFO: Test AUC: 0.584
1:10:46.869164 INFO: Train AUC: 0.592
1:10:46.869196 INFO: AUC difference: 1.37%
1:10:47.176867 INFO: Resetting torch num_threads to 80
1:10:47.188177 PROGRESS: === Extracted 281773 precursors and 1389363 fragments ===
1:10:47.188596 INFO: === FDR correction performed with classifier version 10 ===
1:10:47.189079 PROGRESS: ============================= Precursor FDR =============================
1:10:47.189174 PROGRESS: Total precursors accumulated: 338
1:10:47.189234 PROGRESS: Target precursors: 335 (99.11%)
1:10:47.189283 PROGRESS: Decoy precursors: 3 (0.89%)
1:10:47.189331 PROGRESS: 
1:10:47.189376 PROGRESS: Precursor Summary:
1:10:47.190356 PROGRESS: Channel   0:	 0.050 FDR:   335; 0.010 FDR:   335; 0.001 FDR:   297
1:10:47.190450 PROGRESS: 
1:10:47.190507 PROGRESS: Protein Summary:
1:10:47.191624 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   286
1:10:47.191714 PROGRESS: =========================================================================
1:10:47.195801 INFO: Target number of precursors reached.
1:10:47.287681 INFO: fragments_df: keeping 4111 of 1389363 [sum(precursor_idx_mask)=7089 sum(mass_error_mask)=1389363 stop_rank=4111
1:10:47.529150 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:47.659122 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:48.208258 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:48.208704 INFO: Using score_cutoff 10.993290047836304 (fac=0.99, q=1)
1:10:48.208996 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:48.209077 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:48.209140 INFO: Updating optimization_manager: score_cutoff        : 10.317410160541534 -> 10.993290047836304
1:10:48.209200 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:48.270151 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:48.422338 INFO: === checking if optimization conditions were reached ===
1:10:48.422630 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1:10:48.423745 INFO: Updating optimization_manager: rt_error            : 39.65023128624826 -> 39.65023128624826
1:10:48.423876 INFO: Updating optimization_manager: classifier_version  : 10 -> 19
1:10:48.423975 INFO: Updating optimization_manager: score_cutoff        : 10.993290047836304 -> 10.993290047836304
1:10:48.424062 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:48.424145 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:48.424228 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 39.6502 found after 9 searches.
1:10:48.424290 INFO: ==============================================
1:10:48.424363 PROGRESS: Optimization finished for rt_error.
1:10:48.660398 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:48.721866 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:48.902194 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:10:48.902422 PROGRESS: ==============================================
1:10:48.902489 PROGRESS: ms2_error      : 6.7779
1:10:48.902543 PROGRESS: rt_error       : 39.6502
1:10:48.902591 PROGRESS: ==============================================
1:10:48.903164 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:56.029737 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:11:12.839068 INFO: Using ng extraction backend
1:11:12.839513 PROGRESS: Extracting batch of 11065368 precursors
1:11:28.056619 INFO: === Search parameters used ===
1:11:28.057216 INFO: rt_error       : 39.65023128624826
1:11:28.057282 INFO: mobility_error : 0.1
1:11:28.057329 INFO: num_candidates : 3
1:11:28.057376 INFO: ms1_error      : 30
1:11:28.057419 INFO: ms2_error      : 6.777928779112163
1:11:28.057462 INFO: fwhm_rt        : 3.0
1:11:28.057519 INFO: quant_window   : 3
1:11:28.057559 INFO: ==============================================
1:11:49.148526 INFO: Removed 17676003 precursors with score below cutoff 10.993290047836304
1:12:05.657873 INFO: performing precursor FDR with 40 features
1:12:05.658653 INFO: Decoy channel: -1
1:12:05.658703 INFO: Competetive: True
1:12:07.138458 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:14.962806 INFO: Using random state 831129 for train-test-split
1:17:06.700770 INFO: Test AUC: 0.608
1:17:06.700999 INFO: Train AUC: 0.609
1:17:06.701043 INFO: AUC difference: 0.12%
1:17:12.884355 INFO: Resetting torch num_threads to 80
1:17:14.687242 PROGRESS: ============================= Precursor FDR =============================
1:17:14.687562 PROGRESS: Total precursors accumulated: 44,155
1:17:14.687629 PROGRESS: Target precursors: 43,718 (99.01%)
1:17:14.687681 PROGRESS: Decoy precursors: 437 (0.99%)
1:17:14.687727 PROGRESS: 
1:17:14.687771 PROGRESS: Precursor Summary:
1:17:14.698249 PROGRESS: Channel   0:	 0.050 FDR: 43,718; 0.010 FDR: 43,718; 0.001 FDR: 27,880
1:17:14.698487 PROGRESS: 
1:17:14.698560 PROGRESS: Protein Summary:
1:17:14.714293 PROGRESS: Channel   0:	 0.050 FDR: 8,536; 0.010 FDR: 8,536; 0.001 FDR: 6,174
1:17:14.714540 PROGRESS: =========================================================================
1:17:14.831805 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/psm.parquet
1:17:14.926701 INFO: Saving results to alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/frag.parquet
1:17:15.078897 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
1:17:45.415884 PROGRESS: Processing search outputs
1:17:45.416166 PROGRESS: Performing protein grouping and FDR
1:17:45.416216 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
1:17:45.466261 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
1:17:45.495395 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
1:17:45.527230 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
1:17:45.558422 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
1:17:45.593117 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
1:17:45.621299 INFO: Building combined output
1:17:45.660034 INFO: Performing protein inference
1:17:46.000680 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1:18:04.243359 INFO: Performing protein FDR
1:18:08.397909 INFO: Normalizing q-values using 12,603 targets and 1,951 decoys
1:18:08.401643 INFO: Test AUC: 0.858
1:18:08.401703 INFO: Train AUC: 0.857
1:18:08.401738 INFO: AUC difference: 0.13%
1:18:08.873888 PROGRESS: ================ Protein FDR =================
1:18:08.874038 PROGRESS: Unique protein groups in output
1:18:08.874071 PROGRESS:   1% protein FDR: 7,049
1:18:08.874092 PROGRESS: 
1:18:08.874112 PROGRESS: Unique precursor in output
1:18:08.874130 PROGRESS:   1% protein FDR: 73,874
1:18:08.874173 PROGRESS: ================================================
1:18:08.909986 PROGRESS: Building search statistics
1:18:08.968996 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/optimization_manager.pkl
1:18:08.969223 INFO: Initializing OptimizationManager
1:18:08.969663 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/calibration_manager.pkl
1:18:08.969746 INFO: Initializing CalibrationManager
1:18:08.970116 INFO: Loaded RawFileManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/raw_file_manager.pkl
1:18:08.970199 INFO: Initializing RawFileManager
1:18:08.989863 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/optimization_manager.pkl
1:18:08.990075 INFO: Initializing OptimizationManager
1:18:08.990280 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/calibration_manager.pkl
1:18:08.990353 INFO: Initializing CalibrationManager
1:18:08.990548 INFO: Loaded RawFileManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/raw_file_manager.pkl
1:18:08.990618 INFO: Initializing RawFileManager
1:18:09.010456 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/optimization_manager.pkl
1:18:09.010657 INFO: Initializing OptimizationManager
1:18:09.010873 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/calibration_manager.pkl
1:18:09.010946 INFO: Initializing CalibrationManager
1:18:09.011137 INFO: Loaded RawFileManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/raw_file_manager.pkl
1:18:09.011204 INFO: Initializing RawFileManager
1:18:09.030777 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/optimization_manager.pkl
1:18:09.030974 INFO: Initializing OptimizationManager
1:18:09.031175 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/calibration_manager.pkl
1:18:09.031247 INFO: Initializing CalibrationManager
1:18:09.031452 INFO: Loaded RawFileManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/raw_file_manager.pkl
1:18:09.031520 INFO: Initializing RawFileManager
1:18:09.051452 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/optimization_manager.pkl
1:18:09.051655 INFO: Initializing OptimizationManager
1:18:09.051848 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/calibration_manager.pkl
1:18:09.051920 INFO: Initializing CalibrationManager
1:18:09.052131 INFO: Loaded RawFileManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/raw_file_manager.pkl
1:18:09.052199 INFO: Initializing RawFileManager
1:18:09.070900 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/optimization_manager.pkl
1:18:09.071089 INFO: Initializing OptimizationManager
1:18:09.071278 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/calibration_manager.pkl
1:18:09.071348 INFO: Initializing CalibrationManager
1:18:09.071529 INFO: Loaded RawFileManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/raw_file_manager.pkl
1:18:09.071597 INFO: Initializing RawFileManager
1:18:09.073574 INFO: Writing stat output to disk
1:18:09.073674 INFO: Saving alphadia_zenoswath8600/library/stat.tsv to disk
1:18:09.081945 PROGRESS: Building internal statistics
1:18:09.082251 INFO: Loaded TimingManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/timing_manager.pkl
1:18:09.082297 INFO: Initializing TimingManager
1:18:09.082590 INFO: Loaded TimingManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/timing_manager.pkl
1:18:09.082634 INFO: Initializing TimingManager
1:18:09.082825 INFO: Loaded TimingManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/timing_manager.pkl
1:18:09.082865 INFO: Initializing TimingManager
1:18:09.083046 INFO: Loaded TimingManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/timing_manager.pkl
1:18:09.083084 INFO: Initializing TimingManager
1:18:09.083256 INFO: Loaded TimingManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/timing_manager.pkl
1:18:09.083293 INFO: Initializing TimingManager
1:18:09.083463 INFO: Loaded TimingManager from alphadia_zenoswath8600/library/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/timing_manager.pkl
1:18:09.083501 INFO: Initializing TimingManager
1:18:09.083892 INFO: Writing internal output to disk
1:18:09.083937 INFO: Saving alphadia_zenoswath8600/library/internal.tsv to disk
1:18:09.084399 PROGRESS: Performing label free quantification
1:18:09.121424 INFO: Accumulating fragment data
1:18:09.121617 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
1:18:09.265066 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
1:18:10.001870 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
1:18:10.753231 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
1:18:11.550561 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
1:18:12.404471 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
1:18:13.416607 PROGRESS: Performing label free quantification on the precursor level
1:18:13.416777 INFO: Filtering fragments by quality
1:18:13.610297 INFO: Performing label-free quantification using directLFQ
1:18:14.764792 INFO: 73874 lfq-groups total
1:18:56.590039 INFO: using 80 processes
1:18:56.773162 INFO: lfq-object 0
1:18:56.881235 INFO: lfq-object 100
1:18:56.907075 INFO: lfq-object 300
1:18:56.955714 INFO: lfq-object 500
1:18:56.974579 INFO: lfq-object 700
1:18:57.018280 INFO: lfq-object 400
1:18:57.027371 INFO: lfq-object 200
1:18:57.059825 INFO: lfq-object 600
1:18:57.087017 INFO: lfq-object 1000
1:18:57.108694 INFO: lfq-object 800
1:18:57.111959 INFO: lfq-object 1200
1:18:57.157869 INFO: lfq-object 1400
1:18:57.191149 INFO: lfq-object 1100
1:18:57.212568 INFO: lfq-object 900
1:18:57.219711 INFO: lfq-object 1300
1:18:57.265221 INFO: lfq-object 1700
1:18:57.288787 INFO: lfq-object 1500
1:18:57.336706 INFO: lfq-object 1900
1:18:57.365174 INFO: lfq-object 1800
1:18:57.374303 INFO: lfq-object 2100
1:18:57.394508 INFO: lfq-object 1600
1:18:57.436303 INFO: lfq-object 2000
1:18:57.482575 INFO: lfq-object 2200
1:18:57.562810 INFO: lfq-object 2400
1:18:57.586584 INFO: lfq-object 2300
1:18:57.663078 INFO: lfq-object 2500
1:18:57.673603 INFO: lfq-object 2600
1:18:57.777046 INFO: lfq-object 2700
1:18:57.789668 INFO: lfq-object 2800
1:18:57.904306 INFO: lfq-object 2900
1:18:58.060880 INFO: lfq-object 3000
1:18:58.102540 INFO: lfq-object 3100
1:18:58.145823 INFO: lfq-object 3300
1:18:58.208694 INFO: lfq-object 3200
1:18:58.248454 INFO: lfq-object 3400
1:19:00.836565 INFO: lfq-object 3500
1:19:00.939377 INFO: lfq-object 3600
1:19:00.972757 INFO: lfq-object 3700
1:19:01.090723 INFO: lfq-object 3800
1:19:01.112947 INFO: lfq-object 4000
1:19:01.171390 INFO: lfq-object 4200
1:19:01.181806 INFO: lfq-object 4400
1:19:01.213874 INFO: lfq-object 4100
1:19:01.221006 INFO: lfq-object 3900
1:19:01.277087 INFO: lfq-object 4300
1:19:01.288548 INFO: lfq-object 4500
1:19:01.314272 INFO: lfq-object 4700
1:19:01.384607 INFO: lfq-object 4900
1:19:01.385725 INFO: lfq-object 5100
1:19:01.390698 INFO: lfq-object 4600
1:19:01.420002 INFO: lfq-object 4800
1:19:01.488828 INFO: lfq-object 5000
1:19:01.489140 INFO: lfq-object 5200
1:19:01.583797 INFO: lfq-object 5400
1:19:01.587358 INFO: lfq-object 5300
1:19:01.647234 INFO: lfq-object 5600
1:19:01.695299 INFO: lfq-object 5500
1:19:01.722419 INFO: lfq-object 5800
1:19:01.750949 INFO: lfq-object 5700
1:19:01.827966 INFO: lfq-object 5900
1:19:01.924511 INFO: lfq-object 6100
1:19:01.932617 INFO: lfq-object 6000
1:19:02.030015 INFO: lfq-object 6200
1:19:02.126560 INFO: lfq-object 6300
1:19:02.200881 INFO: lfq-object 6500
1:19:02.228027 INFO: lfq-object 6400
1:19:02.261492 INFO: lfq-object 6700
1:19:02.304404 INFO: lfq-object 6600
1:19:02.370281 INFO: lfq-object 6800
1:19:02.419016 INFO: lfq-object 7000
1:19:02.436457 INFO: lfq-object 7200
1:19:02.477958 INFO: lfq-object 7400
1:19:02.491139 INFO: lfq-object 6900
1:19:02.521611 INFO: lfq-object 7100
1:19:02.547551 INFO: lfq-object 7300
1:19:02.584016 INFO: lfq-object 7500
1:19:02.624100 INFO: lfq-object 7700
1:19:02.682076 INFO: lfq-object 7600
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1:19:02.727377 INFO: lfq-object 7800
1:19:02.730107 INFO: lfq-object 8100
1:19:02.813927 INFO: lfq-object 8000
1:19:02.835760 INFO: lfq-object 8200
1:19:02.923559 INFO: lfq-object 8400
1:19:02.944350 INFO: lfq-object 8300
1:19:02.964457 INFO: lfq-object 8600
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1:19:03.072808 INFO: lfq-object 8700
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1:19:03.137013 INFO: lfq-object 9100
1:19:03.185265 INFO: lfq-object 9000
1:19:03.233410 INFO: lfq-object 9300
1:19:03.245289 INFO: lfq-object 9200
1:19:03.323143 INFO: lfq-object 9500
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1:19:03.571967 INFO: lfq-object 10000
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1:19:03.660285 INFO: lfq-object 10200
1:19:03.663113 INFO: lfq-object 10400
1:19:03.683056 INFO: lfq-object 10100
1:19:03.764800 INFO: lfq-object 10300
1:19:03.785187 INFO: lfq-object 10500
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1:19:03.892828 INFO: lfq-object 10600
1:19:03.947577 INFO: lfq-object 11100
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1:19:04.399156 INFO: lfq-object 12200
1:19:04.484631 INFO: lfq-object 12500
1:19:04.503600 INFO: lfq-object 12400
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1:19:04.823326 INFO: lfq-object 13000
1:19:04.866744 INFO: lfq-object 13200
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1:19:05.157317 INFO: lfq-object 13800
1:19:05.189989 INFO: lfq-object 14000
1:19:05.250941 INFO: lfq-object 14200
1:19:05.281374 INFO: lfq-object 14400
1:19:05.355385 INFO: lfq-object 14300
1:19:05.360585 INFO: lfq-object 14600
1:19:05.390020 INFO: lfq-object 14500
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1:19:05.763975 INFO: lfq-object 15300
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1:19:06.131828 INFO: lfq-object 16200
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1:19:10.304652 INFO: lfq-object 19500
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1:19:11.011814 INFO: lfq-object 21100
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1:19:11.083020 INFO: lfq-object 21500
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1:19:41.004363 INFO: lfq-object 68700
1:19:41.036641 INFO: lfq-object 68900
1:19:41.053127 INFO: lfq-object 68600
1:19:41.094699 INFO: lfq-object 69100
1:19:41.098687 INFO: lfq-object 69300
1:19:41.107404 INFO: lfq-object 68800
1:19:41.141540 INFO: lfq-object 69000
1:19:41.196235 INFO: lfq-object 69200
1:19:41.222986 INFO: lfq-object 69400
1:19:41.238963 INFO: lfq-object 69600
1:19:41.313775 INFO: lfq-object 69800
1:19:41.327491 INFO: lfq-object 69500
1:19:41.339141 INFO: lfq-object 69700
1:19:41.345557 INFO: lfq-object 70000
1:19:41.418552 INFO: lfq-object 69900
1:19:41.457772 INFO: lfq-object 70100
1:19:41.525961 INFO: lfq-object 70300
1:19:41.556440 INFO: lfq-object 70200
1:19:41.622774 INFO: lfq-object 70500
1:19:41.631278 INFO: lfq-object 70400
1:19:41.638416 INFO: lfq-object 70700
1:19:41.725099 INFO: lfq-object 70600
1:19:41.741925 INFO: lfq-object 70800
1:19:41.824349 INFO: lfq-object 71000
1:19:41.846210 INFO: lfq-object 70900
1:19:41.891569 INFO: lfq-object 71200
1:19:41.930627 INFO: lfq-object 71100
1:19:41.964466 INFO: lfq-object 71400
1:19:41.994889 INFO: lfq-object 71300
1:19:42.071948 INFO: lfq-object 71500
1:19:42.174365 INFO: lfq-object 71600
1:19:42.199854 INFO: lfq-object 71700
1:19:42.300433 INFO: lfq-object 71800
1:19:42.373399 INFO: lfq-object 71900
1:19:42.474349 INFO: lfq-object 72000
1:19:42.575910 INFO: lfq-object 72100
1:19:42.676408 INFO: lfq-object 72200
1:19:42.782136 INFO: lfq-object 72300
1:19:42.859580 INFO: lfq-object 72400
1:19:42.966030 INFO: lfq-object 72500
1:19:42.998931 INFO: lfq-object 72600
1:19:43.103150 INFO: lfq-object 72700
1:19:43.142798 INFO: lfq-object 72800
1:19:43.243427 INFO: lfq-object 72900
1:19:43.302012 INFO: lfq-object 73000
1:19:43.420980 INFO: lfq-object 73100
1:19:43.524009 INFO: lfq-object 73200
1:19:43.552447 INFO: lfq-object 73300
1:19:43.632788 INFO: lfq-object 73500
1:19:43.638175 INFO: lfq-object 73700
1:19:43.656340 INFO: lfq-object 73400
1:19:43.734970 INFO: lfq-object 73600
1:19:43.749950 INFO: lfq-object 73800
1:19:47.667895 INFO: Writing precursor output to disk
1:19:47.668127 INFO: Saving alphadia_zenoswath8600/library/precursor.matrix.tsv to disk
1:19:48.008390 PROGRESS: Performing label free quantification on the pg level
1:19:48.008498 INFO: Filtering fragments by quality
1:19:48.214097 INFO: Performing label-free quantification using directLFQ
1:19:48.577253 INFO: 7049 lfq-groups total
1:20:18.820868 INFO: using 80 processes
1:20:18.925779 INFO: lfq-object 0
1:20:19.047023 INFO: lfq-object 300
1:20:19.160137 INFO: lfq-object 600
1:20:19.268070 INFO: lfq-object 100
1:20:19.312906 INFO: lfq-object 900
1:20:19.338197 INFO: lfq-object 200
1:20:19.390075 INFO: lfq-object 400
1:20:19.513925 INFO: lfq-object 1000
1:20:19.534050 INFO: lfq-object 500
1:20:19.541448 INFO: lfq-object 700
1:20:19.628092 INFO: lfq-object 1200
1:20:19.651476 INFO: lfq-object 800
1:20:19.676753 INFO: lfq-object 1300
1:20:19.705688 INFO: lfq-object 1400
1:20:19.709418 INFO: lfq-object 1500
1:20:19.735105 INFO: lfq-object 1100
1:20:19.966612 INFO: lfq-object 1600
1:20:20.025038 INFO: lfq-object 1800
1:20:20.036008 INFO: lfq-object 2100
1:20:20.040232 INFO: lfq-object 1700
1:20:20.052722 INFO: lfq-object 2300
1:20:20.093399 INFO: lfq-object 1900
1:20:20.106002 INFO: lfq-object 2000
1:20:20.116742 INFO: lfq-object 2400
1:20:20.192583 INFO: lfq-object 2600
1:20:20.221686 INFO: lfq-object 2500
1:20:20.293989 INFO: lfq-object 2700
1:20:20.346062 INFO: lfq-object 2200
1:20:20.389960 INFO: lfq-object 2900
1:20:20.440934 INFO: lfq-object 2800
1:20:20.552855 INFO: lfq-object 3000
1:20:20.579047 INFO: lfq-object 3100
1:20:20.646832 INFO: lfq-object 3200
1:20:20.730161 INFO: lfq-object 3500
1:20:20.785058 INFO: lfq-object 3300
1:20:20.806126 INFO: lfq-object 3400
1:20:20.844817 INFO: lfq-object 3600
1:20:20.859465 INFO: lfq-object 3800
1:20:20.976595 INFO: lfq-object 4100
1:20:20.981010 INFO: lfq-object 3900
1:20:21.045478 INFO: lfq-object 3700
1:20:21.095065 INFO: lfq-object 4000
1:20:21.141100 INFO: lfq-object 4200
1:20:21.144624 INFO: lfq-object 4400
1:20:21.173096 INFO: lfq-object 4600
1:20:21.288180 INFO: lfq-object 4700
1:20:21.328331 INFO: lfq-object 4300
1:20:21.335679 INFO: lfq-object 4800
1:20:21.399526 INFO: lfq-object 4900
1:20:21.452086 INFO: lfq-object 4500
1:20:21.483797 INFO: lfq-object 5000
1:20:21.568744 INFO: lfq-object 5200
1:20:21.602395 INFO: lfq-object 5100
1:20:21.620327 INFO: lfq-object 5300
1:20:21.739355 INFO: lfq-object 5400
1:20:21.754370 INFO: lfq-object 5500
1:20:21.811878 INFO: lfq-object 5600
1:20:21.838822 INFO: lfq-object 5700
1:20:21.871655 INFO: lfq-object 5900
1:20:21.901976 INFO: lfq-object 5800
1:20:22.008166 INFO: lfq-object 6000
1:20:22.014320 INFO: lfq-object 6100
1:20:22.112208 INFO: lfq-object 6200
1:20:22.129445 INFO: lfq-object 6400
1:20:22.185371 INFO: lfq-object 6300
1:20:22.238710 INFO: lfq-object 6600
1:20:22.255685 INFO: lfq-object 6500
1:20:22.281131 INFO: lfq-object 6900
1:20:22.331143 INFO: lfq-object 6700
1:20:22.337425 INFO: lfq-object 7000
1:20:22.369134 INFO: lfq-object 6800
1:20:24.450881 INFO: Writing pg output to disk
1:20:24.451057 INFO: Saving alphadia_zenoswath8600/library/pg.matrix.tsv to disk
1:20:24.584888 INFO: Writing psm output to disk
1:20:24.585050 INFO: Saving alphadia_zenoswath8600/library/precursors.tsv to disk
1:20:30.131046 PROGRESS: Building MBR spectral library
1:20:30.173167 INFO: Running MbrLibraryBuilder
1:20:31.446557 INFO: MBR spectral library contains 73,874 precursors, 7,049 proteins
1:20:31.446698 INFO: Writing MBR spectral library to disk
1:20:32.490889 PROGRESS: =================== Search Finished ===================
1:20:33.643056 INFO: Running step 'mbr'
1:20:33.646005 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 6.828943}})
1:20:33.646136 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
1:20:33.657791 INFO: loading additional config provided via CLI
1:20:33.657857 INFO: loading additional config provided via CLI parameters
1:20:33.658280 INFO: Updating config with 'user defined'
1:20:33.658437 INFO: Updating config with 'user defined (cli)'
1:20:33.658478 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default_ng.yaml
1:20:33.659110 INFO: updating config with user defined values: [{'calibration': {'batch_size': 1000, 'optimization_lock_target': 1000, 'min_steps': 5}, 'optimization': {'rt_error': {'automatic_update_percentile_range': 0.999, 'automatic_update_factor': 1.5, 'maximal_decrease': 0.1, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.5}}}, {'version': 1, 'workflow_name': None, 'output_directory': None, 'library_path': None, 'raw_paths': ['/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff'], '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': True, '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': [395, 905], 'fragment_mz': [140, 1750], 'nce': 25.0, 'fragment_types': ['b', 'y'], 'max_fragment_charge': 2, 'instrument': 'SCIEX', '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': 'ng', 'target_ms1_tolerance': 0.0, 'target_ms2_tolerance': 0.0, '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': 'SCIEX'}}, {'raw_paths': ['/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff', '/public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff'], 'fasta_paths': ['./ProteoBenchFASTA_DDAQuantification.fasta']}, {'fasta_paths': [], 'fdr': {'inference_strategy': 'library'}, 'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 6.828943}, 'quant_directory': None, 'general': {'reuse_quant': False}, 'library_prediction': {'enabled': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_path': 'alphadia_zenoswath8600/library/speclib.mbr.hdf', 'output_directory': 'alphadia_zenoswath8600'}]
1:20:33.659754 INFO: Updating config with 'ng_default'
1:20:33.659795 INFO: Updating config with 'user defined'
1:20:33.659908 INFO: Updating config with 'user defined (cli)'
1:20:33.659932 INFO: Updating config with 'multistep search'
1:20:33.659971 INFO: ├──version: 1
1:20:33.659996 INFO: ├──workflow_name: None
1:20:33.660017 INFO: [32;20m├──output_directory: alphadia_zenoswath8600 [multistep search, default: None][0m
1:20:33.660039 INFO: [32;20m├──library_path: alphadia_zenoswath8600/library/speclib.mbr.hdf [multistep search, default: None][0m
1:20:33.660060 INFO: ├──raw_paths:
1:20:33.660086 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff [user defined (cli), default: None][0m
1:20:33.660109 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff [user defined (cli), default: None][0m
1:20:33.660128 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff [user defined (cli), default: None][0m
1:20:33.660148 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff [user defined (cli), default: None][0m
1:20:33.660169 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff [user defined (cli), default: None][0m
1:20:33.660188 INFO: │   [32;20m- /public/compomics2/Robbe/ProteoBench/ZenoSWATH/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff [user defined (cli), default: None][0m
1:20:33.660206 INFO: ├──fasta_paths:
1:20:33.660226 INFO: ├──quant_directory: None
1:20:33.660245 INFO: ├──general
1:20:33.660266 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
1:20:33.660287 INFO: │   ├──transfer_step_enabled: False
1:20:33.660308 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
1:20:33.660328 INFO: │   ├──reuse_calibration: False
1:20:33.660347 INFO: │   ├──reuse_quant: False
1:20:33.660367 INFO: │   ├──astral_ms1: False
1:20:33.660385 INFO: │   ├──log_level: INFO
1:20:33.660403 INFO: │   ├──mmap_detector_events: False
1:20:33.660421 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
1:20:33.660440 INFO: │   ├──save_figures: True
1:20:33.660459 INFO: │   ├──save_library: True
1:20:33.660478 INFO: │   ├──save_flat_library: False
1:20:33.660495 INFO: │   ├──input_library_type: base
1:20:33.660514 INFO: │   ├──save_mbr_library: True
1:20:33.660532 INFO: │   └──random_state: None
1:20:33.660552 INFO: ├──library_loading
1:20:33.660572 INFO: │   └──rt_heuristic: 180
1:20:33.660591 INFO: ├──library_prediction
1:20:33.660609 INFO: │   ├──enabled: False
1:20:33.660629 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
1:20:33.660647 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
1:20:33.660668 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
1:20:33.660689 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
1:20:33.660709 INFO: │   ├──missed_cleavages: 1
1:20:33.660727 INFO: │   ├──precursor_len:
1:20:33.660747 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
1:20:33.660765 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
1:20:33.660785 INFO: │   ├──precursor_charge:
1:20:33.660803 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
1:20:33.660822 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
1:20:33.660840 INFO: │   ├──precursor_mz:
1:20:33.660859 INFO: │   │   [32;20m- 395 [user defined, default: 400][0m
1:20:33.660877 INFO: │   │   [32;20m- 905 [user defined, default: 1200][0m
1:20:33.660896 INFO: │   ├──fragment_mz:
1:20:33.660914 INFO: │   │   [32;20m- 140 [user defined, default: 200][0m
1:20:33.660933 INFO: │   │   [32;20m- 1750 [user defined, default: 2000][0m
1:20:33.660952 INFO: │   ├──nce: 25.0
1:20:33.660973 INFO: │   ├──fragment_types:
1:20:33.660992 INFO: │   │   - b
1:20:33.661011 INFO: │   │   - y
1:20:33.661029 INFO: │   ├──max_fragment_charge: 2
1:20:33.661050 INFO: │   [32;20m├──instrument: SCIEX [user defined, default: Lumos][0m
1:20:33.661068 INFO: │   ├──peptdeep_model_path: None
1:20:33.661093 INFO: │   └──peptdeep_model_type: generic
1:20:33.661113 INFO: ├──custom_modifications:
1:20:33.661133 INFO: │   ├──name: Dimethyl:d12@K
1:20:33.661152 INFO: │   └──composition: H(-2)2H(8)13C(2)
1:20:33.661172 INFO: │   ├──name: Dimethyl:d12@Any_N-term
1:20:33.661191 INFO: │   └──composition: H(-2)2H(8)13C(2)
1:20:33.661209 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
1:20:33.661228 INFO: │   └──composition: H(-2)2H(8)13C(2)
1:20:33.661248 INFO: │   ├──name: mTRAQ:d12@K
1:20:33.661268 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
1:20:33.661286 INFO: │   ├──name: mTRAQ:d12@Any_N-term
1:20:33.661304 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1:20:33.661322 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
1:20:33.661342 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1:20:33.661361 INFO: │   ├──name: Label:13C(12)@K
1:20:33.661381 INFO: │   └──composition: C(12)
1:20:33.661398 INFO: ├──search
1:20:33.661418 INFO: │   [32;20m├──extraction_backend: ng [user defined, default: classic][0m
1:20:33.661439 INFO: │   [32;20m├──target_ms1_tolerance: 30.0 [multistep search, default: 5][0m
1:20:33.661460 INFO: │   [32;20m├──target_ms2_tolerance: 6.828943 [multistep search, default: 10][0m
1:20:33.661488 INFO: │   ├──target_rt_tolerance: 0.0
1:20:33.661506 INFO: │   ├──target_mobility_tolerance: 0.0
1:20:33.661527 INFO: │   ├──quant_window: 3
1:20:33.661545 INFO: │   ├──target_num_candidates: 3
1:20:33.661564 INFO: │   ├──channel_filter: 
1:20:33.661582 INFO: │   ├──exclude_shared_ions: True
1:20:33.661601 INFO: │   ├──compete_for_fragments: True
1:20:33.661619 INFO: │   ├──quant_all: True
1:20:33.661637 INFO: │   ├──top_k_fragments_selection: 12
1:20:33.661655 INFO: │   ├──top_k_fragments_scoring: 12
1:20:33.661675 INFO: │   ├──min_fragment_intensity: 0.01
1:20:33.661692 INFO: │   ├──experimental_xic: True
1:20:33.661713 INFO: │   └──optimized_peak_group_score: False
1:20:33.661731 INFO: ├──calibration
1:20:33.661750 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
1:20:33.661768 INFO: │   ├──optimization_lock_target: 200
1:20:33.661788 INFO: │   ├──max_steps: 20
1:20:33.661806 INFO: │   ├──min_steps: 2
1:20:33.661825 INFO: │   ├──max_skips: 1
1:20:33.661842 INFO: │   ├──max_fragments: 5000
1:20:33.661863 INFO: │   └──min_correlation: 0.7
1:20:33.661880 INFO: ├──search_initial
1:20:33.661899 INFO: │   ├──initial_num_candidates: 1
1:20:33.661918 INFO: │   ├──initial_ms1_tolerance: 30
1:20:33.661937 INFO: │   ├──initial_ms2_tolerance: 30
1:20:33.661956 INFO: │   ├──initial_mobility_tolerance: 0.1
1:20:33.661975 INFO: │   └──initial_rt_tolerance: 0.5
1:20:33.661994 INFO: ├──selection_config
1:20:33.662014 INFO: │   ├──peak_len_rt: 10.0
1:20:33.662032 INFO: │   ├──sigma_scale_rt: 0.5
1:20:33.662051 INFO: │   ├──peak_len_mobility: 0.01
1:20:33.662069 INFO: │   ├──sigma_scale_mobility: 1.0
1:20:33.662088 INFO: │   ├──top_k_precursors: 3
1:20:33.662106 INFO: │   ├──kernel_size: 30
1:20:33.662126 INFO: │   ├──f_mobility: 1.0
1:20:33.662144 INFO: │   ├──f_rt: 0.99
1:20:33.662163 INFO: │   ├──center_fraction: 0.5
1:20:33.662181 INFO: │   ├──min_size_mobility: 8
1:20:33.662200 INFO: │   ├──min_size_rt: 3
1:20:33.662218 INFO: │   ├──max_size_mobility: 20
1:20:33.662237 INFO: │   ├──max_size_rt: 15
1:20:33.662256 INFO: │   ├──group_channels: False
1:20:33.662275 INFO: │   ├──use_weighted_score: True
1:20:33.662294 INFO: │   ├──join_close_candidates: False
1:20:33.662314 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
1:20:33.662332 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
1:20:33.662357 INFO: ├──scoring_config
1:20:33.662375 INFO: │   ├──score_grouped: False
1:20:33.662396 INFO: │   ├──top_k_isotopes: 3
1:20:33.662413 INFO: │   ├──reference_channel: -1
1:20:33.662432 INFO: │   ├──precursor_mz_tolerance: 10
1:20:33.662451 INFO: │   └──fragment_mz_tolerance: 15
1:20:33.662470 INFO: ├──library_multiplexing
1:20:33.662489 INFO: │   ├──enabled: False
1:20:33.662508 INFO: │   ├──input_channel: 0
1:20:33.662524 INFO: │   └──multiplex_mapping:
1:20:33.662543 INFO: ├──multiplexing
1:20:33.662560 INFO: │   ├──enabled: False
1:20:33.662579 INFO: │   ├──target_channels: 4,8
1:20:33.662596 INFO: │   ├──decoy_channel: 12
1:20:33.662615 INFO: │   ├──reference_channel: 0
1:20:33.662632 INFO: │   └──competetive_scoring: True
1:20:33.662650 INFO: ├──fdr
1:20:33.662668 INFO: │   ├──fdr: 0.01
1:20:33.662686 INFO: │   ├──group_level: proteins
1:20:33.662704 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
1:20:33.662724 INFO: │   ├──competetive_scoring: True
1:20:33.662743 INFO: │   ├──keep_decoys: False
1:20:33.662761 INFO: │   ├──channel_wise_fdr: False
1:20:33.662779 INFO: │   ├──enable_two_step_classifier: False
1:20:33.662797 INFO: │   ├──two_step_classifier_max_iterations: 5
1:20:33.662815 INFO: │   └──enable_nn_hyperparameter_tuning: False
1:20:33.662834 INFO: ├──search_output
1:20:33.662851 INFO: │   ├──file_format: tsv
1:20:33.662870 INFO: │   ├──peptide_level_lfq: False
1:20:33.662888 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
1:20:33.662906 INFO: │   ├──save_fragment_quant_matrix: False
1:20:33.662924 INFO: │   ├──min_k_fragments: 12
1:20:33.662943 INFO: │   ├──min_correlation: 0.9
1:20:33.662961 INFO: │   ├──num_samples_quadratic: 50
1:20:33.662978 INFO: │   ├──min_nonnan: 3
1:20:33.662997 INFO: │   └──normalize_lfq: True
1:20:33.663014 INFO: ├──optimization
1:20:33.663033 INFO: │   ├──order_of_optimization: None
1:20:33.663051 INFO: │   ├──ms2_error
1:20:33.663071 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1:20:33.663091 INFO: │   │   ├──targeted_update_factor: 1.0
1:20:33.663110 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1:20:33.663128 INFO: │   │   ├──automatic_update_factor: 1.1
1:20:33.663148 INFO: │   │   ├──try_narrower_values: True
1:20:33.663167 INFO: │   │   ├──maximal_decrease: 0.5
1:20:33.663186 INFO: │   │   ├──favour_narrower_optimum: False
1:20:33.663204 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1:20:33.663222 INFO: │   ├──ms1_error
1:20:33.663241 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1:20:33.663260 INFO: │   │   ├──targeted_update_factor: 1.0
1:20:33.663280 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1:20:33.663299 INFO: │   │   ├──automatic_update_factor: 1.1
1:20:33.663318 INFO: │   │   ├──try_narrower_values: False
1:20:33.663337 INFO: │   │   ├──maximal_decrease: 0.2
1:20:33.663356 INFO: │   │   ├──favour_narrower_optimum: False
1:20:33.663374 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1:20:33.663393 INFO: │   ├──mobility_error
1:20:33.663411 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1:20:33.663431 INFO: │   │   ├──targeted_update_factor: 1.0
1:20:33.663449 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1:20:33.663469 INFO: │   │   ├──automatic_update_factor: 1.1
1:20:33.663486 INFO: │   │   ├──try_narrower_values: False
1:20:33.663505 INFO: │   │   ├──maximal_decrease: 0.2
1:20:33.663522 INFO: │   │   ├──favour_narrower_optimum: False
1:20:33.663546 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1:20:33.663564 INFO: │   └──rt_error
1:20:33.663584 INFO: │       ├──targeted_update_percentile_range: 0.95
1:20:33.663602 INFO: │       ├──targeted_update_factor: 1.0
1:20:33.663621 INFO: │       ├──automatic_update_percentile_range: 0.99
1:20:33.663639 INFO: │       ├──automatic_update_factor: 1.1
1:20:33.663658 INFO: │       ├──try_narrower_values: True
1:20:33.663675 INFO: │       ├──maximal_decrease: 0.2
1:20:33.663694 INFO: │       ├──favour_narrower_optimum: True
1:20:33.663712 INFO: │       └──maximum_decrease_from_maximum: 0.1
1:20:33.663731 INFO: ├──optimization_manager
1:20:33.663749 INFO: │   ├──fwhm_rt: 5
1:20:33.663768 INFO: │   ├──fwhm_mobility: 0.01
1:20:33.663785 INFO: │   └──score_cutoff: 0
1:20:33.663804 INFO: ├──transfer_library
1:20:33.663821 INFO: │   ├──enabled: False
1:20:33.663840 INFO: │   ├──fragment_types:
1:20:33.663857 INFO: │   │   - b
1:20:33.663875 INFO: │   │   - y
1:20:33.663893 INFO: │   ├──max_charge: 2
1:20:33.663910 INFO: │   ├──top_k_samples: 3
1:20:33.663928 INFO: │   ├──norm_delta_max: True
1:20:33.663945 INFO: │   ├──precursor_correlation_cutoff: 0.5
1:20:33.663964 INFO: │   └──fragment_correlation_ratio: 0.75
1:20:33.663981 INFO: └──transfer_learning
1:20:33.664000 INFO:     ├──enabled: False
1:20:33.664017 INFO:     ├──batch_size: 2000
1:20:33.664036 INFO:     ├──max_lr: 0.0001
1:20:33.664053 INFO:     ├──train_fraction: 0.7
1:20:33.664072 INFO:     ├──validation_fraction: 0.2
1:20:33.664089 INFO:     ├──test_fraction: 0.1
1:20:33.664108 INFO:     ├──test_interval: 1
1:20:33.664124 INFO:     ├──lr_patience: 3
1:20:33.664143 INFO:     ├──epochs: 51
1:20:33.664160 INFO:     ├──warmup_epochs: 5
1:20:33.664179 INFO:     ├──nce: 25
1:20:33.664196 INFO:     [32;20m└──instrument: SCIEX [user defined, default: Lumos][0m
1:20:33.669175 INFO: Moved existing config file alphadia_zenoswath8600/frozen_config.yaml to alphadia_zenoswath8600/frozen_config.yaml
1:20:33.669721 INFO: Registering 7 custom modifications
1:20:33.686539 INFO: Searching 6 files:
1:20:33.686605 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff
1:20:33.686628 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff
1:20:33.686648 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff
1:20:33.686665 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff
1:20:33.686682 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff
1:20:33.686700 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff
1:20:33.686720 INFO: Using 0 fasta files:
1:20:33.686739 INFO: Using library: alphadia_zenoswath8600/library/speclib.mbr.hdf
1:20:33.686759 INFO: Saving output to: alphadia_zenoswath8600
1:20:33.686786 PROGRESS: Loading spectral library
1:20:33.686816 PROGRESS: Loading library (type: base) from disk..
