0:00:00.000031 INFO: Moved old log file ./run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/log.txt to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/log.txt
0:00:00.000185 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000221 INFO: User provided config file: config_alphadia112_rs_Astral.yaml.
0:00:00.000250 INFO: User provided config dict: {}.
0:00:00.013074 PROGRESS:           _      _         ___ ___   _   
0:00:00.013134 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.013160 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013186 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013211 PROGRESS:            |_|                           
0:00:00.013231 PROGRESS: 
0:00:00.013252 PROGRESS: version: 1.12.1
0:00:00.013281 INFO: hostname: thestral
0:00:00.013334 INFO: date: 2025-10-15 15:18:53
0:00:00.013357 INFO: ================ AlphaX Environment ===============
0:00:00.013379 INFO: alphatims       : 1.0.8
0:00:00.013402 INFO: alpharaw        : 0.4.5
0:00:00.013420 INFO: alphabase       : 1.5.0
0:00:00.013439 INFO: alphapeptdeep   : 1.3.0
0:00:00.013457 INFO: directlfq       : 0.2.19
0:00:00.013476 INFO: ===================================================
0:00:00.013493 INFO: ================= Pip Environment =================
0:00:00.069922 INFO: alphatims==1.0.8 click==8.1.8 partd==1.4.2 wget==3.2 torchmetrics==1.4.0.post0 uri-template==1.3.0 directlfq==0.2.19 nvidia-nvjitlink-cu12==12.4.127 lxml==5.3.1 fsspec==2025.3.0 fqdn==1.5.1 jsonref==1.1.0 simplejson==3.20.1 tornado==6.4.2 s3transfer==0.11.4 pythonnet==3.0.3 tqdm==4.67.1 psutil==7.0.0 urllib3==2.3.0 fonttools==4.56.0 arrow==1.3.0 dask==2024.11.2 numpy==1.26.4 tzdata==2025.1 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 numba==0.59.1 importlib_resources==6.5.2 packaging==24.2 SQLAlchemy==2.0.39 typing_extensions==4.12.2 pyarrow==19.0.1 alphadia-search-rs==0.2.0 joblib==1.4.2 requests-oauthlib==2.0.0 rdkit==2024.3.3 webcolors==24.11.1 cffi==1.17.1 nvidia-cuda-nvrtc-cu12==12.4.127 protobuf==5.29.3 pyteomics==4.7.5 alphadia==1.12.1 mpmath==1.3.0 pytz==2025.1 multiprocess==0.70.17 MarkupSafe==3.0.2 pyzstd==0.16.2 six==1.17.0 cycler==0.12.1 charset-normalizer==3.4.1 pyparsing==3.2.1 tenacity==9.0.0 llvmlite==0.42.0 attrs==25.2.0 pip==23.0.1 requests==2.32.3 triton==3.2.0 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 alpharaw==0.4.5 regex==2024.11.6 streamlit-aggrid==1.1.1 streamlit==1.43.2 tokenizers==0.19.1 websocket-client==1.8.0 certifi==2025.1.31 narwhals==1.30.0 isoduration==20.11.0 python-dateutil==2.9.0.post0 peptdeep==1.3.0 botocore==1.37.11 locket==1.0.0 referencing==0.36.2 torch==2.6.0 nvidia-cusparse-cu12==12.3.1.170 rocket-fft==0.2.5 lightning-utilities==0.14.0 neptune==1.10.4 importlib_metadata==8.6.1 cloudpickle==3.1.1 clr_loader==0.2.7.post0 setuptools==66.1.1 pandas==2.2.3 dill==0.3.9 jsonschema-specifications==2024.10.1 networkx==3.4.2 transformers==4.40.2 biopython==1.85 filelock==3.17.0 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 greenlet==3.1.1 scipy==1.12.0 matplotlib==3.10.1 contourpy==1.3.1 pydeck==0.9.1 threadpoolctl==3.5.0 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 xxhash==3.4.1 safetensors==0.5.3 idna==3.10 cachetools==5.5.2 huggingface-hub==0.29.3 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 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 alphabase==1.5.0 PyYAML==6.0.2
0:00:00.070041 INFO: ===================================================
0:00:00.070072 INFO: Running step 'library'
0:00:00.070190 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.081282 INFO: loading additional config provided via CLI
0:00:00.081363 INFO: loading additional config provided via CLI parameters
0:00:00.081758 INFO: Updating config with 'user defined'
0:00:00.081909 INFO: Updating config with 'user defined (cli)'
0:00:00.081951 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default_ng.yaml
0:00:00.082547 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': ['./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw'], 'fasta_paths': [], 'quant_directory': None, 'general': {'thread_count': 80, 'transfer_step_enabled': False, 'mbr_step_enabled': True, 'reuse_calibration': False, 'reuse_quant': False, 'astral_ms1': False, 'log_level': 'INFO', 'mmap_detector_events': False, 'use_gpu': False, 'save_figures': True, 'save_library': True, 'save_flat_library': False, 'input_library_type': 'base', 'save_mbr_library': True, 'random_state': None}, 'library_loading': {'rt_heuristic': 180}, 'library_prediction': {'enabled': False, 'enzyme': 'trypsin/p', 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M;Acetyl@Protein_N-term', 'max_var_mod_num': 1, 'missed_cleavages': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [400, 1000], 'fragment_mz': [50, 2000], 'nce': 25.0, 'fragment_types': ['b', 'y'], 'max_fragment_charge': 2, 'instrument': 'Astral', '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': 'Astral'}}, {'raw_paths': ['./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw'], 'library_path': '/home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf', 'fasta_paths': ['./ProteoBenchFASTA_DDAQuantification.fasta']}, {'quant_directory': None, 'general': {'save_mbr_library': True, 'save_library': False, 'reuse_quant': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'output_directory': 'run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library'}]
0:00:00.082828 INFO: Updating config with 'ng_default'
0:00:00.082865 INFO: Updating config with 'user defined'
0:00:00.082982 INFO: Updating config with 'user defined (cli)'
0:00:00.083007 INFO: Updating config with 'multistep search'
0:00:00.083054 INFO: ├──version: 1
0:00:00.083404 INFO: ├──workflow_name: None
0:00:00.083434 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library [multistep search, default: None][0m
0:00:00.083456 INFO: [32;20m├──library_path: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf [user defined (cli), default: None][0m
0:00:00.083476 INFO: ├──raw_paths:
0:00:00.083497 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.083516 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.083535 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.083557 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.083577 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.083596 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.083616 INFO: ├──fasta_paths:
0:00:00.083635 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.083656 INFO: ├──quant_directory: None
0:00:00.083676 INFO: ├──general
0:00:00.083698 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:00:00.083717 INFO: │   ├──transfer_step_enabled: False
0:00:00.083738 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.083757 INFO: │   ├──reuse_calibration: False
0:00:00.083776 INFO: │   ├──reuse_quant: False
0:00:00.083793 INFO: │   ├──astral_ms1: False
0:00:00.083812 INFO: │   ├──log_level: INFO
0:00:00.083832 INFO: │   ├──mmap_detector_events: False
0:00:00.083852 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.083871 INFO: │   ├──save_figures: True
0:00:00.083891 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.083909 INFO: │   ├──save_flat_library: False
0:00:00.083928 INFO: │   ├──input_library_type: base
0:00:00.083946 INFO: │   ├──save_mbr_library: True
0:00:00.083966 INFO: │   └──random_state: None
0:00:00.083984 INFO: ├──library_loading
0:00:00.084004 INFO: │   └──rt_heuristic: 180
0:00:00.084022 INFO: ├──library_prediction
0:00:00.084041 INFO: │   ├──enabled: False
0:00:00.084059 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.084078 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.084096 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.084116 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.084138 INFO: │   ├──missed_cleavages: 1
0:00:00.084157 INFO: │   ├──precursor_len:
0:00:00.084174 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.084192 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.084211 INFO: │   ├──precursor_charge:
0:00:00.084229 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.084246 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.084264 INFO: │   ├──precursor_mz:
0:00:00.084282 INFO: │   │   - 400
0:00:00.084300 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.084317 INFO: │   ├──fragment_mz:
0:00:00.084335 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.084352 INFO: │   │   - 2000
0:00:00.084371 INFO: │   ├──nce: 25.0
0:00:00.084388 INFO: │   ├──fragment_types:
0:00:00.084406 INFO: │   │   - b
0:00:00.084424 INFO: │   │   - y
0:00:00.084447 INFO: │   ├──max_fragment_charge: 2
0:00:00.084465 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:00:00.084483 INFO: │   ├──peptdeep_model_path: None
0:00:00.084502 INFO: │   └──peptdeep_model_type: generic
0:00:00.084521 INFO: ├──custom_modifications:
0:00:00.084540 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.084558 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.084576 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.084595 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.084613 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.084631 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.084649 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.084667 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.084687 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.084704 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.084723 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.084742 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.084760 INFO: │   ├──name: Label:13C(12)@K
0:00:00.084778 INFO: │   └──composition: C(12)
0:00:00.084795 INFO: ├──search
0:00:00.084814 INFO: │   [32;20m├──extraction_backend: ng [user defined, default: classic][0m
0:00:00.084833 INFO: │   [32;20m├──target_ms1_tolerance: 0.0 [user defined, default: 5][0m
0:00:00.084852 INFO: │   [32;20m├──target_ms2_tolerance: 0.0 [user defined, default: 10][0m
0:00:00.084870 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.084888 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.084906 INFO: │   ├──quant_window: 3
0:00:00.084925 INFO: │   ├──target_num_candidates: 3
0:00:00.084943 INFO: │   ├──channel_filter: 
0:00:00.084961 INFO: │   ├──exclude_shared_ions: True
0:00:00.084978 INFO: │   ├──compete_for_fragments: True
0:00:00.084996 INFO: │   ├──quant_all: True
0:00:00.085015 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.085032 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.085050 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.085068 INFO: │   ├──experimental_xic: True
0:00:00.085087 INFO: │   └──optimized_peak_group_score: False
0:00:00.085105 INFO: ├──calibration
0:00:00.085124 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.085144 INFO: │   ├──optimization_lock_target: 200
0:00:00.085162 INFO: │   ├──max_steps: 20
0:00:00.085180 INFO: │   ├──min_steps: 2
0:00:00.085198 INFO: │   ├──max_skips: 1
0:00:00.085217 INFO: │   ├──max_fragments: 5000
0:00:00.085237 INFO: │   └──min_correlation: 0.7
0:00:00.085255 INFO: ├──search_initial
0:00:00.085273 INFO: │   ├──initial_num_candidates: 1
0:00:00.085291 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.085309 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.085327 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.085345 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.085363 INFO: ├──selection_config
0:00:00.085383 INFO: │   ├──peak_len_rt: 10.0
0:00:00.085402 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.085420 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.085438 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.085456 INFO: │   ├──top_k_precursors: 3
0:00:00.085475 INFO: │   ├──kernel_size: 30
0:00:00.085492 INFO: │   ├──f_mobility: 1.0
0:00:00.085510 INFO: │   ├──f_rt: 0.99
0:00:00.085529 INFO: │   ├──center_fraction: 0.5
0:00:00.085547 INFO: │   ├──min_size_mobility: 8
0:00:00.085565 INFO: │   ├──min_size_rt: 3
0:00:00.085582 INFO: │   ├──max_size_mobility: 20
0:00:00.085599 INFO: │   ├──max_size_rt: 15
0:00:00.085616 INFO: │   ├──group_channels: False
0:00:00.085634 INFO: │   ├──use_weighted_score: True
0:00:00.085660 INFO: │   ├──join_close_candidates: False
0:00:00.085679 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.085697 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.085715 INFO: ├──scoring_config
0:00:00.085732 INFO: │   ├──score_grouped: False
0:00:00.085750 INFO: │   ├──top_k_isotopes: 3
0:00:00.085767 INFO: │   ├──reference_channel: -1
0:00:00.085785 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.085803 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.085820 INFO: ├──library_multiplexing
0:00:00.085838 INFO: │   ├──enabled: False
0:00:00.085856 INFO: │   ├──input_channel: 0
0:00:00.085874 INFO: │   └──multiplex_mapping:
0:00:00.085892 INFO: ├──multiplexing
0:00:00.085909 INFO: │   ├──enabled: False
0:00:00.085927 INFO: │   ├──target_channels: 4,8
0:00:00.085946 INFO: │   ├──decoy_channel: 12
0:00:00.085963 INFO: │   ├──reference_channel: 0
0:00:00.085981 INFO: │   └──competetive_scoring: True
0:00:00.085999 INFO: ├──fdr
0:00:00.086017 INFO: │   ├──fdr: 0.01
0:00:00.086036 INFO: │   ├──group_level: proteins
0:00:00.086054 INFO: │   ├──inference_strategy: heuristic
0:00:00.086071 INFO: │   ├──competetive_scoring: True
0:00:00.086089 INFO: │   ├──keep_decoys: False
0:00:00.086107 INFO: │   ├──channel_wise_fdr: False
0:00:00.086125 INFO: │   ├──enable_two_step_classifier: False
0:00:00.086143 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.086160 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.086178 INFO: ├──search_output
0:00:00.086197 INFO: │   ├──file_format: tsv
0:00:00.086215 INFO: │   ├──peptide_level_lfq: False
0:00:00.086234 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.086252 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.086272 INFO: │   ├──min_k_fragments: 12
0:00:00.086290 INFO: │   ├──min_correlation: 0.9
0:00:00.086307 INFO: │   ├──num_samples_quadratic: 50
0:00:00.086325 INFO: │   ├──min_nonnan: 3
0:00:00.086344 INFO: │   └──normalize_lfq: True
0:00:00.086362 INFO: ├──optimization
0:00:00.086380 INFO: │   ├──order_of_optimization: None
0:00:00.086397 INFO: │   ├──ms2_error
0:00:00.086418 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.086437 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.086456 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.086474 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.086494 INFO: │   │   ├──try_narrower_values: True
0:00:00.086512 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.086531 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.086551 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.086575 INFO: │   ├──ms1_error
0:00:00.086593 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.086612 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.086630 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.086649 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.086667 INFO: │   │   ├──try_narrower_values: False
0:00:00.086686 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.086704 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.086722 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.086740 INFO: │   ├──mobility_error
0:00:00.086759 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.086776 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.086794 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.086812 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.086830 INFO: │   │   ├──try_narrower_values: False
0:00:00.086852 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.086870 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.086888 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.086905 INFO: │   └──rt_error
0:00:00.086923 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.086941 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.086959 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.086977 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.086995 INFO: │       ├──try_narrower_values: True
0:00:00.087013 INFO: │       ├──maximal_decrease: 0.2
0:00:00.087031 INFO: │       ├──favour_narrower_optimum: True
0:00:00.087048 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.087067 INFO: ├──optimization_manager
0:00:00.087085 INFO: │   ├──fwhm_rt: 5
0:00:00.087102 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.087120 INFO: │   └──score_cutoff: 0
0:00:00.087137 INFO: ├──transfer_library
0:00:00.087156 INFO: │   ├──enabled: False
0:00:00.087173 INFO: │   ├──fragment_types:
0:00:00.087191 INFO: │   │   - b
0:00:00.087208 INFO: │   │   - y
0:00:00.087227 INFO: │   ├──max_charge: 2
0:00:00.087244 INFO: │   ├──top_k_samples: 3
0:00:00.087262 INFO: │   ├──norm_delta_max: True
0:00:00.087279 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.087297 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.087315 INFO: └──transfer_learning
0:00:00.087333 INFO:     ├──enabled: False
0:00:00.087351 INFO:     ├──batch_size: 2000
0:00:00.087368 INFO:     ├──max_lr: 0.0001
0:00:00.087387 INFO:     ├──train_fraction: 0.7
0:00:00.087405 INFO:     ├──validation_fraction: 0.2
0:00:00.087423 INFO:     ├──test_fraction: 0.1
0:00:00.087441 INFO:     ├──test_interval: 1
0:00:00.087460 INFO:     ├──lr_patience: 3
0:00:00.087478 INFO:     ├──epochs: 51
0:00:00.087496 INFO:     ├──warmup_epochs: 5
0:00:00.087514 INFO:     ├──nce: 25
0:00:00.087532 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:00:00.092155 INFO: Moved existing config file run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/frozen_config.yaml to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/frozen_config.yaml
0:00:00.092308 INFO: Registering 7 custom modifications
0:00:00.119940 INFO: Searching 6 files:
0:00:00.120018 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.120043 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.120064 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.120083 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.120100 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.120118 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.120135 INFO: Using 1 fasta files:
0:00:00.120152 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:00:00.120173 INFO: Using library: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:00.120192 INFO: Saving output to: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library
0:00:00.120218 PROGRESS: Loading spectral library
0:00:00.120242 PROGRESS: Loading library (type: base) from disk..
0:00:00.120270 INFO: Running DynamicLoader
0:00:00.120322 INFO: Loading .hdf library from /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:28.962079 INFO: Running PrecursorInitializer
0:00:28.962442 INFO: Running AnnotateFasta
0:00:29.090987 INFO: Dropping decoys from input library before annotation
0:00:50.410184 INFO: Running IsotopeGenerator
0:00:50.410492 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
0:00:50.410531 INFO: Running RTNormalization
0:00:50.410615 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:00:50.410654 INFO: Saving library to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/speclib.hdf
0:01:25.146988 INFO: Running DecoyGenerator
0:05:11.158536 INFO: Running FlattenLibrary
0:06:45.142144 INFO: Running InitFlatColumns
0:06:45.470924 INFO: Running LogFlatLibraryStats
0:06:45.471091 INFO: ============ Library Stats ============
0:06:45.471143 INFO: Number of precursors: 12,218,312
0:06:48.557289 INFO: 	thereof targets:6,124,046
0:06:48.557431 INFO: 	thereof decoys: 6,094,266
0:06:48.660131 INFO: Number of elution groups: 6,124,046
0:06:48.660261 INFO: 	average size: 2.00
0:06:48.943218 INFO: Number of proteins: 117,993
0:06:48.973128 INFO: Number of channels: 1 ([0])
0:06:48.973350 INFO: Isotopes Distribution for 4 isotopes
0:06:48.973384 INFO: =======================================
0:06:48.984043 PROGRESS: Starting Search Workflows
0:06:48.984396 PROGRESS: 
0:06:48.984598 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
0:06:48.984704 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:06:48.985083 INFO: Initializing TimingManager
0:06:48.985945 INFO: Initializing RawFileManager
0:06:59.643392 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:06:59.647648 INFO: Determining DIA cycle
0:07:00.069275 INFO: Found cycle with start 0.00 min and length 300.
0:07:00.230340 INFO: RT (min)            : 0.0 - 26.9
0:07:00.230438 INFO: RT duration (sec)   : 1611.2
0:07:00.230469 INFO: RT duration (min)   : 26.9
0:07:00.230500 INFO: Cycle len (scans)   : 300
0:07:00.230521 INFO: Cycle len (sec)     : 1.65
0:07:00.230540 INFO: Number of cycles    : 977
0:07:00.230572 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:07:00.230622 INFO: Creating DIA data object took: 11.244563102722168
0:07:01.067903 INFO: Creating DIA data NG object took: 0.837130069732666
0:07:03.031304 INFO: Initializing CalibrationManager
0:07:03.031766 INFO: Setting up calibration estimators ..
0:07:03.031848 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:07:03.032021 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'}' ..
0:07:03.032319 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:07:03.032395 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:07:03.032471 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}}' ..
0:07:03.032539 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:07:03.032591 INFO: Done setting up calibration estimators.
0:07:03.033579 INFO: Initializing OptimizationManager
0:07:03.033794 INFO: initial parameter: ms1_error = 30
0:07:03.033854 INFO: initial parameter: ms2_error = 30
0:07:03.033908 INFO: initial parameter: rt_error = 805.5992431640625
0:07:03.033959 INFO: initial parameter: mobility_error = 0.1
0:07:03.034011 INFO: initial parameter: num_candidates = 1
0:07:03.034051 INFO: initial parameter: fwhm_rt = 5
0:07:03.034092 INFO: initial parameter: fwhm_mobility = 0.01
0:07:03.034133 INFO: initial parameter: score_cutoff = 0
0:07:03.034173 INFO: initial parameter: classifier_version = -1
0:07:03.034258 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:07:03.034922 INFO: FDRManager: loading saved state not requested, will be initialized.
0:07:03.036760 INFO: Initializing FDRManager
0:07:03.036851 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:07:04.362451 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:07:05.773888 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:07:05.774268 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:07:05.774409 PROGRESS: Starting initial search for precursors.
0:07:05.774506 INFO: Starting optimization step 0.
0:07:05.774587 PROGRESS: === Extracting elution groups 0 to 200 ===
0:07:05.774674 INFO: Using ng extraction backend
0:07:05.774786 PROGRESS: Extracting batch of 396 precursors
0:07:05.777187 INFO: === Search parameters used ===
0:07:05.777283 INFO: rt_error       : 805.5992431640625
0:07:05.777332 INFO: mobility_error : 0.1
0:07:05.777374 INFO: num_candidates : 1
0:07:05.777415 INFO: ms1_error      : 30
0:07:05.777453 INFO: ms2_error      : 30
0:07:05.777493 INFO: fwhm_rt        : 5
0:07:05.777532 INFO: quant_window   : 3
0:07:05.777572 INFO: ==============================================
0:07:05.800234 INFO: performing precursor FDR with 40 features
0:07:05.800310 INFO: Decoy channel: -1
0:07:05.800336 INFO: Competetive: True
0:07:05.801357 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:05.805084 INFO: Using random state 112949 for train-test-split
0:07:06.714081 INFO: Test AUC: 0.379
0:07:06.714175 INFO: Train AUC: 0.478
0:07:06.714207 INFO: AUC difference: 20.68%
0:07:06.714230 WARNING: AUC difference > 5%. This may indicate overfitting.
0:07:06.951732 INFO: Resetting torch num_threads to 80
0:07:06.953064 PROGRESS: === Extracted 394 precursors and 1879 fragments ===
0:07:06.953388 INFO: === FDR correction performed with classifier version -1 ===
0:07:06.953828 PROGRESS: ============================= Precursor FDR =============================
0:07:06.953915 PROGRESS: Total precursors accumulated: 2
0:07:06.953974 PROGRESS: Target precursors: 2 (100.00%)
0:07:06.954025 PROGRESS: Decoy precursors: 0 (0.00%)
0:07:06.954072 PROGRESS: 
0:07:06.954117 PROGRESS: Precursor Summary:
0:07:06.955081 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:07:06.955168 PROGRESS: 
0:07:06.955230 PROGRESS: Protein Summary:
0:07:06.956241 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:07:06.956331 PROGRESS: =========================================================================
0:07:06.956479 INFO: Target number of precursors not reached yet.
0:07:07.021591 INFO: Starting optimization step 1.
0:07:07.021930 PROGRESS: === Extracting elution groups 200 to 600 ===
0:07:07.022019 INFO: Using ng extraction backend
0:07:07.022083 PROGRESS: Extracting batch of 786 precursors
0:07:07.024990 INFO: === Search parameters used ===
0:07:07.025087 INFO: rt_error       : 805.5992431640625
0:07:07.025146 INFO: mobility_error : 0.1
0:07:07.025192 INFO: num_candidates : 1
0:07:07.025235 INFO: ms1_error      : 30
0:07:07.025276 INFO: ms2_error      : 30
0:07:07.025315 INFO: fwhm_rt        : 5
0:07:07.025355 INFO: quant_window   : 3
0:07:07.025393 INFO: ==============================================
0:07:07.051309 INFO: performing precursor FDR with 40 features
0:07:07.051382 INFO: Decoy channel: -1
0:07:07.051409 INFO: Competetive: True
0:07:07.054456 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:07.056265 INFO: Using random state 773266 for train-test-split
0:07:07.065930 INFO: Test AUC: 0.460
0:07:07.065992 INFO: Train AUC: 0.473
0:07:07.066023 INFO: AUC difference: 2.83%
0:07:07.278104 INFO: Resetting torch num_threads to 80
0:07:07.280177 PROGRESS: === Extracted 1169 precursors and 5549 fragments ===
0:07:07.280506 INFO: === FDR correction performed with classifier version -1 ===
0:07:07.280931 PROGRESS: ============================= Precursor FDR =============================
0:07:07.281014 PROGRESS: Total precursors accumulated: 0
0:07:07.281082 PROGRESS: Target precursors: 0 (0.00%)
0:07:07.281135 PROGRESS: Decoy precursors: 0 (0.00%)
0:07:07.281181 PROGRESS: 
0:07:07.281224 PROGRESS: Precursor Summary:
0:07:07.281335 PROGRESS: 
0:07:07.281396 PROGRESS: Protein Summary:
0:07:07.281468 PROGRESS: =========================================================================
0:07:07.281638 INFO: Target number of precursors not reached yet.
0:07:07.348639 INFO: Starting optimization step 2.
0:07:07.348835 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:07:07.348917 INFO: Using ng extraction backend
0:07:07.348979 PROGRESS: Extracting batch of 1592 precursors
0:07:07.353055 INFO: === Search parameters used ===
0:07:07.353156 INFO: rt_error       : 805.5992431640625
0:07:07.353208 INFO: mobility_error : 0.1
0:07:07.353251 INFO: num_candidates : 1
0:07:07.353293 INFO: ms1_error      : 30
0:07:07.353335 INFO: ms2_error      : 30
0:07:07.353376 INFO: fwhm_rt        : 5
0:07:07.353418 INFO: quant_window   : 3
0:07:07.353456 INFO: ==============================================
0:07:07.387115 INFO: performing precursor FDR with 40 features
0:07:07.387199 INFO: Decoy channel: -1
0:07:07.387348 INFO: Competetive: True
0:07:07.391149 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:07.393145 INFO: Using random state 619753 for train-test-split
0:07:07.406952 INFO: Test AUC: 0.513
0:07:07.407015 INFO: Train AUC: 0.472
0:07:07.407046 INFO: AUC difference: 8.73%
0:07:07.407068 WARNING: AUC difference > 5%. This may indicate overfitting.
0:07:07.628962 INFO: Resetting torch num_threads to 80
0:07:07.631475 PROGRESS: === Extracted 2751 precursors and 13122 fragments ===
0:07:07.631814 INFO: === FDR correction performed with classifier version -1 ===
0:07:07.632247 PROGRESS: ============================= Precursor FDR =============================
0:07:07.632332 PROGRESS: Total precursors accumulated: 0
0:07:07.632397 PROGRESS: Target precursors: 0 (0.00%)
0:07:07.632448 PROGRESS: Decoy precursors: 0 (0.00%)
0:07:07.632494 PROGRESS: 
0:07:07.632536 PROGRESS: Precursor Summary:
0:07:07.632642 PROGRESS: 
0:07:07.632703 PROGRESS: Protein Summary:
0:07:07.632776 PROGRESS: =========================================================================
0:07:07.632967 INFO: Target number of precursors not reached yet.
0:07:07.705596 INFO: Starting optimization step 3.
0:07:07.705800 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:07:07.705882 INFO: Using ng extraction backend
0:07:07.705945 PROGRESS: Extracting batch of 3177 precursors
0:07:07.712825 INFO: === Search parameters used ===
0:07:07.712952 INFO: rt_error       : 805.5992431640625
0:07:07.713009 INFO: mobility_error : 0.1
0:07:07.713054 INFO: num_candidates : 1
0:07:07.713095 INFO: ms1_error      : 30
0:07:07.713136 INFO: ms2_error      : 30
0:07:07.713174 INFO: fwhm_rt        : 5
0:07:07.713215 INFO: quant_window   : 3
0:07:07.713254 INFO: ==============================================
0:07:07.765237 INFO: performing precursor FDR with 40 features
0:07:07.765327 INFO: Decoy channel: -1
0:07:07.765354 INFO: Competetive: True
0:07:07.771234 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:07.773862 INFO: Using random state 189829 for train-test-split
0:07:07.799182 INFO: Test AUC: 0.472
0:07:07.799261 INFO: Train AUC: 0.479
0:07:07.799291 INFO: AUC difference: 1.43%
0:07:08.014357 INFO: Resetting torch num_threads to 80
0:07:08.017471 PROGRESS: === Extracted 5904 precursors and 28052 fragments ===
0:07:08.017818 INFO: === FDR correction performed with classifier version -1 ===
0:07:08.018253 PROGRESS: ============================= Precursor FDR =============================
0:07:08.018335 PROGRESS: Total precursors accumulated: 0
0:07:08.018391 PROGRESS: Target precursors: 0 (0.00%)
0:07:08.018440 PROGRESS: Decoy precursors: 0 (0.00%)
0:07:08.018486 PROGRESS: 
0:07:08.018529 PROGRESS: Precursor Summary:
0:07:08.018729 PROGRESS: 
0:07:08.018797 PROGRESS: Protein Summary:
0:07:08.018870 PROGRESS: =========================================================================
0:07:08.019112 INFO: Target number of precursors not reached yet.
0:07:08.093786 INFO: Starting optimization step 4.
0:07:08.093998 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:07:08.094080 INFO: Using ng extraction backend
0:07:08.094149 PROGRESS: Extracting batch of 6340 precursors
0:07:08.106446 INFO: === Search parameters used ===
0:07:08.106584 INFO: rt_error       : 805.5992431640625
0:07:08.106649 INFO: mobility_error : 0.1
0:07:08.106716 INFO: num_candidates : 1
0:07:08.106770 INFO: ms1_error      : 30
0:07:08.106816 INFO: ms2_error      : 30
0:07:08.106855 INFO: fwhm_rt        : 5
0:07:08.106893 INFO: quant_window   : 3
0:07:08.106942 INFO: ==============================================
0:07:08.182720 INFO: performing precursor FDR with 40 features
0:07:08.182829 INFO: Decoy channel: -1
0:07:08.182854 INFO: Competetive: True
0:07:08.192598 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:08.197130 INFO: Using random state 797405 for train-test-split
0:07:08.247437 INFO: Test AUC: 0.458
0:07:08.247538 INFO: Train AUC: 0.484
0:07:08.247569 INFO: AUC difference: 5.37%
0:07:08.247597 WARNING: AUC difference > 5%. This may indicate overfitting.
0:07:08.472080 INFO: Resetting torch num_threads to 80
0:07:08.477031 PROGRESS: === Extracted 12173 precursors and 57356 fragments ===
0:07:08.477424 INFO: === FDR correction performed with classifier version -1 ===
0:07:08.477871 PROGRESS: ============================= Precursor FDR =============================
0:07:08.477957 PROGRESS: Total precursors accumulated: 0
0:07:08.478016 PROGRESS: Target precursors: 0 (0.00%)
0:07:08.478067 PROGRESS: Decoy precursors: 0 (0.00%)
0:07:08.478113 PROGRESS: 
0:07:08.478157 PROGRESS: Precursor Summary:
0:07:08.478262 PROGRESS: 
0:07:08.478323 PROGRESS: Protein Summary:
0:07:08.478395 PROGRESS: =========================================================================
0:07:08.479704 INFO: Target number of precursors not reached yet.
0:07:08.564883 INFO: Starting optimization step 5.
0:07:08.565120 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:07:08.565207 INFO: Using ng extraction backend
0:07:08.565271 PROGRESS: Extracting batch of 12663 precursors
0:07:08.588565 INFO: === Search parameters used ===
0:07:08.588741 INFO: rt_error       : 805.5992431640625
0:07:08.588796 INFO: mobility_error : 0.1
0:07:08.588840 INFO: num_candidates : 1
0:07:08.589463 INFO: ms1_error      : 30
0:07:08.589514 INFO: ms2_error      : 30
0:07:08.589554 INFO: fwhm_rt        : 5
0:07:08.589592 INFO: quant_window   : 3
0:07:08.589631 INFO: ==============================================
0:07:08.707319 INFO: performing precursor FDR with 40 features
0:07:08.707430 INFO: Decoy channel: -1
0:07:08.707457 INFO: Competetive: True
0:07:08.724143 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:08.731396 INFO: Using random state 225887 for train-test-split
0:07:08.927892 INFO: Test AUC: 0.487
0:07:08.928005 INFO: Train AUC: 0.499
0:07:08.928034 INFO: AUC difference: 2.31%
0:07:09.401130 INFO: Resetting torch num_threads to 80
0:07:09.407420 PROGRESS: === Extracted 24702 precursors and 116046 fragments ===
0:07:09.407826 INFO: === FDR correction performed with classifier version -1 ===
0:07:09.408318 PROGRESS: ============================= Precursor FDR =============================
0:07:09.408408 PROGRESS: Total precursors accumulated: 22
0:07:09.408466 PROGRESS: Target precursors: 22 (100.00%)
0:07:09.408518 PROGRESS: Decoy precursors: 0 (0.00%)
0:07:09.408566 PROGRESS: 
0:07:09.408608 PROGRESS: Precursor Summary:
0:07:09.409551 PROGRESS: Channel   0:	 0.050 FDR:    22; 0.010 FDR:    22; 0.001 FDR:    22
0:07:09.409637 PROGRESS: 
0:07:09.409693 PROGRESS: Protein Summary:
0:07:09.410743 PROGRESS: Channel   0:	 0.050 FDR:    22; 0.010 FDR:    22; 0.001 FDR:    22
0:07:09.410834 PROGRESS: =========================================================================
0:07:09.411238 INFO: Target number of precursors not reached yet.
0:07:09.513132 INFO: Starting optimization step 6.
0:07:09.513380 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:07:09.514746 INFO: Using ng extraction backend
0:07:09.514829 PROGRESS: Extracting batch of 25339 precursors
0:07:09.559208 INFO: === Search parameters used ===
0:07:09.559406 INFO: rt_error       : 805.5992431640625
0:07:09.559458 INFO: mobility_error : 0.1
0:07:09.559505 INFO: num_candidates : 1
0:07:09.559549 INFO: ms1_error      : 30
0:07:09.559592 INFO: ms2_error      : 30
0:07:09.559632 INFO: fwhm_rt        : 5
0:07:09.559672 INFO: quant_window   : 3
0:07:09.559711 INFO: ==============================================
0:07:09.778131 INFO: performing precursor FDR with 40 features
0:07:09.778248 INFO: Decoy channel: -1
0:07:09.778275 INFO: Competetive: True
0:07:09.799835 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:09.814303 INFO: Using random state 979542 for train-test-split
0:07:10.439886 INFO: Test AUC: 0.554
0:07:10.439998 INFO: Train AUC: 0.561
0:07:10.440029 INFO: AUC difference: 1.19%
0:07:10.676622 INFO: Resetting torch num_threads to 80
0:07:10.686538 PROGRESS: === Extracted 49766 precursors and 233332 fragments ===
0:07:10.687095 INFO: === FDR correction performed with classifier version -1 ===
0:07:10.687601 PROGRESS: ============================= Precursor FDR =============================
0:07:10.687687 PROGRESS: Total precursors accumulated: 111
0:07:10.687749 PROGRESS: Target precursors: 110 (99.10%)
0:07:10.687802 PROGRESS: Decoy precursors: 1 (0.90%)
0:07:10.687849 PROGRESS: 
0:07:10.687895 PROGRESS: Precursor Summary:
0:07:10.688799 PROGRESS: Channel   0:	 0.050 FDR:   110; 0.010 FDR:   110; 0.001 FDR:    77
0:07:10.688888 PROGRESS: 
0:07:10.688944 PROGRESS: Protein Summary:
0:07:10.689982 PROGRESS: Channel   0:	 0.050 FDR:   109; 0.010 FDR:   109; 0.001 FDR:    76
0:07:10.690069 PROGRESS: =========================================================================
0:07:10.690823 INFO: Target number of precursors not reached yet.
0:07:10.824802 INFO: Starting optimization step 7.
0:07:10.825050 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:07:10.825131 INFO: Using ng extraction backend
0:07:10.825198 PROGRESS: Extracting batch of 50691 precursors
0:07:10.913181 INFO: === Search parameters used ===
0:07:10.913443 INFO: rt_error       : 805.5992431640625
0:07:10.913499 INFO: mobility_error : 0.1
0:07:10.913548 INFO: num_candidates : 1
0:07:10.913593 INFO: ms1_error      : 30
0:07:10.913635 INFO: ms2_error      : 30
0:07:10.913676 INFO: fwhm_rt        : 5
0:07:10.913716 INFO: quant_window   : 3
0:07:10.913756 INFO: ==============================================
0:07:11.273895 INFO: performing precursor FDR with 40 features
0:07:11.274009 INFO: Decoy channel: -1
0:07:11.274037 INFO: Competetive: True
0:07:11.317598 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:11.344918 INFO: Using random state 742515 for train-test-split
0:07:13.065534 INFO: Test AUC: 0.581
0:07:13.065659 INFO: Train AUC: 0.592
0:07:13.065690 INFO: AUC difference: 1.78%
0:07:13.326837 INFO: Resetting torch num_threads to 80
0:07:13.366255 PROGRESS: === Extracted 99917 precursors and 469358 fragments ===
0:07:13.366802 INFO: === FDR correction performed with classifier version -1 ===
0:07:13.367362 PROGRESS: ============================= Precursor FDR =============================
0:07:13.367461 PROGRESS: Total precursors accumulated: 272
0:07:13.367523 PROGRESS: Target precursors: 270 (99.26%)
0:07:13.367738 PROGRESS: Decoy precursors: 2 (0.74%)
0:07:13.367791 PROGRESS: 
0:07:13.367838 PROGRESS: Precursor Summary:
0:07:13.368794 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:    33
0:07:13.368886 PROGRESS: 
0:07:13.368943 PROGRESS: Protein Summary:
0:07:13.370000 PROGRESS: Channel   0:	 0.050 FDR:   260; 0.010 FDR:   260; 0.001 FDR:    33
0:07:13.370088 PROGRESS: =========================================================================
0:07:13.371870 INFO: Target number of precursors reached.
0:07:13.428151 INFO: fragments_df: keeping 2307 of 469358 [sum(precursor_idx_mask)=2881 sum(mass_error_mask)=469358 stop_rank=2307
0:07:13.697583 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:13.811815 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:14.065798 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:07:14.066255 INFO: Using score_cutoff 12.883181369018555 (fac=0.99, q=1)
0:07:14.066781 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:07:14.066867 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:07:14.066924 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.883181369018555
0:07:14.066989 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:14.130512 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:14.274753 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:07:14.275000 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:07:14.275098 INFO: Starting optimization step 8.
0:07:14.275161 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:07:14.275248 INFO: Using ng extraction backend
0:07:14.275325 PROGRESS: Extracting batch of 100984 precursors
0:07:14.448284 INFO: === Search parameters used ===
0:07:14.448541 INFO: rt_error       : 805.5992431640625
0:07:14.448598 INFO: mobility_error : 0.1
0:07:14.448645 INFO: num_candidates : 3
0:07:14.448689 INFO: ms1_error      : 30
0:07:14.448731 INFO: ms2_error      : 30
0:07:14.448771 INFO: fwhm_rt        : 3.0
0:07:14.448812 INFO: quant_window   : 3
0:07:14.448853 INFO: ==============================================
0:07:15.694188 INFO: performing precursor FDR with 40 features
0:07:15.694312 INFO: Decoy channel: -1
0:07:15.694339 INFO: Competetive: True
0:07:15.768690 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:15.871012 INFO: Using random state 411945 for train-test-split
0:07:20.386891 INFO: Test AUC: 0.588
0:07:20.387057 INFO: Train AUC: 0.602
0:07:20.387092 INFO: AUC difference: 2.24%
0:07:20.701422 INFO: Resetting torch num_threads to 80
0:07:20.716587 PROGRESS: === Extracted 299716 precursors and 1378030 fragments ===
0:07:20.717079 INFO: === FDR correction performed with classifier version 7 ===
0:07:20.717560 PROGRESS: ============================= Precursor FDR =============================
0:07:20.717645 PROGRESS: Total precursors accumulated: 354
0:07:20.717702 PROGRESS: Target precursors: 351 (99.15%)
0:07:20.717751 PROGRESS: Decoy precursors: 3 (0.85%)
0:07:20.717794 PROGRESS: 
0:07:20.717835 PROGRESS: Precursor Summary:
0:07:20.718790 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   351; 0.001 FDR:   314
0:07:20.718878 PROGRESS: 
0:07:20.718931 PROGRESS: Protein Summary:
0:07:20.720061 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:   331; 0.001 FDR:   296
0:07:20.720152 PROGRESS: =========================================================================
0:07:20.726236 INFO: Target number of precursors reached.
0:07:20.819932 INFO: fragments_df: keeping 4127 of 1378030 [sum(precursor_idx_mask)=8021 sum(mass_error_mask)=1378030 stop_rank=4127
0:07:21.200862 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:21.327574 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:21.885271 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:07:21.885793 INFO: Using score_cutoff 12.049066243171692 (fac=0.99, q=1)
0:07:21.886117 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:21.886195 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:21.886247 INFO: Updating optimization_manager: score_cutoff        : 12.883181369018555 -> 12.049066243171692
0:07:21.886308 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:21.950361 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:22.111889 INFO: === checking if optimization conditions were reached ===
0:07:22.112235 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:07:22.115710 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.003334999259512
0:07:22.115837 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.0033.
0:07:22.115908 INFO: ==============================================
0:07:22.115979 INFO: Starting optimization step 9.
0:07:22.116037 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:07:22.116102 INFO: Using ng extraction backend
0:07:22.116161 PROGRESS: Extracting batch of 100984 precursors
0:07:22.301707 INFO: === Search parameters used ===
0:07:22.302053 INFO: rt_error       : 805.5992431640625
0:07:22.302108 INFO: mobility_error : 0.1
0:07:22.302154 INFO: num_candidates : 3
0:07:22.302195 INFO: ms1_error      : 30
0:07:22.302236 INFO: ms2_error      : 7.003334999259512
0:07:22.302276 INFO: fwhm_rt        : 3.0
0:07:22.302317 INFO: quant_window   : 3
0:07:22.302357 INFO: ==============================================
0:07:23.746445 INFO: performing precursor FDR with 40 features
0:07:23.747342 INFO: Decoy channel: -1
0:07:23.747403 INFO: Competetive: True
0:07:23.830160 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:23.936337 INFO: Using random state 411945 for train-test-split
0:07:27.941254 INFO: Test AUC: 0.594
0:07:27.941383 INFO: Train AUC: 0.601
0:07:27.941416 INFO: AUC difference: 1.24%
0:07:28.268573 INFO: Resetting torch num_threads to 80
0:07:28.279798 PROGRESS: === Extracted 302945 precursors and 1698702 fragments ===
0:07:28.280252 INFO: === FDR correction performed with classifier version 7 ===
0:07:28.280756 PROGRESS: ============================= Precursor FDR =============================
0:07:28.280843 PROGRESS: Total precursors accumulated: 561
0:07:28.280902 PROGRESS: Target precursors: 556 (99.11%)
0:07:28.280954 PROGRESS: Decoy precursors: 5 (0.89%)
0:07:28.281011 PROGRESS: 
0:07:28.281058 PROGRESS: Precursor Summary:
0:07:28.282024 PROGRESS: Channel   0:	 0.050 FDR:   556; 0.010 FDR:   556; 0.001 FDR:   302
0:07:28.282112 PROGRESS: 
0:07:28.282164 PROGRESS: Protein Summary:
0:07:28.283369 PROGRESS: Channel   0:	 0.050 FDR:   523; 0.010 FDR:   523; 0.001 FDR:   284
0:07:28.283462 PROGRESS: =========================================================================
0:07:28.288442 INFO: Target number of precursors reached.
0:07:28.399337 INFO: fragments_df: keeping 5000 of 1698702 [sum(precursor_idx_mask)=13591 sum(mass_error_mask)=1698702 stop_rank=5000
0:07:28.674726 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:28.801110 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:29.583902 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:07:29.584331 INFO: Using score_cutoff 11.58876480960846 (fac=0.99, q=1)
0:07:29.584660 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:29.584739 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:29.584795 INFO: Updating optimization_manager: score_cutoff        : 12.049066243171692 -> 11.58876480960846
0:07:29.584861 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:29.617354 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:29.685219 INFO: === checking if optimization conditions were reached ===
0:07:29.685487 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:07:29.688493 INFO: Updating optimization_manager: ms2_error           : 7.003334999259512 -> 7.245156908120633
0:07:29.688609 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.2452.
0:07:29.688688 INFO: ==============================================
0:07:29.688772 INFO: Starting optimization step 10.
0:07:29.688844 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:07:29.688935 INFO: Using ng extraction backend
0:07:29.689019 PROGRESS: Extracting batch of 50293 precursors
0:07:29.779510 INFO: === Search parameters used ===
0:07:29.779774 INFO: rt_error       : 805.5992431640625
0:07:29.779838 INFO: mobility_error : 0.1
0:07:29.779884 INFO: num_candidates : 3
0:07:29.779938 INFO: ms1_error      : 30
0:07:29.779981 INFO: ms2_error      : 7.245156908120633
0:07:29.780023 INFO: fwhm_rt        : 3.0
0:07:29.780065 INFO: quant_window   : 3
0:07:29.780106 INFO: ==============================================
0:07:30.640620 INFO: performing precursor FDR with 40 features
0:07:30.640732 INFO: Decoy channel: -1
0:07:30.640756 INFO: Competetive: True
0:07:30.680620 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:30.723344 INFO: Using random state 411945 for train-test-split
0:07:32.666034 INFO: Test AUC: 0.586
0:07:32.666157 INFO: Train AUC: 0.599
0:07:32.666189 INFO: AUC difference: 2.16%
0:07:32.940202 INFO: Resetting torch num_threads to 80
0:07:32.955330 PROGRESS: === Extracted 150847 precursors and 841929 fragments ===
0:07:32.955686 INFO: === FDR correction performed with classifier version 7 ===
0:07:32.956119 PROGRESS: ============================= Precursor FDR =============================
0:07:32.956202 PROGRESS: Total precursors accumulated: 226
0:07:32.956267 PROGRESS: Target precursors: 224 (99.12%)
0:07:32.956317 PROGRESS: Decoy precursors: 2 (0.88%)
0:07:32.956362 PROGRESS: 
0:07:32.956404 PROGRESS: Precursor Summary:
0:07:32.957284 PROGRESS: Channel   0:	 0.050 FDR:   224; 0.010 FDR:   224; 0.001 FDR:   192
0:07:32.957369 PROGRESS: 
0:07:32.957423 PROGRESS: Protein Summary:
0:07:32.958468 PROGRESS: Channel   0:	 0.050 FDR:   218; 0.010 FDR:   218; 0.001 FDR:   186
0:07:32.958554 PROGRESS: =========================================================================
0:07:32.960783 INFO: Target number of precursors reached.
0:07:33.016980 INFO: fragments_df: keeping 2677 of 841929 [sum(precursor_idx_mask)=5595 sum(mass_error_mask)=841929 stop_rank=2677
0:07:33.202121 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:33.307559 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:33.601209 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:07:33.601663 INFO: Using score_cutoff 12.917848448467254 (fac=0.99, q=1)
0:07:33.601970 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:33.602048 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:33.602100 INFO: Updating optimization_manager: score_cutoff        : 11.58876480960846 -> 12.917848448467254
0:07:33.602159 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:33.633816 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:33.705004 INFO: === checking if optimization conditions were reached ===
0:07:33.705331 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:07:33.706517 INFO: Updating optimization_manager: ms2_error           : 7.245156908120633 -> 7.003334999259512
0:07:33.706673 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
0:07:33.706786 INFO: Updating optimization_manager: score_cutoff        : 12.917848448467254 -> 11.58876480960846
0:07:33.706894 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:33.706993 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:33.707090 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.0033 found after 3 searches.
0:07:33.707160 INFO: ==============================================
0:07:33.707258 PROGRESS: Optimization finished for ms2_error.
0:07:33.863587 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:33.895211 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:33.985948 INFO: Starting optimization step 0.
0:07:33.986154 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:07:33.986253 INFO: Using ng extraction backend
0:07:33.986333 PROGRESS: Extracting batch of 50293 precursors
0:07:34.074833 INFO: === Search parameters used ===
0:07:34.075099 INFO: rt_error       : 805.5992431640625
0:07:34.075160 INFO: mobility_error : 0.1
0:07:34.075222 INFO: num_candidates : 3
0:07:34.075269 INFO: ms1_error      : 30
0:07:34.075318 INFO: ms2_error      : 7.003334999259512
0:07:34.075361 INFO: fwhm_rt        : 3.0
0:07:34.075402 INFO: quant_window   : 3
0:07:34.075447 INFO: ==============================================
0:07:34.731843 INFO: performing precursor FDR with 40 features
0:07:34.731970 INFO: Decoy channel: -1
0:07:34.731998 INFO: Competetive: True
0:07:34.774088 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:34.812574 INFO: Using random state 513852 for train-test-split
0:07:37.088308 INFO: Test AUC: 0.598
0:07:37.088447 INFO: Train AUC: 0.607
0:07:37.088481 INFO: AUC difference: 1.46%
0:07:37.359309 INFO: Resetting torch num_threads to 80
0:07:37.365495 PROGRESS: === Extracted 150877 precursors and 846129 fragments ===
0:07:37.365895 INFO: === FDR correction performed with classifier version 9 ===
0:07:37.366352 PROGRESS: ============================= Precursor FDR =============================
0:07:37.366440 PROGRESS: Total precursors accumulated: 262
0:07:37.366499 PROGRESS: Target precursors: 260 (99.24%)
0:07:37.366550 PROGRESS: Decoy precursors: 2 (0.76%)
0:07:37.366608 PROGRESS: 
0:07:37.366651 PROGRESS: Precursor Summary:
0:07:37.367577 PROGRESS: Channel   0:	 0.050 FDR:   260; 0.010 FDR:   260; 0.001 FDR:   225
0:07:37.367664 PROGRESS: 
0:07:37.367718 PROGRESS: Protein Summary:
0:07:37.368774 PROGRESS: Channel   0:	 0.050 FDR:   252; 0.010 FDR:   252; 0.001 FDR:   218
0:07:37.368860 PROGRESS: =========================================================================
0:07:37.370863 INFO: Target number of precursors reached.
0:07:37.426448 INFO: fragments_df: keeping 2971 of 846129 [sum(precursor_idx_mask)=6394 sum(mass_error_mask)=846129 stop_rank=2971
0:07:37.589863 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:37.694003 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:38.019141 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:07:38.019563 INFO: Using score_cutoff 12.369116871070862 (fac=0.99, q=1)
0:07:38.019876 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:38.019953 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:38.020006 INFO: Updating optimization_manager: score_cutoff        : 11.58876480960846 -> 12.369116871070862
0:07:38.020062 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:38.051057 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:38.113837 INFO: === checking if optimization conditions were reached ===
0:07:38.114072 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:07:38.115917 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 153.00358274388637
0:07:38.116017 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 153.0036.
0:07:38.116085 INFO: ==============================================
0:07:38.116153 INFO: Starting optimization step 1.
0:07:38.116211 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:07:38.116271 INFO: Using ng extraction backend
0:07:38.116330 PROGRESS: Extracting batch of 50293 precursors
0:07:38.203317 INFO: === Search parameters used ===
0:07:38.203599 INFO: rt_error       : 153.00358274388637
0:07:38.203656 INFO: mobility_error : 0.1
0:07:38.203702 INFO: num_candidates : 3
0:07:38.203747 INFO: ms1_error      : 30
0:07:38.203787 INFO: ms2_error      : 7.003334999259512
0:07:38.203828 INFO: fwhm_rt        : 3.0
0:07:38.203869 INFO: quant_window   : 3
0:07:38.203909 INFO: ==============================================
0:07:38.780465 INFO: performing precursor FDR with 40 features
0:07:38.780587 INFO: Decoy channel: -1
0:07:38.780614 INFO: Competetive: True
0:07:38.819281 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:38.854970 INFO: Using random state 513852 for train-test-split
0:07:41.031186 INFO: Test AUC: 0.596
0:07:41.031541 INFO: Train AUC: 0.603
0:07:41.031576 INFO: AUC difference: 1.20%
0:07:41.697697 INFO: Resetting torch num_threads to 80
0:07:41.704070 PROGRESS: === Extracted 150076 precursors and 677282 fragments ===
0:07:41.704417 INFO: === FDR correction performed with classifier version 9 ===
0:07:41.704876 PROGRESS: ============================= Precursor FDR =============================
0:07:41.704967 PROGRESS: Total precursors accumulated: 304
0:07:41.705024 PROGRESS: Target precursors: 301 (99.01%)
0:07:41.705072 PROGRESS: Decoy precursors: 3 (0.99%)
0:07:41.705115 PROGRESS: 
0:07:41.705159 PROGRESS: Precursor Summary:
0:07:41.706133 PROGRESS: Channel   0:	 0.050 FDR:   301; 0.010 FDR:   301; 0.001 FDR:   245
0:07:41.706220 PROGRESS: 
0:07:41.706273 PROGRESS: Protein Summary:
0:07:41.707350 PROGRESS: Channel   0:	 0.050 FDR:   291; 0.010 FDR:   291; 0.001 FDR:   237
0:07:41.707439 PROGRESS: =========================================================================
0:07:41.709391 INFO: Target number of precursors reached.
0:07:41.755598 INFO: fragments_df: keeping 3216 of 677282 [sum(precursor_idx_mask)=7090 sum(mass_error_mask)=677282 stop_rank=3216
0:07:41.937855 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:42.046109 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:42.404346 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:07:42.404765 INFO: Using score_cutoff 12.054699440002441 (fac=0.99, q=1)
0:07:42.405048 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:42.405124 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:42.405179 INFO: Updating optimization_manager: score_cutoff        : 12.369116871070862 -> 12.054699440002441
0:07:42.405234 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:42.437259 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:42.503175 INFO: === checking if optimization conditions were reached ===
0:07:42.503454 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:07:42.505381 INFO: Updating optimization_manager: rt_error            : 153.00358274388637 -> 101.94582268308439
0:07:42.505494 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 101.9458.
0:07:42.505579 INFO: ==============================================
0:07:42.505666 INFO: Starting optimization step 2.
0:07:42.505740 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:07:42.505818 INFO: Using ng extraction backend
0:07:42.505890 PROGRESS: Extracting batch of 50293 precursors
0:07:42.593109 INFO: === Search parameters used ===
0:07:42.593387 INFO: rt_error       : 101.94582268308439
0:07:42.593459 INFO: mobility_error : 0.1
0:07:42.593525 INFO: num_candidates : 3
0:07:42.593586 INFO: ms1_error      : 30
0:07:42.593643 INFO: ms2_error      : 7.003334999259512
0:07:42.593700 INFO: fwhm_rt        : 3.0
0:07:42.593757 INFO: quant_window   : 3
0:07:42.593815 INFO: ==============================================
0:07:43.164979 INFO: performing precursor FDR with 40 features
0:07:43.165100 INFO: Decoy channel: -1
0:07:43.165127 INFO: Competetive: True
0:07:43.203304 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:43.238188 INFO: Using random state 513852 for train-test-split
0:07:45.268767 INFO: Test AUC: 0.583
0:07:45.268891 INFO: Train AUC: 0.605
0:07:45.268922 INFO: AUC difference: 3.56%
0:07:45.536543 INFO: Resetting torch num_threads to 80
0:07:45.542778 PROGRESS: === Extracted 148809 precursors and 620638 fragments ===
0:07:45.543126 INFO: === FDR correction performed with classifier version 9 ===
0:07:45.543597 PROGRESS: ============================= Precursor FDR =============================
0:07:45.543684 PROGRESS: Total precursors accumulated: 287
0:07:45.543742 PROGRESS: Target precursors: 285 (99.30%)
0:07:45.543793 PROGRESS: Decoy precursors: 2 (0.70%)
0:07:45.543840 PROGRESS: 
0:07:45.543882 PROGRESS: Precursor Summary:
0:07:45.544768 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   285; 0.001 FDR:     3
0:07:45.544873 PROGRESS: 
0:07:45.544956 PROGRESS: Protein Summary:
0:07:45.545998 PROGRESS: Channel   0:	 0.050 FDR:   276; 0.010 FDR:   276; 0.001 FDR:     3
0:07:45.546098 PROGRESS: =========================================================================
0:07:45.548089 INFO: Target number of precursors reached.
0:07:45.591555 INFO: fragments_df: keeping 3051 of 620638 [sum(precursor_idx_mask)=6631 sum(mass_error_mask)=620638 stop_rank=3051
0:07:45.727283 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:45.837152 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:46.173175 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:07:46.173585 INFO: Using score_cutoff 12.110222735595704 (fac=0.99, q=1)
0:07:46.173867 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:46.173945 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:46.173998 INFO: Updating optimization_manager: score_cutoff        : 12.054699440002441 -> 12.110222735595704
0:07:46.174055 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:46.205426 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:46.270976 INFO: === checking if optimization conditions were reached ===
0:07:46.271229 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:07:46.273202 INFO: Updating optimization_manager: rt_error            : 101.94582268308439 -> 81.6764538642128
0:07:46.273301 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 81.6765.
0:07:46.273367 INFO: ==============================================
0:07:46.273435 INFO: Starting optimization step 3.
0:07:46.273493 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:07:46.273566 INFO: Using ng extraction backend
0:07:46.273625 PROGRESS: Extracting batch of 50293 precursors
0:07:46.361927 INFO: === Search parameters used ===
0:07:46.362193 INFO: rt_error       : 81.6764538642128
0:07:46.362249 INFO: mobility_error : 0.1
0:07:46.362293 INFO: num_candidates : 3
0:07:46.362339 INFO: ms1_error      : 30
0:07:46.362382 INFO: ms2_error      : 7.003334999259512
0:07:46.362423 INFO: fwhm_rt        : 3.0
0:07:46.362465 INFO: quant_window   : 3
0:07:46.362507 INFO: ==============================================
0:07:46.922793 INFO: performing precursor FDR with 40 features
0:07:46.922915 INFO: Decoy channel: -1
0:07:46.922942 INFO: Competetive: True
0:07:46.961177 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:46.997724 INFO: Using random state 513852 for train-test-split
0:07:49.025250 INFO: Test AUC: 0.588
0:07:49.025372 INFO: Train AUC: 0.603
0:07:49.025403 INFO: AUC difference: 2.51%
0:07:49.285679 INFO: Resetting torch num_threads to 80
0:07:49.303302 PROGRESS: === Extracted 147512 precursors and 588611 fragments ===
0:07:49.303668 INFO: === FDR correction performed with classifier version 9 ===
0:07:49.304130 PROGRESS: ============================= Precursor FDR =============================
0:07:49.304216 PROGRESS: Total precursors accumulated: 369
0:07:49.304272 PROGRESS: Target precursors: 366 (99.19%)
0:07:49.304321 PROGRESS: Decoy precursors: 3 (0.81%)
0:07:49.304366 PROGRESS: 
0:07:49.304407 PROGRESS: Precursor Summary:
0:07:49.305336 PROGRESS: Channel   0:	 0.050 FDR:   366; 0.010 FDR:   366; 0.001 FDR:   243
0:07:49.305423 PROGRESS: 
0:07:49.305477 PROGRESS: Protein Summary:
0:07:49.306605 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   235
0:07:49.306695 PROGRESS: =========================================================================
0:07:49.308803 INFO: Target number of precursors reached.
0:07:49.351703 INFO: fragments_df: keeping 3574 of 588611 [sum(precursor_idx_mask)=8109 sum(mass_error_mask)=588611 stop_rank=3574
0:07:49.494610 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:49.603369 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:50.005834 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:07:50.006270 INFO: Using score_cutoff 10.617048033714294 (fac=0.99, q=1)
0:07:50.006576 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:50.006656 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:50.006708 INFO: Updating optimization_manager: score_cutoff        : 12.110222735595704 -> 10.617048033714294
0:07:50.006765 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:50.037139 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:50.102153 INFO: === checking if optimization conditions were reached ===
0:07:50.102387 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:07:50.104470 INFO: Updating optimization_manager: rt_error            : 81.6764538642128 -> 64.96369728297921
0:07:50.104572 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 64.9637.
0:07:50.104639 INFO: ==============================================
0:07:50.104721 INFO: Starting optimization step 4.
0:07:50.104781 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:07:50.104842 INFO: Using ng extraction backend
0:07:50.104898 PROGRESS: Extracting batch of 50293 precursors
0:07:50.192742 INFO: === Search parameters used ===
0:07:50.193011 INFO: rt_error       : 64.96369728297921
0:07:50.193068 INFO: mobility_error : 0.1
0:07:50.193112 INFO: num_candidates : 3
0:07:50.193157 INFO: ms1_error      : 30
0:07:50.193201 INFO: ms2_error      : 7.003334999259512
0:07:50.193244 INFO: fwhm_rt        : 3.0
0:07:50.193285 INFO: quant_window   : 3
0:07:50.193327 INFO: ==============================================
0:07:50.757131 INFO: performing precursor FDR with 40 features
0:07:50.757249 INFO: Decoy channel: -1
0:07:50.757275 INFO: Competetive: True
0:07:50.794634 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:50.832873 INFO: Using random state 513852 for train-test-split
0:07:52.980838 INFO: Test AUC: 0.591
0:07:52.981006 INFO: Train AUC: 0.603
0:07:52.981038 INFO: AUC difference: 2.05%
0:07:53.248477 INFO: Resetting torch num_threads to 80
0:07:53.255080 PROGRESS: === Extracted 145011 precursors and 552398 fragments ===
0:07:53.255459 INFO: === FDR correction performed with classifier version 9 ===
0:07:53.255913 PROGRESS: ============================= Precursor FDR =============================
0:07:53.255999 PROGRESS: Total precursors accumulated: 285
0:07:53.256058 PROGRESS: Target precursors: 283 (99.30%)
0:07:53.256118 PROGRESS: Decoy precursors: 2 (0.70%)
0:07:53.256161 PROGRESS: 
0:07:53.256207 PROGRESS: Precursor Summary:
0:07:53.257089 PROGRESS: Channel   0:	 0.050 FDR:   283; 0.010 FDR:   283; 0.001 FDR:   213
0:07:53.257182 PROGRESS: 
0:07:53.257235 PROGRESS: Protein Summary:
0:07:53.258290 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   274; 0.001 FDR:   207
0:07:53.258377 PROGRESS: =========================================================================
0:07:53.260453 INFO: Target number of precursors reached.
0:07:53.298315 INFO: fragments_df: keeping 2899 of 552398 [sum(precursor_idx_mask)=6326 sum(mass_error_mask)=552398 stop_rank=2899
0:07:53.475322 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:53.579405 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:53.898346 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:07:53.898839 INFO: Using score_cutoff 12.01226797142029 (fac=0.99, q=1)
0:07:53.899178 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:53.899256 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:53.899308 INFO: Updating optimization_manager: score_cutoff        : 10.617048033714294 -> 12.01226797142029
0:07:53.899366 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:53.930945 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:54.000452 INFO: === checking if optimization conditions were reached ===
0:07:54.000703 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:07:54.002900 INFO: Updating optimization_manager: rt_error            : 64.96369728297921 -> 52.28020651958449
0:07:54.003003 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 52.2802.
0:07:54.003077 INFO: ==============================================
0:07:54.003152 INFO: Starting optimization step 5.
0:07:54.003211 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:07:54.003288 INFO: Using ng extraction backend
0:07:54.003363 PROGRESS: Extracting batch of 50293 precursors
0:07:54.094697 INFO: === Search parameters used ===
0:07:54.094973 INFO: rt_error       : 52.28020651958449
0:07:54.095028 INFO: mobility_error : 0.1
0:07:54.095072 INFO: num_candidates : 3
0:07:54.095114 INFO: ms1_error      : 30
0:07:54.095155 INFO: ms2_error      : 7.003334999259512
0:07:54.095195 INFO: fwhm_rt        : 3.0
0:07:54.095235 INFO: quant_window   : 3
0:07:54.095273 INFO: ==============================================
0:07:54.613397 INFO: performing precursor FDR with 40 features
0:07:54.613562 INFO: Decoy channel: -1
0:07:54.613591 INFO: Competetive: True
0:07:54.648457 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:54.683323 INFO: Using random state 513852 for train-test-split
0:07:56.641295 INFO: Test AUC: 0.593
0:07:56.641439 INFO: Train AUC: 0.607
0:07:56.641470 INFO: AUC difference: 2.38%
0:07:56.897362 INFO: Resetting torch num_threads to 80
0:07:56.903235 PROGRESS: === Extracted 137722 precursors and 503492 fragments ===
0:07:56.903624 INFO: === FDR correction performed with classifier version 9 ===
0:07:56.904066 PROGRESS: ============================= Precursor FDR =============================
0:07:56.904150 PROGRESS: Total precursors accumulated: 249
0:07:56.904207 PROGRESS: Target precursors: 247 (99.20%)
0:07:56.904257 PROGRESS: Decoy precursors: 2 (0.80%)
0:07:56.904301 PROGRESS: 
0:07:56.904352 PROGRESS: Precursor Summary:
0:07:56.905264 PROGRESS: Channel   0:	 0.050 FDR:   247; 0.010 FDR:   247; 0.001 FDR:   221
0:07:56.905352 PROGRESS: 
0:07:56.905406 PROGRESS: Protein Summary:
0:07:56.906457 PROGRESS: Channel   0:	 0.050 FDR:   240; 0.010 FDR:   240; 0.001 FDR:   215
0:07:56.906543 PROGRESS: =========================================================================
0:07:56.908403 INFO: Target number of precursors reached.
0:07:56.942058 INFO: fragments_df: keeping 2484 of 503492 [sum(precursor_idx_mask)=5112 sum(mass_error_mask)=503492 stop_rank=2484
0:07:57.079945 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:07:57.180261 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:07:57.453044 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:07:57.453469 INFO: Using score_cutoff 11.45145195236206 (fac=0.99, q=1)
0:07:57.453774 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:07:57.453853 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:07:57.453906 INFO: Updating optimization_manager: score_cutoff        : 12.01226797142029 -> 11.45145195236206
0:07:57.453960 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:07:57.486120 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:07:57.552967 INFO: === checking if optimization conditions were reached ===
0:07:57.553198 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:07:57.555208 INFO: Updating optimization_manager: rt_error            : 52.28020651958449 -> 36.35317307814504
0:07:57.555325 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 36.3532.
0:07:57.555395 INFO: ==============================================
0:07:57.555467 INFO: Starting optimization step 6.
0:07:57.555528 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:07:57.555596 INFO: Using ng extraction backend
0:07:57.555658 PROGRESS: Extracting batch of 50293 precursors
0:07:57.642991 INFO: === Search parameters used ===
0:07:57.643269 INFO: rt_error       : 36.35317307814504
0:07:57.643323 INFO: mobility_error : 0.1
0:07:57.643387 INFO: num_candidates : 3
0:07:57.643433 INFO: ms1_error      : 30
0:07:57.643476 INFO: ms2_error      : 7.003334999259512
0:07:57.643518 INFO: fwhm_rt        : 3.0
0:07:57.643557 INFO: quant_window   : 3
0:07:57.643597 INFO: ==============================================
0:07:58.146848 INFO: performing precursor FDR with 40 features
0:07:58.146971 INFO: Decoy channel: -1
0:07:58.146998 INFO: Competetive: True
0:07:58.181079 INFO: Setting torch num_threads to 2 for FDR classification task
0:07:58.212356 INFO: Using random state 513852 for train-test-split
0:08:00.180986 INFO: Test AUC: 0.592
0:08:00.181110 INFO: Train AUC: 0.608
0:08:00.181141 INFO: AUC difference: 2.61%
0:08:00.442211 INFO: Resetting torch num_threads to 80
0:08:00.447868 PROGRESS: === Extracted 134202 precursors and 490086 fragments ===
0:08:00.448216 INFO: === FDR correction performed with classifier version 9 ===
0:08:00.448653 PROGRESS: ============================= Precursor FDR =============================
0:08:00.448735 PROGRESS: Total precursors accumulated: 233
0:08:00.448792 PROGRESS: Target precursors: 231 (99.14%)
0:08:00.448850 PROGRESS: Decoy precursors: 2 (0.86%)
0:08:00.448898 PROGRESS: 
0:08:00.448941 PROGRESS: Precursor Summary:
0:08:00.449808 PROGRESS: Channel   0:	 0.050 FDR:   231; 0.010 FDR:   231; 0.001 FDR:   201
0:08:00.449893 PROGRESS: 
0:08:00.449945 PROGRESS: Protein Summary:
0:08:00.450966 PROGRESS: Channel   0:	 0.050 FDR:   226; 0.010 FDR:   226; 0.001 FDR:   196
0:08:00.451054 PROGRESS: =========================================================================
0:08:00.452854 INFO: Target number of precursors reached.
0:08:00.485879 INFO: fragments_df: keeping 2278 of 490086 [sum(precursor_idx_mask)=4613 sum(mass_error_mask)=490086 stop_rank=2278
0:08:00.647007 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:08:00.745698 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:08:00.999879 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:08:01.000290 INFO: Using score_cutoff 10.136797634124756 (fac=0.99, q=1)
0:08:01.000573 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:08:01.000650 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:08:01.000704 INFO: Updating optimization_manager: score_cutoff        : 11.45145195236206 -> 10.136797634124756
0:08:01.000758 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:08:01.033027 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:08:01.098326 INFO: === checking if optimization conditions were reached ===
0:08:01.098581 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:08:01.100504 INFO: Updating optimization_manager: rt_error            : 36.35317307814504 -> 33.61307550576207
0:08:01.100605 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 33.6131.
0:08:01.100674 INFO: ==============================================
0:08:01.100742 INFO: Starting optimization step 7.
0:08:01.100801 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:08:01.100863 INFO: Using ng extraction backend
0:08:01.100927 PROGRESS: Extracting batch of 50293 precursors
0:08:01.187999 INFO: === Search parameters used ===
0:08:01.188265 INFO: rt_error       : 33.61307550576207
0:08:01.188319 INFO: mobility_error : 0.1
0:08:01.188363 INFO: num_candidates : 3
0:08:01.188409 INFO: ms1_error      : 30
0:08:01.188451 INFO: ms2_error      : 7.003334999259512
0:08:01.188494 INFO: fwhm_rt        : 3.0
0:08:01.188535 INFO: quant_window   : 3
0:08:01.188577 INFO: ==============================================
0:08:01.695852 INFO: performing precursor FDR with 40 features
0:08:01.695973 INFO: Decoy channel: -1
0:08:01.696000 INFO: Competetive: True
0:08:01.731138 INFO: Setting torch num_threads to 2 for FDR classification task
0:08:01.763968 INFO: Using random state 513852 for train-test-split
0:08:03.610303 INFO: Test AUC: 0.592
0:08:03.610426 INFO: Train AUC: 0.605
0:08:03.610469 INFO: AUC difference: 2.11%
0:08:03.872566 INFO: Resetting torch num_threads to 80
0:08:03.878543 PROGRESS: === Extracted 134375 precursors and 494009 fragments ===
0:08:03.878901 INFO: === FDR correction performed with classifier version 9 ===
0:08:03.879354 PROGRESS: ============================= Precursor FDR =============================
0:08:03.879437 PROGRESS: Total precursors accumulated: 306
0:08:03.879501 PROGRESS: Target precursors: 303 (99.02%)
0:08:03.879552 PROGRESS: Decoy precursors: 3 (0.98%)
0:08:03.879596 PROGRESS: 
0:08:03.879638 PROGRESS: Precursor Summary:
0:08:03.880541 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   303; 0.001 FDR:   208
0:08:03.880627 PROGRESS: 
0:08:03.880679 PROGRESS: Protein Summary:
0:08:03.881745 PROGRESS: Channel   0:	 0.050 FDR:   297; 0.010 FDR:   297; 0.001 FDR:   204
0:08:03.881831 PROGRESS: =========================================================================
0:08:03.883688 INFO: Target number of precursors reached.