1:20:33.686924 INFO: Running DynamicLoader
1:20:33.686979 INFO: Loading .hdf library from alphadia_zenoswath8600/library/speclib.mbr.hdf
1:20:34.041244 INFO: Running PrecursorInitializer
1:20:34.041417 INFO: Running AnnotateFasta
1:20:34.041726 INFO: Dropping decoys from input library before annotation
1:20:34.056129 INFO: Running IsotopeGenerator
1:20:34.056388 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
1:20:34.056426 INFO: Running RTNormalization
1:20:34.059570 INFO: Saving library to alphadia_zenoswath8600/speclib.hdf
1:20:34.612444 INFO: Running DecoyGenerator
1:20:39.448328 INFO: Running FlattenLibrary
1:20:40.836794 INFO: Running InitFlatColumns
1:20:40.841387 INFO: Running LogFlatLibraryStats
1:20:40.841518 INFO: ============ Library Stats ============
1:20:40.841562 INFO: Number of precursors: 147,732
1:20:40.870737 INFO: 	thereof targets:73,874
1:20:40.870879 INFO: 	thereof decoys: 73,858
1:20:40.872365 INFO: Number of elution groups: 73,874
1:20:40.872434 INFO: 	average size: 2.00
1:20:40.878655 INFO: Number of proteins: 7,049
1:20:40.879272 INFO: Number of channels: 1 ([0])
1:20:40.879357 INFO: Isotopes Distribution for 4 isotopes
1:20:40.879384 INFO: =======================================
1:20:40.879447 PROGRESS: Starting Search Workflows
1:20:40.879517 PROGRESS: 
1:20:40.879565 INFO: Quantification results path: alphadia_zenoswath8600/quant
1:20:40.879630 INFO: Creating folder alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/figures
1:20:40.879838 INFO: Initializing TimingManager
1:20:40.880179 INFO: Initializing RawFileManager
1:23:04.374791 INFO: Determining DIA cycle
1:23:04.389684 INFO: Found cycle with start 0.00 min and length 86.
1:23:04.623657 INFO: RT (min)            : 0.0 - 55.5
1:23:04.623754 INFO: RT duration (sec)   : 3327.2
1:23:04.623780 INFO: RT duration (min)   : 55.5
1:23:04.623806 INFO: Cycle len (scans)   : 86
1:23:04.623827 INFO: Cycle len (sec)     : 1.90
1:23:04.623845 INFO: Number of cycles    : 1747
1:23:04.623863 INFO: MS2 range (m/z)     : 399.5 - 903.5
1:23:04.623901 INFO: Creating DIA data object took: 143.7436273097992
1:23:05.812477 INFO: Creating DIA data NG object took: 1.188429832458496
1:23:05.829821 INFO: Initializing CalibrationManager
1:23:05.830155 INFO: Setting up calibration estimators ..
1:23:05.830214 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:23:05.830289 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'}' ..
1:23:05.830361 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:23:05.830411 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:23:05.830460 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}}' ..
1:23:05.830507 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:23:05.830550 INFO: Done setting up calibration estimators.
1:23:05.830693 INFO: Initializing OptimizationManager
1:23:05.830826 INFO: initial parameter: ms1_error = 30
1:23:05.830878 INFO: initial parameter: ms2_error = 30
1:23:05.830924 INFO: initial parameter: rt_error = 1663.6044921875
1:23:05.830967 INFO: initial parameter: mobility_error = 0.1
1:23:05.831008 INFO: initial parameter: num_candidates = 1
1:23:05.831050 INFO: initial parameter: fwhm_rt = 5
1:23:05.831091 INFO: initial parameter: fwhm_mobility = 0.01
1:23:05.831131 INFO: initial parameter: score_cutoff = 0
1:23:05.831170 INFO: initial parameter: classifier_version = -1
1:23:05.831237 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
1:23:05.831514 INFO: FDRManager: loading saved state not requested, will be initialized.
1:23:05.831549 INFO: Initializing FDRManager
1:23:05.831585 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:23:05.854790 PROGRESS: Initializing spectral library: 73,874 target precursors potentially observable (0 removed)
1:23:05.869382 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:23:05.869751 INFO: Updating optimization_manager: rt_error            : 1663.6044921875 -> 1663.6044921875
1:23:05.869852 PROGRESS: Starting initial search for precursors.
1:23:05.869933 INFO: Starting optimization step 0.
1:23:05.869994 PROGRESS: === Extracting elution groups 0 to 200 ===
1:23:05.870049 INFO: Using ng extraction backend
1:23:05.870112 PROGRESS: Extracting batch of 394 precursors
1:23:05.872347 INFO: === Search parameters used ===
1:23:05.872445 INFO: rt_error       : 1663.6044921875
1:23:05.872496 INFO: mobility_error : 0.1
1:23:05.872541 INFO: num_candidates : 1
1:23:05.872583 INFO: ms1_error      : 30
1:23:05.872623 INFO: ms2_error      : 30
1:23:05.872664 INFO: fwhm_rt        : 5
1:23:05.872704 INFO: quant_window   : 3
1:23:05.872742 INFO: ==============================================
1:23:05.894840 INFO: performing precursor FDR with 40 features
1:23:05.894916 INFO: Decoy channel: -1
1:23:05.894943 INFO: Competetive: True
1:23:05.895845 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:05.898103 INFO: Using random state 94755 for train-test-split
1:23:05.905692 INFO: Test AUC: 0.581
1:23:05.905750 INFO: Train AUC: 0.466
1:23:05.905781 INFO: AUC difference: 24.53%
1:23:05.905804 WARNING: AUC difference > 5%. This may indicate overfitting.
1:23:06.145251 INFO: Resetting torch num_threads to 80
1:23:06.146553 PROGRESS: === Extracted 394 precursors and 3037 fragments ===
1:23:06.146894 INFO: === FDR correction performed with classifier version -1 ===
1:23:06.147316 PROGRESS: ============================= Precursor FDR =============================
1:23:06.147397 PROGRESS: Total precursors accumulated: 0
1:23:06.147455 PROGRESS: Target precursors: 0 (0.00%)
1:23:06.147505 PROGRESS: Decoy precursors: 0 (0.00%)
1:23:06.147550 PROGRESS: 
1:23:06.147594 PROGRESS: Precursor Summary:
1:23:06.147701 PROGRESS: 
1:23:06.147761 PROGRESS: Protein Summary:
1:23:06.147833 PROGRESS: =========================================================================
1:23:06.147974 INFO: Target number of precursors not reached yet.
1:23:06.151269 INFO: Starting optimization step 1.
1:23:06.151383 PROGRESS: === Extracting elution groups 200 to 600 ===
1:23:06.151455 INFO: Using ng extraction backend
1:23:06.151514 PROGRESS: Extracting batch of 789 precursors
1:23:06.154481 INFO: === Search parameters used ===
1:23:06.154572 INFO: rt_error       : 1663.6044921875
1:23:06.154619 INFO: mobility_error : 0.1
1:23:06.154664 INFO: num_candidates : 1
1:23:06.154708 INFO: ms1_error      : 30
1:23:06.154749 INFO: ms2_error      : 30
1:23:06.154791 INFO: fwhm_rt        : 5
1:23:06.154832 INFO: quant_window   : 3
1:23:06.154872 INFO: ==============================================
1:23:06.200666 INFO: performing precursor FDR with 40 features
1:23:06.200777 INFO: Decoy channel: -1
1:23:06.200804 INFO: Competetive: True
1:23:06.203670 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:06.205203 INFO: Using random state 919861 for train-test-split
1:23:06.213646 INFO: Test AUC: 0.484
1:23:06.213712 INFO: Train AUC: 0.467
1:23:06.213743 INFO: AUC difference: 3.72%
1:23:06.426713 INFO: Resetting torch num_threads to 80
1:23:06.428916 PROGRESS: === Extracted 1183 precursors and 9307 fragments ===
1:23:06.429272 INFO: === FDR correction performed with classifier version -1 ===
1:23:06.429728 PROGRESS: ============================= Precursor FDR =============================
1:23:06.429816 PROGRESS: Total precursors accumulated: 1
1:23:06.429876 PROGRESS: Target precursors: 1 (100.00%)
1:23:06.429926 PROGRESS: Decoy precursors: 0 (0.00%)
1:23:06.429972 PROGRESS: 
1:23:06.430014 PROGRESS: Precursor Summary:
1:23:06.430936 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:23:06.431021 PROGRESS: 
1:23:06.431083 PROGRESS: Protein Summary:
1:23:06.432093 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:23:06.432178 PROGRESS: =========================================================================
1:23:06.432360 INFO: Target number of precursors not reached yet.
1:23:06.436612 INFO: Starting optimization step 2.
1:23:06.436721 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:23:06.436797 INFO: Using ng extraction backend
1:23:06.436857 PROGRESS: Extracting batch of 1588 precursors
1:23:06.441358 INFO: === Search parameters used ===
1:23:06.441449 INFO: rt_error       : 1663.6044921875
1:23:06.441512 INFO: mobility_error : 0.1
1:23:06.442518 INFO: num_candidates : 1
1:23:06.442566 INFO: ms1_error      : 30
1:23:06.442608 INFO: ms2_error      : 30
1:23:06.442647 INFO: fwhm_rt        : 5
1:23:06.442688 INFO: quant_window   : 3
1:23:06.442727 INFO: ==============================================
1:23:06.496134 INFO: performing precursor FDR with 40 features
1:23:06.496255 INFO: Decoy channel: -1
1:23:06.496281 INFO: Competetive: True
1:23:06.499540 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:06.501361 INFO: Using random state 364958 for train-test-split
1:23:06.512940 INFO: Test AUC: 0.462
1:23:06.513005 INFO: Train AUC: 0.470
1:23:06.513034 INFO: AUC difference: 1.63%
1:23:06.740714 INFO: Resetting torch num_threads to 80
1:23:06.743252 PROGRESS: === Extracted 2770 precursors and 21889 fragments ===
1:23:06.743677 INFO: === FDR correction performed with classifier version -1 ===
1:23:06.744121 PROGRESS: ============================= Precursor FDR =============================
1:23:06.744206 PROGRESS: Total precursors accumulated: 2
1:23:06.744275 PROGRESS: Target precursors: 2 (100.00%)
1:23:06.744327 PROGRESS: Decoy precursors: 0 (0.00%)
1:23:06.744375 PROGRESS: 
1:23:06.744420 PROGRESS: Precursor Summary:
1:23:06.745333 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:23:06.745420 PROGRESS: 
1:23:06.745486 PROGRESS: Protein Summary:
1:23:06.746502 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:23:06.746590 PROGRESS: =========================================================================
1:23:06.746792 INFO: Target number of precursors not reached yet.
1:23:06.752769 INFO: Starting optimization step 3.
1:23:06.752899 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:23:06.752971 INFO: Using ng extraction backend
1:23:06.753030 PROGRESS: Extracting batch of 3164 precursors
1:23:06.760311 INFO: === Search parameters used ===
1:23:06.760425 INFO: rt_error       : 1663.6044921875
1:23:06.760478 INFO: mobility_error : 0.1
1:23:06.760524 INFO: num_candidates : 1
1:23:06.760566 INFO: ms1_error      : 30
1:23:06.760610 INFO: ms2_error      : 30
1:23:06.760652 INFO: fwhm_rt        : 5
1:23:06.760693 INFO: quant_window   : 3
1:23:06.760743 INFO: ==============================================
1:23:06.820127 INFO: performing precursor FDR with 40 features
1:23:06.820233 INFO: Decoy channel: -1
1:23:06.820263 INFO: Competetive: True
1:23:06.824292 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:06.826662 INFO: Using random state 696727 for train-test-split
1:23:06.845374 INFO: Test AUC: 0.449
1:23:06.845476 INFO: Train AUC: 0.474
1:23:06.845508 INFO: AUC difference: 5.25%
1:23:06.845530 WARNING: AUC difference > 5%. This may indicate overfitting.
1:23:07.061629 INFO: Resetting torch num_threads to 80
1:23:07.064848 PROGRESS: === Extracted 5934 precursors and 47040 fragments ===
1:23:07.065223 INFO: === FDR correction performed with classifier version -1 ===
1:23:07.065680 PROGRESS: ============================= Precursor FDR =============================
1:23:07.065770 PROGRESS: Total precursors accumulated: 1
1:23:07.065829 PROGRESS: Target precursors: 1 (100.00%)
1:23:07.065876 PROGRESS: Decoy precursors: 0 (0.00%)
1:23:07.065920 PROGRESS: 
1:23:07.065962 PROGRESS: Precursor Summary:
1:23:07.066856 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:23:07.066940 PROGRESS: 
1:23:07.066995 PROGRESS: Protein Summary:
1:23:07.067975 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:23:07.068060 PROGRESS: =========================================================================
1:23:07.068289 INFO: Target number of precursors not reached yet.
1:23:07.077367 INFO: Starting optimization step 4.
1:23:07.077513 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:23:07.077587 INFO: Using ng extraction backend
1:23:07.077643 PROGRESS: Extracting batch of 6329 precursors
1:23:07.090027 INFO: === Search parameters used ===
1:23:07.090195 INFO: rt_error       : 1663.6044921875
1:23:07.090259 INFO: mobility_error : 0.1
1:23:07.090312 INFO: num_candidates : 1
1:23:07.090353 INFO: ms1_error      : 30
1:23:07.090393 INFO: ms2_error      : 30
1:23:07.090433 INFO: fwhm_rt        : 5
1:23:07.090473 INFO: quant_window   : 3
1:23:07.090511 INFO: ==============================================
1:23:07.189323 INFO: performing precursor FDR with 40 features
1:23:07.189448 INFO: Decoy channel: -1
1:23:07.189481 INFO: Competetive: True
1:23:07.194998 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:07.198488 INFO: Using random state 557235 for train-test-split
1:23:07.235087 INFO: Test AUC: 0.474
1:23:07.235194 INFO: Train AUC: 0.469
1:23:07.235224 INFO: AUC difference: 1.17%
1:23:07.448353 INFO: Resetting torch num_threads to 80
1:23:07.452419 PROGRESS: === Extracted 12262 precursors and 96775 fragments ===
1:23:07.452790 INFO: === FDR correction performed with classifier version -1 ===
1:23:07.453218 PROGRESS: ============================= Precursor FDR =============================
1:23:07.453302 PROGRESS: Total precursors accumulated: 0
1:23:07.453363 PROGRESS: Target precursors: 0 (0.00%)
1:23:07.453414 PROGRESS: Decoy precursors: 0 (0.00%)
1:23:07.453460 PROGRESS: 
1:23:07.453514 PROGRESS: Precursor Summary:
1:23:07.453624 PROGRESS: 
1:23:07.453688 PROGRESS: Protein Summary:
1:23:07.453760 PROGRESS: =========================================================================
1:23:07.454018 INFO: Target number of precursors not reached yet.
1:23:07.466213 INFO: Starting optimization step 5.
1:23:07.466413 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:23:07.466493 INFO: Using ng extraction backend
1:23:07.466576 PROGRESS: Extracting batch of 12652 precursors
1:23:07.489637 INFO: === Search parameters used ===
1:23:07.489834 INFO: rt_error       : 1663.6044921875
1:23:07.489886 INFO: mobility_error : 0.1
1:23:07.489929 INFO: num_candidates : 1
1:23:07.489974 INFO: ms1_error      : 30
1:23:07.490016 INFO: ms2_error      : 30
1:23:07.490057 INFO: fwhm_rt        : 5
1:23:07.490096 INFO: quant_window   : 3
1:23:07.490135 INFO: ==============================================
1:23:07.658128 INFO: performing precursor FDR with 40 features
1:23:07.658253 INFO: Decoy channel: -1
1:23:07.658280 INFO: Competetive: True
1:23:07.667419 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:07.673652 INFO: Using random state 63948 for train-test-split
1:23:07.900500 INFO: Test AUC: 0.850
1:23:07.900612 INFO: Train AUC: 0.856
1:23:07.900642 INFO: AUC difference: 0.64%
1:23:08.119456 INFO: Resetting torch num_threads to 80
1:23:08.126405 PROGRESS: === Extracted 24911 precursors and 196483 fragments ===
1:23:08.126843 INFO: === FDR correction performed with classifier version -1 ===
1:23:08.128023 PROGRESS: ============================= Precursor FDR =============================
1:23:08.128115 PROGRESS: Total precursors accumulated: 6,364
1:23:08.128174 PROGRESS: Target precursors: 6,301 (99.01%)
1:23:08.128223 PROGRESS: Decoy precursors: 63 (0.99%)
1:23:08.128269 PROGRESS: 
1:23:08.128313 PROGRESS: Precursor Summary:
1:23:08.130874 PROGRESS: Channel   0:	 0.050 FDR: 6,301; 0.010 FDR: 6,301; 0.001 FDR: 4,407
1:23:08.131004 PROGRESS: 
1:23:08.131065 PROGRESS: Protein Summary:
1:23:08.134766 PROGRESS: Channel   0:	 0.050 FDR: 2,992; 0.010 FDR: 2,992; 0.001 FDR: 2,312
1:23:08.134887 PROGRESS: =========================================================================
1:23:08.135260 INFO: Target number of precursors reached.
1:23:08.166893 INFO: fragments_df: keeping 5000 of 196483 [sum(precursor_idx_mask)=68503 sum(mass_error_mask)=196483 stop_rank=5000
1:23:08.172497 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:09.126710 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:09.811163 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:23:09.811681 INFO: Using score_cutoff 15.787463464736938 (fac=0.99, q=1)
1:23:09.812060 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:23:09.812142 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:23:09.812207 INFO: Updating optimization_manager: score_cutoff        : 0 -> 15.787463464736938
1:23:09.812264 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:09.813863 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:09.816143 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
1:23:09.816238 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:23:09.816316 INFO: Starting optimization step 6.
1:23:09.816376 PROGRESS: === Extracting elution groups 0 to 600 ===
1:23:09.816436 INFO: Using ng extraction backend
1:23:09.816493 PROGRESS: Extracting batch of 1183 precursors
1:23:09.820292 INFO: === Search parameters used ===
1:23:09.820390 INFO: rt_error       : 1663.6044921875
1:23:09.820444 INFO: mobility_error : 0.1
1:23:09.820488 INFO: num_candidates : 3
1:23:09.820529 INFO: ms1_error      : 30
1:23:09.820569 INFO: ms2_error      : 30
1:23:09.820610 INFO: fwhm_rt        : 3.0
1:23:09.820653 INFO: quant_window   : 3
1:23:09.820693 INFO: ==============================================
1:23:09.871120 INFO: performing precursor FDR with 40 features
1:23:09.871215 INFO: Decoy channel: -1
1:23:09.871240 INFO: Competetive: True
1:23:09.873873 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:09.875736 INFO: Using random state 629112 for train-test-split
1:23:09.887647 INFO: Test AUC: 0.713
1:23:09.887716 INFO: Train AUC: 0.663
1:23:09.887746 INFO: AUC difference: 7.57%
1:23:09.887769 WARNING: AUC difference > 5%. This may indicate overfitting.
1:23:10.105049 INFO: Resetting torch num_threads to 80
1:23:10.106649 PROGRESS: === Extracted 3549 precursors and 24515 fragments ===
1:23:10.106990 INFO: === FDR correction performed with classifier version 5 ===
1:23:10.107443 PROGRESS: ============================= Precursor FDR =============================
1:23:10.107528 PROGRESS: Total precursors accumulated: 291
1:23:10.107586 PROGRESS: Target precursors: 289 (99.31%)
1:23:10.107635 PROGRESS: Decoy precursors: 2 (0.69%)
1:23:10.107681 PROGRESS: 
1:23:10.107723 PROGRESS: Precursor Summary:
1:23:10.108653 PROGRESS: Channel   0:	 0.050 FDR:   289; 0.010 FDR:   289; 0.001 FDR:   265
1:23:10.108745 PROGRESS: 
1:23:10.108801 PROGRESS: Protein Summary:
1:23:10.109895 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:   251
1:23:10.109983 PROGRESS: =========================================================================
1:23:10.110381 INFO: Target number of precursors reached.
1:23:10.114345 INFO: fragments_df: keeping 3987 of 24515 [sum(precursor_idx_mask)=6991 sum(mass_error_mask)=24515 stop_rank=3987
1:23:10.118703 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:10.246149 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:10.771254 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:10.771676 INFO: Using score_cutoff 19.30188850021362 (fac=0.99, q=1)
1:23:10.771956 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:10.772035 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:10.772090 INFO: Updating optimization_manager: score_cutoff        : 15.787463464736938 -> 19.30188850021362
1:23:10.772146 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:10.773758 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:10.776026 INFO: === checking if optimization conditions were reached ===
1:23:10.777491 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.828943
1:23:10.777620 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
1:23:10.777681 PROGRESS: ❌ ms2_error      : 6.8289 > 6.8289 or insufficient steps taken.
1:23:10.777738 INFO: ==============================================
1:23:10.777799 INFO: Starting optimization step 7.
1:23:10.777856 PROGRESS: === Extracting elution groups 0 to 600 ===
1:23:10.777911 INFO: Using ng extraction backend
1:23:10.777962 PROGRESS: Extracting batch of 1183 precursors
1:23:10.781659 INFO: === Search parameters used ===
1:23:10.781755 INFO: rt_error       : 1663.6044921875
1:23:10.781804 INFO: mobility_error : 0.1
1:23:10.781847 INFO: num_candidates : 3
1:23:10.781886 INFO: ms1_error      : 30
1:23:10.781925 INFO: ms2_error      : 6.828943
1:23:10.781964 INFO: fwhm_rt        : 3.0
1:23:10.782002 INFO: quant_window   : 3
1:23:10.782041 INFO: ==============================================
1:23:10.825294 INFO: performing precursor FDR with 40 features
1:23:10.825393 INFO: Decoy channel: -1
1:23:10.825421 INFO: Competetive: True
1:23:10.827973 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:10.829849 INFO: Using random state 502024 for train-test-split
1:23:10.841787 INFO: Test AUC: 0.672
1:23:10.841857 INFO: Train AUC: 0.685
1:23:10.841887 INFO: AUC difference: 1.97%
1:23:11.058533 INFO: Resetting torch num_threads to 80
1:23:11.060101 PROGRESS: === Extracted 3549 precursors and 25879 fragments ===
1:23:11.060441 INFO: === FDR correction performed with classifier version 6 ===
1:23:11.060895 PROGRESS: ============================= Precursor FDR =============================
1:23:11.060982 PROGRESS: Total precursors accumulated: 404
1:23:11.061041 PROGRESS: Target precursors: 400 (99.01%)
1:23:11.061089 PROGRESS: Decoy precursors: 4 (0.99%)
1:23:11.061136 PROGRESS: 
1:23:11.061178 PROGRESS: Precursor Summary:
1:23:11.062189 PROGRESS: Channel   0:	 0.050 FDR:   400; 0.010 FDR:   377; 0.001 FDR:   302
1:23:11.062287 PROGRESS: 
1:23:11.062344 PROGRESS: Protein Summary:
1:23:11.063489 PROGRESS: Channel   0:	 0.050 FDR:   364; 0.010 FDR:   343; 0.001 FDR:   283
1:23:11.063577 PROGRESS: =========================================================================
1:23:11.063793 INFO: Target number of precursors reached.
1:23:11.068201 INFO: fragments_df: keeping 5000 of 25879 [sum(precursor_idx_mask)=9380 sum(mass_error_mask)=25879 stop_rank=5000
1:23:11.072385 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:11.202698 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:11.884023 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:11.884442 INFO: Using score_cutoff 13.842626962280274 (fac=0.99, q=1)
1:23:11.884725 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:11.884803 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:11.884859 INFO: Updating optimization_manager: score_cutoff        : 19.30188850021362 -> 13.842626962280274
1:23:11.884913 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:11.886500 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:11.888757 INFO: === checking if optimization conditions were reached ===
1:23:11.890358 INFO: Updating optimization_manager: ms2_error           : 6.828943 -> 6.828943
1:23:11.890455 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:23:11.890517 PROGRESS: ✅ ms2_error      : 6.8289 <= 6.8289
1:23:11.890572 INFO: ==============================================
1:23:11.890635 PROGRESS: Optimization finished for ms2_error.
1:23:11.894659 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:11.895998 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:11.898165 INFO: Starting optimization step 0.
1:23:11.898263 PROGRESS: === Extracting elution groups 0 to 600 ===
1:23:11.898331 INFO: Using ng extraction backend
1:23:11.898389 PROGRESS: Extracting batch of 1183 precursors
1:23:11.902207 INFO: === Search parameters used ===
1:23:11.902310 INFO: rt_error       : 1663.6044921875
1:23:11.902361 INFO: mobility_error : 0.1
1:23:11.902407 INFO: num_candidates : 3
1:23:11.902451 INFO: ms1_error      : 30
1:23:11.902492 INFO: ms2_error      : 6.828943
1:23:11.902534 INFO: fwhm_rt        : 3.0
1:23:11.902573 INFO: quant_window   : 3
1:23:11.902611 INFO: ==============================================
1:23:11.942466 INFO: performing precursor FDR with 40 features
1:23:11.942556 INFO: Decoy channel: -1
1:23:11.942584 INFO: Competetive: True
1:23:11.945136 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:11.946991 INFO: Using random state 972821 for train-test-split
1:23:11.958721 INFO: Test AUC: 0.690
1:23:11.958792 INFO: Train AUC: 0.680
1:23:11.958822 INFO: AUC difference: 1.58%
1:23:12.173410 INFO: Resetting torch num_threads to 80
1:23:12.174994 PROGRESS: === Extracted 3549 precursors and 25892 fragments ===
1:23:12.175328 INFO: === FDR correction performed with classifier version 7 ===
1:23:12.175770 PROGRESS: ============================= Precursor FDR =============================
1:23:12.175852 PROGRESS: Total precursors accumulated: 372
1:23:12.175912 PROGRESS: Target precursors: 369 (99.19%)
1:23:12.175964 PROGRESS: Decoy precursors: 3 (0.81%)
1:23:12.176007 PROGRESS: 
1:23:12.176049 PROGRESS: Precursor Summary:
1:23:12.176990 PROGRESS: Channel   0:	 0.050 FDR:   369; 0.010 FDR:   369; 0.001 FDR:   299
1:23:12.177079 PROGRESS: 
1:23:12.177135 PROGRESS: Protein Summary:
1:23:12.178259 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   338; 0.001 FDR:   281
1:23:12.178355 PROGRESS: =========================================================================
1:23:12.178559 INFO: Target number of precursors reached.
1:23:12.182887 INFO: fragments_df: keeping 5000 of 25892 [sum(precursor_idx_mask)=9183 sum(mass_error_mask)=25892 stop_rank=5000
1:23:12.187073 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:12.314500 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:12.992435 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:12.992852 INFO: Using score_cutoff 14.331574964904785 (fac=0.99, q=1)
1:23:12.993136 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:12.993214 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:12.993268 INFO: Updating optimization_manager: score_cutoff        : 13.842626962280274 -> 14.331574964904785
1:23:12.993322 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:12.994901 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:12.997223 INFO: === checking if optimization conditions were reached ===
1:23:12.997326 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:23:12.998800 INFO: Updating optimization_manager: rt_error            : 1663.6044921875 -> 3.812271555514752
1:23:12.998907 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 3.8123.
1:23:12.998972 INFO: ==============================================
1:23:12.999037 INFO: Starting optimization step 1.
1:23:12.999093 PROGRESS: === Extracting elution groups 0 to 600 ===
1:23:12.999148 INFO: Using ng extraction backend
1:23:12.999203 PROGRESS: Extracting batch of 1183 precursors
1:23:13.002884 INFO: === Search parameters used ===
1:23:13.002972 INFO: rt_error       : 3.812271555514752
1:23:13.003020 INFO: mobility_error : 0.1
1:23:13.003063 INFO: num_candidates : 3
1:23:13.003104 INFO: ms1_error      : 30
1:23:13.003144 INFO: ms2_error      : 6.828943
1:23:13.003184 INFO: fwhm_rt        : 3.0
1:23:13.003223 INFO: quant_window   : 3
1:23:13.003262 INFO: ==============================================
1:23:13.033282 INFO: performing precursor FDR with 40 features
1:23:13.033368 INFO: Decoy channel: -1
1:23:13.033394 INFO: Competetive: True
1:23:13.035948 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:13.037802 INFO: Using random state 972821 for train-test-split
1:23:13.049540 INFO: Test AUC: 0.703
1:23:13.049604 INFO: Train AUC: 0.683
1:23:13.049633 INFO: AUC difference: 2.96%
1:23:13.267219 INFO: Resetting torch num_threads to 80
1:23:13.268743 PROGRESS: === Extracted 3276 precursors and 20940 fragments ===
1:23:13.269089 INFO: === FDR correction performed with classifier version 7 ===
1:23:13.269571 PROGRESS: ============================= Precursor FDR =============================
1:23:13.269661 PROGRESS: Total precursors accumulated: 520
1:23:13.269721 PROGRESS: Target precursors: 515 (99.04%)
1:23:13.269780 PROGRESS: Decoy precursors: 5 (0.96%)
1:23:13.269833 PROGRESS: 
1:23:13.269880 PROGRESS: Precursor Summary:
1:23:13.270800 PROGRESS: Channel   0:	 0.050 FDR:   515; 0.010 FDR:   515; 0.001 FDR:     0
1:23:13.270890 PROGRESS: 
1:23:13.270948 PROGRESS: Protein Summary:
1:23:13.272074 PROGRESS: Channel   0:	 0.050 FDR:   466; 0.010 FDR:   466; 0.001 FDR:     0
1:23:13.272163 PROGRESS: =========================================================================
1:23:13.272365 INFO: Target number of precursors reached.
1:23:13.276508 INFO: fragments_df: keeping 5000 of 20940 [sum(precursor_idx_mask)=10350 sum(mass_error_mask)=20940 stop_rank=5000
1:23:13.280683 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:13.418825 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:14.097214 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:14.097641 INFO: Using score_cutoff 12.865291340446472 (fac=0.99, q=1)
1:23:14.097927 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:14.098007 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:14.098058 INFO: Updating optimization_manager: score_cutoff        : 14.331574964904785 -> 12.865291340446472
1:23:14.098112 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:14.099671 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:14.102014 INFO: === checking if optimization conditions were reached ===
1:23:14.102115 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:23:14.103786 INFO: Updating optimization_manager: rt_error            : 3.812271555514752 -> 3.9711922841354537
1:23:14.103885 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 3.9712.
1:23:14.103947 INFO: ==============================================
1:23:14.104015 INFO: Starting optimization step 2.
1:23:14.104072 PROGRESS: === Extracting elution groups 0 to 600 ===
1:23:14.104129 INFO: Using ng extraction backend
1:23:14.104186 PROGRESS: Extracting batch of 1183 precursors
1:23:14.107980 INFO: === Search parameters used ===
1:23:14.108078 INFO: rt_error       : 3.9711922841354537
1:23:14.108128 INFO: mobility_error : 0.1
1:23:14.108174 INFO: num_candidates : 3
1:23:14.108217 INFO: ms1_error      : 30
1:23:14.108258 INFO: ms2_error      : 6.828943
1:23:14.108297 INFO: fwhm_rt        : 3.0
1:23:14.108336 INFO: quant_window   : 3
1:23:14.108375 INFO: ==============================================
1:23:14.140651 INFO: performing precursor FDR with 40 features
1:23:14.140737 INFO: Decoy channel: -1
1:23:14.140763 INFO: Competetive: True
1:23:14.143316 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:14.145119 INFO: Using random state 972821 for train-test-split
1:23:14.156821 INFO: Test AUC: 0.673
1:23:14.156881 INFO: Train AUC: 0.691
1:23:14.156909 INFO: AUC difference: 2.63%
1:23:14.372816 INFO: Resetting torch num_threads to 80
1:23:14.374335 PROGRESS: === Extracted 3270 precursors and 20893 fragments ===
1:23:14.374675 INFO: === FDR correction performed with classifier version 7 ===
1:23:14.375140 PROGRESS: ============================= Precursor FDR =============================
1:23:14.375228 PROGRESS: Total precursors accumulated: 515
1:23:14.375300 PROGRESS: Target precursors: 510 (99.03%)
1:23:14.375353 PROGRESS: Decoy precursors: 5 (0.97%)
1:23:14.375396 PROGRESS: 
1:23:14.375440 PROGRESS: Precursor Summary:
1:23:14.376359 PROGRESS: Channel   0:	 0.050 FDR:   510; 0.010 FDR:   510; 0.001 FDR:     0
1:23:14.376447 PROGRESS: 
1:23:14.376505 PROGRESS: Protein Summary:
1:23:14.377625 PROGRESS: Channel   0:	 0.050 FDR:   461; 0.010 FDR:   461; 0.001 FDR:     0
1:23:14.377712 PROGRESS: =========================================================================
1:23:14.377916 INFO: Target number of precursors reached.
1:23:14.382059 INFO: fragments_df: keeping 5000 of 20893 [sum(precursor_idx_mask)=10226 sum(mass_error_mask)=20893 stop_rank=5000
1:23:14.386250 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:14.524618 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:15.201051 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:15.201484 INFO: Using score_cutoff 12.855250833892823 (fac=0.99, q=1)
1:23:15.201774 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:15.201852 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:15.201906 INFO: Updating optimization_manager: score_cutoff        : 12.865291340446472 -> 12.855250833892823
1:23:15.201961 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:15.203525 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:15.205881 INFO: === checking if optimization conditions were reached ===
1:23:15.205980 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:23:15.206899 INFO: Updating optimization_manager: rt_error            : 3.9711922841354537 -> 3.812271555514752
1:23:15.207019 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
1:23:15.207114 INFO: Updating optimization_manager: score_cutoff        : 12.855250833892823 -> 12.865291340446472
1:23:15.207201 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:15.207283 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:15.207364 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 3.8123 found after 3 searches.
1:23:15.207423 INFO: ==============================================
1:23:15.207518 PROGRESS: Optimization finished for rt_error.
1:23:15.211445 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:15.212790 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:15.238735 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:23:15.238884 PROGRESS: ==============================================
1:23:15.238948 PROGRESS: ms2_error      : 6.8289
1:23:15.239002 PROGRESS: rt_error       : 3.8123
1:23:15.239050 PROGRESS: ==============================================
1:23:15.239533 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:15.319579 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:15.542572 INFO: Using ng extraction backend
1:23:15.542934 PROGRESS: Extracting batch of 146144 precursors
1:23:15.776554 INFO: === Search parameters used ===
1:23:15.776891 INFO: rt_error       : 3.812271555514752
1:23:15.776949 INFO: mobility_error : 0.1
1:23:15.776994 INFO: num_candidates : 3
1:23:15.777038 INFO: ms1_error      : 30
1:23:15.777081 INFO: ms2_error      : 6.828943
1:23:15.777122 INFO: fwhm_rt        : 3.0
1:23:15.777164 INFO: quant_window   : 3
1:23:15.777205 INFO: ==============================================
1:23:15.944609 INFO: Removed 186268 precursors with score below cutoff 12.865291340446472
1:23:16.167536 INFO: performing precursor FDR with 40 features
1:23:16.167671 INFO: Decoy channel: -1
1:23:16.167698 INFO: Competetive: True
1:23:16.189980 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:16.202108 WARNING: FDR calculation for 131287 target and 88440 decoy PSMs
1:23:16.202250 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:23:16.239230 INFO: Using random state 841899 for train-test-split
1:23:19.166215 INFO: Test AUC: 0.842
1:23:19.166350 INFO: Train AUC: 0.843
1:23:19.166380 INFO: AUC difference: 0.12%
1:23:19.461017 INFO: Resetting torch num_threads to 80
1:23:19.672166 PROGRESS: ============================= Precursor FDR =============================
1:23:19.672450 PROGRESS: Total precursors accumulated: 69,557
1:23:19.672513 PROGRESS: Target precursors: 68,869 (99.01%)
1:23:19.672565 PROGRESS: Decoy precursors: 688 (0.99%)
1:23:19.672612 PROGRESS: 
1:23:19.672656 PROGRESS: Precursor Summary:
1:23:19.692881 PROGRESS: Channel   0:	 0.050 FDR: 68,869; 0.010 FDR: 68,869; 0.001 FDR: 65,346
1:23:19.693184 PROGRESS: 
1:23:19.693249 PROGRESS: Protein Summary:
1:23:19.722938 PROGRESS: Channel   0:	 0.050 FDR: 7,016; 0.010 FDR: 7,016; 0.001 FDR: 6,954
1:23:19.723214 PROGRESS: =========================================================================
1:23:19.724483 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/psm.parquet
1:23:19.859516 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/frag.parquet
1:23:20.061944 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
1:23:20.120056 PROGRESS: 
1:23:20.120192 INFO: Quantification results path: alphadia_zenoswath8600/quant
1:23:20.120265 INFO: Creating folder alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/figures
1:23:20.120425 INFO: Initializing TimingManager
1:23:20.121185 INFO: Initializing RawFileManager
1:25:42.709089 INFO: Determining DIA cycle
1:25:42.723861 INFO: Found cycle with start 0.00 min and length 86.
1:25:42.983041 INFO: RT (min)            : 0.0 - 55.4
1:25:42.983138 INFO: RT duration (sec)   : 3326.9
1:25:42.983167 INFO: RT duration (min)   : 55.4
1:25:42.983189 INFO: Cycle len (scans)   : 86
1:25:42.983209 INFO: Cycle len (sec)     : 1.90
1:25:42.983230 INFO: Number of cycles    : 1747
1:25:42.983250 INFO: MS2 range (m/z)     : 399.5 - 903.5
1:25:42.983284 INFO: Creating DIA data object took: 142.86200094223022
1:25:44.143737 INFO: Creating DIA data NG object took: 1.1603264808654785
1:25:44.172456 INFO: Initializing CalibrationManager
1:25:44.172796 INFO: Setting up calibration estimators ..
1:25:44.172856 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:25:44.172920 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'}' ..
1:25:44.172980 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:25:44.173028 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:25:44.173077 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}}' ..
1:25:44.173124 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:25:44.173169 INFO: Done setting up calibration estimators.
1:25:44.173312 INFO: Initializing OptimizationManager
1:25:44.173446 INFO: initial parameter: ms1_error = 30
1:25:44.173510 INFO: initial parameter: ms2_error = 30
1:25:44.173560 INFO: initial parameter: rt_error = 1663.4844970703125
1:25:44.173603 INFO: initial parameter: mobility_error = 0.1
1:25:44.173645 INFO: initial parameter: num_candidates = 1
1:25:44.173685 INFO: initial parameter: fwhm_rt = 5
1:25:44.173727 INFO: initial parameter: fwhm_mobility = 0.01
1:25:44.173769 INFO: initial parameter: score_cutoff = 0
1:25:44.173809 INFO: initial parameter: classifier_version = -1
1:25:44.173877 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
1:25:44.174072 INFO: FDRManager: loading saved state not requested, will be initialized.
1:25:44.174107 INFO: Initializing FDRManager
1:25:44.174137 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:25:44.196693 PROGRESS: Initializing spectral library: 73,874 target precursors potentially observable (0 removed)
1:25:44.211382 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:25:44.211750 INFO: Updating optimization_manager: rt_error            : 1663.4844970703125 -> 1663.4844970703125
1:25:44.211846 PROGRESS: Starting initial search for precursors.
1:25:44.211926 INFO: Starting optimization step 0.
1:25:44.211984 PROGRESS: === Extracting elution groups 0 to 200 ===
1:25:44.212053 INFO: Using ng extraction backend
1:25:44.212108 PROGRESS: Extracting batch of 394 precursors
1:25:44.214398 INFO: === Search parameters used ===
1:25:44.214493 INFO: rt_error       : 1663.4844970703125
1:25:44.214542 INFO: mobility_error : 0.1
1:25:44.214584 INFO: num_candidates : 1
1:25:44.214627 INFO: ms1_error      : 30
1:25:44.214667 INFO: ms2_error      : 30
1:25:44.214707 INFO: fwhm_rt        : 5
1:25:44.214748 INFO: quant_window   : 3
1:25:44.214789 INFO: ==============================================
1:25:44.235868 INFO: performing precursor FDR with 40 features
1:25:44.235933 INFO: Decoy channel: -1
1:25:44.235959 INFO: Competetive: True
1:25:44.236891 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:44.238905 INFO: Using random state 443750 for train-test-split
1:25:44.245831 INFO: Test AUC: 0.485
1:25:44.245887 INFO: Train AUC: 0.446
1:25:44.245916 INFO: AUC difference: 8.77%
1:25:44.245939 WARNING: AUC difference > 5%. This may indicate overfitting.
1:25:44.461444 INFO: Resetting torch num_threads to 80
1:25:44.462741 PROGRESS: === Extracted 394 precursors and 3045 fragments ===
1:25:44.463081 INFO: === FDR correction performed with classifier version -1 ===
1:25:44.463505 PROGRESS: ============================= Precursor FDR =============================
1:25:44.463591 PROGRESS: Total precursors accumulated: 0
1:25:44.463650 PROGRESS: Target precursors: 0 (0.00%)
1:25:44.463699 PROGRESS: Decoy precursors: 0 (0.00%)
1:25:44.463746 PROGRESS: 
1:25:44.463791 PROGRESS: Precursor Summary:
1:25:44.463896 PROGRESS: 
1:25:44.463960 PROGRESS: Protein Summary:
1:25:44.464035 PROGRESS: =========================================================================
1:25:44.464197 INFO: Target number of precursors not reached yet.
1:25:44.467660 INFO: Starting optimization step 1.
1:25:44.467768 PROGRESS: === Extracting elution groups 200 to 600 ===
1:25:44.467839 INFO: Using ng extraction backend
1:25:44.467896 PROGRESS: Extracting batch of 789 precursors
1:25:44.470694 INFO: === Search parameters used ===
1:25:44.470785 INFO: rt_error       : 1663.4844970703125
1:25:44.470837 INFO: mobility_error : 0.1
1:25:44.470884 INFO: num_candidates : 1
1:25:44.470930 INFO: ms1_error      : 30
1:25:44.470972 INFO: ms2_error      : 30
1:25:44.471011 INFO: fwhm_rt        : 5
1:25:44.471052 INFO: quant_window   : 3
1:25:44.471095 INFO: ==============================================
1:25:44.496460 INFO: performing precursor FDR with 40 features
1:25:44.496532 INFO: Decoy channel: -1
1:25:44.496559 INFO: Competetive: True
1:25:44.499373 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:44.500897 INFO: Using random state 21001 for train-test-split
1:25:44.509004 INFO: Test AUC: 0.487
1:25:44.509064 INFO: Train AUC: 0.487
1:25:44.509094 INFO: AUC difference: 0.00%
1:25:44.719187 INFO: Resetting torch num_threads to 80
1:25:44.721378 PROGRESS: === Extracted 1183 precursors and 9354 fragments ===
1:25:44.721758 INFO: === FDR correction performed with classifier version -1 ===
1:25:44.722188 PROGRESS: ============================= Precursor FDR =============================
1:25:44.722275 PROGRESS: Total precursors accumulated: 0
1:25:44.722334 PROGRESS: Target precursors: 0 (0.00%)
1:25:44.722382 PROGRESS: Decoy precursors: 0 (0.00%)
1:25:44.722426 PROGRESS: 
1:25:44.722471 PROGRESS: Precursor Summary:
1:25:44.722574 PROGRESS: 
1:25:44.722636 PROGRESS: Protein Summary:
1:25:44.722718 PROGRESS: =========================================================================
1:25:44.722912 INFO: Target number of precursors not reached yet.
1:25:44.727488 INFO: Starting optimization step 2.
1:25:44.727598 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:25:44.727668 INFO: Using ng extraction backend
1:25:44.727726 PROGRESS: Extracting batch of 1588 precursors
1:25:44.732144 INFO: === Search parameters used ===
1:25:44.732240 INFO: rt_error       : 1663.4844970703125
1:25:44.732291 INFO: mobility_error : 0.1
1:25:44.732333 INFO: num_candidates : 1
1:25:44.732386 INFO: ms1_error      : 30
1:25:44.732428 INFO: ms2_error      : 30
1:25:44.732468 INFO: fwhm_rt        : 5
1:25:44.732508 INFO: quant_window   : 3
1:25:44.732546 INFO: ==============================================
1:25:44.770250 INFO: performing precursor FDR with 40 features
1:25:44.770341 INFO: Decoy channel: -1
1:25:44.770367 INFO: Competetive: True
1:25:44.773609 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:44.775418 INFO: Using random state 936555 for train-test-split
1:25:44.787023 INFO: Test AUC: 0.502
1:25:44.787084 INFO: Train AUC: 0.493
1:25:44.787113 INFO: AUC difference: 1.71%
1:25:44.998460 INFO: Resetting torch num_threads to 80
1:25:45.000951 PROGRESS: === Extracted 2770 precursors and 21910 fragments ===
1:25:45.001389 INFO: === FDR correction performed with classifier version -1 ===
1:25:45.001827 PROGRESS: ============================= Precursor FDR =============================
1:25:45.001917 PROGRESS: Total precursors accumulated: 0
1:25:45.001978 PROGRESS: Target precursors: 0 (0.00%)
1:25:45.002027 PROGRESS: Decoy precursors: 0 (0.00%)
1:25:45.002074 PROGRESS: 
1:25:45.002126 PROGRESS: Precursor Summary:
1:25:45.002235 PROGRESS: 
1:25:45.002298 PROGRESS: Protein Summary:
1:25:45.002367 PROGRESS: =========================================================================
1:25:45.002566 INFO: Target number of precursors not reached yet.
1:25:45.009284 INFO: Starting optimization step 3.
1:25:45.009408 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:25:45.009487 INFO: Using ng extraction backend
1:25:45.009550 PROGRESS: Extracting batch of 3164 precursors
1:25:45.016744 INFO: === Search parameters used ===
1:25:45.016862 INFO: rt_error       : 1663.4844970703125
1:25:45.016914 INFO: mobility_error : 0.1
1:25:45.016961 INFO: num_candidates : 1
1:25:45.017007 INFO: ms1_error      : 30
1:25:45.017052 INFO: ms2_error      : 30
1:25:45.017092 INFO: fwhm_rt        : 5
1:25:45.017132 INFO: quant_window   : 3
1:25:45.017170 INFO: ==============================================
1:25:45.073208 INFO: performing precursor FDR with 40 features
1:25:45.073319 INFO: Decoy channel: -1
1:25:45.073345 INFO: Competetive: True
1:25:45.077309 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:45.079623 INFO: Using random state 291374 for train-test-split
1:25:45.098691 INFO: Test AUC: 0.474
1:25:45.098784 INFO: Train AUC: 0.500
1:25:45.098814 INFO: AUC difference: 5.17%
1:25:45.098835 WARNING: AUC difference > 5%. This may indicate overfitting.
1:25:45.312786 INFO: Resetting torch num_threads to 80
1:25:45.316083 PROGRESS: === Extracted 5933 precursors and 47025 fragments ===
1:25:45.316476 INFO: === FDR correction performed with classifier version -1 ===
1:25:45.316927 PROGRESS: ============================= Precursor FDR =============================
1:25:45.317017 PROGRESS: Total precursors accumulated: 2
1:25:45.317081 PROGRESS: Target precursors: 2 (100.00%)
1:25:45.317133 PROGRESS: Decoy precursors: 0 (0.00%)
1:25:45.317178 PROGRESS: 
1:25:45.317222 PROGRESS: Precursor Summary:
1:25:45.318139 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:25:45.318228 PROGRESS: 
1:25:45.318282 PROGRESS: Protein Summary:
1:25:45.319287 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:25:45.319373 PROGRESS: =========================================================================
1:25:45.319603 INFO: Target number of precursors not reached yet.
1:25:45.329962 INFO: Starting optimization step 4.
1:25:45.330107 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:25:45.330181 INFO: Using ng extraction backend
1:25:45.330238 PROGRESS: Extracting batch of 6329 precursors
1:25:45.342906 INFO: === Search parameters used ===
1:25:45.343057 INFO: rt_error       : 1663.4844970703125
1:25:45.343107 INFO: mobility_error : 0.1
1:25:45.343149 INFO: num_candidates : 1
1:25:45.343192 INFO: ms1_error      : 30
1:25:45.343232 INFO: ms2_error      : 30
1:25:45.343270 INFO: fwhm_rt        : 5
1:25:45.343325 INFO: quant_window   : 3
1:25:45.343374 INFO: ==============================================
1:25:45.431107 INFO: performing precursor FDR with 40 features
1:25:45.431228 INFO: Decoy channel: -1
1:25:45.431254 INFO: Competetive: True
1:25:45.436506 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:45.439861 INFO: Using random state 148603 for train-test-split
1:25:45.475338 INFO: Test AUC: 0.473
1:25:45.475442 INFO: Train AUC: 0.501
1:25:45.475471 INFO: AUC difference: 5.55%
1:25:45.475494 WARNING: AUC difference > 5%. This may indicate overfitting.
1:25:45.696268 INFO: Resetting torch num_threads to 80
1:25:45.700805 PROGRESS: === Extracted 12260 precursors and 96754 fragments ===
1:25:45.701190 INFO: === FDR correction performed with classifier version -1 ===
1:25:45.701643 PROGRESS: ============================= Precursor FDR =============================
1:25:45.701736 PROGRESS: Total precursors accumulated: 0
1:25:45.701797 PROGRESS: Target precursors: 0 (0.00%)
1:25:45.701848 PROGRESS: Decoy precursors: 0 (0.00%)
1:25:45.701893 PROGRESS: 
1:25:45.701938 PROGRESS: Precursor Summary:
1:25:45.702045 PROGRESS: 
1:25:45.702107 PROGRESS: Protein Summary:
1:25:45.702181 PROGRESS: =========================================================================
1:25:45.702448 INFO: Target number of precursors not reached yet.
1:25:45.716178 INFO: Starting optimization step 5.
1:25:45.716397 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:25:45.716503 INFO: Using ng extraction backend
1:25:45.716581 PROGRESS: Extracting batch of 12652 precursors
1:25:45.739658 INFO: === Search parameters used ===
1:25:45.739850 INFO: rt_error       : 1663.4844970703125
1:25:45.739902 INFO: mobility_error : 0.1
1:25:45.739947 INFO: num_candidates : 1
1:25:45.740007 INFO: ms1_error      : 30
1:25:45.740051 INFO: ms2_error      : 30
1:25:45.740090 INFO: fwhm_rt        : 5
1:25:45.740130 INFO: quant_window   : 3
1:25:45.740168 INFO: ==============================================
1:25:45.904297 INFO: performing precursor FDR with 40 features
1:25:45.904424 INFO: Decoy channel: -1
1:25:45.904450 INFO: Competetive: True
1:25:45.913842 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:45.919686 INFO: Using random state 289214 for train-test-split
1:25:46.155544 INFO: Test AUC: 0.845
1:25:46.155676 INFO: Train AUC: 0.856
1:25:46.155707 INFO: AUC difference: 1.18%
1:25:46.378883 INFO: Resetting torch num_threads to 80
1:25:46.387541 PROGRESS: === Extracted 24909 precursors and 196376 fragments ===
1:25:46.387967 INFO: === FDR correction performed with classifier version -1 ===
1:25:46.389767 PROGRESS: ============================= Precursor FDR =============================
1:25:46.389878 PROGRESS: Total precursors accumulated: 7,885
1:25:46.389938 PROGRESS: Target precursors: 7,807 (99.01%)
1:25:46.389987 PROGRESS: Decoy precursors: 78 (0.99%)
1:25:46.390036 PROGRESS: 
1:25:46.390080 PROGRESS: Precursor Summary:
1:25:46.393353 PROGRESS: Channel   0:	 0.050 FDR: 7,807; 0.010 FDR: 7,807; 0.001 FDR: 7,191
1:25:46.393489 PROGRESS: 
1:25:46.393548 PROGRESS: Protein Summary:
1:25:46.398047 PROGRESS: Channel   0:	 0.050 FDR: 3,433; 0.010 FDR: 3,433; 0.001 FDR: 3,254
1:25:46.398158 PROGRESS: =========================================================================
1:25:46.398570 INFO: Target number of precursors reached.
1:25:46.434523 INFO: fragments_df: keeping 5000 of 196376 [sum(precursor_idx_mask)=81385 sum(mass_error_mask)=196376 stop_rank=5000
1:25:46.440876 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:48.070402 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:48.957806 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:25:48.958519 INFO: Using score_cutoff 14.868214358711244 (fac=0.99, q=1)
1:25:48.958963 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:25:48.959045 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:25:48.959101 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.868214358711244
1:25:48.959172 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:48.960839 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:48.963885 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
1:25:48.964106 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:25:48.964208 INFO: Starting optimization step 6.
1:25:48.964273 PROGRESS: === Extracting elution groups 0 to 600 ===
1:25:48.964349 INFO: Using ng extraction backend
1:25:48.964430 PROGRESS: Extracting batch of 1183 precursors
1:25:48.969050 INFO: === Search parameters used ===
1:25:48.969153 INFO: rt_error       : 1663.4844970703125
1:25:48.969209 INFO: mobility_error : 0.1
1:25:48.969254 INFO: num_candidates : 3
1:25:48.969299 INFO: ms1_error      : 30
1:25:48.969344 INFO: ms2_error      : 30
1:25:48.969394 INFO: fwhm_rt        : 3.0
1:25:48.969436 INFO: quant_window   : 3
1:25:48.969487 INFO: ==============================================
1:25:49.023395 INFO: performing precursor FDR with 40 features
1:25:49.023510 INFO: Decoy channel: -1
1:25:49.023536 INFO: Competetive: True
1:25:49.026422 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:49.028392 INFO: Using random state 988349 for train-test-split
1:25:49.040411 INFO: Test AUC: 0.697
1:25:49.040479 INFO: Train AUC: 0.675
1:25:49.040508 INFO: AUC difference: 3.27%
1:25:49.254183 INFO: Resetting torch num_threads to 80
1:25:49.255808 PROGRESS: === Extracted 3549 precursors and 24539 fragments ===
1:25:49.256175 INFO: === FDR correction performed with classifier version 5 ===
1:25:49.256642 PROGRESS: ============================= Precursor FDR =============================
1:25:49.256732 PROGRESS: Total precursors accumulated: 416
1:25:49.256790 PROGRESS: Target precursors: 412 (99.04%)
1:25:49.256840 PROGRESS: Decoy precursors: 4 (0.96%)
1:25:49.256883 PROGRESS: 
1:25:49.256926 PROGRESS: Precursor Summary:
1:25:49.257890 PROGRESS: Channel   0:	 0.050 FDR:   412; 0.010 FDR:   412; 0.001 FDR:   412
1:25:49.257981 PROGRESS: 
1:25:49.258035 PROGRESS: Protein Summary:
1:25:49.259185 PROGRESS: Channel   0:	 0.050 FDR:   379; 0.010 FDR:   379; 0.001 FDR:   379
1:25:49.259274 PROGRESS: =========================================================================
1:25:49.259717 INFO: Target number of precursors reached.
1:25:49.264065 INFO: fragments_df: keeping 5000 of 24539 [sum(precursor_idx_mask)=9624 sum(mass_error_mask)=24539 stop_rank=5000
1:25:49.270794 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:49.401386 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:50.078829 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:50.079272 INFO: Using score_cutoff 15.995464714050293 (fac=0.99, q=1)
1:25:50.079558 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:50.079640 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:50.079696 INFO: Updating optimization_manager: score_cutoff        : 14.868214358711244 -> 15.995464714050293
1:25:50.079750 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:50.081312 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:50.083714 INFO: === checking if optimization conditions were reached ===
1:25:50.085355 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.828943
1:25:50.085455 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
1:25:50.085536 PROGRESS: ❌ ms2_error      : 6.8289 > 6.8289 or insufficient steps taken.
1:25:50.085594 INFO: ==============================================
1:25:50.085657 INFO: Starting optimization step 7.
1:25:50.085712 PROGRESS: === Extracting elution groups 0 to 600 ===
1:25:50.085770 INFO: Using ng extraction backend
1:25:50.085824 PROGRESS: Extracting batch of 1183 precursors
1:25:50.089495 INFO: === Search parameters used ===
1:25:50.089583 INFO: rt_error       : 1663.4844970703125
1:25:50.089633 INFO: mobility_error : 0.1
1:25:50.089677 INFO: num_candidates : 3
1:25:50.089729 INFO: ms1_error      : 30
1:25:50.089780 INFO: ms2_error      : 6.828943
1:25:50.089826 INFO: fwhm_rt        : 3.0
1:25:50.089867 INFO: quant_window   : 3
1:25:50.089908 INFO: ==============================================
1:25:50.131145 INFO: performing precursor FDR with 40 features
1:25:50.131234 INFO: Decoy channel: -1
1:25:50.131259 INFO: Competetive: True
1:25:50.133920 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:50.135755 INFO: Using random state 954797 for train-test-split
1:25:50.147821 INFO: Test AUC: 0.699
1:25:50.147887 INFO: Train AUC: 0.666
1:25:50.147915 INFO: AUC difference: 4.91%
1:25:50.358798 INFO: Resetting torch num_threads to 80
1:25:50.360375 PROGRESS: === Extracted 3549 precursors and 25854 fragments ===
1:25:50.360727 INFO: === FDR correction performed with classifier version 6 ===
1:25:50.361186 PROGRESS: ============================= Precursor FDR =============================
1:25:50.361272 PROGRESS: Total precursors accumulated: 448
1:25:50.361333 PROGRESS: Target precursors: 444 (99.11%)
1:25:50.361383 PROGRESS: Decoy precursors: 4 (0.89%)
1:25:50.361427 PROGRESS: 
1:25:50.361482 PROGRESS: Precursor Summary:
1:25:50.362423 PROGRESS: Channel   0:	 0.050 FDR:   444; 0.010 FDR:   444; 0.001 FDR:   410
1:25:50.362513 PROGRESS: 
1:25:50.362568 PROGRESS: Protein Summary:
1:25:50.363732 PROGRESS: Channel   0:	 0.050 FDR:   405; 0.010 FDR:   405; 0.001 FDR:   380
1:25:50.363830 PROGRESS: =========================================================================
1:25:50.364031 INFO: Target number of precursors reached.
1:25:50.368579 INFO: fragments_df: keeping 5000 of 25854 [sum(precursor_idx_mask)=10823 sum(mass_error_mask)=25854 stop_rank=5000
1:25:50.373037 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:50.504297 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:51.188733 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:51.189159 INFO: Using score_cutoff 13.717142024517058 (fac=0.99, q=1)
1:25:51.189441 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:51.189538 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:51.189595 INFO: Updating optimization_manager: score_cutoff        : 15.995464714050293 -> 13.717142024517058
1:25:51.189649 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:51.191208 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:51.193609 INFO: === checking if optimization conditions were reached ===
1:25:51.195203 INFO: Updating optimization_manager: ms2_error           : 6.828943 -> 6.828943
1:25:51.195303 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:25:51.195369 PROGRESS: ✅ ms2_error      : 6.8289 <= 6.8289
1:25:51.195428 INFO: ==============================================
1:25:51.195495 PROGRESS: Optimization finished for ms2_error.
1:25:51.199751 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:51.201094 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:51.203356 INFO: Starting optimization step 0.
1:25:51.203465 PROGRESS: === Extracting elution groups 0 to 600 ===
1:25:51.203535 INFO: Using ng extraction backend
1:25:51.203597 PROGRESS: Extracting batch of 1183 precursors
1:25:51.207261 INFO: === Search parameters used ===
1:25:51.207355 INFO: rt_error       : 1663.4844970703125
1:25:51.207408 INFO: mobility_error : 0.1
1:25:51.207452 INFO: num_candidates : 3
1:25:51.207495 INFO: ms1_error      : 30
1:25:51.207538 INFO: ms2_error      : 6.828943
1:25:51.207577 INFO: fwhm_rt        : 3.0
1:25:51.207618 INFO: quant_window   : 3
1:25:51.207659 INFO: ==============================================
1:25:51.248006 INFO: performing precursor FDR with 40 features
1:25:51.248099 INFO: Decoy channel: -1
1:25:51.248124 INFO: Competetive: True
1:25:51.250767 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:51.252650 INFO: Using random state 553103 for train-test-split
1:25:51.265746 INFO: Test AUC: 0.659
1:25:51.265828 INFO: Train AUC: 0.676
1:25:51.265858 INFO: AUC difference: 2.58%
1:25:51.476719 INFO: Resetting torch num_threads to 80
1:25:51.478317 PROGRESS: === Extracted 3549 precursors and 25833 fragments ===
1:25:51.478663 INFO: === FDR correction performed with classifier version 7 ===
1:25:51.479116 PROGRESS: ============================= Precursor FDR =============================
1:25:51.479202 PROGRESS: Total precursors accumulated: 448
1:25:51.479261 PROGRESS: Target precursors: 444 (99.11%)
1:25:51.479312 PROGRESS: Decoy precursors: 4 (0.89%)
1:25:51.479357 PROGRESS: 
1:25:51.479400 PROGRESS: Precursor Summary:
1:25:51.480331 PROGRESS: Channel   0:	 0.050 FDR:   444; 0.010 FDR:   444; 0.001 FDR:   406
1:25:51.480420 PROGRESS: 
1:25:51.480473 PROGRESS: Protein Summary:
1:25:51.481619 PROGRESS: Channel   0:	 0.050 FDR:   405; 0.010 FDR:   405; 0.001 FDR:   377
1:25:51.481711 PROGRESS: =========================================================================
1:25:51.481922 INFO: Target number of precursors reached.
1:25:51.486489 INFO: fragments_df: keeping 5000 of 25833 [sum(precursor_idx_mask)=10801 sum(mass_error_mask)=25833 stop_rank=5000
1:25:51.490932 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:51.621990 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:53.811238 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:53.811670 INFO: Using score_cutoff 13.717142024517058 (fac=0.99, q=1)
1:25:53.811957 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:53.812038 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:53.812091 INFO: Updating optimization_manager: score_cutoff        : 13.717142024517058 -> 13.717142024517058
1:25:53.812144 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:53.813730 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:53.816072 INFO: === checking if optimization conditions were reached ===
1:25:53.816172 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:25:53.817704 INFO: Updating optimization_manager: rt_error            : 1663.4844970703125 -> 7.263855344218502
1:25:53.817806 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 7.2639.
1:25:53.817870 INFO: ==============================================
1:25:53.817934 INFO: Starting optimization step 1.
1:25:53.817989 PROGRESS: === Extracting elution groups 0 to 600 ===
1:25:53.818051 INFO: Using ng extraction backend
1:25:53.818106 PROGRESS: Extracting batch of 1183 precursors
1:25:53.821826 INFO: === Search parameters used ===
1:25:53.821928 INFO: rt_error       : 7.263855344218502
1:25:53.821981 INFO: mobility_error : 0.1
1:25:53.822027 INFO: num_candidates : 3
1:25:53.822068 INFO: ms1_error      : 30
1:25:53.822110 INFO: ms2_error      : 6.828943
1:25:53.822149 INFO: fwhm_rt        : 3.0
1:25:53.822188 INFO: quant_window   : 3
1:25:53.822226 INFO: ==============================================
1:25:53.857010 INFO: performing precursor FDR with 40 features
1:25:53.857107 INFO: Decoy channel: -1
1:25:53.857133 INFO: Competetive: True
1:25:53.859878 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:53.861749 INFO: Using random state 553103 for train-test-split
1:25:53.873729 INFO: Test AUC: 0.676
1:25:53.873791 INFO: Train AUC: 0.687
1:25:53.873821 INFO: AUC difference: 1.56%
1:25:54.087538 INFO: Resetting torch num_threads to 80
1:25:54.089125 PROGRESS: === Extracted 3275 precursors and 20899 fragments ===
1:25:54.089480 INFO: === FDR correction performed with classifier version 7 ===
1:25:54.089970 PROGRESS: ============================= Precursor FDR =============================
1:25:54.090064 PROGRESS: Total precursors accumulated: 558
1:25:54.090122 PROGRESS: Target precursors: 553 (99.10%)
1:25:54.090172 PROGRESS: Decoy precursors: 5 (0.90%)
1:25:54.090218 PROGRESS: 
1:25:54.090261 PROGRESS: Precursor Summary:
1:25:54.091265 PROGRESS: Channel   0:	 0.050 FDR:   553; 0.010 FDR:   553; 0.001 FDR:   492
1:25:54.092180 PROGRESS: 
1:25:54.092237 PROGRESS: Protein Summary:
1:25:54.093520 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   501; 0.001 FDR:   448
1:25:54.093616 PROGRESS: =========================================================================
1:25:54.093834 INFO: Target number of precursors reached.
1:25:54.098286 INFO: fragments_df: keeping 5000 of 20899 [sum(precursor_idx_mask)=10968 sum(mass_error_mask)=20899 stop_rank=5000
1:25:54.102789 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:54.244796 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:54.927590 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:54.928513 INFO: Using score_cutoff 12.14549428024292 (fac=0.99, q=1)
1:25:54.928833 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:54.928915 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:54.928969 INFO: Updating optimization_manager: score_cutoff        : 13.717142024517058 -> 12.14549428024292
1:25:54.929032 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:54.930775 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:54.933139 INFO: === checking if optimization conditions were reached ===
1:25:54.933245 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:25:54.935004 INFO: Updating optimization_manager: rt_error            : 7.263855344218502 -> 6.1473351704598205
1:25:54.935115 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 6.1473.
1:25:54.935183 INFO: ==============================================
1:25:54.935263 INFO: Starting optimization step 2.
1:25:54.935326 PROGRESS: === Extracting elution groups 0 to 600 ===
1:25:54.935392 INFO: Using ng extraction backend
1:25:54.935452 PROGRESS: Extracting batch of 1183 precursors
1:25:54.939501 INFO: === Search parameters used ===
1:25:54.939604 INFO: rt_error       : 6.1473351704598205
1:25:54.939657 INFO: mobility_error : 0.1
1:25:54.939703 INFO: num_candidates : 3
1:25:54.939751 INFO: ms1_error      : 30
1:25:54.939795 INFO: ms2_error      : 6.828943
1:25:54.939836 INFO: fwhm_rt        : 3.0
1:25:54.939876 INFO: quant_window   : 3
1:25:54.939915 INFO: ==============================================
1:25:54.972595 INFO: performing precursor FDR with 40 features
1:25:54.972674 INFO: Decoy channel: -1
1:25:54.972698 INFO: Competetive: True
1:25:54.975501 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:54.977389 INFO: Using random state 553103 for train-test-split
1:25:54.989652 INFO: Test AUC: 0.689
1:25:54.989715 INFO: Train AUC: 0.687
1:25:54.989742 INFO: AUC difference: 0.33%
1:25:55.202925 INFO: Resetting torch num_threads to 80
1:25:55.204517 PROGRESS: === Extracted 3275 precursors and 20920 fragments ===
1:25:55.204872 INFO: === FDR correction performed with classifier version 7 ===
1:25:55.205368 PROGRESS: ============================= Precursor FDR =============================
1:25:55.205459 PROGRESS: Total precursors accumulated: 563
1:25:55.205533 PROGRESS: Target precursors: 558 (99.11%)
1:25:55.205581 PROGRESS: Decoy precursors: 5 (0.89%)
1:25:55.205626 PROGRESS: 
1:25:55.205669 PROGRESS: Precursor Summary:
1:25:55.206686 PROGRESS: Channel   0:	 0.050 FDR:   558; 0.010 FDR:   558; 0.001 FDR:   490
1:25:55.206783 PROGRESS: 
1:25:55.206841 PROGRESS: Protein Summary:
1:25:55.208076 PROGRESS: Channel   0:	 0.050 FDR:   505; 0.010 FDR:   505; 0.001 FDR:   446
1:25:55.208169 PROGRESS: =========================================================================
1:25:55.208383 INFO: Target number of precursors reached.
1:25:55.212818 INFO: fragments_df: keeping 5000 of 20920 [sum(precursor_idx_mask)=11083 sum(mass_error_mask)=20920 stop_rank=5000
1:25:55.227945 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:55.370682 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:56.044760 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:56.045194 INFO: Using score_cutoff 12.15044500722885 (fac=0.99, q=1)
1:25:56.045491 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:56.045574 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:56.045628 INFO: Updating optimization_manager: score_cutoff        : 12.14549428024292 -> 12.15044500722885
1:25:56.045679 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:56.047238 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:56.049591 INFO: === checking if optimization conditions were reached ===
1:25:56.049694 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:25:56.051449 INFO: Updating optimization_manager: rt_error            : 6.1473351704598205 -> 6.181995690303085
1:25:56.051552 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 6.1820.
1:25:56.051622 INFO: ==============================================
1:25:56.051688 INFO: Starting optimization step 3.
1:25:56.051745 PROGRESS: === Extracting elution groups 0 to 600 ===
1:25:56.051800 INFO: Using ng extraction backend
1:25:56.051852 PROGRESS: Extracting batch of 1183 precursors
1:25:56.055526 INFO: === Search parameters used ===
1:25:56.055618 INFO: rt_error       : 6.181995690303085
1:25:56.055667 INFO: mobility_error : 0.1
1:25:56.055710 INFO: num_candidates : 3
1:25:56.055750 INFO: ms1_error      : 30
1:25:56.055792 INFO: ms2_error      : 6.828943
1:25:56.055833 INFO: fwhm_rt        : 3.0
1:25:56.055872 INFO: quant_window   : 3
1:25:56.055909 INFO: ==============================================
1:25:56.088373 INFO: performing precursor FDR with 40 features
1:25:56.088457 INFO: Decoy channel: -1
1:25:56.088481 INFO: Competetive: True
1:25:56.091149 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:56.092972 INFO: Using random state 553103 for train-test-split
1:25:56.105026 INFO: Test AUC: 0.708
1:25:56.105089 INFO: Train AUC: 0.680
1:25:56.105117 INFO: AUC difference: 4.08%
1:25:56.320048 INFO: Resetting torch num_threads to 80
1:25:56.321607 PROGRESS: === Extracted 3277 precursors and 20924 fragments ===
1:25:56.321965 INFO: === FDR correction performed with classifier version 7 ===
1:25:56.322461 PROGRESS: ============================= Precursor FDR =============================
1:25:56.322554 PROGRESS: Total precursors accumulated: 562
1:25:56.322615 PROGRESS: Target precursors: 557 (99.11%)
1:25:56.322663 PROGRESS: Decoy precursors: 5 (0.89%)
1:25:56.322710 PROGRESS: 
1:25:56.322760 PROGRESS: Precursor Summary:
1:25:56.323763 PROGRESS: Channel   0:	 0.050 FDR:   557; 0.010 FDR:   557; 0.001 FDR:   490
1:25:56.323853 PROGRESS: 
1:25:56.323911 PROGRESS: Protein Summary:
1:25:56.325141 PROGRESS: Channel   0:	 0.050 FDR:   504; 0.010 FDR:   504; 0.001 FDR:   446
1:25:56.325233 PROGRESS: =========================================================================
1:25:56.325444 INFO: Target number of precursors reached.