0:08:03.918396 INFO: fragments_df: keeping 2733 of 494009 [sum(precursor_idx_mask)=5846 sum(mass_error_mask)=494009 stop_rank=2733
0:08:04.084327 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:08:04.188090 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:08:04.488439 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:08:04.488866 INFO: Using score_cutoff 10.57063451385498 (fac=0.99, q=1)
0:08:04.489151 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:08:04.489228 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:08:04.489281 INFO: Updating optimization_manager: score_cutoff        : 10.136797634124756 -> 10.57063451385498
0:08:04.489333 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:08:04.520902 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:08:04.582308 INFO: === checking if optimization conditions were reached ===
0:08:04.582534 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:08:04.584519 INFO: Updating optimization_manager: rt_error            : 33.61307550576207 -> 33.116820865652784
0:08:04.584619 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 33.1168.
0:08:04.584683 INFO: ==============================================
0:08:04.584751 INFO: Starting optimization step 8.
0:08:04.584807 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:08:04.584866 INFO: Using ng extraction backend
0:08:04.584921 PROGRESS: Extracting batch of 50293 precursors
0:08:04.671968 INFO: === Search parameters used ===
0:08:04.672229 INFO: rt_error       : 33.116820865652784
0:08:04.672284 INFO: mobility_error : 0.1
0:08:04.672330 INFO: num_candidates : 3
0:08:04.672374 INFO: ms1_error      : 30
0:08:04.672416 INFO: ms2_error      : 7.003334999259512
0:08:04.672458 INFO: fwhm_rt        : 3.0
0:08:04.672499 INFO: quant_window   : 3
0:08:04.672540 INFO: ==============================================
0:08:05.175141 INFO: performing precursor FDR with 40 features
0:08:05.175252 INFO: Decoy channel: -1
0:08:05.175283 INFO: Competetive: True
0:08:05.211571 INFO: Setting torch num_threads to 2 for FDR classification task
0:08:05.242078 INFO: Using random state 513852 for train-test-split
0:08:06.994555 INFO: Test AUC: 0.594
0:08:06.994688 INFO: Train AUC: 0.605
0:08:06.994720 INFO: AUC difference: 1.95%
0:08:07.247371 INFO: Resetting torch num_threads to 80
0:08:07.253003 PROGRESS: === Extracted 134461 precursors and 496985 fragments ===
0:08:07.253345 INFO: === FDR correction performed with classifier version 9 ===
0:08:07.253800 PROGRESS: ============================= Precursor FDR =============================
0:08:07.253885 PROGRESS: Total precursors accumulated: 239
0:08:07.253942 PROGRESS: Target precursors: 237 (99.16%)
0:08:07.253991 PROGRESS: Decoy precursors: 2 (0.84%)
0:08:07.254035 PROGRESS: 
0:08:07.254078 PROGRESS: Precursor Summary:
0:08:07.254982 PROGRESS: Channel   0:	 0.050 FDR:   237; 0.010 FDR:   237; 0.001 FDR:   195
0:08:07.255088 PROGRESS: 
0:08:07.255141 PROGRESS: Protein Summary:
0:08:07.256180 PROGRESS: Channel   0:	 0.050 FDR:   233; 0.010 FDR:   233; 0.001 FDR:   191
0:08:07.256267 PROGRESS: =========================================================================
0:08:07.258051 INFO: Target number of precursors reached.
0:08:07.292533 INFO: fragments_df: keeping 2326 of 496985 [sum(precursor_idx_mask)=4683 sum(mass_error_mask)=496985 stop_rank=2326
0:08:07.428376 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:08:08.006074 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:08:08.264479 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:08:08.264896 INFO: Using score_cutoff 11.854281881332396 (fac=0.99, q=1)
0:08:08.265177 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:08:08.265257 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:08:08.265310 INFO: Updating optimization_manager: score_cutoff        : 10.57063451385498 -> 11.854281881332396
0:08:08.265371 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:08:08.297546 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:08:08.363245 INFO: === checking if optimization conditions were reached ===
0:08:08.363484 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:08:08.364560 INFO: Updating optimization_manager: rt_error            : 33.116820865652784 -> 81.6764538642128
0:08:08.364689 INFO: Updating optimization_manager: classifier_version  : 9 -> 14
0:08:08.364787 INFO: Updating optimization_manager: score_cutoff        : 11.854281881332396 -> 10.617048033714294
0:08:08.364874 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:08:08.364956 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:08:08.365038 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 81.6765 found after 9 searches.
0:08:08.365102 INFO: ==============================================
0:08:08.365169 PROGRESS: Optimization finished for rt_error.
0:08:08.499778 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:08:08.532326 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:08:08.624432 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:08:08.624629 PROGRESS: ==============================================
0:08:08.624697 PROGRESS: ms2_error      : 7.0033
0:08:08.624753 PROGRESS: rt_error       : 81.6765
0:08:08.624800 PROGRESS: ==============================================
0:08:08.625276 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:08:16.593961 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:08:34.298750 INFO: Using ng extraction backend
0:08:34.299330 PROGRESS: Extracting batch of 12001526 precursors
0:08:50.221047 INFO: === Search parameters used ===
0:08:50.221622 INFO: rt_error       : 81.6764538642128
0:08:50.221691 INFO: mobility_error : 0.1
0:08:50.221739 INFO: num_candidates : 3
0:08:50.221781 INFO: ms1_error      : 30
0:08:50.221822 INFO: ms2_error      : 7.003334999259512
0:08:50.221860 INFO: fwhm_rt        : 3.0
0:08:50.221898 INFO: quant_window   : 3
0:08:50.221934 INFO: ==============================================
0:09:31.212907 INFO: Removed 24738427 precursors with score below cutoff 10.617048033714294
0:09:43.744406 INFO: performing precursor FDR with 40 features
0:09:43.744534 INFO: Decoy channel: -1
0:09:43.744567 INFO: Competetive: True
0:09:44.882431 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:49.174943 INFO: Using random state 446031 for train-test-split
0:12:21.475329 INFO: Test AUC: 0.629
0:12:21.475609 INFO: Train AUC: 0.630
0:12:21.475648 INFO: AUC difference: 0.13%
0:12:24.798739 INFO: Resetting torch num_threads to 80
0:12:26.448332 PROGRESS: ============================= Precursor FDR =============================
0:12:26.448618 PROGRESS: Total precursors accumulated: 89,343
0:12:26.448698 PROGRESS: Target precursors: 88,459 (99.01%)
0:12:26.448750 PROGRESS: Decoy precursors: 884 (0.99%)
0:12:26.448798 PROGRESS: 
0:12:26.448842 PROGRESS: Precursor Summary:
0:12:26.474378 PROGRESS: Channel   0:	 0.050 FDR: 88,459; 0.010 FDR: 88,459; 0.001 FDR: 61,622
0:12:26.474631 PROGRESS: 
0:12:26.474699 PROGRESS: Protein Summary:
0:12:26.508054 PROGRESS: Channel   0:	 0.050 FDR: 13,276; 0.010 FDR: 13,276; 0.001 FDR: 9,891
0:12:26.508278 PROGRESS: =========================================================================
0:12:26.569260 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:12:26.739033 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:12:26.982241 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:12:27.516380 PROGRESS: 
0:12:27.516534 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
0:12:27.516607 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
0:12:27.516775 INFO: Initializing TimingManager
0:12:27.517235 INFO: Initializing RawFileManager
0:12:40.465287 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:12:40.469533 INFO: Determining DIA cycle
0:12:40.485014 INFO: Found cycle with start 0.00 min and length 300.
0:12:40.649821 INFO: RT (min)            : 0.0 - 26.9
0:12:40.649916 INFO: RT duration (sec)   : 1611.2
0:12:40.649947 INFO: RT duration (min)   : 26.9
0:12:40.649973 INFO: Cycle len (scans)   : 300
0:12:40.649992 INFO: Cycle len (sec)     : 1.65
0:12:40.650011 INFO: Number of cycles    : 978
0:12:40.650030 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:12:40.650083 INFO: Creating DIA data object took: 13.132750034332275
0:12:41.323201 INFO: Creating DIA data NG object took: 0.6729884147644043
0:12:43.025380 INFO: Initializing CalibrationManager
0:12:43.025651 INFO: Setting up calibration estimators ..
0:12:43.025711 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:12:43.025812 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'}' ..
0:12:43.025948 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:12:43.026006 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:12:43.026062 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}}' ..
0:12:43.026115 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:12:43.026162 INFO: Done setting up calibration estimators.
0:12:43.026371 INFO: Initializing OptimizationManager
0:12:43.026525 INFO: initial parameter: ms1_error = 30
0:12:43.026588 INFO: initial parameter: ms2_error = 30
0:12:43.026638 INFO: initial parameter: rt_error = 805.6019897460938
0:12:43.026686 INFO: initial parameter: mobility_error = 0.1
0:12:43.026727 INFO: initial parameter: num_candidates = 1
0:12:43.026769 INFO: initial parameter: fwhm_rt = 5
0:12:43.026812 INFO: initial parameter: fwhm_mobility = 0.01
0:12:43.026850 INFO: initial parameter: score_cutoff = 0
0:12:43.026894 INFO: initial parameter: classifier_version = -1
0:12:43.026976 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:12:43.027328 INFO: FDRManager: loading saved state not requested, will be initialized.
0:12:43.027370 INFO: Initializing FDRManager
0:12:43.027413 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:12:44.221217 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:12:44.951429 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:12:44.951800 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:12:44.951941 PROGRESS: Starting initial search for precursors.
0:12:44.952026 INFO: Starting optimization step 0.
0:12:44.952088 PROGRESS: === Extracting elution groups 0 to 200 ===
0:12:44.952152 INFO: Using ng extraction backend
0:12:44.952219 PROGRESS: Extracting batch of 396 precursors
0:12:44.954153 INFO: === Search parameters used ===
0:12:44.954250 INFO: rt_error       : 805.6019897460938
0:12:44.954300 INFO: mobility_error : 0.1
0:12:44.954344 INFO: num_candidates : 1
0:12:44.954388 INFO: ms1_error      : 30
0:12:44.954427 INFO: ms2_error      : 30
0:12:44.954468 INFO: fwhm_rt        : 5
0:12:44.954509 INFO: quant_window   : 3
0:12:44.954547 INFO: ==============================================
0:12:44.978787 INFO: performing precursor FDR with 40 features
0:12:44.978887 INFO: Decoy channel: -1
0:12:44.978912 INFO: Competetive: True
0:12:44.979898 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:44.982345 INFO: Using random state 813372 for train-test-split
0:12:44.989807 INFO: Test AUC: 0.403
0:12:44.989866 INFO: Train AUC: 0.525
0:12:44.989897 INFO: AUC difference: 23.28%
0:12:44.989919 WARNING: AUC difference > 5%. This may indicate overfitting.
0:12:45.201604 INFO: Resetting torch num_threads to 80
0:12:45.202953 PROGRESS: === Extracted 391 precursors and 1831 fragments ===
0:12:45.203288 INFO: === FDR correction performed with classifier version -1 ===
0:12:45.203740 PROGRESS: ============================= Precursor FDR =============================
0:12:45.203827 PROGRESS: Total precursors accumulated: 1
0:12:45.203886 PROGRESS: Target precursors: 1 (100.00%)
0:12:45.203936 PROGRESS: Decoy precursors: 0 (0.00%)
0:12:45.203981 PROGRESS: 
0:12:45.204026 PROGRESS: Precursor Summary:
0:12:45.204948 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:12:45.205033 PROGRESS: 
0:12:45.205088 PROGRESS: Protein Summary:
0:12:45.206098 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:12:45.206183 PROGRESS: =========================================================================
0:12:45.206345 INFO: Target number of precursors not reached yet.
0:12:45.270387 INFO: Starting optimization step 1.
0:12:45.270588 PROGRESS: === Extracting elution groups 200 to 600 ===
0:12:45.270671 INFO: Using ng extraction backend
0:12:45.270738 PROGRESS: Extracting batch of 786 precursors
0:12:45.273395 INFO: === Search parameters used ===
0:12:45.273511 INFO: rt_error       : 805.6019897460938
0:12:45.273560 INFO: mobility_error : 0.1
0:12:45.273605 INFO: num_candidates : 1
0:12:45.273646 INFO: ms1_error      : 30
0:12:45.273686 INFO: ms2_error      : 30
0:12:45.273725 INFO: fwhm_rt        : 5
0:12:45.273766 INFO: quant_window   : 3
0:12:45.273803 INFO: ==============================================
0:12:45.300151 INFO: performing precursor FDR with 40 features
0:12:45.300254 INFO: Decoy channel: -1
0:12:45.300279 INFO: Competetive: True
0:12:45.303361 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:45.305022 INFO: Using random state 728503 for train-test-split
0:12:45.313372 INFO: Test AUC: 0.499
0:12:45.313427 INFO: Train AUC: 0.489
0:12:45.313456 INFO: AUC difference: 2.07%
0:12:45.526258 INFO: Resetting torch num_threads to 80
0:12:45.528356 PROGRESS: === Extracted 1172 precursors and 5506 fragments ===
0:12:45.528701 INFO: === FDR correction performed with classifier version -1 ===
0:12:45.529151 PROGRESS: ============================= Precursor FDR =============================
0:12:45.529238 PROGRESS: Total precursors accumulated: 2
0:12:45.529305 PROGRESS: Target precursors: 2 (100.00%)
0:12:45.529355 PROGRESS: Decoy precursors: 0 (0.00%)
0:12:45.529399 PROGRESS: 
0:12:45.529445 PROGRESS: Precursor Summary:
0:12:45.530369 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:12:45.530458 PROGRESS: 
0:12:45.530512 PROGRESS: Protein Summary:
0:12:45.531520 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:12:45.531610 PROGRESS: =========================================================================
0:12:45.531800 INFO: Target number of precursors not reached yet.
0:12:45.598485 INFO: Starting optimization step 2.
0:12:45.598688 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:12:45.598768 INFO: Using ng extraction backend
0:12:45.598831 PROGRESS: Extracting batch of 1592 precursors
0:12:45.602988 INFO: === Search parameters used ===
0:12:45.603107 INFO: rt_error       : 805.6019897460938
0:12:45.603155 INFO: mobility_error : 0.1
0:12:45.603201 INFO: num_candidates : 1
0:12:45.603244 INFO: ms1_error      : 30
0:12:45.603284 INFO: ms2_error      : 30
0:12:45.603326 INFO: fwhm_rt        : 5
0:12:45.603366 INFO: quant_window   : 3
0:12:45.603404 INFO: ==============================================
0:12:45.638177 INFO: performing precursor FDR with 40 features
0:12:45.638250 INFO: Decoy channel: -1
0:12:45.638275 INFO: Competetive: True
0:12:45.641888 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:45.644012 INFO: Using random state 725350 for train-test-split
0:12:45.656620 INFO: Test AUC: 0.475
0:12:45.656682 INFO: Train AUC: 0.508
0:12:45.656711 INFO: AUC difference: 6.54%
0:12:45.656733 WARNING: AUC difference > 5%. This may indicate overfitting.
0:12:45.871163 INFO: Resetting torch num_threads to 80
0:12:45.873650 PROGRESS: === Extracted 2752 precursors and 12933 fragments ===
0:12:45.873992 INFO: === FDR correction performed with classifier version -1 ===
0:12:45.874430 PROGRESS: ============================= Precursor FDR =============================
0:12:45.874515 PROGRESS: Total precursors accumulated: 0
0:12:45.874583 PROGRESS: Target precursors: 0 (0.00%)
0:12:45.874636 PROGRESS: Decoy precursors: 0 (0.00%)
0:12:45.874679 PROGRESS: 
0:12:45.874722 PROGRESS: Precursor Summary:
0:12:45.874826 PROGRESS: 
0:12:45.874886 PROGRESS: Protein Summary:
0:12:45.874958 PROGRESS: =========================================================================
0:12:45.875154 INFO: Target number of precursors not reached yet.
0:12:45.944170 INFO: Starting optimization step 3.
0:12:45.944380 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:12:45.944458 INFO: Using ng extraction backend
0:12:45.944515 PROGRESS: Extracting batch of 3177 precursors
0:12:45.951657 INFO: === Search parameters used ===
0:12:45.951795 INFO: rt_error       : 805.6019897460938
0:12:45.951844 INFO: mobility_error : 0.1
0:12:45.951889 INFO: num_candidates : 1
0:12:45.951931 INFO: ms1_error      : 30
0:12:45.951971 INFO: ms2_error      : 30
0:12:45.952011 INFO: fwhm_rt        : 5
0:12:45.952053 INFO: quant_window   : 3
0:12:45.952104 INFO: ==============================================
0:12:46.000046 INFO: performing precursor FDR with 40 features
0:12:46.000134 INFO: Decoy channel: -1
0:12:46.000160 INFO: Competetive: True
0:12:46.004738 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:46.007223 INFO: Using random state 885714 for train-test-split
0:12:46.029116 INFO: Test AUC: 0.491
0:12:46.029195 INFO: Train AUC: 0.505
0:12:46.029225 INFO: AUC difference: 2.79%
0:12:46.247733 INFO: Resetting torch num_threads to 80
0:12:46.250924 PROGRESS: === Extracted 5885 precursors and 27703 fragments ===
0:12:46.251274 INFO: === FDR correction performed with classifier version -1 ===
0:12:46.251714 PROGRESS: ============================= Precursor FDR =============================
0:12:46.251802 PROGRESS: Total precursors accumulated: 0
0:12:46.251860 PROGRESS: Target precursors: 0 (0.00%)
0:12:46.251910 PROGRESS: Decoy precursors: 0 (0.00%)
0:12:46.251955 PROGRESS: 
0:12:46.251999 PROGRESS: Precursor Summary:
0:12:46.252113 PROGRESS: 
0:12:46.252176 PROGRESS: Protein Summary:
0:12:46.252249 PROGRESS: =========================================================================
0:12:46.252479 INFO: Target number of precursors not reached yet.
0:12:46.327281 INFO: Starting optimization step 4.
0:12:46.327493 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:12:46.327573 INFO: Using ng extraction backend
0:12:46.327643 PROGRESS: Extracting batch of 6340 precursors
0:12:46.339936 INFO: === Search parameters used ===
0:12:46.340084 INFO: rt_error       : 805.6019897460938
0:12:46.340139 INFO: mobility_error : 0.1
0:12:46.340183 INFO: num_candidates : 1
0:12:46.340225 INFO: ms1_error      : 30
0:12:46.340280 INFO: ms2_error      : 30
0:12:46.340322 INFO: fwhm_rt        : 5
0:12:46.340362 INFO: quant_window   : 3
0:12:46.340400 INFO: ==============================================
0:12:46.412719 INFO: performing precursor FDR with 40 features
0:12:46.412819 INFO: Decoy channel: -1
0:12:46.412845 INFO: Competetive: True
0:12:46.419164 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:46.422815 INFO: Using random state 61113 for train-test-split
0:12:46.461506 INFO: Test AUC: 0.520
0:12:46.461610 INFO: Train AUC: 0.503
0:12:46.461639 INFO: AUC difference: 3.44%
0:12:46.682290 INFO: Resetting torch num_threads to 80
0:12:46.687171 PROGRESS: === Extracted 12138 precursors and 56682 fragments ===
0:12:46.687551 INFO: === FDR correction performed with classifier version -1 ===
0:12:46.687992 PROGRESS: ============================= Precursor FDR =============================
0:12:46.688076 PROGRESS: Total precursors accumulated: 0
0:12:46.688132 PROGRESS: Target precursors: 0 (0.00%)
0:12:46.688181 PROGRESS: Decoy precursors: 0 (0.00%)
0:12:46.688226 PROGRESS: 
0:12:46.688270 PROGRESS: Precursor Summary:
0:12:46.688376 PROGRESS: 
0:12:46.688437 PROGRESS: Protein Summary:
0:12:46.688508 PROGRESS: =========================================================================
0:12:46.688786 INFO: Target number of precursors not reached yet.
0:12:46.772010 INFO: Starting optimization step 5.
0:12:46.772238 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:12:46.772317 INFO: Using ng extraction backend
0:12:46.772383 PROGRESS: Extracting batch of 12663 precursors
0:12:46.795547 INFO: === Search parameters used ===
0:12:46.795737 INFO: rt_error       : 805.6019897460938
0:12:46.795802 INFO: mobility_error : 0.1
0:12:46.795849 INFO: num_candidates : 1
0:12:46.795891 INFO: ms1_error      : 30
0:12:46.795933 INFO: ms2_error      : 30
0:12:46.795976 INFO: fwhm_rt        : 5
0:12:46.796015 INFO: quant_window   : 3
0:12:46.796054 INFO: ==============================================
0:12:46.927373 INFO: performing precursor FDR with 40 features
0:12:46.927488 INFO: Decoy channel: -1
0:12:46.927514 INFO: Competetive: True
0:12:46.942436 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:46.948750 INFO: Using random state 855142 for train-test-split
0:12:47.197942 INFO: Test AUC: 0.525
0:12:47.198041 INFO: Train AUC: 0.511
0:12:47.198072 INFO: AUC difference: 2.67%
0:12:47.421886 INFO: Resetting torch num_threads to 80
0:12:47.428036 PROGRESS: === Extracted 24633 precursors and 115281 fragments ===
0:12:47.428430 INFO: === FDR correction performed with classifier version -1 ===
0:12:47.428885 PROGRESS: ============================= Precursor FDR =============================
0:12:47.428975 PROGRESS: Total precursors accumulated: 0
0:12:47.429032 PROGRESS: Target precursors: 0 (0.00%)
0:12:47.429081 PROGRESS: Decoy precursors: 0 (0.00%)
0:12:47.429126 PROGRESS: 
0:12:47.429168 PROGRESS: Precursor Summary:
0:12:47.429280 PROGRESS: 
0:12:47.429341 PROGRESS: Protein Summary:
0:12:47.429413 PROGRESS: =========================================================================
0:12:47.429826 INFO: Target number of precursors not reached yet.
0:12:47.528649 INFO: Starting optimization step 6.
0:12:47.528887 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:12:47.528981 INFO: Using ng extraction backend
0:12:47.529068 PROGRESS: Extracting batch of 25339 precursors
0:12:47.574088 INFO: === Search parameters used ===
0:12:47.574293 INFO: rt_error       : 805.6019897460938
0:12:47.574345 INFO: mobility_error : 0.1
0:12:47.574389 INFO: num_candidates : 1
0:12:47.574431 INFO: ms1_error      : 30
0:12:47.574472 INFO: ms2_error      : 30
0:12:47.574511 INFO: fwhm_rt        : 5
0:12:47.574552 INFO: quant_window   : 3
0:12:47.574632 INFO: ==============================================
0:12:47.786901 INFO: performing precursor FDR with 40 features
0:12:47.787017 INFO: Decoy channel: -1
0:12:47.787044 INFO: Competetive: True
0:12:47.806513 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:47.818346 INFO: Using random state 681178 for train-test-split
0:12:48.424369 INFO: Test AUC: 0.543
0:12:48.424486 INFO: Train AUC: 0.547
0:12:48.424517 INFO: AUC difference: 0.78%
0:12:48.656672 INFO: Resetting torch num_threads to 80
0:12:48.666579 PROGRESS: === Extracted 49665 precursors and 231545 fragments ===
0:12:48.667134 INFO: === FDR correction performed with classifier version -1 ===
0:12:48.667709 PROGRESS: ============================= Precursor FDR =============================
0:12:48.667801 PROGRESS: Total precursors accumulated: 19
0:12:48.667859 PROGRESS: Target precursors: 19 (100.00%)
0:12:48.667911 PROGRESS: Decoy precursors: 0 (0.00%)
0:12:48.667958 PROGRESS: 
0:12:48.668003 PROGRESS: Precursor Summary:
0:12:48.668959 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:12:48.669045 PROGRESS: 
0:12:48.669104 PROGRESS: Protein Summary:
0:12:48.670156 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:12:48.670245 PROGRESS: =========================================================================
0:12:48.671010 INFO: Target number of precursors not reached yet.
0:12:48.804515 INFO: Starting optimization step 7.
0:12:48.804768 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:12:48.804851 INFO: Using ng extraction backend
0:12:48.804913 PROGRESS: Extracting batch of 50691 precursors
0:12:48.892789 INFO: === Search parameters used ===
0:12:48.893053 INFO: rt_error       : 805.6019897460938
0:12:48.893105 INFO: mobility_error : 0.1
0:12:48.893155 INFO: num_candidates : 1
0:12:48.893197 INFO: ms1_error      : 30
0:12:48.893239 INFO: ms2_error      : 30
0:12:48.893281 INFO: fwhm_rt        : 5
0:12:48.893322 INFO: quant_window   : 3
0:12:48.893361 INFO: ==============================================
0:12:49.258278 INFO: performing precursor FDR with 40 features
0:12:49.258389 INFO: Decoy channel: -1
0:12:49.258415 INFO: Competetive: True
0:12:49.297856 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:49.323464 INFO: Using random state 786235 for train-test-split
0:12:50.678051 INFO: Test AUC: 0.569
0:12:50.678177 INFO: Train AUC: 0.590
0:12:50.678208 INFO: AUC difference: 3.59%
0:12:50.930050 INFO: Resetting torch num_threads to 80
0:12:50.948801 PROGRESS: === Extracted 99812 precursors and 465578 fragments ===
0:12:50.949396 INFO: === FDR correction performed with classifier version -1 ===
0:12:50.949984 PROGRESS: ============================= Precursor FDR =============================
0:12:50.950090 PROGRESS: Total precursors accumulated: 216
0:12:50.950152 PROGRESS: Target precursors: 214 (99.07%)
0:12:50.950216 PROGRESS: Decoy precursors: 2 (0.93%)
0:12:50.950265 PROGRESS: 
0:12:50.950309 PROGRESS: Precursor Summary:
0:12:50.951275 PROGRESS: Channel   0:	 0.050 FDR:   214; 0.010 FDR:   214; 0.001 FDR:   193
0:12:50.951371 PROGRESS: 
0:12:50.951428 PROGRESS: Protein Summary:
0:12:50.952484 PROGRESS: Channel   0:	 0.050 FDR:   202; 0.010 FDR:   202; 0.001 FDR:   184
0:12:50.952574 PROGRESS: =========================================================================
0:12:50.953890 INFO: Target number of precursors reached.
0:12:50.988069 INFO: fragments_df: keeping 1925 of 465578 [sum(precursor_idx_mask)=2379 sum(mass_error_mask)=465578 stop_rank=1925
0:12:51.191780 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:12:51.293064 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:12:51.512232 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:12:51.512653 INFO: Using score_cutoff 15.024009417057037 (fac=0.99, q=1)
0:12:51.512954 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:12:51.513034 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:12:51.513088 INFO: Updating optimization_manager: score_cutoff        : 0 -> 15.024009417057037
0:12:51.513146 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:12:51.575769 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:12:51.731820 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:12:51.732097 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:12:51.732205 INFO: Starting optimization step 8.
0:12:51.732276 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:12:51.732352 INFO: Using ng extraction backend
0:12:51.732422 PROGRESS: Extracting batch of 100984 precursors
0:12:51.907264 INFO: === Search parameters used ===
0:12:51.907520 INFO: rt_error       : 805.6019897460938
0:12:51.907576 INFO: mobility_error : 0.1
0:12:51.907622 INFO: num_candidates : 3
0:12:51.907668 INFO: ms1_error      : 30
0:12:51.907708 INFO: ms2_error      : 30
0:12:51.907748 INFO: fwhm_rt        : 3.0
0:12:51.907788 INFO: quant_window   : 3
0:12:51.907828 INFO: ==============================================
0:12:53.205858 INFO: performing precursor FDR with 40 features
0:12:53.205974 INFO: Decoy channel: -1
0:12:53.206000 INFO: Competetive: True
0:12:53.278628 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:53.379638 INFO: Using random state 393924 for train-test-split
0:12:57.428702 INFO: Test AUC: 0.591
0:12:57.428818 INFO: Train AUC: 0.603
0:12:57.428849 INFO: AUC difference: 1.84%
0:12:57.739722 INFO: Resetting torch num_threads to 80
0:12:57.748412 PROGRESS: === Extracted 299627 precursors and 1368172 fragments ===
0:12:57.748795 INFO: === FDR correction performed with classifier version 7 ===
0:12:57.749221 PROGRESS: ============================= Precursor FDR =============================
0:12:57.749305 PROGRESS: Total precursors accumulated: 0
0:12:57.749364 PROGRESS: Target precursors: 0 (0.00%)
0:12:57.749414 PROGRESS: Decoy precursors: 0 (0.00%)
0:12:57.749462 PROGRESS: 
0:12:57.749505 PROGRESS: Precursor Summary:
0:12:57.749623 PROGRESS: 
0:12:57.749686 PROGRESS: Protein Summary:
0:12:57.749757 PROGRESS: =========================================================================
0:12:57.753856 INFO: Target number of precursors not reached yet.
0:12:57.956736 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:12:58.020565 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:12:58.173090 INFO: === skipping optimization until target number of precursors are found ===
0:12:58.173375 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:12:58.173484 INFO: Starting optimization step 9.
0:12:58.173558 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:12:58.173636 INFO: Using ng extraction backend
0:12:58.173706 PROGRESS: Extracting batch of 101368 precursors
0:12:58.351276 INFO: === Search parameters used ===
0:12:58.351527 INFO: rt_error       : 805.6019897460938
0:12:58.351580 INFO: mobility_error : 0.1
0:12:58.351626 INFO: num_candidates : 3
0:12:58.351668 INFO: ms1_error      : 30
0:12:58.351707 INFO: ms2_error      : 30
0:12:58.351748 INFO: fwhm_rt        : 3.0
0:12:58.351790 INFO: quant_window   : 3
0:12:58.351831 INFO: ==============================================
0:12:59.643193 INFO: performing precursor FDR with 40 features
0:12:59.643307 INFO: Decoy channel: -1
0:12:59.643334 INFO: Competetive: True
0:12:59.870744 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:00.112397 INFO: Using random state 393924 for train-test-split
0:13:08.351296 INFO: Test AUC: 0.596
0:13:08.351429 INFO: Train AUC: 0.602
0:13:08.351475 INFO: AUC difference: 0.94%
0:13:08.760062 INFO: Resetting torch num_threads to 80
0:13:08.847003 PROGRESS: === Extracted 600338 precursors and 2735919 fragments ===
0:13:08.847627 INFO: === FDR correction performed with classifier version 7 ===
0:13:08.848224 PROGRESS: ============================= Precursor FDR =============================
0:13:08.848314 PROGRESS: Total precursors accumulated: 330
0:13:08.848372 PROGRESS: Target precursors: 327 (99.09%)
0:13:08.848423 PROGRESS: Decoy precursors: 3 (0.91%)
0:13:08.848467 PROGRESS: 
0:13:08.848513 PROGRESS: Precursor Summary:
0:13:08.849421 PROGRESS: Channel   0:	 0.050 FDR:   327; 0.010 FDR:   327; 0.001 FDR:     0
0:13:08.849514 PROGRESS: 
0:13:08.849568 PROGRESS: Protein Summary:
0:13:08.850631 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   304; 0.001 FDR:     0
0:13:08.850726 PROGRESS: =========================================================================
0:13:08.858161 INFO: Target number of precursors reached.
0:13:09.053249 INFO: fragments_df: keeping 4409 of 2735919 [sum(precursor_idx_mask)=7726 sum(mass_error_mask)=2735919 stop_rank=4409
0:13:09.432083 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:09.552814 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:10.104775 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:10.105208 INFO: Using score_cutoff 15.939338341140747 (fac=0.99, q=1)
0:13:10.105497 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:10.105586 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:10.105641 INFO: Updating optimization_manager: score_cutoff        : 15.024009417057037 -> 15.939338341140747
0:13:10.105697 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:10.231455 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:10.508290 INFO: === checking if optimization conditions were reached ===
0:13:10.508542 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:13:10.510797 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.220784409191484
0:13:10.510902 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.2208.
0:13:10.510967 INFO: ==============================================
0:13:10.511033 INFO: Starting optimization step 10.
0:13:10.511087 PROGRESS: === Extracting elution groups 0 to 102200 ===
0:13:10.511147 INFO: Using ng extraction backend
0:13:10.511202 PROGRESS: Extracting batch of 202352 precursors
0:13:10.854308 INFO: === Search parameters used ===
0:13:10.854584 INFO: rt_error       : 805.6019897460938
0:13:10.854641 INFO: mobility_error : 0.1
0:13:10.854687 INFO: num_candidates : 3
0:13:10.854727 INFO: ms1_error      : 30
0:13:10.854768 INFO: ms2_error      : 7.220784409191484
0:13:10.854806 INFO: fwhm_rt        : 3.0
0:13:10.854857 INFO: quant_window   : 3
0:13:10.854896 INFO: ==============================================
0:13:13.192313 INFO: performing precursor FDR with 40 features
0:13:13.192433 INFO: Decoy channel: -1
0:13:13.192459 INFO: Competetive: True
0:13:13.355671 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:13.597806 INFO: Using random state 393924 for train-test-split
0:13:22.018467 INFO: Test AUC: 0.598
0:13:22.018726 INFO: Train AUC: 0.603
0:13:22.018767 INFO: AUC difference: 0.78%
0:13:22.994277 INFO: Resetting torch num_threads to 80
0:13:23.016536 PROGRESS: === Extracted 606912 precursors and 3366048 fragments ===
0:13:23.016975 INFO: === FDR correction performed with classifier version 7 ===
0:13:23.017627 PROGRESS: ============================= Precursor FDR =============================
0:13:23.017720 PROGRESS: Total precursors accumulated: 969
0:13:23.017785 PROGRESS: Target precursors: 960 (99.07%)
0:13:23.017842 PROGRESS: Decoy precursors: 9 (0.93%)
0:13:23.017893 PROGRESS: 
0:13:23.017943 PROGRESS: Precursor Summary:
0:13:23.019080 PROGRESS: Channel   0:	 0.050 FDR:   960; 0.010 FDR:   960; 0.001 FDR:   734
0:13:23.019191 PROGRESS: 
0:13:23.019254 PROGRESS: Protein Summary:
0:13:23.020680 PROGRESS: Channel   0:	 0.050 FDR:   853; 0.010 FDR:   853; 0.001 FDR:   652
0:13:23.020778 PROGRESS: =========================================================================
0:13:23.032564 INFO: Target number of precursors reached.
0:13:23.251976 INFO: fragments_df: keeping 5000 of 3366048 [sum(precursor_idx_mask)=23439 sum(mass_error_mask)=3366048 stop_rank=5000
0:13:23.547500 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:23.722728 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:24.409328 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:24.409768 INFO: Using score_cutoff 12.714511446475983 (fac=0.99, q=1)
0:13:24.410062 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:24.410141 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:24.410196 INFO: Updating optimization_manager: score_cutoff        : 15.939338341140747 -> 12.714511446475983
0:13:24.410249 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:24.441605 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:24.507910 INFO: === checking if optimization conditions were reached ===
0:13:24.508181 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:13:24.511112 INFO: Updating optimization_manager: ms2_error           : 7.220784409191484 -> 7.3625755757222215
0:13:24.511234 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.3626.
0:13:24.511312 INFO: ==============================================
0:13:24.511391 INFO: Starting optimization step 11.
0:13:24.511457 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:24.511528 INFO: Using ng extraction backend
0:13:24.511597 PROGRESS: Extracting batch of 50293 precursors
0:13:24.603715 INFO: === Search parameters used ===
0:13:24.603989 INFO: rt_error       : 805.6019897460938
0:13:24.604044 INFO: mobility_error : 0.1
0:13:24.604090 INFO: num_candidates : 3
0:13:24.604131 INFO: ms1_error      : 30
0:13:24.604184 INFO: ms2_error      : 7.3625755757222215
0:13:24.604230 INFO: fwhm_rt        : 3.0
0:13:24.604270 INFO: quant_window   : 3
0:13:24.604309 INFO: ==============================================
0:13:25.246638 INFO: performing precursor FDR with 40 features
0:13:25.246757 INFO: Decoy channel: -1
0:13:25.246783 INFO: Competetive: True
0:13:25.285407 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:25.319251 INFO: Using random state 393924 for train-test-split
0:13:27.181530 INFO: Test AUC: 0.587
0:13:27.181648 INFO: Train AUC: 0.601
0:13:27.181678 INFO: AUC difference: 2.30%
0:13:27.455307 INFO: Resetting torch num_threads to 80
0:13:27.461387 PROGRESS: === Extracted 150817 precursors and 835433 fragments ===
0:13:27.461738 INFO: === FDR correction performed with classifier version 7 ===
0:13:27.462189 PROGRESS: ============================= Precursor FDR =============================
0:13:27.462281 PROGRESS: Total precursors accumulated: 251
0:13:27.462340 PROGRESS: Target precursors: 249 (99.20%)
0:13:27.462389 PROGRESS: Decoy precursors: 2 (0.80%)
0:13:27.462434 PROGRESS: 
0:13:27.462475 PROGRESS: Precursor Summary:
0:13:27.463386 PROGRESS: Channel   0:	 0.050 FDR:   249; 0.010 FDR:   249; 0.001 FDR:   141
0:13:27.463477 PROGRESS: 
0:13:27.463532 PROGRESS: Protein Summary:
0:13:27.464582 PROGRESS: Channel   0:	 0.050 FDR:   241; 0.010 FDR:   241; 0.001 FDR:   138
0:13:27.464672 PROGRESS: =========================================================================
0:13:27.466628 INFO: Target number of precursors reached.
0:13:27.522090 INFO: fragments_df: keeping 2946 of 835433 [sum(precursor_idx_mask)=6054 sum(mass_error_mask)=835433 stop_rank=2946
0:13:27.658446 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:27.774688 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:28.165150 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:28.165575 INFO: Using score_cutoff 11.581279781341552 (fac=0.99, q=1)
0:13:28.165861 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:28.165943 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:28.165997 INFO: Updating optimization_manager: score_cutoff        : 12.714511446475983 -> 11.581279781341552
0:13:28.166053 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:28.196404 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:28.260955 INFO: === checking if optimization conditions were reached ===
0:13:28.261245 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:13:28.262211 INFO: Updating optimization_manager: ms2_error           : 7.3625755757222215 -> 7.3625755757222215
0:13:28.262351 INFO: Updating optimization_manager: classifier_version  : 7 -> 11
0:13:28.262460 INFO: Updating optimization_manager: score_cutoff        : 11.581279781341552 -> 11.581279781341552
0:13:28.262559 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:28.262673 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:28.262775 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.3626 found after 3 searches.
0:13:28.262848 INFO: ==============================================
0:13:28.262927 PROGRESS: Optimization finished for ms2_error.
0:13:28.412277 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:28.442734 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:28.537979 INFO: Starting optimization step 0.
0:13:28.538211 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:28.538303 INFO: Using ng extraction backend
0:13:28.538372 PROGRESS: Extracting batch of 50293 precursors
0:13:28.626847 INFO: === Search parameters used ===
0:13:28.627113 INFO: rt_error       : 805.6019897460938
0:13:28.627167 INFO: mobility_error : 0.1
0:13:28.627214 INFO: num_candidates : 3
0:13:28.627258 INFO: ms1_error      : 30
0:13:28.627300 INFO: ms2_error      : 7.3625755757222215
0:13:28.627344 INFO: fwhm_rt        : 3.0
0:13:28.627387 INFO: quant_window   : 3
0:13:28.627429 INFO: ==============================================
0:13:29.253254 INFO: performing precursor FDR with 40 features
0:13:29.253374 INFO: Decoy channel: -1
0:13:29.253402 INFO: Competetive: True
0:13:29.291467 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:29.325318 INFO: Using random state 1600 for train-test-split
0:13:31.270907 INFO: Test AUC: 0.595
0:13:31.271030 INFO: Train AUC: 0.605
0:13:31.271062 INFO: AUC difference: 1.61%
0:13:31.542771 INFO: Resetting torch num_threads to 80
0:13:31.548612 PROGRESS: === Extracted 150824 precursors and 835612 fragments ===
0:13:31.548965 INFO: === FDR correction performed with classifier version 11 ===
0:13:31.549409 PROGRESS: ============================= Precursor FDR =============================
0:13:31.549498 PROGRESS: Total precursors accumulated: 215
0:13:31.549554 PROGRESS: Target precursors: 213 (99.07%)
0:13:31.549605 PROGRESS: Decoy precursors: 2 (0.93%)
0:13:31.549649 PROGRESS: 
0:13:31.549692 PROGRESS: Precursor Summary:
0:13:31.550597 PROGRESS: Channel   0:	 0.050 FDR:   213; 0.010 FDR:   213; 0.001 FDR:   185
0:13:31.550692 PROGRESS: 
0:13:31.550745 PROGRESS: Protein Summary:
0:13:31.551781 PROGRESS: Channel   0:	 0.050 FDR:   206; 0.010 FDR:   206; 0.001 FDR:   179
0:13:31.551869 PROGRESS: =========================================================================
0:13:31.553888 INFO: Target number of precursors reached.
0:13:31.608924 INFO: fragments_df: keeping 2555 of 835612 [sum(precursor_idx_mask)=5208 sum(mass_error_mask)=835612 stop_rank=2555
0:13:31.745767 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:31.862604 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:32.200563 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:32.200984 INFO: Using score_cutoff 12.507943747329712 (fac=0.99, q=1)
0:13:32.201267 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:32.201346 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:32.201400 INFO: Updating optimization_manager: score_cutoff        : 11.581279781341552 -> 12.507943747329712
0:13:32.201454 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:32.232393 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:32.298593 INFO: === checking if optimization conditions were reached ===
0:13:32.298882 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:13:32.300937 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 138.89431682484644
0:13:32.301066 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 138.8943.
0:13:32.301144 INFO: ==============================================
0:13:32.301226 INFO: Starting optimization step 1.
0:13:32.301293 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:32.301363 INFO: Using ng extraction backend
0:13:32.301429 PROGRESS: Extracting batch of 50293 precursors
0:13:32.391115 INFO: === Search parameters used ===
0:13:32.391378 INFO: rt_error       : 138.89431682484644
0:13:32.391433 INFO: mobility_error : 0.1
0:13:32.391479 INFO: num_candidates : 3
0:13:32.391522 INFO: ms1_error      : 30
0:13:32.391562 INFO: ms2_error      : 7.3625755757222215
0:13:32.391602 INFO: fwhm_rt        : 3.0
0:13:32.391643 INFO: quant_window   : 3
0:13:32.391684 INFO: ==============================================
0:13:32.988403 INFO: performing precursor FDR with 40 features
0:13:32.988521 INFO: Decoy channel: -1
0:13:32.988548 INFO: Competetive: True
0:13:33.026382 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:33.061975 INFO: Using random state 1600 for train-test-split
0:13:35.384225 INFO: Test AUC: 0.592
0:13:35.384350 INFO: Train AUC: 0.599
0:13:35.384381 INFO: AUC difference: 1.14%
0:13:35.656328 INFO: Resetting torch num_threads to 80
0:13:35.662396 PROGRESS: === Extracted 149676 precursors and 665173 fragments ===
0:13:35.662761 INFO: === FDR correction performed with classifier version 11 ===
0:13:35.663206 PROGRESS: ============================= Precursor FDR =============================
0:13:35.663310 PROGRESS: Total precursors accumulated: 238
0:13:35.663368 PROGRESS: Target precursors: 236 (99.16%)
0:13:35.663419 PROGRESS: Decoy precursors: 2 (0.84%)
0:13:35.663475 PROGRESS: 
0:13:35.663523 PROGRESS: Precursor Summary:
0:13:35.664434 PROGRESS: Channel   0:	 0.050 FDR:   236; 0.010 FDR:   236; 0.001 FDR:   209
0:13:35.664522 PROGRESS: 
0:13:35.664578 PROGRESS: Protein Summary:
0:13:35.665641 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:   203
0:13:35.665730 PROGRESS: =========================================================================
0:13:35.667852 INFO: Target number of precursors reached.
0:13:35.712392 INFO: fragments_df: keeping 2763 of 665173 [sum(precursor_idx_mask)=5648 sum(mass_error_mask)=665173 stop_rank=2763
0:13:35.849115 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:35.966986 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:36.333405 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:36.333823 INFO: Using score_cutoff 12.758940483570099 (fac=0.99, q=1)
0:13:36.334107 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:36.334188 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:36.334244 INFO: Updating optimization_manager: score_cutoff        : 12.507943747329712 -> 12.758940483570099
0:13:36.334298 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:36.365030 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:36.432765 INFO: === checking if optimization conditions were reached ===
0:13:36.433028 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:13:36.435253 INFO: Updating optimization_manager: rt_error            : 138.89431682484644 -> 91.12856168294651
0:13:36.435373 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 91.1286.
0:13:36.435450 INFO: ==============================================
0:13:36.435528 INFO: Starting optimization step 2.
0:13:36.435594 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:36.435665 INFO: Using ng extraction backend
0:13:36.435730 PROGRESS: Extracting batch of 50293 precursors
0:13:36.526024 INFO: === Search parameters used ===
0:13:36.526284 INFO: rt_error       : 91.12856168294651
0:13:36.526337 INFO: mobility_error : 0.1
0:13:36.526385 INFO: num_candidates : 3
0:13:36.526429 INFO: ms1_error      : 30
0:13:36.526469 INFO: ms2_error      : 7.3625755757222215
0:13:36.526510 INFO: fwhm_rt        : 3.0
0:13:36.526549 INFO: quant_window   : 3
0:13:36.526599 INFO: ==============================================
0:13:37.095250 INFO: performing precursor FDR with 40 features
0:13:37.095367 INFO: Decoy channel: -1
0:13:37.095396 INFO: Competetive: True
0:13:37.131941 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:37.166835 INFO: Using random state 1600 for train-test-split
0:13:39.175409 INFO: Test AUC: 0.589
0:13:39.175520 INFO: Train AUC: 0.602
0:13:39.175551 INFO: AUC difference: 2.13%
0:13:39.437615 INFO: Resetting torch num_threads to 80
0:13:39.444129 PROGRESS: === Extracted 147905 precursors and 599994 fragments ===
0:13:39.444483 INFO: === FDR correction performed with classifier version 11 ===
0:13:39.444942 PROGRESS: ============================= Precursor FDR =============================
0:13:39.445029 PROGRESS: Total precursors accumulated: 330
0:13:39.445098 PROGRESS: Target precursors: 327 (99.09%)
0:13:39.445152 PROGRESS: Decoy precursors: 3 (0.91%)
0:13:39.445197 PROGRESS: 
0:13:39.445246 PROGRESS: Precursor Summary:
0:13:39.446167 PROGRESS: Channel   0:	 0.050 FDR:   327; 0.010 FDR:   327; 0.001 FDR:   251
0:13:39.446257 PROGRESS: 
0:13:39.446312 PROGRESS: Protein Summary:
0:13:39.447416 PROGRESS: Channel   0:	 0.050 FDR:   315; 0.010 FDR:   315; 0.001 FDR:   242
0:13:39.447508 PROGRESS: =========================================================================
0:13:39.449469 INFO: Target number of precursors reached.
0:13:39.491262 INFO: fragments_df: keeping 3402 of 599994 [sum(precursor_idx_mask)=7473 sum(mass_error_mask)=599994 stop_rank=3402
0:13:39.628727 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:39.751705 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:40.197237 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:40.197656 INFO: Using score_cutoff 10.329094457817078 (fac=0.99, q=1)
0:13:40.197943 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:40.198022 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:40.198076 INFO: Updating optimization_manager: score_cutoff        : 12.758940483570099 -> 10.329094457817078
0:13:40.198128 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:40.228567 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:40.297092 INFO: === checking if optimization conditions were reached ===
0:13:40.297376 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:13:40.299785 INFO: Updating optimization_manager: rt_error            : 91.12856168294651 -> 75.5487694340087
0:13:40.299929 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 75.5488.
0:13:40.300009 INFO: ==============================================
0:13:40.300089 INFO: Starting optimization step 3.
0:13:40.300157 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:40.300229 INFO: Using ng extraction backend
0:13:40.300297 PROGRESS: Extracting batch of 50293 precursors
0:13:40.391710 INFO: === Search parameters used ===
0:13:40.392397 INFO: rt_error       : 75.5487694340087
0:13:40.392469 INFO: mobility_error : 0.1
0:13:40.392518 INFO: num_candidates : 3
0:13:40.392563 INFO: ms1_error      : 30
0:13:40.392604 INFO: ms2_error      : 7.3625755757222215
0:13:40.392645 INFO: fwhm_rt        : 3.0
0:13:40.392684 INFO: quant_window   : 3
0:13:40.392725 INFO: ==============================================
0:13:40.964482 INFO: performing precursor FDR with 40 features
0:13:40.964597 INFO: Decoy channel: -1
0:13:40.964623 INFO: Competetive: True
0:13:41.004328 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:41.041152 INFO: Using random state 1600 for train-test-split
0:13:43.266855 INFO: Test AUC: 0.595
0:13:43.266974 INFO: Train AUC: 0.601
0:13:43.267004 INFO: AUC difference: 1.01%
0:13:43.528708 INFO: Resetting torch num_threads to 80
0:13:43.535162 PROGRESS: === Extracted 146800 precursors and 578142 fragments ===
0:13:43.535520 INFO: === FDR correction performed with classifier version 11 ===
0:13:43.536029 PROGRESS: ============================= Precursor FDR =============================
0:13:43.536127 PROGRESS: Total precursors accumulated: 339
0:13:43.536189 PROGRESS: Target precursors: 336 (99.12%)
0:13:43.536237 PROGRESS: Decoy precursors: 3 (0.88%)
0:13:43.536283 PROGRESS: 
0:13:43.536326 PROGRESS: Precursor Summary:
0:13:43.537229 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   336; 0.001 FDR:   230
0:13:43.537316 PROGRESS: 
0:13:43.537372 PROGRESS: Protein Summary:
0:13:43.538438 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   224
0:13:43.538525 PROGRESS: =========================================================================
0:13:43.540585 INFO: Target number of precursors reached.
0:13:43.580537 INFO: fragments_df: keeping 3446 of 578142 [sum(precursor_idx_mask)=7542 sum(mass_error_mask)=578142 stop_rank=3446
0:13:43.718616 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:43.821325 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:44.206164 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:44.206599 INFO: Using score_cutoff 11.232840758800506 (fac=0.99, q=1)
0:13:44.206889 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:44.206969 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:44.207026 INFO: Updating optimization_manager: score_cutoff        : 10.329094457817078 -> 11.232840758800506
0:13:44.207080 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:44.238433 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:44.308274 INFO: === checking if optimization conditions were reached ===
0:13:44.308508 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:13:44.310495 INFO: Updating optimization_manager: rt_error            : 75.5487694340087 -> 63.94240510475293
0:13:44.310610 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 63.9424.
0:13:44.310678 INFO: ==============================================
0:13:44.310747 INFO: Starting optimization step 4.
0:13:44.310805 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:44.310864 INFO: Using ng extraction backend
0:13:44.310921 PROGRESS: Extracting batch of 50293 precursors
0:13:44.398284 INFO: === Search parameters used ===
0:13:44.398551 INFO: rt_error       : 63.94240510475293
0:13:44.398622 INFO: mobility_error : 0.1
0:13:44.398669 INFO: num_candidates : 3
0:13:44.398712 INFO: ms1_error      : 30
0:13:44.398751 INFO: ms2_error      : 7.3625755757222215
0:13:44.398792 INFO: fwhm_rt        : 3.0
0:13:44.398832 INFO: quant_window   : 3
0:13:44.398873 INFO: ==============================================
0:13:44.971492 INFO: performing precursor FDR with 40 features
0:13:44.971610 INFO: Decoy channel: -1
0:13:44.971638 INFO: Competetive: True
0:13:45.007034 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:45.042141 INFO: Using random state 1600 for train-test-split
0:13:47.020837 INFO: Test AUC: 0.597
0:13:47.021066 INFO: Train AUC: 0.602
0:13:47.021098 INFO: AUC difference: 0.87%
0:13:47.277741 INFO: Resetting torch num_threads to 80
0:13:47.284253 PROGRESS: === Extracted 145228 precursors and 562140 fragments ===
0:13:47.284602 INFO: === FDR correction performed with classifier version 11 ===
0:13:47.285091 PROGRESS: ============================= Precursor FDR =============================
0:13:47.285178 PROGRESS: Total precursors accumulated: 351
0:13:47.285235 PROGRESS: Target precursors: 348 (99.15%)
0:13:47.285284 PROGRESS: Decoy precursors: 3 (0.85%)
0:13:47.285326 PROGRESS: 
0:13:47.285369 PROGRESS: Precursor Summary:
0:13:47.286280 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   219
0:13:47.286371 PROGRESS: 
0:13:47.286427 PROGRESS: Protein Summary:
0:13:47.287504 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   336; 0.001 FDR:   214
0:13:47.287596 PROGRESS: =========================================================================
0:13:47.289535 INFO: Target number of precursors reached.
0:13:47.327871 INFO: fragments_df: keeping 3545 of 562140 [sum(precursor_idx_mask)=7637 sum(mass_error_mask)=562140 stop_rank=3545
0:13:47.465289 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:47.568530 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:47.968358 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:47.968782 INFO: Using score_cutoff 11.180931971168517 (fac=0.99, q=1)
0:13:47.969067 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:47.969147 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:47.969207 INFO: Updating optimization_manager: score_cutoff        : 11.232840758800506 -> 11.180931971168517
0:13:47.969264 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:48.001032 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:48.069834 INFO: === checking if optimization conditions were reached ===
0:13:48.070048 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:13:48.072072 INFO: Updating optimization_manager: rt_error            : 63.94240510475293 -> 49.4094485947709
0:13:48.072176 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 49.4094.
0:13:48.072244 INFO: ==============================================
0:13:48.072315 INFO: Starting optimization step 5.
0:13:48.072375 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:48.072436 INFO: Using ng extraction backend
0:13:48.072492 PROGRESS: Extracting batch of 50293 precursors
0:13:48.160174 INFO: === Search parameters used ===
0:13:48.160432 INFO: rt_error       : 49.4094485947709
0:13:48.160486 INFO: mobility_error : 0.1
0:13:48.160533 INFO: num_candidates : 3
0:13:48.160574 INFO: ms1_error      : 30
0:13:48.160614 INFO: ms2_error      : 7.3625755757222215
0:13:48.160655 INFO: fwhm_rt        : 3.0
0:13:48.160692 INFO: quant_window   : 3
0:13:48.160731 INFO: ==============================================
0:13:48.682764 INFO: performing precursor FDR with 40 features
0:13:48.682894 INFO: Decoy channel: -1
0:13:48.682922 INFO: Competetive: True
0:13:48.716472 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:48.747917 INFO: Using random state 1600 for train-test-split
0:13:50.472029 INFO: Test AUC: 0.590
0:13:50.472153 INFO: Train AUC: 0.603
0:13:50.472184 INFO: AUC difference: 2.12%
0:13:50.739252 INFO: Resetting torch num_threads to 80
0:13:50.745166 PROGRESS: === Extracted 134809 precursors and 500487 fragments ===
0:13:50.745514 INFO: === FDR correction performed with classifier version 11 ===
0:13:50.745963 PROGRESS: ============================= Precursor FDR =============================
0:13:50.746049 PROGRESS: Total precursors accumulated: 294
0:13:50.746108 PROGRESS: Target precursors: 292 (99.32%)
0:13:50.746157 PROGRESS: Decoy precursors: 2 (0.68%)
0:13:50.746201 PROGRESS: 
0:13:50.746245 PROGRESS: Precursor Summary:
0:13:50.747147 PROGRESS: Channel   0:	 0.050 FDR:   292; 0.010 FDR:   292; 0.001 FDR:   213
0:13:50.747242 PROGRESS: 
0:13:50.747298 PROGRESS: Protein Summary:
0:13:50.748347 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   285; 0.001 FDR:   208
0:13:50.748437 PROGRESS: =========================================================================
0:13:50.750186 INFO: Target number of precursors reached.
0:13:50.784673 INFO: fragments_df: keeping 2859 of 500487 [sum(precursor_idx_mask)=5820 sum(mass_error_mask)=500487 stop_rank=2859
0:13:50.922761 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:51.049008 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:51.426367 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:51.426803 INFO: Using score_cutoff 11.401108393764495 (fac=0.99, q=1)
0:13:51.427088 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:51.427176 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:51.427231 INFO: Updating optimization_manager: score_cutoff        : 11.180931971168517 -> 11.401108393764495
0:13:51.427285 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:51.459245 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:51.526055 INFO: === checking if optimization conditions were reached ===
0:13:51.526287 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:13:51.528256 INFO: Updating optimization_manager: rt_error            : 49.4094485947709 -> 33.04867649100769
0:13:51.528360 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 33.0487.
0:13:51.528424 INFO: ==============================================
0:13:51.528492 INFO: Starting optimization step 6.
0:13:51.528550 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:51.528611 INFO: Using ng extraction backend
0:13:51.528665 PROGRESS: Extracting batch of 50293 precursors
0:13:51.615789 INFO: === Search parameters used ===
0:13:51.616046 INFO: rt_error       : 33.04867649100769
0:13:51.616097 INFO: mobility_error : 0.1
0:13:51.616142 INFO: num_candidates : 3
0:13:51.616183 INFO: ms1_error      : 30
0:13:51.616223 INFO: ms2_error      : 7.3625755757222215
0:13:51.616264 INFO: fwhm_rt        : 3.0
0:13:51.616313 INFO: quant_window   : 3
0:13:51.616354 INFO: ==============================================
0:13:52.134647 INFO: performing precursor FDR with 40 features
0:13:52.134762 INFO: Decoy channel: -1
0:13:52.134789 INFO: Competetive: True
0:13:52.172063 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:52.203792 INFO: Using random state 1600 for train-test-split
0:13:54.030458 INFO: Test AUC: 0.594
0:13:54.030588 INFO: Train AUC: 0.602
0:13:54.030620 INFO: AUC difference: 1.30%
0:13:54.294020 INFO: Resetting torch num_threads to 80
0:13:54.299969 PROGRESS: === Extracted 134784 precursors and 501560 fragments ===
0:13:54.300326 INFO: === FDR correction performed with classifier version 11 ===
0:13:54.300774 PROGRESS: ============================= Precursor FDR =============================
0:13:54.300861 PROGRESS: Total precursors accumulated: 287
0:13:54.300918 PROGRESS: Target precursors: 285 (99.30%)
0:13:54.300969 PROGRESS: Decoy precursors: 2 (0.70%)
0:13:54.301012 PROGRESS: 
0:13:54.301057 PROGRESS: Precursor Summary:
0:13:54.301959 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   285; 0.001 FDR:   206
0:13:54.302045 PROGRESS: 
0:13:54.302102 PROGRESS: Protein Summary:
0:13:54.303182 PROGRESS: Channel   0:	 0.050 FDR:   277; 0.010 FDR:   277; 0.001 FDR:   202
0:13:54.303273 PROGRESS: =========================================================================
0:13:54.305120 INFO: Target number of precursors reached.
0:13:54.341191 INFO: fragments_df: keeping 2780 of 501560 [sum(precursor_idx_mask)=5702 sum(mass_error_mask)=501560 stop_rank=2780
0:13:54.477650 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:54.599948 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:54.946528 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:54.946964 INFO: Using score_cutoff 11.380029833221435 (fac=0.99, q=1)
0:13:54.947247 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:54.947326 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:54.947377 INFO: Updating optimization_manager: score_cutoff        : 11.401108393764495 -> 11.380029833221435
0:13:54.947431 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:54.979505 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:55.047282 INFO: === checking if optimization conditions were reached ===
0:13:55.047510 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:13:55.049500 INFO: Updating optimization_manager: rt_error            : 33.04867649100769 -> 31.55978232564488
0:13:55.049604 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 31.5598.
0:13:55.049670 INFO: ==============================================
0:13:55.049740 INFO: Starting optimization step 7.
0:13:55.049798 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:55.049861 INFO: Using ng extraction backend
0:13:55.049918 PROGRESS: Extracting batch of 50293 precursors
0:13:55.136997 INFO: === Search parameters used ===
0:13:55.137260 INFO: rt_error       : 31.55978232564488
0:13:55.137316 INFO: mobility_error : 0.1
0:13:55.137363 INFO: num_candidates : 3
0:13:55.137406 INFO: ms1_error      : 30
0:13:55.137459 INFO: ms2_error      : 7.3625755757222215
0:13:55.137501 INFO: fwhm_rt        : 3.0
0:13:55.137541 INFO: quant_window   : 3
0:13:55.137580 INFO: ==============================================
0:13:55.657051 INFO: performing precursor FDR with 40 features
0:13:55.657168 INFO: Decoy channel: -1
0:13:55.657194 INFO: Competetive: True
0:13:55.691373 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:55.723361 INFO: Using random state 1600 for train-test-split
0:13:57.453018 INFO: Test AUC: 0.587
0:13:57.453498 INFO: Train AUC: 0.603
0:13:57.453540 INFO: AUC difference: 2.69%
0:13:57.712287 INFO: Resetting torch num_threads to 80
0:13:57.718221 PROGRESS: === Extracted 134723 precursors and 500234 fragments ===
0:13:57.718583 INFO: === FDR correction performed with classifier version 11 ===
0:13:57.719031 PROGRESS: ============================= Precursor FDR =============================
0:13:57.719118 PROGRESS: Total precursors accumulated: 289
0:13:57.719174 PROGRESS: Target precursors: 287 (99.31%)
0:13:57.719223 PROGRESS: Decoy precursors: 2 (0.69%)
0:13:57.719266 PROGRESS: 
0:13:57.719309 PROGRESS: Precursor Summary:
0:13:57.720201 PROGRESS: Channel   0:	 0.050 FDR:   287; 0.010 FDR:   287; 0.001 FDR:   189
0:13:57.720289 PROGRESS: 
0:13:57.720346 PROGRESS: Protein Summary:
0:13:57.721391 PROGRESS: Channel   0:	 0.050 FDR:   279; 0.010 FDR:   279; 0.001 FDR:   186
0:13:57.721479 PROGRESS: =========================================================================
0:13:57.723373 INFO: Target number of precursors reached.
0:13:57.757599 INFO: fragments_df: keeping 2787 of 500234 [sum(precursor_idx_mask)=5743 sum(mass_error_mask)=500234 stop_rank=2787
0:13:57.893594 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:57.995864 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:58.300649 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:58.301071 INFO: Using score_cutoff 11.38605227909088 (fac=0.99, q=1)
0:13:58.301357 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:58.301435 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:58.301487 INFO: Updating optimization_manager: score_cutoff        : 11.380029833221435 -> 11.38605227909088
0:13:58.301543 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:58.333573 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:58.401745 INFO: === checking if optimization conditions were reached ===
0:13:58.401985 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:13:58.403062 INFO: Updating optimization_manager: rt_error            : 31.55978232564488 -> 63.94240510475293
0:13:58.403192 INFO: Updating optimization_manager: classifier_version  : 11 -> 16
0:13:58.403286 INFO: Updating optimization_manager: score_cutoff        : 11.38605227909088 -> 11.180931971168517
0:13:58.403371 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:58.403453 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:58.403536 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 63.9424 found after 8 searches.
0:13:58.403598 INFO: ==============================================
0:13:58.403662 PROGRESS: Optimization finished for rt_error.
0:13:58.537909 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:58.570339 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:58.665059 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:13:58.665264 PROGRESS: ==============================================
0:13:58.665331 PROGRESS: ms2_error      : 7.3626
0:13:58.665385 PROGRESS: rt_error       : 63.9424
0:13:58.665432 PROGRESS: ==============================================
0:13:58.665894 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:06.909761 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:24.935468 INFO: Using ng extraction backend
0:14:24.935967 PROGRESS: Extracting batch of 12001526 precursors
0:14:40.851855 INFO: === Search parameters used ===
0:14:40.852155 INFO: rt_error       : 63.94240510475293
0:14:40.852227 INFO: mobility_error : 0.1
0:14:40.852286 INFO: num_candidates : 3
0:14:40.852338 INFO: ms1_error      : 30
0:14:40.852386 INFO: ms2_error      : 7.3625755757222215
0:14:40.852429 INFO: fwhm_rt        : 3.0
0:14:40.852473 INFO: quant_window   : 3
0:14:40.852514 INFO: ==============================================
0:15:10.306305 INFO: Removed 26738743 precursors with score below cutoff 11.180931971168517
0:15:17.865257 INFO: performing precursor FDR with 40 features
0:15:17.865379 INFO: Decoy channel: -1
0:15:17.865410 INFO: Competetive: True
0:15:18.647609 INFO: Setting torch num_threads to 2 for FDR classification task
0:15:21.774429 INFO: Using random state 959783 for train-test-split
0:17:18.512975 INFO: Test AUC: 0.630
0:17:18.513240 INFO: Train AUC: 0.631
0:17:18.513280 INFO: AUC difference: 0.14%
0:17:21.203476 INFO: Resetting torch num_threads to 80
0:17:22.803394 PROGRESS: ============================= Precursor FDR =============================
0:17:22.803688 PROGRESS: Total precursors accumulated: 82,465
0:17:22.803756 PROGRESS: Target precursors: 81,649 (99.01%)
0:17:22.803809 PROGRESS: Decoy precursors: 816 (0.99%)
0:17:22.803854 PROGRESS: 
0:17:22.803898 PROGRESS: Precursor Summary:
0:17:22.827901 PROGRESS: Channel   0:	 0.050 FDR: 81,649; 0.010 FDR: 81,649; 0.001 FDR: 57,006
0:17:22.828138 PROGRESS: 
0:17:22.828202 PROGRESS: Protein Summary:
0:17:22.860760 PROGRESS: Channel   0:	 0.050 FDR: 12,940; 0.010 FDR: 12,940; 0.001 FDR: 9,463
0:17:22.860988 PROGRESS: =========================================================================
0:17:22.911978 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
0:17:23.078659 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
0:17:23.311069 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:17:23.908106 PROGRESS: 
0:17:23.908261 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
0:17:23.908337 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
0:17:23.908514 INFO: Initializing TimingManager
0:17:23.908965 INFO: Initializing RawFileManager
0:17:35.364997 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:17:35.369276 INFO: Determining DIA cycle
0:17:35.387183 INFO: Found cycle with start 0.00 min and length 300.
0:17:35.550385 INFO: RT (min)            : 0.0 - 26.9
0:17:35.550477 INFO: RT duration (sec)   : 1611.2
0:17:35.550505 INFO: RT duration (min)   : 26.9
0:17:35.550530 INFO: Cycle len (scans)   : 300
0:17:35.550550 INFO: Cycle len (sec)     : 1.65
0:17:35.550582 INFO: Number of cycles    : 977
0:17:35.550610 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:17:35.550645 INFO: Creating DIA data object took: 11.641589879989624
0:17:36.232027 INFO: Creating DIA data NG object took: 0.6812641620635986
0:17:37.597538 INFO: Initializing CalibrationManager
0:17:37.597811 INFO: Setting up calibration estimators ..
0:17:37.597872 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:17:37.597949 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'}' ..
0:17:37.598046 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:17:37.598097 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:17:37.598150 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}}' ..
0:17:37.598198 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:17:37.598243 INFO: Done setting up calibration estimators.
0:17:37.598431 INFO: Initializing OptimizationManager
0:17:37.598589 INFO: initial parameter: ms1_error = 30
0:17:37.598656 INFO: initial parameter: ms2_error = 30
0:17:37.598714 INFO: initial parameter: rt_error = 805.6004638671875
0:17:37.598758 INFO: initial parameter: mobility_error = 0.1
0:17:37.598799 INFO: initial parameter: num_candidates = 1
0:17:37.598837 INFO: initial parameter: fwhm_rt = 5
0:17:37.598878 INFO: initial parameter: fwhm_mobility = 0.01
0:17:37.598918 INFO: initial parameter: score_cutoff = 0
0:17:37.598956 INFO: initial parameter: classifier_version = -1
0:17:37.599024 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:17:37.599278 INFO: FDRManager: loading saved state not requested, will be initialized.
0:17:37.599312 INFO: Initializing FDRManager
0:17:37.599348 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:17:38.824262 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:17:39.598286 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:17:39.598644 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
0:17:39.598751 PROGRESS: Starting initial search for precursors.
0:17:39.598834 INFO: Starting optimization step 0.
0:17:39.598897 PROGRESS: === Extracting elution groups 0 to 200 ===
0:17:39.598954 INFO: Using ng extraction backend
0:17:39.599016 PROGRESS: Extracting batch of 396 precursors
0:17:39.600912 INFO: === Search parameters used ===
0:17:39.601001 INFO: rt_error       : 805.6004638671875
0:17:39.601050 INFO: mobility_error : 0.1
0:17:39.601095 INFO: num_candidates : 1
0:17:39.601136 INFO: ms1_error      : 30
0:17:39.601177 INFO: ms2_error      : 30
0:17:39.601216 INFO: fwhm_rt        : 5
0:17:39.601254 INFO: quant_window   : 3
0:17:39.601295 INFO: ==============================================
0:17:39.631609 INFO: performing precursor FDR with 40 features
0:17:39.631727 INFO: Decoy channel: -1
0:17:39.631757 INFO: Competetive: True
0:17:39.632703 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:39.634911 INFO: Using random state 974050 for train-test-split
0:17:39.642060 INFO: Test AUC: 0.444
0:17:39.642120 INFO: Train AUC: 0.487
0:17:39.642153 INFO: AUC difference: 8.82%
0:17:39.642179 WARNING: AUC difference > 5%. This may indicate overfitting.
0:17:40.622919 INFO: Resetting torch num_threads to 80
0:17:40.625034 PROGRESS: === Extracted 393 precursors and 1883 fragments ===
0:17:40.625896 INFO: === FDR correction performed with classifier version -1 ===
0:17:40.626846 PROGRESS: ============================= Precursor FDR =============================
0:17:40.627238 PROGRESS: Total precursors accumulated: 5
0:17:40.627584 PROGRESS: Target precursors: 5 (100.00%)
0:17:40.628056 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:40.628387 PROGRESS: 
0:17:40.628712 PROGRESS: Precursor Summary:
0:17:40.630383 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
0:17:40.630719 PROGRESS: 
0:17:40.630994 PROGRESS: Protein Summary:
0:17:40.632623 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
0:17:40.632928 PROGRESS: =========================================================================
0:17:40.633178 INFO: Target number of precursors not reached yet.
0:17:40.707571 INFO: Starting optimization step 1.
0:17:40.707819 PROGRESS: === Extracting elution groups 200 to 600 ===
0:17:40.707929 INFO: Using ng extraction backend
0:17:40.708014 PROGRESS: Extracting batch of 786 precursors
0:17:40.711874 INFO: === Search parameters used ===
0:17:40.712002 INFO: rt_error       : 805.6004638671875
0:17:40.712072 INFO: mobility_error : 0.1
0:17:40.712136 INFO: num_candidates : 1
0:17:40.712195 INFO: ms1_error      : 30
0:17:40.712255 INFO: ms2_error      : 30
0:17:40.712312 INFO: fwhm_rt        : 5
0:17:40.712371 INFO: quant_window   : 3
0:17:40.712427 INFO: ==============================================
0:17:40.756623 INFO: performing precursor FDR with 40 features
0:17:40.756722 INFO: Decoy channel: -1
0:17:40.756748 INFO: Competetive: True
0:17:40.759639 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:40.761175 INFO: Using random state 752471 for train-test-split
0:17:40.769616 INFO: Test AUC: 0.495
0:17:40.769674 INFO: Train AUC: 0.491
0:17:40.769706 INFO: AUC difference: 0.81%
0:17:40.988126 INFO: Resetting torch num_threads to 80
0:17:40.990164 PROGRESS: === Extracted 1169 precursors and 5518 fragments ===
0:17:40.990499 INFO: === FDR correction performed with classifier version -1 ===
0:17:40.990952 PROGRESS: ============================= Precursor FDR =============================
0:17:40.991038 PROGRESS: Total precursors accumulated: 0
0:17:40.991095 PROGRESS: Target precursors: 0 (0.00%)
0:17:40.991145 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:40.991189 PROGRESS: 
0:17:40.991233 PROGRESS: Precursor Summary:
0:17:40.991346 PROGRESS: 
0:17:40.991409 PROGRESS: Protein Summary:
0:17:40.991482 PROGRESS: =========================================================================
0:17:40.991667 INFO: Target number of precursors not reached yet.