1:25:56.329888 INFO: fragments_df: keeping 5000 of 20924 [sum(precursor_idx_mask)=11062 sum(mass_error_mask)=20924 stop_rank=5000
1:25:56.334028 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:56.476156 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:57.152251 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:57.152677 INFO: Using score_cutoff 12.149454861831666 (fac=0.99, q=1)
1:25:57.152964 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:57.153045 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:57.153099 INFO: Updating optimization_manager: score_cutoff        : 12.15044500722885 -> 12.149454861831666
1:25:57.153149 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:57.154718 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:57.157107 INFO: === checking if optimization conditions were reached ===
1:25:57.157208 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:25:57.158113 INFO: Updating optimization_manager: rt_error            : 6.181995690303085 -> 6.1473351704598205
1:25:57.158257 INFO: Updating optimization_manager: classifier_version  : 7 -> 10
1:25:57.158353 INFO: Updating optimization_manager: score_cutoff        : 12.149454861831666 -> 12.15044500722885
1:25:57.158441 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:57.158523 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:57.158602 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 6.1473 found after 4 searches.
1:25:57.158662 INFO: ==============================================
1:25:57.158726 PROGRESS: Optimization finished for rt_error.
1:25:57.162611 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:57.163947 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:57.188993 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:25:57.189150 PROGRESS: ==============================================
1:25:57.189218 PROGRESS: ms2_error      : 6.8289
1:25:57.189273 PROGRESS: rt_error       : 6.1473
1:25:57.189320 PROGRESS: ==============================================
1:25:57.189851 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:57.277491 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:57.503552 INFO: Using ng extraction backend
1:25:57.503913 PROGRESS: Extracting batch of 146144 precursors
1:25:57.740664 INFO: === Search parameters used ===
1:25:57.741040 INFO: rt_error       : 6.1473351704598205
1:25:57.741098 INFO: mobility_error : 0.1
1:25:57.741143 INFO: num_candidates : 3
1:25:57.741187 INFO: ms1_error      : 30
1:25:57.741227 INFO: ms2_error      : 6.828943
1:25:57.741265 INFO: fwhm_rt        : 3.0
1:25:57.741303 INFO: quant_window   : 3
1:25:57.741342 INFO: ==============================================
1:25:57.919001 INFO: Removed 171854 precursors with score below cutoff 12.15044500722885
1:25:58.168743 INFO: performing precursor FDR with 40 features
1:25:58.168869 INFO: Decoy channel: -1
1:25:58.168894 INFO: Competetive: True
1:25:58.194679 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:58.207464 WARNING: FDR calculation for 137532 target and 96839 decoy PSMs
1:25:58.207614 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:25:58.251422 INFO: Using random state 489739 for train-test-split
1:26:01.257326 INFO: Test AUC: 0.842
1:26:01.257477 INFO: Train AUC: 0.841
1:26:01.257508 INFO: AUC difference: 0.19%
1:26:01.557933 INFO: Resetting torch num_threads to 80
1:26:01.777671 PROGRESS: ============================= Precursor FDR =============================
1:26:01.777949 PROGRESS: Total precursors accumulated: 70,418
1:26:01.778019 PROGRESS: Target precursors: 69,721 (99.01%)
1:26:01.778072 PROGRESS: Decoy precursors: 697 (0.99%)
1:26:01.778120 PROGRESS: 
1:26:01.778166 PROGRESS: Precursor Summary:
1:26:01.797971 PROGRESS: Channel   0:	 0.050 FDR: 69,721; 0.010 FDR: 69,721; 0.001 FDR: 66,443
1:26:01.798335 PROGRESS: 
1:26:01.798401 PROGRESS: Protein Summary:
1:26:01.827038 PROGRESS: Channel   0:	 0.050 FDR: 7,015; 0.010 FDR: 7,015; 0.001 FDR: 6,972
1:26:01.827320 PROGRESS: =========================================================================
1:26:01.828542 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/psm.parquet
1:26:01.959160 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/frag.parquet
1:26:02.161667 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
1:26:02.223916 PROGRESS: 
1:26:02.224059 INFO: Quantification results path: alphadia_zenoswath8600/quant
1:26:02.224129 INFO: Creating folder alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/figures
1:26:02.224303 INFO: Initializing TimingManager
1:26:02.225136 INFO: Initializing RawFileManager
1:28:22.453723 INFO: Determining DIA cycle
1:28:22.468473 INFO: Found cycle with start 0.00 min and length 86.
1:28:22.711741 INFO: RT (min)            : 0.0 - 55.5
1:28:22.711836 INFO: RT duration (sec)   : 3327.1
1:28:22.711866 INFO: RT duration (min)   : 55.5
1:28:22.711889 INFO: Cycle len (scans)   : 86
1:28:22.711910 INFO: Cycle len (sec)     : 1.90
1:28:22.711928 INFO: Number of cycles    : 1747
1:28:22.711946 INFO: MS2 range (m/z)     : 399.5 - 903.5
1:28:22.711972 INFO: Creating DIA data object took: 140.48673939704895
1:28:23.899675 INFO: Creating DIA data NG object took: 1.1875853538513184
1:28:23.918469 INFO: Initializing CalibrationManager
1:28:23.918769 INFO: Setting up calibration estimators ..
1:28:23.918827 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:28:23.918888 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'}' ..
1:28:23.918949 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:28:23.918996 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:28:23.919045 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}}' ..
1:28:23.919095 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:28:23.919139 INFO: Done setting up calibration estimators.
1:28:23.919269 INFO: Initializing OptimizationManager
1:28:23.919391 INFO: initial parameter: ms1_error = 30
1:28:23.919441 INFO: initial parameter: ms2_error = 30
1:28:23.919487 INFO: initial parameter: rt_error = 1663.596435546875
1:28:23.919530 INFO: initial parameter: mobility_error = 0.1
1:28:23.919571 INFO: initial parameter: num_candidates = 1
1:28:23.919611 INFO: initial parameter: fwhm_rt = 5
1:28:23.919651 INFO: initial parameter: fwhm_mobility = 0.01
1:28:23.919692 INFO: initial parameter: score_cutoff = 0
1:28:23.919732 INFO: initial parameter: classifier_version = -1
1:28:23.919796 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
1:28:23.919979 INFO: FDRManager: loading saved state not requested, will be initialized.
1:28:23.920012 INFO: Initializing FDRManager
1:28:23.920040 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:28:23.942546 PROGRESS: Initializing spectral library: 73,874 target precursors potentially observable (0 removed)
1:28:23.957129 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:28:23.957491 INFO: Updating optimization_manager: rt_error            : 1663.596435546875 -> 1663.596435546875
1:28:23.957582 PROGRESS: Starting initial search for precursors.
1:28:23.957658 INFO: Starting optimization step 0.
1:28:23.957723 PROGRESS: === Extracting elution groups 0 to 200 ===
1:28:23.957776 INFO: Using ng extraction backend
1:28:23.957829 PROGRESS: Extracting batch of 394 precursors
1:28:23.959767 INFO: === Search parameters used ===
1:28:23.959858 INFO: rt_error       : 1663.596435546875
1:28:23.959905 INFO: mobility_error : 0.1
1:28:23.959947 INFO: num_candidates : 1
1:28:23.959987 INFO: ms1_error      : 30
1:28:23.960027 INFO: ms2_error      : 30
1:28:23.960064 INFO: fwhm_rt        : 5
1:28:23.960103 INFO: quant_window   : 3
1:28:23.960143 INFO: ==============================================
1:28:23.981741 INFO: performing precursor FDR with 40 features
1:28:23.981812 INFO: Decoy channel: -1
1:28:23.981838 INFO: Competetive: True
1:28:23.982730 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:23.984669 INFO: Using random state 463179 for train-test-split
1:28:23.991244 INFO: Test AUC: 0.459
1:28:23.991298 INFO: Train AUC: 0.532
1:28:23.991328 INFO: AUC difference: 13.71%
1:28:23.991349 WARNING: AUC difference > 5%. This may indicate overfitting.
1:28:24.201880 INFO: Resetting torch num_threads to 80
1:28:24.203197 PROGRESS: === Extracted 394 precursors and 3020 fragments ===
1:28:24.203539 INFO: === FDR correction performed with classifier version -1 ===
1:28:24.203959 PROGRESS: ============================= Precursor FDR =============================
1:28:24.204042 PROGRESS: Total precursors accumulated: 0
1:28:24.204100 PROGRESS: Target precursors: 0 (0.00%)
1:28:24.204146 PROGRESS: Decoy precursors: 0 (0.00%)
1:28:24.204191 PROGRESS: 
1:28:24.204233 PROGRESS: Precursor Summary:
1:28:24.204339 PROGRESS: 
1:28:24.204400 PROGRESS: Protein Summary:
1:28:24.204472 PROGRESS: =========================================================================
1:28:24.204635 INFO: Target number of precursors not reached yet.
1:28:24.207816 INFO: Starting optimization step 1.
1:28:24.207924 PROGRESS: === Extracting elution groups 200 to 600 ===
1:28:24.207993 INFO: Using ng extraction backend
1:28:24.208049 PROGRESS: Extracting batch of 789 precursors
1:28:24.210731 INFO: === Search parameters used ===
1:28:24.210816 INFO: rt_error       : 1663.596435546875
1:28:24.210866 INFO: mobility_error : 0.1
1:28:24.210909 INFO: num_candidates : 1
1:28:24.210948 INFO: ms1_error      : 30
1:28:24.210986 INFO: ms2_error      : 30
1:28:24.211025 INFO: fwhm_rt        : 5
1:28:24.211063 INFO: quant_window   : 3
1:28:24.211101 INFO: ==============================================
1:28:24.236896 INFO: performing precursor FDR with 40 features
1:28:24.236976 INFO: Decoy channel: -1
1:28:24.237002 INFO: Competetive: True
1:28:24.239772 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:24.241273 INFO: Using random state 218661 for train-test-split
1:28:24.249680 INFO: Test AUC: 0.483
1:28:24.249734 INFO: Train AUC: 0.525
1:28:24.249764 INFO: AUC difference: 8.05%
1:28:24.249785 WARNING: AUC difference > 5%. This may indicate overfitting.
1:28:24.454680 INFO: Resetting torch num_threads to 80
1:28:24.456854 PROGRESS: === Extracted 1183 precursors and 9270 fragments ===
1:28:24.457208 INFO: === FDR correction performed with classifier version -1 ===
1:28:24.457644 PROGRESS: ============================= Precursor FDR =============================
1:28:24.457731 PROGRESS: Total precursors accumulated: 0
1:28:24.457789 PROGRESS: Target precursors: 0 (0.00%)
1:28:24.457836 PROGRESS: Decoy precursors: 0 (0.00%)
1:28:24.457882 PROGRESS: 
1:28:24.457925 PROGRESS: Precursor Summary:
1:28:24.458031 PROGRESS: 
1:28:24.458092 PROGRESS: Protein Summary:
1:28:24.458171 PROGRESS: =========================================================================
1:28:24.458364 INFO: Target number of precursors not reached yet.
1:28:24.462464 INFO: Starting optimization step 2.
1:28:24.462573 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:28:24.462642 INFO: Using ng extraction backend
1:28:24.462700 PROGRESS: Extracting batch of 1588 precursors
1:28:24.466959 INFO: === Search parameters used ===
1:28:24.467059 INFO: rt_error       : 1663.596435546875
1:28:24.467108 INFO: mobility_error : 0.1
1:28:24.467152 INFO: num_candidates : 1
1:28:24.467193 INFO: ms1_error      : 30
1:28:24.467235 INFO: ms2_error      : 30
1:28:24.467275 INFO: fwhm_rt        : 5
1:28:24.467315 INFO: quant_window   : 3
1:28:24.467355 INFO: ==============================================
1:28:24.503079 INFO: performing precursor FDR with 40 features
1:28:24.503158 INFO: Decoy channel: -1
1:28:24.503184 INFO: Competetive: True
1:28:24.506371 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:24.508179 INFO: Using random state 736974 for train-test-split
1:28:24.520055 INFO: Test AUC: 0.512
1:28:24.520118 INFO: Train AUC: 0.518
1:28:24.520146 INFO: AUC difference: 1.16%
1:28:24.728692 INFO: Resetting torch num_threads to 80
1:28:24.731266 PROGRESS: === Extracted 2770 precursors and 21900 fragments ===
1:28:24.731700 INFO: === FDR correction performed with classifier version -1 ===
1:28:24.732143 PROGRESS: ============================= Precursor FDR =============================
1:28:24.732234 PROGRESS: Total precursors accumulated: 0
1:28:24.732293 PROGRESS: Target precursors: 0 (0.00%)
1:28:24.732341 PROGRESS: Decoy precursors: 0 (0.00%)
1:28:24.732387 PROGRESS: 
1:28:24.732436 PROGRESS: Precursor Summary:
1:28:24.732543 PROGRESS: 
1:28:24.732606 PROGRESS: Protein Summary:
1:28:24.732679 PROGRESS: =========================================================================
1:28:24.732880 INFO: Target number of precursors not reached yet.
1:28:24.738766 INFO: Starting optimization step 3.
1:28:24.738890 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:28:24.738964 INFO: Using ng extraction backend
1:28:24.739019 PROGRESS: Extracting batch of 3164 precursors
1:28:24.746295 INFO: === Search parameters used ===
1:28:24.746414 INFO: rt_error       : 1663.596435546875
1:28:24.746465 INFO: mobility_error : 0.1
1:28:24.746510 INFO: num_candidates : 1
1:28:24.746551 INFO: ms1_error      : 30
1:28:24.746592 INFO: ms2_error      : 30
1:28:24.746633 INFO: fwhm_rt        : 5
1:28:24.746673 INFO: quant_window   : 3
1:28:24.746713 INFO: ==============================================
1:28:24.801296 INFO: performing precursor FDR with 40 features
1:28:24.801397 INFO: Decoy channel: -1
1:28:24.801423 INFO: Competetive: True
1:28:24.806082 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:24.808476 INFO: Using random state 704437 for train-test-split
1:28:24.827947 INFO: Test AUC: 0.519
1:28:24.828026 INFO: Train AUC: 0.514
1:28:24.828056 INFO: AUC difference: 0.97%
1:28:25.038574 INFO: Resetting torch num_threads to 80
1:28:25.041800 PROGRESS: === Extracted 5934 precursors and 47002 fragments ===
1:28:25.042180 INFO: === FDR correction performed with classifier version -1 ===
1:28:25.042614 PROGRESS: ============================= Precursor FDR =============================
1:28:25.042699 PROGRESS: Total precursors accumulated: 0
1:28:25.042764 PROGRESS: Target precursors: 0 (0.00%)
1:28:25.042816 PROGRESS: Decoy precursors: 0 (0.00%)
1:28:25.042862 PROGRESS: 
1:28:25.042907 PROGRESS: Precursor Summary:
1:28:25.043017 PROGRESS: 
1:28:25.043081 PROGRESS: Protein Summary:
1:28:25.043155 PROGRESS: =========================================================================
1:28:25.043381 INFO: Target number of precursors not reached yet.
1:28:25.052600 INFO: Starting optimization step 4.
1:28:25.052734 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:28:25.052809 INFO: Using ng extraction backend
1:28:25.052866 PROGRESS: Extracting batch of 6329 precursors
1:28:25.065154 INFO: === Search parameters used ===
1:28:25.065304 INFO: rt_error       : 1663.596435546875
1:28:25.065354 INFO: mobility_error : 0.1
1:28:25.065400 INFO: num_candidates : 1
1:28:25.065444 INFO: ms1_error      : 30
1:28:25.065494 INFO: ms2_error      : 30
1:28:25.065535 INFO: fwhm_rt        : 5
1:28:25.065574 INFO: quant_window   : 3
1:28:25.065614 INFO: ==============================================
1:28:25.157189 INFO: performing precursor FDR with 40 features
1:28:25.157307 INFO: Decoy channel: -1
1:28:25.157333 INFO: Competetive: True
1:28:25.162612 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:25.166070 INFO: Using random state 338010 for train-test-split
1:28:25.203001 INFO: Test AUC: 0.514
1:28:25.203108 INFO: Train AUC: 0.511
1:28:25.203139 INFO: AUC difference: 0.49%
1:28:25.414176 INFO: Resetting torch num_threads to 80
1:28:25.418275 PROGRESS: === Extracted 12262 precursors and 96669 fragments ===
1:28:25.418652 INFO: === FDR correction performed with classifier version -1 ===
1:28:25.419085 PROGRESS: ============================= Precursor FDR =============================
1:28:25.419169 PROGRESS: Total precursors accumulated: 0
1:28:25.419228 PROGRESS: Target precursors: 0 (0.00%)
1:28:25.419277 PROGRESS: Decoy precursors: 0 (0.00%)
1:28:25.419322 PROGRESS: 
1:28:25.419365 PROGRESS: Precursor Summary:
1:28:25.419471 PROGRESS: 
1:28:25.419861 PROGRESS: Protein Summary:
1:28:25.419940 PROGRESS: =========================================================================
1:28:25.420209 INFO: Target number of precursors not reached yet.
1:28:25.432343 INFO: Starting optimization step 5.
1:28:25.432566 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:28:25.432645 INFO: Using ng extraction backend
1:28:25.432708 PROGRESS: Extracting batch of 12652 precursors
1:28:25.455321 INFO: === Search parameters used ===
1:28:25.455529 INFO: rt_error       : 1663.596435546875
1:28:25.455582 INFO: mobility_error : 0.1
1:28:25.455626 INFO: num_candidates : 1
1:28:25.455669 INFO: ms1_error      : 30
1:28:25.455710 INFO: ms2_error      : 30
1:28:25.455748 INFO: fwhm_rt        : 5
1:28:25.455805 INFO: quant_window   : 3
1:28:25.455848 INFO: ==============================================
1:28:25.615466 INFO: performing precursor FDR with 40 features
1:28:25.615603 INFO: Decoy channel: -1
1:28:25.615630 INFO: Competetive: True
1:28:25.624302 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:25.630052 INFO: Using random state 629466 for train-test-split
1:28:25.867616 INFO: Test AUC: 0.857
1:28:25.867745 INFO: Train AUC: 0.860
1:28:25.867773 INFO: AUC difference: 0.40%
1:28:26.090749 INFO: Resetting torch num_threads to 80
1:28:26.097846 PROGRESS: === Extracted 24912 precursors and 196455 fragments ===
1:28:26.098306 INFO: === FDR correction performed with classifier version -1 ===
1:28:26.099540 PROGRESS: ============================= Precursor FDR =============================
1:28:26.099641 PROGRESS: Total precursors accumulated: 7,324
1:28:26.099701 PROGRESS: Target precursors: 7,252 (99.02%)
1:28:26.099751 PROGRESS: Decoy precursors: 72 (0.98%)
1:28:26.099797 PROGRESS: 
1:28:26.099841 PROGRESS: Precursor Summary:
1:28:26.102669 PROGRESS: Channel   0:	 0.050 FDR: 7,252; 0.010 FDR: 7,252; 0.001 FDR: 5,297
1:28:26.102796 PROGRESS: 
1:28:26.102855 PROGRESS: Protein Summary:
1:28:26.106901 PROGRESS: Channel   0:	 0.050 FDR: 3,279; 0.010 FDR: 3,279; 0.001 FDR: 2,615
1:28:26.107020 PROGRESS: =========================================================================
1:28:26.107413 INFO: Target number of precursors reached.
1:28:26.141666 INFO: fragments_df: keeping 5000 of 196455 [sum(precursor_idx_mask)=76743 sum(mass_error_mask)=196455 stop_rank=5000
1:28:26.147232 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:27.274328 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:27.947110 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:28:27.947572 INFO: Using score_cutoff 14.823486832523345 (fac=0.99, q=1)
1:28:27.947931 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:28:27.948014 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:28:27.948068 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.823486832523345
1:28:27.948122 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:27.949679 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:27.951980 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
1:28:27.952078 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:28:27.952151 INFO: Starting optimization step 6.
1:28:27.952211 PROGRESS: === Extracting elution groups 0 to 600 ===
1:28:27.952272 INFO: Using ng extraction backend
1:28:27.952323 PROGRESS: Extracting batch of 1183 precursors
1:28:27.955803 INFO: === Search parameters used ===
1:28:27.955898 INFO: rt_error       : 1663.596435546875
1:28:27.955947 INFO: mobility_error : 0.1
1:28:27.955991 INFO: num_candidates : 3
1:28:27.956030 INFO: ms1_error      : 30
1:28:27.956070 INFO: ms2_error      : 30
1:28:27.956108 INFO: fwhm_rt        : 3.0
1:28:27.956148 INFO: quant_window   : 3
1:28:27.956186 INFO: ==============================================
1:28:28.000496 INFO: performing precursor FDR with 40 features
1:28:28.000605 INFO: Decoy channel: -1
1:28:28.000630 INFO: Competetive: True
1:28:28.003307 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:28.005177 INFO: Using random state 776831 for train-test-split
1:28:28.016161 INFO: Test AUC: 0.654
1:28:28.016233 INFO: Train AUC: 0.668
1:28:28.016262 INFO: AUC difference: 2.10%
1:28:28.227173 INFO: Resetting torch num_threads to 80
1:28:28.228764 PROGRESS: === Extracted 3548 precursors and 24380 fragments ===
1:28:28.229114 INFO: === FDR correction performed with classifier version 5 ===
1:28:28.229610 PROGRESS: ============================= Precursor FDR =============================
1:28:28.229710 PROGRESS: Total precursors accumulated: 358
1:28:28.229769 PROGRESS: Target precursors: 355 (99.16%)
1:28:28.229817 PROGRESS: Decoy precursors: 3 (0.84%)
1:28:28.229866 PROGRESS: 
1:28:28.229909 PROGRESS: Precursor Summary:
1:28:28.230829 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   238
1:28:28.230920 PROGRESS: 
1:28:28.230980 PROGRESS: Protein Summary:
1:28:28.232069 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   226
1:28:28.232159 PROGRESS: =========================================================================
1:28:28.232588 INFO: Target number of precursors reached.
1:28:28.236667 INFO: fragments_df: keeping 4712 of 24380 [sum(precursor_idx_mask)=8302 sum(mass_error_mask)=24380 stop_rank=4712
1:28:28.240910 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:28.362369 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:28.991086 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:28.991509 INFO: Using score_cutoff 16.347115362167358 (fac=0.99, q=1)
1:28:28.991790 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:28.992007 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:28.992065 INFO: Updating optimization_manager: score_cutoff        : 14.823486832523345 -> 16.347115362167358
1:28:28.992117 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:28.993685 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:28.996046 INFO: === checking if optimization conditions were reached ===
1:28:28.997598 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.828943
1:28:28.997703 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
1:28:28.997767 PROGRESS: ❌ ms2_error      : 6.8289 > 6.8289 or insufficient steps taken.
1:28:28.997825 INFO: ==============================================
1:28:28.997886 INFO: Starting optimization step 7.
1:28:28.997940 PROGRESS: === Extracting elution groups 0 to 600 ===
1:28:28.997994 INFO: Using ng extraction backend
1:28:28.998049 PROGRESS: Extracting batch of 1183 precursors
1:28:29.003251 INFO: === Search parameters used ===
1:28:29.003352 INFO: rt_error       : 1663.596435546875
1:28:29.003407 INFO: mobility_error : 0.1
1:28:29.003454 INFO: num_candidates : 3
1:28:29.003497 INFO: ms1_error      : 30
1:28:29.003541 INFO: ms2_error      : 6.828943
1:28:29.003582 INFO: fwhm_rt        : 3.0
1:28:29.003631 INFO: quant_window   : 3
1:28:29.003676 INFO: ==============================================
1:28:29.043658 INFO: performing precursor FDR with 40 features
1:28:29.043754 INFO: Decoy channel: -1
1:28:29.043780 INFO: Competetive: True
1:28:29.046373 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:29.048209 INFO: Using random state 791857 for train-test-split
1:28:29.060017 INFO: Test AUC: 0.669
1:28:29.060081 INFO: Train AUC: 0.661
1:28:29.060111 INFO: AUC difference: 1.31%
1:28:29.270419 INFO: Resetting torch num_threads to 80
1:28:29.272028 PROGRESS: === Extracted 3549 precursors and 25820 fragments ===
1:28:29.272380 INFO: === FDR correction performed with classifier version 6 ===
1:28:29.272842 PROGRESS: ============================= Precursor FDR =============================
1:28:29.272931 PROGRESS: Total precursors accumulated: 356
1:28:29.272990 PROGRESS: Target precursors: 353 (99.16%)
1:28:29.273038 PROGRESS: Decoy precursors: 3 (0.84%)
1:28:29.273085 PROGRESS: 
1:28:29.273141 PROGRESS: Precursor Summary:
1:28:29.274085 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   353; 0.001 FDR:   209
1:28:29.274179 PROGRESS: 
1:28:29.274235 PROGRESS: Protein Summary:
1:28:29.275334 PROGRESS: Channel   0:	 0.050 FDR:   325; 0.010 FDR:   325; 0.001 FDR:   200
1:28:29.275425 PROGRESS: =========================================================================
1:28:29.275636 INFO: Target number of precursors reached.
1:28:29.279918 INFO: fragments_df: keeping 4840 of 25820 [sum(precursor_idx_mask)=8677 sum(mass_error_mask)=25820 stop_rank=4840
1:28:29.284041 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:29.413239 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:30.060759 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:30.061180 INFO: Using score_cutoff 14.102030271148681 (fac=0.99, q=1)
1:28:30.061482 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:30.061566 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:30.061622 INFO: Updating optimization_manager: score_cutoff        : 16.347115362167358 -> 14.102030271148681
1:28:30.061675 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:30.063215 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:30.065647 INFO: === checking if optimization conditions were reached ===
1:28:30.067212 INFO: Updating optimization_manager: ms2_error           : 6.828943 -> 6.828943
1:28:30.067316 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:28:30.067383 PROGRESS: ✅ ms2_error      : 6.8289 <= 6.8289
1:28:30.067442 INFO: ==============================================
1:28:30.067508 PROGRESS: Optimization finished for ms2_error.
1:28:30.071389 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:30.072721 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:30.074998 INFO: Starting optimization step 0.
1:28:30.075097 PROGRESS: === Extracting elution groups 0 to 600 ===
1:28:30.075167 INFO: Using ng extraction backend
1:28:30.075226 PROGRESS: Extracting batch of 1183 precursors
1:28:30.078790 INFO: === Search parameters used ===
1:28:30.078877 INFO: rt_error       : 1663.596435546875
1:28:30.078936 INFO: mobility_error : 0.1
1:28:30.078983 INFO: num_candidates : 3
1:28:30.079027 INFO: ms1_error      : 30
1:28:30.079071 INFO: ms2_error      : 6.828943
1:28:30.079115 INFO: fwhm_rt        : 3.0
1:28:30.079155 INFO: quant_window   : 3
1:28:30.079196 INFO: ==============================================
1:28:30.119676 INFO: performing precursor FDR with 40 features
1:28:30.119766 INFO: Decoy channel: -1
1:28:30.119792 INFO: Competetive: True
1:28:30.122301 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:30.124167 INFO: Using random state 300629 for train-test-split
1:28:30.135148 INFO: Test AUC: 0.659
1:28:30.135217 INFO: Train AUC: 0.664
1:28:30.135246 INFO: AUC difference: 0.70%
1:28:30.345996 INFO: Resetting torch num_threads to 80
1:28:30.347521 PROGRESS: === Extracted 3549 precursors and 25795 fragments ===
1:28:30.347857 INFO: === FDR correction performed with classifier version 7 ===
1:28:30.348329 PROGRESS: ============================= Precursor FDR =============================
1:28:30.348415 PROGRESS: Total precursors accumulated: 358
1:28:30.348473 PROGRESS: Target precursors: 355 (99.16%)
1:28:30.348519 PROGRESS: Decoy precursors: 3 (0.84%)
1:28:30.348564 PROGRESS: 
1:28:30.348606 PROGRESS: Precursor Summary:
1:28:30.349524 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   209
1:28:30.349614 PROGRESS: 
1:28:30.349669 PROGRESS: Protein Summary:
1:28:30.350761 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   326; 0.001 FDR:   200
1:28:30.350850 PROGRESS: =========================================================================
1:28:30.351051 INFO: Target number of precursors reached.
1:28:30.355325 INFO: fragments_df: keeping 4872 of 25795 [sum(precursor_idx_mask)=8726 sum(mass_error_mask)=25795 stop_rank=4872
1:28:30.359461 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:30.488221 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:31.152906 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:31.153332 INFO: Using score_cutoff 14.577381068801879 (fac=0.99, q=1)
1:28:31.153625 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:31.153706 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:31.153760 INFO: Updating optimization_manager: score_cutoff        : 14.102030271148681 -> 14.577381068801879
1:28:31.153813 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:31.155348 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:31.157654 INFO: === checking if optimization conditions were reached ===
1:28:31.157755 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:28:31.159198 INFO: Updating optimization_manager: rt_error            : 1663.596435546875 -> 2.212469643907068
1:28:31.159294 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 2.2125.
1:28:31.159361 INFO: ==============================================
1:28:31.159425 INFO: Starting optimization step 1.
1:28:31.159481 PROGRESS: === Extracting elution groups 0 to 600 ===
1:28:31.159537 INFO: Using ng extraction backend
1:28:31.159587 PROGRESS: Extracting batch of 1183 precursors
1:28:31.163271 INFO: === Search parameters used ===
1:28:31.163366 INFO: rt_error       : 2.212469643907068
1:28:31.163418 INFO: mobility_error : 0.1
1:28:31.163462 INFO: num_candidates : 3
1:28:31.163502 INFO: ms1_error      : 30
1:28:31.163541 INFO: ms2_error      : 6.828943
1:28:31.163579 INFO: fwhm_rt        : 3.0
1:28:31.163616 INFO: quant_window   : 3
1:28:31.163654 INFO: ==============================================
1:28:31.200275 INFO: performing precursor FDR with 40 features
1:28:31.200360 INFO: Decoy channel: -1
1:28:31.200389 INFO: Competetive: True
1:28:31.203419 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:31.206145 INFO: Using random state 300629 for train-test-split
1:28:31.217906 INFO: Test AUC: 0.688
1:28:31.217977 INFO: Train AUC: 0.683
1:28:31.218007 INFO: AUC difference: 0.77%
1:28:31.430887 INFO: Resetting torch num_threads to 80
1:28:31.432365 PROGRESS: === Extracted 3261 precursors and 20941 fragments ===
1:28:31.432698 INFO: === FDR correction performed with classifier version 7 ===
1:28:31.433163 PROGRESS: ============================= Precursor FDR =============================
1:28:31.433249 PROGRESS: Total precursors accumulated: 556
1:28:31.433303 PROGRESS: Target precursors: 551 (99.10%)
1:28:31.433350 PROGRESS: Decoy precursors: 5 (0.90%)
1:28:31.433393 PROGRESS: 
1:28:31.433434 PROGRESS: Precursor Summary:
1:28:31.434422 PROGRESS: Channel   0:	 0.050 FDR:   551; 0.010 FDR:   551; 0.001 FDR:   485
1:28:31.434512 PROGRESS: 
1:28:31.434563 PROGRESS: Protein Summary:
1:28:31.435754 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   500; 0.001 FDR:   443
1:28:31.435841 PROGRESS: =========================================================================
1:28:31.436041 INFO: Target number of precursors reached.
1:28:31.440331 INFO: fragments_df: keeping 5000 of 20941 [sum(precursor_idx_mask)=10952 sum(mass_error_mask)=20941 stop_rank=5000
1:28:31.444464 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:31.584566 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:32.270718 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:32.271143 INFO: Using score_cutoff 13.265819764137268 (fac=0.99, q=1)
1:28:32.271421 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:32.271497 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:32.271549 INFO: Updating optimization_manager: score_cutoff        : 14.577381068801879 -> 13.265819764137268
1:28:32.271599 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:32.273143 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:32.275503 INFO: === checking if optimization conditions were reached ===
1:28:32.275603 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:28:32.277253 INFO: Updating optimization_manager: rt_error            : 2.212469643907068 -> 6.592528360857637
1:28:32.277349 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 6.5925.
1:28:32.277411 INFO: ==============================================
1:28:32.277486 INFO: Starting optimization step 2.
1:28:32.277546 PROGRESS: === Extracting elution groups 0 to 600 ===
1:28:32.277601 INFO: Using ng extraction backend
1:28:32.277662 PROGRESS: Extracting batch of 1183 precursors
1:28:32.281165 INFO: === Search parameters used ===
1:28:32.281249 INFO: rt_error       : 6.592528360857637
1:28:32.281298 INFO: mobility_error : 0.1
1:28:32.281341 INFO: num_candidates : 3
1:28:32.281381 INFO: ms1_error      : 30
1:28:32.281421 INFO: ms2_error      : 6.828943
1:28:32.281460 INFO: fwhm_rt        : 3.0
1:28:32.281510 INFO: quant_window   : 3
1:28:32.281551 INFO: ==============================================
1:28:32.316456 INFO: performing precursor FDR with 40 features
1:28:32.316543 INFO: Decoy channel: -1
1:28:32.316569 INFO: Competetive: True
1:28:32.319079 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:32.320901 INFO: Using random state 300629 for train-test-split
1:28:32.331800 INFO: Test AUC: 0.673
1:28:32.331864 INFO: Train AUC: 0.686
1:28:32.331895 INFO: AUC difference: 1.89%
1:28:32.544993 INFO: Resetting torch num_threads to 80
1:28:32.546505 PROGRESS: === Extracted 3258 precursors and 20912 fragments ===
1:28:32.546856 INFO: === FDR correction performed with classifier version 7 ===
1:28:32.547313 PROGRESS: ============================= Precursor FDR =============================
1:28:32.547400 PROGRESS: Total precursors accumulated: 557
1:28:32.547455 PROGRESS: Target precursors: 552 (99.10%)
1:28:32.547502 PROGRESS: Decoy precursors: 5 (0.90%)
1:28:32.547545 PROGRESS: 
1:28:32.547586 PROGRESS: Precursor Summary:
1:28:32.548580 PROGRESS: Channel   0:	 0.050 FDR:   552; 0.010 FDR:   552; 0.001 FDR:   467
1:28:32.548668 PROGRESS: 
1:28:32.548723 PROGRESS: Protein Summary:
1:28:32.549933 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   501; 0.001 FDR:   427
1:28:32.550029 PROGRESS: =========================================================================
1:28:32.550224 INFO: Target number of precursors reached.
1:28:32.554503 INFO: fragments_df: keeping 5000 of 20912 [sum(precursor_idx_mask)=10966 sum(mass_error_mask)=20912 stop_rank=5000
1:28:32.558601 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:32.699311 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:33.378849 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:33.379283 INFO: Using score_cutoff 13.266364767551423 (fac=0.99, q=1)
1:28:33.379564 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:33.379642 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:33.379696 INFO: Updating optimization_manager: score_cutoff        : 13.265819764137268 -> 13.266364767551423
1:28:33.379748 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:33.381297 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:33.383712 INFO: === checking if optimization conditions were reached ===
1:28:33.383813 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:28:33.385552 INFO: Updating optimization_manager: rt_error            : 6.592528360857637 -> 5.009915453042979
1:28:33.385654 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 5.0099.
1:28:33.385718 INFO: ==============================================
1:28:33.385782 INFO: Starting optimization step 3.
1:28:33.385845 PROGRESS: === Extracting elution groups 0 to 600 ===
1:28:33.385908 INFO: Using ng extraction backend
1:28:33.385964 PROGRESS: Extracting batch of 1183 precursors
1:28:33.389501 INFO: === Search parameters used ===
1:28:33.389590 INFO: rt_error       : 5.009915453042979
1:28:33.389639 INFO: mobility_error : 0.1
1:28:33.389682 INFO: num_candidates : 3
1:28:33.389721 INFO: ms1_error      : 30
1:28:33.389760 INFO: ms2_error      : 6.828943
1:28:33.389797 INFO: fwhm_rt        : 3.0
1:28:33.389835 INFO: quant_window   : 3
1:28:33.389873 INFO: ==============================================
1:28:33.428822 INFO: performing precursor FDR with 40 features
1:28:33.428932 INFO: Decoy channel: -1
1:28:33.428959 INFO: Competetive: True
1:28:33.431533 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:33.433336 INFO: Using random state 300629 for train-test-split
1:28:33.444824 INFO: Test AUC: 0.732
1:28:33.444890 INFO: Train AUC: 0.672
1:28:33.444921 INFO: AUC difference: 8.94%
1:28:33.444942 WARNING: AUC difference > 5%. This may indicate overfitting.
1:28:33.657997 INFO: Resetting torch num_threads to 80
1:28:33.659515 PROGRESS: === Extracted 3264 precursors and 20929 fragments ===
1:28:33.659857 INFO: === FDR correction performed with classifier version 7 ===
1:28:33.660330 PROGRESS: ============================= Precursor FDR =============================
1:28:33.660418 PROGRESS: Total precursors accumulated: 556
1:28:33.660475 PROGRESS: Target precursors: 551 (99.10%)
1:28:33.660522 PROGRESS: Decoy precursors: 5 (0.90%)
1:28:33.660565 PROGRESS: 
1:28:33.660608 PROGRESS: Precursor Summary:
1:28:33.661591 PROGRESS: Channel   0:	 0.050 FDR:   551; 0.010 FDR:   551; 0.001 FDR:   467
1:28:33.661679 PROGRESS: 
1:28:33.661743 PROGRESS: Protein Summary:
1:28:33.662948 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   500; 0.001 FDR:   427
1:28:33.663037 PROGRESS: =========================================================================
1:28:33.663231 INFO: Target number of precursors reached.
1:28:33.667467 INFO: fragments_df: keeping 5000 of 20929 [sum(precursor_idx_mask)=10994 sum(mass_error_mask)=20929 stop_rank=5000
1:28:33.671562 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:33.816722 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:34.492457 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:34.492886 INFO: Using score_cutoff 13.265819764137268 (fac=0.99, q=1)
1:28:34.493174 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:34.493255 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:34.493309 INFO: Updating optimization_manager: score_cutoff        : 13.266364767551423 -> 13.265819764137268
1:28:34.493362 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:34.494912 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:34.497254 INFO: === checking if optimization conditions were reached ===
1:28:34.497355 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:28:34.499092 INFO: Updating optimization_manager: rt_error            : 5.009915453042979 -> 5.021112916006791
1:28:34.499206 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 5.0211.
1:28:34.499282 INFO: ==============================================
1:28:34.499349 INFO: Starting optimization step 4.
1:28:34.499406 PROGRESS: === Extracting elution groups 0 to 600 ===
1:28:34.499462 INFO: Using ng extraction backend
1:28:34.499514 PROGRESS: Extracting batch of 1183 precursors
1:28:34.502952 INFO: === Search parameters used ===
1:28:34.503038 INFO: rt_error       : 5.021112916006791
1:28:34.503088 INFO: mobility_error : 0.1
1:28:34.503131 INFO: num_candidates : 3
1:28:34.503173 INFO: ms1_error      : 30
1:28:34.503215 INFO: ms2_error      : 6.828943
1:28:34.503256 INFO: fwhm_rt        : 3.0
1:28:34.503295 INFO: quant_window   : 3
1:28:34.503335 INFO: ==============================================
1:28:34.538286 INFO: performing precursor FDR with 40 features
1:28:34.538380 INFO: Decoy channel: -1
1:28:34.538405 INFO: Competetive: True
1:28:34.540973 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:34.542813 INFO: Using random state 300629 for train-test-split
1:28:34.554953 INFO: Test AUC: 0.681
1:28:34.555026 INFO: Train AUC: 0.684
1:28:34.555055 INFO: AUC difference: 0.43%
1:28:34.768175 INFO: Resetting torch num_threads to 80
1:28:34.769744 PROGRESS: === Extracted 3266 precursors and 20924 fragments ===
1:28:34.770089 INFO: === FDR correction performed with classifier version 7 ===
1:28:34.770559 PROGRESS: ============================= Precursor FDR =============================
1:28:34.770647 PROGRESS: Total precursors accumulated: 557
1:28:34.770704 PROGRESS: Target precursors: 552 (99.10%)
1:28:34.770751 PROGRESS: Decoy precursors: 5 (0.90%)
1:28:34.770795 PROGRESS: 
1:28:34.770836 PROGRESS: Precursor Summary:
1:28:34.771814 PROGRESS: Channel   0:	 0.050 FDR:   552; 0.010 FDR:   552; 0.001 FDR:   498
1:28:34.771901 PROGRESS: 
1:28:34.771955 PROGRESS: Protein Summary:
1:28:34.773161 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   501; 0.001 FDR:   452
1:28:34.773249 PROGRESS: =========================================================================
1:28:34.773443 INFO: Target number of precursors reached.
1:28:34.777684 INFO: fragments_df: keeping 5000 of 20924 [sum(precursor_idx_mask)=11010 sum(mass_error_mask)=20924 stop_rank=5000
1:28:34.781795 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:34.923050 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:35.603449 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:35.603879 INFO: Using score_cutoff 13.27696232471466 (fac=0.99, q=1)
1:28:35.604166 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:35.604245 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:35.604298 INFO: Updating optimization_manager: score_cutoff        : 13.265819764137268 -> 13.27696232471466
1:28:35.604349 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:35.605914 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:35.608230 INFO: === checking if optimization conditions were reached ===
1:28:35.608326 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:28:35.609183 INFO: Updating optimization_manager: rt_error            : 5.021112916006791 -> 2.212469643907068
1:28:35.609311 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
1:28:35.609406 INFO: Updating optimization_manager: score_cutoff        : 13.27696232471466 -> 13.265819764137268
1:28:35.609504 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:35.609589 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:35.609668 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 2.2125 found after 5 searches.
1:28:35.609727 INFO: ==============================================
1:28:35.609793 PROGRESS: Optimization finished for rt_error.
1:28:35.613642 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:35.614973 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:35.640333 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:28:35.640480 PROGRESS: ==============================================
1:28:35.640546 PROGRESS: ms2_error      : 6.8289
1:28:35.640600 PROGRESS: rt_error       : 2.2125
1:28:35.640647 PROGRESS: ==============================================
1:28:35.641169 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:35.735466 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:35.986192 INFO: Using ng extraction backend
1:28:35.986534 PROGRESS: Extracting batch of 146144 precursors
1:28:36.221341 INFO: === Search parameters used ===
1:28:36.221725 INFO: rt_error       : 2.212469643907068
1:28:36.221804 INFO: mobility_error : 0.1
1:28:36.221859 INFO: num_candidates : 3
1:28:36.221901 INFO: ms1_error      : 30
1:28:36.221942 INFO: ms2_error      : 6.828943
1:28:36.221982 INFO: fwhm_rt        : 3.0
1:28:36.222022 INFO: quant_window   : 3
1:28:36.222063 INFO: ==============================================
1:28:36.405324 INFO: Removed 194765 precursors with score below cutoff 13.265819764137268
1:28:36.632994 INFO: performing precursor FDR with 40 features
1:28:36.633129 INFO: Decoy channel: -1
1:28:36.633156 INFO: Competetive: True
1:28:36.653071 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:36.663850 WARNING: FDR calculation for 127733 target and 83690 decoy PSMs
1:28:36.663997 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:28:36.700465 INFO: Using random state 13446 for train-test-split
1:28:39.404673 INFO: Test AUC: 0.843
1:28:39.404814 INFO: Train AUC: 0.846
1:28:39.404843 INFO: AUC difference: 0.24%
1:28:39.680418 INFO: Resetting torch num_threads to 80
1:28:39.900496 PROGRESS: ============================= Precursor FDR =============================
1:28:39.900770 PROGRESS: Total precursors accumulated: 69,692
1:28:39.900838 PROGRESS: Target precursors: 69,002 (99.01%)
1:28:39.900889 PROGRESS: Decoy precursors: 690 (0.99%)
1:28:39.900934 PROGRESS: 
1:28:39.900977 PROGRESS: Precursor Summary:
1:28:39.919314 PROGRESS: Channel   0:	 0.050 FDR: 69,002; 0.010 FDR: 69,002; 0.001 FDR: 65,512
1:28:39.919595 PROGRESS: 
1:28:39.919655 PROGRESS: Protein Summary:
1:28:39.946409 PROGRESS: Channel   0:	 0.050 FDR: 7,020; 0.010 FDR: 7,020; 0.001 FDR: 6,951
1:28:39.946679 PROGRESS: =========================================================================
1:28:39.948184 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/psm.parquet
1:28:40.081044 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/frag.parquet
1:28:40.282500 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
1:28:40.323651 PROGRESS: 
1:28:40.323798 INFO: Quantification results path: alphadia_zenoswath8600/quant
1:28:40.323877 INFO: Creating folder alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/figures
1:28:40.324042 INFO: Initializing TimingManager
1:28:40.324690 INFO: Initializing RawFileManager
1:31:03.213106 INFO: Determining DIA cycle
1:31:03.228257 INFO: Found cycle with start 0.00 min and length 86.
1:31:03.462491 INFO: RT (min)            : 0.0 - 55.4
1:31:03.462610 INFO: RT duration (sec)   : 3325.7
1:31:03.462639 INFO: RT duration (min)   : 55.4
1:31:03.462666 INFO: Cycle len (scans)   : 86
1:31:03.462685 INFO: Cycle len (sec)     : 1.90
1:31:03.462706 INFO: Number of cycles    : 1747
1:31:03.462726 INFO: MS2 range (m/z)     : 399.5 - 903.5
1:31:03.462784 INFO: Creating DIA data object took: 143.13799118995667
1:31:04.538577 INFO: Creating DIA data NG object took: 1.0756142139434814
1:31:04.583180 INFO: Initializing CalibrationManager
1:31:04.583518 INFO: Setting up calibration estimators ..
1:31:04.583584 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:31:04.583699 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'}' ..
1:31:04.583803 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:31:04.583861 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:31:04.583923 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}}' ..
1:31:04.583978 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:31:04.584025 INFO: Done setting up calibration estimators.
1:31:04.584203 INFO: Initializing OptimizationManager
1:31:04.584337 INFO: initial parameter: ms1_error = 30
1:31:04.584389 INFO: initial parameter: ms2_error = 30
1:31:04.584437 INFO: initial parameter: rt_error = 1662.873046875
1:31:04.584481 INFO: initial parameter: mobility_error = 0.1
1:31:04.584529 INFO: initial parameter: num_candidates = 1
1:31:04.584572 INFO: initial parameter: fwhm_rt = 5
1:31:04.584614 INFO: initial parameter: fwhm_mobility = 0.01
1:31:04.584656 INFO: initial parameter: score_cutoff = 0
1:31:04.584699 INFO: initial parameter: classifier_version = -1
1:31:04.584780 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
1:31:04.585156 INFO: FDRManager: loading saved state not requested, will be initialized.
1:31:04.585195 INFO: Initializing FDRManager
1:31:04.585246 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:31:04.619098 PROGRESS: Initializing spectral library: 73,874 target precursors potentially observable (0 removed)
1:31:04.640332 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:31:04.640743 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 1662.873046875
1:31:04.640854 PROGRESS: Starting initial search for precursors.
1:31:04.640945 INFO: Starting optimization step 0.
1:31:04.641013 PROGRESS: === Extracting elution groups 0 to 200 ===
1:31:04.641077 INFO: Using ng extraction backend
1:31:04.641152 PROGRESS: Extracting batch of 394 precursors
1:31:04.644886 INFO: === Search parameters used ===
1:31:04.644997 INFO: rt_error       : 1662.873046875
1:31:04.645049 INFO: mobility_error : 0.1
1:31:04.645095 INFO: num_candidates : 1
1:31:04.645138 INFO: ms1_error      : 30
1:31:04.645181 INFO: ms2_error      : 30
1:31:04.645222 INFO: fwhm_rt        : 5
1:31:04.645262 INFO: quant_window   : 3
1:31:04.645302 INFO: ==============================================
1:31:04.667961 INFO: performing precursor FDR with 40 features
1:31:04.668037 INFO: Decoy channel: -1
1:31:04.668063 INFO: Competetive: True
1:31:04.669229 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:04.672010 INFO: Using random state 583173 for train-test-split
1:31:04.680754 INFO: Test AUC: 0.500
1:31:04.680812 INFO: Train AUC: 0.500
1:31:04.680844 INFO: AUC difference: 0.00%
1:31:04.911708 INFO: Resetting torch num_threads to 80
1:31:04.913442 PROGRESS: === Extracted 394 precursors and 3059 fragments ===
1:31:04.913835 INFO: === FDR correction performed with classifier version -1 ===
1:31:04.914222 PROGRESS: ============================= Precursor FDR =============================
1:31:04.914309 PROGRESS: Total precursors accumulated: 200
1:31:04.914367 PROGRESS: Target precursors: 200 (100.00%)
1:31:04.914415 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:04.914461 PROGRESS: 
1:31:04.914505 PROGRESS: Precursor Summary:
1:31:04.915285 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1:31:04.915372 PROGRESS: 
1:31:04.915427 PROGRESS: Protein Summary:
1:31:04.916346 PROGRESS: Channel   0:	 0.050 FDR:   194; 0.010 FDR:   194; 0.001 FDR:   194
1:31:04.916436 PROGRESS: =========================================================================
1:31:04.916670 INFO: Target number of precursors reached.
1:31:04.918397 INFO: fragments_df: keeping 1247 of 3059 [sum(precursor_idx_mask)=1812 sum(mass_error_mask)=3059 stop_rank=1247
1:31:04.921509 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:05.018201 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:05.186068 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:31:05.186625 INFO: Using score_cutoff 14.606017497825622 (fac=0.99, q=1)
1:31:05.186979 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:31:05.187061 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:31:05.187118 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.606017497825622
1:31:05.187184 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:05.188585 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:05.190134 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1:31:05.190234 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:31:05.190311 INFO: Starting optimization step 1.
1:31:05.190373 PROGRESS: === Extracting elution groups 0 to 200 ===
1:31:05.190435 INFO: Using ng extraction backend
1:31:05.190490 PROGRESS: Extracting batch of 394 precursors
1:31:05.192838 INFO: === Search parameters used ===
1:31:05.192975 INFO: rt_error       : 1662.873046875
1:31:05.193030 INFO: mobility_error : 0.1
1:31:05.193082 INFO: num_candidates : 3
1:31:05.193127 INFO: ms1_error      : 30
1:31:05.193168 INFO: ms2_error      : 30
1:31:05.193208 INFO: fwhm_rt        : 3.0
1:31:05.193250 INFO: quant_window   : 3
1:31:05.193289 INFO: ==============================================
1:31:05.218645 INFO: performing precursor FDR with 40 features
1:31:05.218726 INFO: Decoy channel: -1
1:31:05.218752 INFO: Competetive: True
1:31:05.221348 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:05.222922 INFO: Using random state 78486 for train-test-split
1:31:05.231578 INFO: Test AUC: 0.500
1:31:05.231638 INFO: Train AUC: 0.499
1:31:05.231668 INFO: AUC difference: 0.22%
1:31:05.453708 INFO: Resetting torch num_threads to 80
1:31:05.455511 PROGRESS: === Extracted 1182 precursors and 8027 fragments ===
1:31:05.455887 INFO: === FDR correction performed with classifier version 0 ===
1:31:05.456357 PROGRESS: ============================= Precursor FDR =============================
1:31:05.456446 PROGRESS: Total precursors accumulated: 200
1:31:05.456505 PROGRESS: Target precursors: 199 (99.50%)
1:31:05.456554 PROGRESS: Decoy precursors: 1 (0.50%)
1:31:05.456600 PROGRESS: 
1:31:05.456645 PROGRESS: Precursor Summary:
1:31:05.457508 PROGRESS: Channel   0:	 0.050 FDR:   199; 0.010 FDR:   199; 0.001 FDR:     0
1:31:05.457597 PROGRESS: 
1:31:05.457652 PROGRESS: Protein Summary:
1:31:05.458646 PROGRESS: Channel   0:	 0.050 FDR:   193; 0.010 FDR:   193; 0.001 FDR:     0
1:31:05.458738 PROGRESS: =========================================================================
1:31:05.458956 INFO: Target number of precursors not reached yet.
1:31:05.462879 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:05.464321 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:05.466062 INFO: === skipping optimization until target number of precursors are found ===
1:31:05.466180 INFO: Starting optimization step 2.
1:31:05.466246 PROGRESS: === Extracting elution groups 200 to 600 ===
1:31:05.466312 INFO: Using ng extraction backend
1:31:05.466372 PROGRESS: Extracting batch of 789 precursors
1:31:05.469649 INFO: === Search parameters used ===
1:31:05.469745 INFO: rt_error       : 1662.873046875
1:31:05.469795 INFO: mobility_error : 0.1
1:31:05.469840 INFO: num_candidates : 3
1:31:05.469881 INFO: ms1_error      : 30
1:31:05.469923 INFO: ms2_error      : 30
1:31:05.469964 INFO: fwhm_rt        : 3.0
1:31:05.470004 INFO: quant_window   : 3
1:31:05.470042 INFO: ==============================================
1:31:05.507062 INFO: performing precursor FDR with 40 features
1:31:05.507193 INFO: Decoy channel: -1
1:31:05.507219 INFO: Competetive: True
1:31:05.511077 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:05.513161 INFO: Using random state 78486 for train-test-split
1:31:05.524919 INFO: Test AUC: 0.500
1:31:05.524983 INFO: Train AUC: 0.500
1:31:05.525013 INFO: AUC difference: 0.07%
1:31:05.745540 INFO: Resetting torch num_threads to 80
1:31:05.748688 PROGRESS: === Extracted 3549 precursors and 24536 fragments ===
1:31:05.749187 INFO: === FDR correction performed with classifier version 0 ===
1:31:05.749705 PROGRESS: ============================= Precursor FDR =============================
1:31:05.749804 PROGRESS: Total precursors accumulated: 600
1:31:05.749865 PROGRESS: Target precursors: 599 (99.83%)
1:31:05.749925 PROGRESS: Decoy precursors: 1 (0.17%)
1:31:05.749978 PROGRESS: 
1:31:05.750024 PROGRESS: Precursor Summary:
1:31:05.750992 PROGRESS: Channel   0:	 0.050 FDR:   599; 0.010 FDR:   599; 0.001 FDR:     0
1:31:05.751085 PROGRESS: 
1:31:05.751141 PROGRESS: Protein Summary:
1:31:05.752304 PROGRESS: Channel   0:	 0.050 FDR:   544; 0.010 FDR:   544; 0.001 FDR:     0
1:31:05.752395 PROGRESS: =========================================================================
1:31:05.752654 INFO: Target number of precursors reached.
1:31:05.758111 INFO: fragments_df: keeping 5000 of 24536 [sum(precursor_idx_mask)=13483 sum(mass_error_mask)=24536 stop_rank=5000
1:31:05.763201 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:05.888740 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:06.505380 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:06.505993 INFO: Using score_cutoff 14.667789643478393 (fac=0.99, q=1)
1:31:06.506342 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:06.506433 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:06.506495 INFO: Updating optimization_manager: score_cutoff        : 14.606017497825622 -> 14.667789643478393
1:31:06.506552 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:06.508498 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:06.511177 INFO: === checking if optimization conditions were reached ===
1:31:06.513146 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.828943
1:31:06.513275 INFO: Updating optimization_manager: classifier_version  : 0 -> 2
1:31:06.513346 PROGRESS: ❌ ms2_error      : 6.8289 > 6.8289 or insufficient steps taken.
1:31:06.513407 INFO: ==============================================
1:31:06.513483 INFO: Starting optimization step 3.
1:31:06.513546 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:06.513614 INFO: Using ng extraction backend
1:31:06.513678 PROGRESS: Extracting batch of 1183 precursors
1:31:06.520111 INFO: === Search parameters used ===
1:31:06.520278 INFO: rt_error       : 1662.873046875
1:31:06.520334 INFO: mobility_error : 0.1
1:31:06.520386 INFO: num_candidates : 3
1:31:06.520433 INFO: ms1_error      : 30
1:31:06.520478 INFO: ms2_error      : 6.828943
1:31:06.520520 INFO: fwhm_rt        : 3.0
1:31:06.520562 INFO: quant_window   : 3
1:31:06.520604 INFO: ==============================================
1:31:06.570004 INFO: performing precursor FDR with 40 features
1:31:06.570112 INFO: Decoy channel: -1
1:31:06.570138 INFO: Competetive: True
1:31:06.573236 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:06.575383 INFO: Using random state 474153 for train-test-split
1:31:06.587747 INFO: Test AUC: 0.501
1:31:06.587818 INFO: Train AUC: 0.500
1:31:06.587848 INFO: AUC difference: 0.35%
1:31:09.905092 INFO: Resetting torch num_threads to 80
1:31:09.907222 PROGRESS: === Extracted 3549 precursors and 25922 fragments ===
1:31:09.907605 INFO: === FDR correction performed with classifier version 2 ===
1:31:09.908116 PROGRESS: ============================= Precursor FDR =============================
1:31:09.908208 PROGRESS: Total precursors accumulated: 600
1:31:09.908264 PROGRESS: Target precursors: 598 (99.67%)
1:31:09.908317 PROGRESS: Decoy precursors: 2 (0.33%)
1:31:09.908362 PROGRESS: 
1:31:09.908406 PROGRESS: Precursor Summary:
1:31:09.909385 PROGRESS: Channel   0:	 0.050 FDR:   598; 0.010 FDR:   598; 0.001 FDR:     0
1:31:09.909485 PROGRESS: 
1:31:09.909543 PROGRESS: Protein Summary:
1:31:09.910736 PROGRESS: Channel   0:	 0.050 FDR:   543; 0.010 FDR:   543; 0.001 FDR:     0
1:31:09.910827 PROGRESS: =========================================================================
1:31:09.911075 INFO: Target number of precursors reached.
1:31:09.916785 INFO: fragments_df: keeping 5000 of 25922 [sum(precursor_idx_mask)=14123 sum(mass_error_mask)=25922 stop_rank=5000
1:31:09.921919 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:10.050310 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:10.673641 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:10.674169 INFO: Using score_cutoff 11.771535228538513 (fac=0.99, q=1)
1:31:10.674496 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:10.674580 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:10.674636 INFO: Updating optimization_manager: score_cutoff        : 14.667789643478393 -> 11.771535228538513
1:31:10.674690 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:10.676518 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:10.678943 INFO: === checking if optimization conditions were reached ===
1:31:10.680696 INFO: Updating optimization_manager: ms2_error           : 6.828943 -> 6.828943
1:31:10.680801 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
1:31:10.680870 PROGRESS: ✅ ms2_error      : 6.8289 <= 6.8289
1:31:10.680933 INFO: ==============================================
1:31:10.680997 PROGRESS: Optimization finished for ms2_error.
1:31:10.685796 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:10.687178 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:10.689423 INFO: Starting optimization step 0.
1:31:10.689538 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:10.689617 INFO: Using ng extraction backend
1:31:10.689681 PROGRESS: Extracting batch of 1183 precursors
1:31:10.693805 INFO: === Search parameters used ===
1:31:10.693912 INFO: rt_error       : 1662.873046875
1:31:10.693964 INFO: mobility_error : 0.1
1:31:10.694009 INFO: num_candidates : 3
1:31:10.694052 INFO: ms1_error      : 30
1:31:10.694093 INFO: ms2_error      : 6.828943
1:31:10.694132 INFO: fwhm_rt        : 3.0
1:31:10.694173 INFO: quant_window   : 3
1:31:10.694212 INFO: ==============================================
1:31:10.743598 INFO: performing precursor FDR with 40 features
1:31:10.743706 INFO: Decoy channel: -1
1:31:10.743733 INFO: Competetive: True
1:31:10.747009 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:10.749183 INFO: Using random state 715891 for train-test-split
1:31:10.760252 INFO: Test AUC: 0.500
1:31:10.760326 INFO: Train AUC: 0.500
1:31:10.760357 INFO: AUC difference: 0.00%
1:31:10.986371 INFO: Resetting torch num_threads to 80
1:31:10.988467 PROGRESS: === Extracted 3549 precursors and 25926 fragments ===
1:31:10.988859 INFO: === FDR correction performed with classifier version 3 ===
1:31:10.989358 PROGRESS: ============================= Precursor FDR =============================
1:31:10.989449 PROGRESS: Total precursors accumulated: 600
1:31:10.989524 PROGRESS: Target precursors: 599 (99.83%)
1:31:10.989574 PROGRESS: Decoy precursors: 1 (0.17%)
1:31:10.989621 PROGRESS: 
1:31:10.989665 PROGRESS: Precursor Summary:
1:31:10.990643 PROGRESS: Channel   0:	 0.050 FDR:   599; 0.010 FDR:   599; 0.001 FDR:     1
1:31:10.990737 PROGRESS: 
1:31:10.990792 PROGRESS: Protein Summary:
1:31:10.991980 PROGRESS: Channel   0:	 0.050 FDR:   544; 0.010 FDR:   544; 0.001 FDR:     1
1:31:10.992069 PROGRESS: =========================================================================
1:31:10.992342 INFO: Target number of precursors reached.
1:31:10.998138 INFO: fragments_df: keeping 5000 of 25926 [sum(precursor_idx_mask)=14157 sum(mass_error_mask)=25926 stop_rank=5000
1:31:11.003260 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:11.124888 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:11.750288 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:11.750820 INFO: Using score_cutoff 11.905493413925171 (fac=0.99, q=1)
1:31:11.751151 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:11.751232 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:11.751294 INFO: Updating optimization_manager: score_cutoff        : 11.771535228538513 -> 11.905493413925171
1:31:11.751349 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:11.753202 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:11.755639 INFO: === checking if optimization conditions were reached ===
1:31:11.755749 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:31:11.757477 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 422.2207650684523
1:31:11.757602 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 422.2208.
1:31:11.757667 INFO: ==============================================
1:31:11.757754 INFO: Starting optimization step 1.
1:31:11.757812 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:11.757876 INFO: Using ng extraction backend
1:31:11.757934 PROGRESS: Extracting batch of 1183 precursors
1:31:11.762116 INFO: === Search parameters used ===
1:31:11.762225 INFO: rt_error       : 422.2207650684523
1:31:11.762275 INFO: mobility_error : 0.1
1:31:11.762321 INFO: num_candidates : 3
1:31:11.762361 INFO: ms1_error      : 30
1:31:11.762402 INFO: ms2_error      : 6.828943
1:31:11.762444 INFO: fwhm_rt        : 3.0
1:31:11.762483 INFO: quant_window   : 3
1:31:11.762529 INFO: ==============================================
1:31:11.804356 INFO: performing precursor FDR with 40 features
1:31:11.804471 INFO: Decoy channel: -1
1:31:11.804498 INFO: Competetive: True
1:31:11.807576 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:11.809735 INFO: Using random state 715891 for train-test-split
1:31:11.823862 INFO: Test AUC: 0.500
1:31:11.823955 INFO: Train AUC: 0.500
1:31:11.823985 INFO: AUC difference: 0.00%
1:31:12.063449 INFO: Resetting torch num_threads to 80
1:31:12.065512 PROGRESS: === Extracted 3549 precursors and 25857 fragments ===
1:31:12.065901 INFO: === FDR correction performed with classifier version 3 ===
1:31:12.066335 PROGRESS: ============================= Precursor FDR =============================
1:31:12.066426 PROGRESS: Total precursors accumulated: 600
1:31:12.066485 PROGRESS: Target precursors: 600 (100.00%)
1:31:12.066534 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:12.066581 PROGRESS: 
1:31:12.066624 PROGRESS: Precursor Summary:
1:31:12.067492 PROGRESS: Channel   0:	 0.050 FDR:   600; 0.010 FDR:   600; 0.001 FDR:   600
1:31:12.067583 PROGRESS: 
1:31:12.067640 PROGRESS: Protein Summary:
1:31:12.068745 PROGRESS: Channel   0:	 0.050 FDR:   545; 0.010 FDR:   545; 0.001 FDR:   545
1:31:12.068839 PROGRESS: =========================================================================
1:31:12.069121 INFO: Target number of precursors reached.
1:31:12.074778 INFO: fragments_df: keeping 5000 of 25857 [sum(precursor_idx_mask)=14154 sum(mass_error_mask)=25857 stop_rank=5000
1:31:12.078234 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:12.220436 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:12.845577 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:12.846103 INFO: Using score_cutoff 12.104365287208557 (fac=0.99, q=1)
1:31:12.846436 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:12.846519 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:12.846573 INFO: Updating optimization_manager: score_cutoff        : 11.905493413925171 -> 12.104365287208557
1:31:12.846629 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:12.848019 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:12.849233 INFO: === checking if optimization conditions were reached ===
1:31:12.849337 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:31:12.851173 INFO: Updating optimization_manager: rt_error            : 422.2207650684523 -> 371.76397613090455
1:31:12.851279 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 371.7640.
1:31:12.851346 INFO: ==============================================
1:31:12.851415 INFO: Starting optimization step 2.
1:31:12.851484 PROGRESS: === Extracting elution groups 0 to 200 ===
1:31:12.851550 INFO: Using ng extraction backend
1:31:12.851608 PROGRESS: Extracting batch of 394 precursors
1:31:12.854074 INFO: === Search parameters used ===
1:31:12.854166 INFO: rt_error       : 371.76397613090455
1:31:12.854219 INFO: mobility_error : 0.1
1:31:12.854263 INFO: num_candidates : 3
1:31:12.854308 INFO: ms1_error      : 30
1:31:12.854349 INFO: ms2_error      : 6.828943
1:31:12.854398 INFO: fwhm_rt        : 3.0
1:31:12.854443 INFO: quant_window   : 3
1:31:12.854483 INFO: ==============================================
1:31:12.881494 INFO: performing precursor FDR with 40 features
1:31:12.881577 INFO: Decoy channel: -1
1:31:12.881603 INFO: Competetive: True
1:31:12.884153 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:12.885779 INFO: Using random state 715891 for train-test-split
1:31:12.894188 INFO: Test AUC: 0.500
1:31:12.894249 INFO: Train AUC: 0.500
1:31:12.894279 INFO: AUC difference: 0.00%
1:31:13.118290 INFO: Resetting torch num_threads to 80
1:31:13.120174 PROGRESS: === Extracted 1182 precursors and 8398 fragments ===
1:31:13.120555 INFO: === FDR correction performed with classifier version 3 ===
1:31:13.120943 PROGRESS: ============================= Precursor FDR =============================
1:31:13.121030 PROGRESS: Total precursors accumulated: 200
1:31:13.121089 PROGRESS: Target precursors: 200 (100.00%)
1:31:13.121136 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:13.121184 PROGRESS: 
1:31:13.121229 PROGRESS: Precursor Summary:
1:31:13.122019 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1:31:13.122110 PROGRESS: 
1:31:13.122165 PROGRESS: Protein Summary:
1:31:13.123089 PROGRESS: Channel   0:	 0.050 FDR:   194; 0.010 FDR:   194; 0.001 FDR:   194
1:31:13.123183 PROGRESS: =========================================================================
1:31:13.123489 INFO: Target number of precursors reached.
1:31:13.126014 INFO: fragments_df: keeping 2336 of 8398 [sum(precursor_idx_mask)=4654 sum(mass_error_mask)=8398 stop_rank=2336
1:31:13.129667 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:13.230918 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:13.498320 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:13.498849 INFO: Using score_cutoff 9.851826135635376 (fac=0.99, q=1)
1:31:13.499178 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:13.499259 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:13.499315 INFO: Updating optimization_manager: score_cutoff        : 12.104365287208557 -> 9.851826135635376
1:31:13.499371 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:13.500757 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:13.502036 INFO: === checking if optimization conditions were reached ===
1:31:13.502136 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:31:13.503822 INFO: Updating optimization_manager: rt_error            : 371.76397613090455 -> 329.61106924916476
1:31:13.503924 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 329.6111.
1:31:13.503991 INFO: ==============================================
1:31:13.504062 INFO: Starting optimization step 3.
1:31:13.504123 PROGRESS: === Extracting elution groups 0 to 200 ===
1:31:13.504187 INFO: Using ng extraction backend
1:31:13.504245 PROGRESS: Extracting batch of 394 precursors
1:31:13.506666 INFO: === Search parameters used ===
1:31:13.506753 INFO: rt_error       : 329.61106924916476
1:31:13.506806 INFO: mobility_error : 0.1
1:31:13.506853 INFO: num_candidates : 3
1:31:13.506902 INFO: ms1_error      : 30
1:31:13.506950 INFO: ms2_error      : 6.828943
1:31:13.506991 INFO: fwhm_rt        : 3.0
1:31:13.507031 INFO: quant_window   : 3
1:31:13.507071 INFO: ==============================================
1:31:13.534027 INFO: performing precursor FDR with 40 features
1:31:13.534168 INFO: Decoy channel: -1
1:31:13.534206 INFO: Competetive: True
1:31:13.536838 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:13.538504 INFO: Using random state 715891 for train-test-split
1:31:13.546833 INFO: Test AUC: 0.500
1:31:13.546898 INFO: Train AUC: 0.500
1:31:13.546927 INFO: AUC difference: 0.00%
1:31:13.773930 INFO: Resetting torch num_threads to 80
1:31:13.775761 PROGRESS: === Extracted 1182 precursors and 8401 fragments ===
1:31:13.776144 INFO: === FDR correction performed with classifier version 3 ===
1:31:13.776529 PROGRESS: ============================= Precursor FDR =============================
1:31:13.776616 PROGRESS: Total precursors accumulated: 200
1:31:13.776674 PROGRESS: Target precursors: 200 (100.00%)
1:31:13.776721 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:13.776767 PROGRESS: 
1:31:13.776811 PROGRESS: Precursor Summary:
1:31:13.777590 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1:31:13.777680 PROGRESS: 
1:31:13.777734 PROGRESS: Protein Summary:
1:31:13.778646 PROGRESS: Channel   0:	 0.050 FDR:   194; 0.010 FDR:   194; 0.001 FDR:   194
1:31:13.778733 PROGRESS: =========================================================================
1:31:13.778976 INFO: Target number of precursors reached.
1:31:13.781511 INFO: fragments_df: keeping 2337 of 8401 [sum(precursor_idx_mask)=4644 sum(mass_error_mask)=8401 stop_rank=2337
1:31:13.785132 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:13.887822 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:14.150172 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:14.150704 INFO: Using score_cutoff 9.851826135635376 (fac=0.99, q=1)
1:31:14.151042 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:14.151124 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:14.151180 INFO: Updating optimization_manager: score_cutoff        : 9.851826135635376 -> 9.851826135635376
1:31:14.151235 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:14.152641 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:14.153970 INFO: === checking if optimization conditions were reached ===
1:31:14.154073 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:31:14.155788 INFO: Updating optimization_manager: rt_error            : 329.61106924916476 -> 279.57869133625877
1:31:14.155894 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 279.5787.
1:31:14.155958 INFO: ==============================================
1:31:14.156028 INFO: Starting optimization step 4.
1:31:14.156086 PROGRESS: === Extracting elution groups 0 to 200 ===
1:31:14.156147 INFO: Using ng extraction backend
1:31:14.156205 PROGRESS: Extracting batch of 394 precursors
1:31:14.159496 INFO: === Search parameters used ===
1:31:14.159598 INFO: rt_error       : 279.57869133625877
1:31:14.159657 INFO: mobility_error : 0.1
1:31:14.159704 INFO: num_candidates : 3
1:31:14.159745 INFO: ms1_error      : 30
1:31:14.159786 INFO: ms2_error      : 6.828943
1:31:14.159827 INFO: fwhm_rt        : 3.0
1:31:14.159865 INFO: quant_window   : 3
1:31:14.159904 INFO: ==============================================
1:31:14.189351 INFO: performing precursor FDR with 40 features
1:31:14.189444 INFO: Decoy channel: -1
1:31:14.189480 INFO: Competetive: True
1:31:14.192022 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:14.193648 INFO: Using random state 715891 for train-test-split
1:31:14.201869 INFO: Test AUC: 0.500
1:31:14.201930 INFO: Train AUC: 0.500
1:31:14.201959 INFO: AUC difference: 0.00%
1:31:14.426792 INFO: Resetting torch num_threads to 80
1:31:14.428754 PROGRESS: === Extracted 1182 precursors and 8391 fragments ===
1:31:14.429189 INFO: === FDR correction performed with classifier version 3 ===
1:31:14.429646 PROGRESS: ============================= Precursor FDR =============================
1:31:14.429742 PROGRESS: Total precursors accumulated: 200
1:31:14.429810 PROGRESS: Target precursors: 200 (100.00%)
1:31:14.429860 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:14.429905 PROGRESS: 
1:31:14.429948 PROGRESS: Precursor Summary:
1:31:14.430747 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1:31:14.430838 PROGRESS: 
1:31:14.430892 PROGRESS: Protein Summary:
1:31:14.431828 PROGRESS: Channel   0:	 0.050 FDR:   194; 0.010 FDR:   194; 0.001 FDR:   194
1:31:14.431917 PROGRESS: =========================================================================
1:31:14.432188 INFO: Target number of precursors reached.
1:31:14.434834 INFO: fragments_df: keeping 2332 of 8391 [sum(precursor_idx_mask)=4635 sum(mass_error_mask)=8391 stop_rank=2332
1:31:14.438272 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:14.536675 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:14.801621 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:14.802155 INFO: Using score_cutoff 10.726729817390442 (fac=0.99, q=1)
1:31:14.802506 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:14.802593 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:14.802649 INFO: Updating optimization_manager: score_cutoff        : 9.851826135635376 -> 10.726729817390442
1:31:14.802709 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:14.804151 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:14.805501 INFO: === checking if optimization conditions were reached ===
1:31:14.805608 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:31:14.807369 INFO: Updating optimization_manager: rt_error            : 279.57869133625877 -> 257.1411225499147
1:31:14.807481 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 257.1411.