0:17:41.058779 INFO: Starting optimization step 2.
0:17:41.058973 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:17:41.059053 INFO: Using ng extraction backend
0:17:41.059114 PROGRESS: Extracting batch of 1592 precursors
0:17:41.063344 INFO: === Search parameters used ===
0:17:41.063465 INFO: rt_error       : 805.6004638671875
0:17:41.063513 INFO: mobility_error : 0.1
0:17:41.063558 INFO: num_candidates : 1
0:17:41.063599 INFO: ms1_error      : 30
0:17:41.063641 INFO: ms2_error      : 30
0:17:41.063681 INFO: fwhm_rt        : 5
0:17:41.063720 INFO: quant_window   : 3
0:17:41.063760 INFO: ==============================================
0:17:41.095795 INFO: performing precursor FDR with 40 features
0:17:41.095877 INFO: Decoy channel: -1
0:17:41.095902 INFO: Competetive: True
0:17:41.099339 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:41.101263 INFO: Using random state 278117 for train-test-split
0:17:41.113955 INFO: Test AUC: 0.506
0:17:41.114017 INFO: Train AUC: 0.479
0:17:41.114047 INFO: AUC difference: 5.72%
0:17:41.114069 WARNING: AUC difference > 5%. This may indicate overfitting.
0:17:41.331122 INFO: Resetting torch num_threads to 80
0:17:41.333752 PROGRESS: === Extracted 2751 precursors and 13057 fragments ===
0:17:41.334097 INFO: === FDR correction performed with classifier version -1 ===
0:17:41.334527 PROGRESS: ============================= Precursor FDR =============================
0:17:41.334625 PROGRESS: Total precursors accumulated: 0
0:17:41.334690 PROGRESS: Target precursors: 0 (0.00%)
0:17:41.334743 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:41.334788 PROGRESS: 
0:17:41.334834 PROGRESS: Precursor Summary:
0:17:41.334941 PROGRESS: 
0:17:41.335003 PROGRESS: Protein Summary:
0:17:41.335079 PROGRESS: =========================================================================
0:17:41.335280 INFO: Target number of precursors not reached yet.
0:17:41.405751 INFO: Starting optimization step 3.
0:17:41.405950 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:17:41.406032 INFO: Using ng extraction backend
0:17:41.406096 PROGRESS: Extracting batch of 3177 precursors
0:17:41.413661 INFO: === Search parameters used ===
0:17:41.413788 INFO: rt_error       : 805.6004638671875
0:17:41.413840 INFO: mobility_error : 0.1
0:17:41.413887 INFO: num_candidates : 1
0:17:41.413932 INFO: ms1_error      : 30
0:17:41.413974 INFO: ms2_error      : 30
0:17:41.414014 INFO: fwhm_rt        : 5
0:17:41.414056 INFO: quant_window   : 3
0:17:41.414096 INFO: ==============================================
0:17:41.460361 INFO: performing precursor FDR with 40 features
0:17:41.460459 INFO: Decoy channel: -1
0:17:41.460485 INFO: Competetive: True
0:17:41.464807 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:41.467139 INFO: Using random state 253942 for train-test-split
0:17:41.488236 INFO: Test AUC: 0.499
0:17:41.488313 INFO: Train AUC: 0.480
0:17:41.488344 INFO: AUC difference: 3.95%
0:17:41.707829 INFO: Resetting torch num_threads to 80
0:17:41.711063 PROGRESS: === Extracted 5894 precursors and 27935 fragments ===
0:17:41.711410 INFO: === FDR correction performed with classifier version -1 ===
0:17:41.711878 PROGRESS: ============================= Precursor FDR =============================
0:17:41.711968 PROGRESS: Total precursors accumulated: 1
0:17:41.712026 PROGRESS: Target precursors: 1 (100.00%)
0:17:41.712079 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:41.712123 PROGRESS: 
0:17:41.712169 PROGRESS: Precursor Summary:
0:17:41.713084 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:17:41.713170 PROGRESS: 
0:17:41.713226 PROGRESS: Protein Summary:
0:17:41.714241 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:17:41.714327 PROGRESS: =========================================================================
0:17:41.714577 INFO: Target number of precursors not reached yet.
0:17:41.790098 INFO: Starting optimization step 4.
0:17:41.790308 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:17:41.790391 INFO: Using ng extraction backend
0:17:41.790454 PROGRESS: Extracting batch of 6340 precursors
0:17:41.803425 INFO: === Search parameters used ===
0:17:41.803566 INFO: rt_error       : 805.6004638671875
0:17:41.803618 INFO: mobility_error : 0.1
0:17:41.803664 INFO: num_candidates : 1
0:17:41.803707 INFO: ms1_error      : 30
0:17:41.803763 INFO: ms2_error      : 30
0:17:41.803808 INFO: fwhm_rt        : 5
0:17:41.803848 INFO: quant_window   : 3
0:17:41.803888 INFO: ==============================================
0:17:41.876566 INFO: performing precursor FDR with 40 features
0:17:41.877361 INFO: Decoy channel: -1
0:17:41.877393 INFO: Competetive: True
0:17:41.884063 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:41.887509 INFO: Using random state 196808 for train-test-split
0:17:41.924916 INFO: Test AUC: 0.488
0:17:41.925010 INFO: Train AUC: 0.487
0:17:41.925051 INFO: AUC difference: 0.24%
0:17:42.146129 INFO: Resetting torch num_threads to 80
0:17:42.150381 PROGRESS: === Extracted 12164 precursors and 57205 fragments ===
0:17:42.150759 INFO: === FDR correction performed with classifier version -1 ===
0:17:42.151205 PROGRESS: ============================= Precursor FDR =============================
0:17:42.151295 PROGRESS: Total precursors accumulated: 0
0:17:42.151354 PROGRESS: Target precursors: 0 (0.00%)
0:17:42.151406 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:42.151451 PROGRESS: 
0:17:42.151496 PROGRESS: Precursor Summary:
0:17:42.151601 PROGRESS: 
0:17:42.151661 PROGRESS: Protein Summary:
0:17:42.151736 PROGRESS: =========================================================================
0:17:42.152024 INFO: Target number of precursors not reached yet.
0:17:42.236470 INFO: Starting optimization step 5.
0:17:42.236699 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:17:42.236782 INFO: Using ng extraction backend
0:17:42.236849 PROGRESS: Extracting batch of 12663 precursors
0:17:42.260043 INFO: === Search parameters used ===
0:17:42.260240 INFO: rt_error       : 805.6004638671875
0:17:42.260294 INFO: mobility_error : 0.1
0:17:42.260340 INFO: num_candidates : 1
0:17:42.260383 INFO: ms1_error      : 30
0:17:42.260422 INFO: ms2_error      : 30
0:17:42.260465 INFO: fwhm_rt        : 5
0:17:42.260505 INFO: quant_window   : 3
0:17:42.260546 INFO: ==============================================
0:17:42.398123 INFO: performing precursor FDR with 40 features
0:17:42.398401 INFO: Decoy channel: -1
0:17:42.398470 INFO: Competetive: True
0:17:42.414043 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:42.420167 INFO: Using random state 61326 for train-test-split
0:17:42.643187 INFO: Test AUC: 0.535
0:17:42.643301 INFO: Train AUC: 0.534
0:17:42.643330 INFO: AUC difference: 0.13%
0:17:42.872361 INFO: Resetting torch num_threads to 80
0:17:42.878927 PROGRESS: === Extracted 24689 precursors and 116108 fragments ===
0:17:42.879368 INFO: === FDR correction performed with classifier version -1 ===
0:17:42.879885 PROGRESS: ============================= Precursor FDR =============================
0:17:42.879979 PROGRESS: Total precursors accumulated: 38
0:17:42.880037 PROGRESS: Target precursors: 38 (100.00%)
0:17:42.880088 PROGRESS: Decoy precursors: 0 (0.00%)
0:17:42.880131 PROGRESS: 
0:17:42.880173 PROGRESS: Precursor Summary:
0:17:42.881144 PROGRESS: Channel   0:	 0.050 FDR:    38; 0.010 FDR:    38; 0.001 FDR:    38
0:17:42.881231 PROGRESS: 
0:17:42.881286 PROGRESS: Protein Summary:
0:17:42.882308 PROGRESS: Channel   0:	 0.050 FDR:    38; 0.010 FDR:    38; 0.001 FDR:    38
0:17:42.882396 PROGRESS: =========================================================================
0:17:42.882875 INFO: Target number of precursors not reached yet.
0:17:42.984417 INFO: Starting optimization step 6.
0:17:42.984650 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:17:42.984730 INFO: Using ng extraction backend
0:17:42.984798 PROGRESS: Extracting batch of 25339 precursors
0:17:43.029483 INFO: === Search parameters used ===
0:17:43.029690 INFO: rt_error       : 805.6004638671875
0:17:43.029743 INFO: mobility_error : 0.1
0:17:43.029790 INFO: num_candidates : 1
0:17:43.029836 INFO: ms1_error      : 30
0:17:43.029878 INFO: ms2_error      : 30
0:17:43.029919 INFO: fwhm_rt        : 5
0:17:43.029959 INFO: quant_window   : 3
0:17:43.029996 INFO: ==============================================
0:17:43.244203 INFO: performing precursor FDR with 40 features
0:17:43.245267 INFO: Decoy channel: -1
0:17:43.245301 INFO: Competetive: True
0:17:43.264516 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:43.276212 INFO: Using random state 623144 for train-test-split
0:17:43.856728 INFO: Test AUC: 0.559
0:17:43.856846 INFO: Train AUC: 0.575
0:17:43.856876 INFO: AUC difference: 2.80%
0:17:44.095189 INFO: Resetting torch num_threads to 80
0:17:44.105929 PROGRESS: === Extracted 49754 precursors and 233575 fragments ===
0:17:44.106361 INFO: === FDR correction performed with classifier version -1 ===
0:17:44.106953 PROGRESS: ============================= Precursor FDR =============================
0:17:44.107051 PROGRESS: Total precursors accumulated: 115
0:17:44.107111 PROGRESS: Target precursors: 114 (99.13%)
0:17:44.107162 PROGRESS: Decoy precursors: 1 (0.87%)
0:17:44.107205 PROGRESS: 
0:17:44.107249 PROGRESS: Precursor Summary:
0:17:44.108118 PROGRESS: Channel   0:	 0.050 FDR:   114; 0.010 FDR:   114; 0.001 FDR:    90
0:17:44.108216 PROGRESS: 
0:17:44.108274 PROGRESS: Protein Summary:
0:17:44.109256 PROGRESS: Channel   0:	 0.050 FDR:   112; 0.010 FDR:   112; 0.001 FDR:    88
0:17:44.109345 PROGRESS: =========================================================================
0:17:44.110022 INFO: Target number of precursors not reached yet.
0:17:44.244864 INFO: Starting optimization step 7.
0:17:44.245108 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:17:44.245188 INFO: Using ng extraction backend
0:17:44.245251 PROGRESS: Extracting batch of 50691 precursors
0:17:44.332633 INFO: === Search parameters used ===
0:17:44.332876 INFO: rt_error       : 805.6004638671875
0:17:44.332930 INFO: mobility_error : 0.1
0:17:44.332976 INFO: num_candidates : 1
0:17:44.333016 INFO: ms1_error      : 30
0:17:44.333056 INFO: ms2_error      : 30
0:17:44.333098 INFO: fwhm_rt        : 5
0:17:44.333136 INFO: quant_window   : 3
0:17:44.333174 INFO: ==============================================
0:17:44.690213 INFO: performing precursor FDR with 40 features
0:17:44.690324 INFO: Decoy channel: -1
0:17:44.690351 INFO: Competetive: True
0:17:44.726945 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:44.750814 INFO: Using random state 454289 for train-test-split
0:17:46.050456 INFO: Test AUC: 0.583
0:17:46.050581 INFO: Train AUC: 0.598
0:17:46.050613 INFO: AUC difference: 2.58%
0:17:46.309796 INFO: Resetting torch num_threads to 80
0:17:46.328468 PROGRESS: === Extracted 99883 precursors and 469354 fragments ===
0:17:46.328954 INFO: === FDR correction performed with classifier version -1 ===
0:17:46.329488 PROGRESS: ============================= Precursor FDR =============================
0:17:46.329595 PROGRESS: Total precursors accumulated: 248
0:17:46.329656 PROGRESS: Target precursors: 246 (99.19%)
0:17:46.329705 PROGRESS: Decoy precursors: 2 (0.81%)
0:17:46.329749 PROGRESS: 
0:17:46.329792 PROGRESS: Precursor Summary:
0:17:46.332284 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   246; 0.001 FDR:   221
0:17:46.332388 PROGRESS: 
0:17:46.332444 PROGRESS: Protein Summary:
0:17:46.333554 PROGRESS: Channel   0:	 0.050 FDR:   230; 0.010 FDR:   230; 0.001 FDR:   206
0:17:46.333645 PROGRESS: =========================================================================
0:17:46.335292 INFO: Target number of precursors reached.
0:17:46.371375 INFO: fragments_df: keeping 2195 of 469354 [sum(precursor_idx_mask)=2700 sum(mass_error_mask)=469354 stop_rank=2195
0:17:46.580625 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:46.676756 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:46.921462 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:17:46.921886 INFO: Using score_cutoff 14.260303945541382 (fac=0.99, q=1)
0:17:46.922169 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:17:46.922247 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:17:46.922303 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.260303945541382
0:17:46.922355 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:46.984265 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:47.136740 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:17:47.137029 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:17:47.137141 INFO: Starting optimization step 8.
0:17:47.137213 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:17:47.137288 INFO: Using ng extraction backend
0:17:47.137356 PROGRESS: Extracting batch of 100984 precursors
0:17:47.312475 INFO: === Search parameters used ===
0:17:47.312721 INFO: rt_error       : 805.6004638671875
0:17:47.312774 INFO: mobility_error : 0.1
0:17:47.312820 INFO: num_candidates : 3
0:17:47.312862 INFO: ms1_error      : 30
0:17:47.312908 INFO: ms2_error      : 30
0:17:47.312950 INFO: fwhm_rt        : 3.0
0:17:47.312990 INFO: quant_window   : 3
0:17:47.313029 INFO: ==============================================
0:17:48.695707 INFO: performing precursor FDR with 40 features
0:17:48.696035 INFO: Decoy channel: -1
0:17:48.696127 INFO: Competetive: True
0:17:48.786222 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:48.915030 INFO: Using random state 265433 for train-test-split
0:17:52.906480 INFO: Test AUC: 0.591
0:17:52.906616 INFO: Train AUC: 0.606
0:17:52.906650 INFO: AUC difference: 2.45%
0:17:53.229788 INFO: Resetting torch num_threads to 80
0:17:53.258855 PROGRESS: === Extracted 299693 precursors and 1374186 fragments ===
0:17:53.259267 INFO: === FDR correction performed with classifier version 7 ===
0:17:53.259729 PROGRESS: ============================= Precursor FDR =============================
0:17:53.259817 PROGRESS: Total precursors accumulated: 265
0:17:53.259875 PROGRESS: Target precursors: 263 (99.25%)
0:17:53.259935 PROGRESS: Decoy precursors: 2 (0.75%)
0:17:53.259980 PROGRESS: 
0:17:53.260021 PROGRESS: Precursor Summary:
0:17:53.260906 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   263; 0.001 FDR:   158
0:17:53.260992 PROGRESS: 
0:17:53.261046 PROGRESS: Protein Summary:
0:17:53.262074 PROGRESS: Channel   0:	 0.050 FDR:   248; 0.010 FDR:   248; 0.001 FDR:   148
0:17:53.262160 PROGRESS: =========================================================================
0:17:53.266889 INFO: Target number of precursors reached.
0:17:53.361492 INFO: fragments_df: keeping 3288 of 1374186 [sum(precursor_idx_mask)=6052 sum(mass_error_mask)=1374186 stop_rank=3288
0:17:53.670559 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:53.777462 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:54.204043 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:54.204740 INFO: Using score_cutoff 14.239091836738586 (fac=0.99, q=1)
0:17:54.205115 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:54.205195 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:54.205250 INFO: Updating optimization_manager: score_cutoff        : 14.260303945541382 -> 14.239091836738586
0:17:54.205319 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:54.269848 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:54.414249 INFO: === checking if optimization conditions were reached ===
0:17:54.414577 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:17:54.417006 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.096255767741883
0:17:54.417115 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.0963.
0:17:54.417187 INFO: ==============================================
0:17:54.417269 INFO: Starting optimization step 9.
0:17:54.417339 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:17:54.417429 INFO: Using ng extraction backend
0:17:54.417515 PROGRESS: Extracting batch of 100984 precursors
0:17:54.591040 INFO: === Search parameters used ===
0:17:54.591314 INFO: rt_error       : 805.6004638671875
0:17:54.591370 INFO: mobility_error : 0.1
0:17:54.591417 INFO: num_candidates : 3
0:17:54.591458 INFO: ms1_error      : 30
0:17:54.591501 INFO: ms2_error      : 7.096255767741883
0:17:54.591541 INFO: fwhm_rt        : 3.0
0:17:54.591583 INFO: quant_window   : 3
0:17:54.591622 INFO: ==============================================
0:17:55.798335 INFO: performing precursor FDR with 40 features
0:17:55.798455 INFO: Decoy channel: -1
0:17:55.798481 INFO: Competetive: True
0:17:55.874514 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:55.978586 INFO: Using random state 265433 for train-test-split
0:18:00.237533 INFO: Test AUC: 0.593
0:18:00.237680 INFO: Train AUC: 0.603
0:18:00.237714 INFO: AUC difference: 1.58%
0:18:00.559822 INFO: Resetting torch num_threads to 80
0:18:00.571272 PROGRESS: === Extracted 302913 precursors and 1693154 fragments ===
0:18:00.571696 INFO: === FDR correction performed with classifier version 7 ===
0:18:00.572149 PROGRESS: ============================= Precursor FDR =============================
0:18:00.572244 PROGRESS: Total precursors accumulated: 160
0:18:00.572308 PROGRESS: Target precursors: 159 (99.38%)
0:18:00.572361 PROGRESS: Decoy precursors: 1 (0.62%)
0:18:00.572405 PROGRESS: 
0:18:00.572451 PROGRESS: Precursor Summary:
0:18:00.573327 PROGRESS: Channel   0:	 0.050 FDR:   159; 0.010 FDR:   159; 0.001 FDR:   144
0:18:00.573415 PROGRESS: 
0:18:00.573470 PROGRESS: Protein Summary:
0:18:00.574483 PROGRESS: Channel   0:	 0.050 FDR:   151; 0.010 FDR:   151; 0.001 FDR:   136
0:18:00.574584 PROGRESS: =========================================================================
0:18:00.579224 INFO: Target number of precursors not reached yet.
0:18:00.869987 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:00.933489 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:01.071206 INFO: === skipping optimization until target number of precursors are found ===
0:18:01.071485 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:18:01.071589 INFO: Starting optimization step 10.
0:18:01.071663 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:18:01.071738 INFO: Using ng extraction backend
0:18:01.071809 PROGRESS: Extracting batch of 101368 precursors
0:18:01.245551 INFO: === Search parameters used ===
0:18:01.245838 INFO: rt_error       : 805.6004638671875
0:18:01.245924 INFO: mobility_error : 0.1
0:18:01.245982 INFO: num_candidates : 3
0:18:01.246034 INFO: ms1_error      : 30
0:18:01.246084 INFO: ms2_error      : 7.096255767741883
0:18:01.246132 INFO: fwhm_rt        : 3.0
0:18:01.246178 INFO: quant_window   : 3
0:18:01.246223 INFO: ==============================================
0:18:02.544827 INFO: performing precursor FDR with 40 features
0:18:02.544950 INFO: Decoy channel: -1
0:18:02.544977 INFO: Competetive: True
0:18:02.773492 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:03.023975 INFO: Using random state 265433 for train-test-split
0:18:12.387287 INFO: Test AUC: 0.596
0:18:12.387882 INFO: Train AUC: 0.604
0:18:12.387926 INFO: AUC difference: 1.45%
0:18:12.804451 INFO: Resetting torch num_threads to 80
0:18:12.898042 PROGRESS: === Extracted 606960 precursors and 3386521 fragments ===
0:18:12.898694 INFO: === FDR correction performed with classifier version 7 ===
0:18:12.899472 PROGRESS: ============================= Precursor FDR =============================
0:18:12.899567 PROGRESS: Total precursors accumulated: 945
0:18:12.899632 PROGRESS: Target precursors: 936 (99.05%)
0:18:12.899688 PROGRESS: Decoy precursors: 9 (0.95%)
0:18:12.899740 PROGRESS: 
0:18:12.899791 PROGRESS: Precursor Summary:
0:18:12.900876 PROGRESS: Channel   0:	 0.050 FDR:   936; 0.010 FDR:   936; 0.001 FDR:   282
0:18:12.900972 PROGRESS: 
0:18:12.901033 PROGRESS: Protein Summary:
0:18:12.902389 PROGRESS: Channel   0:	 0.050 FDR:   825; 0.010 FDR:   825; 0.001 FDR:   260
0:18:12.902485 PROGRESS: =========================================================================
0:18:12.910067 INFO: Target number of precursors reached.
0:18:13.149389 INFO: fragments_df: keeping 5000 of 3386521 [sum(precursor_idx_mask)=23342 sum(mass_error_mask)=3386521 stop_rank=5000
0:18:13.380913 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:13.554187 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:14.277466 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:14.277937 INFO: Using score_cutoff 13.10376128768921 (fac=0.99, q=1)
0:18:14.278266 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:14.278366 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:14.278441 INFO: Updating optimization_manager: score_cutoff        : 14.239091836738586 -> 13.10376128768921
0:18:14.278495 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:14.315773 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:14.384596 INFO: === checking if optimization conditions were reached ===
0:18:14.384890 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:18:14.387523 INFO: Updating optimization_manager: ms2_error           : 7.096255767741883 -> 7.332132306888475
0:18:14.387649 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.3321.
0:18:14.387742 INFO: ==============================================
0:18:14.387838 INFO: Starting optimization step 11.
0:18:14.387927 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:14.388023 INFO: Using ng extraction backend
0:18:14.388111 PROGRESS: Extracting batch of 50293 precursors
0:18:14.482596 INFO: === Search parameters used ===
0:18:14.482940 INFO: rt_error       : 805.6004638671875
0:18:14.483008 INFO: mobility_error : 0.1
0:18:14.483069 INFO: num_candidates : 3
0:18:14.483131 INFO: ms1_error      : 30
0:18:14.483178 INFO: ms2_error      : 7.332132306888475
0:18:14.483231 INFO: fwhm_rt        : 3.0
0:18:14.483279 INFO: quant_window   : 3
0:18:14.483326 INFO: ==============================================
0:18:15.110131 INFO: performing precursor FDR with 40 features
0:18:15.110253 INFO: Decoy channel: -1
0:18:15.110286 INFO: Competetive: True
0:18:15.148380 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:15.184557 INFO: Using random state 265433 for train-test-split
0:18:17.114410 INFO: Test AUC: 0.587
0:18:17.114532 INFO: Train AUC: 0.602
0:18:17.114570 INFO: AUC difference: 2.42%
0:18:17.384786 INFO: Resetting torch num_threads to 80
0:18:17.391150 PROGRESS: === Extracted 150814 precursors and 839049 fragments ===
0:18:17.391514 INFO: === FDR correction performed with classifier version 7 ===
0:18:17.392008 PROGRESS: ============================= Precursor FDR =============================
0:18:17.392101 PROGRESS: Total precursors accumulated: 128
0:18:17.392159 PROGRESS: Target precursors: 127 (99.22%)
0:18:17.392209 PROGRESS: Decoy precursors: 1 (0.78%)
0:18:17.392252 PROGRESS: 
0:18:17.392294 PROGRESS: Precursor Summary:
0:18:17.393150 PROGRESS: Channel   0:	 0.050 FDR:   127; 0.010 FDR:   127; 0.001 FDR:    98
0:18:17.393259 PROGRESS: 
0:18:17.393314 PROGRESS: Protein Summary:
0:18:17.394295 PROGRESS: Channel   0:	 0.050 FDR:   125; 0.010 FDR:   125; 0.001 FDR:    96
0:18:17.394386 PROGRESS: =========================================================================
0:18:17.396556 INFO: Target number of precursors not reached yet.
0:18:17.542832 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:17.574115 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:17.635844 INFO: === skipping optimization until target number of precursors are found ===
0:18:17.636083 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:18:17.636172 INFO: Starting optimization step 12.
0:18:17.636236 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:18:17.636302 INFO: Using ng extraction backend
0:18:17.636361 PROGRESS: Extracting batch of 50691 precursors
0:18:17.724392 INFO: === Search parameters used ===
0:18:17.724667 INFO: rt_error       : 805.6004638671875
0:18:17.724725 INFO: mobility_error : 0.1
0:18:17.724774 INFO: num_candidates : 3
0:18:17.724817 INFO: ms1_error      : 30
0:18:17.724860 INFO: ms2_error      : 7.332132306888475
0:18:17.724902 INFO: fwhm_rt        : 3.0
0:18:17.724945 INFO: quant_window   : 3
0:18:17.724984 INFO: ==============================================
0:18:18.394036 INFO: performing precursor FDR with 40 features
0:18:18.394165 INFO: Decoy channel: -1
0:18:18.394202 INFO: Competetive: True
0:18:18.496637 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:18.597135 INFO: Using random state 265433 for train-test-split
0:18:22.791003 INFO: Test AUC: 0.590
0:18:22.791135 INFO: Train AUC: 0.603
0:18:22.791165 INFO: AUC difference: 2.10%
0:18:23.108324 INFO: Resetting torch num_threads to 80
0:18:23.153470 PROGRESS: === Extracted 302840 precursors and 1684941 fragments ===
0:18:23.154124 INFO: === FDR correction performed with classifier version 7 ===
0:18:23.154752 PROGRESS: ============================= Precursor FDR =============================
0:18:23.154848 PROGRESS: Total precursors accumulated: 1
0:18:23.154907 PROGRESS: Target precursors: 1 (100.00%)
0:18:23.154958 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:23.155001 PROGRESS: 
0:18:23.155046 PROGRESS: Precursor Summary:
0:18:23.155986 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:23.156073 PROGRESS: 
0:18:23.156128 PROGRESS: Protein Summary:
0:18:23.157135 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:23.157223 PROGRESS: =========================================================================
0:18:23.161173 INFO: Target number of precursors not reached yet.
0:18:23.369677 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:23.431641 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:23.580211 INFO: === skipping optimization until target number of precursors are found ===
0:18:23.580501 PROGRESS: === Optimization of ms2_error has been skipped 2 time(s); maximum number is 1 ===
0:18:23.580890 INFO: Updating optimization_manager: ms2_error           : 7.332132306888475 -> 7.096255767741883
0:18:23.581026 INFO: Updating optimization_manager: classifier_version  : 7 -> 10
0:18:23.581139 INFO: Updating optimization_manager: score_cutoff        : 13.10376128768921 -> 13.10376128768921
0:18:23.581249 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:23.581372 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:23.581477 PROGRESS: ✅ ms2_error      : optimization complete (batch_substantially_bigger). Optimal parameter 7.0963 found after 2 searches.
0:18:23.581579 PROGRESS: Optimization finished for ms2_error.
0:18:23.735786 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:23.766936 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:23.858536 INFO: Starting optimization step 0.
0:18:23.858806 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:23.858910 INFO: Using ng extraction backend
0:18:23.858994 PROGRESS: Extracting batch of 50293 precursors
0:18:23.946859 INFO: === Search parameters used ===
0:18:23.947119 INFO: rt_error       : 805.6004638671875
0:18:23.947173 INFO: mobility_error : 0.1
0:18:23.947222 INFO: num_candidates : 3
0:18:23.947265 INFO: ms1_error      : 30
0:18:23.947307 INFO: ms2_error      : 7.096255767741883
0:18:23.947348 INFO: fwhm_rt        : 3.0
0:18:23.947392 INFO: quant_window   : 3
0:18:23.947432 INFO: ==============================================
0:18:24.591559 INFO: performing precursor FDR with 40 features
0:18:24.591682 INFO: Decoy channel: -1
0:18:24.591708 INFO: Competetive: True
0:18:24.629704 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:24.664835 INFO: Using random state 78487 for train-test-split
0:18:26.631263 INFO: Test AUC: 0.601
0:18:26.631388 INFO: Train AUC: 0.611
0:18:26.631417 INFO: AUC difference: 1.55%
0:18:26.900611 INFO: Resetting torch num_threads to 80
0:18:26.908042 PROGRESS: === Extracted 150862 precursors and 843210 fragments ===
0:18:26.908808 INFO: === FDR correction performed with classifier version 10 ===
0:18:26.909289 PROGRESS: ============================= Precursor FDR =============================
0:18:26.909386 PROGRESS: Total precursors accumulated: 159
0:18:26.909445 PROGRESS: Target precursors: 158 (99.37%)
0:18:26.909494 PROGRESS: Decoy precursors: 1 (0.63%)
0:18:26.909537 PROGRESS: 
0:18:26.909580 PROGRESS: Precursor Summary:
0:18:26.910460 PROGRESS: Channel   0:	 0.050 FDR:   158; 0.010 FDR:   158; 0.001 FDR:    95
0:18:26.910555 PROGRESS: 
0:18:26.910619 PROGRESS: Protein Summary:
0:18:26.911621 PROGRESS: Channel   0:	 0.050 FDR:   155; 0.010 FDR:   155; 0.001 FDR:    93
0:18:26.911708 PROGRESS: =========================================================================
0:18:26.914592 INFO: Target number of precursors not reached yet.
0:18:27.048807 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:27.080325 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:27.162247 INFO: === skipping optimization until target number of precursors are found ===
0:18:27.162521 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:18:27.162642 INFO: Starting optimization step 1.
0:18:27.162720 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:18:27.162795 INFO: Using ng extraction backend
0:18:27.162866 PROGRESS: Extracting batch of 50691 precursors
0:18:27.276291 INFO: === Search parameters used ===
0:18:27.276571 INFO: rt_error       : 805.6004638671875
0:18:27.276629 INFO: mobility_error : 0.1
0:18:27.276676 INFO: num_candidates : 3
0:18:27.276720 INFO: ms1_error      : 30
0:18:27.276763 INFO: ms2_error      : 7.096255767741883
0:18:27.276804 INFO: fwhm_rt        : 3.0
0:18:27.276845 INFO: quant_window   : 3
0:18:27.276884 INFO: ==============================================
0:18:27.983619 INFO: performing precursor FDR with 40 features
0:18:27.983742 INFO: Decoy channel: -1
0:18:27.983767 INFO: Competetive: True
0:18:28.085683 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:28.185794 INFO: Using random state 78487 for train-test-split
0:18:32.252773 INFO: Test AUC: 0.598
0:18:32.252918 INFO: Train AUC: 0.611
0:18:32.252954 INFO: AUC difference: 2.13%
0:18:32.595519 INFO: Resetting torch num_threads to 80
0:18:32.639279 PROGRESS: === Extracted 302924 precursors and 1693050 fragments ===
0:18:32.639912 INFO: === FDR correction performed with classifier version 10 ===
0:18:32.640516 PROGRESS: ============================= Precursor FDR =============================
0:18:32.640606 PROGRESS: Total precursors accumulated: 315
0:18:32.640663 PROGRESS: Target precursors: 312 (99.05%)
0:18:32.640715 PROGRESS: Decoy precursors: 3 (0.95%)
0:18:32.640761 PROGRESS: 
0:18:32.640805 PROGRESS: Precursor Summary:
0:18:32.641738 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   312; 0.001 FDR:    14
0:18:32.641825 PROGRESS: 
0:18:32.641880 PROGRESS: Protein Summary:
0:18:32.642954 PROGRESS: Channel   0:	 0.050 FDR:   293; 0.010 FDR:   293; 0.001 FDR:    14
0:18:32.643047 PROGRESS: =========================================================================
0:18:32.646968 INFO: Target number of precursors reached.
0:18:32.768272 INFO: fragments_df: keeping 3886 of 1693050 [sum(precursor_idx_mask)=7920 sum(mass_error_mask)=1693050 stop_rank=3886
0:18:33.000629 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:33.120067 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:33.632612 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:33.633032 INFO: Using score_cutoff 13.0279278840065 (fac=0.99, q=1)
0:18:33.633326 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:33.633406 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:33.633460 INFO: Updating optimization_manager: score_cutoff        : 13.10376128768921 -> 13.0279278840065
0:18:33.633513 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:33.699554 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:33.918467 INFO: === checking if optimization conditions were reached ===
0:18:33.918776 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:18:33.920875 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 283.7553438515995
0:18:33.921012 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 283.7553.
0:18:33.921102 INFO: ==============================================
0:18:33.921180 INFO: Starting optimization step 2.
0:18:33.921241 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:33.921306 INFO: Using ng extraction backend
0:18:33.921366 PROGRESS: Extracting batch of 100984 precursors
0:18:34.096912 INFO: === Search parameters used ===
0:18:34.097186 INFO: rt_error       : 283.7553438515995
0:18:34.097243 INFO: mobility_error : 0.1
0:18:34.097291 INFO: num_candidates : 3
0:18:34.097336 INFO: ms1_error      : 30
0:18:34.097377 INFO: ms2_error      : 7.096255767741883
0:18:34.097417 INFO: fwhm_rt        : 3.0
0:18:34.097459 INFO: quant_window   : 3
0:18:34.097499 INFO: ==============================================
0:18:35.317316 INFO: performing precursor FDR with 40 features
0:18:35.317432 INFO: Decoy channel: -1
0:18:35.317459 INFO: Competetive: True
0:18:35.390535 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:35.492554 INFO: Using random state 78487 for train-test-split
0:18:39.459845 INFO: Test AUC: 0.598
0:18:39.459991 INFO: Train AUC: 0.608
0:18:39.460028 INFO: AUC difference: 1.73%
0:18:39.788607 INFO: Resetting torch num_threads to 80
0:18:39.800153 PROGRESS: === Extracted 302629 precursors and 1585078 fragments ===
0:18:39.800730 INFO: === FDR correction performed with classifier version 10 ===
0:18:39.801266 PROGRESS: ============================= Precursor FDR =============================
0:18:39.801360 PROGRESS: Total precursors accumulated: 511
0:18:39.801418 PROGRESS: Target precursors: 506 (99.02%)
0:18:39.801468 PROGRESS: Decoy precursors: 5 (0.98%)
0:18:39.801510 PROGRESS: 
0:18:39.801552 PROGRESS: Precursor Summary:
0:18:39.802509 PROGRESS: Channel   0:	 0.050 FDR:   506; 0.010 FDR:   506; 0.001 FDR:   263
0:18:39.802607 PROGRESS: 
0:18:39.802662 PROGRESS: Protein Summary:
0:18:39.803819 PROGRESS: Channel   0:	 0.050 FDR:   470; 0.010 FDR:   470; 0.001 FDR:   247
0:18:39.803924 PROGRESS: =========================================================================
0:18:39.808930 INFO: Target number of precursors reached.
0:18:39.948982 INFO: fragments_df: keeping 5000 of 1585078 [sum(precursor_idx_mask)=12469 sum(mass_error_mask)=1585078 stop_rank=5000
0:18:40.095192 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:40.215869 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:40.898249 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:40.898684 INFO: Using score_cutoff 12.611048272132873 (fac=0.99, q=1)
0:18:40.898979 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:40.899058 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:40.899115 INFO: Updating optimization_manager: score_cutoff        : 13.0279278840065 -> 12.611048272132873
0:18:40.899169 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:40.930247 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:41.058590 INFO: === checking if optimization conditions were reached ===
0:18:41.058871 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:18:41.061290 INFO: Updating optimization_manager: rt_error            : 283.7553438515995 -> 127.8505568281217
0:18:41.061425 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 127.8506.
0:18:41.061517 INFO: ==============================================
0:18:41.061612 INFO: Starting optimization step 3.
0:18:41.061701 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:41.061805 INFO: Using ng extraction backend
0:18:41.061892 PROGRESS: Extracting batch of 50293 precursors
0:18:41.152496 INFO: === Search parameters used ===
0:18:41.152775 INFO: rt_error       : 127.8505568281217
0:18:41.152833 INFO: mobility_error : 0.1
0:18:41.152880 INFO: num_candidates : 3
0:18:41.152924 INFO: ms1_error      : 30
0:18:41.152964 INFO: ms2_error      : 7.096255767741883
0:18:41.153005 INFO: fwhm_rt        : 3.0
0:18:41.153057 INFO: quant_window   : 3
0:18:41.153096 INFO: ==============================================
0:18:41.781401 INFO: performing precursor FDR with 40 features
0:18:41.781533 INFO: Decoy channel: -1
0:18:41.781565 INFO: Competetive: True
0:18:41.833670 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:41.870390 INFO: Using random state 78487 for train-test-split
0:18:43.797938 INFO: Test AUC: 0.599
0:18:43.798161 INFO: Train AUC: 0.609
0:18:43.798197 INFO: AUC difference: 1.57%
0:18:44.839695 INFO: Resetting torch num_threads to 80
0:18:44.846333 PROGRESS: === Extracted 149652 precursors and 652519 fragments ===
0:18:44.846715 INFO: === FDR correction performed with classifier version 10 ===
0:18:44.847188 PROGRESS: ============================= Precursor FDR =============================
0:18:44.847282 PROGRESS: Total precursors accumulated: 245
0:18:44.847340 PROGRESS: Target precursors: 243 (99.18%)
0:18:44.847390 PROGRESS: Decoy precursors: 2 (0.82%)
0:18:44.847432 PROGRESS: 
0:18:44.847474 PROGRESS: Precursor Summary:
0:18:44.848387 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:   243; 0.001 FDR:   224
0:18:44.848475 PROGRESS: 
0:18:44.848530 PROGRESS: Protein Summary:
0:18:44.849598 PROGRESS: Channel   0:	 0.050 FDR:   234; 0.010 FDR:   234; 0.001 FDR:   215
0:18:44.849687 PROGRESS: =========================================================================
0:18:44.852613 INFO: Target number of precursors reached.
0:18:44.897438 INFO: fragments_df: keeping 2780 of 652519 [sum(precursor_idx_mask)=5898 sum(mass_error_mask)=652519 stop_rank=2780
0:18:45.071033 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:45.240346 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:45.648701 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:45.649213 INFO: Using score_cutoff 13.336868760108949 (fac=0.99, q=1)
0:18:45.649524 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:45.649606 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:45.649661 INFO: Updating optimization_manager: score_cutoff        : 12.611048272132873 -> 13.336868760108949
0:18:45.649717 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:45.683361 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:45.751548 INFO: === checking if optimization conditions were reached ===
0:18:45.751876 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:18:45.754324 INFO: Updating optimization_manager: rt_error            : 127.8505568281217 -> 97.74352069896742
0:18:45.754476 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 97.7435.
0:18:45.754558 INFO: ==============================================
0:18:45.754690 INFO: Starting optimization step 4.
0:18:45.754762 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:45.754836 INFO: Using ng extraction backend
0:18:45.754905 PROGRESS: Extracting batch of 50293 precursors
0:18:45.850732 INFO: === Search parameters used ===
0:18:45.851038 INFO: rt_error       : 97.74352069896742
0:18:45.851103 INFO: mobility_error : 0.1
0:18:45.851157 INFO: num_candidates : 3
0:18:45.851203 INFO: ms1_error      : 30
0:18:45.851245 INFO: ms2_error      : 7.096255767741883
0:18:45.851287 INFO: fwhm_rt        : 3.0
0:18:45.851330 INFO: quant_window   : 3
0:18:45.851372 INFO: ==============================================
0:18:46.452442 INFO: performing precursor FDR with 40 features
0:18:46.452559 INFO: Decoy channel: -1
0:18:46.452585 INFO: Competetive: True
0:18:46.489062 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:46.522666 INFO: Using random state 78487 for train-test-split
0:18:48.480175 INFO: Test AUC: 0.590
0:18:48.480303 INFO: Train AUC: 0.608
0:18:48.480335 INFO: AUC difference: 3.08%
0:18:48.759228 INFO: Resetting torch num_threads to 80
0:18:48.765394 PROGRESS: === Extracted 148519 precursors and 616494 fragments ===
0:18:48.765777 INFO: === FDR correction performed with classifier version 10 ===
0:18:48.766243 PROGRESS: ============================= Precursor FDR =============================
0:18:48.766336 PROGRESS: Total precursors accumulated: 235
0:18:48.766397 PROGRESS: Target precursors: 233 (99.15%)
0:18:48.766449 PROGRESS: Decoy precursors: 2 (0.85%)
0:18:48.766493 PROGRESS: 
0:18:48.766537 PROGRESS: Precursor Summary:
0:18:48.767460 PROGRESS: Channel   0:	 0.050 FDR:   233; 0.010 FDR:   233; 0.001 FDR:   194
0:18:48.767559 PROGRESS: 
0:18:48.767616 PROGRESS: Protein Summary:
0:18:48.768669 PROGRESS: Channel   0:	 0.050 FDR:   224; 0.010 FDR:   224; 0.001 FDR:   187
0:18:48.768759 PROGRESS: =========================================================================
0:18:48.770847 INFO: Target number of precursors reached.
0:18:48.812518 INFO: fragments_df: keeping 2675 of 616494 [sum(precursor_idx_mask)=5580 sum(mass_error_mask)=616494 stop_rank=2675
0:18:48.949452 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:49.072956 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:49.378643 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:49.379363 INFO: Using score_cutoff 14.086399658203124 (fac=0.99, q=1)
0:18:49.379870 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:49.380137 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:49.380375 INFO: Updating optimization_manager: score_cutoff        : 13.336868760108949 -> 14.086399658203124
0:18:49.380608 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:49.413651 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:49.481889 INFO: === checking if optimization conditions were reached ===
0:18:49.482407 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:18:49.484906 INFO: Updating optimization_manager: rt_error            : 97.74352069896742 -> 68.50949556124114
0:18:49.485215 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 68.5095.
0:18:49.485476 INFO: ==============================================
0:18:49.485730 INFO: Starting optimization step 5.
0:18:49.485966 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:49.486204 INFO: Using ng extraction backend
0:18:49.486438 PROGRESS: Extracting batch of 50293 precursors
0:18:49.576884 INFO: === Search parameters used ===
0:18:49.577163 INFO: rt_error       : 68.50949556124114
0:18:49.577218 INFO: mobility_error : 0.1
0:18:49.577262 INFO: num_candidates : 3
0:18:49.577305 INFO: ms1_error      : 30
0:18:49.577345 INFO: ms2_error      : 7.096255767741883
0:18:49.577386 INFO: fwhm_rt        : 3.0
0:18:49.577425 INFO: quant_window   : 3
0:18:49.577462 INFO: ==============================================
0:18:50.201429 INFO: performing precursor FDR with 40 features
0:18:50.201549 INFO: Decoy channel: -1
0:18:50.201574 INFO: Competetive: True
0:18:50.236515 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:50.268776 INFO: Using random state 78487 for train-test-split
0:18:52.183688 INFO: Test AUC: 0.595
0:18:52.183808 INFO: Train AUC: 0.609
0:18:52.183838 INFO: AUC difference: 2.30%
0:18:52.454719 INFO: Resetting torch num_threads to 80
0:18:52.460744 PROGRESS: === Extracted 146114 precursors and 573974 fragments ===
0:18:52.461104 INFO: === FDR correction performed with classifier version 10 ===
0:18:52.461576 PROGRESS: ============================= Precursor FDR =============================
0:18:52.461663 PROGRESS: Total precursors accumulated: 222
0:18:52.461720 PROGRESS: Target precursors: 220 (99.10%)
0:18:52.461768 PROGRESS: Decoy precursors: 2 (0.90%)
0:18:52.461811 PROGRESS: 
0:18:52.461860 PROGRESS: Precursor Summary:
0:18:52.462838 PROGRESS: Channel   0:	 0.050 FDR:   220; 0.010 FDR:   220; 0.001 FDR:   181
0:18:52.462929 PROGRESS: 
0:18:52.462985 PROGRESS: Protein Summary:
0:18:52.464028 PROGRESS: Channel   0:	 0.050 FDR:   213; 0.010 FDR:   213; 0.001 FDR:   177
0:18:52.464122 PROGRESS: =========================================================================
0:18:52.466118 INFO: Target number of precursors reached.
0:18:52.529889 INFO: fragments_df: keeping 2502 of 573974 [sum(precursor_idx_mask)=5115 sum(mass_error_mask)=573974 stop_rank=2502
0:18:52.666446 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:52.762723 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:53.040158 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:53.040579 INFO: Using score_cutoff 13.122330538272857 (fac=0.99, q=1)
0:18:53.040861 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:53.040939 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:53.040992 INFO: Updating optimization_manager: score_cutoff        : 14.086399658203124 -> 13.122330538272857
0:18:53.041047 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:53.072676 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:53.139572 INFO: === checking if optimization conditions were reached ===
0:18:53.139868 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:18:53.142159 INFO: Updating optimization_manager: rt_error            : 68.50949556124114 -> 47.801129031157124
0:18:53.142302 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 47.8011.
0:18:53.142381 INFO: ==============================================
0:18:53.142462 INFO: Starting optimization step 6.
0:18:53.142529 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:53.142611 INFO: Using ng extraction backend
0:18:53.142682 PROGRESS: Extracting batch of 50293 precursors
0:18:53.233047 INFO: === Search parameters used ===
0:18:53.233312 INFO: rt_error       : 47.801129031157124
0:18:53.233369 INFO: mobility_error : 0.1
0:18:53.233413 INFO: num_candidates : 3
0:18:53.233454 INFO: ms1_error      : 30
0:18:53.233495 INFO: ms2_error      : 7.096255767741883
0:18:53.233533 INFO: fwhm_rt        : 3.0
0:18:53.233570 INFO: quant_window   : 3
0:18:53.233608 INFO: ==============================================
0:18:53.753899 INFO: performing precursor FDR with 40 features
0:18:53.754018 INFO: Decoy channel: -1
0:18:53.754044 INFO: Competetive: True
0:18:53.787051 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:53.819417 INFO: Using random state 78487 for train-test-split
0:18:55.550036 INFO: Test AUC: 0.591
0:18:55.550158 INFO: Train AUC: 0.609
0:18:55.550187 INFO: AUC difference: 3.01%
0:18:55.815331 INFO: Resetting torch num_threads to 80
0:18:55.821313 PROGRESS: === Extracted 134936 precursors and 504313 fragments ===
0:18:55.821912 INFO: === FDR correction performed with classifier version 10 ===
0:18:55.822384 PROGRESS: ============================= Precursor FDR =============================
0:18:55.822469 PROGRESS: Total precursors accumulated: 284
0:18:55.822525 PROGRESS: Target precursors: 282 (99.30%)
0:18:55.822587 PROGRESS: Decoy precursors: 2 (0.70%)
0:18:55.822655 PROGRESS: 
0:18:55.822709 PROGRESS: Precursor Summary:
0:18:55.823686 PROGRESS: Channel   0:	 0.050 FDR:   282; 0.010 FDR:   282; 0.001 FDR:   211
0:18:55.823772 PROGRESS: 
0:18:55.823826 PROGRESS: Protein Summary:
0:18:55.824894 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   274; 0.001 FDR:   205
0:18:55.824979 PROGRESS: =========================================================================
0:18:55.826977 INFO: Target number of precursors reached.
0:18:55.862505 INFO: fragments_df: keeping 2762 of 504313 [sum(precursor_idx_mask)=5639 sum(mass_error_mask)=504313 stop_rank=2762
0:18:55.998908 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:56.100792 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:56.403001 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:56.403434 INFO: Using score_cutoff 9.833851682281495 (fac=0.99, q=1)
0:18:56.403717 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:56.403806 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:56.403859 INFO: Updating optimization_manager: score_cutoff        : 13.122330538272857 -> 9.833851682281495
0:18:56.403912 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:56.435691 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:56.501347 INFO: === checking if optimization conditions were reached ===
0:18:56.501637 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:18:56.503987 INFO: Updating optimization_manager: rt_error            : 47.801129031157124 -> 36.871384147444545
0:18:56.504106 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 36.8714.
0:18:56.504182 INFO: ==============================================
0:18:56.504262 INFO: Starting optimization step 7.
0:18:56.504328 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:56.504396 INFO: Using ng extraction backend
0:18:56.504461 PROGRESS: Extracting batch of 50293 precursors
0:18:56.594941 INFO: === Search parameters used ===
0:18:56.595212 INFO: rt_error       : 36.871384147444545
0:18:56.595268 INFO: mobility_error : 0.1
0:18:56.595315 INFO: num_candidates : 3
0:18:56.595356 INFO: ms1_error      : 30
0:18:56.595396 INFO: ms2_error      : 7.096255767741883
0:18:56.595433 INFO: fwhm_rt        : 3.0
0:18:56.595471 INFO: quant_window   : 3
0:18:56.595508 INFO: ==============================================
0:18:57.120353 INFO: performing precursor FDR with 40 features
0:18:57.120473 INFO: Decoy channel: -1
0:18:57.120498 INFO: Competetive: True
0:18:57.155927 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:57.186160 INFO: Using random state 78487 for train-test-split
0:18:58.933081 INFO: Test AUC: 0.594
0:18:58.933208 INFO: Train AUC: 0.609
0:18:58.933239 INFO: AUC difference: 2.48%
0:18:59.198604 INFO: Resetting torch num_threads to 80
0:18:59.204703 PROGRESS: === Extracted 134824 precursors and 503944 fragments ===
0:18:59.205061 INFO: === FDR correction performed with classifier version 10 ===
0:18:59.205528 PROGRESS: ============================= Precursor FDR =============================
0:18:59.205612 PROGRESS: Total precursors accumulated: 261
0:18:59.205677 PROGRESS: Target precursors: 259 (99.23%)
0:18:59.205729 PROGRESS: Decoy precursors: 2 (0.77%)
0:18:59.205772 PROGRESS: 
0:18:59.205814 PROGRESS: Precursor Summary:
0:18:59.206717 PROGRESS: Channel   0:	 0.050 FDR:   259; 0.010 FDR:   259; 0.001 FDR:   238
0:18:59.206804 PROGRESS: 
0:18:59.206858 PROGRESS: Protein Summary:
0:18:59.207909 PROGRESS: Channel   0:	 0.050 FDR:   251; 0.010 FDR:   251; 0.001 FDR:   232
0:18:59.207995 PROGRESS: =========================================================================
0:18:59.210027 INFO: Target number of precursors reached.
0:18:59.244481 INFO: fragments_df: keeping 2548 of 503944 [sum(precursor_idx_mask)=5163 sum(mass_error_mask)=503944 stop_rank=2548
0:18:59.381199 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:59.481532 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:59.761154 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:59.761573 INFO: Using score_cutoff 10.384982341575622 (fac=0.99, q=1)
0:18:59.761851 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:59.761927 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:59.761979 INFO: Updating optimization_manager: score_cutoff        : 9.833851682281495 -> 10.384982341575622
0:18:59.762032 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:59.793907 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:59.860065 INFO: === checking if optimization conditions were reached ===
0:18:59.860351 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:18:59.862669 INFO: Updating optimization_manager: rt_error            : 36.871384147444545 -> 32.61198060504226
0:18:59.862798 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 32.6120.
0:18:59.862873 INFO: ==============================================
0:18:59.862951 INFO: Starting optimization step 8.
0:18:59.863014 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:59.863082 INFO: Using ng extraction backend
0:18:59.863147 PROGRESS: Extracting batch of 50293 precursors
0:18:59.952135 INFO: === Search parameters used ===
0:18:59.952404 INFO: rt_error       : 32.61198060504226
0:18:59.952464 INFO: mobility_error : 0.1
0:18:59.952510 INFO: num_candidates : 3
0:18:59.952554 INFO: ms1_error      : 30
0:18:59.952599 INFO: ms2_error      : 7.096255767741883
0:18:59.952638 INFO: fwhm_rt        : 3.0
0:18:59.952677 INFO: quant_window   : 3
0:18:59.952717 INFO: ==============================================
0:19:00.478143 INFO: performing precursor FDR with 40 features
0:19:00.478265 INFO: Decoy channel: -1
0:19:00.478291 INFO: Competetive: True
0:19:00.511864 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:00.543238 INFO: Using random state 78487 for train-test-split
0:19:02.277720 INFO: Test AUC: 0.598
0:19:02.277844 INFO: Train AUC: 0.606
0:19:02.277873 INFO: AUC difference: 1.36%
0:19:02.536916 INFO: Resetting torch num_threads to 80
0:19:02.542834 PROGRESS: === Extracted 134888 precursors and 504566 fragments ===
0:19:02.543191 INFO: === FDR correction performed with classifier version 10 ===
0:19:02.543674 PROGRESS: ============================= Precursor FDR =============================
0:19:02.543760 PROGRESS: Total precursors accumulated: 261
0:19:02.543815 PROGRESS: Target precursors: 259 (99.23%)
0:19:02.543863 PROGRESS: Decoy precursors: 2 (0.77%)
0:19:02.543906 PROGRESS: 
0:19:02.543947 PROGRESS: Precursor Summary:
0:19:02.544863 PROGRESS: Channel   0:	 0.050 FDR:   259; 0.010 FDR:   259; 0.001 FDR:   227
0:19:02.544946 PROGRESS: 
0:19:02.544998 PROGRESS: Protein Summary:
0:19:02.546056 PROGRESS: Channel   0:	 0.050 FDR:   252; 0.010 FDR:   252; 0.001 FDR:   220
0:19:02.546141 PROGRESS: =========================================================================
0:19:02.547964 INFO: Target number of precursors reached.
0:19:02.590676 INFO: fragments_df: keeping 2557 of 504566 [sum(precursor_idx_mask)=5187 sum(mass_error_mask)=504566 stop_rank=2557
0:19:02.727349 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:02.828009 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:03.107650 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:03.108084 INFO: Using score_cutoff 9.759702214050293 (fac=0.99, q=1)
0:19:03.108371 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:03.108450 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:03.108504 INFO: Updating optimization_manager: score_cutoff        : 10.384982341575622 -> 9.759702214050293
0:19:03.108563 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:03.140682 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:03.206730 INFO: === checking if optimization conditions were reached ===
0:19:03.206968 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:19:03.208928 INFO: Updating optimization_manager: rt_error            : 32.61198060504226 -> 32.10092038849501
0:19:03.209039 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 32.1009.
0:19:03.209104 INFO: ==============================================
0:19:03.209171 INFO: Starting optimization step 9.
0:19:03.209228 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:19:03.209287 INFO: Using ng extraction backend
0:19:03.209340 PROGRESS: Extracting batch of 50293 precursors
0:19:03.297309 INFO: === Search parameters used ===
0:19:03.297586 INFO: rt_error       : 32.10092038849501
0:19:03.297651 INFO: mobility_error : 0.1
0:19:03.297701 INFO: num_candidates : 3
0:19:03.297746 INFO: ms1_error      : 30
0:19:03.297804 INFO: ms2_error      : 7.096255767741883
0:19:03.297847 INFO: fwhm_rt        : 3.0
0:19:03.297886 INFO: quant_window   : 3
0:19:03.297926 INFO: ==============================================
0:19:03.834443 INFO: performing precursor FDR with 40 features
0:19:03.834574 INFO: Decoy channel: -1
0:19:03.834602 INFO: Competetive: True
0:19:03.868368 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:03.900960 INFO: Using random state 78487 for train-test-split
0:19:05.582081 INFO: Test AUC: 0.594
0:19:05.582205 INFO: Train AUC: 0.610
0:19:05.582235 INFO: AUC difference: 2.63%
0:19:05.841189 INFO: Resetting torch num_threads to 80
0:19:05.847293 PROGRESS: === Extracted 134912 precursors and 504725 fragments ===
0:19:05.847659 INFO: === FDR correction performed with classifier version 10 ===
0:19:05.848120 PROGRESS: ============================= Precursor FDR =============================
0:19:05.848221 PROGRESS: Total precursors accumulated: 266
0:19:05.848301 PROGRESS: Target precursors: 264 (99.25%)
0:19:05.848358 PROGRESS: Decoy precursors: 2 (0.75%)
0:19:05.848406 PROGRESS: 
0:19:05.848448 PROGRESS: Precursor Summary:
0:19:05.849372 PROGRESS: Channel   0:	 0.050 FDR:   264; 0.010 FDR:   264; 0.001 FDR:   225
0:19:05.849460 PROGRESS: 
0:19:05.849514 PROGRESS: Protein Summary:
0:19:05.850571 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   256; 0.001 FDR:   218
0:19:05.850660 PROGRESS: =========================================================================
0:19:05.852677 INFO: Target number of precursors reached.
0:19:05.887317 INFO: fragments_df: keeping 2592 of 504725 [sum(precursor_idx_mask)=5273 sum(mass_error_mask)=504725 stop_rank=2592
0:19:06.053676 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:06.155090 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:06.439798 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:06.440226 INFO: Using score_cutoff 9.775821663665772 (fac=0.99, q=1)
0:19:06.440519 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:06.440602 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:06.440665 INFO: Updating optimization_manager: score_cutoff        : 9.759702214050293 -> 9.775821663665772
0:19:06.440722 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:06.472324 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:06.536166 INFO: === checking if optimization conditions were reached ===
0:19:06.536443 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:19:06.537543 INFO: Updating optimization_manager: rt_error            : 32.10092038849501 -> 32.10092038849501
0:19:06.537686 INFO: Updating optimization_manager: classifier_version  : 10 -> 22
0:19:06.537800 INFO: Updating optimization_manager: score_cutoff        : 9.775821663665772 -> 9.775821663665772
0:19:06.537908 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:06.538014 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:06.538119 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 32.1009 found after 9 searches.
0:19:06.538196 INFO: ==============================================
0:19:06.538278 PROGRESS: Optimization finished for rt_error.
0:19:06.714843 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:06.748078 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:06.837511 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:19:06.837734 PROGRESS: ==============================================
0:19:06.837820 PROGRESS: ms2_error      : 7.0963
0:19:06.837908 PROGRESS: rt_error       : 32.1009
0:19:06.837975 PROGRESS: ==============================================
0:19:06.838450 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:14.870112 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:32.554950 INFO: Using ng extraction backend
0:19:32.555548 PROGRESS: Extracting batch of 12001526 precursors
0:19:48.439592 INFO: === Search parameters used ===
0:19:48.440121 INFO: rt_error       : 32.10092038849501
0:19:48.440193 INFO: mobility_error : 0.1
0:19:48.440246 INFO: num_candidates : 3
0:19:48.440296 INFO: ms1_error      : 30
0:19:48.440342 INFO: ms2_error      : 7.096255767741883
0:19:48.440388 INFO: fwhm_rt        : 3.0
0:19:48.440433 INFO: quant_window   : 3
0:19:48.440477 INFO: ==============================================
0:20:06.273036 INFO: Removed 23920366 precursors with score below cutoff 9.775821663665772
0:20:14.543528 INFO: performing precursor FDR with 40 features
0:20:14.543655 INFO: Decoy channel: -1
0:20:14.543688 INFO: Competetive: True
0:20:15.366464 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:18.633016 INFO: Using random state 440398 for train-test-split
0:22:20.951955 INFO: Test AUC: 0.631
0:22:20.952197 INFO: Train AUC: 0.633
0:22:20.952237 INFO: AUC difference: 0.19%
0:22:23.718182 INFO: Resetting torch num_threads to 80
0:22:25.341664 PROGRESS: ============================= Precursor FDR =============================
0:22:25.341957 PROGRESS: Total precursors accumulated: 73,932
0:22:25.342025 PROGRESS: Target precursors: 73,200 (99.01%)
0:22:25.342080 PROGRESS: Decoy precursors: 732 (0.99%)
0:22:25.342129 PROGRESS: 
0:22:25.342176 PROGRESS: Precursor Summary:
0:22:25.363051 PROGRESS: Channel   0:	 0.050 FDR: 73,200; 0.010 FDR: 73,183; 0.001 FDR: 51,170
0:22:25.363285 PROGRESS: 
0:22:25.363347 PROGRESS: Protein Summary:
0:22:25.389747 PROGRESS: Channel   0:	 0.050 FDR: 12,300; 0.010 FDR: 12,297; 0.001 FDR: 9,338
0:22:25.389972 PROGRESS: =========================================================================
0:22:25.443510 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
0:22:25.594661 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
0:22:25.808971 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:22:26.465817 PROGRESS: 
0:22:26.465975 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
0:22:26.466051 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
0:22:26.466220 INFO: Initializing TimingManager
0:22:26.466687 INFO: Initializing RawFileManager
0:22:37.367654 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:22:37.371708 INFO: Determining DIA cycle
0:22:37.388068 INFO: Found cycle with start 0.00 min and length 300.
0:22:37.557935 INFO: RT (min)            : 0.0 - 26.9
0:22:37.558031 INFO: RT duration (sec)   : 1611.2
0:22:37.558063 INFO: RT duration (min)   : 26.9
0:22:37.558088 INFO: Cycle len (scans)   : 300
0:22:37.558108 INFO: Cycle len (sec)     : 1.65
0:22:37.558129 INFO: Number of cycles    : 977
0:22:37.558148 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:22:37.558176 INFO: Creating DIA data object took: 11.091397523880005
0:22:38.247941 INFO: Creating DIA data NG object took: 0.6896514892578125
0:22:39.595252 INFO: Initializing CalibrationManager
0:22:39.595508 INFO: Setting up calibration estimators ..
0:22:39.595570 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:22:39.595650 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'}' ..
0:22:39.595765 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:22:39.595824 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:22:39.595894 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}}' ..
0:22:39.595948 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:22:39.595997 INFO: Done setting up calibration estimators.
0:22:39.596201 INFO: Initializing OptimizationManager
0:22:39.596341 INFO: initial parameter: ms1_error = 30
0:22:39.596392 INFO: initial parameter: ms2_error = 30
0:22:39.596440 INFO: initial parameter: rt_error = 805.5982666015625
0:22:39.596483 INFO: initial parameter: mobility_error = 0.1
0:22:39.596524 INFO: initial parameter: num_candidates = 1
0:22:39.596564 INFO: initial parameter: fwhm_rt = 5
0:22:39.596607 INFO: initial parameter: fwhm_mobility = 0.01
0:22:39.596647 INFO: initial parameter: score_cutoff = 0
0:22:39.596688 INFO: initial parameter: classifier_version = -1
0:22:39.596758 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:22:39.597014 INFO: FDRManager: loading saved state not requested, will be initialized.
0:22:39.597049 INFO: Initializing FDRManager
0:22:39.597086 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:22:40.824260 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:22:41.564124 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:22:41.564468 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
0:22:41.564574 PROGRESS: Starting initial search for precursors.
0:22:41.564659 INFO: Starting optimization step 0.
0:22:41.564723 PROGRESS: === Extracting elution groups 0 to 200 ===
0:22:41.564787 INFO: Using ng extraction backend
0:22:41.564849 PROGRESS: Extracting batch of 396 precursors
0:22:41.566757 INFO: === Search parameters used ===
0:22:41.566852 INFO: rt_error       : 805.5982666015625
0:22:41.566902 INFO: mobility_error : 0.1
0:22:41.566947 INFO: num_candidates : 1
0:22:41.566988 INFO: ms1_error      : 30
0:22:41.567029 INFO: ms2_error      : 30
0:22:41.567070 INFO: fwhm_rt        : 5
0:22:41.567108 INFO: quant_window   : 3
0:22:41.567150 INFO: ==============================================
0:22:41.595279 INFO: performing precursor FDR with 40 features
0:22:41.595365 INFO: Decoy channel: -1
0:22:41.595395 INFO: Competetive: True
0:22:41.596497 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:41.599263 INFO: Using random state 290015 for train-test-split
0:22:41.608216 INFO: Test AUC: 0.540
0:22:41.608278 INFO: Train AUC: 0.491
0:22:41.608315 INFO: AUC difference: 9.98%
0:22:41.608341 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:41.817488 INFO: Resetting torch num_threads to 80
0:22:41.818812 PROGRESS: === Extracted 392 precursors and 1853 fragments ===
0:22:41.819153 INFO: === FDR correction performed with classifier version -1 ===
0:22:41.819587 PROGRESS: ============================= Precursor FDR =============================
0:22:41.819670 PROGRESS: Total precursors accumulated: 0
0:22:41.819730 PROGRESS: Target precursors: 0 (0.00%)
0:22:41.819779 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:41.819825 PROGRESS: 
0:22:41.819869 PROGRESS: Precursor Summary:
0:22:41.819974 PROGRESS: 
0:22:41.820035 PROGRESS: Protein Summary:
0:22:41.820107 PROGRESS: =========================================================================
0:22:41.820273 INFO: Target number of precursors not reached yet.
0:22:41.884669 INFO: Starting optimization step 1.
0:22:41.884871 PROGRESS: === Extracting elution groups 200 to 600 ===
0:22:41.884955 INFO: Using ng extraction backend
0:22:41.885016 PROGRESS: Extracting batch of 786 precursors
0:22:41.887914 INFO: === Search parameters used ===
0:22:41.888025 INFO: rt_error       : 805.5982666015625
0:22:41.888075 INFO: mobility_error : 0.1
0:22:41.888143 INFO: num_candidates : 1
0:22:41.888186 INFO: ms1_error      : 30
0:22:41.888227 INFO: ms2_error      : 30
0:22:41.888268 INFO: fwhm_rt        : 5
0:22:41.888306 INFO: quant_window   : 3
0:22:41.888344 INFO: ==============================================
0:22:41.938661 INFO: performing precursor FDR with 40 features
0:22:41.938745 INFO: Decoy channel: -1
0:22:41.938770 INFO: Competetive: True
0:22:41.941654 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:41.943149 INFO: Using random state 48626 for train-test-split
0:22:41.951286 INFO: Test AUC: 0.503
0:22:41.951340 INFO: Train AUC: 0.498
0:22:41.951369 INFO: AUC difference: 1.01%
0:22:42.164611 INFO: Resetting torch num_threads to 80
0:22:42.166656 PROGRESS: === Extracted 1171 precursors and 5469 fragments ===
0:22:42.167012 INFO: === FDR correction performed with classifier version -1 ===
0:22:42.167443 PROGRESS: ============================= Precursor FDR =============================
0:22:42.167528 PROGRESS: Total precursors accumulated: 0
0:22:42.167588 PROGRESS: Target precursors: 0 (0.00%)
0:22:42.167639 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:42.167686 PROGRESS: 
0:22:42.167730 PROGRESS: Precursor Summary:
0:22:42.167837 PROGRESS: 
0:22:42.167900 PROGRESS: Protein Summary:
0:22:42.167981 PROGRESS: =========================================================================
0:22:42.168177 INFO: Target number of precursors not reached yet.
0:22:42.235230 INFO: Starting optimization step 2.
0:22:42.235424 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:22:42.235504 INFO: Using ng extraction backend
0:22:42.235565 PROGRESS: Extracting batch of 1592 precursors
0:22:42.240081 INFO: === Search parameters used ===
0:22:42.240201 INFO: rt_error       : 805.5982666015625
0:22:42.240255 INFO: mobility_error : 0.1
0:22:42.240302 INFO: num_candidates : 1
0:22:42.240344 INFO: ms1_error      : 30
0:22:42.240384 INFO: ms2_error      : 30
0:22:42.240423 INFO: fwhm_rt        : 5
0:22:42.240462 INFO: quant_window   : 3
0:22:42.240500 INFO: ==============================================
0:22:42.278535 INFO: performing precursor FDR with 40 features
0:22:42.278635 INFO: Decoy channel: -1
0:22:42.278661 INFO: Competetive: True
0:22:42.282254 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:42.284222 INFO: Using random state 9584 for train-test-split
0:22:42.296022 INFO: Test AUC: 0.529
0:22:42.296087 INFO: Train AUC: 0.489
0:22:42.296118 INFO: AUC difference: 8.24%
0:22:42.296142 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:42.512408 INFO: Resetting torch num_threads to 80
0:22:42.514887 PROGRESS: === Extracted 2751 precursors and 13038 fragments ===
0:22:42.515230 INFO: === FDR correction performed with classifier version -1 ===
0:22:42.515664 PROGRESS: ============================= Precursor FDR =============================
0:22:42.515751 PROGRESS: Total precursors accumulated: 0
0:22:42.515809 PROGRESS: Target precursors: 0 (0.00%)
0:22:42.515858 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:42.515902 PROGRESS: 
0:22:42.515952 PROGRESS: Precursor Summary:
0:22:42.516061 PROGRESS: 
0:22:42.516132 PROGRESS: Protein Summary:
0:22:42.516203 PROGRESS: =========================================================================
0:22:42.516410 INFO: Target number of precursors not reached yet.
0:22:42.586298 INFO: Starting optimization step 3.
0:22:42.586501 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:22:42.586592 INFO: Using ng extraction backend
0:22:42.586659 PROGRESS: Extracting batch of 3177 precursors
0:22:42.594033 INFO: === Search parameters used ===
0:22:42.594159 INFO: rt_error       : 805.5982666015625
0:22:42.594209 INFO: mobility_error : 0.1
0:22:42.594254 INFO: num_candidates : 1
0:22:42.594299 INFO: ms1_error      : 30
0:22:42.594338 INFO: ms2_error      : 30
0:22:42.594377 INFO: fwhm_rt        : 5
0:22:42.594416 INFO: quant_window   : 3
0:22:42.594455 INFO: ==============================================
0:22:42.640688 INFO: performing precursor FDR with 40 features
0:22:42.640793 INFO: Decoy channel: -1
0:22:42.640820 INFO: Competetive: True
0:22:42.646089 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:42.648414 INFO: Using random state 560195 for train-test-split
0:22:42.667914 INFO: Test AUC: 0.513
0:22:42.667982 INFO: Train AUC: 0.493
0:22:42.668011 INFO: AUC difference: 4.00%
0:22:42.883745 INFO: Resetting torch num_threads to 80
0:22:42.886968 PROGRESS: === Extracted 5898 precursors and 28051 fragments ===
0:22:42.887320 INFO: === FDR correction performed with classifier version -1 ===
0:22:42.887753 PROGRESS: ============================= Precursor FDR =============================
0:22:42.887839 PROGRESS: Total precursors accumulated: 0
0:22:42.887903 PROGRESS: Target precursors: 0 (0.00%)
0:22:42.887954 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:42.887997 PROGRESS: 
0:22:42.888037 PROGRESS: Precursor Summary:
0:22:42.888141 PROGRESS: 
0:22:42.888201 PROGRESS: Protein Summary:
0:22:42.888271 PROGRESS: =========================================================================
0:22:42.888497 INFO: Target number of precursors not reached yet.
0:22:42.963203 INFO: Starting optimization step 4.