1:31:14.807550 INFO: ==============================================
1:31:14.807619 INFO: Starting optimization step 5.
1:31:14.807680 PROGRESS: === Extracting elution groups 0 to 200 ===
1:31:14.807744 INFO: Using ng extraction backend
1:31:14.807804 PROGRESS: Extracting batch of 394 precursors
1:31:14.810697 INFO: === Search parameters used ===
1:31:14.810794 INFO: rt_error       : 257.1411225499147
1:31:14.810849 INFO: mobility_error : 0.1
1:31:14.810899 INFO: num_candidates : 3
1:31:14.810943 INFO: ms1_error      : 30
1:31:14.810985 INFO: ms2_error      : 6.828943
1:31:14.811026 INFO: fwhm_rt        : 3.0
1:31:14.811065 INFO: quant_window   : 3
1:31:14.811106 INFO: ==============================================
1:31:14.835578 INFO: performing precursor FDR with 40 features
1:31:14.835662 INFO: Decoy channel: -1
1:31:14.835689 INFO: Competetive: True
1:31:14.838162 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:14.839706 INFO: Using random state 715891 for train-test-split
1:31:14.847551 INFO: Test AUC: 0.500
1:31:14.847611 INFO: Train AUC: 0.500
1:31:14.847640 INFO: AUC difference: 0.00%
1:31:15.069235 INFO: Resetting torch num_threads to 80
1:31:15.071016 PROGRESS: === Extracted 1182 precursors and 8373 fragments ===
1:31:15.071389 INFO: === FDR correction performed with classifier version 3 ===
1:31:15.071765 PROGRESS: ============================= Precursor FDR =============================
1:31:15.071849 PROGRESS: Total precursors accumulated: 200
1:31:15.071907 PROGRESS: Target precursors: 200 (100.00%)
1:31:15.071954 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:15.072001 PROGRESS: 
1:31:15.072046 PROGRESS: Precursor Summary:
1:31:15.072810 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1:31:15.072896 PROGRESS: 
1:31:15.072950 PROGRESS: Protein Summary:
1:31:15.073871 PROGRESS: Channel   0:	 0.050 FDR:   194; 0.010 FDR:   194; 0.001 FDR:   194
1:31:15.073961 PROGRESS: =========================================================================
1:31:15.074185 INFO: Target number of precursors reached.
1:31:15.076619 INFO: fragments_df: keeping 2329 of 8373 [sum(precursor_idx_mask)=4627 sum(mass_error_mask)=8373 stop_rank=2329
1:31:15.079916 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:15.175074 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:15.434532 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:15.435030 INFO: Using score_cutoff 10.733732561302185 (fac=0.99, q=1)
1:31:15.435342 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:15.435421 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:15.435476 INFO: Updating optimization_manager: score_cutoff        : 10.726729817390442 -> 10.733732561302185
1:31:15.435531 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:15.436887 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:15.438126 INFO: === checking if optimization conditions were reached ===
1:31:15.438223 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:31:15.439873 INFO: Updating optimization_manager: rt_error            : 257.1411225499147 -> 250.21384310568857
1:31:15.439975 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 250.2138.
1:31:15.440042 INFO: ==============================================
1:31:15.440109 INFO: Starting optimization step 6.
1:31:15.440167 PROGRESS: === Extracting elution groups 0 to 200 ===
1:31:15.440230 INFO: Using ng extraction backend
1:31:15.440297 PROGRESS: Extracting batch of 394 precursors
1:31:15.442717 INFO: === Search parameters used ===
1:31:15.442808 INFO: rt_error       : 250.21384310568857
1:31:15.442858 INFO: mobility_error : 0.1
1:31:15.442902 INFO: num_candidates : 3
1:31:15.442944 INFO: ms1_error      : 30
1:31:15.442987 INFO: ms2_error      : 6.828943
1:31:15.443027 INFO: fwhm_rt        : 3.0
1:31:15.443068 INFO: quant_window   : 3
1:31:15.443108 INFO: ==============================================
1:31:15.476144 INFO: performing precursor FDR with 40 features
1:31:15.476221 INFO: Decoy channel: -1
1:31:15.476247 INFO: Competetive: True
1:31:15.478673 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:15.480217 INFO: Using random state 715891 for train-test-split
1:31:15.488005 INFO: Test AUC: 0.500
1:31:15.488063 INFO: Train AUC: 0.500
1:31:15.488092 INFO: AUC difference: 0.00%
1:31:15.706926 INFO: Resetting torch num_threads to 80
1:31:15.708606 PROGRESS: === Extracted 1182 precursors and 8359 fragments ===
1:31:15.708965 INFO: === FDR correction performed with classifier version 3 ===
1:31:15.709351 PROGRESS: ============================= Precursor FDR =============================
1:31:15.709438 PROGRESS: Total precursors accumulated: 200
1:31:15.709507 PROGRESS: Target precursors: 200 (100.00%)
1:31:15.709557 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:15.709603 PROGRESS: 
1:31:15.709646 PROGRESS: Precursor Summary:
1:31:15.710413 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:   200
1:31:15.710498 PROGRESS: 
1:31:15.710551 PROGRESS: Protein Summary:
1:31:15.711479 PROGRESS: Channel   0:	 0.050 FDR:   194; 0.010 FDR:   194; 0.001 FDR:   194
1:31:15.711574 PROGRESS: =========================================================================
1:31:15.711774 INFO: Target number of precursors reached.
1:31:15.714201 INFO: fragments_df: keeping 2336 of 8359 [sum(precursor_idx_mask)=4622 sum(mass_error_mask)=8359 stop_rank=2336
1:31:15.717727 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:15.812116 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:16.069101 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:16.069612 INFO: Using score_cutoff 10.733732561302185 (fac=0.99, q=1)
1:31:16.069927 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:16.070007 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:16.070061 INFO: Updating optimization_manager: score_cutoff        : 10.733732561302185 -> 10.733732561302185
1:31:16.070115 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:16.071465 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:16.072662 INFO: === checking if optimization conditions were reached ===
1:31:16.072760 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:31:16.073794 INFO: Updating optimization_manager: rt_error            : 250.21384310568857 -> 250.21384310568857
1:31:16.073921 INFO: Updating optimization_manager: classifier_version  : 3 -> 10
1:31:16.074014 INFO: Updating optimization_manager: score_cutoff        : 10.733732561302185 -> 10.733732561302185
1:31:16.074101 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:16.074191 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:16.074275 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 250.2138 found after 7 searches.
1:31:16.074335 INFO: ==============================================
1:31:16.074403 PROGRESS: Optimization finished for rt_error.
1:31:16.077323 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:16.078254 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:16.104781 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:31:16.104923 PROGRESS: ==============================================
1:31:16.104992 PROGRESS: ms2_error      : 6.8289
1:31:16.105046 PROGRESS: rt_error       : 250.2138
1:31:16.105094 PROGRESS: ==============================================
1:31:16.105570 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:16.191257 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:16.430192 INFO: Using ng extraction backend
1:31:16.430515 PROGRESS: Extracting batch of 146144 precursors
1:31:16.672756 INFO: === Search parameters used ===
1:31:16.673137 INFO: rt_error       : 250.21384310568857
1:31:16.673198 INFO: mobility_error : 0.1
1:31:16.673244 INFO: num_candidates : 3
1:31:16.673289 INFO: ms1_error      : 30
1:31:16.673343 INFO: ms2_error      : 6.828943
1:31:16.673385 INFO: fwhm_rt        : 3.0
1:31:16.673426 INFO: quant_window   : 3
1:31:16.673473 INFO: ==============================================
1:31:16.936682 INFO: Removed 41774 precursors with score below cutoff 10.733732561302185
1:31:17.297021 INFO: performing precursor FDR with 40 features
1:31:17.297161 INFO: Decoy channel: -1
1:31:17.297188 INFO: Competetive: True
1:31:17.343847 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:17.479288 INFO: Using random state 977674 for train-test-split
1:31:24.581416 INFO: Test AUC: 0.738
1:31:24.581588 INFO: Train AUC: 0.741
1:31:24.581621 INFO: AUC difference: 0.34%
1:31:24.981563 INFO: Resetting torch num_threads to 80
1:31:25.223517 PROGRESS: ============================= Precursor FDR =============================
1:31:25.223807 PROGRESS: Total precursors accumulated: 68,250
1:31:25.223876 PROGRESS: Target precursors: 67,575 (99.01%)
1:31:25.223928 PROGRESS: Decoy precursors: 675 (0.99%)
1:31:25.223974 PROGRESS: 
1:31:25.224018 PROGRESS: Precursor Summary:
1:31:25.253381 PROGRESS: Channel   0:	 0.050 FDR: 67,575; 0.010 FDR: 67,575; 0.001 FDR: 59,909
1:31:25.253719 PROGRESS: 
1:31:25.253785 PROGRESS: Protein Summary:
1:31:25.292964 PROGRESS: Channel   0:	 0.050 FDR: 7,010; 0.010 FDR: 7,010; 0.001 FDR: 6,894
1:31:25.293243 PROGRESS: =========================================================================
1:31:25.295499 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/psm.parquet
1:31:25.435538 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/frag.parquet
1:31:25.647170 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
1:31:25.701581 PROGRESS: 
1:31:25.701733 INFO: Quantification results path: alphadia_zenoswath8600/quant
1:31:25.701806 INFO: Creating folder alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/figures
1:31:25.701981 INFO: Initializing TimingManager
1:31:25.702813 INFO: Initializing RawFileManager
1:33:55.378286 INFO: Determining DIA cycle
1:33:55.393303 INFO: Found cycle with start 0.00 min and length 86.
1:33:55.661980 INFO: RT (min)            : 0.0 - 55.4
1:33:55.662078 INFO: RT duration (sec)   : 3325.7
1:33:55.662106 INFO: RT duration (min)   : 55.4
1:33:55.662131 INFO: Cycle len (scans)   : 86
1:33:55.662153 INFO: Cycle len (sec)     : 1.90
1:33:55.662172 INFO: Number of cycles    : 1747
1:33:55.662191 INFO: MS2 range (m/z)     : 399.5 - 903.5
1:33:55.662235 INFO: Creating DIA data object took: 149.9593107700348
1:33:56.806827 INFO: Creating DIA data NG object took: 1.1444473266601562
1:33:56.833632 INFO: Initializing CalibrationManager
1:33:56.833940 INFO: Setting up calibration estimators ..
1:33:56.834001 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:33:56.834086 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'}' ..
1:33:56.834180 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:33:56.834233 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:33:56.834292 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}}' ..
1:33:56.834345 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:33:56.834390 INFO: Done setting up calibration estimators.
1:33:56.834522 INFO: Initializing OptimizationManager
1:33:56.834659 INFO: initial parameter: ms1_error = 30
1:33:56.834711 INFO: initial parameter: ms2_error = 30
1:33:56.834759 INFO: initial parameter: rt_error = 1662.873046875
1:33:56.834802 INFO: initial parameter: mobility_error = 0.1
1:33:56.834845 INFO: initial parameter: num_candidates = 1
1:33:56.834887 INFO: initial parameter: fwhm_rt = 5
1:33:56.834927 INFO: initial parameter: fwhm_mobility = 0.01
1:33:56.834967 INFO: initial parameter: score_cutoff = 0
1:33:56.835006 INFO: initial parameter: classifier_version = -1
1:33:56.835083 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
1:33:56.835373 INFO: FDRManager: loading saved state not requested, will be initialized.
1:33:56.835413 INFO: Initializing FDRManager
1:33:56.835451 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:33:56.860235 PROGRESS: Initializing spectral library: 73,874 target precursors potentially observable (0 removed)
1:33:56.874785 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:33:56.875156 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 1662.873046875
1:33:56.875256 PROGRESS: Starting initial search for precursors.
1:33:56.875345 INFO: Starting optimization step 0.
1:33:56.875410 PROGRESS: === Extracting elution groups 0 to 200 ===
1:33:56.875476 INFO: Using ng extraction backend
1:33:56.875543 PROGRESS: Extracting batch of 394 precursors
1:33:56.877458 INFO: === Search parameters used ===
1:33:56.877564 INFO: rt_error       : 1662.873046875
1:33:56.877616 INFO: mobility_error : 0.1
1:33:56.877660 INFO: num_candidates : 1
1:33:56.877705 INFO: ms1_error      : 30
1:33:56.877748 INFO: ms2_error      : 30
1:33:56.877788 INFO: fwhm_rt        : 5
1:33:56.877829 INFO: quant_window   : 3
1:33:56.877868 INFO: ==============================================
1:33:56.901209 INFO: performing precursor FDR with 40 features
1:33:56.901277 INFO: Decoy channel: -1
1:33:56.901304 INFO: Competetive: True
1:33:56.902276 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:56.904721 INFO: Using random state 77900 for train-test-split
1:33:56.912454 INFO: Test AUC: 0.491
1:33:56.912512 INFO: Train AUC: 0.524
1:33:56.912544 INFO: AUC difference: 6.24%
1:33:56.912568 WARNING: AUC difference > 5%. This may indicate overfitting.
1:33:57.130786 INFO: Resetting torch num_threads to 80
1:33:57.132139 PROGRESS: === Extracted 394 precursors and 3037 fragments ===
1:33:57.132489 INFO: === FDR correction performed with classifier version -1 ===
1:33:57.132914 PROGRESS: ============================= Precursor FDR =============================
1:33:57.133000 PROGRESS: Total precursors accumulated: 0
1:33:57.133059 PROGRESS: Target precursors: 0 (0.00%)
1:33:57.133109 PROGRESS: Decoy precursors: 0 (0.00%)
1:33:57.133155 PROGRESS: 
1:33:57.133197 PROGRESS: Precursor Summary:
1:33:57.133309 PROGRESS: 
1:33:57.133371 PROGRESS: Protein Summary:
1:33:57.133442 PROGRESS: =========================================================================
1:33:57.133645 INFO: Target number of precursors not reached yet.
1:33:57.136985 INFO: Starting optimization step 1.
1:33:57.137094 PROGRESS: === Extracting elution groups 200 to 600 ===
1:33:57.137165 INFO: Using ng extraction backend
1:33:57.137223 PROGRESS: Extracting batch of 789 precursors
1:33:57.139838 INFO: === Search parameters used ===
1:33:57.139926 INFO: rt_error       : 1662.873046875
1:33:57.139977 INFO: mobility_error : 0.1
1:33:57.140023 INFO: num_candidates : 1
1:33:57.140065 INFO: ms1_error      : 30
1:33:57.140107 INFO: ms2_error      : 30
1:33:57.140151 INFO: fwhm_rt        : 5
1:33:57.140189 INFO: quant_window   : 3
1:33:57.140228 INFO: ==============================================
1:33:57.165989 INFO: performing precursor FDR with 40 features
1:33:57.166064 INFO: Decoy channel: -1
1:33:57.166091 INFO: Competetive: True
1:33:57.168928 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:57.170450 INFO: Using random state 967758 for train-test-split
1:33:57.178636 INFO: Test AUC: 0.550
1:33:57.178694 INFO: Train AUC: 0.506
1:33:57.178722 INFO: AUC difference: 8.55%
1:33:57.178744 WARNING: AUC difference > 5%. This may indicate overfitting.
1:33:57.384756 INFO: Resetting torch num_threads to 80
1:33:57.387102 PROGRESS: === Extracted 1183 precursors and 9253 fragments ===
1:33:57.387471 INFO: === FDR correction performed with classifier version -1 ===
1:33:57.387897 PROGRESS: ============================= Precursor FDR =============================
1:33:57.387982 PROGRESS: Total precursors accumulated: 0
1:33:57.388040 PROGRESS: Target precursors: 0 (0.00%)
1:33:57.388087 PROGRESS: Decoy precursors: 0 (0.00%)
1:33:57.388133 PROGRESS: 
1:33:57.388176 PROGRESS: Precursor Summary:
1:33:57.388282 PROGRESS: 
1:33:57.388345 PROGRESS: Protein Summary:
1:33:57.388423 PROGRESS: =========================================================================
1:33:57.388632 INFO: Target number of precursors not reached yet.
1:33:57.392812 INFO: Starting optimization step 2.
1:33:57.392922 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:33:57.392993 INFO: Using ng extraction backend
1:33:57.393052 PROGRESS: Extracting batch of 1588 precursors
1:33:57.397161 INFO: === Search parameters used ===
1:33:57.397257 INFO: rt_error       : 1662.873046875
1:33:57.397306 INFO: mobility_error : 0.1
1:33:57.397352 INFO: num_candidates : 1
1:33:57.397393 INFO: ms1_error      : 30
1:33:57.397436 INFO: ms2_error      : 30
1:33:57.397486 INFO: fwhm_rt        : 5
1:33:57.397531 INFO: quant_window   : 3
1:33:57.397569 INFO: ==============================================
1:33:57.432851 INFO: performing precursor FDR with 40 features
1:33:57.432935 INFO: Decoy channel: -1
1:33:57.432962 INFO: Competetive: True
1:33:57.436338 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:57.438242 INFO: Using random state 426965 for train-test-split
1:33:57.449500 INFO: Test AUC: 0.557
1:33:57.449563 INFO: Train AUC: 0.492
1:33:57.449592 INFO: AUC difference: 13.31%
1:33:57.449614 WARNING: AUC difference > 5%. This may indicate overfitting.
1:33:57.659961 INFO: Resetting torch num_threads to 80
1:33:57.662648 PROGRESS: === Extracted 2771 precursors and 21839 fragments ===
1:33:57.663026 INFO: === FDR correction performed with classifier version -1 ===
1:33:57.663449 PROGRESS: ============================= Precursor FDR =============================
1:33:57.663535 PROGRESS: Total precursors accumulated: 0
1:33:57.663594 PROGRESS: Target precursors: 0 (0.00%)
1:33:57.663641 PROGRESS: Decoy precursors: 0 (0.00%)
1:33:57.663687 PROGRESS: 
1:33:57.663735 PROGRESS: Precursor Summary:
1:33:57.663844 PROGRESS: 
1:33:57.663907 PROGRESS: Protein Summary:
1:33:57.663980 PROGRESS: =========================================================================
1:33:57.664195 INFO: Target number of precursors not reached yet.
1:33:57.670321 INFO: Starting optimization step 3.
1:33:57.670445 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:33:57.670517 INFO: Using ng extraction backend
1:33:57.670576 PROGRESS: Extracting batch of 3164 precursors
1:33:57.677748 INFO: === Search parameters used ===
1:33:57.677856 INFO: rt_error       : 1662.873046875
1:33:57.677903 INFO: mobility_error : 0.1
1:33:57.677948 INFO: num_candidates : 1
1:33:57.677989 INFO: ms1_error      : 30
1:33:57.678032 INFO: ms2_error      : 30
1:33:57.678072 INFO: fwhm_rt        : 5
1:33:57.678113 INFO: quant_window   : 3
1:33:57.678151 INFO: ==============================================
1:33:57.733356 INFO: performing precursor FDR with 40 features
1:33:57.733459 INFO: Decoy channel: -1
1:33:57.733493 INFO: Competetive: True
1:33:57.737519 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:57.739879 INFO: Using random state 585509 for train-test-split
1:33:57.758669 INFO: Test AUC: 0.501
1:33:57.758747 INFO: Train AUC: 0.506
1:33:57.758777 INFO: AUC difference: 1.09%
1:33:57.973878 INFO: Resetting torch num_threads to 80
1:33:57.977272 PROGRESS: === Extracted 5935 precursors and 46837 fragments ===
1:33:57.977670 INFO: === FDR correction performed with classifier version -1 ===
1:33:57.978098 PROGRESS: ============================= Precursor FDR =============================
1:33:57.978185 PROGRESS: Total precursors accumulated: 0
1:33:57.978252 PROGRESS: Target precursors: 0 (0.00%)
1:33:57.978303 PROGRESS: Decoy precursors: 0 (0.00%)
1:33:57.978348 PROGRESS: 
1:33:57.978392 PROGRESS: Precursor Summary:
1:33:57.978499 PROGRESS: 
1:33:57.978561 PROGRESS: Protein Summary:
1:33:57.978635 PROGRESS: =========================================================================
1:33:57.978863 INFO: Target number of precursors not reached yet.
1:33:57.988240 INFO: Starting optimization step 4.
1:33:57.988367 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:33:57.988440 INFO: Using ng extraction backend
1:33:57.988498 PROGRESS: Extracting batch of 6329 precursors
1:33:58.000484 INFO: === Search parameters used ===
1:33:58.000648 INFO: rt_error       : 1662.873046875
1:33:58.000700 INFO: mobility_error : 0.1
1:33:58.000743 INFO: num_candidates : 1
1:33:58.000786 INFO: ms1_error      : 30
1:33:58.000826 INFO: ms2_error      : 30
1:33:58.000868 INFO: fwhm_rt        : 5
1:33:58.000908 INFO: quant_window   : 3
1:33:58.000949 INFO: ==============================================
1:33:58.091542 INFO: performing precursor FDR with 40 features
1:33:58.091668 INFO: Decoy channel: -1
1:33:58.091695 INFO: Competetive: True
1:33:58.097063 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:58.100464 INFO: Using random state 512225 for train-test-split
1:33:58.136271 INFO: Test AUC: 0.495
1:33:58.136379 INFO: Train AUC: 0.508
1:33:58.136409 INFO: AUC difference: 2.58%
1:33:58.353124 INFO: Resetting torch num_threads to 80
1:33:58.357307 PROGRESS: === Extracted 12264 precursors and 96729 fragments ===
1:33:58.357701 INFO: === FDR correction performed with classifier version -1 ===
1:33:58.358136 PROGRESS: ============================= Precursor FDR =============================
1:33:58.358222 PROGRESS: Total precursors accumulated: 0
1:33:58.358282 PROGRESS: Target precursors: 0 (0.00%)
1:33:58.358333 PROGRESS: Decoy precursors: 0 (0.00%)
1:33:58.358388 PROGRESS: 
1:33:58.358433 PROGRESS: Precursor Summary:
1:33:58.358542 PROGRESS: 
1:33:58.358604 PROGRESS: Protein Summary:
1:33:58.358681 PROGRESS: =========================================================================
1:33:58.358951 INFO: Target number of precursors not reached yet.
1:33:58.371241 INFO: Starting optimization step 5.
1:33:58.371449 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:33:58.371530 INFO: Using ng extraction backend
1:33:58.371593 PROGRESS: Extracting batch of 12652 precursors
1:33:58.393915 INFO: === Search parameters used ===
1:33:58.394117 INFO: rt_error       : 1662.873046875
1:33:58.394171 INFO: mobility_error : 0.1
1:33:58.394216 INFO: num_candidates : 1
1:33:58.394271 INFO: ms1_error      : 30
1:33:58.394313 INFO: ms2_error      : 30
1:33:58.394352 INFO: fwhm_rt        : 5
1:33:58.394408 INFO: quant_window   : 3
1:33:58.394452 INFO: ==============================================
1:33:58.549504 INFO: performing precursor FDR with 40 features
1:33:58.549633 INFO: Decoy channel: -1
1:33:58.549659 INFO: Competetive: True
1:33:58.559481 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:58.565350 INFO: Using random state 183236 for train-test-split
1:33:58.795398 INFO: Test AUC: 0.849
1:33:58.795522 INFO: Train AUC: 0.855
1:33:58.795551 INFO: AUC difference: 0.75%
1:33:59.010476 INFO: Resetting torch num_threads to 80
1:33:59.017598 PROGRESS: === Extracted 24914 precursors and 196571 fragments ===
1:33:59.018042 INFO: === FDR correction performed with classifier version -1 ===
1:33:59.019437 PROGRESS: ============================= Precursor FDR =============================
1:33:59.019529 PROGRESS: Total precursors accumulated: 7,888
1:33:59.019588 PROGRESS: Target precursors: 7,810 (99.01%)
1:33:59.019639 PROGRESS: Decoy precursors: 78 (0.99%)
1:33:59.019684 PROGRESS: 
1:33:59.019728 PROGRESS: Precursor Summary:
1:33:59.022747 PROGRESS: Channel   0:	 0.050 FDR: 7,810; 0.010 FDR: 7,810; 0.001 FDR: 5,470
1:33:59.022881 PROGRESS: 
1:33:59.022937 PROGRESS: Protein Summary:
1:33:59.027340 PROGRESS: Channel   0:	 0.050 FDR: 3,454; 0.010 FDR: 3,454; 0.001 FDR: 2,664
1:33:59.027450 PROGRESS: =========================================================================
1:33:59.027833 INFO: Target number of precursors reached.
1:33:59.063570 INFO: fragments_df: keeping 5000 of 196571 [sum(precursor_idx_mask)=81677 sum(mass_error_mask)=196571 stop_rank=5000
1:33:59.069241 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:00.333384 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:01.011557 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:34:01.012268 INFO: Using score_cutoff 14.993105415058137 (fac=0.99, q=1)
1:34:01.012825 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:34:01.012910 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:34:01.012964 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.993105415058137
1:34:01.013025 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:01.014743 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:01.017026 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
1:34:01.017131 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:34:01.017214 INFO: Starting optimization step 6.
1:34:01.017293 PROGRESS: === Extracting elution groups 0 to 600 ===
1:34:01.017379 INFO: Using ng extraction backend
1:34:01.017473 PROGRESS: Extracting batch of 1183 precursors
1:34:01.021206 INFO: === Search parameters used ===
1:34:01.021300 INFO: rt_error       : 1662.873046875
1:34:01.021351 INFO: mobility_error : 0.1
1:34:01.021395 INFO: num_candidates : 3
1:34:01.021437 INFO: ms1_error      : 30
1:34:01.021486 INFO: ms2_error      : 30
1:34:01.021529 INFO: fwhm_rt        : 3.0
1:34:01.021570 INFO: quant_window   : 3
1:34:01.021608 INFO: ==============================================
1:34:01.065117 INFO: performing precursor FDR with 40 features
1:34:01.065251 INFO: Decoy channel: -1
1:34:01.065278 INFO: Competetive: True
1:34:01.070591 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:01.072660 INFO: Using random state 667355 for train-test-split
1:34:01.084877 INFO: Test AUC: 0.653
1:34:01.084940 INFO: Train AUC: 0.669
1:34:01.084969 INFO: AUC difference: 2.44%
1:34:01.296135 INFO: Resetting torch num_threads to 80
1:34:01.297776 PROGRESS: === Extracted 3548 precursors and 24336 fragments ===
1:34:01.298150 INFO: === FDR correction performed with classifier version 5 ===
1:34:01.298630 PROGRESS: ============================= Precursor FDR =============================
1:34:01.298722 PROGRESS: Total precursors accumulated: 428
1:34:01.298782 PROGRESS: Target precursors: 424 (99.07%)
1:34:01.298832 PROGRESS: Decoy precursors: 4 (0.93%)
1:34:01.298879 PROGRESS: 
1:34:01.298924 PROGRESS: Precursor Summary:
1:34:01.299899 PROGRESS: Channel   0:	 0.050 FDR:   424; 0.010 FDR:   424; 0.001 FDR:   339
1:34:01.299990 PROGRESS: 
1:34:01.300045 PROGRESS: Protein Summary:
1:34:01.301205 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   389; 0.001 FDR:   318
1:34:01.301298 PROGRESS: =========================================================================
1:34:01.301764 INFO: Target number of precursors reached.
1:34:01.306234 INFO: fragments_df: keeping 5000 of 24336 [sum(precursor_idx_mask)=9853 sum(mass_error_mask)=24336 stop_rank=5000
1:34:01.311946 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:01.437084 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:02.111726 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:02.112154 INFO: Using score_cutoff 16.124298498344423 (fac=0.99, q=1)
1:34:02.112437 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:02.112525 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:02.112581 INFO: Updating optimization_manager: score_cutoff        : 14.993105415058137 -> 16.124298498344423
1:34:02.112632 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:02.114200 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:02.116561 INFO: === checking if optimization conditions were reached ===
1:34:02.118192 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.828943
1:34:02.118298 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
1:34:02.118374 PROGRESS: ❌ ms2_error      : 6.8289 > 6.8289 or insufficient steps taken.
1:34:02.118434 INFO: ==============================================
1:34:02.118495 INFO: Starting optimization step 7.
1:34:02.118550 PROGRESS: === Extracting elution groups 0 to 600 ===
1:34:02.118603 INFO: Using ng extraction backend
1:34:02.118655 PROGRESS: Extracting batch of 1183 precursors
1:34:02.121980 INFO: === Search parameters used ===
1:34:02.122069 INFO: rt_error       : 1662.873046875
1:34:02.122119 INFO: mobility_error : 0.1
1:34:02.122163 INFO: num_candidates : 3
1:34:02.122203 INFO: ms1_error      : 30
1:34:02.122242 INFO: ms2_error      : 6.828943
1:34:02.122283 INFO: fwhm_rt        : 3.0
1:34:02.122329 INFO: quant_window   : 3
1:34:02.122369 INFO: ==============================================
1:34:02.162590 INFO: performing precursor FDR with 40 features
1:34:02.162686 INFO: Decoy channel: -1
1:34:02.162712 INFO: Competetive: True
1:34:02.166971 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:02.168823 INFO: Using random state 350080 for train-test-split
1:34:02.179681 INFO: Test AUC: 0.655
1:34:02.179745 INFO: Train AUC: 0.677
1:34:02.179777 INFO: AUC difference: 3.26%
1:34:02.392959 INFO: Resetting torch num_threads to 80
1:34:02.394547 PROGRESS: === Extracted 3549 precursors and 25762 fragments ===
1:34:02.394894 INFO: === FDR correction performed with classifier version 6 ===
1:34:02.395356 PROGRESS: ============================= Precursor FDR =============================
1:34:02.395444 PROGRESS: Total precursors accumulated: 413
1:34:02.395504 PROGRESS: Target precursors: 409 (99.03%)
1:34:02.395564 PROGRESS: Decoy precursors: 4 (0.97%)
1:34:02.395611 PROGRESS: 
1:34:02.395655 PROGRESS: Precursor Summary:
1:34:02.396590 PROGRESS: Channel   0:	 0.050 FDR:   409; 0.010 FDR:   409; 0.001 FDR:   327
1:34:02.396681 PROGRESS: 
1:34:02.396736 PROGRESS: Protein Summary:
1:34:02.397871 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   378; 0.001 FDR:   306
1:34:02.397965 PROGRESS: =========================================================================
1:34:02.398166 INFO: Target number of precursors reached.
1:34:02.402648 INFO: fragments_df: keeping 5000 of 25762 [sum(precursor_idx_mask)=10038 sum(mass_error_mask)=25762 stop_rank=5000
1:34:02.406777 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:02.530210 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:03.207623 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:03.208042 INFO: Using score_cutoff 14.095544574737549 (fac=0.99, q=1)
1:34:03.208333 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:03.208414 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:03.208469 INFO: Updating optimization_manager: score_cutoff        : 16.124298498344423 -> 14.095544574737549
1:34:03.208524 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:03.210076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:03.212426 INFO: === checking if optimization conditions were reached ===
1:34:03.214020 INFO: Updating optimization_manager: ms2_error           : 6.828943 -> 6.828943
1:34:03.214122 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:34:03.214186 PROGRESS: ✅ ms2_error      : 6.8289 <= 6.8289
1:34:03.214243 INFO: ==============================================
1:34:03.214316 PROGRESS: Optimization finished for ms2_error.
1:34:03.218242 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:03.219591 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:03.221801 INFO: Starting optimization step 0.
1:34:03.221900 PROGRESS: === Extracting elution groups 0 to 600 ===
1:34:03.221967 INFO: Using ng extraction backend
1:34:03.222026 PROGRESS: Extracting batch of 1183 precursors
1:34:03.225289 INFO: === Search parameters used ===
1:34:03.225384 INFO: rt_error       : 1662.873046875
1:34:03.225437 INFO: mobility_error : 0.1
1:34:03.225685 INFO: num_candidates : 3
1:34:03.225740 INFO: ms1_error      : 30
1:34:03.225783 INFO: ms2_error      : 6.828943
1:34:03.225825 INFO: fwhm_rt        : 3.0
1:34:03.225864 INFO: quant_window   : 3
1:34:03.225908 INFO: ==============================================
1:34:03.265556 INFO: performing precursor FDR with 40 features
1:34:03.265645 INFO: Decoy channel: -1
1:34:03.265671 INFO: Competetive: True
1:34:03.269484 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:03.271345 INFO: Using random state 348883 for train-test-split
1:34:03.282097 INFO: Test AUC: 0.667
1:34:03.282166 INFO: Train AUC: 0.676
1:34:03.282196 INFO: AUC difference: 1.25%
1:34:03.493265 INFO: Resetting torch num_threads to 80
1:34:03.494840 PROGRESS: === Extracted 3549 precursors and 25785 fragments ===
1:34:03.495183 INFO: === FDR correction performed with classifier version 7 ===
1:34:03.495648 PROGRESS: ============================= Precursor FDR =============================
1:34:03.495736 PROGRESS: Total precursors accumulated: 414
1:34:03.495794 PROGRESS: Target precursors: 410 (99.03%)
1:34:03.495843 PROGRESS: Decoy precursors: 4 (0.97%)
1:34:03.495893 PROGRESS: 
1:34:03.495936 PROGRESS: Precursor Summary:
1:34:03.496867 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   410; 0.001 FDR:   328
1:34:03.496965 PROGRESS: 
1:34:03.497020 PROGRESS: Protein Summary:
1:34:03.498168 PROGRESS: Channel   0:	 0.050 FDR:   379; 0.010 FDR:   379; 0.001 FDR:   307
1:34:03.498261 PROGRESS: =========================================================================
1:34:03.498462 INFO: Target number of precursors reached.
1:34:03.502945 INFO: fragments_df: keeping 5000 of 25785 [sum(precursor_idx_mask)=10069 sum(mass_error_mask)=25785 stop_rank=5000
1:34:03.507116 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:03.632427 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:04.307127 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:04.307554 INFO: Using score_cutoff 14.102887349796294 (fac=0.99, q=1)
1:34:04.307840 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:04.307920 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:04.307973 INFO: Updating optimization_manager: score_cutoff        : 14.095544574737549 -> 14.102887349796294
1:34:04.308023 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:04.309592 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:04.311947 INFO: === checking if optimization conditions were reached ===
1:34:04.312057 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:34:04.313567 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 10.900389743855452
1:34:04.313679 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 10.9004.
1:34:04.313746 INFO: ==============================================
1:34:04.313813 INFO: Starting optimization step 1.
1:34:04.313871 PROGRESS: === Extracting elution groups 0 to 600 ===
1:34:04.313927 INFO: Using ng extraction backend
1:34:04.313982 PROGRESS: Extracting batch of 1183 precursors
1:34:04.317416 INFO: === Search parameters used ===
1:34:04.317528 INFO: rt_error       : 10.900389743855452
1:34:04.317585 INFO: mobility_error : 0.1
1:34:04.317628 INFO: num_candidates : 3
1:34:04.317667 INFO: ms1_error      : 30
1:34:04.317708 INFO: ms2_error      : 6.828943
1:34:04.317750 INFO: fwhm_rt        : 3.0
1:34:04.317787 INFO: quant_window   : 3
1:34:04.317825 INFO: ==============================================
1:34:04.352128 INFO: performing precursor FDR with 40 features
1:34:04.352251 INFO: Decoy channel: -1
1:34:04.352278 INFO: Competetive: True
1:34:04.354865 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:04.356692 INFO: Using random state 348883 for train-test-split
1:34:04.370011 INFO: Test AUC: 0.660
1:34:04.370076 INFO: Train AUC: 0.675
1:34:04.370106 INFO: AUC difference: 2.16%
1:34:04.584315 INFO: Resetting torch num_threads to 80
1:34:04.585935 PROGRESS: === Extracted 3296 precursors and 21074 fragments ===
1:34:04.586287 INFO: === FDR correction performed with classifier version 7 ===
1:34:04.586779 PROGRESS: ============================= Precursor FDR =============================
1:34:04.586871 PROGRESS: Total precursors accumulated: 582
1:34:04.586930 PROGRESS: Target precursors: 577 (99.14%)
1:34:04.586978 PROGRESS: Decoy precursors: 5 (0.86%)
1:34:04.587024 PROGRESS: 
1:34:04.587068 PROGRESS: Precursor Summary:
1:34:04.588057 PROGRESS: Channel   0:	 0.050 FDR:   577; 0.010 FDR:   577; 0.001 FDR:   482
1:34:04.588155 PROGRESS: 
1:34:04.588210 PROGRESS: Protein Summary:
1:34:04.589445 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   525; 0.001 FDR:   441
1:34:04.589547 PROGRESS: =========================================================================
1:34:04.589751 INFO: Target number of precursors reached.
1:34:04.594137 INFO: fragments_df: keeping 5000 of 21074 [sum(precursor_idx_mask)=11475 sum(mass_error_mask)=21074 stop_rank=5000
1:34:04.598318 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:04.738178 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:05.415402 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:05.415840 INFO: Using score_cutoff 12.371459030914306 (fac=0.99, q=1)
1:34:05.416126 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:05.416208 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:05.416265 INFO: Updating optimization_manager: score_cutoff        : 14.102887349796294 -> 12.371459030914306
1:34:05.416329 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:05.417909 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:05.420257 INFO: === checking if optimization conditions were reached ===
1:34:05.420357 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:34:05.422039 INFO: Updating optimization_manager: rt_error            : 10.900389743855452 -> 18.030938812794407
1:34:05.422149 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 18.0309.
1:34:05.422219 INFO: ==============================================
1:34:05.422287 INFO: Starting optimization step 2.
1:34:05.422348 PROGRESS: === Extracting elution groups 0 to 600 ===
1:34:05.422408 INFO: Using ng extraction backend
1:34:05.422472 PROGRESS: Extracting batch of 1183 precursors
1:34:05.425822 INFO: === Search parameters used ===
1:34:05.425914 INFO: rt_error       : 18.030938812794407
1:34:05.425966 INFO: mobility_error : 0.1
1:34:05.426012 INFO: num_candidates : 3
1:34:05.426062 INFO: ms1_error      : 30
1:34:05.426108 INFO: ms2_error      : 6.828943
1:34:05.426151 INFO: fwhm_rt        : 3.0
1:34:05.426192 INFO: quant_window   : 3
1:34:05.426233 INFO: ==============================================
1:34:05.457859 INFO: performing precursor FDR with 40 features
1:34:05.457942 INFO: Decoy channel: -1
1:34:05.457969 INFO: Competetive: True
1:34:05.460611 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:05.462440 INFO: Using random state 348883 for train-test-split
1:34:05.475118 INFO: Test AUC: 0.656
1:34:05.475185 INFO: Train AUC: 0.678
1:34:05.475215 INFO: AUC difference: 3.31%
1:34:05.688378 INFO: Resetting torch num_threads to 80
1:34:05.689969 PROGRESS: === Extracted 3290 precursors and 21049 fragments ===
1:34:05.690316 INFO: === FDR correction performed with classifier version 7 ===
1:34:05.690783 PROGRESS: ============================= Precursor FDR =============================
1:34:05.690871 PROGRESS: Total precursors accumulated: 582
1:34:05.690929 PROGRESS: Target precursors: 577 (99.14%)
1:34:05.690975 PROGRESS: Decoy precursors: 5 (0.86%)
1:34:05.691025 PROGRESS: 
1:34:05.691069 PROGRESS: Precursor Summary:
1:34:05.692032 PROGRESS: Channel   0:	 0.050 FDR:   577; 0.010 FDR:   577; 0.001 FDR:   481
1:34:05.692122 PROGRESS: 
1:34:05.692177 PROGRESS: Protein Summary:
1:34:05.693390 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   525; 0.001 FDR:   440
1:34:05.693496 PROGRESS: =========================================================================
1:34:05.693694 INFO: Target number of precursors reached.
1:34:05.698106 INFO: fragments_df: keeping 5000 of 21049 [sum(precursor_idx_mask)=11463 sum(mass_error_mask)=21049 stop_rank=5000
1:34:05.702267 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:05.843462 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:06.525183 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:06.525919 INFO: Using score_cutoff 12.371459030914306 (fac=0.99, q=1)
1:34:06.526206 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:06.526287 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:06.526341 INFO: Updating optimization_manager: score_cutoff        : 12.371459030914306 -> 12.371459030914306
1:34:06.526392 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:06.527939 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:06.530273 INFO: === checking if optimization conditions were reached ===
1:34:06.530373 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:34:06.532130 INFO: Updating optimization_manager: rt_error            : 18.030938812794407 -> 19.343254840168033
1:34:06.532230 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 19.3433.
1:34:06.532294 INFO: ==============================================
1:34:06.532367 INFO: Starting optimization step 3.
1:34:06.532430 PROGRESS: === Extracting elution groups 0 to 600 ===
1:34:06.532490 INFO: Using ng extraction backend
1:34:06.532543 PROGRESS: Extracting batch of 1183 precursors
1:34:06.535886 INFO: === Search parameters used ===
1:34:06.535974 INFO: rt_error       : 19.343254840168033
1:34:06.536025 INFO: mobility_error : 0.1
1:34:06.536068 INFO: num_candidates : 3
1:34:06.536107 INFO: ms1_error      : 30
1:34:06.536148 INFO: ms2_error      : 6.828943
1:34:06.536187 INFO: fwhm_rt        : 3.0
1:34:06.536225 INFO: quant_window   : 3
1:34:06.536263 INFO: ==============================================
1:34:06.567597 INFO: performing precursor FDR with 40 features
1:34:06.567678 INFO: Decoy channel: -1
1:34:06.567704 INFO: Competetive: True
1:34:06.571509 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:06.573350 INFO: Using random state 348883 for train-test-split
1:34:06.585506 INFO: Test AUC: 0.701
1:34:06.585577 INFO: Train AUC: 0.668
1:34:06.585606 INFO: AUC difference: 4.98%
1:34:06.798695 INFO: Resetting torch num_threads to 80
1:34:06.800318 PROGRESS: === Extracted 3291 precursors and 21054 fragments ===
1:34:06.800658 INFO: === FDR correction performed with classifier version 7 ===
1:34:06.801131 PROGRESS: ============================= Precursor FDR =============================
1:34:06.801220 PROGRESS: Total precursors accumulated: 582
1:34:06.801280 PROGRESS: Target precursors: 577 (99.14%)
1:34:06.801328 PROGRESS: Decoy precursors: 5 (0.86%)
1:34:06.801375 PROGRESS: 
1:34:06.801418 PROGRESS: Precursor Summary:
1:34:06.802412 PROGRESS: Channel   0:	 0.050 FDR:   577; 0.010 FDR:   577; 0.001 FDR:   481
1:34:06.802508 PROGRESS: 
1:34:06.802571 PROGRESS: Protein Summary:
1:34:06.803785 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   525; 0.001 FDR:   441
1:34:06.803879 PROGRESS: =========================================================================
1:34:06.804084 INFO: Target number of precursors reached.
1:34:06.808453 INFO: fragments_df: keeping 5000 of 21054 [sum(precursor_idx_mask)=11462 sum(mass_error_mask)=21054 stop_rank=5000
1:34:06.812599 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:06.955193 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:07.625854 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:07.626266 INFO: Using score_cutoff 12.371459030914306 (fac=0.99, q=1)
1:34:07.626549 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:07.626631 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:07.626685 INFO: Updating optimization_manager: score_cutoff        : 12.371459030914306 -> 12.371459030914306
1:34:07.626735 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:07.628289 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:07.630650 INFO: === checking if optimization conditions were reached ===
1:34:07.630749 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:34:07.632489 INFO: Updating optimization_manager: rt_error            : 19.343254840168033 -> 19.363640077554166
1:34:07.632588 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 19.3636.
1:34:07.632660 INFO: ==============================================
1:34:07.632726 INFO: Starting optimization step 4.
1:34:07.632784 PROGRESS: === Extracting elution groups 0 to 600 ===
1:34:07.632840 INFO: Using ng extraction backend
1:34:07.632893 PROGRESS: Extracting batch of 1183 precursors
1:34:07.636281 INFO: === Search parameters used ===
1:34:07.636371 INFO: rt_error       : 19.363640077554166
1:34:07.636421 INFO: mobility_error : 0.1
1:34:07.636467 INFO: num_candidates : 3
1:34:07.636510 INFO: ms1_error      : 30
1:34:07.636550 INFO: ms2_error      : 6.828943
1:34:07.636589 INFO: fwhm_rt        : 3.0
1:34:07.636627 INFO: quant_window   : 3
1:34:07.636666 INFO: ==============================================
1:34:07.668833 INFO: performing precursor FDR with 40 features
1:34:07.668955 INFO: Decoy channel: -1
1:34:07.668983 INFO: Competetive: True
1:34:07.673367 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:07.675197 INFO: Using random state 348883 for train-test-split
1:34:07.687607 INFO: Test AUC: 0.694
1:34:07.687676 INFO: Train AUC: 0.670
1:34:07.687707 INFO: AUC difference: 3.67%
1:34:07.902053 INFO: Resetting torch num_threads to 80
1:34:07.903975 PROGRESS: === Extracted 3288 precursors and 21042 fragments ===
1:34:07.904370 INFO: === FDR correction performed with classifier version 7 ===
1:34:07.904847 PROGRESS: ============================= Precursor FDR =============================
1:34:07.904934 PROGRESS: Total precursors accumulated: 516
1:34:07.904994 PROGRESS: Target precursors: 511 (99.03%)
1:34:07.905043 PROGRESS: Decoy precursors: 5 (0.97%)
1:34:07.905090 PROGRESS: 
1:34:07.905133 PROGRESS: Precursor Summary:
1:34:07.906154 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   511; 0.001 FDR:   481
1:34:07.906249 PROGRESS: 
1:34:07.906306 PROGRESS: Protein Summary:
1:34:07.907517 PROGRESS: Channel   0:	 0.050 FDR:   466; 0.010 FDR:   466; 0.001 FDR:   442
1:34:07.907609 PROGRESS: =========================================================================
1:34:07.907825 INFO: Target number of precursors reached.
1:34:07.912313 INFO: fragments_df: keeping 5000 of 21042 [sum(precursor_idx_mask)=10381 sum(mass_error_mask)=21042 stop_rank=5000
1:34:07.918413 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:08.054026 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:08.726524 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:08.726953 INFO: Using score_cutoff 13.486723408699035 (fac=0.99, q=1)
1:34:08.727247 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:08.727328 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:08.727382 INFO: Updating optimization_manager: score_cutoff        : 12.371459030914306 -> 13.486723408699035
1:34:08.727439 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:08.729027 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:08.731456 INFO: === checking if optimization conditions were reached ===
1:34:08.731561 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:34:08.732480 INFO: Updating optimization_manager: rt_error            : 19.363640077554166 -> 10.900389743855452
1:34:08.732614 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
1:34:08.732710 INFO: Updating optimization_manager: score_cutoff        : 13.486723408699035 -> 12.371459030914306
1:34:08.732798 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:08.732884 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:08.732966 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 10.9004 found after 5 searches.
1:34:08.733029 INFO: ==============================================
1:34:08.733093 PROGRESS: Optimization finished for rt_error.
1:34:08.737343 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:08.738696 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:08.765902 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:34:08.766056 PROGRESS: ==============================================
1:34:08.766125 PROGRESS: ms2_error      : 6.8289
1:34:08.766182 PROGRESS: rt_error       : 10.9004
1:34:08.766231 PROGRESS: ==============================================
1:34:08.766958 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:08.851906 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:09.080712 INFO: Using ng extraction backend
1:34:09.081044 PROGRESS: Extracting batch of 146144 precursors
1:34:09.317479 INFO: === Search parameters used ===
1:34:09.317859 INFO: rt_error       : 10.900389743855452
1:34:09.317936 INFO: mobility_error : 0.1
1:34:09.317992 INFO: num_candidates : 3
1:34:09.318038 INFO: ms1_error      : 30
1:34:09.318081 INFO: ms2_error      : 6.828943
1:34:09.318122 INFO: fwhm_rt        : 3.0
1:34:09.318163 INFO: quant_window   : 3
1:34:09.318206 INFO: ==============================================
1:34:09.488361 INFO: Removed 175648 precursors with score below cutoff 12.371459030914306
1:34:09.726613 INFO: performing precursor FDR with 40 features
1:34:09.726741 INFO: Decoy channel: -1
1:34:09.726768 INFO: Competetive: True
1:34:09.755430 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:09.774237 WARNING: FDR calculation for 135790 target and 94380 decoy PSMs
1:34:09.774385 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:34:09.814085 INFO: Using random state 151090 for train-test-split
1:34:12.817476 INFO: Test AUC: 0.839
1:34:12.817614 INFO: Train AUC: 0.842
1:34:12.817645 INFO: AUC difference: 0.44%
1:34:13.112658 INFO: Resetting torch num_threads to 80
1:34:13.327922 PROGRESS: ============================= Precursor FDR =============================
1:34:13.328190 PROGRESS: Total precursors accumulated: 70,434
1:34:13.328254 PROGRESS: Target precursors: 69,737 (99.01%)
1:34:13.328307 PROGRESS: Decoy precursors: 697 (0.99%)
1:34:13.328356 PROGRESS: 
1:34:13.328400 PROGRESS: Precursor Summary:
1:34:13.349257 PROGRESS: Channel   0:	 0.050 FDR: 69,737; 0.010 FDR: 69,737; 0.001 FDR: 67,264
1:34:13.349695 PROGRESS: 
1:34:13.349764 PROGRESS: Protein Summary:
1:34:13.379783 PROGRESS: Channel   0:	 0.050 FDR: 7,033; 0.010 FDR: 7,033; 0.001 FDR: 7,007
1:34:13.380048 PROGRESS: =========================================================================
1:34:13.381733 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/psm.parquet
1:34:13.517844 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/frag.parquet
1:34:13.720009 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
1:34:13.757710 PROGRESS: 
1:34:13.757857 INFO: Quantification results path: alphadia_zenoswath8600/quant
1:34:13.757935 INFO: Creating folder alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/figures
1:34:13.758123 INFO: Initializing TimingManager
1:34:13.758929 INFO: Initializing RawFileManager
1:36:41.288187 INFO: Determining DIA cycle
1:36:41.303130 INFO: Found cycle with start 0.00 min and length 86.
1:36:41.594222 INFO: RT (min)            : 0.0 - 55.4
1:36:41.594316 INFO: RT duration (sec)   : 3325.6
1:36:41.594345 INFO: RT duration (min)   : 55.4
1:36:41.594371 INFO: Cycle len (scans)   : 86
1:36:41.594391 INFO: Cycle len (sec)     : 1.90
1:36:41.594409 INFO: Number of cycles    : 1747
1:36:41.594430 INFO: MS2 range (m/z)     : 399.5 - 903.5
1:36:41.594474 INFO: Creating DIA data object took: 147.8354434967041
1:36:42.754531 INFO: Creating DIA data NG object took: 1.1599128246307373
1:36:42.791148 INFO: Initializing CalibrationManager
1:36:42.791589 INFO: Setting up calibration estimators ..
1:36:42.791654 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:36:42.791746 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'}' ..
1:36:42.791830 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:36:42.791883 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:36:42.791935 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}}' ..
1:36:42.791987 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:36:42.792048 INFO: Done setting up calibration estimators.
1:36:42.792193 INFO: Initializing OptimizationManager
1:36:42.792325 INFO: initial parameter: ms1_error = 30
1:36:42.792378 INFO: initial parameter: ms2_error = 30
1:36:42.792424 INFO: initial parameter: rt_error = 1662.8485107421875
1:36:42.792468 INFO: initial parameter: mobility_error = 0.1
1:36:42.792511 INFO: initial parameter: num_candidates = 1
1:36:42.792551 INFO: initial parameter: fwhm_rt = 5
1:36:42.792591 INFO: initial parameter: fwhm_mobility = 0.01
1:36:42.792629 INFO: initial parameter: score_cutoff = 0
1:36:42.792671 INFO: initial parameter: classifier_version = -1
1:36:42.792745 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
1:36:42.793021 INFO: FDRManager: loading saved state not requested, will be initialized.
1:36:42.793057 INFO: Initializing FDRManager
1:36:42.793093 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:36:42.817142 PROGRESS: Initializing spectral library: 73,874 target precursors potentially observable (0 removed)
1:36:42.831967 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:36:42.832350 INFO: Updating optimization_manager: rt_error            : 1662.8485107421875 -> 1662.8485107421875
1:36:42.832452 PROGRESS: Starting initial search for precursors.
1:36:42.832540 INFO: Starting optimization step 0.
1:36:42.832607 PROGRESS: === Extracting elution groups 0 to 200 ===
1:36:42.832668 INFO: Using ng extraction backend
1:36:42.832736 PROGRESS: Extracting batch of 394 precursors
1:36:42.835205 INFO: === Search parameters used ===
1:36:42.835395 INFO: rt_error       : 1662.8485107421875
1:36:42.835452 INFO: mobility_error : 0.1
1:36:42.835498 INFO: num_candidates : 1
1:36:42.835542 INFO: ms1_error      : 30
1:36:42.835583 INFO: ms2_error      : 30
1:36:42.835624 INFO: fwhm_rt        : 5
1:36:42.835664 INFO: quant_window   : 3
1:36:42.835705 INFO: ==============================================
1:36:42.857305 INFO: performing precursor FDR with 40 features
1:36:42.857375 INFO: Decoy channel: -1
1:36:42.857401 INFO: Competetive: True
1:36:42.858422 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:42.860889 INFO: Using random state 231209 for train-test-split
1:36:42.868539 INFO: Test AUC: 0.503
1:36:42.868593 INFO: Train AUC: 0.484
1:36:42.868624 INFO: AUC difference: 3.88%
1:36:43.078679 INFO: Resetting torch num_threads to 80
1:36:43.079957 PROGRESS: === Extracted 394 precursors and 3038 fragments ===
1:36:43.080299 INFO: === FDR correction performed with classifier version -1 ===
1:36:43.080726 PROGRESS: ============================= Precursor FDR =============================
1:36:43.080811 PROGRESS: Total precursors accumulated: 0
1:36:43.080870 PROGRESS: Target precursors: 0 (0.00%)
1:36:43.080920 PROGRESS: Decoy precursors: 0 (0.00%)
1:36:43.080966 PROGRESS: 
1:36:43.081010 PROGRESS: Precursor Summary:
1:36:43.081119 PROGRESS: 
1:36:43.081182 PROGRESS: Protein Summary:
1:36:43.081252 PROGRESS: =========================================================================
1:36:43.081418 INFO: Target number of precursors not reached yet.
1:36:43.084682 INFO: Starting optimization step 1.
1:36:43.084796 PROGRESS: === Extracting elution groups 200 to 600 ===
1:36:43.084869 INFO: Using ng extraction backend
1:36:43.084928 PROGRESS: Extracting batch of 789 precursors
1:36:43.087505 INFO: === Search parameters used ===
1:36:43.087613 INFO: rt_error       : 1662.8485107421875
1:36:43.087664 INFO: mobility_error : 0.1
1:36:43.087711 INFO: num_candidates : 1
1:36:43.087754 INFO: ms1_error      : 30
1:36:43.087795 INFO: ms2_error      : 30
1:36:43.087837 INFO: fwhm_rt        : 5
1:36:43.087883 INFO: quant_window   : 3
1:36:43.087927 INFO: ==============================================
1:36:43.112431 INFO: performing precursor FDR with 40 features
1:36:43.112510 INFO: Decoy channel: -1
1:36:43.112538 INFO: Competetive: True
1:36:43.115411 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:43.116909 INFO: Using random state 960013 for train-test-split
1:36:43.125496 INFO: Test AUC: 0.460
1:36:43.125557 INFO: Train AUC: 0.500
1:36:43.125589 INFO: AUC difference: 8.07%
1:36:43.125613 WARNING: AUC difference > 5%. This may indicate overfitting.
1:36:43.333115 INFO: Resetting torch num_threads to 80
1:36:43.335278 PROGRESS: === Extracted 1183 precursors and 9335 fragments ===
1:36:43.335642 INFO: === FDR correction performed with classifier version -1 ===
1:36:43.336080 PROGRESS: ============================= Precursor FDR =============================
1:36:43.336170 PROGRESS: Total precursors accumulated: 0
1:36:43.336234 PROGRESS: Target precursors: 0 (0.00%)
1:36:43.336287 PROGRESS: Decoy precursors: 0 (0.00%)
1:36:43.336339 PROGRESS: 
1:36:43.336388 PROGRESS: Precursor Summary:
1:36:43.336499 PROGRESS: 
1:36:43.336566 PROGRESS: Protein Summary:
1:36:43.336654 PROGRESS: =========================================================================
1:36:43.336852 INFO: Target number of precursors not reached yet.
1:36:43.340997 INFO: Starting optimization step 2.
1:36:43.341112 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:36:43.341189 INFO: Using ng extraction backend
1:36:43.341250 PROGRESS: Extracting batch of 1588 precursors
1:36:43.345296 INFO: === Search parameters used ===
1:36:43.345402 INFO: rt_error       : 1662.8485107421875
1:36:43.345459 INFO: mobility_error : 0.1
1:36:43.345525 INFO: num_candidates : 1
1:36:43.345574 INFO: ms1_error      : 30
1:36:43.345624 INFO: ms2_error      : 30
1:36:43.345669 INFO: fwhm_rt        : 5
1:36:43.345711 INFO: quant_window   : 3
1:36:43.345755 INFO: ==============================================
1:36:43.381531 INFO: performing precursor FDR with 40 features
1:36:43.381621 INFO: Decoy channel: -1
1:36:43.381649 INFO: Competetive: True
1:36:43.385802 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:43.387671 INFO: Using random state 208764 for train-test-split
1:36:43.399211 INFO: Test AUC: 0.491
1:36:43.399271 INFO: Train AUC: 0.493
1:36:43.399300 INFO: AUC difference: 0.36%
1:36:43.616338 INFO: Resetting torch num_threads to 80
1:36:43.618877 PROGRESS: === Extracted 2771 precursors and 21921 fragments ===
1:36:43.619339 INFO: === FDR correction performed with classifier version -1 ===
1:36:43.619765 PROGRESS: ============================= Precursor FDR =============================
1:36:43.619852 PROGRESS: Total precursors accumulated: 0
1:36:43.619911 PROGRESS: Target precursors: 0 (0.00%)
1:36:43.619960 PROGRESS: Decoy precursors: 0 (0.00%)
1:36:43.620010 PROGRESS: 
1:36:43.620064 PROGRESS: Precursor Summary:
1:36:43.620173 PROGRESS: 
1:36:43.620234 PROGRESS: Protein Summary:
1:36:43.620306 PROGRESS: =========================================================================
1:36:43.620505 INFO: Target number of precursors not reached yet.
1:36:43.626467 INFO: Starting optimization step 3.
1:36:43.626595 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:36:43.626665 INFO: Using ng extraction backend
1:36:43.626723 PROGRESS: Extracting batch of 3164 precursors
1:36:43.633477 INFO: === Search parameters used ===
1:36:43.633599 INFO: rt_error       : 1662.8485107421875
1:36:43.633650 INFO: mobility_error : 0.1
1:36:43.633696 INFO: num_candidates : 1
1:36:43.633737 INFO: ms1_error      : 30
1:36:43.633782 INFO: ms2_error      : 30
1:36:43.633824 INFO: fwhm_rt        : 5
1:36:43.633864 INFO: quant_window   : 3
1:36:43.633903 INFO: ==============================================
1:36:43.687844 INFO: performing precursor FDR with 40 features
1:36:43.687949 INFO: Decoy channel: -1
1:36:43.687978 INFO: Competetive: True
1:36:43.691915 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:43.694467 INFO: Using random state 799913 for train-test-split
1:36:43.714539 INFO: Test AUC: 0.484
1:36:43.714616 INFO: Train AUC: 0.499
1:36:43.714646 INFO: AUC difference: 3.12%
1:36:43.925383 INFO: Resetting torch num_threads to 80
1:36:43.928639 PROGRESS: === Extracted 5935 precursors and 47047 fragments ===
1:36:43.929036 INFO: === FDR correction performed with classifier version -1 ===
1:36:43.929475 PROGRESS: ============================= Precursor FDR =============================
1:36:43.929573 PROGRESS: Total precursors accumulated: 0
1:36:43.929634 PROGRESS: Target precursors: 0 (0.00%)
1:36:43.929682 PROGRESS: Decoy precursors: 0 (0.00%)
1:36:43.929729 PROGRESS: 
1:36:43.929773 PROGRESS: Precursor Summary:
1:36:43.929880 PROGRESS: 
1:36:43.929941 PROGRESS: Protein Summary:
1:36:43.930015 PROGRESS: =========================================================================
1:36:43.930242 INFO: Target number of precursors not reached yet.
1:36:43.939092 INFO: Starting optimization step 4.
1:36:43.939221 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:36:43.939293 INFO: Using ng extraction backend
1:36:43.939356 PROGRESS: Extracting batch of 6329 precursors
1:36:43.951321 INFO: === Search parameters used ===
1:36:43.951521 INFO: rt_error       : 1662.8485107421875
1:36:43.951575 INFO: mobility_error : 0.1
1:36:43.951619 INFO: num_candidates : 1
1:36:43.951663 INFO: ms1_error      : 30
1:36:43.951706 INFO: ms2_error      : 30
1:36:43.951745 INFO: fwhm_rt        : 5
1:36:43.951787 INFO: quant_window   : 3
1:36:43.951825 INFO: ==============================================
1:36:44.041349 INFO: performing precursor FDR with 40 features
1:36:44.041472 INFO: Decoy channel: -1
1:36:44.041499 INFO: Competetive: True
1:36:44.046789 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:44.050202 INFO: Using random state 130349 for train-test-split
1:36:44.085625 INFO: Test AUC: 0.489
1:36:44.085750 INFO: Train AUC: 0.502
1:36:44.085779 INFO: AUC difference: 2.65%
1:36:44.301903 INFO: Resetting torch num_threads to 80
1:36:44.306060 PROGRESS: === Extracted 12264 precursors and 96853 fragments ===
1:36:44.306433 INFO: === FDR correction performed with classifier version -1 ===
1:36:44.306895 PROGRESS: ============================= Precursor FDR =============================
1:36:44.306985 PROGRESS: Total precursors accumulated: 1
1:36:44.307046 PROGRESS: Target precursors: 1 (100.00%)
1:36:44.307096 PROGRESS: Decoy precursors: 0 (0.00%)
1:36:44.307147 PROGRESS: 
1:36:44.307192 PROGRESS: Precursor Summary:
1:36:44.308105 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:36:44.308202 PROGRESS: 
1:36:44.308257 PROGRESS: Protein Summary:
1:36:44.309265 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:36:44.309354 PROGRESS: =========================================================================
1:36:44.309635 INFO: Target number of precursors not reached yet.
1:36:44.321863 INFO: Starting optimization step 5.
1:36:44.322068 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:36:44.322147 INFO: Using ng extraction backend
1:36:44.322213 PROGRESS: Extracting batch of 12652 precursors
1:36:44.345957 INFO: === Search parameters used ===
1:36:44.346185 INFO: rt_error       : 1662.8485107421875
1:36:44.346240 INFO: mobility_error : 0.1
1:36:44.346285 INFO: num_candidates : 1
1:36:44.346348 INFO: ms1_error      : 30
1:36:44.346393 INFO: ms2_error      : 30
1:36:44.346433 INFO: fwhm_rt        : 5
1:36:44.346474 INFO: quant_window   : 3
1:36:44.346513 INFO: ==============================================
1:36:44.500385 INFO: performing precursor FDR with 40 features
1:36:44.500504 INFO: Decoy channel: -1
1:36:44.500531 INFO: Competetive: True
1:36:44.508977 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:44.514779 INFO: Using random state 862241 for train-test-split
1:36:44.753493 INFO: Test AUC: 0.863
1:36:44.753613 INFO: Train AUC: 0.855
1:36:44.753644 INFO: AUC difference: 0.93%
1:36:46.910271 INFO: Resetting torch num_threads to 80
1:36:46.917619 PROGRESS: === Extracted 24912 precursors and 196676 fragments ===
1:36:46.918063 INFO: === FDR correction performed with classifier version -1 ===
1:36:46.919337 PROGRESS: ============================= Precursor FDR =============================
1:36:46.919430 PROGRESS: Total precursors accumulated: 7,134
1:36:46.919499 PROGRESS: Target precursors: 7,064 (99.02%)
1:36:46.919549 PROGRESS: Decoy precursors: 70 (0.98%)
1:36:46.919594 PROGRESS: 
1:36:46.919639 PROGRESS: Precursor Summary:
1:36:46.922565 PROGRESS: Channel   0:	 0.050 FDR: 7,064; 0.010 FDR: 7,064; 0.001 FDR: 4,635
1:36:46.922710 PROGRESS: 
1:36:46.922771 PROGRESS: Protein Summary:
1:36:46.926782 PROGRESS: Channel   0:	 0.050 FDR: 3,246; 0.010 FDR: 3,246; 0.001 FDR: 2,386
1:36:46.926898 PROGRESS: =========================================================================
1:36:46.927282 INFO: Target number of precursors reached.
1:36:46.961963 INFO: fragments_df: keeping 5000 of 196676 [sum(precursor_idx_mask)=75383 sum(mass_error_mask)=196676 stop_rank=5000
1:36:46.967690 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:48.074026 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:48.753681 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:36:48.754157 INFO: Using score_cutoff 15.323661933803558 (fac=0.99, q=1)
1:36:48.754513 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:36:48.754595 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:36:48.754650 INFO: Updating optimization_manager: score_cutoff        : 0 -> 15.323661933803558
1:36:48.754702 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:48.756259 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:48.758511 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
1:36:48.758608 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:36:48.758683 INFO: Starting optimization step 6.
1:36:48.758744 PROGRESS: === Extracting elution groups 0 to 600 ===
1:36:48.758802 INFO: Using ng extraction backend
1:36:48.758857 PROGRESS: Extracting batch of 1183 precursors
1:36:48.762167 INFO: === Search parameters used ===
1:36:48.762265 INFO: rt_error       : 1662.8485107421875
1:36:48.762316 INFO: mobility_error : 0.1
1:36:48.762361 INFO: num_candidates : 3
1:36:48.762403 INFO: ms1_error      : 30
1:36:48.762444 INFO: ms2_error      : 30
1:36:48.762494 INFO: fwhm_rt        : 3.0
1:36:48.762537 INFO: quant_window   : 3
1:36:48.762580 INFO: ==============================================
1:36:48.803178 INFO: performing precursor FDR with 40 features
1:36:48.803275 INFO: Decoy channel: -1
1:36:48.803301 INFO: Competetive: True
1:36:48.806084 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:48.808001 INFO: Using random state 740097 for train-test-split
1:36:48.820236 INFO: Test AUC: 0.662
1:36:48.820311 INFO: Train AUC: 0.685
1:36:48.820340 INFO: AUC difference: 3.36%
1:36:49.034343 INFO: Resetting torch num_threads to 80
1:36:49.035944 PROGRESS: === Extracted 3549 precursors and 24497 fragments ===
1:36:49.036282 INFO: === FDR correction performed with classifier version 5 ===
1:36:49.036768 PROGRESS: ============================= Precursor FDR =============================
1:36:49.036857 PROGRESS: Total precursors accumulated: 366
1:36:49.036918 PROGRESS: Target precursors: 363 (99.18%)
1:36:49.036968 PROGRESS: Decoy precursors: 3 (0.82%)
1:36:49.037017 PROGRESS: 
1:36:49.037062 PROGRESS: Precursor Summary:
1:36:49.038026 PROGRESS: Channel   0:	 0.050 FDR:   363; 0.010 FDR:   363; 0.001 FDR:   317
1:36:49.038125 PROGRESS: 
1:36:49.038182 PROGRESS: Protein Summary:
1:36:49.039335 PROGRESS: Channel   0:	 0.050 FDR:   340; 0.010 FDR:   340; 0.001 FDR:   300
1:36:49.039426 PROGRESS: =========================================================================
1:36:49.039851 INFO: Target number of precursors reached.
1:36:49.044224 INFO: fragments_df: keeping 4796 of 24497 [sum(precursor_idx_mask)=8611 sum(mass_error_mask)=24497 stop_rank=4796
1:36:49.048543 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:49.174975 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:49.820484 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:49.820915 INFO: Using score_cutoff 16.04123695678711 (fac=0.99, q=1)
1:36:49.821204 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:49.821285 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:49.821340 INFO: Updating optimization_manager: score_cutoff        : 15.323661933803558 -> 16.04123695678711
1:36:49.821392 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:49.822982 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:49.825407 INFO: === checking if optimization conditions were reached ===
1:36:49.827125 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.828943
1:36:49.827231 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
1:36:49.827293 PROGRESS: ❌ ms2_error      : 6.8289 > 6.8289 or insufficient steps taken.
1:36:49.827352 INFO: ==============================================
1:36:49.827415 INFO: Starting optimization step 7.
1:36:49.827470 PROGRESS: === Extracting elution groups 0 to 600 ===
1:36:49.827527 INFO: Using ng extraction backend
1:36:49.827583 PROGRESS: Extracting batch of 1183 precursors
1:36:49.830952 INFO: === Search parameters used ===
1:36:49.831047 INFO: rt_error       : 1662.8485107421875
1:36:49.831098 INFO: mobility_error : 0.1
1:36:49.831142 INFO: num_candidates : 3
1:36:49.831184 INFO: ms1_error      : 30
1:36:49.831233 INFO: ms2_error      : 6.828943
1:36:49.831275 INFO: fwhm_rt        : 3.0
1:36:49.831315 INFO: quant_window   : 3
1:36:49.831355 INFO: ==============================================
1:36:49.871752 INFO: performing precursor FDR with 40 features
1:36:49.871832 INFO: Decoy channel: -1
1:36:49.871857 INFO: Competetive: True
1:36:49.876505 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:49.878422 INFO: Using random state 240293 for train-test-split
1:36:49.890282 INFO: Test AUC: 0.691
1:36:49.890350 INFO: Train AUC: 0.678
1:36:49.890379 INFO: AUC difference: 1.84%
1:36:50.103313 INFO: Resetting torch num_threads to 80
1:36:50.104903 PROGRESS: === Extracted 3549 precursors and 25880 fragments ===
1:36:50.105243 INFO: === FDR correction performed with classifier version 6 ===
1:36:50.105722 PROGRESS: ============================= Precursor FDR =============================
1:36:50.105815 PROGRESS: Total precursors accumulated: 350
1:36:50.105874 PROGRESS: Target precursors: 347 (99.14%)
1:36:50.105924 PROGRESS: Decoy precursors: 3 (0.86%)
1:36:50.105971 PROGRESS: 
1:36:50.106016 PROGRESS: Precursor Summary:
1:36:50.106987 PROGRESS: Channel   0:	 0.050 FDR:   347; 0.010 FDR:   347; 0.001 FDR:   288
1:36:50.107078 PROGRESS: 
1:36:50.107134 PROGRESS: Protein Summary:
1:36:50.108310 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   322; 0.001 FDR:   273
1:36:50.108401 PROGRESS: =========================================================================
1:36:50.108608 INFO: Target number of precursors reached.
1:36:50.112907 INFO: fragments_df: keeping 4812 of 25880 [sum(precursor_idx_mask)=8645 sum(mass_error_mask)=25880 stop_rank=4812
1:36:50.117061 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:50.241812 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:50.887973 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:50.888384 INFO: Using score_cutoff 14.794350888633728 (fac=0.99, q=1)
1:36:50.888670 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:50.888751 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:50.888806 INFO: Updating optimization_manager: score_cutoff        : 16.04123695678711 -> 14.794350888633728
1:36:50.888858 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:50.890455 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:50.892832 INFO: === checking if optimization conditions were reached ===
1:36:50.894438 INFO: Updating optimization_manager: ms2_error           : 6.828943 -> 6.828943
1:36:50.894544 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:36:50.894887 PROGRESS: ✅ ms2_error      : 6.8289 <= 6.8289
1:36:50.894948 INFO: ==============================================
1:36:50.895010 PROGRESS: Optimization finished for ms2_error.
1:36:50.899038 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:50.900399 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:50.902677 INFO: Starting optimization step 0.
1:36:50.902775 PROGRESS: === Extracting elution groups 0 to 600 ===
1:36:50.902843 INFO: Using ng extraction backend
1:36:50.902900 PROGRESS: Extracting batch of 1183 precursors
1:36:50.906310 INFO: === Search parameters used ===
1:36:50.906434 INFO: rt_error       : 1662.8485107421875
1:36:50.906485 INFO: mobility_error : 0.1
1:36:50.906529 INFO: num_candidates : 3
1:36:50.906574 INFO: ms1_error      : 30
1:36:50.906615 INFO: ms2_error      : 6.828943
1:36:50.906653 INFO: fwhm_rt        : 3.0
1:36:50.906693 INFO: quant_window   : 3
1:36:50.906732 INFO: ==============================================
1:36:50.948556 INFO: performing precursor FDR with 40 features
1:36:50.948654 INFO: Decoy channel: -1
1:36:50.948681 INFO: Competetive: True
1:36:50.951421 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:50.953325 INFO: Using random state 479284 for train-test-split
1:36:50.964376 INFO: Test AUC: 0.686
1:36:50.964443 INFO: Train AUC: 0.679
1:36:50.964473 INFO: AUC difference: 0.99%
1:36:51.178315 INFO: Resetting torch num_threads to 80
1:36:51.179911 PROGRESS: === Extracted 3549 precursors and 25889 fragments ===
1:36:51.180251 INFO: === FDR correction performed with classifier version 7 ===
1:36:51.180709 PROGRESS: ============================= Precursor FDR =============================
1:36:51.180799 PROGRESS: Total precursors accumulated: 351
1:36:51.180859 PROGRESS: Target precursors: 348 (99.15%)
1:36:51.180910 PROGRESS: Decoy precursors: 3 (0.85%)
1:36:51.180956 PROGRESS: 
1:36:51.181001 PROGRESS: Precursor Summary:
1:36:51.181968 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   288
1:36:51.182068 PROGRESS: 
1:36:51.182124 PROGRESS: Protein Summary:
1:36:51.183244 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   322; 0.001 FDR:   274
1:36:51.183335 PROGRESS: =========================================================================
1:36:51.183568 INFO: Target number of precursors reached.