0:22:42.963413 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:22:42.963500 INFO: Using ng extraction backend
0:22:42.963560 PROGRESS: Extracting batch of 6340 precursors
0:22:42.976053 INFO: === Search parameters used ===
0:22:42.976222 INFO: rt_error       : 805.5982666015625
0:22:42.976277 INFO: mobility_error : 0.1
0:22:42.976324 INFO: num_candidates : 1
0:22:42.976366 INFO: ms1_error      : 30
0:22:42.976408 INFO: ms2_error      : 30
0:22:42.976448 INFO: fwhm_rt        : 5
0:22:42.976486 INFO: quant_window   : 3
0:22:42.976526 INFO: ==============================================
0:22:43.063869 INFO: performing precursor FDR with 40 features
0:22:43.063972 INFO: Decoy channel: -1
0:22:43.063999 INFO: Competetive: True
0:22:43.070237 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:43.073713 INFO: Using random state 491838 for train-test-split
0:22:43.118287 INFO: Test AUC: 0.505
0:22:43.118385 INFO: Train AUC: 0.495
0:22:43.118414 INFO: AUC difference: 2.02%
0:22:43.340962 INFO: Resetting torch num_threads to 80
0:22:43.345170 PROGRESS: === Extracted 12176 precursors and 57532 fragments ===
0:22:43.345552 INFO: === FDR correction performed with classifier version -1 ===
0:22:43.345994 PROGRESS: ============================= Precursor FDR =============================
0:22:43.346081 PROGRESS: Total precursors accumulated: 0
0:22:43.346141 PROGRESS: Target precursors: 0 (0.00%)
0:22:43.346190 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:43.346237 PROGRESS: 
0:22:43.346281 PROGRESS: Precursor Summary:
0:22:43.346387 PROGRESS: 
0:22:43.346450 PROGRESS: Protein Summary:
0:22:43.346522 PROGRESS: =========================================================================
0:22:43.346817 INFO: Target number of precursors not reached yet.
0:22:43.430431 INFO: Starting optimization step 5.
0:22:43.430673 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:22:43.430757 INFO: Using ng extraction backend
0:22:43.430820 PROGRESS: Extracting batch of 12663 precursors
0:22:43.453717 INFO: === Search parameters used ===
0:22:43.453886 INFO: rt_error       : 805.5982666015625
0:22:43.453938 INFO: mobility_error : 0.1
0:22:43.453984 INFO: num_candidates : 1
0:22:43.454027 INFO: ms1_error      : 30
0:22:43.454067 INFO: ms2_error      : 30
0:22:43.454106 INFO: fwhm_rt        : 5
0:22:43.454170 INFO: quant_window   : 3
0:22:43.454212 INFO: ==============================================
0:22:43.585139 INFO: performing precursor FDR with 40 features
0:22:43.585251 INFO: Decoy channel: -1
0:22:43.585277 INFO: Competetive: True
0:22:43.601044 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:43.607654 INFO: Using random state 309881 for train-test-split
0:22:43.862745 INFO: Test AUC: 0.523
0:22:43.862859 INFO: Train AUC: 0.542
0:22:43.862889 INFO: AUC difference: 3.54%
0:22:44.086579 INFO: Resetting torch num_threads to 80
0:22:44.092867 PROGRESS: === Extracted 24724 precursors and 116398 fragments ===
0:22:44.093252 INFO: === FDR correction performed with classifier version -1 ===
0:22:44.093747 PROGRESS: ============================= Precursor FDR =============================
0:22:44.093838 PROGRESS: Total precursors accumulated: 33
0:22:44.093897 PROGRESS: Target precursors: 33 (100.00%)
0:22:44.093949 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:44.093994 PROGRESS: 
0:22:44.094036 PROGRESS: Precursor Summary:
0:22:44.094994 PROGRESS: Channel   0:	 0.050 FDR:    33; 0.010 FDR:    33; 0.001 FDR:    33
0:22:44.095085 PROGRESS: 
0:22:44.095142 PROGRESS: Protein Summary:
0:22:44.096187 PROGRESS: Channel   0:	 0.050 FDR:    33; 0.010 FDR:    33; 0.001 FDR:    33
0:22:44.096276 PROGRESS: =========================================================================
0:22:44.096702 INFO: Target number of precursors not reached yet.
0:22:44.197014 INFO: Starting optimization step 6.
0:22:44.197265 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:22:44.197348 INFO: Using ng extraction backend
0:22:44.197411 PROGRESS: Extracting batch of 25339 precursors
0:22:44.242086 INFO: === Search parameters used ===
0:22:44.242319 INFO: rt_error       : 805.5982666015625
0:22:44.242375 INFO: mobility_error : 0.1
0:22:44.242422 INFO: num_candidates : 1
0:22:44.242465 INFO: ms1_error      : 30
0:22:44.242504 INFO: ms2_error      : 30
0:22:44.242546 INFO: fwhm_rt        : 5
0:22:44.242606 INFO: quant_window   : 3
0:22:44.242649 INFO: ==============================================
0:22:44.447939 INFO: performing precursor FDR with 40 features
0:22:44.448050 INFO: Decoy channel: -1
0:22:44.448079 INFO: Competetive: True
0:22:44.466851 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:44.478016 INFO: Using random state 479661 for train-test-split
0:22:45.059633 INFO: Test AUC: 0.560
0:22:45.059749 INFO: Train AUC: 0.576
0:22:45.059779 INFO: AUC difference: 2.80%
0:22:45.291887 INFO: Resetting torch num_threads to 80
0:22:45.302050 PROGRESS: === Extracted 49832 precursors and 234547 fragments ===
0:22:45.302477 INFO: === FDR correction performed with classifier version -1 ===
0:22:45.303001 PROGRESS: ============================= Precursor FDR =============================
0:22:45.303096 PROGRESS: Total precursors accumulated: 44
0:22:45.303155 PROGRESS: Target precursors: 44 (100.00%)
0:22:45.303204 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:45.303247 PROGRESS: 
0:22:45.303292 PROGRESS: Precursor Summary:
0:22:45.304226 PROGRESS: Channel   0:	 0.050 FDR:    44; 0.010 FDR:    44; 0.001 FDR:    44
0:22:45.304315 PROGRESS: 
0:22:45.304371 PROGRESS: Protein Summary:
0:22:45.305417 PROGRESS: Channel   0:	 0.050 FDR:    43; 0.010 FDR:    43; 0.001 FDR:    43
0:22:45.305508 PROGRESS: =========================================================================
0:22:45.306213 INFO: Target number of precursors not reached yet.
0:22:45.439689 INFO: Starting optimization step 7.
0:22:45.439939 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:22:45.440024 INFO: Using ng extraction backend
0:22:45.440088 PROGRESS: Extracting batch of 50691 precursors
0:22:45.527896 INFO: === Search parameters used ===
0:22:45.528136 INFO: rt_error       : 805.5982666015625
0:22:45.528189 INFO: mobility_error : 0.1
0:22:45.528237 INFO: num_candidates : 1
0:22:45.528280 INFO: ms1_error      : 30
0:22:45.528320 INFO: ms2_error      : 30
0:22:45.528362 INFO: fwhm_rt        : 5
0:22:45.528400 INFO: quant_window   : 3
0:22:45.528440 INFO: ==============================================
0:22:45.867286 INFO: performing precursor FDR with 40 features
0:22:45.867399 INFO: Decoy channel: -1
0:22:45.867425 INFO: Competetive: True
0:22:45.903811 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:45.929505 INFO: Using random state 31308 for train-test-split
0:22:47.346015 INFO: Test AUC: 0.574
0:22:47.346135 INFO: Train AUC: 0.596
0:22:47.346166 INFO: AUC difference: 3.74%
0:22:47.598841 INFO: Resetting torch num_threads to 80
0:22:47.616041 PROGRESS: === Extracted 100023 precursors and 471000 fragments ===
0:22:47.618104 INFO: === FDR correction performed with classifier version -1 ===
0:22:47.618697 PROGRESS: ============================= Precursor FDR =============================
0:22:47.618801 PROGRESS: Total precursors accumulated: 272
0:22:47.618862 PROGRESS: Target precursors: 270 (99.26%)
0:22:47.618916 PROGRESS: Decoy precursors: 2 (0.74%)
0:22:47.618962 PROGRESS: 
0:22:47.619007 PROGRESS: Precursor Summary:
0:22:47.619981 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:   223
0:22:47.620075 PROGRESS: 
0:22:47.620132 PROGRESS: Protein Summary:
0:22:47.621242 PROGRESS: Channel   0:	 0.050 FDR:   253; 0.010 FDR:   253; 0.001 FDR:   209
0:22:47.621333 PROGRESS: =========================================================================
0:22:47.622621 INFO: Target number of precursors reached.
0:22:47.658377 INFO: fragments_df: keeping 2381 of 471000 [sum(precursor_idx_mask)=2977 sum(mass_error_mask)=471000 stop_rank=2381
0:22:47.911736 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:22:48.054651 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:22:48.429879 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:22:48.430312 INFO: Using score_cutoff 14.393230613422395 (fac=0.99, q=1)
0:22:48.430632 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:22:48.430713 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:22:48.430769 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.393230613422395
0:22:48.430829 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:48.526051 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:48.738462 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:22:48.738779 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:22:48.738910 INFO: Starting optimization step 8.
0:22:48.739016 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:22:48.739108 INFO: Using ng extraction backend
0:22:48.739192 PROGRESS: Extracting batch of 100984 precursors
0:22:48.920702 INFO: === Search parameters used ===
0:22:48.920957 INFO: rt_error       : 805.5982666015625
0:22:48.921018 INFO: mobility_error : 0.1
0:22:48.921063 INFO: num_candidates : 3
0:22:48.921108 INFO: ms1_error      : 30
0:22:48.921148 INFO: ms2_error      : 30
0:22:48.921187 INFO: fwhm_rt        : 3.0
0:22:48.921227 INFO: quant_window   : 3
0:22:48.921266 INFO: ==============================================
0:22:50.149104 INFO: performing precursor FDR with 40 features
0:22:50.149220 INFO: Decoy channel: -1
0:22:50.149246 INFO: Competetive: True
0:22:50.220975 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:50.322628 INFO: Using random state 227026 for train-test-split
0:22:54.207006 INFO: Test AUC: 0.593
0:22:54.207131 INFO: Train AUC: 0.603
0:22:54.207163 INFO: AUC difference: 1.60%
0:22:54.522317 INFO: Resetting torch num_threads to 80
0:22:54.534478 PROGRESS: === Extracted 300250 precursors and 1383222 fragments ===
0:22:54.534874 INFO: === FDR correction performed with classifier version 7 ===
0:22:54.535369 PROGRESS: ============================= Precursor FDR =============================
0:22:54.535460 PROGRESS: Total precursors accumulated: 315
0:22:54.535519 PROGRESS: Target precursors: 312 (99.05%)
0:22:54.535568 PROGRESS: Decoy precursors: 3 (0.95%)
0:22:54.535612 PROGRESS: 
0:22:54.535655 PROGRESS: Precursor Summary:
0:22:54.536575 PROGRESS: Channel   0:	 0.050 FDR:   312; 0.010 FDR:   312; 0.001 FDR:   229
0:22:54.536665 PROGRESS: 
0:22:54.536728 PROGRESS: Protein Summary:
0:22:54.537798 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   296; 0.001 FDR:   214
0:22:54.537888 PROGRESS: =========================================================================
0:22:54.543004 INFO: Target number of precursors reached.
0:22:54.638550 INFO: fragments_df: keeping 3457 of 1383222 [sum(precursor_idx_mask)=6598 sum(mass_error_mask)=1383222 stop_rank=3457
0:22:54.848042 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:22:54.966579 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:22:56.311783 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:22:56.312212 INFO: Using score_cutoff 8.029124402618407 (fac=0.99, q=1)
0:22:56.312499 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:22:56.312582 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:22:56.312636 INFO: Updating optimization_manager: score_cutoff        : 14.393230613422395 -> 8.029124402618407
0:22:56.312692 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:56.373641 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:56.527290 INFO: === checking if optimization conditions were reached ===
0:22:56.527528 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:22:56.529697 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.246735808105685
0:22:56.529800 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.2467.
0:22:56.529879 INFO: ==============================================
0:22:56.529949 INFO: Starting optimization step 9.
0:22:56.530007 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:22:56.530069 INFO: Using ng extraction backend
0:22:56.530125 PROGRESS: Extracting batch of 100984 precursors
0:22:56.703089 INFO: === Search parameters used ===
0:22:56.703345 INFO: rt_error       : 805.5982666015625
0:22:56.703400 INFO: mobility_error : 0.1
0:22:56.703448 INFO: num_candidates : 3
0:22:56.703490 INFO: ms1_error      : 30
0:22:56.703531 INFO: ms2_error      : 7.246735808105685
0:22:56.703573 INFO: fwhm_rt        : 3.0
0:22:56.703612 INFO: quant_window   : 3
0:22:56.703652 INFO: ==============================================
0:22:57.927953 INFO: performing precursor FDR with 40 features
0:22:57.928067 INFO: Decoy channel: -1
0:22:57.928093 INFO: Competetive: True
0:22:58.001015 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:58.103605 INFO: Using random state 227026 for train-test-split
0:23:02.039819 INFO: Test AUC: 0.591
0:23:02.039949 INFO: Train AUC: 0.604
0:23:02.039981 INFO: AUC difference: 2.05%
0:23:02.371436 INFO: Resetting torch num_threads to 80
0:23:02.398159 PROGRESS: === Extracted 302891 precursors and 1700956 fragments ===
0:23:02.398580 INFO: === FDR correction performed with classifier version 7 ===
0:23:02.399125 PROGRESS: ============================= Precursor FDR =============================
0:23:02.399221 PROGRESS: Total precursors accumulated: 438
0:23:02.399280 PROGRESS: Target precursors: 434 (99.09%)
0:23:02.399330 PROGRESS: Decoy precursors: 4 (0.91%)
0:23:02.399374 PROGRESS: 
0:23:02.399416 PROGRESS: Precursor Summary:
0:23:02.400429 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   434; 0.001 FDR:   307
0:23:02.400528 PROGRESS: 
0:23:02.400582 PROGRESS: Protein Summary:
0:23:02.401760 PROGRESS: Channel   0:	 0.050 FDR:   405; 0.010 FDR:   405; 0.001 FDR:   283
0:23:02.401856 PROGRESS: =========================================================================
0:23:02.407521 INFO: Target number of precursors reached.
0:23:02.519859 INFO: fragments_df: keeping 5000 of 1700956 [sum(precursor_idx_mask)=10863 sum(mass_error_mask)=1700956 stop_rank=5000
0:23:02.725267 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:02.855587 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:03.505604 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:03.506314 INFO: Using score_cutoff 9.802296621894836 (fac=0.99, q=1)
0:23:03.506721 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:03.506805 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:03.506862 INFO: Updating optimization_manager: score_cutoff        : 8.029124402618407 -> 9.802296621894836
0:23:03.506938 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:03.538102 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:03.602100 INFO: === checking if optimization conditions were reached ===
0:23:03.602371 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:23:03.605119 INFO: Updating optimization_manager: ms2_error           : 7.246735808105685 -> 7.303303597899703
0:23:03.605232 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.3033.
0:23:03.605298 INFO: ==============================================
0:23:03.605377 INFO: Starting optimization step 10.
0:23:03.605446 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:03.605525 INFO: Using ng extraction backend
0:23:03.605608 PROGRESS: Extracting batch of 50293 precursors
0:23:03.694324 INFO: === Search parameters used ===
0:23:03.694626 INFO: rt_error       : 805.5982666015625
0:23:03.694687 INFO: mobility_error : 0.1
0:23:03.694735 INFO: num_candidates : 3
0:23:03.694777 INFO: ms1_error      : 30
0:23:03.694818 INFO: ms2_error      : 7.303303597899703
0:23:03.694858 INFO: fwhm_rt        : 3.0
0:23:03.694898 INFO: quant_window   : 3
0:23:03.694937 INFO: ==============================================
0:23:04.339470 INFO: performing precursor FDR with 40 features
0:23:04.339639 INFO: Decoy channel: -1
0:23:04.339668 INFO: Competetive: True
0:23:04.378181 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:04.414101 INFO: Using random state 227026 for train-test-split
0:23:06.305561 INFO: Test AUC: 0.587
0:23:06.305701 INFO: Train AUC: 0.602
0:23:06.305735 INFO: AUC difference: 2.54%
0:23:06.577157 INFO: Resetting torch num_threads to 80
0:23:06.583206 PROGRESS: === Extracted 150842 precursors and 846022 fragments ===
0:23:06.583617 INFO: === FDR correction performed with classifier version 7 ===
0:23:06.584080 PROGRESS: ============================= Precursor FDR =============================
0:23:06.584169 PROGRESS: Total precursors accumulated: 203
0:23:06.584231 PROGRESS: Target precursors: 201 (99.01%)
0:23:06.584283 PROGRESS: Decoy precursors: 2 (0.99%)
0:23:06.584334 PROGRESS: 
0:23:06.584380 PROGRESS: Precursor Summary:
0:23:06.585269 PROGRESS: Channel   0:	 0.050 FDR:   201; 0.010 FDR:   201; 0.001 FDR:   145
0:23:06.585359 PROGRESS: 
0:23:06.585413 PROGRESS: Protein Summary:
0:23:06.586428 PROGRESS: Channel   0:	 0.050 FDR:   195; 0.010 FDR:   195; 0.001 FDR:   141
0:23:06.586515 PROGRESS: =========================================================================
0:23:06.588704 INFO: Target number of precursors reached.
0:23:06.644922 INFO: fragments_df: keeping 2460 of 846022 [sum(precursor_idx_mask)=5069 sum(mass_error_mask)=846022 stop_rank=2460
0:23:06.785461 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:06.880444 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:07.152197 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:07.152625 INFO: Using score_cutoff 15.047917671203614 (fac=0.99, q=1)
0:23:07.152932 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:07.153014 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:07.153069 INFO: Updating optimization_manager: score_cutoff        : 9.802296621894836 -> 15.047917671203614
0:23:07.153128 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:07.184085 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:07.250323 INFO: === checking if optimization conditions were reached ===
0:23:07.250617 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:23:07.251677 INFO: Updating optimization_manager: ms2_error           : 7.303303597899703 -> 7.246735808105685
0:23:07.251823 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
0:23:07.251935 INFO: Updating optimization_manager: score_cutoff        : 15.047917671203614 -> 9.802296621894836
0:23:07.252038 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:07.252152 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:07.252254 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.2467 found after 3 searches.
0:23:07.252328 INFO: ==============================================
0:23:07.252405 PROGRESS: Optimization finished for ms2_error.
0:23:07.402940 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:07.434320 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:07.530911 INFO: Starting optimization step 0.
0:23:07.531145 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:07.531238 INFO: Using ng extraction backend
0:23:07.531311 PROGRESS: Extracting batch of 50293 precursors
0:23:07.621946 INFO: === Search parameters used ===
0:23:07.622219 INFO: rt_error       : 805.5982666015625
0:23:07.622277 INFO: mobility_error : 0.1
0:23:07.622325 INFO: num_candidates : 3
0:23:07.622368 INFO: ms1_error      : 30
0:23:07.622409 INFO: ms2_error      : 7.246735808105685
0:23:07.622462 INFO: fwhm_rt        : 3.0
0:23:07.622503 INFO: quant_window   : 3
0:23:07.622543 INFO: ==============================================
0:23:08.252944 INFO: performing precursor FDR with 40 features
0:23:08.253060 INFO: Decoy channel: -1
0:23:08.253088 INFO: Competetive: True
0:23:08.290692 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:08.326292 INFO: Using random state 521042 for train-test-split
0:23:10.292525 INFO: Test AUC: 0.599
0:23:10.292650 INFO: Train AUC: 0.613
0:23:10.292680 INFO: AUC difference: 2.30%
0:23:10.565581 INFO: Resetting torch num_threads to 80
0:23:10.571535 PROGRESS: === Extracted 150843 precursors and 847152 fragments ===
0:23:10.571892 INFO: === FDR correction performed with classifier version 9 ===
0:23:10.572345 PROGRESS: ============================= Precursor FDR =============================
0:23:10.572439 PROGRESS: Total precursors accumulated: 212
0:23:10.572499 PROGRESS: Target precursors: 210 (99.06%)
0:23:10.572550 PROGRESS: Decoy precursors: 2 (0.94%)
0:23:10.572596 PROGRESS: 
0:23:10.572639 PROGRESS: Precursor Summary:
0:23:10.573535 PROGRESS: Channel   0:	 0.050 FDR:   210; 0.010 FDR:   210; 0.001 FDR:   169
0:23:10.573626 PROGRESS: 
0:23:10.573681 PROGRESS: Protein Summary:
0:23:10.574724 PROGRESS: Channel   0:	 0.050 FDR:   202; 0.010 FDR:   202; 0.001 FDR:   164
0:23:10.574820 PROGRESS: =========================================================================
0:23:10.576834 INFO: Target number of precursors reached.
0:23:10.636295 INFO: fragments_df: keeping 2533 of 847152 [sum(precursor_idx_mask)=5326 sum(mass_error_mask)=847152 stop_rank=2533
0:23:10.773452 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:10.870373 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:11.150386 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:11.150823 INFO: Using score_cutoff 15.052578321361542 (fac=0.99, q=1)
0:23:11.151116 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:11.151196 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:11.151251 INFO: Updating optimization_manager: score_cutoff        : 9.802296621894836 -> 15.052578321361542
0:23:11.151307 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:11.182306 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:11.249421 INFO: === checking if optimization conditions were reached ===
0:23:11.249713 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:23:11.251821 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 142.79423393057604
0:23:11.251941 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 142.7942.
0:23:11.252016 INFO: ==============================================
0:23:11.252096 INFO: Starting optimization step 1.
0:23:11.252161 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:11.252231 INFO: Using ng extraction backend
0:23:11.252314 PROGRESS: Extracting batch of 50293 precursors
0:23:11.342509 INFO: === Search parameters used ===
0:23:11.342783 INFO: rt_error       : 142.79423393057604
0:23:11.342839 INFO: mobility_error : 0.1
0:23:11.342887 INFO: num_candidates : 3
0:23:11.342941 INFO: ms1_error      : 30
0:23:11.342986 INFO: ms2_error      : 7.246735808105685
0:23:11.343031 INFO: fwhm_rt        : 3.0
0:23:11.343074 INFO: quant_window   : 3
0:23:11.343115 INFO: ==============================================
0:23:11.915426 INFO: performing precursor FDR with 40 features
0:23:11.915547 INFO: Decoy channel: -1
0:23:11.915576 INFO: Competetive: True
0:23:11.952436 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:11.988116 INFO: Using random state 521042 for train-test-split
0:23:13.816691 INFO: Test AUC: 0.595
0:23:13.816808 INFO: Train AUC: 0.607
0:23:13.816839 INFO: AUC difference: 2.07%
0:23:14.084330 INFO: Resetting torch num_threads to 80
0:23:14.090347 PROGRESS: === Extracted 149589 precursors and 671768 fragments ===
0:23:14.090717 INFO: === FDR correction performed with classifier version 9 ===
0:23:14.091192 PROGRESS: ============================= Precursor FDR =============================
0:23:14.091283 PROGRESS: Total precursors accumulated: 243
0:23:14.091341 PROGRESS: Target precursors: 241 (99.18%)
0:23:14.091391 PROGRESS: Decoy precursors: 2 (0.82%)
0:23:14.091435 PROGRESS: 
0:23:14.091480 PROGRESS: Precursor Summary:
0:23:14.092384 PROGRESS: Channel   0:	 0.050 FDR:   241; 0.010 FDR:   241; 0.001 FDR:   206
0:23:14.092474 PROGRESS: 
0:23:14.092529 PROGRESS: Protein Summary:
0:23:14.093584 PROGRESS: Channel   0:	 0.050 FDR:   232; 0.010 FDR:   232; 0.001 FDR:   198
0:23:14.093675 PROGRESS: =========================================================================
0:23:14.095662 INFO: Target number of precursors reached.
0:23:14.140430 INFO: fragments_df: keeping 2760 of 671768 [sum(precursor_idx_mask)=5910 sum(mass_error_mask)=671768 stop_rank=2760
0:23:14.276086 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:14.401607 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:14.706617 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:14.707039 INFO: Using score_cutoff 14.515542474746704 (fac=0.99, q=1)
0:23:14.707330 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:14.707411 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:14.707465 INFO: Updating optimization_manager: score_cutoff        : 15.052578321361542 -> 14.515542474746704
0:23:14.707520 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:14.738523 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:14.804022 INFO: === checking if optimization conditions were reached ===
0:23:14.804292 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:23:14.806490 INFO: Updating optimization_manager: rt_error            : 142.79423393057604 -> 97.47135347047276
0:23:14.806618 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 97.4714.
0:23:14.806699 INFO: ==============================================
0:23:14.806778 INFO: Starting optimization step 2.
0:23:14.806845 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:14.806917 INFO: Using ng extraction backend
0:23:14.806982 PROGRESS: Extracting batch of 50293 precursors
0:23:14.896952 INFO: === Search parameters used ===
0:23:14.897215 INFO: rt_error       : 97.47135347047276
0:23:14.897285 INFO: mobility_error : 0.1
0:23:14.897334 INFO: num_candidates : 3
0:23:14.897377 INFO: ms1_error      : 30
0:23:14.897418 INFO: ms2_error      : 7.246735808105685
0:23:14.897457 INFO: fwhm_rt        : 3.0
0:23:14.897497 INFO: quant_window   : 3
0:23:14.897538 INFO: ==============================================
0:23:15.473108 INFO: performing precursor FDR with 40 features
0:23:15.473230 INFO: Decoy channel: -1
0:23:15.473255 INFO: Competetive: True
0:23:15.511463 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:15.548770 INFO: Using random state 521042 for train-test-split
0:23:17.510076 INFO: Test AUC: 0.593
0:23:17.510197 INFO: Train AUC: 0.606
0:23:17.510227 INFO: AUC difference: 2.22%
0:23:17.770595 INFO: Resetting torch num_threads to 80
0:23:17.776748 PROGRESS: === Extracted 148357 precursors and 623908 fragments ===
0:23:17.777104 INFO: === FDR correction performed with classifier version 9 ===
0:23:17.777555 PROGRESS: ============================= Precursor FDR =============================
0:23:17.777644 PROGRESS: Total precursors accumulated: 240
0:23:17.777704 PROGRESS: Target precursors: 238 (99.17%)
0:23:17.777758 PROGRESS: Decoy precursors: 2 (0.83%)
0:23:17.777805 PROGRESS: 
0:23:17.777851 PROGRESS: Precursor Summary:
0:23:17.778760 PROGRESS: Channel   0:	 0.050 FDR:   238; 0.010 FDR:   238; 0.001 FDR:   190
0:23:17.778852 PROGRESS: 
0:23:17.778910 PROGRESS: Protein Summary:
0:23:17.779951 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:   183
0:23:17.780039 PROGRESS: =========================================================================
0:23:17.782070 INFO: Target number of precursors reached.
0:23:17.823900 INFO: fragments_df: keeping 2676 of 623908 [sum(precursor_idx_mask)=5719 sum(mass_error_mask)=623908 stop_rank=2676
0:23:17.960107 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:18.062730 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:18.356200 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:18.356624 INFO: Using score_cutoff 14.88239665517807 (fac=0.99, q=1)
0:23:18.356907 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:18.356986 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:18.357040 INFO: Updating optimization_manager: score_cutoff        : 14.515542474746704 -> 14.88239665517807
0:23:18.357095 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:18.388149 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:18.452042 INFO: === checking if optimization conditions were reached ===
0:23:18.452307 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:23:18.454631 INFO: Updating optimization_manager: rt_error            : 97.47135347047276 -> 80.670793682143
0:23:18.454748 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 80.6708.
0:23:18.454826 INFO: ==============================================
0:23:18.454905 INFO: Starting optimization step 3.
0:23:18.454972 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:18.455041 INFO: Using ng extraction backend
0:23:18.455107 PROGRESS: Extracting batch of 50293 precursors
0:23:18.545147 INFO: === Search parameters used ===
0:23:18.545412 INFO: rt_error       : 80.670793682143
0:23:18.545467 INFO: mobility_error : 0.1
0:23:18.545513 INFO: num_candidates : 3
0:23:18.545557 INFO: ms1_error      : 30
0:23:18.545596 INFO: ms2_error      : 7.246735808105685
0:23:18.545638 INFO: fwhm_rt        : 3.0
0:23:18.545677 INFO: quant_window   : 3
0:23:18.545716 INFO: ==============================================
0:23:19.122114 INFO: performing precursor FDR with 40 features
0:23:19.122235 INFO: Decoy channel: -1
0:23:19.122262 INFO: Competetive: True
0:23:19.161686 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:19.196259 INFO: Using random state 521042 for train-test-split
0:23:21.173090 INFO: Test AUC: 0.594
0:23:21.173213 INFO: Train AUC: 0.609
0:23:21.173244 INFO: AUC difference: 2.51%
0:23:21.432749 INFO: Resetting torch num_threads to 80
0:23:21.439180 PROGRESS: === Extracted 147308 precursors and 596918 fragments ===
0:23:21.439534 INFO: === FDR correction performed with classifier version 9 ===
0:23:21.440005 PROGRESS: ============================= Precursor FDR =============================
0:23:21.440095 PROGRESS: Total precursors accumulated: 314
0:23:21.440154 PROGRESS: Target precursors: 311 (99.04%)
0:23:21.440212 PROGRESS: Decoy precursors: 3 (0.96%)
0:23:21.440258 PROGRESS: 
0:23:21.440302 PROGRESS: Precursor Summary:
0:23:21.441211 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   311; 0.001 FDR:   186
0:23:21.441303 PROGRESS: 
0:23:21.441359 PROGRESS: Protein Summary:
0:23:21.442444 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   295; 0.001 FDR:   177
0:23:21.442534 PROGRESS: =========================================================================
0:23:21.444641 INFO: Target number of precursors reached.
0:23:21.485314 INFO: fragments_df: keeping 3213 of 596918 [sum(precursor_idx_mask)=7088 sum(mass_error_mask)=596918 stop_rank=3213
0:23:21.621721 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:21.729069 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:22.083637 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:22.084064 INFO: Using score_cutoff 7.3003539662361145 (fac=0.99, q=1)
0:23:22.084352 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:22.084433 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:22.084487 INFO: Updating optimization_manager: score_cutoff        : 14.88239665517807 -> 7.3003539662361145
0:23:22.084541 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:22.114771 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:22.177302 INFO: === checking if optimization conditions were reached ===
0:23:22.177557 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:23:22.179872 INFO: Updating optimization_manager: rt_error            : 80.670793682143 -> 64.22379566807277
0:23:22.179990 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 64.2238.
0:23:22.180065 INFO: ==============================================
0:23:22.180145 INFO: Starting optimization step 4.
0:23:22.180211 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:22.180292 INFO: Using ng extraction backend
0:23:22.180358 PROGRESS: Extracting batch of 50293 precursors
0:23:22.270204 INFO: === Search parameters used ===
0:23:22.270464 INFO: rt_error       : 64.22379566807277
0:23:22.270519 INFO: mobility_error : 0.1
0:23:22.270569 INFO: num_candidates : 3
0:23:22.270613 INFO: ms1_error      : 30
0:23:22.270652 INFO: ms2_error      : 7.246735808105685
0:23:22.270691 INFO: fwhm_rt        : 3.0
0:23:22.270728 INFO: quant_window   : 3
0:23:22.270767 INFO: ==============================================
0:23:22.828587 INFO: performing precursor FDR with 40 features
0:23:22.828704 INFO: Decoy channel: -1
0:23:22.828731 INFO: Competetive: True
0:23:22.867624 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:22.903262 INFO: Using random state 521042 for train-test-split
0:23:24.824937 INFO: Test AUC: 0.595
0:23:24.825058 INFO: Train AUC: 0.610
0:23:24.825089 INFO: AUC difference: 2.43%
0:23:25.083830 INFO: Resetting torch num_threads to 80
0:23:25.089864 PROGRESS: === Extracted 145301 precursors and 563438 fragments ===
0:23:25.090231 INFO: === FDR correction performed with classifier version 9 ===
0:23:25.090704 PROGRESS: ============================= Precursor FDR =============================
0:23:25.090797 PROGRESS: Total precursors accumulated: 253
0:23:25.090854 PROGRESS: Target precursors: 251 (99.21%)
0:23:25.090906 PROGRESS: Decoy precursors: 2 (0.79%)
0:23:25.090950 PROGRESS: 
0:23:25.090995 PROGRESS: Precursor Summary:
0:23:25.091887 PROGRESS: Channel   0:	 0.050 FDR:   251; 0.010 FDR:   251; 0.001 FDR:   202
0:23:25.091977 PROGRESS: 
0:23:25.092035 PROGRESS: Protein Summary:
0:23:25.093082 PROGRESS: Channel   0:	 0.050 FDR:   241; 0.010 FDR:   241; 0.001 FDR:   196
0:23:25.093171 PROGRESS: =========================================================================
0:23:25.095116 INFO: Target number of precursors reached.
0:23:25.133645 INFO: fragments_df: keeping 2700 of 563438 [sum(precursor_idx_mask)=5721 sum(mass_error_mask)=563438 stop_rank=2700
0:23:25.270108 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:25.369051 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:25.665255 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:25.665672 INFO: Using score_cutoff 13.934062399864196 (fac=0.99, q=1)
0:23:25.665953 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:25.666034 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:25.666089 INFO: Updating optimization_manager: score_cutoff        : 7.3003539662361145 -> 13.934062399864196
0:23:25.666143 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:25.697276 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:25.763833 INFO: === checking if optimization conditions were reached ===
0:23:25.764114 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:23:25.766377 INFO: Updating optimization_manager: rt_error            : 64.22379566807277 -> 50.974479517841914
0:23:25.766497 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 50.9745.
0:23:25.766593 INFO: ==============================================
0:23:25.766676 INFO: Starting optimization step 5.
0:23:25.766758 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:25.766829 INFO: Using ng extraction backend
0:23:25.766894 PROGRESS: Extracting batch of 50293 precursors
0:23:25.856708 INFO: === Search parameters used ===
0:23:25.856968 INFO: rt_error       : 50.974479517841914
0:23:25.857019 INFO: mobility_error : 0.1
0:23:25.857066 INFO: num_candidates : 3
0:23:25.857109 INFO: ms1_error      : 30
0:23:25.857148 INFO: ms2_error      : 7.246735808105685
0:23:25.857189 INFO: fwhm_rt        : 3.0
0:23:25.857227 INFO: quant_window   : 3
0:23:25.857265 INFO: ==============================================
0:23:26.391779 INFO: performing precursor FDR with 40 features
0:23:26.391897 INFO: Decoy channel: -1
0:23:26.391924 INFO: Competetive: True
0:23:26.425849 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:26.456297 INFO: Using random state 521042 for train-test-split
0:23:28.198724 INFO: Test AUC: 0.595
0:23:28.199112 INFO: Train AUC: 0.608
0:23:28.199147 INFO: AUC difference: 2.09%
0:23:28.459793 INFO: Resetting torch num_threads to 80
0:23:28.465643 PROGRESS: === Extracted 137024 precursors and 506642 fragments ===
0:23:28.466002 INFO: === FDR correction performed with classifier version 9 ===
0:23:28.466448 PROGRESS: ============================= Precursor FDR =============================
0:23:28.466538 PROGRESS: Total precursors accumulated: 255
0:23:28.466606 PROGRESS: Target precursors: 253 (99.22%)
0:23:28.466658 PROGRESS: Decoy precursors: 2 (0.78%)
0:23:28.466702 PROGRESS: 
0:23:28.466747 PROGRESS: Precursor Summary:
0:23:28.467635 PROGRESS: Channel   0:	 0.050 FDR:   253; 0.010 FDR:   253; 0.001 FDR:   244
0:23:28.467736 PROGRESS: 
0:23:28.467793 PROGRESS: Protein Summary:
0:23:28.468836 PROGRESS: Channel   0:	 0.050 FDR:   242; 0.010 FDR:   242; 0.001 FDR:   234
0:23:28.468926 PROGRESS: =========================================================================
0:23:28.470728 INFO: Target number of precursors reached.
0:23:28.505364 INFO: fragments_df: keeping 2513 of 506642 [sum(precursor_idx_mask)=5342 sum(mass_error_mask)=506642 stop_rank=2513
0:23:28.641300 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:28.737601 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:29.015047 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:29.015468 INFO: Using score_cutoff 12.946492288970948 (fac=0.99, q=1)
0:23:29.015755 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:29.015836 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:29.015891 INFO: Updating optimization_manager: score_cutoff        : 13.934062399864196 -> 12.946492288970948
0:23:29.015945 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:29.048226 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:29.114041 INFO: === checking if optimization conditions were reached ===
0:23:29.114326 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:23:29.116653 INFO: Updating optimization_manager: rt_error            : 50.974479517841914 -> 38.12219693935354
0:23:29.116777 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 38.1222.
0:23:29.116868 INFO: ==============================================
0:23:29.116951 INFO: Starting optimization step 6.
0:23:29.117020 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:29.117088 INFO: Using ng extraction backend
0:23:29.117155 PROGRESS: Extracting batch of 50293 precursors
0:23:29.206854 INFO: === Search parameters used ===
0:23:29.207111 INFO: rt_error       : 38.12219693935354
0:23:29.207166 INFO: mobility_error : 0.1
0:23:29.207213 INFO: num_candidates : 3
0:23:29.207254 INFO: ms1_error      : 30
0:23:29.207296 INFO: ms2_error      : 7.246735808105685
0:23:29.207338 INFO: fwhm_rt        : 3.0
0:23:29.207376 INFO: quant_window   : 3
0:23:29.207417 INFO: ==============================================
0:23:29.725502 INFO: performing precursor FDR with 40 features
0:23:29.725623 INFO: Decoy channel: -1
0:23:29.725653 INFO: Competetive: True
0:23:29.760554 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:29.791597 INFO: Using random state 521042 for train-test-split
0:23:31.534538 INFO: Test AUC: 0.591
0:23:31.534664 INFO: Train AUC: 0.610
0:23:31.534694 INFO: AUC difference: 3.00%
0:23:31.797390 INFO: Resetting torch num_threads to 80
0:23:31.803234 PROGRESS: === Extracted 134985 precursors and 500140 fragments ===
0:23:31.803596 INFO: === FDR correction performed with classifier version 9 ===
0:23:31.804048 PROGRESS: ============================= Precursor FDR =============================
0:23:31.804138 PROGRESS: Total precursors accumulated: 256
0:23:31.804197 PROGRESS: Target precursors: 254 (99.22%)
0:23:31.804248 PROGRESS: Decoy precursors: 2 (0.78%)
0:23:31.804292 PROGRESS: 
0:23:31.804335 PROGRESS: Precursor Summary:
0:23:31.805238 PROGRESS: Channel   0:	 0.050 FDR:   254; 0.010 FDR:   254; 0.001 FDR:   182
0:23:31.805326 PROGRESS: 
0:23:31.805382 PROGRESS: Protein Summary:
0:23:31.806404 PROGRESS: Channel   0:	 0.050 FDR:   245; 0.010 FDR:   245; 0.001 FDR:   176
0:23:31.806494 PROGRESS: =========================================================================
0:23:31.808264 INFO: Target number of precursors reached.
0:23:31.842706 INFO: fragments_df: keeping 2475 of 500140 [sum(precursor_idx_mask)=5177 sum(mass_error_mask)=500140 stop_rank=2475
0:23:31.978845 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:32.078900 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:32.350334 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:32.350762 INFO: Using score_cutoff 11.649846649074554 (fac=0.99, q=1)
0:23:32.351044 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:32.351123 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:32.351179 INFO: Updating optimization_manager: score_cutoff        : 12.946492288970948 -> 11.649846649074554
0:23:32.351234 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:32.383220 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:32.449201 INFO: === checking if optimization conditions were reached ===
0:23:32.449479 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:23:32.451771 INFO: Updating optimization_manager: rt_error            : 38.12219693935354 -> 32.891094613318224
0:23:32.451905 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 32.8911.
0:23:32.451983 INFO: ==============================================
0:23:32.452065 INFO: Starting optimization step 7.
0:23:32.452673 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:32.452749 INFO: Using ng extraction backend
0:23:32.452818 PROGRESS: Extracting batch of 50293 precursors
0:23:32.542486 INFO: === Search parameters used ===
0:23:32.542745 INFO: rt_error       : 32.891094613318224
0:23:32.542799 INFO: mobility_error : 0.1
0:23:32.542846 INFO: num_candidates : 3
0:23:32.542888 INFO: ms1_error      : 30
0:23:32.542928 INFO: ms2_error      : 7.246735808105685
0:23:32.542968 INFO: fwhm_rt        : 3.0
0:23:32.543006 INFO: quant_window   : 3
0:23:32.543045 INFO: ==============================================
0:23:33.065154 INFO: performing precursor FDR with 40 features
0:23:33.065275 INFO: Decoy channel: -1
0:23:33.065300 INFO: Competetive: True
0:23:33.099449 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:33.132364 INFO: Using random state 521042 for train-test-split
0:23:34.865160 INFO: Test AUC: 0.591
0:23:34.865279 INFO: Train AUC: 0.607
0:23:34.865309 INFO: AUC difference: 2.70%
0:23:35.123633 INFO: Resetting torch num_threads to 80
0:23:35.129524 PROGRESS: === Extracted 135305 precursors and 505752 fragments ===
0:23:35.129883 INFO: === FDR correction performed with classifier version 9 ===
0:23:35.130338 PROGRESS: ============================= Precursor FDR =============================
0:23:35.130427 PROGRESS: Total precursors accumulated: 271
0:23:35.130484 PROGRESS: Target precursors: 269 (99.26%)
0:23:35.130534 PROGRESS: Decoy precursors: 2 (0.74%)
0:23:35.130601 PROGRESS: 
0:23:35.130650 PROGRESS: Precursor Summary:
0:23:35.131538 PROGRESS: Channel   0:	 0.050 FDR:   269; 0.010 FDR:   269; 0.001 FDR:   212
0:23:35.131627 PROGRESS: 
0:23:35.131685 PROGRESS: Protein Summary:
0:23:35.132734 PROGRESS: Channel   0:	 0.050 FDR:   261; 0.010 FDR:   261; 0.001 FDR:   206
0:23:35.132822 PROGRESS: =========================================================================
0:23:35.134656 INFO: Target number of precursors reached.
0:23:35.169312 INFO: fragments_df: keeping 2603 of 505752 [sum(precursor_idx_mask)=5505 sum(mass_error_mask)=505752 stop_rank=2603
0:23:35.305066 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:35.409897 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:35.694690 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:35.695111 INFO: Using score_cutoff 12.602596446990967 (fac=0.99, q=1)
0:23:35.695392 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:35.695472 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:35.695528 INFO: Updating optimization_manager: score_cutoff        : 11.649846649074554 -> 12.602596446990967
0:23:35.695582 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:35.727105 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:35.793368 INFO: === checking if optimization conditions were reached ===
0:23:35.793672 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:23:35.795992 INFO: Updating optimization_manager: rt_error            : 32.891094613318224 -> 33.98021329821879
0:23:35.796107 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 33.9802.
0:23:35.796181 INFO: ==============================================
0:23:35.796262 INFO: Starting optimization step 8.
0:23:35.796326 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:35.796393 INFO: Using ng extraction backend
0:23:35.796457 PROGRESS: Extracting batch of 50293 precursors
0:23:35.886206 INFO: === Search parameters used ===
0:23:35.886456 INFO: rt_error       : 33.98021329821879
0:23:35.886508 INFO: mobility_error : 0.1
0:23:35.886556 INFO: num_candidates : 3
0:23:35.886609 INFO: ms1_error      : 30
0:23:35.886648 INFO: ms2_error      : 7.246735808105685
0:23:35.886688 INFO: fwhm_rt        : 3.0
0:23:35.886725 INFO: quant_window   : 3
0:23:35.886763 INFO: ==============================================
0:23:36.411694 INFO: performing precursor FDR with 40 features
0:23:36.411823 INFO: Decoy channel: -1
0:23:36.411850 INFO: Competetive: True
0:23:36.446271 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:36.477381 INFO: Using random state 521042 for train-test-split
0:23:38.244496 INFO: Test AUC: 0.587
0:23:38.244621 INFO: Train AUC: 0.609
0:23:38.244652 INFO: AUC difference: 3.57%
0:23:38.501833 INFO: Resetting torch num_threads to 80
0:23:38.507867 PROGRESS: === Extracted 135528 precursors and 511011 fragments ===
0:23:38.508224 INFO: === FDR correction performed with classifier version 9 ===
0:23:38.508685 PROGRESS: ============================= Precursor FDR =============================
0:23:38.508776 PROGRESS: Total precursors accumulated: 303
0:23:38.508841 PROGRESS: Target precursors: 300 (99.01%)
0:23:38.508893 PROGRESS: Decoy precursors: 3 (0.99%)
0:23:38.508937 PROGRESS: 
0:23:38.508979 PROGRESS: Precursor Summary:
0:23:38.509894 PROGRESS: Channel   0:	 0.050 FDR:   300; 0.010 FDR:   284; 0.001 FDR:   184
0:23:38.509982 PROGRESS: 
0:23:38.510036 PROGRESS: Protein Summary:
0:23:38.511109 PROGRESS: Channel   0:	 0.050 FDR:   292; 0.010 FDR:   276; 0.001 FDR:   180
0:23:38.511205 PROGRESS: =========================================================================
0:23:38.513061 INFO: Target number of precursors reached.
0:23:38.549416 INFO: fragments_df: keeping 2713 of 511011 [sum(precursor_idx_mask)=5786 sum(mass_error_mask)=511011 stop_rank=2713
0:23:38.685459 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:38.788273 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:39.236945 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:39.237369 INFO: Using score_cutoff 12.720415610790253 (fac=0.99, q=1)
0:23:39.237663 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:39.237743 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:39.237797 INFO: Updating optimization_manager: score_cutoff        : 12.602596446990967 -> 12.720415610790253
0:23:39.237850 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:39.271988 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:39.336129 INFO: === checking if optimization conditions were reached ===
0:23:39.336390 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:23:39.337666 INFO: Updating optimization_manager: rt_error            : 33.98021329821879 -> 33.98021329821879
0:23:39.337812 INFO: Updating optimization_manager: classifier_version  : 9 -> 19
0:23:39.337924 INFO: Updating optimization_manager: score_cutoff        : 12.720415610790253 -> 12.720415610790253
0:23:39.338022 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:39.338118 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:39.338214 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 33.9802 found after 9 searches.
0:23:39.338288 INFO: ==============================================
0:23:39.338366 PROGRESS: Optimization finished for rt_error.
0:23:39.486742 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:39.518425 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:39.611084 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:23:39.611319 PROGRESS: ==============================================
0:23:39.611396 PROGRESS: ms2_error      : 7.2467
0:23:39.611460 PROGRESS: rt_error       : 33.9802
0:23:39.611515 PROGRESS: ==============================================
0:23:39.614123 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:47.569695 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:06.138235 INFO: Using ng extraction backend
0:24:06.138724 PROGRESS: Extracting batch of 12001526 precursors
0:24:22.003284 INFO: === Search parameters used ===
0:24:22.003791 INFO: rt_error       : 33.98021329821879
0:24:22.003862 INFO: mobility_error : 0.1
0:24:22.003913 INFO: num_candidates : 3
0:24:22.003972 INFO: ms1_error      : 30
0:24:22.004022 INFO: ms2_error      : 7.246735808105685
0:24:22.004073 INFO: fwhm_rt        : 3.0
0:24:22.004117 INFO: quant_window   : 3
0:24:22.004158 INFO: ==============================================
0:24:41.869059 INFO: Removed 28141159 precursors with score below cutoff 12.720415610790253
0:24:46.352104 INFO: performing precursor FDR with 40 features
0:24:46.352223 INFO: Decoy channel: -1
0:24:46.352253 INFO: Competetive: True
0:24:46.783896 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:48.453524 INFO: Using random state 751854 for train-test-split
0:25:54.345096 INFO: Test AUC: 0.634
0:25:54.345392 INFO: Train AUC: 0.635
0:25:54.345429 INFO: AUC difference: 0.17%
0:25:55.894977 INFO: Resetting torch num_threads to 80
0:25:57.380263 PROGRESS: ============================= Precursor FDR =============================
0:25:57.380552 PROGRESS: Total precursors accumulated: 72,354
0:25:57.380619 PROGRESS: Target precursors: 71,638 (99.01%)
0:25:57.380670 PROGRESS: Decoy precursors: 716 (0.99%)
0:25:57.380715 PROGRESS: 
0:25:57.380757 PROGRESS: Precursor Summary:
0:25:57.401401 PROGRESS: Channel   0:	 0.050 FDR: 71,638; 0.010 FDR: 71,638; 0.001 FDR: 52,276
0:25:57.401634 PROGRESS: 
0:25:57.401692 PROGRESS: Protein Summary:
0:25:57.429400 PROGRESS: Channel   0:	 0.050 FDR: 12,045; 0.010 FDR: 12,045; 0.001 FDR: 9,270
0:25:57.429646 PROGRESS: =========================================================================
0:25:57.462072 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
0:25:57.603834 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
0:25:57.812153 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:25:58.438083 PROGRESS: 
0:25:58.438233 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
0:25:58.438303 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
0:25:58.438475 INFO: Initializing TimingManager
0:25:58.438932 INFO: Initializing RawFileManager
0:26:09.400417 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:26:09.404477 INFO: Determining DIA cycle
0:26:09.419918 INFO: Found cycle with start 0.00 min and length 300.
0:26:09.594101 INFO: RT (min)            : 0.0 - 26.9
0:26:09.594194 INFO: RT duration (sec)   : 1611.2
0:26:09.594224 INFO: RT duration (min)   : 26.9
0:26:09.594250 INFO: Cycle len (scans)   : 300
0:26:09.594271 INFO: Cycle len (sec)     : 1.65
0:26:09.594292 INFO: Number of cycles    : 977
0:26:09.594310 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:26:09.594337 INFO: Creating DIA data object took: 11.155310869216919
0:26:10.288823 INFO: Creating DIA data NG object took: 0.6943767070770264
0:26:11.634308 INFO: Initializing CalibrationManager
0:26:11.634599 INFO: Setting up calibration estimators ..
0:26:11.634659 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:26:11.634734 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'}' ..
0:26:11.634815 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:26:11.634865 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:26:11.634916 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}}' ..
0:26:11.634977 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:26:11.635020 INFO: Done setting up calibration estimators.
0:26:11.635219 INFO: Initializing OptimizationManager
0:26:11.635350 INFO: initial parameter: ms1_error = 30
0:26:11.635400 INFO: initial parameter: ms2_error = 30
0:26:11.635444 INFO: initial parameter: rt_error = 805.6002197265625
0:26:11.635487 INFO: initial parameter: mobility_error = 0.1
0:26:11.635528 INFO: initial parameter: num_candidates = 1
0:26:11.635567 INFO: initial parameter: fwhm_rt = 5
0:26:11.635608 INFO: initial parameter: fwhm_mobility = 0.01
0:26:11.635650 INFO: initial parameter: score_cutoff = 0
0:26:11.635690 INFO: initial parameter: classifier_version = -1
0:26:11.635760 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:26:11.636035 INFO: FDRManager: loading saved state not requested, will be initialized.
0:26:11.636072 INFO: Initializing FDRManager
0:26:11.636112 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:26:12.839126 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:26:13.584472 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:26:13.585029 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
0:26:13.585133 PROGRESS: Starting initial search for precursors.
0:26:13.585215 INFO: Starting optimization step 0.
0:26:13.585276 PROGRESS: === Extracting elution groups 0 to 200 ===
0:26:13.585338 INFO: Using ng extraction backend
0:26:13.585397 PROGRESS: Extracting batch of 396 precursors
0:26:13.587111 INFO: === Search parameters used ===
0:26:13.587199 INFO: rt_error       : 805.6002197265625
0:26:13.587249 INFO: mobility_error : 0.1
0:26:13.587293 INFO: num_candidates : 1
0:26:13.587333 INFO: ms1_error      : 30
0:26:13.587373 INFO: ms2_error      : 30
0:26:13.587413 INFO: fwhm_rt        : 5
0:26:13.587451 INFO: quant_window   : 3
0:26:13.587489 INFO: ==============================================
0:26:13.604635 INFO: performing precursor FDR with 40 features
0:26:13.604747 INFO: Decoy channel: -1
0:26:13.604774 INFO: Competetive: True
0:26:13.605680 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:13.607856 INFO: Using random state 256395 for train-test-split
0:26:13.615420 INFO: Test AUC: 0.484
0:26:13.615475 INFO: Train AUC: 0.493
0:26:13.615506 INFO: AUC difference: 1.76%
0:26:13.830855 INFO: Resetting torch num_threads to 80
0:26:13.832148 PROGRESS: === Extracted 393 precursors and 1847 fragments ===
0:26:13.832485 INFO: === FDR correction performed with classifier version -1 ===
0:26:13.832913 PROGRESS: ============================= Precursor FDR =============================
0:26:13.833004 PROGRESS: Total precursors accumulated: 0
0:26:13.833062 PROGRESS: Target precursors: 0 (0.00%)
0:26:13.833112 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:13.833156 PROGRESS: 
0:26:13.833201 PROGRESS: Precursor Summary:
0:26:13.833307 PROGRESS: 
0:26:13.833368 PROGRESS: Protein Summary:
0:26:13.833440 PROGRESS: =========================================================================
0:26:13.833605 INFO: Target number of precursors not reached yet.
0:26:13.897923 INFO: Starting optimization step 1.
0:26:13.898127 PROGRESS: === Extracting elution groups 200 to 600 ===
0:26:13.898207 INFO: Using ng extraction backend
0:26:13.898266 PROGRESS: Extracting batch of 786 precursors
0:26:13.900835 INFO: === Search parameters used ===
0:26:13.900948 INFO: rt_error       : 805.6002197265625
0:26:13.901000 INFO: mobility_error : 0.1
0:26:13.901050 INFO: num_candidates : 1
0:26:13.901095 INFO: ms1_error      : 30
0:26:13.901140 INFO: ms2_error      : 30
0:26:13.901184 INFO: fwhm_rt        : 5
0:26:13.901223 INFO: quant_window   : 3
0:26:13.901264 INFO: ==============================================
0:26:13.957409 INFO: performing precursor FDR with 40 features
0:26:13.957516 INFO: Decoy channel: -1
0:26:13.957542 INFO: Competetive: True
0:26:13.960426 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:13.961910 INFO: Using random state 895212 for train-test-split
0:26:13.970124 INFO: Test AUC: 0.457
0:26:13.970185 INFO: Train AUC: 0.508
0:26:13.970215 INFO: AUC difference: 10.00%
0:26:13.970238 WARNING: AUC difference > 5%. This may indicate overfitting.
0:26:14.178536 INFO: Resetting torch num_threads to 80
0:26:14.180601 PROGRESS: === Extracted 1172 precursors and 5527 fragments ===
0:26:14.180939 INFO: === FDR correction performed with classifier version -1 ===
0:26:14.181394 PROGRESS: ============================= Precursor FDR =============================
0:26:14.181483 PROGRESS: Total precursors accumulated: 1
0:26:14.181543 PROGRESS: Target precursors: 1 (100.00%)
0:26:14.181594 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:14.181638 PROGRESS: 
0:26:14.181682 PROGRESS: Precursor Summary:
0:26:14.182615 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:26:14.182704 PROGRESS: 
0:26:14.183567 PROGRESS: Protein Summary:
0:26:14.184613 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:26:14.184702 PROGRESS: =========================================================================
0:26:14.184901 INFO: Target number of precursors not reached yet.
0:26:14.252675 INFO: Starting optimization step 2.
0:26:14.252873 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:26:14.252954 INFO: Using ng extraction backend
0:26:14.253016 PROGRESS: Extracting batch of 1592 precursors
0:26:14.257068 INFO: === Search parameters used ===
0:26:14.257193 INFO: rt_error       : 805.6002197265625
0:26:14.257246 INFO: mobility_error : 0.1
0:26:14.257296 INFO: num_candidates : 1
0:26:14.257340 INFO: ms1_error      : 30
0:26:14.257382 INFO: ms2_error      : 30
0:26:14.257425 INFO: fwhm_rt        : 5
0:26:14.257467 INFO: quant_window   : 3
0:26:14.257507 INFO: ==============================================
0:26:14.288667 INFO: performing precursor FDR with 40 features
0:26:14.288757 INFO: Decoy channel: -1
0:26:14.288783 INFO: Competetive: True
0:26:14.292062 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:14.293776 INFO: Using random state 260353 for train-test-split
0:26:14.305328 INFO: Test AUC: 0.512
0:26:14.305392 INFO: Train AUC: 0.491
0:26:14.305422 INFO: AUC difference: 4.26%
0:26:14.528144 INFO: Resetting torch num_threads to 80
0:26:14.530644 PROGRESS: === Extracted 2754 precursors and 13075 fragments ===
0:26:14.530983 INFO: === FDR correction performed with classifier version -1 ===
0:26:14.531438 PROGRESS: ============================= Precursor FDR =============================
0:26:14.531525 PROGRESS: Total precursors accumulated: 3
0:26:14.531590 PROGRESS: Target precursors: 3 (100.00%)
0:26:14.531641 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:14.531686 PROGRESS: 
0:26:14.531731 PROGRESS: Precursor Summary:
0:26:14.532639 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:26:14.532724 PROGRESS: 
0:26:14.532779 PROGRESS: Protein Summary:
0:26:14.533786 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:26:14.533875 PROGRESS: =========================================================================
0:26:14.534099 INFO: Target number of precursors not reached yet.
0:26:14.604116 INFO: Starting optimization step 3.
0:26:14.604321 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:26:14.604402 INFO: Using ng extraction backend
0:26:14.604465 PROGRESS: Extracting batch of 3177 precursors
0:26:14.611243 INFO: === Search parameters used ===
0:26:14.611383 INFO: rt_error       : 805.6002197265625
0:26:14.611434 INFO: mobility_error : 0.1
0:26:14.611480 INFO: num_candidates : 1
0:26:14.611523 INFO: ms1_error      : 30
0:26:14.611565 INFO: ms2_error      : 30
0:26:14.611607 INFO: fwhm_rt        : 5
0:26:14.611646 INFO: quant_window   : 3
0:26:14.611696 INFO: ==============================================
0:26:14.663236 INFO: performing precursor FDR with 40 features
0:26:14.663345 INFO: Decoy channel: -1
0:26:14.663372 INFO: Competetive: True
0:26:14.667844 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:14.670151 INFO: Using random state 390276 for train-test-split
0:26:14.689613 INFO: Test AUC: 0.515
0:26:14.689682 INFO: Train AUC: 0.491
0:26:14.689713 INFO: AUC difference: 4.79%
0:26:14.903573 INFO: Resetting torch num_threads to 80
0:26:14.906820 PROGRESS: === Extracted 5901 precursors and 27847 fragments ===
0:26:14.907158 INFO: === FDR correction performed with classifier version -1 ===
0:26:14.907633 PROGRESS: ============================= Precursor FDR =============================
0:26:14.907720 PROGRESS: Total precursors accumulated: 4
0:26:14.907779 PROGRESS: Target precursors: 4 (100.00%)
0:26:14.907828 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:14.907873 PROGRESS: 
0:26:14.907916 PROGRESS: Precursor Summary:
0:26:14.908834 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:26:14.908919 PROGRESS: 
0:26:14.908973 PROGRESS: Protein Summary:
0:26:14.909974 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:26:14.910061 PROGRESS: =========================================================================
0:26:14.910313 INFO: Target number of precursors not reached yet.
0:26:14.984990 INFO: Starting optimization step 4.
0:26:14.985200 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:26:14.985279 INFO: Using ng extraction backend
0:26:14.985338 PROGRESS: Extracting batch of 6340 precursors
0:26:14.997950 INFO: === Search parameters used ===
0:26:14.998085 INFO: rt_error       : 805.6002197265625
0:26:14.998146 INFO: mobility_error : 0.1
0:26:14.998195 INFO: num_candidates : 1
0:26:14.998240 INFO: ms1_error      : 30
0:26:14.998280 INFO: ms2_error      : 30
0:26:14.998320 INFO: fwhm_rt        : 5
0:26:14.998358 INFO: quant_window   : 3
0:26:14.998396 INFO: ==============================================
0:26:15.079240 INFO: performing precursor FDR with 40 features
0:26:15.079348 INFO: Decoy channel: -1
0:26:15.079375 INFO: Competetive: True
0:26:15.086674 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:15.090019 INFO: Using random state 459347 for train-test-split
0:26:15.129944 INFO: Test AUC: 0.492
0:26:15.130042 INFO: Train AUC: 0.495
0:26:15.130072 INFO: AUC difference: 0.49%
0:26:15.346862 INFO: Resetting torch num_threads to 80
0:26:15.351058 PROGRESS: === Extracted 12165 precursors and 57133 fragments ===
0:26:15.351425 INFO: === FDR correction performed with classifier version -1 ===
0:26:15.351889 PROGRESS: ============================= Precursor FDR =============================
0:26:15.351973 PROGRESS: Total precursors accumulated: 0
0:26:15.352030 PROGRESS: Target precursors: 0 (0.00%)
0:26:15.352078 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:15.352123 PROGRESS: 
0:26:15.352165 PROGRESS: Precursor Summary:
0:26:15.352273 PROGRESS: 
0:26:15.352335 PROGRESS: Protein Summary:
0:26:15.352406 PROGRESS: =========================================================================
0:26:15.352704 INFO: Target number of precursors not reached yet.
0:26:15.434722 INFO: Starting optimization step 5.
0:26:15.434948 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:26:15.435031 INFO: Using ng extraction backend
0:26:15.435106 PROGRESS: Extracting batch of 12663 precursors
0:26:15.458483 INFO: === Search parameters used ===
0:26:15.458652 INFO: rt_error       : 805.6002197265625
0:26:15.458707 INFO: mobility_error : 0.1
0:26:15.458753 INFO: num_candidates : 1
0:26:15.458795 INFO: ms1_error      : 30
0:26:15.458835 INFO: ms2_error      : 30
0:26:15.458875 INFO: fwhm_rt        : 5
0:26:15.458915 INFO: quant_window   : 3
0:26:15.458954 INFO: ==============================================
0:26:15.587379 INFO: performing precursor FDR with 40 features
0:26:15.587488 INFO: Decoy channel: -1
0:26:15.587522 INFO: Competetive: True
0:26:15.599826 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:15.605738 INFO: Using random state 998334 for train-test-split
0:26:15.852611 INFO: Test AUC: 0.517
0:26:15.852714 INFO: Train AUC: 0.511
0:26:15.852749 INFO: AUC difference: 1.16%
0:26:16.083135 INFO: Resetting torch num_threads to 80
0:26:16.089648 PROGRESS: === Extracted 24723 precursors and 116071 fragments ===
0:26:16.090082 INFO: === FDR correction performed with classifier version -1 ===
0:26:16.090595 PROGRESS: ============================= Precursor FDR =============================
0:26:16.090698 PROGRESS: Total precursors accumulated: 0
0:26:16.090771 PROGRESS: Target precursors: 0 (0.00%)
0:26:16.090835 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:16.090891 PROGRESS: 
0:26:16.090947 PROGRESS: Precursor Summary:
0:26:16.091082 PROGRESS: 
0:26:16.091155 PROGRESS: Protein Summary:
0:26:16.091244 PROGRESS: =========================================================================
0:26:16.091826 INFO: Target number of precursors not reached yet.
0:26:16.193397 INFO: Starting optimization step 6.
0:26:16.193676 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:26:16.193784 INFO: Using ng extraction backend
0:26:16.193861 PROGRESS: Extracting batch of 25339 precursors
0:26:16.238398 INFO: === Search parameters used ===
0:26:16.238637 INFO: rt_error       : 805.6002197265625
0:26:16.238709 INFO: mobility_error : 0.1
0:26:16.238769 INFO: num_candidates : 1
0:26:16.238824 INFO: ms1_error      : 30
0:26:16.238880 INFO: ms2_error      : 30
0:26:16.238932 INFO: fwhm_rt        : 5
0:26:16.238981 INFO: quant_window   : 3
0:26:16.239032 INFO: ==============================================
0:26:16.459037 INFO: performing precursor FDR with 40 features
0:26:16.459153 INFO: Decoy channel: -1
0:26:16.459184 INFO: Competetive: True
0:26:16.477556 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:16.488936 INFO: Using random state 346818 for train-test-split
0:26:17.070688 INFO: Test AUC: 0.547
0:26:17.070796 INFO: Train AUC: 0.562
0:26:17.070834 INFO: AUC difference: 2.70%
0:26:17.307063 INFO: Resetting torch num_threads to 80
0:26:17.316806 PROGRESS: === Extracted 49768 precursors and 233056 fragments ===
0:26:17.317286 INFO: === FDR correction performed with classifier version -1 ===
0:26:17.317982 PROGRESS: ============================= Precursor FDR =============================
0:26:17.318091 PROGRESS: Total precursors accumulated: 0
0:26:17.318168 PROGRESS: Target precursors: 0 (0.00%)
0:26:17.318235 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:17.318295 PROGRESS: 
0:26:17.318352 PROGRESS: Precursor Summary:
0:26:17.318489 PROGRESS: 
0:26:17.318585 PROGRESS: Protein Summary:
0:26:17.318689 PROGRESS: =========================================================================
0:26:17.319521 INFO: Target number of precursors not reached yet.
0:26:17.459020 INFO: Starting optimization step 7.
0:26:17.459283 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:26:17.459388 INFO: Using ng extraction backend
0:26:17.459471 PROGRESS: Extracting batch of 50691 precursors
0:26:17.552587 INFO: === Search parameters used ===
0:26:17.552870 INFO: rt_error       : 805.6002197265625
0:26:17.552948 INFO: mobility_error : 0.1
0:26:17.553009 INFO: num_candidates : 1
0:26:17.553064 INFO: ms1_error      : 30
0:26:17.553118 INFO: ms2_error      : 30
0:26:17.553173 INFO: fwhm_rt        : 5
0:26:17.553225 INFO: quant_window   : 3
0:26:17.553276 INFO: ==============================================
0:26:17.971652 INFO: performing precursor FDR with 40 features
0:26:17.971812 INFO: Decoy channel: -1
0:26:17.971854 INFO: Competetive: True
0:26:18.024300 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:18.061780 INFO: Using random state 560464 for train-test-split
0:26:19.629311 INFO: Test AUC: 0.575
0:26:19.629436 INFO: Train AUC: 0.588
0:26:19.629466 INFO: AUC difference: 2.29%
0:26:19.880800 INFO: Resetting torch num_threads to 80
0:26:19.898507 PROGRESS: === Extracted 99957 precursors and 468918 fragments ===
0:26:19.898999 INFO: === FDR correction performed with classifier version -1 ===
0:26:19.899529 PROGRESS: ============================= Precursor FDR =============================
0:26:19.899834 PROGRESS: Total precursors accumulated: 231
0:26:19.899894 PROGRESS: Target precursors: 229 (99.13%)
0:26:19.899949 PROGRESS: Decoy precursors: 2 (0.87%)
0:26:19.899993 PROGRESS: 
0:26:19.900034 PROGRESS: Precursor Summary:
0:26:19.900951 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:     9
0:26:19.901040 PROGRESS: 
0:26:19.901093 PROGRESS: Protein Summary:
0:26:19.902127 PROGRESS: Channel   0:	 0.050 FDR:   215; 0.010 FDR:   215; 0.001 FDR:     9
0:26:19.902216 PROGRESS: =========================================================================
0:26:19.903445 INFO: Target number of precursors reached.
0:26:19.939321 INFO: fragments_df: keeping 2070 of 468918 [sum(precursor_idx_mask)=2526 sum(mass_error_mask)=468918 stop_rank=2070
0:26:20.144767 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:20.238282 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:20.471095 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:26:20.471516 INFO: Using score_cutoff 14.63133464126587 (fac=0.99, q=1)
0:26:20.471819 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:26:20.471899 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:26:20.471954 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.63133464126587
0:26:20.472013 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:20.534513 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:20.677289 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:26:20.677564 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:26:20.677671 INFO: Starting optimization step 8.
0:26:20.677748 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:26:20.677829 INFO: Using ng extraction backend
0:26:20.677906 PROGRESS: Extracting batch of 100984 precursors
0:26:20.850888 INFO: === Search parameters used ===
0:26:20.851155 INFO: rt_error       : 805.6002197265625
0:26:20.851230 INFO: mobility_error : 0.1
0:26:20.851294 INFO: num_candidates : 3
0:26:20.851353 INFO: ms1_error      : 30
0:26:20.851411 INFO: ms2_error      : 30
0:26:20.851469 INFO: fwhm_rt        : 3.0
0:26:20.851524 INFO: quant_window   : 3
0:26:20.851580 INFO: ==============================================
0:26:22.088482 INFO: performing precursor FDR with 40 features
0:26:22.088603 INFO: Decoy channel: -1
0:26:22.088629 INFO: Competetive: True
0:26:22.164432 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:22.266008 INFO: Using random state 187038 for train-test-split
0:26:26.440943 INFO: Test AUC: 0.589
0:26:26.441124 INFO: Train AUC: 0.601
0:26:26.441162 INFO: AUC difference: 1.97%
0:26:27.837410 INFO: Resetting torch num_threads to 80
0:26:27.848692 PROGRESS: === Extracted 300122 precursors and 1379034 fragments ===
0:26:27.849071 INFO: === FDR correction performed with classifier version 7 ===
0:26:27.849528 PROGRESS: ============================= Precursor FDR =============================
0:26:27.849616 PROGRESS: Total precursors accumulated: 206
0:26:27.849674 PROGRESS: Target precursors: 204 (99.03%)
0:26:27.849723 PROGRESS: Decoy precursors: 2 (0.97%)
0:26:27.849766 PROGRESS: 
0:26:27.849807 PROGRESS: Precursor Summary:
0:26:27.850702 PROGRESS: Channel   0:	 0.050 FDR:   204; 0.010 FDR:   204; 0.001 FDR:     0
0:26:27.850792 PROGRESS: 
0:26:27.850848 PROGRESS: Protein Summary:
0:26:27.851841 PROGRESS: Channel   0:	 0.050 FDR:   192; 0.010 FDR:   192; 0.001 FDR:     0
0:26:27.851928 PROGRESS: =========================================================================
0:26:27.856914 INFO: Target number of precursors reached.
0:26:27.951014 INFO: fragments_df: keeping 2662 of 1379034 [sum(precursor_idx_mask)=4719 sum(mass_error_mask)=1379034 stop_rank=2662
0:26:28.225827 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:28.318594 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:28.613695 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:28.614113 INFO: Using score_cutoff 15.381844525051116 (fac=0.99, q=1)
0:26:28.614395 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:28.614474 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:28.614529 INFO: Updating optimization_manager: score_cutoff        : 14.63133464126587 -> 15.381844525051116
0:26:28.614594 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:28.677876 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:28.829673 INFO: === checking if optimization conditions were reached ===
0:26:28.829965 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:26:28.832342 INFO: Updating optimization_manager: ms2_error           : 30 -> 6.985299009071708
0:26:28.832474 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 6.9853.
0:26:28.832554 INFO: ==============================================
0:26:28.832631 INFO: Starting optimization step 9.