1:36:51.187879 INFO: fragments_df: keeping 4823 of 25889 [sum(precursor_idx_mask)=8672 sum(mass_error_mask)=25889 stop_rank=4823
1:36:51.192062 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:51.317877 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:52.020971 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:52.022573 INFO: Using score_cutoff 14.797290753650666 (fac=0.99, q=1)
1:36:52.022860 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:52.022941 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:52.022998 INFO: Updating optimization_manager: score_cutoff        : 14.794350888633728 -> 14.797290753650666
1:36:52.023052 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:52.024632 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:52.027038 INFO: === checking if optimization conditions were reached ===
1:36:52.027144 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:36:52.028602 INFO: Updating optimization_manager: rt_error            : 1662.8485107421875 -> 5.504170195900387
1:36:52.028702 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 5.5042.
1:36:52.028769 INFO: ==============================================
1:36:52.028836 INFO: Starting optimization step 1.
1:36:52.028892 PROGRESS: === Extracting elution groups 0 to 600 ===
1:36:52.028958 INFO: Using ng extraction backend
1:36:52.029015 PROGRESS: Extracting batch of 1183 precursors
1:36:52.032391 INFO: === Search parameters used ===
1:36:52.032485 INFO: rt_error       : 5.504170195900387
1:36:52.032546 INFO: mobility_error : 0.1
1:36:52.032590 INFO: num_candidates : 3
1:36:52.032634 INFO: ms1_error      : 30
1:36:52.032677 INFO: ms2_error      : 6.828943
1:36:52.032720 INFO: fwhm_rt        : 3.0
1:36:52.032759 INFO: quant_window   : 3
1:36:52.032800 INFO: ==============================================
1:36:52.062897 INFO: performing precursor FDR with 40 features
1:36:52.062973 INFO: Decoy channel: -1
1:36:52.063000 INFO: Competetive: True
1:36:52.065640 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:52.067479 INFO: Using random state 479284 for train-test-split
1:36:52.078137 INFO: Test AUC: 0.674
1:36:52.078200 INFO: Train AUC: 0.695
1:36:52.078228 INFO: AUC difference: 3.06%
1:36:52.294614 INFO: Resetting torch num_threads to 80
1:36:52.296142 PROGRESS: === Extracted 3269 precursors and 20919 fragments ===
1:36:52.296482 INFO: === FDR correction performed with classifier version 7 ===
1:36:52.296961 PROGRESS: ============================= Precursor FDR =============================
1:36:52.297050 PROGRESS: Total precursors accumulated: 542
1:36:52.297108 PROGRESS: Target precursors: 537 (99.08%)
1:36:52.297158 PROGRESS: Decoy precursors: 5 (0.92%)
1:36:52.297204 PROGRESS: 
1:36:52.297247 PROGRESS: Precursor Summary:
1:36:52.298250 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   537; 0.001 FDR:   447
1:36:52.298343 PROGRESS: 
1:36:52.298397 PROGRESS: Protein Summary:
1:36:52.301244 PROGRESS: Channel   0:	 0.050 FDR:   490; 0.010 FDR:   490; 0.001 FDR:   414
1:36:52.301339 PROGRESS: =========================================================================
1:36:52.301566 INFO: Target number of precursors reached.
1:36:52.305856 INFO: fragments_df: keeping 5000 of 20919 [sum(precursor_idx_mask)=10722 sum(mass_error_mask)=20919 stop_rank=5000
1:36:52.310065 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:52.447998 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:53.128264 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:53.128692 INFO: Using score_cutoff 11.880416855621338 (fac=0.99, q=1)
1:36:53.128977 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:53.129056 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:53.129110 INFO: Updating optimization_manager: score_cutoff        : 14.797290753650666 -> 11.880416855621338
1:36:53.129160 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:53.130740 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:53.133145 INFO: === checking if optimization conditions were reached ===
1:36:53.133244 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:36:53.134912 INFO: Updating optimization_manager: rt_error            : 5.504170195900387 -> 3.7107578023124694
1:36:53.135014 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 3.7108.
1:36:53.135078 INFO: ==============================================
1:36:53.135165 INFO: Starting optimization step 2.
1:36:53.135226 PROGRESS: === Extracting elution groups 0 to 600 ===
1:36:53.135283 INFO: Using ng extraction backend
1:36:53.135337 PROGRESS: Extracting batch of 1183 precursors
1:36:53.138715 INFO: === Search parameters used ===
1:36:53.138805 INFO: rt_error       : 3.7107578023124694
1:36:53.138855 INFO: mobility_error : 0.1
1:36:53.138898 INFO: num_candidates : 3
1:36:53.138941 INFO: ms1_error      : 30
1:36:53.138981 INFO: ms2_error      : 6.828943
1:36:53.139020 INFO: fwhm_rt        : 3.0
1:36:53.139062 INFO: quant_window   : 3
1:36:53.139103 INFO: ==============================================
1:36:53.172340 INFO: performing precursor FDR with 40 features
1:36:53.172423 INFO: Decoy channel: -1
1:36:53.172449 INFO: Competetive: True
1:36:53.175021 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:53.176847 INFO: Using random state 479284 for train-test-split
1:36:53.188604 INFO: Test AUC: 0.655
1:36:53.188672 INFO: Train AUC: 0.699
1:36:53.188715 INFO: AUC difference: 6.37%
1:36:53.188738 WARNING: AUC difference > 5%. This may indicate overfitting.
1:36:53.405945 INFO: Resetting torch num_threads to 80
1:36:53.407496 PROGRESS: === Extracted 3270 precursors and 20924 fragments ===
1:36:53.407843 INFO: === FDR correction performed with classifier version 7 ===
1:36:53.408315 PROGRESS: ============================= Precursor FDR =============================
1:36:53.408404 PROGRESS: Total precursors accumulated: 542
1:36:53.408465 PROGRESS: Target precursors: 537 (99.08%)
1:36:53.408517 PROGRESS: Decoy precursors: 5 (0.92%)
1:36:53.408561 PROGRESS: 
1:36:53.408605 PROGRESS: Precursor Summary:
1:36:53.409606 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   537; 0.001 FDR:   445
1:36:53.409711 PROGRESS: 
1:36:53.409768 PROGRESS: Protein Summary:
1:36:53.410984 PROGRESS: Channel   0:	 0.050 FDR:   490; 0.010 FDR:   490; 0.001 FDR:   411
1:36:53.411073 PROGRESS: =========================================================================
1:36:53.411276 INFO: Target number of precursors reached.
1:36:53.415549 INFO: fragments_df: keeping 5000 of 20924 [sum(precursor_idx_mask)=10742 sum(mass_error_mask)=20924 stop_rank=5000
1:36:53.419705 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:53.556712 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:54.231700 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:54.232111 INFO: Using score_cutoff 11.880416855621338 (fac=0.99, q=1)
1:36:54.232391 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:54.232470 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:54.232524 INFO: Updating optimization_manager: score_cutoff        : 11.880416855621338 -> 11.880416855621338
1:36:54.232574 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:54.234138 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:54.236464 INFO: === checking if optimization conditions were reached ===
1:36:54.236560 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:36:54.238300 INFO: Updating optimization_manager: rt_error            : 3.7107578023124694 -> 3.7037918463842434
1:36:54.238400 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 3.7038.
1:36:54.238470 INFO: ==============================================
1:36:54.238537 INFO: Starting optimization step 3.
1:36:54.238592 PROGRESS: === Extracting elution groups 0 to 600 ===
1:36:54.238646 INFO: Using ng extraction backend
1:36:54.238697 PROGRESS: Extracting batch of 1183 precursors
1:36:54.242033 INFO: === Search parameters used ===
1:36:54.242125 INFO: rt_error       : 3.7037918463842434
1:36:54.242174 INFO: mobility_error : 0.1
1:36:54.242216 INFO: num_candidates : 3
1:36:54.242255 INFO: ms1_error      : 30
1:36:54.242296 INFO: ms2_error      : 6.828943
1:36:54.242334 INFO: fwhm_rt        : 3.0
1:36:54.242373 INFO: quant_window   : 3
1:36:54.242410 INFO: ==============================================
1:36:54.275284 INFO: performing precursor FDR with 40 features
1:36:54.275369 INFO: Decoy channel: -1
1:36:54.275398 INFO: Competetive: True
1:36:54.278016 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:54.279843 INFO: Using random state 479284 for train-test-split
1:36:54.291981 INFO: Test AUC: 0.698
1:36:54.292063 INFO: Train AUC: 0.688
1:36:54.292096 INFO: AUC difference: 1.40%
1:36:54.507166 INFO: Resetting torch num_threads to 80
1:36:54.508696 PROGRESS: === Extracted 3262 precursors and 20879 fragments ===
1:36:54.509047 INFO: === FDR correction performed with classifier version 7 ===
1:36:54.509536 PROGRESS: ============================= Precursor FDR =============================
1:36:54.509632 PROGRESS: Total precursors accumulated: 542
1:36:54.509696 PROGRESS: Target precursors: 537 (99.08%)
1:36:54.509754 PROGRESS: Decoy precursors: 5 (0.92%)
1:36:54.509810 PROGRESS: 
1:36:54.509871 PROGRESS: Precursor Summary:
1:36:54.511739 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   537; 0.001 FDR:   448
1:36:54.511836 PROGRESS: 
1:36:54.511896 PROGRESS: Protein Summary:
1:36:54.513130 PROGRESS: Channel   0:	 0.050 FDR:   491; 0.010 FDR:   491; 0.001 FDR:   415
1:36:54.513231 PROGRESS: =========================================================================
1:36:54.513435 INFO: Target number of precursors reached.
1:36:54.517705 INFO: fragments_df: keeping 5000 of 20879 [sum(precursor_idx_mask)=10738 sum(mass_error_mask)=20879 stop_rank=5000
1:36:54.521888 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:54.658813 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:55.329662 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:55.330215 INFO: Using score_cutoff 12.109076779174805 (fac=0.99, q=1)
1:36:55.330496 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:55.330579 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:55.330636 INFO: Updating optimization_manager: score_cutoff        : 11.880416855621338 -> 12.109076779174805
1:36:55.330688 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:55.332239 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:55.334569 INFO: === checking if optimization conditions were reached ===
1:36:55.334676 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:36:55.335560 INFO: Updating optimization_manager: rt_error            : 3.7037918463842434 -> 3.7037918463842434
1:36:55.335684 INFO: Updating optimization_manager: classifier_version  : 7 -> 11
1:36:55.335778 INFO: Updating optimization_manager: score_cutoff        : 12.109076779174805 -> 12.109076779174805
1:36:55.335865 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:55.335947 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:55.336025 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 3.7038 found after 4 searches.
1:36:55.336085 INFO: ==============================================
1:36:55.336150 PROGRESS: Optimization finished for rt_error.
1:36:55.340030 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:55.341363 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:55.366080 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:36:55.366231 PROGRESS: ==============================================
1:36:55.366298 PROGRESS: ms2_error      : 6.8289
1:36:55.366356 PROGRESS: rt_error       : 3.7038
1:36:55.366403 PROGRESS: ==============================================
1:36:55.366866 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:55.448455 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:55.672168 INFO: Using ng extraction backend
1:36:55.672504 PROGRESS: Extracting batch of 146144 precursors
1:36:55.907435 INFO: === Search parameters used ===
1:36:55.907838 INFO: rt_error       : 3.7037918463842434
1:36:55.907897 INFO: mobility_error : 0.1
1:36:55.907944 INFO: num_candidates : 3
1:36:55.907987 INFO: ms1_error      : 30
1:36:55.908032 INFO: ms2_error      : 6.828943
1:36:55.908075 INFO: fwhm_rt        : 3.0
1:36:55.908115 INFO: quant_window   : 3
1:36:55.908158 INFO: ==============================================
1:36:56.080706 INFO: Removed 169762 precursors with score below cutoff 12.109076779174805
1:36:56.315370 INFO: performing precursor FDR with 40 features
1:36:56.315507 INFO: Decoy channel: -1
1:36:56.315534 INFO: Competetive: True
1:36:56.337330 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:56.349376 WARNING: FDR calculation for 138263 target and 98117 decoy PSMs
1:36:56.349550 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:36:56.392043 INFO: Using random state 800222 for train-test-split
1:36:59.591109 INFO: Test AUC: 0.839
1:36:59.591245 INFO: Train AUC: 0.841
1:36:59.591292 INFO: AUC difference: 0.16%
1:36:59.890509 INFO: Resetting torch num_threads to 80
1:37:00.099193 PROGRESS: ============================= Precursor FDR =============================
1:37:00.100370 PROGRESS: Total precursors accumulated: 70,496
1:37:00.100444 PROGRESS: Target precursors: 69,799 (99.01%)
1:37:00.100496 PROGRESS: Decoy precursors: 697 (0.99%)
1:37:00.100546 PROGRESS: 
1:37:00.100589 PROGRESS: Precursor Summary:
1:37:00.120542 PROGRESS: Channel   0:	 0.050 FDR: 69,799; 0.010 FDR: 69,799; 0.001 FDR: 67,198
1:37:00.120933 PROGRESS: 
1:37:00.121001 PROGRESS: Protein Summary:
1:37:00.150326 PROGRESS: Channel   0:	 0.050 FDR: 7,037; 0.010 FDR: 7,037; 0.001 FDR: 7,008
1:37:00.150601 PROGRESS: =========================================================================
1:37:00.152213 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/psm.parquet
1:37:00.290014 INFO: Saving results to alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/frag.parquet
1:37:00.494272 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
1:37:00.864813 PROGRESS: Processing search outputs
1:37:00.864921 PROGRESS: Performing protein grouping and FDR
1:37:00.864952 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
1:37:00.903533 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
1:37:00.939627 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
1:37:00.974316 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
1:37:01.012880 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
1:37:01.048121 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
1:37:01.084620 INFO: Building combined output
1:37:01.105429 INFO: Performing protein inference
1:37:01.562461 INFO: Inference strategy: library. Using library grouping for protein inference
1:37:01.564449 INFO: Performing protein FDR
1:37:03.800454 INFO: Normalizing q-values using 7,049 targets and 2,251 decoys
1:37:03.802463 INFO: Test AUC: 1.000
1:37:03.802517 INFO: Train AUC: 1.000
1:37:03.802547 INFO: AUC difference: 0.01%
1:37:04.317640 PROGRESS: ================ Protein FDR =================
1:37:04.317794 PROGRESS: Unique protein groups in output
1:37:04.317825 PROGRESS:   1% protein FDR: 7,047
1:37:04.317845 PROGRESS: 
1:37:04.317863 PROGRESS: Unique precursor in output
1:37:04.317881 PROGRESS:   1% protein FDR: 73,722
1:37:04.317897 PROGRESS: ================================================
1:37:04.365295 PROGRESS: Building search statistics
1:37:04.435109 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/optimization_manager.pkl
1:37:04.435316 INFO: Initializing OptimizationManager
1:37:04.435554 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/calibration_manager.pkl
1:37:04.435631 INFO: Initializing CalibrationManager
1:37:04.435839 INFO: Loaded RawFileManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/raw_file_manager.pkl
1:37:04.435913 INFO: Initializing RawFileManager
1:37:04.460634 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/optimization_manager.pkl
1:37:04.460835 INFO: Initializing OptimizationManager
1:37:04.461033 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/calibration_manager.pkl
1:37:04.461106 INFO: Initializing CalibrationManager
1:37:04.461312 INFO: Loaded RawFileManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/raw_file_manager.pkl
1:37:04.461384 INFO: Initializing RawFileManager
1:37:04.487055 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/optimization_manager.pkl
1:37:04.487258 INFO: Initializing OptimizationManager
1:37:04.487458 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/calibration_manager.pkl
1:37:04.487532 INFO: Initializing CalibrationManager
1:37:04.487734 INFO: Loaded RawFileManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/raw_file_manager.pkl
1:37:04.487808 INFO: Initializing RawFileManager
1:37:04.512367 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/optimization_manager.pkl
1:37:04.512567 INFO: Initializing OptimizationManager
1:37:04.512761 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/calibration_manager.pkl
1:37:04.512832 INFO: Initializing CalibrationManager
1:37:04.513041 INFO: Loaded RawFileManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/raw_file_manager.pkl
1:37:04.513116 INFO: Initializing RawFileManager
1:37:04.537854 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/optimization_manager.pkl
1:37:04.538055 INFO: Initializing OptimizationManager
1:37:04.538254 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/calibration_manager.pkl
1:37:04.538325 INFO: Initializing CalibrationManager
1:37:04.538525 INFO: Loaded RawFileManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/raw_file_manager.pkl
1:37:04.538596 INFO: Initializing RawFileManager
1:37:04.563401 INFO: Loaded OptimizationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/optimization_manager.pkl
1:37:04.563596 INFO: Initializing OptimizationManager
1:37:04.563792 INFO: Loaded CalibrationManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/calibration_manager.pkl
1:37:04.563863 INFO: Initializing CalibrationManager
1:37:04.564064 INFO: Loaded RawFileManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/raw_file_manager.pkl
1:37:04.564135 INFO: Initializing RawFileManager
1:37:04.566588 INFO: Writing stat output to disk
1:37:04.566648 INFO: Saving alphadia_zenoswath8600/stat.tsv to disk
1:37:04.572002 PROGRESS: Building internal statistics
1:37:04.572280 INFO: Loaded TimingManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1/timing_manager.pkl
1:37:04.572324 INFO: Initializing TimingManager
1:37:04.572723 INFO: Loaded TimingManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2/timing_manager.pkl
1:37:04.572765 INFO: Initializing TimingManager
1:37:04.572953 INFO: Loaded TimingManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3/timing_manager.pkl
1:37:04.572991 INFO: Initializing TimingManager
1:37:04.573166 INFO: Loaded TimingManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1/timing_manager.pkl
1:37:04.573202 INFO: Initializing TimingManager
1:37:04.573372 INFO: Loaded TimingManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2/timing_manager.pkl
1:37:04.573408 INFO: Initializing TimingManager
1:37:04.573590 INFO: Loaded TimingManager from alphadia_zenoswath8600/quant/LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3/timing_manager.pkl
1:37:04.573627 INFO: Initializing TimingManager
1:37:04.574032 INFO: Writing internal output to disk
1:37:04.574094 INFO: Saving alphadia_zenoswath8600/internal.tsv to disk
1:37:04.574590 PROGRESS: Performing label free quantification
1:37:04.620842 INFO: Accumulating fragment data
1:37:04.621011 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
1:37:04.664981 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
1:37:05.511478 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
1:37:06.341570 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
1:37:07.191823 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
1:37:08.051449 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
1:37:09.065723 PROGRESS: Performing label free quantification on the precursor level
1:37:09.065864 INFO: Filtering fragments by quality
1:37:09.270108 INFO: Performing label-free quantification using directLFQ
1:37:10.018865 INFO: 73722 lfq-groups total
1:37:46.570316 INFO: using 80 processes
1:37:46.760094 INFO: lfq-object 0
1:37:46.879284 INFO: lfq-object 100
1:37:46.924440 INFO: lfq-object 300
1:37:46.952877 INFO: lfq-object 500
1:37:46.967216 INFO: lfq-object 700
1:37:47.008410 INFO: lfq-object 200
1:37:47.043798 INFO: lfq-object 400
1:37:47.071792 INFO: lfq-object 600
1:37:47.085590 INFO: lfq-object 800
1:37:47.092488 INFO: lfq-object 1000
1:37:47.117903 INFO: lfq-object 1200
1:37:47.161119 INFO: lfq-object 1400
1:37:47.202049 INFO: lfq-object 900
1:37:47.210238 INFO: lfq-object 1100
1:37:47.233883 INFO: lfq-object 1300
1:37:47.282375 INFO: lfq-object 1500
1:37:47.303624 INFO: lfq-object 1700
1:37:47.382354 INFO: lfq-object 1900
1:37:47.399358 INFO: lfq-object 1600
1:37:47.417775 INFO: lfq-object 1800
1:37:47.495359 INFO: lfq-object 2100
1:37:47.495991 INFO: lfq-object 2000
1:37:47.613945 INFO: lfq-object 2200
1:37:47.730988 INFO: lfq-object 2300
1:37:51.017197 INFO: lfq-object 2400
1:37:51.073807 INFO: lfq-object 2600
1:37:51.096191 INFO: lfq-object 2800
1:37:51.155980 INFO: lfq-object 2500
1:37:51.192177 INFO: lfq-object 2700
1:37:51.211816 INFO: lfq-object 2900
1:37:51.234324 INFO: lfq-object 3100
1:37:51.262328 INFO: lfq-object 3300
1:37:51.289798 INFO: lfq-object 3500
1:37:51.309117 INFO: lfq-object 3700
1:37:51.330210 INFO: lfq-object 3000
1:37:51.352218 INFO: lfq-object 3200
1:37:51.378539 INFO: lfq-object 3400
1:37:51.406509 INFO: lfq-object 3600
1:37:51.435989 INFO: lfq-object 3800
1:37:51.457192 INFO: lfq-object 4000
1:37:51.483309 INFO: lfq-object 4200
1:37:51.552372 INFO: lfq-object 4400
1:37:51.577389 INFO: lfq-object 4100
1:37:51.580896 INFO: lfq-object 3900
1:37:51.600212 INFO: lfq-object 4300
1:37:51.686416 INFO: lfq-object 4500
1:37:51.695074 INFO: lfq-object 4700
1:37:51.755497 INFO: lfq-object 4900
1:37:51.814958 INFO: lfq-object 4800
1:37:51.825866 INFO: lfq-object 4600
1:37:51.872992 INFO: lfq-object 5000
1:37:51.902080 INFO: lfq-object 5100
1:37:52.018912 INFO: lfq-object 5200
1:37:52.131804 INFO: lfq-object 5300
1:37:52.158376 INFO: lfq-object 5400
1:37:52.278247 INFO: lfq-object 5500
1:37:52.367129 INFO: lfq-object 5600
1:37:52.472838 INFO: lfq-object 5800
1:37:52.483242 INFO: lfq-object 5700
1:37:52.599597 INFO: lfq-object 5900
1:37:52.603289 INFO: lfq-object 6100
1:37:52.634996 INFO: lfq-object 6300
1:37:52.685655 INFO: lfq-object 6500
1:37:52.698584 INFO: lfq-object 6700
1:37:52.717022 INFO: lfq-object 6200
1:37:52.727082 INFO: lfq-object 6000
1:37:52.751980 INFO: lfq-object 6400
1:37:52.801666 INFO: lfq-object 6600
1:37:52.825892 INFO: lfq-object 6800
1:37:52.843697 INFO: lfq-object 7000
1:37:52.892108 INFO: lfq-object 7200
1:37:52.896360 INFO: lfq-object 7400
1:37:52.946593 INFO: lfq-object 6900
1:37:52.960525 INFO: lfq-object 7100
1:37:53.012440 INFO: lfq-object 7300
1:37:53.013918 INFO: lfq-object 7500
1:37:53.127451 INFO: lfq-object 7600
1:37:53.131162 INFO: lfq-object 7700
1:37:53.229084 INFO: lfq-object 7900
1:37:53.248526 INFO: lfq-object 7800
1:37:53.345739 INFO: lfq-object 8000
1:37:53.453960 INFO: lfq-object 8100
1:37:53.570257 INFO: lfq-object 8200
1:37:53.689194 INFO: lfq-object 8300
1:37:53.767400 INFO: lfq-object 8400
1:37:53.842949 INFO: lfq-object 8600
1:37:53.871186 INFO: lfq-object 8800
1:37:53.883438 INFO: lfq-object 8500
1:37:53.961362 INFO: lfq-object 8700
1:37:53.984033 INFO: lfq-object 8900
1:37:54.006649 INFO: lfq-object 9100
1:37:54.055274 INFO: lfq-object 9300
1:37:54.081176 INFO: lfq-object 9500
1:37:54.100510 INFO: lfq-object 9000
1:37:54.121605 INFO: lfq-object 9200
1:37:54.173077 INFO: lfq-object 9400
1:37:54.199035 INFO: lfq-object 9600
1:37:54.252139 INFO: lfq-object 9800
1:37:54.281336 INFO: lfq-object 10000
1:37:54.315021 INFO: lfq-object 9700
1:37:54.365235 INFO: lfq-object 10200
1:37:54.370692 INFO: lfq-object 9900
1:37:54.401886 INFO: lfq-object 10100
1:37:54.483396 INFO: lfq-object 10300
1:37:54.492119 INFO: lfq-object 10400
1:37:54.622104 INFO: lfq-object 10700
1:37:54.622337 INFO: lfq-object 10500
1:37:54.704857 INFO: lfq-object 10900
1:37:54.737007 INFO: lfq-object 11100
1:37:54.739892 INFO: lfq-object 10800
1:37:54.750857 INFO: lfq-object 10600
1:37:54.823777 INFO: lfq-object 11000
1:37:54.849031 INFO: lfq-object 11200
1:37:54.913979 INFO: lfq-object 11400
1:37:54.963987 INFO: lfq-object 11600
1:37:54.965258 INFO: lfq-object 11300
1:37:55.030230 INFO: lfq-object 11500
1:37:55.042745 INFO: lfq-object 11800
1:37:55.080830 INFO: lfq-object 11700
1:37:55.158633 INFO: lfq-object 11900
1:37:55.273302 INFO: lfq-object 12100
1:37:55.277388 INFO: lfq-object 12000
1:37:55.342394 INFO: lfq-object 12300
1:37:55.384244 INFO: lfq-object 12500
1:37:55.405057 INFO: lfq-object 12200
1:37:55.460705 INFO: lfq-object 12400
1:37:55.501721 INFO: lfq-object 12600
1:37:55.525388 INFO: lfq-object 12800
1:37:55.559728 INFO: lfq-object 13000
1:37:55.609414 INFO: lfq-object 13200
1:37:55.618833 INFO: lfq-object 12700
1:37:55.628193 INFO: lfq-object 13400
1:37:55.644521 INFO: lfq-object 12900
1:37:55.676269 INFO: lfq-object 13100
1:37:55.727992 INFO: lfq-object 13300
1:37:55.742634 INFO: lfq-object 13500
1:37:55.799431 INFO: lfq-object 13700
1:37:55.846856 INFO: lfq-object 13900
1:37:55.860122 INFO: lfq-object 13600
1:37:55.915844 INFO: lfq-object 13800
1:37:55.928025 INFO: lfq-object 14100
1:37:55.962752 INFO: lfq-object 14000
1:37:56.049260 INFO: lfq-object 14200
1:37:56.084085 INFO: lfq-object 14400
1:37:56.126085 INFO: lfq-object 14600
1:37:56.158879 INFO: lfq-object 14800
1:37:56.165016 INFO: lfq-object 14300
1:37:56.202804 INFO: lfq-object 14500
1:37:56.248463 INFO: lfq-object 14700
1:37:56.276663 INFO: lfq-object 14900
1:37:56.301512 INFO: lfq-object 15100
1:37:56.367396 INFO: lfq-object 15300
1:37:56.369819 INFO: lfq-object 15500
1:37:56.390104 INFO: lfq-object 15000
1:37:56.423755 INFO: lfq-object 15200
1:37:56.486464 INFO: lfq-object 15400
1:37:56.487231 INFO: lfq-object 15600
1:37:56.580024 INFO: lfq-object 15800
1:37:56.604839 INFO: lfq-object 16000
1:37:56.607332 INFO: lfq-object 15700
1:37:56.695552 INFO: lfq-object 16200
1:37:56.696985 INFO: lfq-object 15900
1:37:56.721112 INFO: lfq-object 16100
1:37:56.812762 INFO: lfq-object 16500
1:37:56.812994 INFO: lfq-object 16300
1:37:56.868301 INFO: lfq-object 16700
1:37:56.915707 INFO: lfq-object 16900
1:37:56.929094 INFO: lfq-object 16600
1:37:56.929573 INFO: lfq-object 16400
1:37:56.949647 INFO: lfq-object 17100
1:37:56.986039 INFO: lfq-object 16800
1:37:57.031471 INFO: lfq-object 17000
1:37:57.066461 INFO: lfq-object 17200
1:37:57.143036 INFO: lfq-object 17400
1:37:57.152638 INFO: lfq-object 17600
1:37:57.202060 INFO: lfq-object 17800
1:37:57.205288 INFO: lfq-object 17300
1:37:57.259599 INFO: lfq-object 17500
1:37:57.272229 INFO: lfq-object 17700
1:37:57.317118 INFO: lfq-object 17900
1:37:57.432551 INFO: lfq-object 18000
1:38:00.690106 INFO: lfq-object 18100
1:38:00.750873 INFO: lfq-object 18300
1:38:00.808325 INFO: lfq-object 18200
1:38:00.828036 INFO: lfq-object 18500
1:38:00.868066 INFO: lfq-object 18400
1:38:00.944184 INFO: lfq-object 18600
1:38:01.019445 INFO: lfq-object 19200
1:38:01.032788 INFO: lfq-object 18800
1:38:01.032865 INFO: lfq-object 19000
1:38:01.059036 INFO: lfq-object 18700
1:38:01.154392 INFO: lfq-object 19500
1:38:01.158761 INFO: lfq-object 18900
1:38:01.160911 INFO: lfq-object 19100
1:38:01.162593 INFO: lfq-object 19300
1:38:01.224945 INFO: lfq-object 19700
1:38:01.245823 INFO: lfq-object 19900
1:38:01.267180 INFO: lfq-object 19600
1:38:01.269917 INFO: lfq-object 20100
1:38:01.275594 INFO: lfq-object 19400
1:38:01.336930 INFO: lfq-object 19800
1:38:01.360729 INFO: lfq-object 20000
1:38:01.382893 INFO: lfq-object 20200
1:38:01.432874 INFO: lfq-object 20400
1:38:01.496592 INFO: lfq-object 20300
1:38:01.510405 INFO: lfq-object 20600
1:38:01.538307 INFO: lfq-object 20800
1:38:01.546040 INFO: lfq-object 20500
1:38:01.625951 INFO: lfq-object 20700
1:38:01.658234 INFO: lfq-object 20900
1:38:01.718205 INFO: lfq-object 21100
1:38:01.774271 INFO: lfq-object 21000
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1:38:01.833173 INFO: lfq-object 21200
1:38:01.923243 INFO: lfq-object 21400
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1:38:02.368428 INFO: lfq-object 22000
1:38:02.398625 INFO: lfq-object 22200
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1:38:30.029238 INFO: lfq-object 69400
1:38:30.051202 INFO: lfq-object 69600
1:38:30.102779 INFO: lfq-object 69800
1:38:30.124934 INFO: lfq-object 70000
1:38:30.144951 INFO: lfq-object 69500
1:38:30.168539 INFO: lfq-object 69700
1:38:30.216691 INFO: lfq-object 69900
1:38:30.238604 INFO: lfq-object 70100
1:38:30.295961 INFO: lfq-object 70300
1:38:30.355575 INFO: lfq-object 70200
1:38:30.372397 INFO: lfq-object 70500
1:38:30.417494 INFO: lfq-object 70400
1:38:30.437629 INFO: lfq-object 70700
1:38:30.492712 INFO: lfq-object 70600
1:38:30.565385 INFO: lfq-object 70800
1:38:30.641990 INFO: lfq-object 71000
1:38:30.666418 INFO: lfq-object 71200
1:38:30.681862 INFO: lfq-object 70900
1:38:30.744169 INFO: lfq-object 71400
1:38:30.758335 INFO: lfq-object 71100
1:38:30.782162 INFO: lfq-object 71300
1:38:30.860111 INFO: lfq-object 71500
1:38:30.922816 INFO: lfq-object 71700
1:38:30.973599 INFO: lfq-object 71600
1:38:30.989345 INFO: lfq-object 71900
1:38:31.004356 INFO: lfq-object 72100
1:38:31.037106 INFO: lfq-object 71800
1:38:31.104421 INFO: lfq-object 72000
1:38:31.118958 INFO: lfq-object 72200
1:38:31.176273 INFO: lfq-object 72400
1:38:31.238985 INFO: lfq-object 72300
1:38:31.244756 INFO: lfq-object 72600
1:38:31.265947 INFO: lfq-object 72800
1:38:31.289520 INFO: lfq-object 73000
1:38:31.289737 INFO: lfq-object 72500
1:38:31.359535 INFO: lfq-object 72700
1:38:31.379369 INFO: lfq-object 72900
1:38:31.404821 INFO: lfq-object 73100
1:38:31.452472 INFO: lfq-object 73700
1:38:31.463453 INFO: lfq-object 73300
1:38:31.477823 INFO: lfq-object 73500
1:38:31.524499 INFO: lfq-object 73200
1:38:31.576878 INFO: lfq-object 73400
1:38:31.597851 INFO: lfq-object 73600
1:38:38.280941 INFO: Writing precursor output to disk
1:38:38.281095 INFO: Saving alphadia_zenoswath8600/precursor.matrix.tsv to disk
1:38:38.693202 PROGRESS: Performing label free quantification on the pg level
1:38:38.693302 INFO: Filtering fragments by quality
1:38:38.906157 INFO: Performing label-free quantification using directLFQ
1:38:39.456166 INFO: 7047 lfq-groups total
1:39:05.765046 INFO: using 80 processes
1:39:05.852124 INFO: lfq-object 0
1:39:06.111736 INFO: lfq-object 600
1:39:06.212855 INFO: lfq-object 300
1:39:06.238906 INFO: lfq-object 100
1:39:06.351437 INFO: lfq-object 400
1:39:06.410341 INFO: lfq-object 900
1:39:06.526746 INFO: lfq-object 200
1:39:06.530696 INFO: lfq-object 800
1:39:06.545341 INFO: lfq-object 700
1:39:06.613530 INFO: lfq-object 1000
1:39:06.641184 INFO: lfq-object 500
1:39:06.808034 INFO: lfq-object 1200
1:39:06.825369 INFO: lfq-object 1100
1:39:06.848469 INFO: lfq-object 1500
1:39:06.849479 INFO: lfq-object 1300
1:39:06.901828 INFO: lfq-object 1400
1:39:06.932365 INFO: lfq-object 2100
1:39:06.967396 INFO: lfq-object 1600
1:39:06.991631 INFO: lfq-object 2300
1:39:07.015826 INFO: lfq-object 2000
1:39:07.051396 INFO: lfq-object 1700
1:39:07.069241 INFO: lfq-object 1900
1:39:07.077523 INFO: lfq-object 2400
1:39:07.106757 INFO: lfq-object 1800
1:39:07.130891 INFO: lfq-object 2600
1:39:07.205789 INFO: lfq-object 2200
1:39:07.211017 INFO: lfq-object 2700
1:39:07.234799 INFO: lfq-object 2500
1:39:07.250826 INFO: lfq-object 2900
1:39:07.359571 INFO: lfq-object 3000
1:39:07.434087 INFO: lfq-object 2800
1:39:07.445211 INFO: lfq-object 3100
1:39:07.502158 INFO: lfq-object 3200
1:39:07.559055 INFO: lfq-object 3500
1:39:07.625776 INFO: lfq-object 3300
1:39:07.721735 INFO: lfq-object 3800
1:39:07.765071 INFO: lfq-object 3600
1:39:07.812098 INFO: lfq-object 3400
1:39:07.817538 INFO: lfq-object 4100
1:39:07.850938 INFO: lfq-object 3900
1:39:07.961255 INFO: lfq-object 3700
1:39:07.986304 INFO: lfq-object 4000
1:39:08.019989 INFO: lfq-object 4400
1:39:08.039274 INFO: lfq-object 4600
1:39:08.053713 INFO: lfq-object 4200
1:39:08.132858 INFO: lfq-object 4700
1:39:08.177819 INFO: lfq-object 4900
1:39:08.245359 INFO: lfq-object 4300
1:39:08.248326 INFO: lfq-object 4800
1:39:08.256085 INFO: lfq-object 4500
1:39:08.268462 INFO: lfq-object 5000
1:39:08.315325 INFO: lfq-object 5200
1:39:08.412710 INFO: lfq-object 5300
1:39:08.429614 INFO: lfq-object 5100
1:39:08.469721 INFO: lfq-object 5500
1:39:08.535655 INFO: lfq-object 5600
1:39:08.544536 INFO: lfq-object 5400
1:39:08.616217 INFO: lfq-object 5700
1:39:08.671144 INFO: lfq-object 5800
1:39:08.726493 INFO: lfq-object 5900
1:39:08.757979 INFO: lfq-object 6100
1:39:08.893700 INFO: lfq-object 6000
1:39:08.935333 INFO: lfq-object 6200
1:39:08.962886 INFO: lfq-object 6400
1:39:09.000107 INFO: lfq-object 6300
1:39:09.040628 INFO: lfq-object 6500
1:39:09.091246 INFO: lfq-object 6700
1:39:09.106117 INFO: lfq-object 6900
1:39:09.211354 INFO: lfq-object 6600
1:39:09.226747 INFO: lfq-object 7000
1:39:09.254534 INFO: lfq-object 6800
1:39:11.379533 INFO: Writing pg output to disk
1:39:11.379724 INFO: Saving alphadia_zenoswath8600/pg.matrix.tsv to disk
1:39:11.547364 INFO: Writing psm output to disk
1:39:11.547529 INFO: Saving alphadia_zenoswath8600/precursors.tsv to disk
1:39:19.343744 PROGRESS: Building MBR spectral library
1:39:19.406881 INFO: Running MbrLibraryBuilder
1:39:19.627635 INFO: MBR spectral library contains 73,722 precursors, 7,047 proteins
1:39:19.628105 INFO: Writing MBR spectral library to disk
1:39:20.385824 PROGRESS: =================== Search Finished ===================