0:26:28.832696 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:26:28.832765 INFO: Using ng extraction backend
0:26:28.832830 PROGRESS: Extracting batch of 100984 precursors
0:26:29.007910 INFO: === Search parameters used ===
0:26:29.008164 INFO: rt_error       : 805.6002197265625
0:26:29.008219 INFO: mobility_error : 0.1
0:26:29.008264 INFO: num_candidates : 3
0:26:29.008308 INFO: ms1_error      : 30
0:26:29.008348 INFO: ms2_error      : 6.985299009071708
0:26:29.008389 INFO: fwhm_rt        : 3.0
0:26:29.008428 INFO: quant_window   : 3
0:26:29.008468 INFO: ==============================================
0:26:30.186177 INFO: performing precursor FDR with 40 features
0:26:30.186300 INFO: Decoy channel: -1
0:26:30.186326 INFO: Competetive: True
0:26:30.260321 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:30.360918 INFO: Using random state 187038 for train-test-split
0:26:34.500565 INFO: Test AUC: 0.595
0:26:34.500697 INFO: Train AUC: 0.602
0:26:34.500728 INFO: AUC difference: 1.22%
0:26:34.826296 INFO: Resetting torch num_threads to 80
0:26:34.837601 PROGRESS: === Extracted 302950 precursors and 1704817 fragments ===
0:26:34.837992 INFO: === FDR correction performed with classifier version 7 ===
0:26:34.838497 PROGRESS: ============================= Precursor FDR =============================
0:26:34.838600 PROGRESS: Total precursors accumulated: 451
0:26:34.838660 PROGRESS: Target precursors: 447 (99.11%)
0:26:34.838711 PROGRESS: Decoy precursors: 4 (0.89%)
0:26:34.838764 PROGRESS: 
0:26:34.838811 PROGRESS: Precursor Summary:
0:26:34.839767 PROGRESS: Channel   0:	 0.050 FDR:   447; 0.010 FDR:   447; 0.001 FDR:   340
0:26:34.839861 PROGRESS: 
0:26:34.839915 PROGRESS: Protein Summary:
0:26:34.841062 PROGRESS: Channel   0:	 0.050 FDR:   417; 0.010 FDR:   417; 0.001 FDR:   315
0:26:34.841153 PROGRESS: =========================================================================
0:26:34.846191 INFO: Target number of precursors reached.
0:26:34.958992 INFO: fragments_df: keeping 5000 of 1704817 [sum(precursor_idx_mask)=11076 sum(mass_error_mask)=1704817 stop_rank=5000
0:26:35.127346 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:35.261705 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:35.943467 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:35.943908 INFO: Using score_cutoff 12.72551245250702 (fac=0.99, q=1)
0:26:35.944200 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:35.944283 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:35.944337 INFO: Updating optimization_manager: score_cutoff        : 15.381844525051116 -> 12.72551245250702
0:26:35.944390 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:35.975048 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:36.040736 INFO: === checking if optimization conditions were reached ===
0:26:36.041039 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:26:36.043988 INFO: Updating optimization_manager: ms2_error           : 6.985299009071708 -> 7.206637673903375
0:26:36.044111 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.2066.
0:26:36.044190 INFO: ==============================================
0:26:36.044271 INFO: Starting optimization step 10.
0:26:36.044338 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:26:36.044407 INFO: Using ng extraction backend
0:26:36.044473 PROGRESS: Extracting batch of 50293 precursors
0:26:36.136162 INFO: === Search parameters used ===
0:26:36.136423 INFO: rt_error       : 805.6002197265625
0:26:36.136476 INFO: mobility_error : 0.1
0:26:36.136521 INFO: num_candidates : 3
0:26:36.136561 INFO: ms1_error      : 30
0:26:36.136601 INFO: ms2_error      : 7.206637673903375
0:26:36.136642 INFO: fwhm_rt        : 3.0
0:26:36.136680 INFO: quant_window   : 3
0:26:36.136719 INFO: ==============================================
0:26:36.748537 INFO: performing precursor FDR with 40 features
0:26:36.748665 INFO: Decoy channel: -1
0:26:36.748697 INFO: Competetive: True
0:26:36.788555 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:36.824240 INFO: Using random state 187038 for train-test-split
0:26:38.740915 INFO: Test AUC: 0.588
0:26:38.741065 INFO: Train AUC: 0.598
0:26:38.741101 INFO: AUC difference: 1.68%
0:26:39.097380 INFO: Resetting torch num_threads to 80
0:26:39.109532 PROGRESS: === Extracted 150848 precursors and 845004 fragments ===
0:26:39.110063 INFO: === FDR correction performed with classifier version 7 ===
0:26:39.110755 PROGRESS: ============================= Precursor FDR =============================
0:26:39.110875 PROGRESS: Total precursors accumulated: 158
0:26:39.110966 PROGRESS: Target precursors: 157 (99.37%)
0:26:39.111034 PROGRESS: Decoy precursors: 1 (0.63%)
0:26:39.111100 PROGRESS: 
0:26:39.111172 PROGRESS: Precursor Summary:
0:26:39.112599 PROGRESS: Channel   0:	 0.050 FDR:   157; 0.010 FDR:   157; 0.001 FDR:   148
0:26:39.112728 PROGRESS: 
0:26:39.112813 PROGRESS: Protein Summary:
0:26:39.114216 PROGRESS: Channel   0:	 0.050 FDR:   151; 0.010 FDR:   151; 0.001 FDR:   142
0:26:39.114314 PROGRESS: =========================================================================
0:26:39.117871 INFO: Target number of precursors not reached yet.
0:26:39.296423 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:39.333962 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:39.432345 INFO: === skipping optimization until target number of precursors are found ===
0:26:39.432888 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:26:39.433204 INFO: Starting optimization step 11.
0:26:39.433450 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:26:39.433717 INFO: Using ng extraction backend
0:26:39.433967 PROGRESS: Extracting batch of 50691 precursors
0:26:39.534990 INFO: === Search parameters used ===
0:26:39.535289 INFO: rt_error       : 805.6002197265625
0:26:39.535352 INFO: mobility_error : 0.1
0:26:39.535428 INFO: num_candidates : 3
0:26:39.535476 INFO: ms1_error      : 30
0:26:39.535519 INFO: ms2_error      : 7.206637673903375
0:26:39.535564 INFO: fwhm_rt        : 3.0
0:26:39.535603 INFO: quant_window   : 3
0:26:39.535644 INFO: ==============================================
0:26:40.491982 INFO: performing precursor FDR with 40 features
0:26:40.493604 INFO: Decoy channel: -1
0:26:40.493718 INFO: Competetive: True
0:26:40.634159 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:40.773958 INFO: Using random state 187038 for train-test-split
0:26:45.012852 INFO: Test AUC: 0.590
0:26:45.012982 INFO: Train AUC: 0.602
0:26:45.013013 INFO: AUC difference: 1.99%
0:26:45.336454 INFO: Resetting torch num_threads to 80
0:26:45.383356 PROGRESS: === Extracted 302895 precursors and 1697739 fragments ===
0:26:45.384252 INFO: === FDR correction performed with classifier version 7 ===
0:26:45.384921 PROGRESS: ============================= Precursor FDR =============================
0:26:45.385012 PROGRESS: Total precursors accumulated: 443
0:26:45.385072 PROGRESS: Target precursors: 439 (99.10%)
0:26:45.385123 PROGRESS: Decoy precursors: 4 (0.90%)
0:26:45.385168 PROGRESS: 
0:26:45.385214 PROGRESS: Precursor Summary:
0:26:45.386210 PROGRESS: Channel   0:	 0.050 FDR:   439; 0.010 FDR:   439; 0.001 FDR:   257
0:26:45.386304 PROGRESS: 
0:26:45.386359 PROGRESS: Protein Summary:
0:26:45.387562 PROGRESS: Channel   0:	 0.050 FDR:   410; 0.010 FDR:   410; 0.001 FDR:   237
0:26:45.387656 PROGRESS: =========================================================================
0:26:45.391647 INFO: Target number of precursors reached.
0:26:45.508728 INFO: fragments_df: keeping 5000 of 1697739 [sum(precursor_idx_mask)=10885 sum(mass_error_mask)=1697739 stop_rank=5000
0:26:45.699778 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:45.809539 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:46.427364 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:46.427793 INFO: Using score_cutoff 12.900892143630982 (fac=0.99, q=1)
0:26:46.428083 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:46.428164 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:46.428221 INFO: Updating optimization_manager: score_cutoff        : 12.72551245250702 -> 12.900892143630982
0:26:46.428275 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:46.460851 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:46.526152 INFO: === checking if optimization conditions were reached ===
0:26:46.526426 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:26:46.527409 INFO: Updating optimization_manager: ms2_error           : 7.206637673903375 -> 6.985299009071708
0:26:46.527552 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
0:26:46.527657 INFO: Updating optimization_manager: score_cutoff        : 12.900892143630982 -> 12.72551245250702
0:26:46.527755 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:46.527849 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:46.527944 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 6.9853 found after 3 searches.
0:26:46.528014 INFO: ==============================================
0:26:46.528105 PROGRESS: Optimization finished for ms2_error.
0:26:46.677168 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:46.708243 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:46.803059 INFO: Starting optimization step 0.
0:26:46.803295 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:26:46.803384 INFO: Using ng extraction backend
0:26:46.803454 PROGRESS: Extracting batch of 50293 precursors
0:26:46.892562 INFO: === Search parameters used ===
0:26:46.892832 INFO: rt_error       : 805.6002197265625
0:26:46.892889 INFO: mobility_error : 0.1
0:26:46.892937 INFO: num_candidates : 3
0:26:46.892981 INFO: ms1_error      : 30
0:26:46.893021 INFO: ms2_error      : 6.985299009071708
0:26:46.893062 INFO: fwhm_rt        : 3.0
0:26:46.893101 INFO: quant_window   : 3
0:26:46.893142 INFO: ==============================================
0:26:47.526430 INFO: performing precursor FDR with 40 features
0:26:47.526546 INFO: Decoy channel: -1
0:26:47.526581 INFO: Competetive: True
0:26:47.564716 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:47.600624 INFO: Using random state 861621 for train-test-split
0:26:49.504719 INFO: Test AUC: 0.593
0:26:49.504824 INFO: Train AUC: 0.611
0:26:49.504854 INFO: AUC difference: 2.82%
0:26:49.777715 INFO: Resetting torch num_threads to 80
0:26:49.784018 PROGRESS: === Extracted 150879 precursors and 848698 fragments ===
0:26:49.784375 INFO: === FDR correction performed with classifier version 9 ===
0:26:49.784815 PROGRESS: ============================= Precursor FDR =============================
0:26:49.784913 PROGRESS: Total precursors accumulated: 137
0:26:49.784972 PROGRESS: Target precursors: 136 (99.27%)
0:26:49.785027 PROGRESS: Decoy precursors: 1 (0.73%)
0:26:49.785073 PROGRESS: 
0:26:49.785121 PROGRESS: Precursor Summary:
0:26:49.785968 PROGRESS: Channel   0:	 0.050 FDR:   136; 0.010 FDR:   136; 0.001 FDR:     0
0:26:49.786054 PROGRESS: 
0:26:49.786108 PROGRESS: Protein Summary:
0:26:49.787066 PROGRESS: Channel   0:	 0.050 FDR:   132; 0.010 FDR:   132; 0.001 FDR:     0
0:26:49.787156 PROGRESS: =========================================================================
0:26:49.789206 INFO: Target number of precursors not reached yet.
0:26:49.928898 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:49.962682 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:50.028563 INFO: === skipping optimization until target number of precursors are found ===
0:26:50.028831 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:26:50.028934 INFO: Starting optimization step 1.
0:26:50.029006 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:26:50.029081 INFO: Using ng extraction backend
0:26:50.029151 PROGRESS: Extracting batch of 50691 precursors
0:26:50.123037 INFO: === Search parameters used ===
0:26:50.123309 INFO: rt_error       : 805.6002197265625
0:26:50.123372 INFO: mobility_error : 0.1
0:26:50.123419 INFO: num_candidates : 3
0:26:50.123476 INFO: ms1_error      : 30
0:26:50.123519 INFO: ms2_error      : 6.985299009071708
0:26:50.123561 INFO: fwhm_rt        : 3.0
0:26:50.123599 INFO: quant_window   : 3
0:26:50.123639 INFO: ==============================================
0:26:50.787652 INFO: performing precursor FDR with 40 features
0:26:50.787778 INFO: Decoy channel: -1
0:26:50.787805 INFO: Competetive: True
0:26:50.888713 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:50.987956 INFO: Using random state 861621 for train-test-split
0:26:55.050248 INFO: Test AUC: 0.595
0:26:55.050380 INFO: Train AUC: 0.609
0:26:55.050414 INFO: AUC difference: 2.22%
0:26:55.364505 INFO: Resetting torch num_threads to 80
0:26:55.409501 PROGRESS: === Extracted 302950 precursors and 1705002 fragments ===
0:26:55.410138 INFO: === FDR correction performed with classifier version 9 ===
0:26:55.410784 PROGRESS: ============================= Precursor FDR =============================
0:26:55.410881 PROGRESS: Total precursors accumulated: 449
0:26:55.410941 PROGRESS: Target precursors: 445 (99.11%)
0:26:55.410993 PROGRESS: Decoy precursors: 4 (0.89%)
0:26:55.411040 PROGRESS: 
0:26:55.411085 PROGRESS: Precursor Summary:
0:26:55.412083 PROGRESS: Channel   0:	 0.050 FDR:   445; 0.010 FDR:   445; 0.001 FDR:   420
0:26:55.412177 PROGRESS: 
0:26:55.412232 PROGRESS: Protein Summary:
0:26:55.413401 PROGRESS: Channel   0:	 0.050 FDR:   416; 0.010 FDR:   416; 0.001 FDR:   392
0:26:55.413493 PROGRESS: =========================================================================
0:26:55.417361 INFO: Target number of precursors reached.
0:26:55.536680 INFO: fragments_df: keeping 5000 of 1705002 [sum(precursor_idx_mask)=11123 sum(mass_error_mask)=1705002 stop_rank=5000
0:26:55.677153 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:55.810503 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:56.484359 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:56.484785 INFO: Using score_cutoff 13.80504556617737 (fac=0.99, q=1)
0:26:56.485070 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:56.485150 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:56.485204 INFO: Updating optimization_manager: score_cutoff        : 12.72551245250702 -> 13.80504556617737
0:26:56.485258 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:56.515988 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:56.582523 INFO: === checking if optimization conditions were reached ===
0:26:56.582817 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:26:56.585020 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 180.8415409471168
0:26:56.585137 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 180.8415.
0:26:56.585215 INFO: ==============================================
0:26:56.585296 INFO: Starting optimization step 2.
0:26:56.585366 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:26:56.585437 INFO: Using ng extraction backend
0:26:56.585503 PROGRESS: Extracting batch of 50293 precursors
0:26:56.675554 INFO: === Search parameters used ===
0:26:56.675801 INFO: rt_error       : 180.8415409471168
0:26:56.675873 INFO: mobility_error : 0.1
0:26:56.675926 INFO: num_candidates : 3
0:26:56.675970 INFO: ms1_error      : 30
0:26:56.676011 INFO: ms2_error      : 6.985299009071708
0:26:56.676052 INFO: fwhm_rt        : 3.0
0:26:56.676093 INFO: quant_window   : 3
0:26:56.676132 INFO: ==============================================
0:26:57.254573 INFO: performing precursor FDR with 40 features
0:26:57.254686 INFO: Decoy channel: -1
0:26:57.254713 INFO: Competetive: True
0:26:57.293190 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:57.328243 INFO: Using random state 861621 for train-test-split
0:26:59.379248 INFO: Test AUC: 0.589
0:26:59.379372 INFO: Train AUC: 0.605
0:26:59.379402 INFO: AUC difference: 2.54%
0:26:59.648881 INFO: Resetting torch num_threads to 80
0:26:59.658607 PROGRESS: === Extracted 150264 precursors and 708700 fragments ===
0:26:59.659018 INFO: === FDR correction performed with classifier version 9 ===
0:26:59.659498 PROGRESS: ============================= Precursor FDR =============================
0:26:59.659589 PROGRESS: Total precursors accumulated: 259
0:26:59.659647 PROGRESS: Target precursors: 257 (99.23%)
0:26:59.659697 PROGRESS: Decoy precursors: 2 (0.77%)
0:26:59.659740 PROGRESS: 
0:26:59.659782 PROGRESS: Precursor Summary:
0:26:59.660683 PROGRESS: Channel   0:	 0.050 FDR:   257; 0.010 FDR:   257; 0.001 FDR:   225
0:26:59.660769 PROGRESS: 
0:26:59.660824 PROGRESS: Protein Summary:
0:26:59.661866 PROGRESS: Channel   0:	 0.050 FDR:   247; 0.010 FDR:   247; 0.001 FDR:   216
0:26:59.661955 PROGRESS: =========================================================================
0:26:59.665118 INFO: Target number of precursors reached.
0:26:59.711027 INFO: fragments_df: keeping 2957 of 708700 [sum(precursor_idx_mask)=6181 sum(mass_error_mask)=708700 stop_rank=2957
0:26:59.888459 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:00.010313 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:00.400606 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:00.401134 INFO: Using score_cutoff 11.240489812088013 (fac=0.99, q=1)
0:27:00.401524 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:00.401604 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:00.401659 INFO: Updating optimization_manager: score_cutoff        : 13.80504556617737 -> 11.240489812088013
0:27:00.401720 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:00.432616 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:00.503540 INFO: === checking if optimization conditions were reached ===
0:27:00.503817 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:27:00.506266 INFO: Updating optimization_manager: rt_error            : 180.8415409471168 -> 137.9223124118572
0:27:00.506384 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 137.9223.
0:27:00.506465 INFO: ==============================================
0:27:00.506551 INFO: Starting optimization step 3.
0:27:00.506637 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:00.506741 INFO: Using ng extraction backend
0:27:00.506834 PROGRESS: Extracting batch of 50293 precursors
0:27:00.597874 INFO: === Search parameters used ===
0:27:00.598128 INFO: rt_error       : 137.9223124118572
0:27:00.598183 INFO: mobility_error : 0.1
0:27:00.598230 INFO: num_candidates : 3
0:27:00.598272 INFO: ms1_error      : 30
0:27:00.598313 INFO: ms2_error      : 6.985299009071708
0:27:00.598353 INFO: fwhm_rt        : 3.0
0:27:00.598392 INFO: quant_window   : 3
0:27:00.598428 INFO: ==============================================
0:27:01.172722 INFO: performing precursor FDR with 40 features
0:27:01.172837 INFO: Decoy channel: -1
0:27:01.172863 INFO: Competetive: True
0:27:01.212183 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:01.248043 INFO: Using random state 861621 for train-test-split
0:27:03.103096 INFO: Test AUC: 0.587
0:27:03.103221 INFO: Train AUC: 0.604
0:27:03.103256 INFO: AUC difference: 2.83%
0:27:03.362392 INFO: Resetting torch num_threads to 80
0:27:03.369717 PROGRESS: === Extracted 149698 precursors and 669230 fragments ===
0:27:03.370116 INFO: === FDR correction performed with classifier version 9 ===
0:27:03.370615 PROGRESS: ============================= Precursor FDR =============================
0:27:03.370711 PROGRESS: Total precursors accumulated: 279
0:27:03.370770 PROGRESS: Target precursors: 277 (99.28%)
0:27:03.370820 PROGRESS: Decoy precursors: 2 (0.72%)
0:27:03.370862 PROGRESS: 
0:27:03.370906 PROGRESS: Precursor Summary:
0:27:03.371812 PROGRESS: Channel   0:	 0.050 FDR:   277; 0.010 FDR:   277; 0.001 FDR:   266
0:27:03.371898 PROGRESS: 
0:27:03.371954 PROGRESS: Protein Summary:
0:27:03.373031 PROGRESS: Channel   0:	 0.050 FDR:   267; 0.010 FDR:   267; 0.001 FDR:   256
0:27:03.373118 PROGRESS: =========================================================================
0:27:03.375948 INFO: Target number of precursors reached.
0:27:03.422516 INFO: fragments_df: keeping 3111 of 669230 [sum(precursor_idx_mask)=6615 sum(mass_error_mask)=669230 stop_rank=3111
0:27:03.560832 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:03.676555 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:04.084681 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:04.085096 INFO: Using score_cutoff 12.67801657333374 (fac=0.99, q=1)
0:27:04.085376 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:04.085455 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:04.085510 INFO: Updating optimization_manager: score_cutoff        : 11.240489812088013 -> 12.67801657333374
0:27:04.085565 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:04.116970 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:04.202333 INFO: === checking if optimization conditions were reached ===
0:27:04.202617 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:27:04.204978 INFO: Updating optimization_manager: rt_error            : 137.9223124118572 -> 101.57762598508589
0:27:04.205102 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 101.5776.
0:27:04.205182 INFO: ==============================================
0:27:04.205263 INFO: Starting optimization step 4.
0:27:04.205333 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:04.205407 INFO: Using ng extraction backend
0:27:04.205490 PROGRESS: Extracting batch of 50293 precursors
0:27:04.318363 INFO: === Search parameters used ===
0:27:04.318635 INFO: rt_error       : 101.57762598508589
0:27:04.318699 INFO: mobility_error : 0.1
0:27:04.318748 INFO: num_candidates : 3
0:27:04.318792 INFO: ms1_error      : 30
0:27:04.318833 INFO: ms2_error      : 6.985299009071708
0:27:04.318873 INFO: fwhm_rt        : 3.0
0:27:04.318912 INFO: quant_window   : 3
0:27:04.318950 INFO: ==============================================
0:27:04.897138 INFO: performing precursor FDR with 40 features
0:27:04.897257 INFO: Decoy channel: -1
0:27:04.897283 INFO: Competetive: True
0:27:04.936208 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:04.971853 INFO: Using random state 861621 for train-test-split
0:27:06.876652 INFO: Test AUC: 0.590
0:27:06.876786 INFO: Train AUC: 0.604
0:27:06.876824 INFO: AUC difference: 2.36%
0:27:07.142090 INFO: Resetting torch num_threads to 80
0:27:07.148504 PROGRESS: === Extracted 148673 precursors and 626982 fragments ===
0:27:07.148875 INFO: === FDR correction performed with classifier version 9 ===
0:27:07.149347 PROGRESS: ============================= Precursor FDR =============================
0:27:07.149436 PROGRESS: Total precursors accumulated: 262
0:27:07.149493 PROGRESS: Target precursors: 260 (99.24%)
0:27:07.149543 PROGRESS: Decoy precursors: 2 (0.76%)
0:27:07.149588 PROGRESS: 
0:27:07.149632 PROGRESS: Precursor Summary:
0:27:07.150519 PROGRESS: Channel   0:	 0.050 FDR:   260; 0.010 FDR:   260; 0.001 FDR:   236
0:27:07.150613 PROGRESS: 
0:27:07.150669 PROGRESS: Protein Summary:
0:27:07.151719 PROGRESS: Channel   0:	 0.050 FDR:   250; 0.010 FDR:   250; 0.001 FDR:   226
0:27:07.151816 PROGRESS: =========================================================================
0:27:07.153935 INFO: Target number of precursors reached.
0:27:07.196804 INFO: fragments_df: keeping 2927 of 626982 [sum(precursor_idx_mask)=6130 sum(mass_error_mask)=626982 stop_rank=2927
0:27:07.361017 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:07.480028 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:07.868249 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:07.868670 INFO: Using score_cutoff 14.293539344215393 (fac=0.99, q=1)
0:27:07.868953 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:07.869035 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:07.869092 INFO: Updating optimization_manager: score_cutoff        : 12.67801657333374 -> 14.293539344215393
0:27:07.869144 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:07.900195 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:07.982869 INFO: === checking if optimization conditions were reached ===
0:27:07.983140 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:27:07.985432 INFO: Updating optimization_manager: rt_error            : 101.57762598508589 -> 69.6648651372815
0:27:07.985559 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 69.6649.
0:27:07.985638 INFO: ==============================================
0:27:07.985720 INFO: Starting optimization step 5.
0:27:07.985806 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:07.985879 INFO: Using ng extraction backend
0:27:07.985947 PROGRESS: Extracting batch of 50293 precursors
0:27:08.101290 INFO: === Search parameters used ===
0:27:08.101565 INFO: rt_error       : 69.6648651372815
0:27:08.101628 INFO: mobility_error : 0.1
0:27:08.101679 INFO: num_candidates : 3
0:27:08.101726 INFO: ms1_error      : 30
0:27:08.101769 INFO: ms2_error      : 6.985299009071708
0:27:08.101809 INFO: fwhm_rt        : 3.0
0:27:08.101848 INFO: quant_window   : 3
0:27:08.101887 INFO: ==============================================
0:27:08.667116 INFO: performing precursor FDR with 40 features
0:27:08.667235 INFO: Decoy channel: -1
0:27:08.667261 INFO: Competetive: True
0:27:08.703096 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:08.737281 INFO: Using random state 861621 for train-test-split
0:27:10.873035 INFO: Test AUC: 0.591
0:27:10.873151 INFO: Train AUC: 0.605
0:27:10.873180 INFO: AUC difference: 2.33%
0:27:11.139763 INFO: Resetting torch num_threads to 80
0:27:11.148810 PROGRESS: === Extracted 146076 precursors and 572316 fragments ===
0:27:11.149255 INFO: === FDR correction performed with classifier version 9 ===
0:27:11.149853 PROGRESS: ============================= Precursor FDR =============================
0:27:11.149971 PROGRESS: Total precursors accumulated: 276
0:27:11.150053 PROGRESS: Target precursors: 274 (99.28%)
0:27:11.150125 PROGRESS: Decoy precursors: 2 (0.72%)
0:27:11.150209 PROGRESS: 
0:27:11.150276 PROGRESS: Precursor Summary:
0:27:11.151450 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   274; 0.001 FDR:   215
0:27:11.151581 PROGRESS: 
0:27:11.151668 PROGRESS: Protein Summary:
0:27:11.153035 PROGRESS: Channel   0:	 0.050 FDR:   264; 0.010 FDR:   264; 0.001 FDR:   207
0:27:11.153164 PROGRESS: =========================================================================
0:27:11.156454 INFO: Target number of precursors reached.
0:27:11.221672 INFO: fragments_df: keeping 2934 of 572316 [sum(precursor_idx_mask)=6174 sum(mass_error_mask)=572316 stop_rank=2934
0:27:11.401404 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:11.520384 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:11.932966 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:11.933386 INFO: Using score_cutoff 12.624003916740417 (fac=0.99, q=1)
0:27:11.933675 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:11.933760 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:11.933820 INFO: Updating optimization_manager: score_cutoff        : 14.293539344215393 -> 12.624003916740417
0:27:11.933881 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:11.966458 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:12.043093 INFO: === checking if optimization conditions were reached ===
0:27:12.043362 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:27:12.045688 INFO: Updating optimization_manager: rt_error            : 69.6648651372815 -> 49.2916721626452
0:27:12.045802 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 49.2917.
0:27:12.045878 INFO: ==============================================
0:27:12.045972 INFO: Starting optimization step 6.
0:27:12.046044 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:12.046113 INFO: Using ng extraction backend
0:27:12.046178 PROGRESS: Extracting batch of 50293 precursors
0:27:12.136277 INFO: === Search parameters used ===
0:27:12.136537 INFO: rt_error       : 49.2916721626452
0:27:12.136594 INFO: mobility_error : 0.1
0:27:12.136652 INFO: num_candidates : 3
0:27:12.136707 INFO: ms1_error      : 30
0:27:12.136750 INFO: ms2_error      : 6.985299009071708
0:27:12.136791 INFO: fwhm_rt        : 3.0
0:27:12.136833 INFO: quant_window   : 3
0:27:12.136873 INFO: ==============================================
0:27:12.663942 INFO: performing precursor FDR with 40 features
0:27:12.664065 INFO: Decoy channel: -1
0:27:12.664090 INFO: Competetive: True
0:27:12.696317 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:12.727021 INFO: Using random state 861621 for train-test-split
0:27:14.627345 INFO: Test AUC: 0.595
0:27:14.627466 INFO: Train AUC: 0.606
0:27:14.627496 INFO: AUC difference: 1.96%
0:27:14.897434 INFO: Resetting torch num_threads to 80
0:27:14.903124 PROGRESS: === Extracted 133729 precursors and 488190 fragments ===
0:27:14.903481 INFO: === FDR correction performed with classifier version 9 ===
0:27:14.903927 PROGRESS: ============================= Precursor FDR =============================
0:27:14.904015 PROGRESS: Total precursors accumulated: 253
0:27:14.904073 PROGRESS: Target precursors: 251 (99.21%)
0:27:14.904124 PROGRESS: Decoy precursors: 2 (0.79%)
0:27:14.904169 PROGRESS: 
0:27:14.904213 PROGRESS: Precursor Summary:
0:27:14.905090 PROGRESS: Channel   0:	 0.050 FDR:   251; 0.010 FDR:   251; 0.001 FDR:   189
0:27:14.905177 PROGRESS: 
0:27:14.905233 PROGRESS: Protein Summary:
0:27:14.906265 PROGRESS: Channel   0:	 0.050 FDR:   245; 0.010 FDR:   245; 0.001 FDR:   184
0:27:14.906352 PROGRESS: =========================================================================
0:27:14.908127 INFO: Target number of precursors reached.
0:27:14.941724 INFO: fragments_df: keeping 2517 of 488190 [sum(precursor_idx_mask)=5038 sum(mass_error_mask)=488190 stop_rank=2517
0:27:15.077698 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:15.201251 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:15.522491 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:15.522925 INFO: Using score_cutoff 11.219591345787048 (fac=0.99, q=1)
0:27:15.523209 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:15.523290 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:15.523345 INFO: Updating optimization_manager: score_cutoff        : 12.624003916740417 -> 11.219591345787048
0:27:15.523400 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:15.555025 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:15.697633 INFO: === checking if optimization conditions were reached ===
0:27:15.698038 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:27:15.700105 INFO: Updating optimization_manager: rt_error            : 49.2916721626452 -> 38.95686516778016
0:27:15.700348 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 38.9569.
0:27:15.700526 INFO: ==============================================
0:27:15.700708 INFO: Starting optimization step 7.
0:27:15.700880 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:15.701054 INFO: Using ng extraction backend
0:27:15.701222 PROGRESS: Extracting batch of 50293 precursors
0:27:15.788173 INFO: === Search parameters used ===
0:27:15.788413 INFO: rt_error       : 38.95686516778016
0:27:15.788468 INFO: mobility_error : 0.1
0:27:15.788512 INFO: num_candidates : 3
0:27:15.788553 INFO: ms1_error      : 30
0:27:15.788594 INFO: ms2_error      : 6.985299009071708
0:27:15.788633 INFO: fwhm_rt        : 3.0
0:27:15.788672 INFO: quant_window   : 3
0:27:15.788710 INFO: ==============================================
0:27:16.330905 INFO: performing precursor FDR with 40 features
0:27:16.331029 INFO: Decoy channel: -1
0:27:16.331056 INFO: Competetive: True
0:27:16.370442 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:16.406721 INFO: Using random state 861621 for train-test-split
0:27:18.293527 INFO: Test AUC: 0.595
0:27:18.293653 INFO: Train AUC: 0.607
0:27:18.293684 INFO: AUC difference: 1.85%
0:27:18.583808 INFO: Resetting torch num_threads to 80
0:27:18.606316 PROGRESS: === Extracted 133664 precursors and 484391 fragments ===
0:27:18.606697 INFO: === FDR correction performed with classifier version 9 ===
0:27:18.607134 PROGRESS: ============================= Precursor FDR =============================
0:27:18.607218 PROGRESS: Total precursors accumulated: 193
0:27:18.607277 PROGRESS: Target precursors: 192 (99.48%)
0:27:18.607326 PROGRESS: Decoy precursors: 1 (0.52%)
0:27:18.607378 PROGRESS: 
0:27:18.607422 PROGRESS: Precursor Summary:
0:27:18.608286 PROGRESS: Channel   0:	 0.050 FDR:   192; 0.010 FDR:   192; 0.001 FDR:    54
0:27:18.608375 PROGRESS: 
0:27:18.608429 PROGRESS: Protein Summary:
0:27:18.609422 PROGRESS: Channel   0:	 0.050 FDR:   186; 0.010 FDR:   186; 0.001 FDR:    54
0:27:18.609506 PROGRESS: =========================================================================
0:27:18.611438 INFO: Target number of precursors not reached yet.
0:27:18.840497 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:18.872252 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:18.958661 INFO: === skipping optimization until target number of precursors are found ===
0:27:18.958962 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:27:18.959071 INFO: Starting optimization step 8.
0:27:18.959142 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:27:18.959216 INFO: Using ng extraction backend
0:27:18.959282 PROGRESS: Extracting batch of 50691 precursors
0:27:19.075347 INFO: === Search parameters used ===
0:27:19.076012 INFO: rt_error       : 38.95686516778016
0:27:19.076291 INFO: mobility_error : 0.1
0:27:19.076554 INFO: num_candidates : 3
0:27:19.076816 INFO: ms1_error      : 30
0:27:19.077103 INFO: ms2_error      : 6.985299009071708
0:27:19.077373 INFO: fwhm_rt        : 3.0
0:27:19.077644 INFO: quant_window   : 3
0:27:19.077901 INFO: ==============================================
0:27:19.695927 INFO: performing precursor FDR with 40 features
0:27:19.696041 INFO: Decoy channel: -1
0:27:19.696072 INFO: Competetive: True
0:27:19.797210 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:19.906203 INFO: Using random state 861621 for train-test-split
0:27:23.530173 INFO: Test AUC: 0.595
0:27:23.530398 INFO: Train AUC: 0.606
0:27:23.530433 INFO: AUC difference: 1.92%
0:27:23.845537 INFO: Resetting torch num_threads to 80
0:27:23.886952 PROGRESS: === Extracted 268590 precursors and 970141 fragments ===
0:27:23.887664 INFO: === FDR correction performed with classifier version 9 ===
0:27:23.888295 PROGRESS: ============================= Precursor FDR =============================
0:27:23.888383 PROGRESS: Total precursors accumulated: 432
0:27:23.888443 PROGRESS: Target precursors: 428 (99.07%)
0:27:23.888493 PROGRESS: Decoy precursors: 4 (0.93%)
0:27:23.888537 PROGRESS: 
0:27:23.888580 PROGRESS: Precursor Summary:
0:27:23.889564 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   428; 0.001 FDR:   335
0:27:23.889651 PROGRESS: 
0:27:23.889705 PROGRESS: Protein Summary:
0:27:23.890878 PROGRESS: Channel   0:	 0.050 FDR:   404; 0.010 FDR:   404; 0.001 FDR:   315
0:27:23.890966 PROGRESS: =========================================================================
0:27:23.894805 INFO: Target number of precursors reached.
0:27:23.965734 INFO: fragments_df: keeping 4437 of 970141 [sum(precursor_idx_mask)=8680 sum(mass_error_mask)=970141 stop_rank=4437
0:27:24.182879 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:24.357135 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:24.946922 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:24.947361 INFO: Using score_cutoff 11.559306282234191 (fac=0.99, q=1)
0:27:24.947681 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:24.947762 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:24.947815 INFO: Updating optimization_manager: score_cutoff        : 11.219591345787048 -> 11.559306282234191
0:27:24.947875 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:24.978889 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:25.044480 INFO: === checking if optimization conditions were reached ===
0:27:25.044721 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:27:25.046879 INFO: Updating optimization_manager: rt_error            : 38.95686516778016 -> 36.18380957821414
0:27:25.046984 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 36.1838.
0:27:25.047051 INFO: ==============================================
0:27:25.047125 INFO: Starting optimization step 9.
0:27:25.047184 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:25.047265 INFO: Using ng extraction backend
0:27:25.047341 PROGRESS: Extracting batch of 50293 precursors
0:27:25.135372 INFO: === Search parameters used ===
0:27:25.135642 INFO: rt_error       : 36.18380957821414
0:27:25.135699 INFO: mobility_error : 0.1
0:27:25.135744 INFO: num_candidates : 3
0:27:25.135799 INFO: ms1_error      : 30
0:27:25.135843 INFO: ms2_error      : 6.985299009071708
0:27:25.135885 INFO: fwhm_rt        : 3.0
0:27:25.135926 INFO: quant_window   : 3
0:27:25.135966 INFO: ==============================================
0:27:25.630194 INFO: performing precursor FDR with 40 features
0:27:25.630316 INFO: Decoy channel: -1
0:27:25.630341 INFO: Competetive: True
0:27:25.663652 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:25.698000 INFO: Using random state 861621 for train-test-split
0:27:27.647544 INFO: Test AUC: 0.595
0:27:27.647667 INFO: Train AUC: 0.606
0:27:27.647698 INFO: AUC difference: 1.94%
0:27:27.914016 INFO: Resetting torch num_threads to 80
0:27:27.919696 PROGRESS: === Extracted 133765 precursors and 484594 fragments ===
0:27:27.920053 INFO: === FDR correction performed with classifier version 9 ===
0:27:27.920506 PROGRESS: ============================= Precursor FDR =============================
0:27:27.920594 PROGRESS: Total precursors accumulated: 236
0:27:27.920651 PROGRESS: Target precursors: 234 (99.15%)
0:27:27.920701 PROGRESS: Decoy precursors: 2 (0.85%)
0:27:27.920744 PROGRESS: 
0:27:27.920787 PROGRESS: Precursor Summary:
0:27:27.921672 PROGRESS: Channel   0:	 0.050 FDR:   234; 0.010 FDR:   234; 0.001 FDR:   174
0:27:27.921757 PROGRESS: 
0:27:27.921811 PROGRESS: Protein Summary:
0:27:27.922842 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:   170
0:27:27.922932 PROGRESS: =========================================================================
0:27:27.924713 INFO: Target number of precursors reached.
0:27:27.957893 INFO: fragments_df: keeping 2381 of 484594 [sum(precursor_idx_mask)=4679 sum(mass_error_mask)=484594 stop_rank=2381
0:27:28.095041 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:28.219622 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:28.531111 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:28.531530 INFO: Using score_cutoff 11.908289637851716 (fac=0.99, q=1)
0:27:28.531815 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:28.531894 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:28.531950 INFO: Updating optimization_manager: score_cutoff        : 11.559306282234191 -> 11.908289637851716
0:27:28.532002 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:28.563146 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:28.626518 INFO: === checking if optimization conditions were reached ===
0:27:28.626778 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:27:28.628715 INFO: Updating optimization_manager: rt_error            : 36.18380957821414 -> 33.36358368211233
0:27:28.628818 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 33.3636.
0:27:28.628884 INFO: ==============================================
0:27:28.628953 INFO: Starting optimization step 10.
0:27:28.629013 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:28.629072 INFO: Using ng extraction backend
0:27:28.629132 PROGRESS: Extracting batch of 50293 precursors
0:27:28.724393 INFO: === Search parameters used ===
0:27:28.724930 INFO: rt_error       : 33.36358368211233
0:27:28.725174 INFO: mobility_error : 0.1
0:27:28.725396 INFO: num_candidates : 3
0:27:28.725611 INFO: ms1_error      : 30
0:27:28.725821 INFO: ms2_error      : 6.985299009071708
0:27:28.726029 INFO: fwhm_rt        : 3.0
0:27:28.726234 INFO: quant_window   : 3
0:27:28.726440 INFO: ==============================================
0:27:29.243658 INFO: performing precursor FDR with 40 features
0:27:29.243775 INFO: Decoy channel: -1
0:27:29.243807 INFO: Competetive: True
0:27:29.278629 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:29.309904 INFO: Using random state 861621 for train-test-split
0:27:31.144323 INFO: Test AUC: 0.594
0:27:31.144442 INFO: Train AUC: 0.606
0:27:31.144479 INFO: AUC difference: 1.99%
0:27:31.409776 INFO: Resetting torch num_threads to 80
0:27:31.415670 PROGRESS: === Extracted 133742 precursors and 484244 fragments ===
0:27:31.416054 INFO: === FDR correction performed with classifier version 9 ===
0:27:31.416533 PROGRESS: ============================= Precursor FDR =============================
0:27:31.416631 PROGRESS: Total precursors accumulated: 226
0:27:31.416703 PROGRESS: Target precursors: 224 (99.12%)
0:27:31.416764 PROGRESS: Decoy precursors: 2 (0.88%)
0:27:31.416820 PROGRESS: 
0:27:31.416874 PROGRESS: Precursor Summary:
0:27:31.417869 PROGRESS: Channel   0:	 0.050 FDR:   224; 0.010 FDR:   224; 0.001 FDR:   165
0:27:31.417964 PROGRESS: 
0:27:31.418033 PROGRESS: Protein Summary:
0:27:31.419147 PROGRESS: Channel   0:	 0.050 FDR:   219; 0.010 FDR:   219; 0.001 FDR:   161
0:27:31.419256 PROGRESS: =========================================================================
0:27:31.421286 INFO: Target number of precursors reached.
0:27:31.453920 INFO: fragments_df: keeping 2294 of 484244 [sum(precursor_idx_mask)=4504 sum(mass_error_mask)=484244 stop_rank=2294
0:27:31.590047 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:31.688224 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:31.940893 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:31.941341 INFO: Using score_cutoff 13.119761001777649 (fac=0.99, q=1)
0:27:31.941654 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:31.941742 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:31.941810 INFO: Updating optimization_manager: score_cutoff        : 11.908289637851716 -> 13.119761001777649
0:27:31.941877 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:31.973196 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:32.037962 INFO: === checking if optimization conditions were reached ===
0:27:32.038224 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:27:32.040198 INFO: Updating optimization_manager: rt_error            : 33.36358368211233 -> 35.239817867142165
0:27:32.040300 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 35.2398.
0:27:32.040365 INFO: ==============================================
0:27:32.040432 INFO: Starting optimization step 11.
0:27:32.040489 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:32.040547 INFO: Using ng extraction backend
0:27:32.040603 PROGRESS: Extracting batch of 50293 precursors
0:27:32.130135 INFO: === Search parameters used ===
0:27:32.130397 INFO: rt_error       : 35.239817867142165
0:27:32.130459 INFO: mobility_error : 0.1
0:27:32.130507 INFO: num_candidates : 3
0:27:32.130551 INFO: ms1_error      : 30
0:27:32.130605 INFO: ms2_error      : 6.985299009071708
0:27:32.130646 INFO: fwhm_rt        : 3.0
0:27:32.130686 INFO: quant_window   : 3
0:27:32.130725 INFO: ==============================================
0:27:32.631863 INFO: performing precursor FDR with 40 features
0:27:32.631981 INFO: Decoy channel: -1
0:27:32.632008 INFO: Competetive: True
0:27:32.665510 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:32.696353 INFO: Using random state 861621 for train-test-split
0:27:34.487327 INFO: Test AUC: 0.588
0:27:34.487446 INFO: Train AUC: 0.609
0:27:34.487477 INFO: AUC difference: 3.34%
0:27:34.749522 INFO: Resetting torch num_threads to 80
0:27:34.755355 PROGRESS: === Extracted 133563 precursors and 482794 fragments ===
0:27:34.755702 INFO: === FDR correction performed with classifier version 9 ===
0:27:34.756159 PROGRESS: ============================= Precursor FDR =============================
0:27:34.756248 PROGRESS: Total precursors accumulated: 241
0:27:34.756304 PROGRESS: Target precursors: 239 (99.17%)
0:27:34.756356 PROGRESS: Decoy precursors: 2 (0.83%)
0:27:34.756401 PROGRESS: 
0:27:34.756444 PROGRESS: Precursor Summary:
0:27:34.757324 PROGRESS: Channel   0:	 0.050 FDR:   239; 0.010 FDR:   239; 0.001 FDR:   149
0:27:34.757410 PROGRESS: 
0:27:34.757466 PROGRESS: Protein Summary:
0:27:34.758483 PROGRESS: Channel   0:	 0.050 FDR:   234; 0.010 FDR:   234; 0.001 FDR:   145
0:27:34.758582 PROGRESS: =========================================================================
0:27:34.760459 INFO: Target number of precursors reached.
0:27:34.793571 INFO: fragments_df: keeping 2394 of 482794 [sum(precursor_idx_mask)=4754 sum(mass_error_mask)=482794 stop_rank=2394
0:27:34.930259 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:35.051596 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:35.315379 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:35.315798 INFO: Using score_cutoff 11.994407211112977 (fac=0.99, q=1)
0:27:35.316090 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:35.316170 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:35.316224 INFO: Updating optimization_manager: score_cutoff        : 13.119761001777649 -> 11.994407211112977
0:27:35.316277 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:35.347599 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:35.412299 INFO: === checking if optimization conditions were reached ===
0:27:35.412579 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
0:27:35.414857 INFO: Updating optimization_manager: rt_error            : 35.239817867142165 -> 32.16373412629726
0:27:35.414976 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 32.1637.
0:27:35.415053 INFO: ==============================================
0:27:35.415133 INFO: Starting optimization step 12.
0:27:35.415203 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:35.415290 INFO: Using ng extraction backend
0:27:35.415365 PROGRESS: Extracting batch of 50293 precursors
0:27:35.504931 INFO: === Search parameters used ===
0:27:35.505193 INFO: rt_error       : 32.16373412629726
0:27:35.505253 INFO: mobility_error : 0.1
0:27:35.505300 INFO: num_candidates : 3
0:27:35.505343 INFO: ms1_error      : 30
0:27:35.505382 INFO: ms2_error      : 6.985299009071708
0:27:35.505422 INFO: fwhm_rt        : 3.0
0:27:35.505462 INFO: quant_window   : 3
0:27:35.505502 INFO: ==============================================
0:27:36.000525 INFO: performing precursor FDR with 40 features
0:27:36.000640 INFO: Decoy channel: -1
0:27:36.000667 INFO: Competetive: True
0:27:36.035046 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:36.066061 INFO: Using random state 861621 for train-test-split
0:27:37.843151 INFO: Test AUC: 0.594
0:27:37.843268 INFO: Train AUC: 0.608
0:27:37.843303 INFO: AUC difference: 2.24%
0:27:38.106822 INFO: Resetting torch num_threads to 80
0:27:38.112518 PROGRESS: === Extracted 133559 precursors and 482244 fragments ===
0:27:38.112872 INFO: === FDR correction performed with classifier version 9 ===
0:27:38.113330 PROGRESS: ============================= Precursor FDR =============================
0:27:38.113418 PROGRESS: Total precursors accumulated: 239
0:27:38.113475 PROGRESS: Target precursors: 237 (99.16%)
0:27:38.113524 PROGRESS: Decoy precursors: 2 (0.84%)
0:27:38.113568 PROGRESS: 
0:27:38.113611 PROGRESS: Precursor Summary:
0:27:38.114486 PROGRESS: Channel   0:	 0.050 FDR:   237; 0.010 FDR:   237; 0.001 FDR:   203
0:27:38.114583 PROGRESS: 
0:27:38.114640 PROGRESS: Protein Summary:
0:27:38.115670 PROGRESS: Channel   0:	 0.050 FDR:   232; 0.010 FDR:   232; 0.001 FDR:   199
0:27:38.115757 PROGRESS: =========================================================================
0:27:38.117517 INFO: Target number of precursors reached.
0:27:38.150580 INFO: fragments_df: keeping 2392 of 482244 [sum(precursor_idx_mask)=4799 sum(mass_error_mask)=482244 stop_rank=2392
0:27:38.286234 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:38.385951 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:38.649032 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:38.649449 INFO: Using score_cutoff 11.962288764953612 (fac=0.99, q=1)
0:27:38.649734 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:38.649814 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:38.649869 INFO: Updating optimization_manager: score_cutoff        : 11.994407211112977 -> 11.962288764953612
0:27:38.649922 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:38.680830 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:38.743593 INFO: === checking if optimization conditions were reached ===
0:27:38.743866 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
0:27:38.746167 INFO: Updating optimization_manager: rt_error            : 32.16373412629726 -> 32.91828917758878
0:27:38.746282 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 32.9183.
0:27:38.746357 INFO: ==============================================
0:27:38.746444 INFO: Starting optimization step 13.
0:27:38.746514 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:38.746596 INFO: Using ng extraction backend
0:27:38.746666 PROGRESS: Extracting batch of 50293 precursors
0:27:38.836124 INFO: === Search parameters used ===
0:27:38.836387 INFO: rt_error       : 32.91828917758878
0:27:38.836441 INFO: mobility_error : 0.1
0:27:38.836488 INFO: num_candidates : 3
0:27:38.836532 INFO: ms1_error      : 30
0:27:38.836572 INFO: ms2_error      : 6.985299009071708
0:27:38.836613 INFO: fwhm_rt        : 3.0
0:27:38.836653 INFO: quant_window   : 3
0:27:38.836692 INFO: ==============================================
0:27:39.337963 INFO: performing precursor FDR with 40 features
0:27:39.338083 INFO: Decoy channel: -1
0:27:39.338110 INFO: Competetive: True
0:27:39.371596 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:39.402193 INFO: Using random state 861621 for train-test-split
0:27:41.254365 INFO: Test AUC: 0.596
0:27:41.254483 INFO: Train AUC: 0.607
0:27:41.254515 INFO: AUC difference: 1.87%
0:27:41.518849 INFO: Resetting torch num_threads to 80
0:27:41.524603 PROGRESS: === Extracted 133497 precursors and 481416 fragments ===
0:27:41.524951 INFO: === FDR correction performed with classifier version 9 ===
0:27:41.525407 PROGRESS: ============================= Precursor FDR =============================
0:27:41.525495 PROGRESS: Total precursors accumulated: 234
0:27:41.525552 PROGRESS: Target precursors: 232 (99.15%)
0:27:41.525602 PROGRESS: Decoy precursors: 2 (0.85%)
0:27:41.525646 PROGRESS: 
0:27:41.525689 PROGRESS: Precursor Summary:
0:27:41.526587 PROGRESS: Channel   0:	 0.050 FDR:   232; 0.010 FDR:   232; 0.001 FDR:   171
0:27:41.526685 PROGRESS: 
0:27:41.526743 PROGRESS: Protein Summary:
0:27:41.527778 PROGRESS: Channel   0:	 0.050 FDR:   227; 0.010 FDR:   227; 0.001 FDR:   166
0:27:41.527867 PROGRESS: =========================================================================
0:27:41.529672 INFO: Target number of precursors reached.
0:27:41.562621 INFO: fragments_df: keeping 2364 of 481416 [sum(precursor_idx_mask)=4649 sum(mass_error_mask)=481416 stop_rank=2364
0:27:41.699905 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:41.797507 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:42.059142 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:42.059558 INFO: Using score_cutoff 11.173868868541717 (fac=0.99, q=1)
0:27:42.059840 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:42.059920 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:42.059973 INFO: Updating optimization_manager: score_cutoff        : 11.962288764953612 -> 11.173868868541717
0:27:42.060025 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:42.090932 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:42.156458 INFO: === checking if optimization conditions were reached ===
0:27:42.156735 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
0:27:42.158035 INFO: Updating optimization_manager: rt_error            : 32.91828917758878 -> 49.2916721626452
0:27:42.158177 INFO: Updating optimization_manager: classifier_version  : 9 -> 18
0:27:42.158301 INFO: Updating optimization_manager: score_cutoff        : 11.173868868541717 -> 11.219591345787048
0:27:42.158409 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:42.158509 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:42.158647 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 49.2917 found after 12 searches.
0:27:42.158727 INFO: ==============================================
0:27:42.158821 PROGRESS: Optimization finished for rt_error.
0:27:42.306457 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:42.337736 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:42.433674 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:27:42.433899 PROGRESS: ==============================================
0:27:42.433984 PROGRESS: ms2_error      : 6.9853
0:27:42.434049 PROGRESS: rt_error       : 49.2917
0:27:42.434103 PROGRESS: ==============================================
0:27:42.435022 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:50.330291 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:08.006518 INFO: Using ng extraction backend
0:28:08.006832 PROGRESS: Extracting batch of 12001526 precursors
0:28:23.895313 INFO: === Search parameters used ===
0:28:23.895799 INFO: rt_error       : 49.2916721626452
0:28:23.895864 INFO: mobility_error : 0.1
0:28:23.895924 INFO: num_candidates : 3
0:28:23.895968 INFO: ms1_error      : 30
0:28:23.896022 INFO: ms2_error      : 6.985299009071708
0:28:23.896081 INFO: fwhm_rt        : 3.0
0:28:23.896125 INFO: quant_window   : 3
0:28:23.896165 INFO: ==============================================
0:28:43.748318 INFO: Removed 26485359 precursors with score below cutoff 11.219591345787048
0:28:49.416867 INFO: performing precursor FDR with 40 features
0:28:49.416992 INFO: Decoy channel: -1
0:28:49.417025 INFO: Competetive: True
0:28:49.954138 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:52.057825 INFO: Using random state 990116 for train-test-split
0:30:08.954853 INFO: Test AUC: 0.634
0:30:08.955128 INFO: Train AUC: 0.637
0:30:08.955168 INFO: AUC difference: 0.43%
0:30:10.906677 INFO: Resetting torch num_threads to 80
0:30:12.408755 PROGRESS: ============================= Precursor FDR =============================
0:30:12.409052 PROGRESS: Total precursors accumulated: 71,616
0:30:12.409122 PROGRESS: Target precursors: 70,907 (99.01%)
0:30:12.409175 PROGRESS: Decoy precursors: 709 (0.99%)
0:30:12.409226 PROGRESS: 
0:30:12.409269 PROGRESS: Precursor Summary:
0:30:12.428778 PROGRESS: Channel   0:	 0.050 FDR: 70,907; 0.010 FDR: 70,907; 0.001 FDR: 48,564
0:30:12.429029 PROGRESS: 
0:30:12.429090 PROGRESS: Protein Summary:
0:30:12.455666 PROGRESS: Channel   0:	 0.050 FDR: 12,164; 0.010 FDR: 12,164; 0.001 FDR: 8,919
0:30:12.455902 PROGRESS: =========================================================================
0:30:12.489750 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
0:30:12.629945 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
0:30:12.835950 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:30:13.497275 PROGRESS: 
0:30:13.497426 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant
0:30:13.497496 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
0:30:13.497663 INFO: Initializing TimingManager
0:30:13.498108 INFO: Initializing RawFileManager
0:30:27.331087 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:30:27.335468 INFO: Determining DIA cycle
0:30:27.351855 INFO: Found cycle with start 0.00 min and length 300.
0:30:27.524034 INFO: RT (min)            : 0.0 - 26.9
0:30:27.524129 INFO: RT duration (sec)   : 1611.2
0:30:27.524161 INFO: RT duration (min)   : 26.9
0:30:27.524186 INFO: Cycle len (scans)   : 300
0:30:27.524204 INFO: Cycle len (sec)     : 1.65
0:30:27.524221 INFO: Number of cycles    : 978
0:30:27.524239 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:30:27.524309 INFO: Creating DIA data object took: 14.026103258132935
0:30:28.192597 INFO: Creating DIA data NG object took: 0.6681578159332275
0:30:29.909431 INFO: Initializing CalibrationManager
0:30:29.909710 INFO: Setting up calibration estimators ..
0:30:29.909769 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:30:29.909868 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'}' ..
0:30:29.909962 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:30:29.910018 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:30:29.910072 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}}' ..
0:30:29.910125 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:30:29.910172 INFO: Done setting up calibration estimators.
0:30:29.910378 INFO: Initializing OptimizationManager
0:30:29.910522 INFO: initial parameter: ms1_error = 30
0:30:29.910584 INFO: initial parameter: ms2_error = 30
0:30:29.910633 INFO: initial parameter: rt_error = 805.611083984375
0:30:29.910676 INFO: initial parameter: mobility_error = 0.1
0:30:29.910716 INFO: initial parameter: num_candidates = 1
0:30:29.910755 INFO: initial parameter: fwhm_rt = 5
0:30:29.910795 INFO: initial parameter: fwhm_mobility = 0.01
0:30:29.910833 INFO: initial parameter: score_cutoff = 0
0:30:29.910871 INFO: initial parameter: classifier_version = -1
0:30:29.910947 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:30:29.911305 INFO: FDRManager: loading saved state not requested, will be initialized.
0:30:29.911343 INFO: Initializing FDRManager
0:30:29.911384 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:30:31.108428 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:30:31.841715 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:30:31.842070 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
0:30:31.842171 PROGRESS: Starting initial search for precursors.
0:30:31.842255 INFO: Starting optimization step 0.
0:30:31.842318 PROGRESS: === Extracting elution groups 0 to 200 ===
0:30:31.842379 INFO: Using ng extraction backend
0:30:31.842448 PROGRESS: Extracting batch of 396 precursors
0:30:31.844356 INFO: === Search parameters used ===
0:30:31.844455 INFO: rt_error       : 805.611083984375
0:30:31.844506 INFO: mobility_error : 0.1
0:30:31.844551 INFO: num_candidates : 1
0:30:31.844591 INFO: ms1_error      : 30
0:30:31.844630 INFO: ms2_error      : 30
0:30:31.844671 INFO: fwhm_rt        : 5
0:30:31.844709 INFO: quant_window   : 3
0:30:31.844748 INFO: ==============================================
0:30:31.863858 INFO: performing precursor FDR with 40 features
0:30:31.863922 INFO: Decoy channel: -1
0:30:31.863947 INFO: Competetive: True
0:30:31.864866 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:31.867376 INFO: Using random state 751901 for train-test-split
0:30:31.875042 INFO: Test AUC: 0.536
0:30:31.875100 INFO: Train AUC: 0.508
0:30:31.875131 INFO: AUC difference: 5.51%
0:30:31.875153 WARNING: AUC difference > 5%. This may indicate overfitting.
0:30:33.309426 INFO: Resetting torch num_threads to 80
0:30:33.310749 PROGRESS: === Extracted 393 precursors and 1907 fragments ===
0:30:33.311084 INFO: === FDR correction performed with classifier version -1 ===
0:30:33.311520 PROGRESS: ============================= Precursor FDR =============================
0:30:33.311602 PROGRESS: Total precursors accumulated: 0
0:30:33.311660 PROGRESS: Target precursors: 0 (0.00%)
0:30:33.311718 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:33.311763 PROGRESS: 
0:30:33.311806 PROGRESS: Precursor Summary:
0:30:33.311911 PROGRESS: 
0:30:33.311971 PROGRESS: Protein Summary:
0:30:33.312041 PROGRESS: =========================================================================
0:30:33.312197 INFO: Target number of precursors not reached yet.
0:30:33.376612 INFO: Starting optimization step 1.
0:30:33.376830 PROGRESS: === Extracting elution groups 200 to 600 ===
0:30:33.376909 INFO: Using ng extraction backend
0:30:33.376968 PROGRESS: Extracting batch of 786 precursors
0:30:33.379593 INFO: === Search parameters used ===
0:30:33.379691 INFO: rt_error       : 805.611083984375
0:30:33.379746 INFO: mobility_error : 0.1
0:30:33.379789 INFO: num_candidates : 1
0:30:33.379829 INFO: ms1_error      : 30
0:30:33.379868 INFO: ms2_error      : 30
0:30:33.379908 INFO: fwhm_rt        : 5
0:30:33.379947 INFO: quant_window   : 3
0:30:33.379985 INFO: ==============================================
0:30:33.432398 INFO: performing precursor FDR with 40 features
0:30:33.432480 INFO: Decoy channel: -1
0:30:33.432505 INFO: Competetive: True
0:30:33.435410 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:33.436993 INFO: Using random state 431770 for train-test-split
0:30:33.445189 INFO: Test AUC: 0.513
0:30:33.445244 INFO: Train AUC: 0.506
0:30:33.445274 INFO: AUC difference: 1.27%
0:30:33.654595 INFO: Resetting torch num_threads to 80
0:30:33.656651 PROGRESS: === Extracted 1172 precursors and 5583 fragments ===
0:30:33.656999 INFO: === FDR correction performed with classifier version -1 ===
0:30:33.657429 PROGRESS: ============================= Precursor FDR =============================
0:30:33.657515 PROGRESS: Total precursors accumulated: 0
0:30:33.657573 PROGRESS: Target precursors: 0 (0.00%)
0:30:33.657624 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:33.657667 PROGRESS: 
0:30:33.657710 PROGRESS: Precursor Summary:
0:30:33.657819 PROGRESS: 
0:30:33.657885 PROGRESS: Protein Summary:
0:30:33.657966 PROGRESS: =========================================================================
0:30:33.658143 INFO: Target number of precursors not reached yet.
0:30:33.725127 INFO: Starting optimization step 2.
0:30:33.725333 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:30:33.725414 INFO: Using ng extraction backend
0:30:33.725482 PROGRESS: Extracting batch of 1592 precursors
0:30:33.730045 INFO: === Search parameters used ===
0:30:33.730177 INFO: rt_error       : 805.611083984375
0:30:33.730229 INFO: mobility_error : 0.1
0:30:33.730274 INFO: num_candidates : 1
0:30:33.730323 INFO: ms1_error      : 30
0:30:33.730362 INFO: ms2_error      : 30
0:30:33.730403 INFO: fwhm_rt        : 5
0:30:33.730443 INFO: quant_window   : 3
0:30:33.730484 INFO: ==============================================
0:30:33.776424 INFO: performing precursor FDR with 40 features
0:30:33.776512 INFO: Decoy channel: -1
0:30:33.776536 INFO: Competetive: True
0:30:33.779783 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:33.781651 INFO: Using random state 29062 for train-test-split
0:30:33.793592 INFO: Test AUC: 0.534
0:30:33.793658 INFO: Train AUC: 0.503
0:30:33.793687 INFO: AUC difference: 6.14%
0:30:33.793708 WARNING: AUC difference > 5%. This may indicate overfitting.
0:30:34.006830 INFO: Resetting torch num_threads to 80
0:30:34.009315 PROGRESS: === Extracted 2760 precursors and 13238 fragments ===
0:30:34.009659 INFO: === FDR correction performed with classifier version -1 ===
0:30:34.010109 PROGRESS: ============================= Precursor FDR =============================
0:30:34.010197 PROGRESS: Total precursors accumulated: 1
0:30:34.010255 PROGRESS: Target precursors: 1 (100.00%)
0:30:34.010303 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:34.010346 PROGRESS: 
0:30:34.010397 PROGRESS: Precursor Summary:
0:30:34.011313 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:30:34.011405 PROGRESS: 
0:30:34.011461 PROGRESS: Protein Summary:
0:30:34.012452 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:30:34.012551 PROGRESS: =========================================================================
0:30:34.012752 INFO: Target number of precursors not reached yet.
0:30:34.082762 INFO: Starting optimization step 3.
0:30:34.082967 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:30:34.083050 INFO: Using ng extraction backend
0:30:34.083116 PROGRESS: Extracting batch of 3177 precursors
0:30:34.090627 INFO: === Search parameters used ===
0:30:34.090773 INFO: rt_error       : 805.611083984375
0:30:34.090826 INFO: mobility_error : 0.1
0:30:34.090873 INFO: num_candidates : 1
0:30:34.090919 INFO: ms1_error      : 30
0:30:34.090960 INFO: ms2_error      : 30
0:30:34.090999 INFO: fwhm_rt        : 5
0:30:34.091038 INFO: quant_window   : 3
0:30:34.091077 INFO: ==============================================
0:30:34.137981 INFO: performing precursor FDR with 40 features
0:30:34.138073 INFO: Decoy channel: -1
0:30:34.138098 INFO: Competetive: True
0:30:34.142200 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:34.144463 INFO: Using random state 228962 for train-test-split
0:30:34.164551 INFO: Test AUC: 0.520
0:30:34.164637 INFO: Train AUC: 0.507
0:30:34.164667 INFO: AUC difference: 2.48%
0:30:34.378062 INFO: Resetting torch num_threads to 80
0:30:34.381305 PROGRESS: === Extracted 5916 precursors and 28236 fragments ===
0:30:34.381664 INFO: === FDR correction performed with classifier version -1 ===
0:30:34.382130 PROGRESS: ============================= Precursor FDR =============================
0:30:34.382219 PROGRESS: Total precursors accumulated: 1
0:30:34.382278 PROGRESS: Target precursors: 1 (100.00%)
0:30:34.382329 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:34.382374 PROGRESS: 
0:30:34.382418 PROGRESS: Precursor Summary:
0:30:34.383329 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:30:34.383419 PROGRESS: 
0:30:34.383475 PROGRESS: Protein Summary:
0:30:34.384465 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:30:34.384554 PROGRESS: =========================================================================
0:30:34.384798 INFO: Target number of precursors not reached yet.
0:30:34.459595 INFO: Starting optimization step 4.
0:30:34.459816 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:30:34.459898 INFO: Using ng extraction backend
0:30:34.459961 PROGRESS: Extracting batch of 6340 precursors
0:30:34.472542 INFO: === Search parameters used ===
0:30:34.472709 INFO: rt_error       : 805.611083984375
0:30:34.472759 INFO: mobility_error : 0.1
0:30:34.472806 INFO: num_candidates : 1
0:30:34.472852 INFO: ms1_error      : 30
0:30:34.472903 INFO: ms2_error      : 30
0:30:34.472947 INFO: fwhm_rt        : 5
0:30:34.472987 INFO: quant_window   : 3
0:30:34.473026 INFO: ==============================================
0:30:34.544577 INFO: performing precursor FDR with 40 features
0:30:34.544694 INFO: Decoy channel: -1
0:30:34.544721 INFO: Competetive: True
0:30:34.550483 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:34.553823 INFO: Using random state 353022 for train-test-split
0:30:34.592765 INFO: Test AUC: 0.524
0:30:34.592879 INFO: Train AUC: 0.506
0:30:34.592908 INFO: AUC difference: 3.70%
0:30:34.816542 INFO: Resetting torch num_threads to 80
0:30:34.820787 PROGRESS: === Extracted 12186 precursors and 57773 fragments ===
0:30:34.821154 INFO: === FDR correction performed with classifier version -1 ===
0:30:34.821619 PROGRESS: ============================= Precursor FDR =============================
0:30:34.821709 PROGRESS: Total precursors accumulated: 4
0:30:34.821768 PROGRESS: Target precursors: 4 (100.00%)
0:30:34.821816 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:34.821862 PROGRESS: 
0:30:34.821905 PROGRESS: Precursor Summary:
0:30:34.822832 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:30:34.822919 PROGRESS: 
0:30:34.822975 PROGRESS: Protein Summary:
0:30:34.823976 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:30:34.824070 PROGRESS: =========================================================================
0:30:34.824369 INFO: Target number of precursors not reached yet.
0:30:34.907496 INFO: Starting optimization step 5.
0:30:34.907734 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:30:34.907816 INFO: Using ng extraction backend
0:30:34.907898 PROGRESS: Extracting batch of 12663 precursors
0:30:34.931187 INFO: === Search parameters used ===
0:30:34.931368 INFO: rt_error       : 805.611083984375
0:30:34.931420 INFO: mobility_error : 0.1
0:30:34.931468 INFO: num_candidates : 1
0:30:34.931512 INFO: ms1_error      : 30
0:30:34.931553 INFO: ms2_error      : 30
0:30:34.931593 INFO: fwhm_rt        : 5
0:30:34.931631 INFO: quant_window   : 3
0:30:34.931669 INFO: ==============================================
0:30:35.065801 INFO: performing precursor FDR with 40 features
0:30:35.065908 INFO: Decoy channel: -1
0:30:35.065934 INFO: Competetive: True
0:30:35.077633 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:35.083846 INFO: Using random state 433367 for train-test-split
0:30:35.325703 INFO: Test AUC: 0.545
0:30:35.325810 INFO: Train AUC: 0.547
0:30:35.325840 INFO: AUC difference: 0.41%
0:30:35.554620 INFO: Resetting torch num_threads to 80
0:30:35.561041 PROGRESS: === Extracted 24708 precursors and 116540 fragments ===
0:30:35.561431 INFO: === FDR correction performed with classifier version -1 ===
0:30:35.561916 PROGRESS: ============================= Precursor FDR =============================
0:30:35.562039 PROGRESS: Total precursors accumulated: 1
0:30:35.562101 PROGRESS: Target precursors: 1 (100.00%)
0:30:35.562152 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:35.562199 PROGRESS: 
0:30:35.562242 PROGRESS: Precursor Summary:
0:30:35.563189 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:30:35.563282 PROGRESS: 
0:30:35.563340 PROGRESS: Protein Summary:
0:30:35.564373 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:30:35.564472 PROGRESS: =========================================================================
0:30:35.564923 INFO: Target number of precursors not reached yet.
0:30:35.664984 INFO: Starting optimization step 6.
0:30:35.665227 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:30:35.665311 INFO: Using ng extraction backend
0:30:35.665375 PROGRESS: Extracting batch of 25339 precursors
0:30:35.710244 INFO: === Search parameters used ===
0:30:35.710472 INFO: rt_error       : 805.611083984375
0:30:35.710527 INFO: mobility_error : 0.1
0:30:35.710588 INFO: num_candidates : 1
0:30:35.710639 INFO: ms1_error      : 30
0:30:35.710686 INFO: ms2_error      : 30
0:30:35.710729 INFO: fwhm_rt        : 5
0:30:35.710771 INFO: quant_window   : 3
0:30:35.710812 INFO: ==============================================
0:30:35.926118 INFO: performing precursor FDR with 40 features
0:30:35.926234 INFO: Decoy channel: -1
0:30:35.926260 INFO: Competetive: True
0:30:35.945430 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:35.956678 INFO: Using random state 387068 for train-test-split
0:30:36.523025 INFO: Test AUC: 0.554
0:30:36.523142 INFO: Train AUC: 0.582
0:30:36.523172 INFO: AUC difference: 4.78%
0:30:36.762878 INFO: Resetting torch num_threads to 80
0:30:36.773242 PROGRESS: === Extracted 49785 precursors and 233156 fragments ===
0:30:36.773738 INFO: === FDR correction performed with classifier version -1 ===
0:30:36.774261 PROGRESS: ============================= Precursor FDR =============================
0:30:36.774351 PROGRESS: Total precursors accumulated: 19
0:30:36.774412 PROGRESS: Target precursors: 19 (100.00%)
0:30:36.774462 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:36.774518 PROGRESS: 
0:30:36.774572 PROGRESS: Precursor Summary:
0:30:36.775522 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:30:36.775611 PROGRESS: 
0:30:36.775669 PROGRESS: Protein Summary:
0:30:36.776733 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:30:36.776826 PROGRESS: =========================================================================
0:30:36.777580 INFO: Target number of precursors not reached yet.
0:30:36.911516 INFO: Starting optimization step 7.
0:30:36.911760 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:30:36.911845 INFO: Using ng extraction backend
0:30:36.911910 PROGRESS: Extracting batch of 50691 precursors
0:30:36.999454 INFO: === Search parameters used ===
0:30:36.999699 INFO: rt_error       : 805.611083984375
0:30:36.999753 INFO: mobility_error : 0.1
0:30:36.999800 INFO: num_candidates : 1
0:30:36.999846 INFO: ms1_error      : 30
0:30:36.999888 INFO: ms2_error      : 30
0:30:36.999930 INFO: fwhm_rt        : 5
0:30:36.999971 INFO: quant_window   : 3
0:30:37.000012 INFO: ==============================================
0:30:37.369038 INFO: performing precursor FDR with 40 features
0:30:37.369152 INFO: Decoy channel: -1
0:30:37.369179 INFO: Competetive: True
0:30:37.408946 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:37.433795 INFO: Using random state 465003 for train-test-split
0:30:38.771122 INFO: Test AUC: 0.579
0:30:38.771676 INFO: Train AUC: 0.593
0:30:38.771721 INFO: AUC difference: 2.47%
0:30:39.021797 INFO: Resetting torch num_threads to 80
0:30:39.040351 PROGRESS: === Extracted 99985 precursors and 468362 fragments ===
0:30:39.040887 INFO: === FDR correction performed with classifier version -1 ===
0:30:39.041420 PROGRESS: ============================= Precursor FDR =============================
0:30:39.041523 PROGRESS: Total precursors accumulated: 242
0:30:39.041584 PROGRESS: Target precursors: 240 (99.17%)
0:30:39.041635 PROGRESS: Decoy precursors: 2 (0.83%)
0:30:39.041683 PROGRESS: 
0:30:39.041727 PROGRESS: Precursor Summary:
0:30:39.042631 PROGRESS: Channel   0:	 0.050 FDR:   240; 0.010 FDR:   240; 0.001 FDR:     0
0:30:39.042725 PROGRESS: 
0:30:39.042781 PROGRESS: Protein Summary:
0:30:39.043816 PROGRESS: Channel   0:	 0.050 FDR:   222; 0.010 FDR:   222; 0.001 FDR:     0
0:30:39.043907 PROGRESS: =========================================================================
0:30:39.045176 INFO: Target number of precursors reached.
0:30:39.080352 INFO: fragments_df: keeping 2171 of 468362 [sum(precursor_idx_mask)=2624 sum(mass_error_mask)=468362 stop_rank=2171
0:30:39.285514 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:39.407705 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:39.680719 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:30:39.681142 INFO: Using score_cutoff 14.8951129986763 (fac=0.99, q=1)
0:30:39.681426 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:30:39.681506 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:30:39.681569 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.8951129986763
0:30:39.681624 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:39.760419 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:39.912422 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:30:39.912685 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:30:39.912790 INFO: Starting optimization step 8.
0:30:39.912863 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:30:39.912940 INFO: Using ng extraction backend
0:30:39.913008 PROGRESS: Extracting batch of 100984 precursors
0:30:40.088582 INFO: === Search parameters used ===
0:30:40.088836 INFO: rt_error       : 805.611083984375
0:30:40.088891 INFO: mobility_error : 0.1
0:30:40.088938 INFO: num_candidates : 3
0:30:40.088982 INFO: ms1_error      : 30
0:30:40.089025 INFO: ms2_error      : 30
0:30:40.089064 INFO: fwhm_rt        : 3.0
0:30:40.089103 INFO: quant_window   : 3
0:30:40.089143 INFO: ==============================================
0:30:41.371773 INFO: performing precursor FDR with 40 features
0:30:41.371887 INFO: Decoy channel: -1
0:30:41.371912 INFO: Competetive: True
0:30:41.444976 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:41.547398 INFO: Using random state 750973 for train-test-split
0:30:45.447292 INFO: Test AUC: 0.593
0:30:45.447419 INFO: Train AUC: 0.605
0:30:45.447450 INFO: AUC difference: 1.97%
0:30:45.771628 INFO: Resetting torch num_threads to 80
0:30:45.782537 PROGRESS: === Extracted 300155 precursors and 1376486 fragments ===
0:30:45.782936 INFO: === FDR correction performed with classifier version 7 ===
0:30:45.783395 PROGRESS: ============================= Precursor FDR =============================
0:30:45.783493 PROGRESS: Total precursors accumulated: 112
0:30:45.783552 PROGRESS: Target precursors: 111 (99.11%)
0:30:45.783603 PROGRESS: Decoy precursors: 1 (0.89%)
0:30:45.783646 PROGRESS: 
0:30:45.783690 PROGRESS: Precursor Summary:
0:30:45.784553 PROGRESS: Channel   0:	 0.050 FDR:   111; 0.010 FDR:   111; 0.001 FDR:   104
0:30:45.784638 PROGRESS: 
0:30:45.784692 PROGRESS: Protein Summary:
0:30:45.785659 PROGRESS: Channel   0:	 0.050 FDR:   104; 0.010 FDR:   104; 0.001 FDR:    98
0:30:45.785748 PROGRESS: =========================================================================
0:30:45.790761 INFO: Target number of precursors not reached yet.
0:30:46.076548 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:46.139576 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:46.291693 INFO: === skipping optimization until target number of precursors are found ===
0:30:46.291951 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:30:46.292045 INFO: Starting optimization step 9.
0:30:46.292113 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:30:46.292182 INFO: Using ng extraction backend
0:30:46.292242 PROGRESS: Extracting batch of 101368 precursors
0:30:46.469875 INFO: === Search parameters used ===
0:30:46.470146 INFO: rt_error       : 805.611083984375
0:30:46.470201 INFO: mobility_error : 0.1
0:30:46.470248 INFO: num_candidates : 3
0:30:46.470291 INFO: ms1_error      : 30
0:30:46.470331 INFO: ms2_error      : 30
0:30:46.470371 INFO: fwhm_rt        : 3.0
0:30:46.470412 INFO: quant_window   : 3
0:30:46.470452 INFO: ==============================================
0:30:47.786292 INFO: performing precursor FDR with 40 features
0:30:47.786420 INFO: Decoy channel: -1
0:30:47.786446 INFO: Competetive: True
0:30:48.020692 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:48.262746 INFO: Using random state 750973 for train-test-split
0:30:57.126118 INFO: Test AUC: 0.595
0:30:57.126363 INFO: Train AUC: 0.606
0:30:57.126399 INFO: AUC difference: 1.74%
0:30:57.544139 INFO: Resetting torch num_threads to 80
0:30:57.639979 PROGRESS: === Extracted 601347 precursors and 2754353 fragments ===
0:30:57.640691 INFO: === FDR correction performed with classifier version 7 ===
0:30:57.641353 PROGRESS: ============================= Precursor FDR =============================
0:30:57.641445 PROGRESS: Total precursors accumulated: 508
0:30:57.641510 PROGRESS: Target precursors: 503 (99.02%)
0:30:57.641562 PROGRESS: Decoy precursors: 5 (0.98%)
0:30:57.641605 PROGRESS: 
0:30:57.641648 PROGRESS: Precursor Summary:
0:30:57.642678 PROGRESS: Channel   0:	 0.050 FDR:   503; 0.010 FDR:   503; 0.001 FDR:   331
0:30:57.642771 PROGRESS: 
0:30:57.642839 PROGRESS: Protein Summary:
0:30:57.644046 PROGRESS: Channel   0:	 0.050 FDR:   451; 0.010 FDR:   451; 0.001 FDR:   300
0:30:57.644138 PROGRESS: =========================================================================
0:30:57.652301 INFO: Target number of precursors reached.
0:30:57.849005 INFO: fragments_df: keeping 5000 of 2754353 [sum(precursor_idx_mask)=11436 sum(mass_error_mask)=2754353 stop_rank=5000
0:30:58.170056 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:58.290909 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:58.906355 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:30:58.906816 INFO: Using score_cutoff 12.538607220840454 (fac=0.99, q=1)
0:30:58.907149 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:30:58.907238 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:30:58.907292 INFO: Updating optimization_manager: score_cutoff        : 14.8951129986763 -> 12.538607220840454
0:30:58.907350 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:58.968587 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:59.109885 INFO: === checking if optimization conditions were reached ===
0:30:59.110127 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:30:59.112582 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.064276041331647
0:30:59.112685 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.0643.
0:30:59.112751 INFO: ==============================================
0:30:59.112825 INFO: Starting optimization step 10.
0:30:59.112885 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:30:59.112964 INFO: Using ng extraction backend
0:30:59.113035 PROGRESS: Extracting batch of 100984 precursors
0:30:59.287254 INFO: === Search parameters used ===
0:30:59.287533 INFO: rt_error       : 805.611083984375
0:30:59.287593 INFO: mobility_error : 0.1
0:30:59.287642 INFO: num_candidates : 3
0:30:59.287686 INFO: ms1_error      : 30
0:30:59.287730 INFO: ms2_error      : 7.064276041331647
0:30:59.287770 INFO: fwhm_rt        : 3.0
0:30:59.287809 INFO: quant_window   : 3
0:30:59.287847 INFO: ==============================================
0:31:00.485258 INFO: performing precursor FDR with 40 features
0:31:00.485375 INFO: Decoy channel: -1
0:31:00.485402 INFO: Competetive: True
0:31:00.559119 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:00.664507 INFO: Using random state 750973 for train-test-split
0:31:04.582867 INFO: Test AUC: 0.591
0:31:04.583002 INFO: Train AUC: 0.604
0:31:04.583037 INFO: AUC difference: 2.11%
0:31:04.904081 INFO: Resetting torch num_threads to 80
0:31:04.915585 PROGRESS: === Extracted 302933 precursors and 1702001 fragments ===
0:31:04.915967 INFO: === FDR correction performed with classifier version 7 ===
0:31:04.916495 PROGRESS: ============================= Precursor FDR =============================
0:31:04.916585 PROGRESS: Total precursors accumulated: 407
0:31:04.916644 PROGRESS: Target precursors: 403 (99.02%)
0:31:04.916694 PROGRESS: Decoy precursors: 4 (0.98%)
0:31:04.916738 PROGRESS: 
0:31:04.916780 PROGRESS: Precursor Summary:
0:31:04.917747 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   403; 0.001 FDR:   244
0:31:04.917834 PROGRESS: 
0:31:04.917888 PROGRESS: Protein Summary:
0:31:04.919042 PROGRESS: Channel   0:	 0.050 FDR:   379; 0.010 FDR:   379; 0.001 FDR:   225
0:31:04.919139 PROGRESS: =========================================================================
0:31:04.924703 INFO: Target number of precursors reached.
0:31:05.036643 INFO: fragments_df: keeping 4840 of 1702001 [sum(precursor_idx_mask)=10048 sum(mass_error_mask)=1702001 stop_rank=4840
0:31:05.204661 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:05.315975 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:06.030903 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:06.031361 INFO: Using score_cutoff 12.907754626464843 (fac=0.99, q=1)
0:31:06.031656 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:06.031738 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:06.031792 INFO: Updating optimization_manager: score_cutoff        : 12.538607220840454 -> 12.907754626464843
0:31:06.031868 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:06.066771 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:06.142426 INFO: === checking if optimization conditions were reached ===
0:31:06.143182 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:31:06.146810 INFO: Updating optimization_manager: ms2_error           : 7.064276041331647 -> 7.326093683622706
0:31:06.147112 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.3261.
0:31:06.147220 INFO: ==============================================
0:31:06.147328 INFO: Starting optimization step 11.
0:31:06.147418 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:06.147518 INFO: Using ng extraction backend
0:31:06.147605 PROGRESS: Extracting batch of 50293 precursors
0:31:06.243660 INFO: === Search parameters used ===
0:31:06.244489 INFO: rt_error       : 805.611083984375
0:31:06.244595 INFO: mobility_error : 0.1
0:31:06.244661 INFO: num_candidates : 3
0:31:06.244720 INFO: ms1_error      : 30
0:31:06.244776 INFO: ms2_error      : 7.326093683622706
0:31:06.244836 INFO: fwhm_rt        : 3.0
0:31:06.244887 INFO: quant_window   : 3
0:31:06.244942 INFO: ==============================================
0:31:07.036125 INFO: performing precursor FDR with 40 features
0:31:07.036246 INFO: Decoy channel: -1
0:31:07.036276 INFO: Competetive: True
0:31:07.075363 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:07.116622 INFO: Using random state 750973 for train-test-split
0:31:09.149203 INFO: Test AUC: 0.590
0:31:09.149325 INFO: Train AUC: 0.601
0:31:09.149356 INFO: AUC difference: 1.87%
0:31:09.419394 INFO: Resetting torch num_threads to 80
0:31:09.425901 PROGRESS: === Extracted 150837 precursors and 842691 fragments ===
0:31:09.426264 INFO: === FDR correction performed with classifier version 7 ===
0:31:09.426745 PROGRESS: ============================= Precursor FDR =============================
0:31:09.426838 PROGRESS: Total precursors accumulated: 253
0:31:09.426895 PROGRESS: Target precursors: 251 (99.21%)
0:31:09.426945 PROGRESS: Decoy precursors: 2 (0.79%)
0:31:09.426990 PROGRESS: 
0:31:09.427035 PROGRESS: Precursor Summary:
0:31:09.427925 PROGRESS: Channel   0:	 0.050 FDR:   251; 0.010 FDR:   251; 0.001 FDR:   134
0:31:09.428013 PROGRESS: 
0:31:09.428068 PROGRESS: Protein Summary:
0:31:09.429108 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   246; 0.001 FDR:   131
0:31:09.429197 PROGRESS: =========================================================================
0:31:09.431418 INFO: Target number of precursors reached.
0:31:09.489314 INFO: fragments_df: keeping 2877 of 842691 [sum(precursor_idx_mask)=5982 sum(mass_error_mask)=842691 stop_rank=2877
0:31:09.669009 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:09.786541 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:10.169032 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:10.169454 INFO: Using score_cutoff 7.695281567573547 (fac=0.99, q=1)
0:31:10.169736 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:10.169817 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:10.169871 INFO: Updating optimization_manager: score_cutoff        : 12.907754626464843 -> 7.695281567573547
0:31:10.169924 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:10.200361 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:10.263710 INFO: === checking if optimization conditions were reached ===
0:31:10.263941 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:31:10.264827 INFO: Updating optimization_manager: ms2_error           : 7.326093683622706 -> 7.326093683622706
0:31:10.264965 INFO: Updating optimization_manager: classifier_version  : 7 -> 11
0:31:10.265061 INFO: Updating optimization_manager: score_cutoff        : 7.695281567573547 -> 7.695281567573547
0:31:10.265162 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:10.265248 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:10.265332 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.3261 found after 3 searches.
0:31:10.265397 INFO: ==============================================
0:31:10.265464 PROGRESS: Optimization finished for ms2_error.
0:31:10.403507 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:10.434268 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:10.523849 INFO: Starting optimization step 0.
0:31:10.524056 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:10.524132 INFO: Using ng extraction backend
0:31:10.524192 PROGRESS: Extracting batch of 50293 precursors
0:31:10.610871 INFO: === Search parameters used ===
0:31:10.611120 INFO: rt_error       : 805.611083984375
0:31:10.611174 INFO: mobility_error : 0.1
0:31:10.611221 INFO: num_candidates : 3
0:31:10.611264 INFO: ms1_error      : 30
0:31:10.611306 INFO: ms2_error      : 7.326093683622706
0:31:10.611346 INFO: fwhm_rt        : 3.0
0:31:10.611386 INFO: quant_window   : 3
0:31:10.611425 INFO: ==============================================
0:31:11.238914 INFO: performing precursor FDR with 40 features
0:31:11.239031 INFO: Decoy channel: -1
0:31:11.239056 INFO: Competetive: True
0:31:11.279351 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:11.328501 INFO: Using random state 632367 for train-test-split
0:31:13.351889 INFO: Test AUC: 0.598
0:31:13.352012 INFO: Train AUC: 0.607
0:31:13.352043 INFO: AUC difference: 1.53%
0:31:13.627257 INFO: Resetting torch num_threads to 80
0:31:13.642209 PROGRESS: === Extracted 150835 precursors and 843340 fragments ===
0:31:13.642596 INFO: === FDR correction performed with classifier version 11 ===
0:31:13.643052 PROGRESS: ============================= Precursor FDR =============================
0:31:13.643145 PROGRESS: Total precursors accumulated: 220
0:31:13.643203 PROGRESS: Target precursors: 218 (99.09%)
0:31:13.643253 PROGRESS: Decoy precursors: 2 (0.91%)
0:31:13.643297 PROGRESS: 
0:31:13.643339 PROGRESS: Precursor Summary:
0:31:13.644224 PROGRESS: Channel   0:	 0.050 FDR:   218; 0.010 FDR:   218; 0.001 FDR:   130
0:31:13.644311 PROGRESS: 
0:31:13.644366 PROGRESS: Protein Summary:
0:31:13.645400 PROGRESS: Channel   0:	 0.050 FDR:   213; 0.010 FDR:   213; 0.001 FDR:   127
0:31:13.645490 PROGRESS: =========================================================================
0:31:13.647887 INFO: Target number of precursors reached.
0:31:13.708461 INFO: fragments_df: keeping 2645 of 843340 [sum(precursor_idx_mask)=5417 sum(mass_error_mask)=843340 stop_rank=2645
0:31:13.884788 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:14.001720 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:14.354647 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:14.355126 INFO: Using score_cutoff 13.466294622516632 (fac=0.99, q=1)
0:31:14.355416 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:14.355500 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:14.355561 INFO: Updating optimization_manager: score_cutoff        : 7.695281567573547 -> 13.466294622516632
0:31:14.355628 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:14.386693 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:14.452453 INFO: === checking if optimization conditions were reached ===
0:31:14.452692 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:31:14.454510 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 234.8521199283685
0:31:14.454622 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 234.8521.
0:31:14.454689 INFO: ==============================================
0:31:14.454769 INFO: Starting optimization step 1.
0:31:14.454836 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:14.454921 INFO: Using ng extraction backend
0:31:14.454998 PROGRESS: Extracting batch of 50293 precursors
0:31:14.543253 INFO: === Search parameters used ===
0:31:14.543548 INFO: rt_error       : 234.8521199283685
0:31:14.543603 INFO: mobility_error : 0.1
0:31:14.543649 INFO: num_candidates : 3
0:31:14.543690 INFO: ms1_error      : 30
0:31:14.543731 INFO: ms2_error      : 7.326093683622706
0:31:14.543771 INFO: fwhm_rt        : 3.0
0:31:14.543823 INFO: quant_window   : 3
0:31:14.543864 INFO: ==============================================
0:31:15.138062 INFO: performing precursor FDR with 40 features
0:31:15.138254 INFO: Decoy channel: -1
0:31:15.138282 INFO: Competetive: True
0:31:15.178292 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:15.215327 INFO: Using random state 632367 for train-test-split
0:31:17.253153 INFO: Test AUC: 0.592
0:31:17.253278 INFO: Train AUC: 0.605
0:31:17.253309 INFO: AUC difference: 2.11%
0:31:17.520870 INFO: Resetting torch num_threads to 80
0:31:17.527184 PROGRESS: === Extracted 150591 precursors and 749726 fragments ===
0:31:17.527595 INFO: === FDR correction performed with classifier version 11 ===
0:31:17.528065 PROGRESS: ============================= Precursor FDR =============================
0:31:17.528153 PROGRESS: Total precursors accumulated: 265
0:31:17.528213 PROGRESS: Target precursors: 263 (99.25%)
0:31:17.528262 PROGRESS: Decoy precursors: 2 (0.75%)
0:31:17.528306 PROGRESS: 
0:31:17.528347 PROGRESS: Precursor Summary:
0:31:17.529244 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   263; 0.001 FDR:   202
0:31:17.529332 PROGRESS: 
0:31:17.529385 PROGRESS: Protein Summary:
0:31:17.530416 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   256; 0.001 FDR:   196
0:31:17.530503 PROGRESS: =========================================================================
0:31:17.532658 INFO: Target number of precursors reached.
0:31:17.581775 INFO: fragments_df: keeping 2945 of 749726 [sum(precursor_idx_mask)=6263 sum(mass_error_mask)=749726 stop_rank=2945
0:31:17.721568 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:17.838891 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:18.193793 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:18.194236 INFO: Using score_cutoff 8.45565869922638 (fac=0.99, q=1)
0:31:18.194549 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:18.194651 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:18.194707 INFO: Updating optimization_manager: score_cutoff        : 13.466294622516632 -> 8.45565869922638
0:31:18.194760 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:18.225296 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:18.290933 INFO: === checking if optimization conditions were reached ===
0:31:18.291205 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:31:18.293152 INFO: Updating optimization_manager: rt_error            : 234.8521199283685 -> 182.2082287201937
0:31:18.293266 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 182.2082.
0:31:18.293349 INFO: ==============================================
0:31:18.293437 INFO: Starting optimization step 2.
0:31:18.293515 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:18.293595 INFO: Using ng extraction backend
0:31:18.293671 PROGRESS: Extracting batch of 50293 precursors
0:31:18.380940 INFO: === Search parameters used ===
0:31:18.381226 INFO: rt_error       : 182.2082287201937
0:31:18.381301 INFO: mobility_error : 0.1
0:31:18.381367 INFO: num_candidates : 3
0:31:18.381429 INFO: ms1_error      : 30
0:31:18.381491 INFO: ms2_error      : 7.326093683622706
0:31:18.381551 INFO: fwhm_rt        : 3.0
0:31:18.381617 INFO: quant_window   : 3
0:31:18.381680 INFO: ==============================================
0:31:18.962066 INFO: performing precursor FDR with 40 features
0:31:18.962188 INFO: Decoy channel: -1
0:31:18.962220 INFO: Competetive: True
0:31:18.999842 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:19.037344 INFO: Using random state 632367 for train-test-split
0:31:20.955127 INFO: Test AUC: 0.589
0:31:20.955246 INFO: Train AUC: 0.604
0:31:20.955275 INFO: AUC difference: 2.42%
0:31:21.226521 INFO: Resetting torch num_threads to 80
0:31:21.232410 PROGRESS: === Extracted 150137 precursors and 704637 fragments ===
0:31:21.232917 INFO: === FDR correction performed with classifier version 11 ===
0:31:21.233365 PROGRESS: ============================= Precursor FDR =============================
0:31:21.233452 PROGRESS: Total precursors accumulated: 206
0:31:21.233510 PROGRESS: Target precursors: 204 (99.03%)
0:31:21.233559 PROGRESS: Decoy precursors: 2 (0.97%)
0:31:21.233603 PROGRESS: 
0:31:21.233647 PROGRESS: Precursor Summary:
0:31:21.234531 PROGRESS: Channel   0:	 0.050 FDR:   204; 0.010 FDR:   204; 0.001 FDR:     1
0:31:21.234637 PROGRESS: 
0:31:21.234696 PROGRESS: Protein Summary:
0:31:21.235709 PROGRESS: Channel   0:	 0.050 FDR:   199; 0.010 FDR:   199; 0.001 FDR:     1
0:31:21.235805 PROGRESS: =========================================================================
0:31:21.237887 INFO: Target number of precursors reached.
0:31:21.285900 INFO: fragments_df: keeping 2476 of 704637 [sum(precursor_idx_mask)=5044 sum(mass_error_mask)=704637 stop_rank=2476
0:31:21.422334 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:21.530196 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:21.856349 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:21.856775 INFO: Using score_cutoff 13.43362915248871 (fac=0.99, q=1)
0:31:21.857066 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:21.857145 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:21.857199 INFO: Updating optimization_manager: score_cutoff        : 8.45565869922638 -> 13.43362915248871
0:31:21.857254 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:21.888011 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:21.954991 INFO: === checking if optimization conditions were reached ===
0:31:21.955258 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:31:21.957242 INFO: Updating optimization_manager: rt_error            : 182.2082287201937 -> 117.59432889573576
0:31:21.957359 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 117.5943.
0:31:21.957442 INFO: ==============================================
0:31:21.957533 INFO: Starting optimization step 3.
0:31:21.957612 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:21.957691 INFO: Using ng extraction backend
0:31:21.957767 PROGRESS: Extracting batch of 50293 precursors
0:31:22.044586 INFO: === Search parameters used ===
0:31:22.044875 INFO: rt_error       : 117.59432889573576
0:31:22.044953 INFO: mobility_error : 0.1
0:31:22.045020 INFO: num_candidates : 3
0:31:22.045080 INFO: ms1_error      : 30
0:31:22.045151 INFO: ms2_error      : 7.326093683622706
0:31:22.045212 INFO: fwhm_rt        : 3.0
0:31:22.045269 INFO: quant_window   : 3
0:31:22.045327 INFO: ==============================================
0:31:22.622921 INFO: performing precursor FDR with 40 features
0:31:22.623044 INFO: Decoy channel: -1
0:31:22.623070 INFO: Competetive: True
0:31:22.660486 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:22.694688 INFO: Using random state 632367 for train-test-split
0:31:24.779191 INFO: Test AUC: 0.586
0:31:24.779308 INFO: Train AUC: 0.605
0:31:24.779338 INFO: AUC difference: 3.07%
0:31:25.050331 INFO: Resetting torch num_threads to 80
0:31:25.056706 PROGRESS: === Extracted 149133 precursors and 643718 fragments ===
0:31:25.057079 INFO: === FDR correction performed with classifier version 11 ===
0:31:25.057540 PROGRESS: ============================= Precursor FDR =============================
0:31:25.057629 PROGRESS: Total precursors accumulated: 272
0:31:25.057686 PROGRESS: Target precursors: 270 (99.26%)
0:31:25.057735 PROGRESS: Decoy precursors: 2 (0.74%)
0:31:25.057777 PROGRESS: 
0:31:25.057820 PROGRESS: Precursor Summary:
0:31:25.058710 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:    58
0:31:25.058800 PROGRESS: 
0:31:25.058855 PROGRESS: Protein Summary:
0:31:25.059878 PROGRESS: Channel   0:	 0.050 FDR:   261; 0.010 FDR:   261; 0.001 FDR:    58
0:31:25.059975 PROGRESS: =========================================================================
0:31:25.062129 INFO: Target number of precursors reached.
0:31:25.104492 INFO: fragments_df: keeping 3023 of 643718 [sum(precursor_idx_mask)=6354 sum(mass_error_mask)=643718 stop_rank=3023
0:31:25.241344 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:25.360360 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:25.740947 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:25.741370 INFO: Using score_cutoff 10.855490723705293 (fac=0.99, q=1)
0:31:25.741657 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:25.741737 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:25.741793 INFO: Updating optimization_manager: score_cutoff        : 13.43362915248871 -> 10.855490723705293
0:31:25.741847 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:25.772528 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:25.838361 INFO: === checking if optimization conditions were reached ===
0:31:25.838664 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:31:25.840971 INFO: Updating optimization_manager: rt_error            : 117.59432889573576 -> 100.12873113809059
0:31:25.841083 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 100.1287.
0:31:25.841162 INFO: ==============================================
0:31:25.841243 INFO: Starting optimization step 4.
0:31:25.841311 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:25.841380 INFO: Using ng extraction backend
0:31:25.841444 PROGRESS: Extracting batch of 50293 precursors
0:31:25.929576 INFO: === Search parameters used ===
0:31:25.929852 INFO: rt_error       : 100.12873113809059
0:31:25.929910 INFO: mobility_error : 0.1
0:31:25.929983 INFO: num_candidates : 3
0:31:25.930031 INFO: ms1_error      : 30
0:31:25.930072 INFO: ms2_error      : 7.326093683622706
0:31:25.930114 INFO: fwhm_rt        : 3.0
0:31:25.930155 INFO: quant_window   : 3
0:31:25.930193 INFO: ==============================================
0:31:26.506338 INFO: performing precursor FDR with 40 features
0:31:26.506459 INFO: Decoy channel: -1
0:31:26.506483 INFO: Competetive: True
0:31:26.543414 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:26.579401 INFO: Using random state 632367 for train-test-split
0:31:28.890802 INFO: Test AUC: 0.594
0:31:28.890951 INFO: Train AUC: 0.605
0:31:28.890993 INFO: AUC difference: 1.81%
0:31:29.257878 INFO: Resetting torch num_threads to 80
0:31:29.268547 PROGRESS: === Extracted 148693 precursors and 625106 fragments ===
0:31:29.269214 INFO: === FDR correction performed with classifier version 11 ===
0:31:29.269769 PROGRESS: ============================= Precursor FDR =============================
0:31:29.269864 PROGRESS: Total precursors accumulated: 238
0:31:29.269925 PROGRESS: Target precursors: 236 (99.16%)
0:31:29.269975 PROGRESS: Decoy precursors: 2 (0.84%)
0:31:29.270022 PROGRESS: 
0:31:29.270066 PROGRESS: Precursor Summary:
0:31:29.271331 PROGRESS: Channel   0:	 0.050 FDR:   236; 0.010 FDR:   236; 0.001 FDR:   177
0:31:29.271440 PROGRESS: 
0:31:29.271501 PROGRESS: Protein Summary:
0:31:29.272731 PROGRESS: Channel   0:	 0.050 FDR:   230; 0.010 FDR:   230; 0.001 FDR:   174
0:31:29.272825 PROGRESS: =========================================================================
0:31:29.278326 INFO: Target number of precursors reached.
0:31:29.335731 INFO: fragments_df: keeping 2719 of 625106 [sum(precursor_idx_mask)=5603 sum(mass_error_mask)=625106 stop_rank=2719
0:31:29.516193 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:29.644927 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:30.062419 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:30.063018 INFO: Using score_cutoff 10.56661848306656 (fac=0.99, q=1)
0:31:30.063377 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:30.063482 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:30.063556 INFO: Updating optimization_manager: score_cutoff        : 10.855490723705293 -> 10.56661848306656
0:31:30.063631 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:30.098011 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:30.174704 INFO: === checking if optimization conditions were reached ===
0:31:30.175006 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:31:30.177477 INFO: Updating optimization_manager: rt_error            : 100.12873113809059 -> 76.45056204146984
0:31:30.177893 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 76.4506.
0:31:30.178150 INFO: ==============================================
0:31:30.178403 INFO: Starting optimization step 5.
0:31:30.178663 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:30.178895 INFO: Using ng extraction backend
0:31:30.179114 PROGRESS: Extracting batch of 50293 precursors
0:31:30.277154 INFO: === Search parameters used ===
0:31:30.277932 INFO: rt_error       : 76.45056204146984
0:31:30.278296 INFO: mobility_error : 0.1
0:31:30.278527 INFO: num_candidates : 3
0:31:30.278624 INFO: ms1_error      : 30
0:31:30.278691 INFO: ms2_error      : 7.326093683622706
0:31:30.278752 INFO: fwhm_rt        : 3.0
0:31:30.278812 INFO: quant_window   : 3
0:31:30.278869 INFO: ==============================================
0:31:30.934592 INFO: performing precursor FDR with 40 features
0:31:30.934715 INFO: Decoy channel: -1
0:31:30.934741 INFO: Competetive: True
0:31:30.973100 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:31.008157 INFO: Using random state 632367 for train-test-split
0:31:32.813131 INFO: Test AUC: 0.594
0:31:32.813258 INFO: Train AUC: 0.605
0:31:32.813287 INFO: AUC difference: 1.85%
0:31:33.082741 INFO: Resetting torch num_threads to 80
0:31:33.088748 PROGRESS: === Extracted 147308 precursors and 587895 fragments ===
0:31:33.089108 INFO: === FDR correction performed with classifier version 11 ===
0:31:33.089551 PROGRESS: ============================= Precursor FDR =============================
0:31:33.089639 PROGRESS: Total precursors accumulated: 238
0:31:33.089695 PROGRESS: Target precursors: 236 (99.16%)
0:31:33.089750 PROGRESS: Decoy precursors: 2 (0.84%)
0:31:33.089794 PROGRESS: 
0:31:33.089837 PROGRESS: Precursor Summary:
0:31:33.090709 PROGRESS: Channel   0:	 0.050 FDR:   236; 0.010 FDR:   236; 0.001 FDR:    46
0:31:33.090797 PROGRESS: 
0:31:33.090851 PROGRESS: Protein Summary:
0:31:33.091842 PROGRESS: Channel   0:	 0.050 FDR:   228; 0.010 FDR:   228; 0.001 FDR:    45
0:31:33.091929 PROGRESS: =========================================================================
0:31:33.093859 INFO: Target number of precursors reached.
0:31:33.133559 INFO: fragments_df: keeping 2713 of 587895 [sum(precursor_idx_mask)=5496 sum(mass_error_mask)=587895 stop_rank=2713
0:31:33.270022 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:33.383569 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:33.714722 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:33.715140 INFO: Using score_cutoff 13.069908102035521 (fac=0.99, q=1)
0:31:33.715425 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:33.715503 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:33.715560 INFO: Updating optimization_manager: score_cutoff        : 10.56661848306656 -> 13.069908102035521
0:31:33.715614 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:33.746636 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:33.813539 INFO: === checking if optimization conditions were reached ===
0:31:33.813801 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:31:33.816095 INFO: Updating optimization_manager: rt_error            : 76.45056204146984 -> 57.371323646751655
0:31:33.816236 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 57.3713.
0:31:33.816312 INFO: ==============================================
0:31:33.816393 INFO: Starting optimization step 6.
0:31:33.816460 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:33.816529 INFO: Using ng extraction backend
0:31:33.816596 PROGRESS: Extracting batch of 50293 precursors
0:31:33.906299 INFO: === Search parameters used ===
0:31:33.906558 INFO: rt_error       : 57.371323646751655
0:31:33.906629 INFO: mobility_error : 0.1
0:31:33.906676 INFO: num_candidates : 3
0:31:33.906722 INFO: ms1_error      : 30
0:31:33.906764 INFO: ms2_error      : 7.326093683622706
0:31:33.906804 INFO: fwhm_rt        : 3.0
0:31:33.906844 INFO: quant_window   : 3
0:31:33.906883 INFO: ==============================================
0:31:34.445398 INFO: performing precursor FDR with 40 features
0:31:34.445506 INFO: Decoy channel: -1
0:31:34.445533 INFO: Competetive: True
0:31:34.481327 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:34.516395 INFO: Using random state 632367 for train-test-split
0:31:36.345680 INFO: Test AUC: 0.590
0:31:36.345801 INFO: Train AUC: 0.605
0:31:36.345832 INFO: AUC difference: 2.45%
0:31:36.615535 INFO: Resetting torch num_threads to 80
0:31:36.621453 PROGRESS: === Extracted 142380 precursors and 533544 fragments ===
0:31:36.621796 INFO: === FDR correction performed with classifier version 11 ===
0:31:36.622249 PROGRESS: ============================= Precursor FDR =============================
0:31:36.622335 PROGRESS: Total precursors accumulated: 244
0:31:36.622392 PROGRESS: Target precursors: 242 (99.18%)
0:31:36.622441 PROGRESS: Decoy precursors: 2 (0.82%)
0:31:36.622485 PROGRESS: 
0:31:36.622528 PROGRESS: Precursor Summary:
0:31:36.623417 PROGRESS: Channel   0:	 0.050 FDR:   242; 0.010 FDR:   242; 0.001 FDR:   206
0:31:36.623508 PROGRESS: 
0:31:36.623564 PROGRESS: Protein Summary:
0:31:36.624609 PROGRESS: Channel   0:	 0.050 FDR:   236; 0.010 FDR:   236; 0.001 FDR:   200
0:31:36.624705 PROGRESS: =========================================================================
0:31:36.626620 INFO: Target number of precursors reached.
0:31:36.662527 INFO: fragments_df: keeping 2638 of 533544 [sum(precursor_idx_mask)=5297 sum(mass_error_mask)=533544 stop_rank=2638
0:31:36.798483 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:36.894836 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:37.184212 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:37.184628 INFO: Using score_cutoff 13.100965167617797 (fac=0.99, q=1)
0:31:37.184911 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:37.184991 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:37.185047 INFO: Updating optimization_manager: score_cutoff        : 13.069908102035521 -> 13.100965167617797
0:31:37.185099 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:37.216107 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:37.280492 INFO: === checking if optimization conditions were reached ===
0:31:37.280772 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:31:37.283088 INFO: Updating optimization_manager: rt_error            : 57.371323646751655 -> 42.621976104609814
0:31:37.283204 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 42.6220.
0:31:37.283281 INFO: ==============================================
0:31:37.283361 INFO: Starting optimization step 7.
0:31:37.283430 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:37.283521 INFO: Using ng extraction backend
0:31:37.283587 PROGRESS: Extracting batch of 50293 precursors
0:31:37.373289 INFO: === Search parameters used ===
0:31:37.373547 INFO: rt_error       : 42.621976104609814
0:31:37.373604 INFO: mobility_error : 0.1
0:31:37.373649 INFO: num_candidates : 3
0:31:37.373693 INFO: ms1_error      : 30
0:31:37.373749 INFO: ms2_error      : 7.326093683622706
0:31:37.373791 INFO: fwhm_rt        : 3.0
0:31:37.373831 INFO: quant_window   : 3
0:31:37.373869 INFO: ==============================================
0:31:37.880494 INFO: performing precursor FDR with 40 features
0:31:37.880611 INFO: Decoy channel: -1
0:31:37.880637 INFO: Competetive: True
0:31:37.914805 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:37.946236 INFO: Using random state 632367 for train-test-split
0:31:39.644106 INFO: Test AUC: 0.586
0:31:39.644230 INFO: Train AUC: 0.606
0:31:39.644261 INFO: AUC difference: 3.27%
0:31:39.907445 INFO: Resetting torch num_threads to 80
0:31:39.913198 PROGRESS: === Extracted 133773 precursors and 485043 fragments ===
0:31:39.913552 INFO: === FDR correction performed with classifier version 11 ===
0:31:39.914006 PROGRESS: ============================= Precursor FDR =============================
0:31:39.914093 PROGRESS: Total precursors accumulated: 248
0:31:39.914151 PROGRESS: Target precursors: 246 (99.19%)
0:31:39.914201 PROGRESS: Decoy precursors: 2 (0.81%)
0:31:39.914244 PROGRESS: 
0:31:39.914285 PROGRESS: Precursor Summary:
0:31:39.915180 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   246; 0.001 FDR:   202
0:31:39.915269 PROGRESS: 
0:31:39.915325 PROGRESS: Protein Summary:
0:31:39.916374 PROGRESS: Channel   0:	 0.050 FDR:   240; 0.010 FDR:   240; 0.001 FDR:   197
0:31:39.916461 PROGRESS: =========================================================================
0:31:39.918280 INFO: Target number of precursors reached.
0:31:39.950850 INFO: fragments_df: keeping 2477 of 485043 [sum(precursor_idx_mask)=4877 sum(mass_error_mask)=485043 stop_rank=2477
0:31:40.087069 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:40.195032 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:40.466884 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:40.467297 INFO: Using score_cutoff 12.310627850532532 (fac=0.99, q=1)
0:31:40.467580 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:40.467660 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:40.467716 INFO: Updating optimization_manager: score_cutoff        : 13.100965167617797 -> 12.310627850532532
0:31:40.467767 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:40.498841 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:40.564259 INFO: === checking if optimization conditions were reached ===
0:31:40.564538 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:31:40.566839 INFO: Updating optimization_manager: rt_error            : 42.621976104609814 -> 34.651222230983386
0:31:40.566956 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 34.6512.
0:31:40.567033 INFO: ==============================================
0:31:40.567128 INFO: Starting optimization step 8.
0:31:40.567200 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:40.567269 INFO: Using ng extraction backend
0:31:40.567334 PROGRESS: Extracting batch of 50293 precursors
0:31:40.656969 INFO: === Search parameters used ===
0:31:40.657220 INFO: rt_error       : 34.651222230983386
0:31:40.657272 INFO: mobility_error : 0.1
0:31:40.657318 INFO: num_candidates : 3
0:31:40.657358 INFO: ms1_error      : 30
0:31:40.657396 INFO: ms2_error      : 7.326093683622706
0:31:40.657436 INFO: fwhm_rt        : 3.0
0:31:40.657475 INFO: quant_window   : 3
0:31:40.657516 INFO: ==============================================
0:31:41.170691 INFO: performing precursor FDR with 40 features
0:31:41.170812 INFO: Decoy channel: -1
0:31:41.170840 INFO: Competetive: True
0:31:41.204887 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:41.235050 INFO: Using random state 632367 for train-test-split
0:31:42.940108 INFO: Test AUC: 0.594
0:31:42.940225 INFO: Train AUC: 0.606
0:31:42.940256 INFO: AUC difference: 1.99%
0:31:43.210464 INFO: Resetting torch num_threads to 80
0:31:43.216167 PROGRESS: === Extracted 134293 precursors and 486102 fragments ===
0:31:43.216533 INFO: === FDR correction performed with classifier version 11 ===
0:31:43.216993 PROGRESS: ============================= Precursor FDR =============================
0:31:43.217079 PROGRESS: Total precursors accumulated: 243
0:31:43.217139 PROGRESS: Target precursors: 241 (99.18%)
0:31:43.217188 PROGRESS: Decoy precursors: 2 (0.82%)
0:31:43.217233 PROGRESS: 
0:31:43.217276 PROGRESS: Precursor Summary:
0:31:43.218204 PROGRESS: Channel   0:	 0.050 FDR:   241; 0.010 FDR:   241; 0.001 FDR:   211
0:31:43.218301 PROGRESS: 
0:31:43.218358 PROGRESS: Protein Summary:
0:31:43.219392 PROGRESS: Channel   0:	 0.050 FDR:   236; 0.010 FDR:   236; 0.001 FDR:   206
0:31:43.219481 PROGRESS: =========================================================================
0:31:43.221218 INFO: Target number of precursors reached.
0:31:43.253977 INFO: fragments_df: keeping 2442 of 486102 [sum(precursor_idx_mask)=4792 sum(mass_error_mask)=486102 stop_rank=2442
0:31:43.388778 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:43.504468 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:43.826360 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:43.826782 INFO: Using score_cutoff 12.290345792770385 (fac=0.99, q=1)
0:31:43.827065 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:43.827145 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:43.827200 INFO: Updating optimization_manager: score_cutoff        : 12.310627850532532 -> 12.290345792770385
0:31:43.827255 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:43.858553 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:43.923881 INFO: === checking if optimization conditions were reached ===
0:31:43.924147 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:31:43.926432 INFO: Updating optimization_manager: rt_error            : 34.651222230983386 -> 33.3594738653242
0:31:43.926548 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 33.3595.
0:31:43.927517 INFO: ==============================================
0:31:43.927618 INFO: Starting optimization step 9.
0:31:43.927685 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:43.927758 INFO: Using ng extraction backend
0:31:43.927824 PROGRESS: Extracting batch of 50293 precursors
0:31:44.017234 INFO: === Search parameters used ===
0:31:44.017484 INFO: rt_error       : 33.3594738653242
0:31:44.017538 INFO: mobility_error : 0.1
0:31:44.017583 INFO: num_candidates : 3
0:31:44.017625 INFO: ms1_error      : 30
0:31:44.017667 INFO: ms2_error      : 7.326093683622706
0:31:44.017705 INFO: fwhm_rt        : 3.0
0:31:44.017744 INFO: quant_window   : 3
0:31:44.017782 INFO: ==============================================
0:31:44.529027 INFO: performing precursor FDR with 40 features
0:31:44.529145 INFO: Decoy channel: -1
0:31:44.529172 INFO: Competetive: True
0:31:44.562551 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:44.593234 INFO: Using random state 632367 for train-test-split
0:31:46.330803 INFO: Test AUC: 0.595
0:31:46.330918 INFO: Train AUC: 0.604
0:31:46.330950 INFO: AUC difference: 1.51%
0:31:46.600914 INFO: Resetting torch num_threads to 80
0:31:46.606841 PROGRESS: === Extracted 134317 precursors and 486139 fragments ===
0:31:46.607202 INFO: === FDR correction performed with classifier version 11 ===
0:31:46.607675 PROGRESS: ============================= Precursor FDR =============================
0:31:46.607764 PROGRESS: Total precursors accumulated: 239
0:31:46.607825 PROGRESS: Target precursors: 237 (99.16%)
0:31:46.607877 PROGRESS: Decoy precursors: 2 (0.84%)
0:31:46.607924 PROGRESS: 
0:31:46.607977 PROGRESS: Precursor Summary:
0:31:46.608885 PROGRESS: Channel   0:	 0.050 FDR:   237; 0.010 FDR:   237; 0.001 FDR:   217
0:31:46.608974 PROGRESS: 
0:31:46.609030 PROGRESS: Protein Summary:
0:31:46.610087 PROGRESS: Channel   0:	 0.050 FDR:   231; 0.010 FDR:   231; 0.001 FDR:   213
0:31:46.610177 PROGRESS: =========================================================================
0:31:46.612172 INFO: Target number of precursors reached.
0:31:46.644854 INFO: fragments_df: keeping 2404 of 486139 [sum(precursor_idx_mask)=4740 sum(mass_error_mask)=486139 stop_rank=2404
0:31:46.781579 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:46.900878 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:47.218208 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:47.218631 INFO: Using score_cutoff 12.61032764968872 (fac=0.99, q=1)
0:31:47.218920 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:47.219001 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:47.219057 INFO: Updating optimization_manager: score_cutoff        : 12.290345792770385 -> 12.61032764968872
0:31:47.219114 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:47.249995 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:47.315727 INFO: === checking if optimization conditions were reached ===
0:31:47.315986 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
0:31:47.317255 INFO: Updating optimization_manager: rt_error            : 33.3594738653242 -> 42.621976104609814
0:31:47.317412 INFO: Updating optimization_manager: classifier_version  : 11 -> 19
0:31:47.317521 INFO: Updating optimization_manager: score_cutoff        : 12.61032764968872 -> 12.310627850532532
0:31:47.317621 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:47.317716 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:47.317809 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 42.6220 found after 10 searches.
0:31:47.317878 INFO: ==============================================
0:31:47.317963 PROGRESS: Optimization finished for rt_error.
0:31:47.466777 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:47.498039 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:47.594571 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:31:47.594802 PROGRESS: ==============================================
0:31:47.594885 PROGRESS: ms2_error      : 7.3261
0:31:47.594951 PROGRESS: rt_error       : 42.6220
0:31:47.595007 PROGRESS: ==============================================
0:31:47.597039 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:55.349928 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:12.964259 INFO: Using ng extraction backend
0:32:12.964746 PROGRESS: Extracting batch of 12001526 precursors
0:32:29.012514 INFO: === Search parameters used ===
0:32:29.013177 INFO: rt_error       : 42.621976104609814
0:32:29.013280 INFO: mobility_error : 0.1
0:32:29.013335 INFO: num_candidates : 3
0:32:29.013384 INFO: ms1_error      : 30
0:32:29.013429 INFO: ms2_error      : 7.326093683622706
0:32:29.013478 INFO: fwhm_rt        : 3.0
0:32:29.013526 INFO: quant_window   : 3
0:32:29.013575 INFO: ==============================================
0:32:49.552374 INFO: Removed 27694707 precursors with score below cutoff 12.310627850532532
0:32:54.093095 INFO: performing precursor FDR with 40 features
0:32:54.093340 INFO: Decoy channel: -1
0:32:54.093370 INFO: Competetive: True
0:32:54.532154 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:56.222723 INFO: Using random state 522594 for train-test-split
0:34:03.343760 INFO: Test AUC: 0.636
0:34:03.344006 INFO: Train AUC: 0.637
0:34:03.344044 INFO: AUC difference: 0.19%
0:34:04.976690 INFO: Resetting torch num_threads to 80
0:34:06.449494 PROGRESS: ============================= Precursor FDR =============================
0:34:06.450245 PROGRESS: Total precursors accumulated: 71,646
0:34:06.450320 PROGRESS: Target precursors: 70,937 (99.01%)
0:34:06.450387 PROGRESS: Decoy precursors: 709 (0.99%)
0:34:06.450437 PROGRESS: 
0:34:06.450482 PROGRESS: Precursor Summary:
0:34:06.470237 PROGRESS: Channel   0:	 0.050 FDR: 70,937; 0.010 FDR: 70,937; 0.001 FDR: 51,198
0:34:06.470477 PROGRESS: 
0:34:06.470535 PROGRESS: Protein Summary:
0:34:06.497241 PROGRESS: Channel   0:	 0.050 FDR: 11,857; 0.010 FDR: 11,857; 0.001 FDR: 9,167
0:34:06.497480 PROGRESS: =========================================================================
0:34:06.529881 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
0:34:06.667512 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
0:34:06.876838 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:34:33.668991 PROGRESS: Processing search outputs
0:34:33.669110 PROGRESS: Performing protein grouping and FDR
0:34:33.669145 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:34:33.724819 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:34:33.769733 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:34:33.811054 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:34:33.847819 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:34:33.889103 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:34:33.925844 INFO: Building combined output
0:34:33.947515 INFO: Performing protein inference
0:34:34.460119 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
0:35:14.631591 INFO: Performing protein FDR
0:35:19.813171 INFO: Normalizing q-values using 17,500 targets and 3,362 decoys
0:35:19.817416 INFO: Test AUC: 0.865
0:35:19.817477 INFO: Train AUC: 0.864
0:35:19.817511 INFO: AUC difference: 0.16%
0:35:20.375221 PROGRESS: ================ Protein FDR =================
0:35:20.375364 PROGRESS: Unique protein groups in output
0:35:20.375393 PROGRESS:   1% protein FDR: 10,145
0:35:20.375412 PROGRESS: 
0:35:20.375431 PROGRESS: Unique precursor in output
0:35:20.375449 PROGRESS:   1% protein FDR: 120,580
0:35:20.375469 PROGRESS: ================================================
0:35:20.434211 PROGRESS: Building search statistics
0:35:20.516455 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
0:35:20.516643 INFO: Initializing OptimizationManager
0:35:20.516855 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
0:35:20.516930 INFO: Initializing CalibrationManager
0:35:20.517141 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
0:35:20.517215 INFO: Initializing RawFileManager
0:35:20.546010 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
0:35:20.546197 INFO: Initializing OptimizationManager
0:35:20.546396 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
0:35:20.546472 INFO: Initializing CalibrationManager
0:35:20.546945 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
0:35:20.547031 INFO: Initializing RawFileManager
0:35:20.574854 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
0:35:20.575056 INFO: Initializing OptimizationManager
0:35:20.575250 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
0:35:20.575321 INFO: Initializing CalibrationManager
0:35:20.575521 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
0:35:20.575597 INFO: Initializing RawFileManager
0:35:20.603250 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
0:35:20.603440 INFO: Initializing OptimizationManager
0:35:20.603637 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
0:35:20.603711 INFO: Initializing CalibrationManager
0:35:20.603908 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
0:35:20.603984 INFO: Initializing RawFileManager
0:35:20.631007 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
0:35:20.631184 INFO: Initializing OptimizationManager
0:35:20.631378 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
0:35:20.631451 INFO: Initializing CalibrationManager
0:35:20.631644 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
0:35:20.631720 INFO: Initializing RawFileManager
0:35:20.659124 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
0:35:20.659307 INFO: Initializing OptimizationManager
0:35:20.659497 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
0:35:20.659569 INFO: Initializing CalibrationManager
0:35:20.659755 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
0:35:20.659829 INFO: Initializing RawFileManager
0:35:20.662315 INFO: Writing stat output to disk
0:35:20.662373 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/stat.tsv to disk
0:35:20.669387 PROGRESS: Building internal statistics
0:35:20.669714 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
0:35:20.669761 INFO: Initializing TimingManager
0:35:20.670102 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
0:35:20.670145 INFO: Initializing TimingManager
0:35:20.670335 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
0:35:20.670373 INFO: Initializing TimingManager
0:35:20.670555 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
0:35:20.670604 INFO: Initializing TimingManager
0:35:20.670783 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
0:35:20.670830 INFO: Initializing TimingManager
0:35:20.671007 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
0:35:20.671043 INFO: Initializing TimingManager
0:35:20.671460 INFO: Writing internal output to disk
0:35:20.671504 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/internal.tsv to disk
0:35:20.672004 PROGRESS: Performing label free quantification
0:35:20.725924 INFO: Accumulating fragment data
0:35:20.726072 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:35:20.935483 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:35:22.132752 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:35:23.358400 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:35:24.665091 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:35:26.041378 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:35:27.738081 PROGRESS: Performing label free quantification on the precursor level
0:35:27.738214 INFO: Filtering fragments by quality
0:35:28.086790 INFO: Performing label-free quantification using directLFQ
0:35:29.768001 INFO: 120580 lfq-groups total
0:36:17.503775 INFO: using 80 processes
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0:37:34.862386 INFO: lfq-object 117500
0:37:34.954233 INFO: lfq-object 117600
0:37:35.082954 INFO: lfq-object 117700
0:37:35.180897 INFO: lfq-object 117800
0:37:35.268499 INFO: lfq-object 118100
0:37:35.279687 INFO: lfq-object 117900
0:37:35.357975 INFO: lfq-object 118400
0:37:35.368228 INFO: lfq-object 118200
0:37:35.371257 INFO: lfq-object 118000
0:37:35.460065 INFO: lfq-object 118500
0:37:35.464016 INFO: lfq-object 118300
0:37:35.504293 INFO: lfq-object 118800
0:37:35.555653 INFO: lfq-object 118600
0:37:35.601755 INFO: lfq-object 118900
0:37:35.639188 INFO: lfq-object 119200
0:37:35.653840 INFO: lfq-object 118700
0:37:35.695578 INFO: lfq-object 119000
0:37:35.735200 INFO: lfq-object 119300
0:37:35.786424 INFO: lfq-object 119100
0:37:35.792570 INFO: lfq-object 119600
0:37:35.832968 INFO: lfq-object 119400
0:37:35.884746 INFO: lfq-object 119700
0:37:35.896376 INFO: lfq-object 119900
0:37:35.932358 INFO: lfq-object 119500
0:37:35.971513 INFO: lfq-object 119800
0:37:35.999721 INFO: lfq-object 120000
0:37:36.092903 INFO: lfq-object 120100
0:37:36.096313 INFO: lfq-object 120300
0:37:36.189479 INFO: lfq-object 120200
0:37:36.193059 INFO: lfq-object 120400
0:37:36.289066 INFO: lfq-object 120500
0:37:41.776837 INFO: Writing precursor output to disk
0:37:41.777267 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/precursor.matrix.tsv to disk
0:37:42.280368 PROGRESS: Performing label free quantification on the pg level
0:37:42.280480 INFO: Filtering fragments by quality
0:37:42.631883 INFO: Performing label-free quantification using directLFQ
0:37:42.942529 INFO: 10145 lfq-groups total
0:38:09.087487 INFO: using 80 processes
0:38:09.223208 INFO: lfq-object 0
0:38:09.377352 INFO: lfq-object 100
0:38:09.430193 INFO: lfq-object 200
0:38:09.515200 INFO: lfq-object 800
0:38:09.656666 INFO: lfq-object 400
0:38:09.692854 INFO: lfq-object 300
0:38:09.794952 INFO: lfq-object 900
0:38:09.828759 INFO: lfq-object 500
0:38:09.872027 INFO: lfq-object 1600
0:38:09.919655 INFO: lfq-object 1000
0:38:09.952775 INFO: lfq-object 700
0:38:09.958514 INFO: lfq-object 1100
0:38:09.986434 INFO: lfq-object 600
0:38:10.041397 INFO: lfq-object 1300
0:38:10.049216 INFO: lfq-object 1700
0:38:10.052142 INFO: lfq-object 1400
0:38:10.066488 INFO: lfq-object 1200
0:38:10.126829 INFO: lfq-object 1800
0:38:10.225270 INFO: lfq-object 1500
0:38:10.274195 INFO: lfq-object 1900
0:38:10.313811 INFO: lfq-object 2400
0:38:10.383552 INFO: lfq-object 2000
0:38:10.464213 INFO: lfq-object 2700
0:38:10.502808 INFO: lfq-object 2200
0:38:10.526068 INFO: lfq-object 2600
0:38:10.573771 INFO: lfq-object 2300
0:38:10.585384 INFO: lfq-object 2900
0:38:10.605825 INFO: lfq-object 2500
0:38:10.616335 INFO: lfq-object 3200
0:38:10.634716 INFO: lfq-object 2800
0:38:10.653012 INFO: lfq-object 2100
0:38:10.659468 INFO: lfq-object 3300
0:38:10.703403 INFO: lfq-object 3400
0:38:10.747683 INFO: lfq-object 3500
0:38:10.761543 INFO: lfq-object 3000
0:38:10.780733 INFO: lfq-object 3100
0:38:10.860588 INFO: lfq-object 3700
0:38:10.890015 INFO: lfq-object 3600
0:38:10.972940 INFO: lfq-object 3800
0:38:11.022759 INFO: lfq-object 4000
0:38:11.059516 INFO: lfq-object 4100
0:38:11.102453 INFO: lfq-object 3900
0:38:11.179087 INFO: lfq-object 4200
0:38:11.200806 INFO: lfq-object 4400
0:38:11.318676 INFO: lfq-object 4600
0:38:11.320322 INFO: lfq-object 4300
0:38:11.332259 INFO: lfq-object 4800
0:38:11.394218 INFO: lfq-object 4500
0:38:11.430172 INFO: lfq-object 4900
0:38:11.452051 INFO: lfq-object 5000
0:38:11.500543 INFO: lfq-object 5100
0:38:11.579234 INFO: lfq-object 4700
0:38:11.672118 INFO: lfq-object 5600
0:38:11.703249 INFO: lfq-object 5300
0:38:11.713297 INFO: lfq-object 5700
0:38:11.719899 INFO: lfq-object 5500
0:38:11.748723 INFO: lfq-object 5200
0:38:11.748903 INFO: lfq-object 5800
0:38:11.784907 INFO: lfq-object 5400
0:38:11.827555 INFO: lfq-object 5900
0:38:11.836137 INFO: lfq-object 6000
0:38:11.946970 INFO: lfq-object 6100
0:38:11.987623 INFO: lfq-object 6300
0:38:12.001756 INFO: lfq-object 6400
0:38:12.028337 INFO: lfq-object 6200
0:38:12.130171 INFO: lfq-object 6600
0:38:12.215413 INFO: lfq-object 6500
0:38:12.223027 INFO: lfq-object 6800
0:38:12.285972 INFO: lfq-object 6900
0:38:12.289648 INFO: lfq-object 7000
0:38:12.324166 INFO: lfq-object 6700
0:38:12.330419 INFO: lfq-object 7200
0:38:12.358612 INFO: lfq-object 7100
0:38:12.374228 INFO: lfq-object 7300
0:38:12.474057 INFO: lfq-object 7400
0:38:12.513173 INFO: lfq-object 7500
0:38:12.525101 INFO: lfq-object 7600
0:38:12.573243 INFO: lfq-object 7700
0:38:12.621742 INFO: lfq-object 7800
0:38:12.670537 INFO: lfq-object 8000
0:38:12.733118 INFO: lfq-object 7900
0:38:14.649169 INFO: lfq-object 8100
0:38:14.661764 INFO: lfq-object 8200
0:38:14.700826 INFO: lfq-object 8300
0:38:14.779108 INFO: lfq-object 8400
0:38:14.825340 INFO: lfq-object 8500
0:38:14.886406 INFO: lfq-object 8800
0:38:14.888528 INFO: lfq-object 8700
0:38:14.922140 INFO: lfq-object 8900
0:38:14.956457 INFO: lfq-object 9000
0:38:14.974548 INFO: lfq-object 8600
0:38:15.007351 INFO: lfq-object 9100
0:38:15.090446 INFO: lfq-object 9200
0:38:15.165891 INFO: lfq-object 9400
0:38:15.173653 INFO: lfq-object 9300
0:38:15.198283 INFO: lfq-object 9600
0:38:15.231182 INFO: lfq-object 9500
0:38:15.270427 INFO: lfq-object 9700
0:38:15.323161 INFO: lfq-object 9800
0:38:15.455786 INFO: lfq-object 9900
0:38:15.499030 INFO: lfq-object 10100
0:38:15.509073 INFO: lfq-object 10000
0:38:17.629730 INFO: Writing pg output to disk
0:38:17.629973 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/pg.matrix.tsv to disk
0:38:17.911553 INFO: Writing psm output to disk
0:38:17.911752 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/precursors.tsv to disk
0:38:26.151078 PROGRESS: Building MBR spectral library
0:38:26.243341 INFO: Running MbrLibraryBuilder
0:38:31.367345 INFO: MBR spectral library contains 120,580 precursors, 10,145 proteins
0:38:31.367495 INFO: Writing MBR spectral library to disk
0:38:32.833322 PROGRESS: =================== Search Finished ===================
0:38:34.927907 INFO: Running step 'mbr'
0:38:34.932324 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 7.171496}})
0:38:34.932541 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:38:34.944627 INFO: loading additional config provided via CLI
0:38:34.944718 INFO: loading additional config provided via CLI parameters
0:38:34.945179 INFO: Updating config with 'user defined'
0:38:34.945342 INFO: Updating config with 'user defined (cli)'
0:38:34.945385 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default_ng.yaml
0:38:34.946116 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': ['./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw'], 'fasta_paths': [], 'quant_directory': None, 'general': {'thread_count': 80, 'transfer_step_enabled': False, 'mbr_step_enabled': True, 'reuse_calibration': False, 'reuse_quant': False, 'astral_ms1': False, 'log_level': 'INFO', 'mmap_detector_events': False, 'use_gpu': False, 'save_figures': True, 'save_library': True, 'save_flat_library': False, 'input_library_type': 'base', 'save_mbr_library': True, 'random_state': None}, 'library_loading': {'rt_heuristic': 180}, 'library_prediction': {'enabled': False, 'enzyme': 'trypsin/p', 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M;Acetyl@Protein_N-term', 'max_var_mod_num': 1, 'missed_cleavages': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [400, 1000], 'fragment_mz': [50, 2000], 'nce': 25.0, 'fragment_types': ['b', 'y'], 'max_fragment_charge': 2, 'instrument': 'Astral', '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': 'Astral'}}, {'raw_paths': ['./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', './Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw'], 'library_path': '/home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf', 'fasta_paths': ['./ProteoBenchFASTA_DDAQuantification.fasta']}, {'fasta_paths': [], 'fdr': {'inference_strategy': 'library'}, 'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 7.171496}, 'quant_directory': None, 'general': {'reuse_quant': False}, 'library_prediction': {'enabled': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_path': 'run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/speclib.mbr.hdf', 'output_directory': 'run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol'}]
0:38:34.946419 INFO: Updating config with 'ng_default'
0:38:34.946456 INFO: Updating config with 'user defined'
0:38:34.946585 INFO: Updating config with 'user defined (cli)'
0:38:34.946610 INFO: Updating config with 'multistep search'
0:38:34.946658 INFO: ├──version: 1
0:38:34.946684 INFO: ├──workflow_name: None
0:38:34.946709 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol [multistep search, default: None][0m
0:38:34.946731 INFO: [32;20m├──library_path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/speclib.mbr.hdf [multistep search, default: None][0m
0:38:34.946753 INFO: ├──raw_paths:
0:38:34.946772 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:38:34.946792 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:38:34.946809 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:38:34.946834 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:38:34.946851 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:38:34.946870 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:38:34.946887 INFO: ├──fasta_paths:
0:38:34.946906 INFO: ├──quant_directory: None
0:38:34.946923 INFO: ├──general
0:38:34.946944 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:38:34.946963 INFO: │   ├──transfer_step_enabled: False
0:38:34.946983 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:38:34.947001 INFO: │   ├──reuse_calibration: False
0:38:34.947021 INFO: │   ├──reuse_quant: False
0:38:34.947039 INFO: │   ├──astral_ms1: False
0:38:34.947056 INFO: │   ├──log_level: INFO
0:38:34.947074 INFO: │   ├──mmap_detector_events: False
0:38:34.947093 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:38:34.947113 INFO: │   ├──save_figures: True
0:38:34.947130 INFO: │   ├──save_library: True
0:38:34.947147 INFO: │   ├──save_flat_library: False
0:38:34.947166 INFO: │   ├──input_library_type: base
0:38:34.947183 INFO: │   ├──save_mbr_library: True
0:38:34.947201 INFO: │   └──random_state: None
0:38:34.947218 INFO: ├──library_loading
0:38:34.947238 INFO: │   └──rt_heuristic: 180
0:38:34.947255 INFO: ├──library_prediction
0:38:34.947272 INFO: │   ├──enabled: False
0:38:34.947289 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:38:34.947309 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:38:34.947326 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:38:34.947344 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:38:34.947361 INFO: │   ├──missed_cleavages: 1
0:38:34.947379 INFO: │   ├──precursor_len:
0:38:34.947398 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:38:34.947416 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:38:34.947433 INFO: │   ├──precursor_charge:
0:38:34.947452 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:38:34.947469 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:38:34.947486 INFO: │   ├──precursor_mz:
0:38:34.947504 INFO: │   │   - 400
0:38:34.947524 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:38:34.947541 INFO: │   ├──fragment_mz:
0:38:34.947558 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:38:34.947575 INFO: │   │   - 2000
0:38:34.947593 INFO: │   ├──nce: 25.0
0:38:34.947612 INFO: │   ├──fragment_types:
0:38:34.947629 INFO: │   │   - b
0:38:34.947647 INFO: │   │   - y
0:38:34.947665 INFO: │   ├──max_fragment_charge: 2
0:38:34.947685 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:38:34.947703 INFO: │   ├──peptdeep_model_path: None
0:38:34.947722 INFO: │   └──peptdeep_model_type: generic
0:38:34.947740 INFO: ├──custom_modifications:
0:38:34.947759 INFO: │   ├──name: Dimethyl:d12@K
0:38:34.947777 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:38:34.947795 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:38:34.947813 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:38:34.947831 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:38:34.947849 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:38:34.947867 INFO: │   ├──name: mTRAQ:d12@K
0:38:34.947884 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:38:34.947904 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:38:34.947922 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:38:34.947939 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:38:34.947966 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:38:34.947984 INFO: │   ├──name: Label:13C(12)@K
0:38:34.948002 INFO: │   └──composition: C(12)
0:38:34.948019 INFO: ├──search
0:38:34.948038 INFO: │   [32;20m├──extraction_backend: ng [user defined, default: classic][0m
0:38:34.948059 INFO: │   [32;20m├──target_ms1_tolerance: 30.0 [multistep search, default: 5][0m
0:38:34.948078 INFO: │   [32;20m├──target_ms2_tolerance: 7.171496 [multistep search, default: 10][0m
0:38:34.948096 INFO: │   ├──target_rt_tolerance: 0.0
0:38:34.948115 INFO: │   ├──target_mobility_tolerance: 0.0
0:38:34.948132 INFO: │   ├──quant_window: 3
0:38:34.948150 INFO: │   ├──target_num_candidates: 3
0:38:34.948167 INFO: │   ├──channel_filter: 
0:38:34.948186 INFO: │   ├──exclude_shared_ions: True
0:38:34.948203 INFO: │   ├──compete_for_fragments: True
0:38:34.948220 INFO: │   ├──quant_all: True
0:38:34.948238 INFO: │   ├──top_k_fragments_selection: 12
0:38:34.948256 INFO: │   ├──top_k_fragments_scoring: 12
0:38:34.948274 INFO: │   ├──min_fragment_intensity: 0.01
0:38:34.948292 INFO: │   ├──experimental_xic: True
0:38:34.948309 INFO: │   └──optimized_peak_group_score: False
0:38:34.948326 INFO: ├──calibration
0:38:34.948347 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:38:34.948364 INFO: │   ├──optimization_lock_target: 200
0:38:34.948381 INFO: │   ├──max_steps: 20
0:38:34.948399 INFO: │   ├──min_steps: 2
0:38:34.948417 INFO: │   ├──max_skips: 1
0:38:34.948435 INFO: │   ├──max_fragments: 5000
0:38:34.948452 INFO: │   └──min_correlation: 0.7
0:38:34.948469 INFO: ├──search_initial
0:38:34.948488 INFO: │   ├──initial_num_candidates: 1
0:38:34.948505 INFO: │   ├──initial_ms1_tolerance: 30
0:38:34.948522 INFO: │   ├──initial_ms2_tolerance: 30
0:38:34.948539 INFO: │   ├──initial_mobility_tolerance: 0.1
0:38:34.948558 INFO: │   └──initial_rt_tolerance: 0.5
0:38:34.948575 INFO: ├──selection_config
0:38:34.948592 INFO: │   ├──peak_len_rt: 10.0
0:38:34.948610 INFO: │   ├──sigma_scale_rt: 0.5
0:38:34.948628 INFO: │   ├──peak_len_mobility: 0.01
0:38:34.948646 INFO: │   ├──sigma_scale_mobility: 1.0
0:38:34.948663 INFO: │   ├──top_k_precursors: 3
0:38:34.948680 INFO: │   ├──kernel_size: 30
0:38:34.948697 INFO: │   ├──f_mobility: 1.0
0:38:34.948716 INFO: │   ├──f_rt: 0.99
0:38:34.948734 INFO: │   ├──center_fraction: 0.5
0:38:34.948751 INFO: │   ├──min_size_mobility: 8
0:38:34.948770 INFO: │   ├──min_size_rt: 3
0:38:34.948789 INFO: │   ├──max_size_mobility: 20
0:38:34.948806 INFO: │   ├──max_size_rt: 15
0:38:34.948824 INFO: │   ├──group_channels: False
0:38:34.948842 INFO: │   ├──use_weighted_score: True
0:38:34.948861 INFO: │   ├──join_close_candidates: False
0:38:34.948879 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:38:34.948896 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:38:34.948914 INFO: ├──scoring_config
0:38:34.948934 INFO: │   ├──score_grouped: False
0:38:34.948951 INFO: │   ├──top_k_isotopes: 3
0:38:34.948969 INFO: │   ├──reference_channel: -1
0:38:34.948986 INFO: │   ├──precursor_mz_tolerance: 10
0:38:34.949004 INFO: │   └──fragment_mz_tolerance: 15
0:38:34.949022 INFO: ├──library_multiplexing
0:38:34.949039 INFO: │   ├──enabled: False
0:38:34.949056 INFO: │   ├──input_channel: 0
0:38:34.949075 INFO: │   └──multiplex_mapping:
0:38:34.949091 INFO: ├──multiplexing
0:38:34.949109 INFO: │   ├──enabled: False
0:38:34.949126 INFO: │   ├──target_channels: 4,8
0:38:34.949145 INFO: │   ├──decoy_channel: 12
0:38:34.949162 INFO: │   ├──reference_channel: 0
0:38:34.949986 INFO: │   └──competetive_scoring: True
0:38:34.950013 INFO: ├──fdr
0:38:34.950033 INFO: │   ├──fdr: 0.01
0:38:34.950051 INFO: │   ├──group_level: proteins
0:38:34.950069 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
0:38:34.950087 INFO: │   ├──competetive_scoring: True
0:38:34.950104 INFO: │   ├──keep_decoys: False
0:38:34.950123 INFO: │   ├──channel_wise_fdr: False
0:38:34.950140 INFO: │   ├──enable_two_step_classifier: False
0:38:34.950158 INFO: │   ├──two_step_classifier_max_iterations: 5
0:38:34.950176 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:38:34.950194 INFO: ├──search_output
0:38:34.950212 INFO: │   ├──file_format: tsv
0:38:34.950229 INFO: │   ├──peptide_level_lfq: False
0:38:34.950247 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:38:34.950267 INFO: │   ├──save_fragment_quant_matrix: False
0:38:34.950284 INFO: │   ├──min_k_fragments: 12
0:38:34.950302 INFO: │   ├──min_correlation: 0.9
0:38:34.950319 INFO: │   ├──num_samples_quadratic: 50
0:38:34.950336 INFO: │   ├──min_nonnan: 3
0:38:34.950354 INFO: │   └──normalize_lfq: True
0:38:34.950371 INFO: ├──optimization
0:38:34.950389 INFO: │   ├──order_of_optimization: None
0:38:34.950406 INFO: │   ├──ms2_error
0:38:34.950425 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:38:34.950442 INFO: │   │   ├──targeted_update_factor: 1.0
0:38:34.950460 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:38:34.950477 INFO: │   │   ├──automatic_update_factor: 1.1
0:38:34.950496 INFO: │   │   ├──try_narrower_values: True
0:38:34.950513 INFO: │   │   ├──maximal_decrease: 0.5
0:38:34.950531 INFO: │   │   ├──favour_narrower_optimum: False
0:38:34.950548 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:38:34.950574 INFO: │   ├──ms1_error
0:38:34.950593 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:38:34.950610 INFO: │   │   ├──targeted_update_factor: 1.0
0:38:34.950628 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:38:34.950644 INFO: │   │   ├──automatic_update_factor: 1.1
0:38:34.950663 INFO: │   │   ├──try_narrower_values: False
0:38:34.950680 INFO: │   │   ├──maximal_decrease: 0.2
0:38:34.950697 INFO: │   │   ├──favour_narrower_optimum: False
0:38:34.950714 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:38:34.950732 INFO: │   ├──mobility_error
0:38:34.950750 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:38:34.950768 INFO: │   │   ├──targeted_update_factor: 1.0
0:38:34.950786 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:38:34.950805 INFO: │   │   ├──automatic_update_factor: 1.1
0:38:34.950823 INFO: │   │   ├──try_narrower_values: False
0:38:34.950840 INFO: │   │   ├──maximal_decrease: 0.2
0:38:34.950858 INFO: │   │   ├──favour_narrower_optimum: False
0:38:34.950877 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:38:34.950895 INFO: │   └──rt_error
0:38:34.950913 INFO: │       ├──targeted_update_percentile_range: 0.95
0:38:34.950930 INFO: │       ├──targeted_update_factor: 1.0
0:38:34.950949 INFO: │       ├──automatic_update_percentile_range: 0.99
0:38:34.950968 INFO: │       ├──automatic_update_factor: 1.1
0:38:34.950985 INFO: │       ├──try_narrower_values: True
0:38:34.951003 INFO: │       ├──maximal_decrease: 0.2
0:38:34.951020 INFO: │       ├──favour_narrower_optimum: True
0:38:34.951039 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:38:34.951056 INFO: ├──optimization_manager
0:38:34.951074 INFO: │   ├──fwhm_rt: 5
0:38:34.951092 INFO: │   ├──fwhm_mobility: 0.01
0:38:34.951115 INFO: │   └──score_cutoff: 0
0:38:34.951132 INFO: ├──transfer_library
0:38:34.951150 INFO: │   ├──enabled: False
0:38:34.951166 INFO: │   ├──fragment_types:
0:38:34.951184 INFO: │   │   - b
0:38:34.951202 INFO: │   │   - y
0:38:34.951219 INFO: │   ├──max_charge: 2
0:38:34.951237 INFO: │   ├──top_k_samples: 3
0:38:34.951256 INFO: │   ├──norm_delta_max: True
0:38:34.951274 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:38:34.951291 INFO: │   └──fragment_correlation_ratio: 0.75
0:38:34.951308 INFO: └──transfer_learning
0:38:34.951327 INFO:     ├──enabled: False
0:38:34.951345 INFO:     ├──batch_size: 2000
0:38:34.951363 INFO:     ├──max_lr: 0.0001
0:38:34.951381 INFO:     ├──train_fraction: 0.7
0:38:34.951399 INFO:     ├──validation_fraction: 0.2
0:38:34.951417 INFO:     ├──test_fraction: 0.1
0:38:34.951434 INFO:     ├──test_interval: 1
0:38:34.951452 INFO:     ├──lr_patience: 3
0:38:34.951470 INFO:     ├──epochs: 51
0:38:34.951488 INFO:     ├──warmup_epochs: 5
0:38:34.951504 INFO:     ├──nce: 25
0:38:34.951523 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:38:34.956727 INFO: Moved existing config file run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/frozen_config.yaml to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/frozen_config.yaml
0:38:34.957692 INFO: Registering 7 custom modifications
0:38:34.977271 INFO: Searching 6 files:
0:38:34.977337 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:38:34.977362 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:38:34.977381 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:38:34.977399 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:38:34.977416 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:38:34.977432 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:38:34.977450 INFO: Using 0 fasta files:
0:38:34.977468 INFO: Using library: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/speclib.mbr.hdf
0:38:34.977487 INFO: Saving output to: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol
0:38:34.977518 PROGRESS: Loading spectral library
0:38:34.977552 PROGRESS: Loading library (type: base) from disk..
0:38:34.977586 INFO: Running DynamicLoader
0:38:34.977643 INFO: Loading .hdf library from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/library/speclib.mbr.hdf
0:38:35.506957 INFO: Running PrecursorInitializer
0:38:35.507123 INFO: Running AnnotateFasta
0:38:35.507521 INFO: Dropping decoys from input library before annotation
0:38:35.527230 INFO: Running IsotopeGenerator
0:38:35.527436 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
0:38:35.527480 INFO: Running RTNormalization
0:38:35.530841 INFO: Saving library to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/speclib.hdf
0:38:36.367787 INFO: Running DecoyGenerator
0:38:43.709549 INFO: Running FlattenLibrary
0:38:44.646915 INFO: Running InitFlatColumns
0:38:44.652889 INFO: Running LogFlatLibraryStats
0:38:44.653013 INFO: ============ Library Stats ============
0:38:44.653045 INFO: Number of precursors: 241,132
0:38:44.692602 INFO: 	thereof targets:120,580
0:38:44.692735 INFO: 	thereof decoys: 120,552
0:38:44.694825 INFO: Number of elution groups: 120,580
0:38:44.694894 INFO: 	average size: 2.00
0:38:44.702540 INFO: Number of proteins: 10,145
0:38:44.703447 INFO: Number of channels: 1 ([0])
0:38:44.703552 INFO: Isotopes Distribution for 4 isotopes
0:38:44.703583 INFO: =======================================
0:38:44.704295 PROGRESS: Starting Search Workflows
0:38:44.704408 PROGRESS: 
0:38:44.704488 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
0:38:44.704555 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:38:44.704797 INFO: Initializing TimingManager
0:38:44.705300 INFO: Initializing RawFileManager
0:38:54.672341 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:38:54.677339 INFO: Determining DIA cycle
0:38:54.693820 INFO: Found cycle with start 0.00 min and length 300.
0:38:54.857523 INFO: RT (min)            : 0.0 - 26.9
0:38:54.857628 INFO: RT duration (sec)   : 1611.2
0:38:54.857658 INFO: RT duration (min)   : 26.9
0:38:54.857682 INFO: Cycle len (scans)   : 300
0:38:54.857702 INFO: Cycle len (sec)     : 1.65
0:38:54.857722 INFO: Number of cycles    : 977
0:38:54.857743 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:38:54.857812 INFO: Creating DIA data object took: 10.152406692504883
0:38:55.590351 INFO: Creating DIA data NG object took: 0.7324004173278809
0:38:55.650311 INFO: Initializing CalibrationManager
0:38:55.650597 INFO: Setting up calibration estimators ..
0:38:55.650662 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:38:55.650760 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'}' ..
0:38:55.650859 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:38:55.650911 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:38:55.650966 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}}' ..
0:38:55.651020 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:38:55.651065 INFO: Done setting up calibration estimators.
0:38:55.651263 INFO: Initializing OptimizationManager
0:38:55.651391 INFO: initial parameter: ms1_error = 30
0:38:55.651442 INFO: initial parameter: ms2_error = 30
0:38:55.651487 INFO: initial parameter: rt_error = 805.5992431640625
0:38:55.651530 INFO: initial parameter: mobility_error = 0.1
0:38:55.651570 INFO: initial parameter: num_candidates = 1
0:38:55.651610 INFO: initial parameter: fwhm_rt = 5
0:38:55.651653 INFO: initial parameter: fwhm_mobility = 0.01
0:38:55.651695 INFO: initial parameter: score_cutoff = 0
0:38:55.651737 INFO: initial parameter: classifier_version = -1
0:38:55.651810 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:38:55.652230 INFO: FDRManager: loading saved state not requested, will be initialized.
0:38:55.652268 INFO: Initializing FDRManager
0:38:55.652310 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:38:55.679832 PROGRESS: Initializing spectral library: 120,580 target precursors potentially observable (0 removed)
0:38:55.698505 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:38:55.698885 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:38:55.699025 PROGRESS: Starting initial search for precursors.
0:38:55.699116 INFO: Starting optimization step 0.
0:38:55.699179 PROGRESS: === Extracting elution groups 0 to 200 ===
0:38:55.699241 INFO: Using ng extraction backend
0:38:55.699312 PROGRESS: Extracting batch of 398 precursors
0:38:55.701186 INFO: === Search parameters used ===
0:38:55.701280 INFO: rt_error       : 805.5992431640625
0:38:55.701331 INFO: mobility_error : 0.1
0:38:55.701376 INFO: num_candidates : 1
0:38:55.701418 INFO: ms1_error      : 30
0:38:55.701458 INFO: ms2_error      : 30
0:38:55.701498 INFO: fwhm_rt        : 5
0:38:55.701536 INFO: quant_window   : 3
0:38:55.701572 INFO: ==============================================
0:38:55.724325 INFO: performing precursor FDR with 40 features
0:38:55.724399 INFO: Decoy channel: -1
0:38:55.724424 INFO: Competetive: True
0:38:55.725726 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:55.728421 INFO: Using random state 38106 for train-test-split
0:38:55.736683 INFO: Test AUC: 0.417
0:38:55.736742 INFO: Train AUC: 0.517
0:38:55.736775 INFO: AUC difference: 19.35%
0:38:55.736797 WARNING: AUC difference > 5%. This may indicate overfitting.
0:38:55.992699 INFO: Resetting torch num_threads to 80
0:38:55.994013 PROGRESS: === Extracted 398 precursors and 2863 fragments ===
0:38:55.994344 INFO: === FDR correction performed with classifier version -1 ===
0:38:55.994782 PROGRESS: ============================= Precursor FDR =============================
0:38:55.994866 PROGRESS: Total precursors accumulated: 0
0:38:55.994924 PROGRESS: Target precursors: 0 (0.00%)
0:38:55.994974 PROGRESS: Decoy precursors: 0 (0.00%)
0:38:55.995017 PROGRESS: 
0:38:55.995061 PROGRESS: Precursor Summary:
0:38:55.995169 PROGRESS: 
0:38:55.995231 PROGRESS: Protein Summary:
0:38:55.995304 PROGRESS: =========================================================================
0:38:55.995452 INFO: Target number of precursors not reached yet.
0:38:55.999351 INFO: Starting optimization step 1.
0:38:55.999460 PROGRESS: === Extracting elution groups 200 to 600 ===
0:38:55.999531 INFO: Using ng extraction backend
0:38:55.999589 PROGRESS: Extracting batch of 798 precursors
0:38:56.002241 INFO: === Search parameters used ===
0:38:56.002327 INFO: rt_error       : 805.5992431640625
0:38:56.002374 INFO: mobility_error : 0.1
0:38:56.002417 INFO: num_candidates : 1
0:38:56.002459 INFO: ms1_error      : 30
0:38:56.002499 INFO: ms2_error      : 30
0:38:56.002537 INFO: fwhm_rt        : 5
0:38:56.002594 INFO: quant_window   : 3
0:38:56.002638 INFO: ==============================================
0:38:56.057762 INFO: performing precursor FDR with 40 features
0:38:56.057848 INFO: Decoy channel: -1
0:38:56.057874 INFO: Competetive: True
0:38:56.061187 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:56.062989 INFO: Using random state 763538 for train-test-split
0:38:56.072132 INFO: Test AUC: 0.460
0:38:56.072193 INFO: Train AUC: 0.500
0:38:56.072223 INFO: AUC difference: 7.95%
0:38:56.072245 WARNING: AUC difference > 5%. This may indicate overfitting.
0:38:56.285600 INFO: Resetting torch num_threads to 80
0:38:56.287824 PROGRESS: === Extracted 1196 precursors and 8494 fragments ===
0:38:56.288162 INFO: === FDR correction performed with classifier version -1 ===
0:38:56.288584 PROGRESS: ============================= Precursor FDR =============================
0:38:56.288669 PROGRESS: Total precursors accumulated: 0
0:38:56.288726 PROGRESS: Target precursors: 0 (0.00%)
0:38:56.288774 PROGRESS: Decoy precursors: 0 (0.00%)
0:38:56.288817 PROGRESS: 
0:38:56.288860 PROGRESS: Precursor Summary:
0:38:56.288964 PROGRESS: 
0:38:56.289039 PROGRESS: Protein Summary:
0:38:56.289123 PROGRESS: =========================================================================
0:38:56.289302 INFO: Target number of precursors not reached yet.
0:38:56.294257 INFO: Starting optimization step 2.
0:38:56.294360 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:38:56.294429 INFO: Using ng extraction backend
0:38:56.294487 PROGRESS: Extracting batch of 1598 precursors
0:38:56.298715 INFO: === Search parameters used ===
0:38:56.298812 INFO: rt_error       : 805.5992431640625
0:38:56.298861 INFO: mobility_error : 0.1
0:38:56.298903 INFO: num_candidates : 1
0:38:56.298945 INFO: ms1_error      : 30
0:38:56.298984 INFO: ms2_error      : 30
0:38:56.299024 INFO: fwhm_rt        : 5
0:38:56.299062 INFO: quant_window   : 3
0:38:56.299103 INFO: ==============================================
0:38:56.338748 INFO: performing precursor FDR with 40 features
0:38:56.338853 INFO: Decoy channel: -1
0:38:56.338879 INFO: Competetive: True
0:38:56.342575 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:56.344348 INFO: Using random state 471590 for train-test-split
0:38:56.356213 INFO: Test AUC: 0.464
0:38:56.356274 INFO: Train AUC: 0.504
0:38:56.356304 INFO: AUC difference: 7.84%
0:38:56.356329 WARNING: AUC difference > 5%. This may indicate overfitting.
0:38:56.575772 INFO: Resetting torch num_threads to 80
0:38:56.578528 PROGRESS: === Extracted 2790 precursors and 19493 fragments ===
0:38:56.578886 INFO: === FDR correction performed with classifier version -1 ===
0:38:56.579337 PROGRESS: ============================= Precursor FDR =============================
0:38:56.579423 PROGRESS: Total precursors accumulated: 1
0:38:56.579480 PROGRESS: Target precursors: 1 (100.00%)
0:38:56.579529 PROGRESS: Decoy precursors: 0 (0.00%)
0:38:56.579574 PROGRESS: 
0:38:56.579623 PROGRESS: Precursor Summary:
0:38:56.580563 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:38:56.580650 PROGRESS: 
0:38:56.580704 PROGRESS: Protein Summary:
0:38:56.581709 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:38:56.581797 PROGRESS: =========================================================================
0:38:56.582031 INFO: Target number of precursors not reached yet.
0:38:56.589536 INFO: Starting optimization step 3.
0:38:56.589653 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:38:56.589732 INFO: Using ng extraction backend
0:38:56.589795 PROGRESS: Extracting batch of 3190 precursors
0:38:56.597265 INFO: === Search parameters used ===
0:38:56.597380 INFO: rt_error       : 805.5992431640625
0:38:56.597431 INFO: mobility_error : 0.1
0:38:56.597475 INFO: num_candidates : 1
0:38:56.597519 INFO: ms1_error      : 30
0:38:56.597561 INFO: ms2_error      : 30
0:38:56.597602 INFO: fwhm_rt        : 5
0:38:56.597643 INFO: quant_window   : 3
0:38:56.597682 INFO: ==============================================
0:38:56.649390 INFO: performing precursor FDR with 40 features
0:38:56.649479 INFO: Decoy channel: -1
0:38:56.649505 INFO: Competetive: True
0:38:56.653883 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:56.657295 INFO: Using random state 850573 for train-test-split
0:38:56.678377 INFO: Test AUC: 0.479
0:38:56.678457 INFO: Train AUC: 0.507
0:38:56.678488 INFO: AUC difference: 5.42%
0:38:56.678511 WARNING: AUC difference > 5%. This may indicate overfitting.
0:38:56.898489 INFO: Resetting torch num_threads to 80
0:38:56.902043 PROGRESS: === Extracted 5978 precursors and 41786 fragments ===
0:38:56.902421 INFO: === FDR correction performed with classifier version -1 ===
0:38:56.902895 PROGRESS: ============================= Precursor FDR =============================
0:38:56.902985 PROGRESS: Total precursors accumulated: 1
0:38:56.903044 PROGRESS: Target precursors: 1 (100.00%)
0:38:56.903093 PROGRESS: Decoy precursors: 0 (0.00%)
0:38:56.903138 PROGRESS: 
0:38:56.903180 PROGRESS: Precursor Summary:
0:38:56.904102 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:38:56.904188 PROGRESS: 
0:38:56.904241 PROGRESS: Protein Summary:
0:38:56.905243 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:38:56.905330 PROGRESS: =========================================================================
0:38:56.905601 INFO: Target number of precursors not reached yet.
0:38:56.918469 INFO: Starting optimization step 4.
0:38:56.918616 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:38:56.918692 INFO: Using ng extraction backend
0:38:56.918750 PROGRESS: Extracting batch of 6370 precursors
0:38:56.930849 INFO: === Search parameters used ===
0:38:56.930974 INFO: rt_error       : 805.5992431640625
0:38:56.931023 INFO: mobility_error : 0.1
0:38:56.931067 INFO: num_candidates : 1
0:38:56.931110 INFO: ms1_error      : 30
0:38:56.931159 INFO: ms2_error      : 30
0:38:56.931207 INFO: fwhm_rt        : 5
0:38:56.931246 INFO: quant_window   : 3
0:38:56.931282 INFO: ==============================================
0:38:57.013628 INFO: performing precursor FDR with 40 features
0:38:57.013740 INFO: Decoy channel: -1
0:38:57.013766 INFO: Competetive: True
0:38:57.021718 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:57.026022 INFO: Using random state 889617 for train-test-split
0:38:57.064280 INFO: Test AUC: 0.500
0:38:57.064394 INFO: Train AUC: 0.507
0:38:57.064424 INFO: AUC difference: 1.36%
0:38:57.287589 INFO: Resetting torch num_threads to 80
0:38:57.292576 PROGRESS: === Extracted 12342 precursors and 86376 fragments ===
0:38:57.292978 INFO: === FDR correction performed with classifier version -1 ===
0:38:57.293470 PROGRESS: ============================= Precursor FDR =============================
0:38:57.293561 PROGRESS: Total precursors accumulated: 1
0:38:57.293617 PROGRESS: Target precursors: 1 (100.00%)
0:38:57.293664 PROGRESS: Decoy precursors: 0 (0.00%)
0:38:57.293708 PROGRESS: 
0:38:57.293750 PROGRESS: Precursor Summary:
0:38:57.294693 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:38:57.294783 PROGRESS: 
0:38:57.294838 PROGRESS: Protein Summary:
0:38:57.295868 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:38:57.295955 PROGRESS: =========================================================================
0:38:57.296299 INFO: Target number of precursors not reached yet.
0:38:57.313736 INFO: Starting optimization step 5.
0:38:57.313903 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:38:57.313977 INFO: Using ng extraction backend
0:38:57.314046 PROGRESS: Extracting batch of 12737 precursors
0:38:57.338610 INFO: === Search parameters used ===
0:38:57.339080 INFO: rt_error       : 805.5992431640625
0:38:57.339142 INFO: mobility_error : 0.1
0:38:57.339196 INFO: num_candidates : 1
0:38:57.339243 INFO: ms1_error      : 30
0:38:57.339288 INFO: ms2_error      : 30
0:38:57.339327 INFO: fwhm_rt        : 5
0:38:57.339368 INFO: quant_window   : 3
0:38:57.339408 INFO: ==============================================
0:38:57.485878 INFO: performing precursor FDR with 40 features
0:38:57.485983 INFO: Decoy channel: -1
0:38:57.486014 INFO: Competetive: True
0:38:57.500697 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:57.508844 INFO: Using random state 605767 for train-test-split
0:38:57.833592 INFO: Test AUC: 0.806
0:38:57.833705 INFO: Train AUC: 0.800
0:38:57.833734 INFO: AUC difference: 0.71%
0:38:58.091039 INFO: Resetting torch num_threads to 80
0:38:58.102490 PROGRESS: === Extracted 25055 precursors and 175639 fragments ===
0:38:58.103132 INFO: === FDR correction performed with classifier version -1 ===
0:38:58.105107 PROGRESS: ============================= Precursor FDR =============================
0:38:58.105248 PROGRESS: Total precursors accumulated: 3,288
0:38:58.105328 PROGRESS: Target precursors: 3,256 (99.03%)
0:38:58.105397 PROGRESS: Decoy precursors: 32 (0.97%)
0:38:58.105458 PROGRESS: 
0:38:58.105518 PROGRESS: Precursor Summary:
0:38:58.107669 PROGRESS: Channel   0:	 0.050 FDR: 3,256; 0.010 FDR: 3,256; 0.001 FDR: 1,410
0:38:58.107797 PROGRESS: 
0:38:58.107876 PROGRESS: Protein Summary:
0:38:58.110267 PROGRESS: Channel   0:	 0.050 FDR: 2,126; 0.010 FDR: 2,126; 0.001 FDR: 1,052
0:38:58.110380 PROGRESS: =========================================================================
0:38:58.111335 INFO: Target number of precursors reached.
0:38:58.142374 INFO: fragments_df: keeping 5000 of 175639 [sum(precursor_idx_mask)=36340 sum(mass_error_mask)=175639 stop_rank=5000
0:38:58.156247 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:58.704243 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:59.406261 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:38:59.407158 INFO: Using score_cutoff 14.58962819480896 (fac=0.99, q=1)
0:38:59.407679 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:38:59.407758 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:38:59.407827 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.58962819480896
0:38:59.407903 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:59.410967 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:59.415681 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:38:59.415784 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:38:59.415886 INFO: Starting optimization step 6.
0:38:59.415959 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:38:59.416049 INFO: Using ng extraction backend
0:38:59.416129 PROGRESS: Extracting batch of 2794 precursors
0:38:59.423263 INFO: === Search parameters used ===
0:38:59.423376 INFO: rt_error       : 805.5992431640625
0:38:59.423429 INFO: mobility_error : 0.1
0:38:59.423475 INFO: num_candidates : 3
0:38:59.423518 INFO: ms1_error      : 30
0:38:59.423559 INFO: ms2_error      : 30
0:38:59.423599 INFO: fwhm_rt        : 3.0
0:38:59.423637 INFO: quant_window   : 3
0:38:59.423675 INFO: ==============================================
0:38:59.495857 INFO: performing precursor FDR with 40 features
0:38:59.495961 INFO: Decoy channel: -1
0:38:59.495986 INFO: Competetive: True
0:38:59.500194 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:59.503015 INFO: Using random state 512275 for train-test-split
0:38:59.525237 INFO: Test AUC: 0.637
0:38:59.525329 INFO: Train AUC: 0.645
0:38:59.525361 INFO: AUC difference: 1.23%
0:38:59.747422 INFO: Resetting torch num_threads to 80
0:38:59.749213 PROGRESS: === Extracted 8372 precursors and 51242 fragments ===
0:38:59.749558 INFO: === FDR correction performed with classifier version 5 ===
0:38:59.750035 PROGRESS: ============================= Precursor FDR =============================
0:38:59.750121 PROGRESS: Total precursors accumulated: 357
0:38:59.750181 PROGRESS: Target precursors: 354 (99.16%)
0:38:59.750231 PROGRESS: Decoy precursors: 3 (0.84%)
0:38:59.750274 PROGRESS: 
0:38:59.750315 PROGRESS: Precursor Summary:
0:38:59.751284 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   354; 0.001 FDR:   318
0:38:59.751374 PROGRESS: 
0:38:59.751427 PROGRESS: Protein Summary:
0:38:59.752542 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   326; 0.001 FDR:   293
0:38:59.752628 PROGRESS: =========================================================================
0:38:59.754621 INFO: Target number of precursors reached.
0:38:59.760570 INFO: fragments_df: keeping 4483 of 51242 [sum(precursor_idx_mask)=8247 sum(mass_error_mask)=51242 stop_rank=4483
0:38:59.769374 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:59.881125 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:00.414721 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:00.415149 INFO: Using score_cutoff 15.977131450653076 (fac=0.99, q=1)
0:39:00.415442 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:00.415518 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:00.415570 INFO: Updating optimization_manager: score_cutoff        : 14.58962819480896 -> 15.977131450653076
0:39:00.415622 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:00.417925 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:00.422024 INFO: === checking if optimization conditions were reached ===
0:39:00.423627 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.171496
0:39:00.423728 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:39:00.423791 PROGRESS: ❌ ms2_error      : 7.1715 > 7.1715 or insufficient steps taken.
0:39:00.423847 INFO: ==============================================
0:39:00.423908 INFO: Starting optimization step 7.
0:39:00.423962 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:39:00.424018 INFO: Using ng extraction backend
0:39:00.424068 PROGRESS: Extracting batch of 2794 precursors
0:39:00.430110 INFO: === Search parameters used ===
0:39:00.430212 INFO: rt_error       : 805.5992431640625
0:39:00.430262 INFO: mobility_error : 0.1
0:39:00.430305 INFO: num_candidates : 3
0:39:00.430343 INFO: ms1_error      : 30
0:39:00.430381 INFO: ms2_error      : 7.171496
0:39:00.430418 INFO: fwhm_rt        : 3.0
0:39:00.430462 INFO: quant_window   : 3
0:39:00.430499 INFO: ==============================================
0:39:00.492668 INFO: performing precursor FDR with 40 features
0:39:00.492773 INFO: Decoy channel: -1
0:39:00.492799 INFO: Competetive: True
0:39:00.496406 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:00.499050 INFO: Using random state 798691 for train-test-split
0:39:00.519714 INFO: Test AUC: 0.674
0:39:00.519803 INFO: Train AUC: 0.676
0:39:00.519832 INFO: AUC difference: 0.25%
0:39:02.184344 INFO: Resetting torch num_threads to 80
0:39:02.186160 PROGRESS: === Extracted 8382 precursors and 59331 fragments ===
0:39:02.186494 INFO: === FDR correction performed with classifier version 6 ===
0:39:02.187026 PROGRESS: ============================= Precursor FDR =============================
0:39:02.187111 PROGRESS: Total precursors accumulated: 707
0:39:02.187168 PROGRESS: Target precursors: 700 (99.01%)
0:39:02.187215 PROGRESS: Decoy precursors: 7 (0.99%)
0:39:02.187258 PROGRESS: 
0:39:02.187299 PROGRESS: Precursor Summary:
0:39:02.188317 PROGRESS: Channel   0:	 0.050 FDR:   700; 0.010 FDR:   684; 0.001 FDR:   332
0:39:02.188405 PROGRESS: 
0:39:02.188459 PROGRESS: Protein Summary:
0:39:02.189720 PROGRESS: Channel   0:	 0.050 FDR:   635; 0.010 FDR:   621; 0.001 FDR:   310
0:39:02.189815 PROGRESS: =========================================================================
0:39:02.190068 INFO: Target number of precursors reached.
0:39:02.197771 INFO: fragments_df: keeping 5000 of 59331 [sum(precursor_idx_mask)=17078 sum(mass_error_mask)=59331 stop_rank=5000
0:39:02.202813 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:02.335467 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:02.953083 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:02.953511 INFO: Using score_cutoff 12.883429781055451 (fac=0.99, q=1)
0:39:02.953798 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:02.953875 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:02.953928 INFO: Updating optimization_manager: score_cutoff        : 15.977131450653076 -> 12.883429781055451
0:39:02.953980 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:02.955518 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:02.957678 INFO: === checking if optimization conditions were reached ===
0:39:02.959285 INFO: Updating optimization_manager: ms2_error           : 7.171496 -> 7.171496
0:39:02.959385 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:39:02.959446 PROGRESS: ✅ ms2_error      : 7.1715 <= 7.1715
0:39:02.959503 INFO: ==============================================
0:39:02.959565 PROGRESS: Optimization finished for ms2_error.
0:39:02.964309 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:02.965602 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:02.967737 INFO: Starting optimization step 0.
0:39:02.967830 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:02.967898 INFO: Using ng extraction backend
0:39:02.967956 PROGRESS: Extracting batch of 1196 precursors
0:39:02.971293 INFO: === Search parameters used ===
0:39:02.971392 INFO: rt_error       : 805.5992431640625
0:39:02.971444 INFO: mobility_error : 0.1
0:39:02.971488 INFO: num_candidates : 3
0:39:02.971531 INFO: ms1_error      : 30
0:39:02.971570 INFO: ms2_error      : 7.171496
0:39:02.971610 INFO: fwhm_rt        : 3.0
0:39:02.971649 INFO: quant_window   : 3
0:39:02.971687 INFO: ==============================================
0:39:03.008927 INFO: performing precursor FDR with 40 features
0:39:03.009011 INFO: Decoy channel: -1
0:39:03.009037 INFO: Competetive: True
0:39:03.011650 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:03.013404 INFO: Using random state 179364 for train-test-split
0:39:03.025976 INFO: Test AUC: 0.664
0:39:03.026044 INFO: Train AUC: 0.686
0:39:03.026073 INFO: AUC difference: 3.18%
0:39:03.247084 INFO: Resetting torch num_threads to 80
0:39:03.248672 PROGRESS: === Extracted 3588 precursors and 25494 fragments ===
0:39:03.249014 INFO: === FDR correction performed with classifier version 7 ===
0:39:03.249476 PROGRESS: ============================= Precursor FDR =============================
0:39:03.249562 PROGRESS: Total precursors accumulated: 330
0:39:03.249618 PROGRESS: Target precursors: 327 (99.09%)
0:39:03.249667 PROGRESS: Decoy precursors: 3 (0.91%)
0:39:03.249712 PROGRESS: 
0:39:03.249754 PROGRESS: Precursor Summary:
0:39:03.250722 PROGRESS: Channel   0:	 0.050 FDR:   327; 0.010 FDR:   327; 0.001 FDR:   274
0:39:03.250814 PROGRESS: 
0:39:03.250871 PROGRESS: Protein Summary:
0:39:03.252022 PROGRESS: Channel   0:	 0.050 FDR:   313; 0.010 FDR:   313; 0.001 FDR:   261
0:39:03.252114 PROGRESS: =========================================================================
0:39:03.252350 INFO: Target number of precursors reached.
0:39:03.256450 INFO: fragments_df: keeping 3692 of 25494 [sum(precursor_idx_mask)=8163 sum(mass_error_mask)=25494 stop_rank=3692
0:39:03.261345 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:03.383855 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:03.867074 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:03.867501 INFO: Using score_cutoff 12.571093389701842 (fac=0.99, q=1)
0:39:03.867783 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:03.867859 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:03.867911 INFO: Updating optimization_manager: score_cutoff        : 12.883429781055451 -> 12.571093389701842
0:39:03.867962 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:03.869509 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:03.871693 INFO: === checking if optimization conditions were reached ===
0:39:03.871804 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:39:03.873241 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 57.54242207230214
0:39:03.873347 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 57.5424.
0:39:03.873410 INFO: ==============================================
0:39:03.873475 INFO: Starting optimization step 1.
0:39:03.873530 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:03.873587 INFO: Using ng extraction backend
0:39:03.873641 PROGRESS: Extracting batch of 1196 precursors
0:39:03.876926 INFO: === Search parameters used ===
0:39:03.877018 INFO: rt_error       : 57.54242207230214
0:39:03.877069 INFO: mobility_error : 0.1
0:39:03.877112 INFO: num_candidates : 3
0:39:03.877155 INFO: ms1_error      : 30
0:39:03.877196 INFO: ms2_error      : 7.171496
0:39:03.877236 INFO: fwhm_rt        : 3.0
0:39:03.877273 INFO: quant_window   : 3
0:39:03.877311 INFO: ==============================================
0:39:03.911308 INFO: performing precursor FDR with 40 features
0:39:03.911388 INFO: Decoy channel: -1
0:39:03.911412 INFO: Competetive: True
0:39:03.913989 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:03.915731 INFO: Using random state 179364 for train-test-split
0:39:03.927488 INFO: Test AUC: 0.701
0:39:03.927551 INFO: Train AUC: 0.679
0:39:03.927580 INFO: AUC difference: 3.17%
0:39:04.145322 INFO: Resetting torch num_threads to 80
0:39:04.146884 PROGRESS: === Extracted 3504 precursors and 21266 fragments ===
0:39:04.147226 INFO: === FDR correction performed with classifier version 7 ===
0:39:04.147710 PROGRESS: ============================= Precursor FDR =============================
0:39:04.147796 PROGRESS: Total precursors accumulated: 424
0:39:04.147852 PROGRESS: Target precursors: 420 (99.06%)
0:39:04.147901 PROGRESS: Decoy precursors: 4 (0.94%)
0:39:04.147949 PROGRESS: 
0:39:04.147993 PROGRESS: Precursor Summary:
0:39:04.148954 PROGRESS: Channel   0:	 0.050 FDR:   420; 0.010 FDR:   420; 0.001 FDR:   296
0:39:04.149042 PROGRESS: 
0:39:04.149095 PROGRESS: Protein Summary:
0:39:04.150274 PROGRESS: Channel   0:	 0.050 FDR:   406; 0.010 FDR:   406; 0.001 FDR:   284
0:39:04.150361 PROGRESS: =========================================================================
0:39:04.150586 INFO: Target number of precursors reached.
0:39:04.154447 INFO: fragments_df: keeping 4039 of 21266 [sum(precursor_idx_mask)=8997 sum(mass_error_mask)=21266 stop_rank=4039
0:39:04.159332 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:04.286969 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:04.816793 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:04.817221 INFO: Using score_cutoff 11.774121041965484 (fac=0.99, q=1)
0:39:04.817508 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:04.817585 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:04.817640 INFO: Updating optimization_manager: score_cutoff        : 12.571093389701842 -> 11.774121041965484
0:39:04.817694 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:04.819229 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:04.821465 INFO: === checking if optimization conditions were reached ===
0:39:04.821559 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:39:04.823159 INFO: Updating optimization_manager: rt_error            : 57.54242207230214 -> 17.963156733961107
0:39:04.823255 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 17.9632.
0:39:04.823322 INFO: ==============================================
0:39:04.823389 INFO: Starting optimization step 2.
0:39:04.823447 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:04.823506 INFO: Using ng extraction backend
0:39:04.823563 PROGRESS: Extracting batch of 1196 precursors
0:39:04.826885 INFO: === Search parameters used ===
0:39:04.826975 INFO: rt_error       : 17.963156733961107
0:39:04.827026 INFO: mobility_error : 0.1
0:39:04.827070 INFO: num_candidates : 3
0:39:04.827110 INFO: ms1_error      : 30
0:39:04.827149 INFO: ms2_error      : 7.171496
0:39:04.827187 INFO: fwhm_rt        : 3.0
0:39:04.827227 INFO: quant_window   : 3
0:39:04.827266 INFO: ==============================================
0:39:04.858837 INFO: performing precursor FDR with 40 features
0:39:04.858913 INFO: Decoy channel: -1
0:39:04.858939 INFO: Competetive: True
0:39:04.861462 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:04.863169 INFO: Using random state 179364 for train-test-split
0:39:04.874905 INFO: Test AUC: 0.703
0:39:04.874967 INFO: Train AUC: 0.686
0:39:04.874995 INFO: AUC difference: 2.55%
0:39:05.091442 INFO: Resetting torch num_threads to 80
0:39:05.092995 PROGRESS: === Extracted 3292 precursors and 19771 fragments ===
0:39:05.093328 INFO: === FDR correction performed with classifier version 7 ===
0:39:05.093794 PROGRESS: ============================= Precursor FDR =============================
0:39:05.093879 PROGRESS: Total precursors accumulated: 468
0:39:05.093946 PROGRESS: Target precursors: 464 (99.15%)
0:39:05.093998 PROGRESS: Decoy precursors: 4 (0.85%)
0:39:05.094043 PROGRESS: 
0:39:05.094085 PROGRESS: Precursor Summary:
0:39:05.095063 PROGRESS: Channel   0:	 0.050 FDR:   464; 0.010 FDR:   464; 0.001 FDR:   297
0:39:05.095151 PROGRESS: 
0:39:05.095203 PROGRESS: Protein Summary:
0:39:05.096345 PROGRESS: Channel   0:	 0.050 FDR:   446; 0.010 FDR:   446; 0.001 FDR:   285
0:39:05.096433 PROGRESS: =========================================================================
0:39:05.096626 INFO: Target number of precursors reached.
0:39:05.100326 INFO: fragments_df: keeping 4101 of 19771 [sum(precursor_idx_mask)=9104 sum(mass_error_mask)=19771 stop_rank=4101
0:39:05.105197 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:05.224103 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:05.697429 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:05.697876 INFO: Using score_cutoff 11.379256678962706 (fac=0.99, q=1)
0:39:05.698189 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:05.698279 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:05.698352 INFO: Updating optimization_manager: score_cutoff        : 11.774121041965484 -> 11.379256678962706
0:39:05.698422 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:05.699985 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:05.702257 INFO: === checking if optimization conditions were reached ===
0:39:05.702362 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:39:05.704132 INFO: Updating optimization_manager: rt_error            : 17.963156733961107 -> 16.73808264476773
0:39:05.704243 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 16.7381.
0:39:05.704324 INFO: ==============================================
0:39:05.704407 INFO: Starting optimization step 3.
0:39:05.704482 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:05.704559 INFO: Using ng extraction backend
0:39:05.704631 PROGRESS: Extracting batch of 1196 precursors
0:39:05.707998 INFO: === Search parameters used ===
0:39:05.708102 INFO: rt_error       : 16.73808264476773
0:39:05.708169 INFO: mobility_error : 0.1
0:39:05.708231 INFO: num_candidates : 3
0:39:05.708290 INFO: ms1_error      : 30
0:39:05.708347 INFO: ms2_error      : 7.171496
0:39:05.708403 INFO: fwhm_rt        : 3.0
0:39:05.708459 INFO: quant_window   : 3
0:39:05.708515 INFO: ==============================================
0:39:05.743345 INFO: performing precursor FDR with 40 features
0:39:05.743459 INFO: Decoy channel: -1
0:39:05.743486 INFO: Competetive: True
0:39:05.746089 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:05.747870 INFO: Using random state 179364 for train-test-split
0:39:05.760207 INFO: Test AUC: 0.685
0:39:05.760275 INFO: Train AUC: 0.690
0:39:05.760304 INFO: AUC difference: 0.66%
0:39:05.978148 INFO: Resetting torch num_threads to 80
0:39:05.979690 PROGRESS: === Extracted 3295 precursors and 19759 fragments ===
0:39:05.980021 INFO: === FDR correction performed with classifier version 7 ===
0:39:05.980479 PROGRESS: ============================= Precursor FDR =============================
0:39:05.980570 PROGRESS: Total precursors accumulated: 467
0:39:05.980627 PROGRESS: Target precursors: 463 (99.14%)
0:39:05.980676 PROGRESS: Decoy precursors: 4 (0.86%)
0:39:05.980719 PROGRESS: 
0:39:05.980760 PROGRESS: Precursor Summary:
0:39:05.981701 PROGRESS: Channel   0:	 0.050 FDR:   463; 0.010 FDR:   463; 0.001 FDR:   298
0:39:05.981787 PROGRESS: 
0:39:05.981841 PROGRESS: Protein Summary:
0:39:05.983002 PROGRESS: Channel   0:	 0.050 FDR:   445; 0.010 FDR:   445; 0.001 FDR:   286
0:39:05.983094 PROGRESS: =========================================================================
0:39:05.983297 INFO: Target number of precursors reached.
0:39:05.987012 INFO: fragments_df: keeping 4091 of 19759 [sum(precursor_idx_mask)=9086 sum(mass_error_mask)=19759 stop_rank=4091
0:39:05.991906 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:06.122155 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:06.658212 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:06.658650 INFO: Using score_cutoff 11.379163945770264 (fac=0.99, q=1)
0:39:06.658936 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:06.659014 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:06.659069 INFO: Updating optimization_manager: score_cutoff        : 11.379256678962706 -> 11.379163945770264
0:39:06.659125 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:06.660669 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:06.662925 INFO: === checking if optimization conditions were reached ===
0:39:06.663022 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:39:06.664680 INFO: Updating optimization_manager: rt_error            : 16.73808264476773 -> 16.66843787898815
0:39:06.664786 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.6684.
0:39:06.664852 INFO: ==============================================
0:39:06.664919 INFO: Starting optimization step 4.
0:39:06.664978 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:06.665038 INFO: Using ng extraction backend
0:39:06.665093 PROGRESS: Extracting batch of 1196 precursors
0:39:06.668402 INFO: === Search parameters used ===
0:39:06.668490 INFO: rt_error       : 16.66843787898815
0:39:06.668540 INFO: mobility_error : 0.1
0:39:06.668584 INFO: num_candidates : 3
0:39:06.668625 INFO: ms1_error      : 30
0:39:06.668665 INFO: ms2_error      : 7.171496
0:39:06.668705 INFO: fwhm_rt        : 3.0
0:39:06.668744 INFO: quant_window   : 3
0:39:06.668781 INFO: ==============================================
0:39:06.701536 INFO: performing precursor FDR with 40 features
0:39:06.701612 INFO: Decoy channel: -1
0:39:06.701638 INFO: Competetive: True
0:39:06.704291 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:06.706009 INFO: Using random state 179364 for train-test-split
0:39:06.718169 INFO: Test AUC: 0.666
0:39:06.718234 INFO: Train AUC: 0.694
0:39:06.718264 INFO: AUC difference: 4.03%
0:39:06.935221 INFO: Resetting torch num_threads to 80
0:39:06.936761 PROGRESS: === Extracted 3296 precursors and 19763 fragments ===
0:39:06.937105 INFO: === FDR correction performed with classifier version 7 ===
0:39:06.937567 PROGRESS: ============================= Precursor FDR =============================
0:39:06.937651 PROGRESS: Total precursors accumulated: 467
0:39:06.937707 PROGRESS: Target precursors: 463 (99.14%)
0:39:06.937755 PROGRESS: Decoy precursors: 4 (0.86%)
0:39:06.937799 PROGRESS: 
0:39:06.937840 PROGRESS: Precursor Summary:
0:39:06.938794 PROGRESS: Channel   0:	 0.050 FDR:   463; 0.010 FDR:   463; 0.001 FDR:   298
0:39:06.938884 PROGRESS: 
0:39:06.938936 PROGRESS: Protein Summary:
0:39:06.940093 PROGRESS: Channel   0:	 0.050 FDR:   445; 0.010 FDR:   445; 0.001 FDR:   286
0:39:06.940183 PROGRESS: =========================================================================
0:39:06.940382 INFO: Target number of precursors reached.
0:39:06.944010 INFO: fragments_df: keeping 4091 of 19763 [sum(precursor_idx_mask)=9085 sum(mass_error_mask)=19763 stop_rank=4091
0:39:06.948918 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:07.089339 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:07.625628 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:07.626055 INFO: Using score_cutoff 11.379163945770264 (fac=0.99, q=1)
0:39:07.626339 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:07.626416 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:07.626476 INFO: Updating optimization_manager: score_cutoff        : 11.379163945770264 -> 11.379163945770264
0:39:07.626529 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:07.628063 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:07.630253 INFO: === checking if optimization conditions were reached ===
0:39:07.630348 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:39:07.631247 INFO: Updating optimization_manager: rt_error            : 16.66843787898815 -> 16.66843787898815
0:39:07.631371 INFO: Updating optimization_manager: classifier_version  : 7 -> 12
0:39:07.631464 INFO: Updating optimization_manager: score_cutoff        : 11.379163945770264 -> 11.379163945770264
0:39:07.631546 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:07.631626 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:07.631706 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 16.6684 found after 5 searches.
0:39:07.631764 INFO: ==============================================
0:39:07.631827 PROGRESS: Optimization finished for rt_error.
0:39:07.636522 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:07.637820 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:07.665401 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:39:07.665553 PROGRESS: ==============================================
0:39:07.665618 PROGRESS: ms2_error      : 7.1715
0:39:07.665670 PROGRESS: rt_error       : 16.6684
0:39:07.665739 PROGRESS: ==============================================
0:39:07.666581 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:07.798074 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:08.154047 INFO: Using ng extraction backend
0:39:08.154351 PROGRESS: Extracting batch of 240048 precursors
0:39:08.554694 INFO: === Search parameters used ===
0:39:08.554943 INFO: rt_error       : 16.66843787898815
0:39:08.555001 INFO: mobility_error : 0.1
0:39:08.555051 INFO: num_candidates : 3
0:39:08.555097 INFO: ms1_error      : 30
0:39:08.555138 INFO: ms2_error      : 7.171496
0:39:08.555181 INFO: fwhm_rt        : 3.0
0:39:08.555219 INFO: quant_window   : 3
0:39:08.555259 INFO: ==============================================
0:39:08.845940 INFO: Removed 350582 precursors with score below cutoff 11.379163945770264
0:39:09.148094 INFO: performing precursor FDR with 40 features
0:39:09.148214 INFO: Decoy channel: -1
0:39:09.148240 INFO: Competetive: True
0:39:09.183855 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:09.201816 WARNING: FDR calculation for 199077 target and 106621 decoy PSMs
0:39:09.201952 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:39:09.269514 INFO: Using random state 691296 for train-test-split
0:39:13.460415 INFO: Test AUC: 0.879
0:39:13.460544 INFO: Train AUC: 0.881
0:39:13.460574 INFO: AUC difference: 0.19%
0:39:13.770311 INFO: Resetting torch num_threads to 80
0:39:14.101319 PROGRESS: ============================= Precursor FDR =============================
0:39:14.101567 PROGRESS: Total precursors accumulated: 110,228
0:39:14.101636 PROGRESS: Target precursors: 109,137 (99.01%)
0:39:14.101691 PROGRESS: Decoy precursors: 1,091 (0.99%)
0:39:14.101737 PROGRESS: 
0:39:14.101783 PROGRESS: Precursor Summary:
0:39:14.128757 PROGRESS: Channel   0:	 0.050 FDR: 109,137; 0.010 FDR: 109,137; 0.001 FDR: 98,221
0:39:14.129011 PROGRESS: 
0:39:14.129076 PROGRESS: Protein Summary:
0:39:14.166516 PROGRESS: Channel   0:	 0.050 FDR: 10,107; 0.010 FDR: 10,107; 0.001 FDR: 9,966
0:39:14.167300 PROGRESS: =========================================================================
0:39:14.168997 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:39:14.364975 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:39:14.649153 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:39:14.896620 PROGRESS: 
0:39:14.896766 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
0:39:14.896840 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
0:39:14.896997 INFO: Initializing TimingManager
0:39:14.897482 INFO: Initializing RawFileManager
0:39:25.776999 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:39:25.781232 INFO: Determining DIA cycle
0:39:25.797614 INFO: Found cycle with start 0.00 min and length 300.
0:39:25.958856 INFO: RT (min)            : 0.0 - 26.9
0:39:25.958952 INFO: RT duration (sec)   : 1611.2
0:39:25.958981 INFO: RT duration (min)   : 26.9
0:39:25.959006 INFO: Cycle len (scans)   : 300
0:39:25.959036 INFO: Cycle len (sec)     : 1.65
0:39:25.959055 INFO: Number of cycles    : 978
0:39:25.959076 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:39:25.959127 INFO: Creating DIA data object took: 11.061542272567749
0:39:26.591404 INFO: Creating DIA data NG object took: 0.6319479942321777
0:39:26.636479 INFO: Initializing CalibrationManager
0:39:26.636842 INFO: Setting up calibration estimators ..
0:39:26.636917 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:39:26.637047 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'}' ..
0:39:26.637184 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:39:26.637267 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:39:26.637330 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}}' ..
0:39:26.637394 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:39:26.637468 INFO: Done setting up calibration estimators.
0:39:26.637760 INFO: Initializing OptimizationManager
0:39:26.637942 INFO: initial parameter: ms1_error = 30
0:39:26.638036 INFO: initial parameter: ms2_error = 30
0:39:26.638103 INFO: initial parameter: rt_error = 805.6019897460938
0:39:26.638159 INFO: initial parameter: mobility_error = 0.1
0:39:26.638214 INFO: initial parameter: num_candidates = 1
0:39:26.638278 INFO: initial parameter: fwhm_rt = 5
0:39:26.638333 INFO: initial parameter: fwhm_mobility = 0.01
0:39:26.638390 INFO: initial parameter: score_cutoff = 0
0:39:26.638447 INFO: initial parameter: classifier_version = -1
0:39:26.638573 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:39:26.639074 INFO: FDRManager: loading saved state not requested, will be initialized.
0:39:26.639132 INFO: Initializing FDRManager
0:39:26.639198 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:39:26.674265 PROGRESS: Initializing spectral library: 120,580 target precursors potentially observable (0 removed)
0:39:26.694325 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:39:26.694732 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:39:26.694849 PROGRESS: Starting initial search for precursors.
0:39:26.694944 INFO: Starting optimization step 0.
0:39:26.695020 PROGRESS: === Extracting elution groups 0 to 200 ===
0:39:26.695085 INFO: Using ng extraction backend
0:39:26.695156 PROGRESS: Extracting batch of 398 precursors
0:39:26.697186 INFO: === Search parameters used ===
0:39:26.697290 INFO: rt_error       : 805.6019897460938
0:39:26.697348 INFO: mobility_error : 0.1
0:39:26.697394 INFO: num_candidates : 1
0:39:26.697439 INFO: ms1_error      : 30
0:39:26.697479 INFO: ms2_error      : 30
0:39:26.697522 INFO: fwhm_rt        : 5
0:39:26.697564 INFO: quant_window   : 3
0:39:26.697604 INFO: ==============================================
0:39:26.715547 INFO: performing precursor FDR with 40 features
0:39:26.715657 INFO: Decoy channel: -1
0:39:26.715683 INFO: Competetive: True
0:39:26.716669 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:26.719315 INFO: Using random state 15355 for train-test-split
0:39:26.727611 INFO: Test AUC: 0.654
0:39:26.727671 INFO: Train AUC: 0.728
0:39:26.727702 INFO: AUC difference: 10.12%
0:39:26.727724 WARNING: AUC difference > 5%. This may indicate overfitting.
0:39:26.984253 INFO: Resetting torch num_threads to 80
0:39:26.986045 PROGRESS: === Extracted 398 precursors and 2807 fragments ===
0:39:26.986491 INFO: === FDR correction performed with classifier version -1 ===
0:39:26.987024 PROGRESS: ============================= Precursor FDR =============================
0:39:26.987126 PROGRESS: Total precursors accumulated: 5
0:39:26.987196 PROGRESS: Target precursors: 5 (100.00%)
0:39:26.987250 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:26.987295 PROGRESS: 
0:39:26.987340 PROGRESS: Precursor Summary:
0:39:26.988373 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
0:39:26.988467 PROGRESS: 
0:39:26.988527 PROGRESS: Protein Summary:
0:39:26.989683 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
0:39:26.989780 PROGRESS: =========================================================================
0:39:26.989999 INFO: Target number of precursors not reached yet.
0:39:26.994925 INFO: Starting optimization step 1.
0:39:26.995056 PROGRESS: === Extracting elution groups 200 to 600 ===
0:39:26.995132 INFO: Using ng extraction backend
0:39:26.995200 PROGRESS: Extracting batch of 798 precursors
0:39:26.999270 INFO: === Search parameters used ===
0:39:26.999369 INFO: rt_error       : 805.6019897460938
0:39:26.999418 INFO: mobility_error : 0.1
0:39:26.999464 INFO: num_candidates : 1
0:39:26.999507 INFO: ms1_error      : 30
0:39:26.999547 INFO: ms2_error      : 30
0:39:26.999587 INFO: fwhm_rt        : 5
0:39:26.999631 INFO: quant_window   : 3
0:39:26.999675 INFO: ==============================================
0:39:27.027485 INFO: performing precursor FDR with 40 features
0:39:27.027644 INFO: Decoy channel: -1
0:39:27.027671 INFO: Competetive: True
0:39:27.031799 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:27.034067 INFO: Using random state 80125 for train-test-split
0:39:27.045923 INFO: Test AUC: 0.723
0:39:27.046053 INFO: Train AUC: 0.690
0:39:27.046087 INFO: AUC difference: 4.72%
0:39:27.302115 INFO: Resetting torch num_threads to 80
0:39:27.304742 PROGRESS: === Extracted 1195 precursors and 8335 fragments ===
0:39:27.305137 INFO: === FDR correction performed with classifier version -1 ===
0:39:27.305580 PROGRESS: ============================= Precursor FDR =============================
0:39:27.305668 PROGRESS: Total precursors accumulated: 0
0:39:27.305726 PROGRESS: Target precursors: 0 (0.00%)
0:39:27.305776 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:27.305823 PROGRESS: 
0:39:27.305869 PROGRESS: Precursor Summary:
0:39:27.305991 PROGRESS: 
0:39:27.306060 PROGRESS: Protein Summary:
0:39:27.306139 PROGRESS: =========================================================================
0:39:27.306399 INFO: Target number of precursors not reached yet.
0:39:27.312226 INFO: Starting optimization step 2.
0:39:27.312352 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:39:27.312425 INFO: Using ng extraction backend
0:39:27.312492 PROGRESS: Extracting batch of 1598 precursors
0:39:27.317984 INFO: === Search parameters used ===
0:39:27.318090 INFO: rt_error       : 805.6019897460938
0:39:27.318140 INFO: mobility_error : 0.1
0:39:27.318187 INFO: num_candidates : 1
0:39:27.318231 INFO: ms1_error      : 30
0:39:27.318272 INFO: ms2_error      : 30
0:39:27.318312 INFO: fwhm_rt        : 5
0:39:27.318353 INFO: quant_window   : 3
0:39:27.318393 INFO: ==============================================
0:39:27.353913 INFO: performing precursor FDR with 40 features
0:39:27.354050 INFO: Decoy channel: -1
0:39:27.354083 INFO: Competetive: True
0:39:27.358723 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:27.361466 INFO: Using random state 598828 for train-test-split
0:39:27.378382 INFO: Test AUC: 0.694
0:39:27.378473 INFO: Train AUC: 0.690
0:39:27.378511 INFO: AUC difference: 0.63%
0:39:27.602481 INFO: Resetting torch num_threads to 80
0:39:27.605727 PROGRESS: === Extracted 2792 precursors and 19347 fragments ===
0:39:27.606153 INFO: === FDR correction performed with classifier version -1 ===
0:39:27.606663 PROGRESS: ============================= Precursor FDR =============================
0:39:27.606764 PROGRESS: Total precursors accumulated: 0
0:39:27.606848 PROGRESS: Target precursors: 0 (0.00%)
0:39:27.606915 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:27.606972 PROGRESS: 
0:39:27.607036 PROGRESS: Precursor Summary:
0:39:27.607178 PROGRESS: 
0:39:27.607251 PROGRESS: Protein Summary:
0:39:27.607342 PROGRESS: =========================================================================
0:39:27.607696 INFO: Target number of precursors not reached yet.
0:39:27.616408 INFO: Starting optimization step 3.
0:39:27.616569 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:39:27.616658 INFO: Using ng extraction backend
0:39:27.616734 PROGRESS: Extracting batch of 3190 precursors
0:39:27.625952 INFO: === Search parameters used ===
0:39:27.626119 INFO: rt_error       : 805.6019897460938
0:39:27.626190 INFO: mobility_error : 0.1
0:39:27.626250 INFO: num_candidates : 1
0:39:27.626306 INFO: ms1_error      : 30
0:39:27.626365 INFO: ms2_error      : 30
0:39:27.626418 INFO: fwhm_rt        : 5
0:39:27.626471 INFO: quant_window   : 3
0:39:27.626523 INFO: ==============================================
0:39:27.684724 INFO: performing precursor FDR with 40 features
0:39:27.684846 INFO: Decoy channel: -1
0:39:27.684878 INFO: Competetive: True
0:39:27.695088 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:27.699835 INFO: Using random state 24545 for train-test-split
0:39:27.737146 INFO: Test AUC: 0.686
0:39:27.737276 INFO: Train AUC: 0.697
0:39:27.737312 INFO: AUC difference: 1.63%
0:39:27.967994 INFO: Resetting torch num_threads to 80
0:39:27.973198 PROGRESS: === Extracted 5974 precursors and 41512 fragments ===
0:39:27.973650 INFO: === FDR correction performed with classifier version -1 ===
0:39:27.974171 PROGRESS: ============================= Precursor FDR =============================
0:39:27.974270 PROGRESS: Total precursors accumulated: 0
0:39:27.974347 PROGRESS: Target precursors: 0 (0.00%)
0:39:27.974410 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:27.974468 PROGRESS: 
0:39:27.974523 PROGRESS: Precursor Summary:
0:39:27.974678 PROGRESS: 
0:39:27.974758 PROGRESS: Protein Summary:
0:39:27.974859 PROGRESS: =========================================================================
0:39:27.975262 INFO: Target number of precursors not reached yet.
0:39:27.989541 INFO: Starting optimization step 4.
0:39:27.989698 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:39:27.989798 INFO: Using ng extraction backend
0:39:27.989877 PROGRESS: Extracting batch of 6370 precursors
0:39:28.003379 INFO: === Search parameters used ===
0:39:28.003566 INFO: rt_error       : 805.6019897460938
0:39:28.003638 INFO: mobility_error : 0.1
0:39:28.003698 INFO: num_candidates : 1
0:39:28.003757 INFO: ms1_error      : 30
0:39:28.003811 INFO: ms2_error      : 30
0:39:28.003864 INFO: fwhm_rt        : 5
0:39:28.003927 INFO: quant_window   : 3
0:39:28.003984 INFO: ==============================================
0:39:28.089452 INFO: performing precursor FDR with 40 features
0:39:28.089606 INFO: Decoy channel: -1
0:39:28.089641 INFO: Competetive: True
0:39:28.103356 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:28.108776 INFO: Using random state 536104 for train-test-split
0:39:28.169365 INFO: Test AUC: 0.701
0:39:28.169521 INFO: Train AUC: 0.697
0:39:28.169557 INFO: AUC difference: 0.58%
0:39:28.408249 INFO: Resetting torch num_threads to 80
0:39:28.413327 PROGRESS: === Extracted 12330 precursors and 85693 fragments ===
0:39:28.413805 INFO: === FDR correction performed with classifier version -1 ===
0:39:28.414342 PROGRESS: ============================= Precursor FDR =============================
0:39:28.414443 PROGRESS: Total precursors accumulated: 2
0:39:28.414519 PROGRESS: Target precursors: 2 (100.00%)
0:39:28.414597 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:28.414671 PROGRESS: 
0:39:28.414729 PROGRESS: Precursor Summary:
0:39:28.415855 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:39:28.415955 PROGRESS: 
0:39:28.416028 PROGRESS: Protein Summary:
0:39:28.417214 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:39:28.417326 PROGRESS: =========================================================================
0:39:28.417742 INFO: Target number of precursors not reached yet.
0:39:28.441540 INFO: Starting optimization step 5.
0:39:28.441776 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:39:28.441895 INFO: Using ng extraction backend
0:39:28.441983 PROGRESS: Extracting batch of 12737 precursors
0:39:28.468904 INFO: === Search parameters used ===
0:39:28.469460 INFO: rt_error       : 805.6019897460938
0:39:28.469542 INFO: mobility_error : 0.1
0:39:28.469604 INFO: num_candidates : 1
0:39:28.469669 INFO: ms1_error      : 30
0:39:28.469724 INFO: ms2_error      : 30
0:39:28.469779 INFO: fwhm_rt        : 5
0:39:28.469831 INFO: quant_window   : 3
0:39:28.469885 INFO: ==============================================
0:39:28.620043 INFO: performing precursor FDR with 40 features
0:39:28.620161 INFO: Decoy channel: -1
0:39:28.620187 INFO: Competetive: True
0:39:28.631852 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:28.637941 INFO: Using random state 474124 for train-test-split
0:39:29.042273 INFO: Test AUC: 0.791
0:39:29.042423 INFO: Train AUC: 0.796
0:39:29.042454 INFO: AUC difference: 0.64%
0:39:29.276914 INFO: Resetting torch num_threads to 80
0:39:29.284767 PROGRESS: === Extracted 25051 precursors and 174643 fragments ===
0:39:29.285241 INFO: === FDR correction performed with classifier version -1 ===
0:39:29.286122 PROGRESS: ============================= Precursor FDR =============================
0:39:29.286229 PROGRESS: Total precursors accumulated: 2,933
0:39:29.286288 PROGRESS: Target precursors: 2,904 (99.01%)
0:39:29.286337 PROGRESS: Decoy precursors: 29 (0.99%)
0:39:29.286381 PROGRESS: 
0:39:29.286422 PROGRESS: Precursor Summary:
0:39:29.287981 PROGRESS: Channel   0:	 0.050 FDR: 2,904; 0.010 FDR: 2,904; 0.001 FDR:    13
0:39:29.288088 PROGRESS: 
0:39:29.288147 PROGRESS: Protein Summary:
0:39:29.290175 PROGRESS: Channel   0:	 0.050 FDR: 1,947; 0.010 FDR: 1,947; 0.001 FDR:    13
0:39:29.290281 PROGRESS: =========================================================================
0:39:29.290797 INFO: Target number of precursors reached.
0:39:29.313222 INFO: fragments_df: keeping 5000 of 174643 [sum(precursor_idx_mask)=32694 sum(mass_error_mask)=174643 stop_rank=5000
0:39:29.323230 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:29.667260 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:30.287886 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:39:30.288449 INFO: Using score_cutoff 14.54094419403076 (fac=0.99, q=1)
0:39:30.288829 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:39:30.288909 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:39:30.288964 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.54094419403076
0:39:30.289032 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:30.291547 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:30.295811 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:39:30.295924 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:39:30.296006 INFO: Starting optimization step 6.
0:39:30.296069 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:39:30.296131 INFO: Using ng extraction backend
0:39:30.296189 PROGRESS: Extracting batch of 2794 precursors
0:39:30.303324 INFO: === Search parameters used ===
0:39:30.303435 INFO: rt_error       : 805.6019897460938
0:39:30.303486 INFO: mobility_error : 0.1
0:39:30.303534 INFO: num_candidates : 3
0:39:30.303586 INFO: ms1_error      : 30
0:39:30.303629 INFO: ms2_error      : 30
0:39:30.303671 INFO: fwhm_rt        : 3.0
0:39:30.303712 INFO: quant_window   : 3
0:39:30.303754 INFO: ==============================================
0:39:30.371027 INFO: performing precursor FDR with 40 features
0:39:30.371176 INFO: Decoy channel: -1
0:39:30.371202 INFO: Competetive: True
0:39:30.374833 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:30.377578 INFO: Using random state 635338 for train-test-split
0:39:30.400192 INFO: Test AUC: 0.622
0:39:30.400312 INFO: Train AUC: 0.648
0:39:30.400343 INFO: AUC difference: 4.06%
0:39:30.621083 INFO: Resetting torch num_threads to 80
0:39:30.622950 PROGRESS: === Extracted 8371 precursors and 50584 fragments ===
0:39:30.623325 INFO: === FDR correction performed with classifier version 5 ===
0:39:30.623808 PROGRESS: ============================= Precursor FDR =============================
0:39:30.623897 PROGRESS: Total precursors accumulated: 352
0:39:30.623954 PROGRESS: Target precursors: 349 (99.15%)
0:39:30.624004 PROGRESS: Decoy precursors: 3 (0.85%)
0:39:30.624048 PROGRESS: 
0:39:30.624091 PROGRESS: Precursor Summary:
0:39:30.625080 PROGRESS: Channel   0:	 0.050 FDR:   349; 0.010 FDR:   349; 0.001 FDR:   244
0:39:30.625169 PROGRESS: 
0:39:30.625224 PROGRESS: Protein Summary:
0:39:30.626351 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   321; 0.001 FDR:   230
0:39:30.626440 PROGRESS: =========================================================================
0:39:30.626930 INFO: Target number of precursors reached.
0:39:30.632908 INFO: fragments_df: keeping 4438 of 50584 [sum(precursor_idx_mask)=8177 sum(mass_error_mask)=50584 stop_rank=4438
0:39:30.641532 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:30.761720 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:31.354788 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:31.355332 INFO: Using score_cutoff 15.862745860290527 (fac=0.99, q=1)
0:39:31.355646 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:31.355727 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:31.355782 INFO: Updating optimization_manager: score_cutoff        : 14.54094419403076 -> 15.862745860290527
0:39:31.355837 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:31.358299 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:31.362371 INFO: === checking if optimization conditions were reached ===
0:39:31.363947 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.171496
0:39:31.364059 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:39:31.364125 PROGRESS: ❌ ms2_error      : 7.1715 > 7.1715 or insufficient steps taken.
0:39:31.364183 INFO: ==============================================
0:39:31.364246 INFO: Starting optimization step 7.
0:39:31.364303 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:39:31.364362 INFO: Using ng extraction backend
0:39:31.364418 PROGRESS: Extracting batch of 2794 precursors
0:39:31.371301 INFO: === Search parameters used ===
0:39:31.371402 INFO: rt_error       : 805.6019897460938
0:39:31.371459 INFO: mobility_error : 0.1
0:39:31.371506 INFO: num_candidates : 3
0:39:31.371548 INFO: ms1_error      : 30
0:39:31.371587 INFO: ms2_error      : 7.171496
0:39:31.371627 INFO: fwhm_rt        : 3.0
0:39:31.371667 INFO: quant_window   : 3
0:39:31.371709 INFO: ==============================================
0:39:31.440415 INFO: performing precursor FDR with 40 features
0:39:31.440546 INFO: Decoy channel: -1
0:39:31.440574 INFO: Competetive: True
0:39:31.444598 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:31.447538 INFO: Using random state 203155 for train-test-split
0:39:31.470508 INFO: Test AUC: 0.683
0:39:31.470644 INFO: Train AUC: 0.676
0:39:31.470675 INFO: AUC difference: 1.09%
0:39:31.692624 INFO: Resetting torch num_threads to 80
0:39:31.694537 PROGRESS: === Extracted 8381 precursors and 58922 fragments ===
0:39:31.694915 INFO: === FDR correction performed with classifier version 6 ===
0:39:31.695398 PROGRESS: ============================= Precursor FDR =============================
0:39:31.695488 PROGRESS: Total precursors accumulated: 536
0:39:31.695545 PROGRESS: Target precursors: 531 (99.07%)
0:39:31.695595 PROGRESS: Decoy precursors: 5 (0.93%)
0:39:31.695639 PROGRESS: 
0:39:31.695685 PROGRESS: Precursor Summary:
0:39:31.696702 PROGRESS: Channel   0:	 0.050 FDR:   531; 0.010 FDR:   531; 0.001 FDR:   296
0:39:31.697871 PROGRESS: 
0:39:31.697931 PROGRESS: Protein Summary:
0:39:31.699221 PROGRESS: Channel   0:	 0.050 FDR:   489; 0.010 FDR:   489; 0.001 FDR:   274
0:39:31.699318 PROGRESS: =========================================================================
0:39:31.699620 INFO: Target number of precursors reached.
0:39:31.707149 INFO: fragments_df: keeping 5000 of 58922 [sum(precursor_idx_mask)=13501 sum(mass_error_mask)=58922 stop_rank=5000
0:39:31.712915 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:31.852160 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:32.531918 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:32.532431 INFO: Using score_cutoff 14.163505674362183 (fac=0.99, q=1)
0:39:32.532737 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:32.532816 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:32.532872 INFO: Updating optimization_manager: score_cutoff        : 15.862745860290527 -> 14.163505674362183
0:39:32.532928 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:32.534604 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:32.536807 INFO: === checking if optimization conditions were reached ===
0:39:32.538386 INFO: Updating optimization_manager: ms2_error           : 7.171496 -> 7.171496
0:39:32.538490 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:39:32.538555 PROGRESS: ✅ ms2_error      : 7.1715 <= 7.1715
0:39:32.538631 INFO: ==============================================
0:39:32.538696 PROGRESS: Optimization finished for ms2_error.
0:39:32.544102 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:32.545396 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:32.547553 INFO: Starting optimization step 0.
0:39:32.547651 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:32.547731 INFO: Using ng extraction backend
0:39:32.547793 PROGRESS: Extracting batch of 1196 precursors
0:39:32.552205 INFO: === Search parameters used ===
0:39:32.552297 INFO: rt_error       : 805.6019897460938
0:39:32.552347 INFO: mobility_error : 0.1
0:39:32.552391 INFO: num_candidates : 3
0:39:32.552433 INFO: ms1_error      : 30
0:39:32.552472 INFO: ms2_error      : 7.171496
0:39:32.552513 INFO: fwhm_rt        : 3.0
0:39:32.552552 INFO: quant_window   : 3
0:39:32.552595 INFO: ==============================================
0:39:32.592708 INFO: performing precursor FDR with 40 features
0:39:32.592844 INFO: Decoy channel: -1
0:39:32.592872 INFO: Competetive: True
0:39:32.595657 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:32.597628 INFO: Using random state 739375 for train-test-split
0:39:32.609298 INFO: Test AUC: 0.688
0:39:32.609364 INFO: Train AUC: 0.677
0:39:32.609393 INFO: AUC difference: 1.57%
0:39:32.828218 INFO: Resetting torch num_threads to 80
0:39:32.829875 PROGRESS: === Extracted 3588 precursors and 25405 fragments ===
0:39:32.830242 INFO: === FDR correction performed with classifier version 7 ===
0:39:32.830696 PROGRESS: ============================= Precursor FDR =============================
0:39:32.830797 PROGRESS: Total precursors accumulated: 246
0:39:32.830858 PROGRESS: Target precursors: 244 (99.19%)
0:39:32.830908 PROGRESS: Decoy precursors: 2 (0.81%)
0:39:32.830952 PROGRESS: 
0:39:32.830998 PROGRESS: Precursor Summary:
0:39:32.831882 PROGRESS: Channel   0:	 0.050 FDR:   244; 0.010 FDR:   244; 0.001 FDR:   200
0:39:32.831968 PROGRESS: 
0:39:32.832030 PROGRESS: Protein Summary:
0:39:32.833091 PROGRESS: Channel   0:	 0.050 FDR:   232; 0.010 FDR:   232; 0.001 FDR:   191
0:39:32.833180 PROGRESS: =========================================================================
0:39:32.833421 INFO: Target number of precursors reached.
0:39:32.837127 INFO: fragments_df: keeping 2909 of 25405 [sum(precursor_idx_mask)=6206 sum(mass_error_mask)=25405 stop_rank=2909
0:39:32.842799 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:32.942895 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:33.264809 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:33.265301 INFO: Using score_cutoff 14.064753246116638 (fac=0.99, q=1)
0:39:33.265605 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:33.265685 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:33.265741 INFO: Updating optimization_manager: score_cutoff        : 14.163505674362183 -> 14.064753246116638
0:39:33.265794 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:33.267478 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:33.269719 INFO: === checking if optimization conditions were reached ===
0:39:33.269837 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:39:33.271360 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 126.68643498038286
0:39:33.271461 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 126.6864.
0:39:33.271526 INFO: ==============================================
0:39:33.271600 INFO: Starting optimization step 1.
0:39:33.271662 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:33.271725 INFO: Using ng extraction backend
0:39:33.271784 PROGRESS: Extracting batch of 1196 precursors
0:39:33.276072 INFO: === Search parameters used ===
0:39:33.276164 INFO: rt_error       : 126.68643498038286
0:39:33.276214 INFO: mobility_error : 0.1
0:39:33.276260 INFO: num_candidates : 3
0:39:33.276300 INFO: ms1_error      : 30
0:39:33.276341 INFO: ms2_error      : 7.171496
0:39:33.276381 INFO: fwhm_rt        : 3.0
0:39:33.276420 INFO: quant_window   : 3
0:39:33.276458 INFO: ==============================================
0:39:33.311557 INFO: performing precursor FDR with 40 features
0:39:33.311654 INFO: Decoy channel: -1
0:39:33.311680 INFO: Competetive: True
0:39:33.314336 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:33.316197 INFO: Using random state 739375 for train-test-split
0:39:33.329424 INFO: Test AUC: 0.705
0:39:33.329496 INFO: Train AUC: 0.686
0:39:33.329526 INFO: AUC difference: 2.81%
0:39:33.549238 INFO: Resetting torch num_threads to 80
0:39:33.550889 PROGRESS: === Extracted 3588 precursors and 23917 fragments ===
0:39:33.551257 INFO: === FDR correction performed with classifier version 7 ===
0:39:33.551755 PROGRESS: ============================= Precursor FDR =============================
0:39:33.551845 PROGRESS: Total precursors accumulated: 357
0:39:33.551903 PROGRESS: Target precursors: 354 (99.16%)
0:39:33.551952 PROGRESS: Decoy precursors: 3 (0.84%)
0:39:33.551997 PROGRESS: 
0:39:33.552040 PROGRESS: Precursor Summary:
0:39:33.552978 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   354; 0.001 FDR:   228
0:39:33.553075 PROGRESS: 
0:39:33.553132 PROGRESS: Protein Summary:
0:39:33.554261 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   339; 0.001 FDR:   218
0:39:33.554352 PROGRESS: =========================================================================
0:39:33.554575 INFO: Target number of precursors reached.
0:39:33.558649 INFO: fragments_df: keeping 3793 of 23917 [sum(precursor_idx_mask)=8496 sum(mass_error_mask)=23917 stop_rank=3793
0:39:33.564247 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:33.688218 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:34.174922 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:34.175423 INFO: Using score_cutoff 12.11613478345871 (fac=0.99, q=1)
0:39:34.175732 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:34.175814 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:34.175871 INFO: Updating optimization_manager: score_cutoff        : 14.064753246116638 -> 12.11613478345871
0:39:34.175927 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:34.177624 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:34.179868 INFO: === checking if optimization conditions were reached ===
0:39:34.179977 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:39:34.181590 INFO: Updating optimization_manager: rt_error            : 126.68643498038286 -> 38.6391169233681
0:39:34.181689 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 38.6391.
0:39:34.181762 INFO: ==============================================
0:39:34.181830 INFO: Starting optimization step 2.
0:39:34.181890 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:34.181949 INFO: Using ng extraction backend
0:39:34.182004 PROGRESS: Extracting batch of 1196 precursors
0:39:34.186344 INFO: === Search parameters used ===
0:39:34.186432 INFO: rt_error       : 38.6391169233681
0:39:34.186486 INFO: mobility_error : 0.1
0:39:34.186533 INFO: num_candidates : 3
0:39:34.186587 INFO: ms1_error      : 30
0:39:34.186631 INFO: ms2_error      : 7.171496
0:39:34.186677 INFO: fwhm_rt        : 3.0
0:39:34.186719 INFO: quant_window   : 3
0:39:34.186757 INFO: ==============================================
0:39:34.222037 INFO: performing precursor FDR with 40 features
0:39:34.222131 INFO: Decoy channel: -1
0:39:34.222158 INFO: Competetive: True
0:39:34.225036 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:34.226920 INFO: Using random state 739375 for train-test-split
0:39:34.240448 INFO: Test AUC: 0.715
0:39:34.240526 INFO: Train AUC: 0.702
0:39:34.240556 INFO: AUC difference: 1.75%
0:39:34.461900 INFO: Resetting torch num_threads to 80
0:39:34.463538 PROGRESS: === Extracted 3301 precursors and 19855 fragments ===
0:39:34.463909 INFO: === FDR correction performed with classifier version 7 ===
0:39:34.464390 PROGRESS: ============================= Precursor FDR =============================
0:39:34.464478 PROGRESS: Total precursors accumulated: 459
0:39:34.464536 PROGRESS: Target precursors: 455 (99.13%)
0:39:34.464586 PROGRESS: Decoy precursors: 4 (0.87%)
0:39:34.464629 PROGRESS: 
0:39:34.464678 PROGRESS: Precursor Summary:
0:39:34.465669 PROGRESS: Channel   0:	 0.050 FDR:   455; 0.010 FDR:   455; 0.001 FDR:   229
0:39:34.465757 PROGRESS: 
0:39:34.465812 PROGRESS: Protein Summary:
0:39:34.467011 PROGRESS: Channel   0:	 0.050 FDR:   436; 0.010 FDR:   436; 0.001 FDR:   219
0:39:34.467103 PROGRESS: =========================================================================
0:39:34.467300 INFO: Target number of precursors reached.
0:39:34.471077 INFO: fragments_df: keeping 4032 of 19855 [sum(precursor_idx_mask)=8958 sum(mass_error_mask)=19855 stop_rank=4032
0:39:34.476655 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:34.611709 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:35.103907 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:35.104421 INFO: Using score_cutoff 11.762787246322631 (fac=0.99, q=1)
0:39:35.104728 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:35.104807 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:35.104861 INFO: Updating optimization_manager: score_cutoff        : 12.11613478345871 -> 11.762787246322631
0:39:35.104913 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:35.106598 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:35.108829 INFO: === checking if optimization conditions were reached ===
0:39:35.108926 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:39:35.110983 INFO: Updating optimization_manager: rt_error            : 38.6391169233681 -> 17.980134244309756
0:39:35.111082 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 17.9801.
0:39:35.111151 INFO: ==============================================
0:39:35.111217 INFO: Starting optimization step 3.
0:39:35.111276 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:35.111336 INFO: Using ng extraction backend
0:39:35.111391 PROGRESS: Extracting batch of 1196 precursors
0:39:35.115644 INFO: === Search parameters used ===
0:39:35.115736 INFO: rt_error       : 17.980134244309756
0:39:35.115786 INFO: mobility_error : 0.1
0:39:35.115833 INFO: num_candidates : 3
0:39:35.115873 INFO: ms1_error      : 30
0:39:35.115914 INFO: ms2_error      : 7.171496
0:39:35.115953 INFO: fwhm_rt        : 3.0
0:39:35.115991 INFO: quant_window   : 3
0:39:35.116029 INFO: ==============================================
0:39:35.152973 INFO: performing precursor FDR with 40 features
0:39:35.153107 INFO: Decoy channel: -1
0:39:35.153133 INFO: Competetive: True
0:39:35.156278 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:35.158321 INFO: Using random state 739375 for train-test-split
0:39:35.172676 INFO: Test AUC: 0.743
0:39:35.172757 INFO: Train AUC: 0.696
0:39:35.172787 INFO: AUC difference: 6.71%
0:39:35.172810 WARNING: AUC difference > 5%. This may indicate overfitting.
0:39:35.399610 INFO: Resetting torch num_threads to 80
0:39:35.401238 PROGRESS: === Extracted 3292 precursors and 19862 fragments ===
0:39:35.401610 INFO: === FDR correction performed with classifier version 7 ===
0:39:35.402090 PROGRESS: ============================= Precursor FDR =============================
0:39:35.402180 PROGRESS: Total precursors accumulated: 485
0:39:35.402238 PROGRESS: Target precursors: 481 (99.18%)
0:39:35.402296 PROGRESS: Decoy precursors: 4 (0.82%)
0:39:35.402342 PROGRESS: 
0:39:35.402388 PROGRESS: Precursor Summary:
0:39:35.403364 PROGRESS: Channel   0:	 0.050 FDR:   481; 0.010 FDR:   481; 0.001 FDR:   229
0:39:35.403459 PROGRESS: 
0:39:35.403516 PROGRESS: Protein Summary:
0:39:35.404686 PROGRESS: Channel   0:	 0.050 FDR:   460; 0.010 FDR:   460; 0.001 FDR:   219
0:39:35.404781 PROGRESS: =========================================================================
0:39:35.404987 INFO: Target number of precursors reached.
0:39:35.408930 INFO: fragments_df: keeping 4194 of 19862 [sum(precursor_idx_mask)=9388 sum(mass_error_mask)=19862 stop_rank=4194
0:39:35.414597 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:35.531821 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:36.020815 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:36.021320 INFO: Using score_cutoff 11.79765118789673 (fac=0.99, q=1)
0:39:36.021628 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:36.021707 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:36.021761 INFO: Updating optimization_manager: score_cutoff        : 11.762787246322631 -> 11.79765118789673
0:39:36.021816 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:36.023500 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:36.025768 INFO: === checking if optimization conditions were reached ===
0:39:36.026183 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:39:36.027961 INFO: Updating optimization_manager: rt_error            : 17.980134244309756 -> 18.388645529158108
0:39:36.028063 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 18.3886.
0:39:36.028129 INFO: ==============================================
0:39:36.028197 INFO: Starting optimization step 4.
0:39:36.028256 PROGRESS: === Extracting elution groups 0 to 600 ===
0:39:36.028317 INFO: Using ng extraction backend
0:39:36.028375 PROGRESS: Extracting batch of 1196 precursors
0:39:36.032771 INFO: === Search parameters used ===
0:39:36.032859 INFO: rt_error       : 18.388645529158108
0:39:36.032909 INFO: mobility_error : 0.1
0:39:36.032956 INFO: num_candidates : 3
0:39:36.032998 INFO: ms1_error      : 30
0:39:36.033038 INFO: ms2_error      : 7.171496
0:39:36.033077 INFO: fwhm_rt        : 3.0
0:39:36.033116 INFO: quant_window   : 3
0:39:36.033154 INFO: ==============================================
0:39:36.070524 INFO: performing precursor FDR with 40 features
0:39:36.070674 INFO: Decoy channel: -1
0:39:36.070702 INFO: Competetive: True
0:39:36.073601 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:36.075595 INFO: Using random state 739375 for train-test-split
0:39:36.089656 INFO: Test AUC: 0.717
0:39:36.089746 INFO: Train AUC: 0.701
0:39:36.089776 INFO: AUC difference: 2.35%
0:39:36.315630 INFO: Resetting torch num_threads to 80
0:39:36.317559 PROGRESS: === Extracted 3297 precursors and 19875 fragments ===
0:39:36.317973 INFO: === FDR correction performed with classifier version 7 ===
0:39:36.318481 PROGRESS: ============================= Precursor FDR =============================
0:39:36.318594 PROGRESS: Total precursors accumulated: 484
0:39:36.318659 PROGRESS: Target precursors: 480 (99.17%)
0:39:36.318709 PROGRESS: Decoy precursors: 4 (0.83%)
0:39:36.318752 PROGRESS: 
0:39:36.318795 PROGRESS: Precursor Summary:
0:39:36.319806 PROGRESS: Channel   0:	 0.050 FDR:   480; 0.010 FDR:   480; 0.001 FDR:   229
0:39:36.319900 PROGRESS: 
0:39:36.319955 PROGRESS: Protein Summary:
0:39:36.321121 PROGRESS: Channel   0:	 0.050 FDR:   459; 0.010 FDR:   459; 0.001 FDR:   219
0:39:36.321214 PROGRESS: =========================================================================
0:39:36.321436 INFO: Target number of precursors reached.
0:39:36.325436 INFO: fragments_df: keeping 4186 of 19875 [sum(precursor_idx_mask)=9377 sum(mass_error_mask)=19875 stop_rank=4186
0:39:36.331197 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:36.448258 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:36.939847 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:36.940364 INFO: Using score_cutoff 11.796310267066955 (fac=0.99, q=1)
0:39:36.940674 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:36.940754 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:36.940808 INFO: Updating optimization_manager: score_cutoff        : 11.79765118789673 -> 11.796310267066955
0:39:36.940862 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:36.942551 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:36.944787 INFO: === checking if optimization conditions were reached ===
0:39:36.944890 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:39:36.945919 INFO: Updating optimization_manager: rt_error            : 18.388645529158108 -> 17.980134244309756
0:39:36.946043 INFO: Updating optimization_manager: classifier_version  : 7 -> 11
0:39:36.946138 INFO: Updating optimization_manager: score_cutoff        : 11.796310267066955 -> 11.79765118789673
0:39:36.946222 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:36.946300 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:36.946379 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 17.9801 found after 5 searches.
0:39:36.946438 INFO: ==============================================
0:39:36.946505 PROGRESS: Optimization finished for rt_error.
0:39:36.951909 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:36.953224 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:36.983778 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:39:36.983914 PROGRESS: ==============================================
0:39:36.983983 PROGRESS: ms2_error      : 7.1715
0:39:36.984040 PROGRESS: rt_error       : 17.9801
0:39:36.984088 PROGRESS: ==============================================
0:39:36.984619 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:37.114044 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:37.486495 INFO: Using ng extraction backend
0:39:37.486952 PROGRESS: Extracting batch of 240048 precursors
0:39:37.878402 INFO: === Search parameters used ===
0:39:37.878770 INFO: rt_error       : 17.980134244309756
0:39:37.878848 INFO: mobility_error : 0.1
0:39:37.878912 INFO: num_candidates : 3
0:39:37.878973 INFO: ms1_error      : 30
0:39:37.879028 INFO: ms2_error      : 7.171496
0:39:37.879081 INFO: fwhm_rt        : 3.0
0:39:37.879149 INFO: quant_window   : 3
0:39:37.879202 INFO: ==============================================
0:39:38.141222 INFO: Removed 366058 precursors with score below cutoff 11.79765118789673
0:39:38.430502 INFO: performing precursor FDR with 40 features
0:39:38.430629 INFO: Decoy channel: -1
0:39:38.430657 INFO: Competetive: True
0:39:38.469754 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:38.493184 WARNING: FDR calculation for 193056 target and 97596 decoy PSMs
0:39:38.493364 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:39:38.558453 INFO: Using random state 141458 for train-test-split
0:39:43.574650 INFO: Test AUC: 0.883
0:39:43.574824 INFO: Train AUC: 0.886
0:39:43.574855 INFO: AUC difference: 0.39%
0:39:43.881684 INFO: Resetting torch num_threads to 80
0:39:44.247951 PROGRESS: ============================= Precursor FDR =============================
0:39:44.248281 PROGRESS: Total precursors accumulated: 110,798
0:39:44.248358 PROGRESS: Target precursors: 109,701 (99.01%)
0:39:44.248410 PROGRESS: Decoy precursors: 1,097 (0.99%)
0:39:44.248458 PROGRESS: 
0:39:44.248502 PROGRESS: Precursor Summary:
0:39:44.283365 PROGRESS: Channel   0:	 0.050 FDR: 109,701; 0.010 FDR: 109,701; 0.001 FDR: 99,493
0:39:44.283711 PROGRESS: 
0:39:44.283780 PROGRESS: Protein Summary:
0:39:44.335312 PROGRESS: Channel   0:	 0.050 FDR: 10,114; 0.010 FDR: 10,114; 0.001 FDR: 10,000
0:39:44.335632 PROGRESS: =========================================================================
0:39:44.338584 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
0:39:44.527976 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
0:39:44.827286 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:39:44.921089 PROGRESS: 
0:39:44.921232 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
0:39:44.921301 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
0:39:44.921464 INFO: Initializing TimingManager
0:39:44.921958 INFO: Initializing RawFileManager
0:39:55.923663 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:39:55.927909 INFO: Determining DIA cycle
0:39:55.944216 INFO: Found cycle with start 0.00 min and length 300.
0:39:56.100878 INFO: RT (min)            : 0.0 - 26.9
0:39:56.100974 INFO: RT duration (sec)   : 1611.2
0:39:56.101003 INFO: RT duration (min)   : 26.9
0:39:56.101025 INFO: Cycle len (scans)   : 300
0:39:56.101046 INFO: Cycle len (sec)     : 1.65
0:39:56.101065 INFO: Number of cycles    : 977
0:39:56.101084 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:39:56.101117 INFO: Creating DIA data object took: 11.179058074951172
0:39:56.770671 INFO: Creating DIA data NG object took: 0.6694355010986328
0:39:56.802332 INFO: Initializing CalibrationManager
0:39:56.802620 INFO: Setting up calibration estimators ..
0:39:56.802682 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:39:56.802748 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'}' ..
0:39:56.802818 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:39:56.802871 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:39:56.802922 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}}' ..
0:39:56.802983 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:39:56.803027 INFO: Done setting up calibration estimators.
0:39:56.803215 INFO: Initializing OptimizationManager
0:39:56.803332 INFO: initial parameter: ms1_error = 30
0:39:56.803383 INFO: initial parameter: ms2_error = 30
0:39:56.803428 INFO: initial parameter: rt_error = 805.6004638671875
0:39:56.803470 INFO: initial parameter: mobility_error = 0.1
0:39:56.803509 INFO: initial parameter: num_candidates = 1
0:39:56.803550 INFO: initial parameter: fwhm_rt = 5
0:39:56.803589 INFO: initial parameter: fwhm_mobility = 0.01
0:39:56.803626 INFO: initial parameter: score_cutoff = 0
0:39:56.803664 INFO: initial parameter: classifier_version = -1
0:39:56.803727 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:39:56.803933 INFO: FDRManager: loading saved state not requested, will be initialized.
0:39:56.803965 INFO: Initializing FDRManager
0:39:56.803993 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:39:56.831341 PROGRESS: Initializing spectral library: 120,580 target precursors potentially observable (0 removed)
0:39:56.849556 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:39:56.849890 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
0:39:56.849984 PROGRESS: Starting initial search for precursors.
0:39:56.850062 INFO: Starting optimization step 0.
0:39:56.850120 PROGRESS: === Extracting elution groups 0 to 200 ===
0:39:56.850173 INFO: Using ng extraction backend
0:39:56.850226 PROGRESS: Extracting batch of 398 precursors
0:39:56.852625 INFO: === Search parameters used ===
0:39:56.852729 INFO: rt_error       : 805.6004638671875
0:39:56.852780 INFO: mobility_error : 0.1
0:39:56.852824 INFO: num_candidates : 1
0:39:56.852865 INFO: ms1_error      : 30
0:39:56.852908 INFO: ms2_error      : 30
0:39:56.852949 INFO: fwhm_rt        : 5
0:39:56.852990 INFO: quant_window   : 3
0:39:56.853029 INFO: ==============================================
0:39:56.877953 INFO: performing precursor FDR with 40 features
0:39:56.878032 INFO: Decoy channel: -1
0:39:56.878058 INFO: Competetive: True
0:39:56.878999 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:56.881058 INFO: Using random state 330613 for train-test-split
0:39:56.887962 INFO: Test AUC: 0.572
0:39:56.888021 INFO: Train AUC: 0.504
0:39:56.888051 INFO: AUC difference: 13.39%
0:39:56.888073 WARNING: AUC difference > 5%. This may indicate overfitting.
0:39:57.099847 INFO: Resetting torch num_threads to 80
0:39:57.101186 PROGRESS: === Extracted 397 precursors and 2785 fragments ===
0:39:57.101518 INFO: === FDR correction performed with classifier version -1 ===
0:39:57.101948 PROGRESS: ============================= Precursor FDR =============================
0:39:57.102034 PROGRESS: Total precursors accumulated: 0
0:39:57.102091 PROGRESS: Target precursors: 0 (0.00%)
0:39:57.102140 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:57.102184 PROGRESS: 
0:39:57.102229 PROGRESS: Precursor Summary:
0:39:57.102343 PROGRESS: 
0:39:57.102405 PROGRESS: Protein Summary:
0:39:57.102476 PROGRESS: =========================================================================
0:39:57.102676 INFO: Target number of precursors not reached yet.
0:39:57.106426 INFO: Starting optimization step 1.
0:39:57.106532 PROGRESS: === Extracting elution groups 200 to 600 ===
0:39:57.106614 INFO: Using ng extraction backend
0:39:57.106676 PROGRESS: Extracting batch of 798 precursors
0:39:57.109730 INFO: === Search parameters used ===
0:39:57.109814 INFO: rt_error       : 805.6004638671875
0:39:57.109862 INFO: mobility_error : 0.1
0:39:57.109904 INFO: num_candidates : 1
0:39:57.109945 INFO: ms1_error      : 30
0:39:57.109985 INFO: ms2_error      : 30
0:39:57.110023 INFO: fwhm_rt        : 5
0:39:57.110065 INFO: quant_window   : 3
0:39:57.110103 INFO: ==============================================
0:39:57.133333 INFO: performing precursor FDR with 40 features
0:39:57.133409 INFO: Decoy channel: -1
0:39:57.133438 INFO: Competetive: True
0:39:57.136284 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:57.137820 INFO: Using random state 359262 for train-test-split
0:39:57.146011 INFO: Test AUC: 0.506
0:39:57.146068 INFO: Train AUC: 0.528
0:39:57.146097 INFO: AUC difference: 4.11%
0:39:57.360360 INFO: Resetting torch num_threads to 80
0:39:57.362675 PROGRESS: === Extracted 1195 precursors and 8348 fragments ===
0:39:57.363042 INFO: === FDR correction performed with classifier version -1 ===
0:39:57.363500 PROGRESS: ============================= Precursor FDR =============================
0:39:57.363589 PROGRESS: Total precursors accumulated: 0
0:39:57.363647 PROGRESS: Target precursors: 0 (0.00%)
0:39:57.363698 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:57.363744 PROGRESS: 
0:39:57.363787 PROGRESS: Precursor Summary:
0:39:57.363895 PROGRESS: 
0:39:57.363959 PROGRESS: Protein Summary:
0:39:57.364042 PROGRESS: =========================================================================
0:39:57.364287 INFO: Target number of precursors not reached yet.
0:39:57.369207 INFO: Starting optimization step 2.
0:39:57.369316 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:39:57.369390 INFO: Using ng extraction backend
0:39:57.369451 PROGRESS: Extracting batch of 1598 precursors
0:39:57.374390 INFO: === Search parameters used ===
0:39:57.374484 INFO: rt_error       : 805.6004638671875
0:39:57.374534 INFO: mobility_error : 0.1
0:39:57.374586 INFO: num_candidates : 1
0:39:57.374630 INFO: ms1_error      : 30
0:39:57.374675 INFO: ms2_error      : 30
0:39:57.374714 INFO: fwhm_rt        : 5
0:39:57.374754 INFO: quant_window   : 3
0:39:57.374795 INFO: ==============================================
0:39:57.405076 INFO: performing precursor FDR with 40 features
0:39:57.405152 INFO: Decoy channel: -1
0:39:57.405177 INFO: Competetive: True
0:39:57.408532 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:57.410639 INFO: Using random state 23379 for train-test-split
0:39:57.422418 INFO: Test AUC: 0.546
0:39:57.422478 INFO: Train AUC: 0.520
0:39:57.422508 INFO: AUC difference: 4.98%
0:39:57.632393 INFO: Resetting torch num_threads to 80
0:39:57.635393 PROGRESS: === Extracted 2793 precursors and 19470 fragments ===
0:39:57.635805 INFO: === FDR correction performed with classifier version -1 ===
0:39:57.636280 PROGRESS: ============================= Precursor FDR =============================
0:39:57.636369 PROGRESS: Total precursors accumulated: 0
0:39:57.636426 PROGRESS: Target precursors: 0 (0.00%)
0:39:57.636477 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:57.636520 PROGRESS: 
0:39:57.636573 PROGRESS: Precursor Summary:
0:39:57.636693 PROGRESS: 
0:39:57.636756 PROGRESS: Protein Summary:
0:39:57.636829 PROGRESS: =========================================================================
0:39:57.637106 INFO: Target number of precursors not reached yet.
0:39:57.644122 INFO: Starting optimization step 3.
0:39:57.644241 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:39:57.644315 INFO: Using ng extraction backend
0:39:57.644375 PROGRESS: Extracting batch of 3190 precursors
0:39:57.651739 INFO: === Search parameters used ===
0:39:57.651850 INFO: rt_error       : 805.6004638671875
0:39:57.651900 INFO: mobility_error : 0.1
0:39:57.651945 INFO: num_candidates : 1
0:39:57.651988 INFO: ms1_error      : 30
0:39:57.652028 INFO: ms2_error      : 30
0:39:57.652068 INFO: fwhm_rt        : 5
0:39:57.652108 INFO: quant_window   : 3
0:39:57.652148 INFO: ==============================================
0:39:57.708874 INFO: performing precursor FDR with 40 features
0:39:57.709001 INFO: Decoy channel: -1
0:39:57.709037 INFO: Competetive: True
0:39:57.713708 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:57.716176 INFO: Using random state 801491 for train-test-split
0:39:57.737478 INFO: Test AUC: 0.514
0:39:57.737583 INFO: Train AUC: 0.520
0:39:57.737627 INFO: AUC difference: 1.01%
0:39:57.965643 INFO: Resetting torch num_threads to 80
0:39:57.970092 PROGRESS: === Extracted 5977 precursors and 41428 fragments ===
0:39:57.970604 INFO: === FDR correction performed with classifier version -1 ===
0:39:57.971167 PROGRESS: ============================= Precursor FDR =============================
0:39:57.971283 PROGRESS: Total precursors accumulated: 0
0:39:57.971355 PROGRESS: Target precursors: 0 (0.00%)
0:39:57.971408 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:57.971456 PROGRESS: 
0:39:57.971499 PROGRESS: Precursor Summary:
0:39:57.971620 PROGRESS: 
0:39:57.971686 PROGRESS: Protein Summary:
0:39:57.971763 PROGRESS: =========================================================================
0:39:57.972106 INFO: Target number of precursors not reached yet.
0:39:57.983525 INFO: Starting optimization step 4.
0:39:57.983771 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:39:57.983855 INFO: Using ng extraction backend
0:39:57.983916 PROGRESS: Extracting batch of 6370 precursors
0:39:57.996981 INFO: === Search parameters used ===
0:39:57.997235 INFO: rt_error       : 805.6004638671875
0:39:57.997287 INFO: mobility_error : 0.1
0:39:57.997332 INFO: num_candidates : 1
0:39:57.997374 INFO: ms1_error      : 30
0:39:57.997415 INFO: ms2_error      : 30
0:39:57.997455 INFO: fwhm_rt        : 5
0:39:57.997494 INFO: quant_window   : 3
0:39:57.997535 INFO: ==============================================
0:39:58.081339 INFO: performing precursor FDR with 40 features
0:39:58.081453 INFO: Decoy channel: -1
0:39:58.081479 INFO: Competetive: True
0:39:58.087167 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:58.090405 INFO: Using random state 150369 for train-test-split
0:39:58.127164 INFO: Test AUC: 0.509
0:39:58.127266 INFO: Train AUC: 0.523
0:39:58.127296 INFO: AUC difference: 2.74%
0:39:58.342379 INFO: Resetting torch num_threads to 80
0:39:58.346687 PROGRESS: === Extracted 12337 precursors and 85716 fragments ===
0:39:58.347060 INFO: === FDR correction performed with classifier version -1 ===
0:39:58.347507 PROGRESS: ============================= Precursor FDR =============================
0:39:58.347596 PROGRESS: Total precursors accumulated: 0
0:39:58.347654 PROGRESS: Target precursors: 0 (0.00%)
0:39:58.347703 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:58.347746 PROGRESS: 
0:39:58.347791 PROGRESS: Precursor Summary:
0:39:58.347899 PROGRESS: 
0:39:58.347963 PROGRESS: Protein Summary:
0:39:58.348037 PROGRESS: =========================================================================
0:39:58.348327 INFO: Target number of precursors not reached yet.
0:39:58.364771 INFO: Starting optimization step 5.
0:39:58.364938 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:39:58.365017 INFO: Using ng extraction backend
0:39:58.365075 PROGRESS: Extracting batch of 12737 precursors
0:39:58.388508 INFO: === Search parameters used ===
0:39:58.388665 INFO: rt_error       : 805.6004638671875
0:39:58.388715 INFO: mobility_error : 0.1
0:39:58.388762 INFO: num_candidates : 1
0:39:58.388803 INFO: ms1_error      : 30
0:39:58.388843 INFO: ms2_error      : 30
0:39:58.388883 INFO: fwhm_rt        : 5
0:39:58.389217 INFO: quant_window   : 3
0:39:58.389270 INFO: ==============================================
0:39:58.524282 INFO: performing precursor FDR with 40 features
0:39:58.524394 INFO: Decoy channel: -1
0:39:58.524419 INFO: Competetive: True
0:39:58.533755 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:58.539268 INFO: Using random state 311475 for train-test-split
0:39:58.869353 INFO: Test AUC: 0.810
0:39:58.869464 INFO: Train AUC: 0.807
0:39:58.869493 INFO: AUC difference: 0.28%
0:39:59.118372 INFO: Resetting torch num_threads to 80
0:39:59.124908 PROGRESS: === Extracted 25059 precursors and 175055 fragments ===
0:39:59.125311 INFO: === FDR correction performed with classifier version -1 ===
0:39:59.126223 PROGRESS: ============================= Precursor FDR =============================
0:39:59.126324 PROGRESS: Total precursors accumulated: 3,968
0:39:59.126391 PROGRESS: Target precursors: 3,929 (99.02%)
0:39:59.126440 PROGRESS: Decoy precursors: 39 (0.98%)
0:39:59.126484 PROGRESS: 
0:39:59.126527 PROGRESS: Precursor Summary:
0:39:59.128424 PROGRESS: Channel   0:	 0.050 FDR: 3,929; 0.010 FDR: 3,929; 0.001 FDR: 2,084
0:39:59.128524 PROGRESS: 
0:39:59.128581 PROGRESS: Protein Summary:
0:39:59.131150 PROGRESS: Channel   0:	 0.050 FDR: 2,529; 0.010 FDR: 2,529; 0.001 FDR: 1,492
0:39:59.131253 PROGRESS: =========================================================================
0:39:59.131647 INFO: Target number of precursors reached.
0:39:59.157607 INFO: fragments_df: keeping 5000 of 175055 [sum(precursor_idx_mask)=43509 sum(mass_error_mask)=175055 stop_rank=5000
0:39:59.165653 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:59.690791 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:00.371402 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:40:00.371878 INFO: Using score_cutoff 14.339893572235107 (fac=0.99, q=1)
0:40:00.372191 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:40:00.372272 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:40:00.372328 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.339893572235107
0:40:00.372384 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:00.374693 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:00.379026 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:40:00.379146 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:40:00.379236 INFO: Starting optimization step 6.
0:40:00.379306 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:40:00.379378 INFO: Using ng extraction backend
0:40:00.379442 PROGRESS: Extracting batch of 2794 precursors
0:40:00.386247 INFO: === Search parameters used ===
0:40:00.386357 INFO: rt_error       : 805.6004638671875
0:40:00.386417 INFO: mobility_error : 0.1
0:40:00.386473 INFO: num_candidates : 3
0:40:00.386525 INFO: ms1_error      : 30
0:40:00.386585 INFO: ms2_error      : 30
0:40:00.386638 INFO: fwhm_rt        : 3.0
0:40:00.386688 INFO: quant_window   : 3
0:40:00.386737 INFO: ==============================================
0:40:00.482026 INFO: performing precursor FDR with 40 features
0:40:00.482168 INFO: Decoy channel: -1
0:40:00.482197 INFO: Competetive: True
0:40:00.486350 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:00.489176 INFO: Using random state 157271 for train-test-split
0:40:00.512580 INFO: Test AUC: 0.651
0:40:00.512707 INFO: Train AUC: 0.657
0:40:00.512736 INFO: AUC difference: 0.93%
0:40:00.743784 INFO: Resetting torch num_threads to 80
0:40:00.745618 PROGRESS: === Extracted 8373 precursors and 50923 fragments ===
0:40:00.745967 INFO: === FDR correction performed with classifier version 5 ===
0:40:00.746485 PROGRESS: ============================= Precursor FDR =============================
0:40:00.746583 PROGRESS: Total precursors accumulated: 478
0:40:00.746645 PROGRESS: Target precursors: 474 (99.16%)
0:40:00.746695 PROGRESS: Decoy precursors: 4 (0.84%)
0:40:00.746739 PROGRESS: 
0:40:00.746782 PROGRESS: Precursor Summary:
0:40:00.747760 PROGRESS: Channel   0:	 0.050 FDR:   474; 0.010 FDR:   474; 0.001 FDR:   414
0:40:00.747853 PROGRESS: 
0:40:00.747909 PROGRESS: Protein Summary:
0:40:00.749083 PROGRESS: Channel   0:	 0.050 FDR:   438; 0.010 FDR:   438; 0.001 FDR:   387
0:40:00.749177 PROGRESS: =========================================================================
0:40:00.749573 INFO: Target number of precursors reached.
0:40:00.755778 INFO: fragments_df: keeping 5000 of 50923 [sum(precursor_idx_mask)=11048 sum(mass_error_mask)=50923 stop_rank=5000
0:40:00.760962 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:00.909308 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:01.599818 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:01.600393 INFO: Using score_cutoff 15.852298203849791 (fac=0.99, q=1)
0:40:01.600765 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:01.601060 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:01.601121 INFO: Updating optimization_manager: score_cutoff        : 14.339893572235107 -> 15.852298203849791
0:40:01.601179 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:01.603009 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:01.605594 INFO: === checking if optimization conditions were reached ===
0:40:01.607590 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.171496
0:40:01.607703 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:40:01.607769 PROGRESS: ❌ ms2_error      : 7.1715 > 7.1715 or insufficient steps taken.
0:40:01.607826 INFO: ==============================================
0:40:01.607887 INFO: Starting optimization step 7.
0:40:01.607948 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:01.608015 INFO: Using ng extraction backend
0:40:01.608076 PROGRESS: Extracting batch of 1196 precursors
0:40:01.612632 INFO: === Search parameters used ===
0:40:01.612735 INFO: rt_error       : 805.6004638671875
0:40:01.612783 INFO: mobility_error : 0.1
0:40:01.612827 INFO: num_candidates : 3
0:40:01.612882 INFO: ms1_error      : 30
0:40:01.612920 INFO: ms2_error      : 7.171496
0:40:01.612978 INFO: fwhm_rt        : 3.0
0:40:01.613024 INFO: quant_window   : 3
0:40:01.613066 INFO: ==============================================
0:40:01.656684 INFO: performing precursor FDR with 40 features
0:40:01.656800 INFO: Decoy channel: -1
0:40:01.656828 INFO: Competetive: True
0:40:01.660017 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:01.661971 INFO: Using random state 327919 for train-test-split
0:40:01.675719 INFO: Test AUC: 0.670
0:40:01.675799 INFO: Train AUC: 0.665
0:40:01.675829 INFO: AUC difference: 0.80%
0:40:01.901301 INFO: Resetting torch num_threads to 80
0:40:01.903099 PROGRESS: === Extracted 3588 precursors and 25440 fragments ===
0:40:01.903495 INFO: === FDR correction performed with classifier version 6 ===
0:40:01.903980 PROGRESS: ============================= Precursor FDR =============================
0:40:01.904068 PROGRESS: Total precursors accumulated: 421
0:40:01.904127 PROGRESS: Target precursors: 417 (99.05%)
0:40:01.904175 PROGRESS: Decoy precursors: 4 (0.95%)
0:40:01.904218 PROGRESS: 
0:40:01.904261 PROGRESS: Precursor Summary:
0:40:01.905231 PROGRESS: Channel   0:	 0.050 FDR:   417; 0.010 FDR:   417; 0.001 FDR:   328
0:40:01.905322 PROGRESS: 
0:40:01.905379 PROGRESS: Protein Summary:
0:40:01.906553 PROGRESS: Channel   0:	 0.050 FDR:   401; 0.010 FDR:   401; 0.001 FDR:   314
0:40:01.906652 PROGRESS: =========================================================================
0:40:01.908033 INFO: Target number of precursors reached.
0:40:01.912455 INFO: fragments_df: keeping 4444 of 25440 [sum(precursor_idx_mask)=10181 sum(mass_error_mask)=25440 stop_rank=4444
0:40:01.921075 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:02.057417 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:02.663954 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:02.664492 INFO: Using score_cutoff 11.402129223632812 (fac=0.99, q=1)
0:40:02.664822 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:02.664902 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:02.664957 INFO: Updating optimization_manager: score_cutoff        : 15.852298203849791 -> 11.402129223632812
0:40:02.665011 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:02.666717 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:02.669040 INFO: === checking if optimization conditions were reached ===
0:40:02.670577 INFO: Updating optimization_manager: ms2_error           : 7.171496 -> 7.171496
0:40:02.670677 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:40:02.670742 PROGRESS: ✅ ms2_error      : 7.1715 <= 7.1715
0:40:02.670809 INFO: ==============================================
0:40:02.670874 PROGRESS: Optimization finished for ms2_error.
0:40:02.676306 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:02.677620 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:02.679865 INFO: Starting optimization step 0.
0:40:02.679967 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:02.680039 INFO: Using ng extraction backend
0:40:02.680099 PROGRESS: Extracting batch of 1196 precursors
0:40:02.684076 INFO: === Search parameters used ===
0:40:02.684180 INFO: rt_error       : 805.6004638671875
0:40:02.684370 INFO: mobility_error : 0.1
0:40:02.684422 INFO: num_candidates : 3
0:40:02.684464 INFO: ms1_error      : 30
0:40:02.684503 INFO: ms2_error      : 7.171496
0:40:02.684543 INFO: fwhm_rt        : 3.0
0:40:02.684581 INFO: quant_window   : 3
0:40:02.684618 INFO: ==============================================
0:40:02.722680 INFO: performing precursor FDR with 40 features
0:40:02.722778 INFO: Decoy channel: -1
0:40:02.722804 INFO: Competetive: True
0:40:02.725487 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:02.727383 INFO: Using random state 767824 for train-test-split
0:40:02.738699 INFO: Test AUC: 0.669
0:40:02.738768 INFO: Train AUC: 0.664
0:40:02.738797 INFO: AUC difference: 0.73%
0:40:02.963318 INFO: Resetting torch num_threads to 80
0:40:02.965107 PROGRESS: === Extracted 3588 precursors and 25424 fragments ===
0:40:02.965503 INFO: === FDR correction performed with classifier version 7 ===
0:40:02.965964 PROGRESS: ============================= Precursor FDR =============================
0:40:02.966050 PROGRESS: Total precursors accumulated: 416
0:40:02.966108 PROGRESS: Target precursors: 412 (99.04%)
0:40:02.966157 PROGRESS: Decoy precursors: 4 (0.96%)
0:40:02.966202 PROGRESS: 
0:40:02.966247 PROGRESS: Precursor Summary:
0:40:02.967257 PROGRESS: Channel   0:	 0.050 FDR:   412; 0.010 FDR:   412; 0.001 FDR:   327
0:40:02.967347 PROGRESS: 
0:40:02.967403 PROGRESS: Protein Summary:
0:40:02.968572 PROGRESS: Channel   0:	 0.050 FDR:   396; 0.010 FDR:   396; 0.001 FDR:   313
0:40:02.968663 PROGRESS: =========================================================================
0:40:02.968868 INFO: Target number of precursors reached.
0:40:02.973231 INFO: fragments_df: keeping 4410 of 25424 [sum(precursor_idx_mask)=10061 sum(mass_error_mask)=25424 stop_rank=4410
0:40:02.978883 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:03.097573 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:03.621554 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:03.622096 INFO: Using score_cutoff 11.38916541223526 (fac=0.99, q=1)
0:40:03.622422 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:03.622505 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:03.622568 INFO: Updating optimization_manager: score_cutoff        : 11.402129223632812 -> 11.38916541223526
0:40:03.622631 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:03.624340 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:03.626657 INFO: === checking if optimization conditions were reached ===
0:40:03.626754 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:40:03.628363 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 65.45138081470706
0:40:03.628480 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 65.4514.
0:40:03.628546 INFO: ==============================================
0:40:03.628615 INFO: Starting optimization step 1.
0:40:03.628675 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:03.628734 INFO: Using ng extraction backend
0:40:03.628792 PROGRESS: Extracting batch of 1196 precursors
0:40:03.632607 INFO: === Search parameters used ===
0:40:03.632707 INFO: rt_error       : 65.45138081470706
0:40:03.632763 INFO: mobility_error : 0.1
0:40:03.632814 INFO: num_candidates : 3
0:40:03.632856 INFO: ms1_error      : 30
0:40:03.632898 INFO: ms2_error      : 7.171496
0:40:03.632939 INFO: fwhm_rt        : 3.0
0:40:03.632979 INFO: quant_window   : 3
0:40:03.633020 INFO: ==============================================
0:40:03.667083 INFO: performing precursor FDR with 40 features
0:40:03.667174 INFO: Decoy channel: -1
0:40:03.667200 INFO: Competetive: True
0:40:03.669993 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:03.671923 INFO: Using random state 767824 for train-test-split
0:40:03.683321 INFO: Test AUC: 0.700
0:40:03.683402 INFO: Train AUC: 0.686
0:40:03.683432 INFO: AUC difference: 2.12%
0:40:06.081470 INFO: Resetting torch num_threads to 80
0:40:06.086570 PROGRESS: === Extracted 3575 precursors and 22102 fragments ===
0:40:06.087001 INFO: === FDR correction performed with classifier version 7 ===
0:40:06.087626 PROGRESS: ============================= Precursor FDR =============================
0:40:06.087719 PROGRESS: Total precursors accumulated: 444
0:40:06.087779 PROGRESS: Target precursors: 440 (99.10%)
0:40:06.087831 PROGRESS: Decoy precursors: 4 (0.90%)
0:40:06.087874 PROGRESS: 
0:40:06.087919 PROGRESS: Precursor Summary:
0:40:06.088966 PROGRESS: Channel   0:	 0.050 FDR:   440; 0.010 FDR:   440; 0.001 FDR:   389
0:40:06.089061 PROGRESS: 
0:40:06.089114 PROGRESS: Protein Summary:
0:40:06.090366 PROGRESS: Channel   0:	 0.050 FDR:   421; 0.010 FDR:   421; 0.001 FDR:   373
0:40:06.090455 PROGRESS: =========================================================================
0:40:06.090908 INFO: Target number of precursors reached.
0:40:06.096039 INFO: fragments_df: keeping 4364 of 22102 [sum(precursor_idx_mask)=9854 sum(mass_error_mask)=22102 stop_rank=4364
0:40:06.103877 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:06.223337 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:06.745394 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:06.746126 INFO: Using score_cutoff 11.395141028881074 (fac=0.99, q=1)
0:40:06.746484 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:06.746575 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:06.746635 INFO: Updating optimization_manager: score_cutoff        : 11.38916541223526 -> 11.395141028881074
0:40:06.746730 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:06.749232 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:06.751646 INFO: === checking if optimization conditions were reached ===
0:40:06.751768 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:40:06.753640 INFO: Updating optimization_manager: rt_error            : 65.45138081470706 -> 11.473259536736066
0:40:06.753744 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 11.4733.
0:40:06.753812 INFO: ==============================================
0:40:06.753903 INFO: Starting optimization step 2.
0:40:06.753988 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:06.754134 INFO: Using ng extraction backend
0:40:06.754274 PROGRESS: Extracting batch of 1196 precursors
0:40:06.758444 INFO: === Search parameters used ===
0:40:06.758541 INFO: rt_error       : 11.473259536736066
0:40:06.758606 INFO: mobility_error : 0.1
0:40:06.758650 INFO: num_candidates : 3
0:40:06.758690 INFO: ms1_error      : 30
0:40:06.758730 INFO: ms2_error      : 7.171496
0:40:06.758770 INFO: fwhm_rt        : 3.0
0:40:06.758809 INFO: quant_window   : 3
0:40:06.758847 INFO: ==============================================
0:40:06.798718 INFO: performing precursor FDR with 40 features
0:40:06.798826 INFO: Decoy channel: -1
0:40:06.798853 INFO: Competetive: True
0:40:06.804139 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:06.806517 INFO: Using random state 767824 for train-test-split
0:40:06.821070 INFO: Test AUC: 0.687
0:40:06.821145 INFO: Train AUC: 0.708
0:40:06.821193 INFO: AUC difference: 2.89%
0:40:07.048467 INFO: Resetting torch num_threads to 80
0:40:07.050332 PROGRESS: === Extracted 3295 precursors and 19807 fragments ===
0:40:07.050773 INFO: === FDR correction performed with classifier version 7 ===
0:40:07.051345 PROGRESS: ============================= Precursor FDR =============================
0:40:07.051445 PROGRESS: Total precursors accumulated: 442
0:40:07.051522 PROGRESS: Target precursors: 438 (99.10%)
0:40:07.051585 PROGRESS: Decoy precursors: 4 (0.90%)
0:40:07.051640 PROGRESS: 
0:40:07.051695 PROGRESS: Precursor Summary:
0:40:07.052825 PROGRESS: Channel   0:	 0.050 FDR:   438; 0.010 FDR:   438; 0.001 FDR:   390
0:40:07.052932 PROGRESS: 
0:40:07.053001 PROGRESS: Protein Summary:
0:40:07.054316 PROGRESS: Channel   0:	 0.050 FDR:   419; 0.010 FDR:   419; 0.001 FDR:   374
0:40:07.054429 PROGRESS: =========================================================================
0:40:07.054700 INFO: Target number of precursors reached.
0:40:07.058680 INFO: fragments_df: keeping 4055 of 19807 [sum(precursor_idx_mask)=8680 sum(mass_error_mask)=19807 stop_rank=4055
0:40:07.065807 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:07.180753 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:07.663514 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:07.664334 INFO: Using score_cutoff 11.387771185398101 (fac=0.99, q=1)
0:40:07.664759 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:07.664847 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:07.664908 INFO: Updating optimization_manager: score_cutoff        : 11.395141028881074 -> 11.387771185398101
0:40:07.664978 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:07.667064 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:07.669671 INFO: === checking if optimization conditions were reached ===
0:40:07.669779 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:40:07.671762 INFO: Updating optimization_manager: rt_error            : 11.473259536736066 -> 8.945667870633285
0:40:07.671868 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 8.9457.
0:40:07.671937 INFO: ==============================================
0:40:07.672013 INFO: Starting optimization step 3.
0:40:07.672293 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:07.672372 INFO: Using ng extraction backend
0:40:07.672439 PROGRESS: Extracting batch of 1196 precursors
0:40:07.676114 INFO: === Search parameters used ===
0:40:07.676214 INFO: rt_error       : 8.945667870633285
0:40:07.676270 INFO: mobility_error : 0.1
0:40:07.676319 INFO: num_candidates : 3
0:40:07.676368 INFO: ms1_error      : 30
0:40:07.676414 INFO: ms2_error      : 7.171496
0:40:07.676462 INFO: fwhm_rt        : 3.0
0:40:07.676508 INFO: quant_window   : 3
0:40:07.676553 INFO: ==============================================
0:40:07.712761 INFO: performing precursor FDR with 40 features
0:40:07.712893 INFO: Decoy channel: -1
0:40:07.712920 INFO: Competetive: True
0:40:07.716111 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:07.718126 INFO: Using random state 767824 for train-test-split
0:40:07.731235 INFO: Test AUC: 0.686
0:40:07.731311 INFO: Train AUC: 0.710
0:40:07.731339 INFO: AUC difference: 3.34%
0:40:07.956517 INFO: Resetting torch num_threads to 80
0:40:07.959143 PROGRESS: === Extracted 3297 precursors and 19827 fragments ===
0:40:07.959637 INFO: === FDR correction performed with classifier version 7 ===
0:40:07.960130 PROGRESS: ============================= Precursor FDR =============================
0:40:07.960225 PROGRESS: Total precursors accumulated: 444
0:40:07.960287 PROGRESS: Target precursors: 440 (99.10%)
0:40:07.960336 PROGRESS: Decoy precursors: 4 (0.90%)
0:40:07.960380 PROGRESS: 
0:40:07.960422 PROGRESS: Precursor Summary:
0:40:07.961421 PROGRESS: Channel   0:	 0.050 FDR:   440; 0.010 FDR:   440; 0.001 FDR:   390
0:40:07.961522 PROGRESS: 
0:40:07.961586 PROGRESS: Protein Summary:
0:40:07.962809 PROGRESS: Channel   0:	 0.050 FDR:   421; 0.010 FDR:   421; 0.001 FDR:   374
0:40:07.962910 PROGRESS: =========================================================================
0:40:07.963158 INFO: Target number of precursors reached.
0:40:07.967235 INFO: fragments_df: keeping 4077 of 19827 [sum(precursor_idx_mask)=8717 sum(mass_error_mask)=19827 stop_rank=4077
0:40:07.973141 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:08.106967 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:08.627664 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:08.628131 INFO: Using score_cutoff 11.395141028881074 (fac=0.99, q=1)
0:40:08.628451 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:08.628532 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:08.628587 INFO: Updating optimization_manager: score_cutoff        : 11.387771185398101 -> 11.395141028881074
0:40:08.628643 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:08.630320 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:08.632687 INFO: === checking if optimization conditions were reached ===
0:40:08.632794 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:40:08.634544 INFO: Updating optimization_manager: rt_error            : 8.945667870633285 -> 8.945075405257345
0:40:08.634664 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 8.9451.
0:40:08.634738 INFO: ==============================================
0:40:08.634807 INFO: Starting optimization step 4.
0:40:08.634868 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:08.634936 INFO: Using ng extraction backend
0:40:08.634995 PROGRESS: Extracting batch of 1196 precursors
0:40:08.638614 INFO: === Search parameters used ===
0:40:08.638714 INFO: rt_error       : 8.945075405257345
0:40:08.638765 INFO: mobility_error : 0.1
0:40:08.638816 INFO: num_candidates : 3
0:40:08.638870 INFO: ms1_error      : 30
0:40:08.638916 INFO: ms2_error      : 7.171496
0:40:08.638966 INFO: fwhm_rt        : 3.0
0:40:08.639014 INFO: quant_window   : 3
0:40:08.639059 INFO: ==============================================
0:40:08.673516 INFO: performing precursor FDR with 40 features
0:40:08.673635 INFO: Decoy channel: -1
0:40:08.673661 INFO: Competetive: True
0:40:08.676876 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:08.678929 INFO: Using random state 767824 for train-test-split
0:40:08.692137 INFO: Test AUC: 0.716
0:40:08.692204 INFO: Train AUC: 0.702
0:40:08.692236 INFO: AUC difference: 1.96%
0:40:08.920763 INFO: Resetting torch num_threads to 80
0:40:08.922508 PROGRESS: === Extracted 3296 precursors and 19824 fragments ===
0:40:08.922863 INFO: === FDR correction performed with classifier version 7 ===
0:40:08.923353 PROGRESS: ============================= Precursor FDR =============================
0:40:08.923444 PROGRESS: Total precursors accumulated: 445
0:40:08.923501 PROGRESS: Target precursors: 441 (99.10%)
0:40:08.923552 PROGRESS: Decoy precursors: 4 (0.90%)
0:40:08.923598 PROGRESS: 
0:40:08.923643 PROGRESS: Precursor Summary:
0:40:08.924638 PROGRESS: Channel   0:	 0.050 FDR:   441; 0.010 FDR:   441; 0.001 FDR:   390
0:40:08.924733 PROGRESS: 
0:40:08.924791 PROGRESS: Protein Summary:
0:40:08.925997 PROGRESS: Channel   0:	 0.050 FDR:   422; 0.010 FDR:   422; 0.001 FDR:   374
0:40:08.926091 PROGRESS: =========================================================================
0:40:08.926346 INFO: Target number of precursors reached.
0:40:08.930253 INFO: fragments_df: keeping 4085 of 19824 [sum(precursor_idx_mask)=8736 sum(mass_error_mask)=19824 stop_rank=4085
0:40:08.935309 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:09.048058 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:09.528761 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:09.529237 INFO: Using score_cutoff 11.398825950622559 (fac=0.99, q=1)
0:40:09.529544 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:09.529627 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:09.529684 INFO: Updating optimization_manager: score_cutoff        : 11.395141028881074 -> 11.398825950622559
0:40:09.529740 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:09.531437 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:09.533777 INFO: === checking if optimization conditions were reached ===
0:40:09.533878 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:40:09.534880 INFO: Updating optimization_manager: rt_error            : 8.945075405257345 -> 8.945075405257345
0:40:09.535012 INFO: Updating optimization_manager: classifier_version  : 7 -> 12
0:40:09.535108 INFO: Updating optimization_manager: score_cutoff        : 11.398825950622559 -> 11.398825950622559
0:40:09.535202 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:09.535284 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:09.535364 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 8.9451 found after 5 searches.
0:40:09.535424 INFO: ==============================================
0:40:09.535492 PROGRESS: Optimization finished for rt_error.
0:40:09.540291 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:09.541612 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:09.571624 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:40:09.571777 PROGRESS: ==============================================
0:40:09.571848 PROGRESS: ms2_error      : 7.1715
0:40:09.571905 PROGRESS: rt_error       : 8.9451
0:40:09.571951 PROGRESS: ==============================================
0:40:09.572694 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:09.697774 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:10.054131 INFO: Using ng extraction backend
0:40:10.054464 PROGRESS: Extracting batch of 240048 precursors
0:40:10.438418 INFO: === Search parameters used ===
0:40:10.438699 INFO: rt_error       : 8.945075405257345
0:40:10.438771 INFO: mobility_error : 0.1
0:40:10.438821 INFO: num_candidates : 3
0:40:10.438864 INFO: ms1_error      : 30
0:40:10.438908 INFO: ms2_error      : 7.171496
0:40:10.438949 INFO: fwhm_rt        : 3.0
0:40:10.438992 INFO: quant_window   : 3
0:40:10.439031 INFO: ==============================================
0:40:10.704908 INFO: Removed 349691 precursors with score below cutoff 11.398825950622559
0:40:11.002596 INFO: performing precursor FDR with 40 features
0:40:11.002716 INFO: Decoy channel: -1
0:40:11.002743 INFO: Competetive: True
0:40:11.033453 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:11.049857 WARNING: FDR calculation for 200263 target and 106801 decoy PSMs
0:40:11.050007 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:40:11.117587 INFO: Using random state 70938 for train-test-split
0:40:15.587519 INFO: Test AUC: 0.882
0:40:15.587661 INFO: Train AUC: 0.885
0:40:15.587694 INFO: AUC difference: 0.35%
0:40:15.907707 INFO: Resetting torch num_threads to 80
0:40:16.229677 PROGRESS: ============================= Precursor FDR =============================
0:40:16.229956 PROGRESS: Total precursors accumulated: 111,354
0:40:16.230027 PROGRESS: Target precursors: 110,252 (99.01%)
0:40:16.230082 PROGRESS: Decoy precursors: 1,102 (0.99%)
0:40:16.230129 PROGRESS: 
0:40:16.230174 PROGRESS: Precursor Summary:
0:40:16.261089 PROGRESS: Channel   0:	 0.050 FDR: 110,252; 0.010 FDR: 110,252; 0.001 FDR: 99,898
0:40:16.261359 PROGRESS: 
0:40:16.261429 PROGRESS: Protein Summary:
0:40:16.303830 PROGRESS: Channel   0:	 0.050 FDR: 10,111; 0.010 FDR: 10,111; 0.001 FDR: 9,992
0:40:16.304105 PROGRESS: =========================================================================
0:40:16.306252 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
0:40:16.493856 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
0:40:16.792654 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:40:16.894929 PROGRESS: 
0:40:16.895093 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
0:40:16.895168 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
0:40:16.895340 INFO: Initializing TimingManager
0:40:16.895942 INFO: Initializing RawFileManager
0:40:26.894792 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:40:26.900820 INFO: Determining DIA cycle
0:40:26.916102 INFO: Found cycle with start 0.00 min and length 300.
0:40:27.100337 INFO: RT (min)            : 0.0 - 26.9
0:40:27.100443 INFO: RT duration (sec)   : 1611.2
0:40:27.100472 INFO: RT duration (min)   : 26.9
0:40:27.100496 INFO: Cycle len (scans)   : 300
0:40:27.100516 INFO: Cycle len (sec)     : 1.65
0:40:27.100535 INFO: Number of cycles    : 977
0:40:27.100553 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:40:27.100579 INFO: Creating DIA data object took: 10.204533576965332
0:40:27.776075 INFO: Creating DIA data NG object took: 0.6753721237182617
0:40:27.797285 INFO: Initializing CalibrationManager
0:40:27.797591 INFO: Setting up calibration estimators ..
0:40:27.797652 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:40:27.797723 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'}' ..
0:40:27.797798 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:40:27.797848 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:40:27.797897 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}}' ..
0:40:27.797945 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:40:27.797988 INFO: Done setting up calibration estimators.
0:40:27.798175 INFO: Initializing OptimizationManager
0:40:27.798301 INFO: initial parameter: ms1_error = 30
0:40:27.798351 INFO: initial parameter: ms2_error = 30
0:40:27.798396 INFO: initial parameter: rt_error = 805.5982666015625
0:40:27.798439 INFO: initial parameter: mobility_error = 0.1
0:40:27.798479 INFO: initial parameter: num_candidates = 1
0:40:27.798517 INFO: initial parameter: fwhm_rt = 5
0:40:27.798559 INFO: initial parameter: fwhm_mobility = 0.01
0:40:27.798618 INFO: initial parameter: score_cutoff = 0
0:40:27.798657 INFO: initial parameter: classifier_version = -1
0:40:27.798726 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:40:27.798958 INFO: FDRManager: loading saved state not requested, will be initialized.
0:40:27.798992 INFO: Initializing FDRManager
0:40:27.799026 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:40:27.826509 PROGRESS: Initializing spectral library: 120,580 target precursors potentially observable (0 removed)
0:40:27.845338 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:40:27.845721 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
0:40:27.845819 PROGRESS: Starting initial search for precursors.
0:40:27.845915 INFO: Starting optimization step 0.
0:40:27.845974 PROGRESS: === Extracting elution groups 0 to 200 ===
0:40:27.846028 INFO: Using ng extraction backend
0:40:27.846083 PROGRESS: Extracting batch of 398 precursors
0:40:27.848301 INFO: === Search parameters used ===
0:40:27.848403 INFO: rt_error       : 805.5982666015625
0:40:27.848453 INFO: mobility_error : 0.1
0:40:27.848497 INFO: num_candidates : 1
0:40:27.848539 INFO: ms1_error      : 30
0:40:27.848578 INFO: ms2_error      : 30
0:40:27.848619 INFO: fwhm_rt        : 5
0:40:27.848657 INFO: quant_window   : 3
0:40:27.848697 INFO: ==============================================
0:40:27.865201 INFO: performing precursor FDR with 40 features
0:40:27.865271 INFO: Decoy channel: -1
0:40:27.865296 INFO: Competetive: True
0:40:27.866215 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:27.868336 INFO: Using random state 228323 for train-test-split
0:40:27.875125 INFO: Test AUC: 0.690
0:40:27.875183 INFO: Train AUC: 0.682
0:40:27.875211 INFO: AUC difference: 1.23%
0:40:28.087602 INFO: Resetting torch num_threads to 80
0:40:28.089067 PROGRESS: === Extracted 397 precursors and 2803 fragments ===
0:40:28.089411 INFO: === FDR correction performed with classifier version -1 ===
0:40:28.089846 PROGRESS: ============================= Precursor FDR =============================
0:40:28.089932 PROGRESS: Total precursors accumulated: 0
0:40:28.089991 PROGRESS: Target precursors: 0 (0.00%)
0:40:28.090044 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:28.090089 PROGRESS: 
0:40:28.090135 PROGRESS: Precursor Summary:
0:40:28.090241 PROGRESS: 
0:40:28.090302 PROGRESS: Protein Summary:
0:40:28.090374 PROGRESS: =========================================================================
0:40:28.090582 INFO: Target number of precursors not reached yet.
0:40:28.094531 INFO: Starting optimization step 1.
0:40:28.094727 PROGRESS: === Extracting elution groups 200 to 600 ===
0:40:28.094805 INFO: Using ng extraction backend
0:40:28.094865 PROGRESS: Extracting batch of 798 precursors
0:40:28.097662 INFO: === Search parameters used ===
0:40:28.097758 INFO: rt_error       : 805.5982666015625
0:40:28.097809 INFO: mobility_error : 0.1
0:40:28.097853 INFO: num_candidates : 1
0:40:28.097898 INFO: ms1_error      : 30
0:40:28.097938 INFO: ms2_error      : 30
0:40:28.097978 INFO: fwhm_rt        : 5
0:40:28.098018 INFO: quant_window   : 3
0:40:28.098056 INFO: ==============================================
0:40:28.122529 INFO: performing precursor FDR with 40 features
0:40:28.122613 INFO: Decoy channel: -1
0:40:28.122638 INFO: Competetive: True
0:40:28.125603 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:28.127230 INFO: Using random state 390195 for train-test-split
0:40:28.135834 INFO: Test AUC: 0.718
0:40:28.135895 INFO: Train AUC: 0.671
0:40:28.135923 INFO: AUC difference: 7.10%
0:40:28.135945 WARNING: AUC difference > 5%. This may indicate overfitting.
0:40:28.354591 INFO: Resetting torch num_threads to 80
0:40:28.356906 PROGRESS: === Extracted 1194 precursors and 8349 fragments ===
0:40:28.357276 INFO: === FDR correction performed with classifier version -1 ===
0:40:28.357712 PROGRESS: ============================= Precursor FDR =============================
0:40:28.357799 PROGRESS: Total precursors accumulated: 0
0:40:28.357857 PROGRESS: Target precursors: 0 (0.00%)
0:40:28.357909 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:28.357955 PROGRESS: 
0:40:28.358000 PROGRESS: Precursor Summary:
0:40:28.358108 PROGRESS: 
0:40:28.358170 PROGRESS: Protein Summary:
0:40:28.358254 PROGRESS: =========================================================================
0:40:28.358489 INFO: Target number of precursors not reached yet.
0:40:28.363352 INFO: Starting optimization step 2.
0:40:28.363464 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:40:28.363539 INFO: Using ng extraction backend
0:40:28.363599 PROGRESS: Extracting batch of 1598 precursors
0:40:28.368053 INFO: === Search parameters used ===
0:40:28.368159 INFO: rt_error       : 805.5982666015625
0:40:28.368221 INFO: mobility_error : 0.1
0:40:28.368266 INFO: num_candidates : 1
0:40:28.368310 INFO: ms1_error      : 30
0:40:28.368351 INFO: ms2_error      : 30
0:40:28.368392 INFO: fwhm_rt        : 5
0:40:28.368430 INFO: quant_window   : 3
0:40:28.368469 INFO: ==============================================
0:40:28.400617 INFO: performing precursor FDR with 40 features
0:40:28.400694 INFO: Decoy channel: -1
0:40:28.400721 INFO: Competetive: True
0:40:28.404088 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:28.405977 INFO: Using random state 774425 for train-test-split
0:40:28.418822 INFO: Test AUC: 0.648
0:40:28.418887 INFO: Train AUC: 0.671
0:40:28.418915 INFO: AUC difference: 3.39%
0:40:28.631722 INFO: Resetting torch num_threads to 80
0:40:28.634479 PROGRESS: === Extracted 2791 precursors and 19395 fragments ===
0:40:28.634860 INFO: === FDR correction performed with classifier version -1 ===
0:40:28.635324 PROGRESS: ============================= Precursor FDR =============================
0:40:28.635413 PROGRESS: Total precursors accumulated: 1
0:40:28.635472 PROGRESS: Target precursors: 1 (100.00%)
0:40:28.635521 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:28.635566 PROGRESS: 
0:40:28.635615 PROGRESS: Precursor Summary:
0:40:28.636561 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:28.636647 PROGRESS: 
0:40:28.636703 PROGRESS: Protein Summary:
0:40:28.637727 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:28.637816 PROGRESS: =========================================================================
0:40:28.638075 INFO: Target number of precursors not reached yet.
0:40:28.644668 INFO: Starting optimization step 3.
0:40:28.644789 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:40:28.644864 INFO: Using ng extraction backend
0:40:28.644926 PROGRESS: Extracting batch of 3190 precursors
0:40:28.652211 INFO: === Search parameters used ===
0:40:28.652346 INFO: rt_error       : 805.5982666015625
0:40:28.652401 INFO: mobility_error : 0.1
0:40:28.652447 INFO: num_candidates : 1
0:40:28.652490 INFO: ms1_error      : 30
0:40:28.652531 INFO: ms2_error      : 30
0:40:28.652569 INFO: fwhm_rt        : 5
0:40:28.652611 INFO: quant_window   : 3
0:40:28.652648 INFO: ==============================================
0:40:28.699567 INFO: performing precursor FDR with 40 features
0:40:28.699671 INFO: Decoy channel: -1
0:40:28.699696 INFO: Competetive: True
0:40:28.703717 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:28.706060 INFO: Using random state 373926 for train-test-split
0:40:28.726520 INFO: Test AUC: 0.677
0:40:28.726618 INFO: Train AUC: 0.657
0:40:28.726648 INFO: AUC difference: 2.99%
0:40:28.945772 INFO: Resetting torch num_threads to 80
0:40:28.949300 PROGRESS: === Extracted 5980 precursors and 41800 fragments ===
0:40:28.949662 INFO: === FDR correction performed with classifier version -1 ===
0:40:28.950138 PROGRESS: ============================= Precursor FDR =============================
0:40:28.950230 PROGRESS: Total precursors accumulated: 1
0:40:28.950289 PROGRESS: Target precursors: 1 (100.00%)
0:40:28.950339 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:28.950382 PROGRESS: 
0:40:28.950425 PROGRESS: Precursor Summary:
0:40:28.951368 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:28.951457 PROGRESS: 
0:40:28.951511 PROGRESS: Protein Summary:
0:40:28.952543 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:28.952633 PROGRESS: =========================================================================
0:40:28.952926 INFO: Target number of precursors not reached yet.
0:40:28.963179 INFO: Starting optimization step 4.
0:40:28.963317 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:40:28.963394 INFO: Using ng extraction backend
0:40:28.963459 PROGRESS: Extracting batch of 6370 precursors
0:40:28.976240 INFO: === Search parameters used ===
0:40:28.976387 INFO: rt_error       : 805.5982666015625
0:40:28.976437 INFO: mobility_error : 0.1
0:40:28.976502 INFO: num_candidates : 1
0:40:28.976546 INFO: ms1_error      : 30
0:40:28.976597 INFO: ms2_error      : 30
0:40:28.976639 INFO: fwhm_rt        : 5
0:40:28.976679 INFO: quant_window   : 3
0:40:28.976717 INFO: ==============================================
0:40:29.048914 INFO: performing precursor FDR with 40 features
0:40:29.049034 INFO: Decoy channel: -1
0:40:29.049061 INFO: Competetive: True
0:40:29.054557 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:29.058072 INFO: Using random state 76435 for train-test-split
0:40:29.097084 INFO: Test AUC: 0.668
0:40:29.097195 INFO: Train AUC: 0.666
0:40:29.097226 INFO: AUC difference: 0.29%
0:40:29.316132 INFO: Resetting torch num_threads to 80
0:40:29.320459 PROGRESS: === Extracted 12340 precursors and 86232 fragments ===
0:40:29.320876 INFO: === FDR correction performed with classifier version -1 ===
0:40:29.321337 PROGRESS: ============================= Precursor FDR =============================
0:40:29.321424 PROGRESS: Total precursors accumulated: 0
0:40:29.321484 PROGRESS: Target precursors: 0 (0.00%)
0:40:29.321534 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:29.321579 PROGRESS: 
0:40:29.321625 PROGRESS: Precursor Summary:
0:40:29.321736 PROGRESS: 
0:40:29.321797 PROGRESS: Protein Summary:
0:40:29.321870 PROGRESS: =========================================================================
0:40:29.322207 INFO: Target number of precursors not reached yet.
0:40:29.339522 INFO: Starting optimization step 5.
0:40:29.339747 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:40:29.339835 INFO: Using ng extraction backend
0:40:29.339900 PROGRESS: Extracting batch of 12737 precursors
0:40:29.362658 INFO: === Search parameters used ===
0:40:29.362858 INFO: rt_error       : 805.5982666015625
0:40:29.362911 INFO: mobility_error : 0.1
0:40:29.362960 INFO: num_candidates : 1
0:40:29.363003 INFO: ms1_error      : 30
0:40:29.363045 INFO: ms2_error      : 30
0:40:29.363089 INFO: fwhm_rt        : 5
0:40:29.363131 INFO: quant_window   : 3
0:40:29.363172 INFO: ==============================================
0:40:29.499099 INFO: performing precursor FDR with 40 features
0:40:29.499230 INFO: Decoy channel: -1
0:40:29.499255 INFO: Competetive: True
0:40:29.510404 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:29.516129 INFO: Using random state 493509 for train-test-split
0:40:29.835700 INFO: Test AUC: 0.815
0:40:29.835833 INFO: Train AUC: 0.810
0:40:29.835864 INFO: AUC difference: 0.66%
0:40:30.068929 INFO: Resetting torch num_threads to 80
0:40:30.076214 PROGRESS: === Extracted 25064 precursors and 176007 fragments ===
0:40:30.076662 INFO: === FDR correction performed with classifier version -1 ===
0:40:30.077875 PROGRESS: ============================= Precursor FDR =============================
0:40:30.077968 PROGRESS: Total precursors accumulated: 7,001
0:40:30.078029 PROGRESS: Target precursors: 6,932 (99.01%)
0:40:30.078081 PROGRESS: Decoy precursors: 69 (0.99%)
0:40:30.078126 PROGRESS: 
0:40:30.078171 PROGRESS: Precursor Summary:
0:40:30.080948 PROGRESS: Channel   0:	 0.050 FDR: 6,932; 0.010 FDR: 6,932; 0.001 FDR: 6,932
0:40:30.081053 PROGRESS: 
0:40:30.081110 PROGRESS: Protein Summary:
0:40:30.085164 PROGRESS: Channel   0:	 0.050 FDR: 3,808; 0.010 FDR: 3,808; 0.001 FDR: 3,808
0:40:30.085271 PROGRESS: =========================================================================
0:40:30.085730 INFO: Target number of precursors reached.
0:40:30.119222 INFO: fragments_df: keeping 5000 of 176007 [sum(precursor_idx_mask)=71541 sum(mass_error_mask)=176007 stop_rank=5000
0:40:30.126008 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:31.196147 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:31.880713 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:40:31.881252 INFO: Using score_cutoff 12.389557496738433 (fac=0.99, q=1)
0:40:31.881614 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:40:31.881696 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:40:31.881765 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.389557496738433
0:40:31.881822 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:31.883442 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:31.885581 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:40:31.885675 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:40:31.885755 INFO: Starting optimization step 6.
0:40:31.885817 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:31.885880 INFO: Using ng extraction backend
0:40:31.885940 PROGRESS: Extracting batch of 1196 precursors
0:40:31.889514 INFO: === Search parameters used ===
0:40:31.889608 INFO: rt_error       : 805.5982666015625
0:40:31.889659 INFO: mobility_error : 0.1
0:40:31.889704 INFO: num_candidates : 3
0:40:31.889752 INFO: ms1_error      : 30
0:40:31.889796 INFO: ms2_error      : 30
0:40:31.889836 INFO: fwhm_rt        : 3.0
0:40:31.889875 INFO: quant_window   : 3
0:40:31.889913 INFO: ==============================================
0:40:31.931769 INFO: performing precursor FDR with 40 features
0:40:31.931863 INFO: Decoy channel: -1
0:40:31.931889 INFO: Competetive: True
0:40:31.936610 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:31.938541 INFO: Using random state 461633 for train-test-split
0:40:31.951012 INFO: Test AUC: 0.655
0:40:31.951075 INFO: Train AUC: 0.645
0:40:31.951103 INFO: AUC difference: 1.54%
0:40:32.162931 INFO: Resetting torch num_threads to 80
0:40:32.164623 PROGRESS: === Extracted 3585 precursors and 21891 fragments ===
0:40:32.164970 INFO: === FDR correction performed with classifier version 5 ===
0:40:32.165459 PROGRESS: ============================= Precursor FDR =============================
0:40:32.165549 PROGRESS: Total precursors accumulated: 397
0:40:32.165608 PROGRESS: Target precursors: 394 (99.24%)
0:40:32.165658 PROGRESS: Decoy precursors: 3 (0.76%)
0:40:32.165702 PROGRESS: 
0:40:32.165745 PROGRESS: Precursor Summary:
0:40:32.166727 PROGRESS: Channel   0:	 0.050 FDR:   394; 0.010 FDR:   394; 0.001 FDR:   394
0:40:32.166823 PROGRESS: 
0:40:32.166878 PROGRESS: Protein Summary:
0:40:32.168055 PROGRESS: Channel   0:	 0.050 FDR:   376; 0.010 FDR:   376; 0.001 FDR:   376
0:40:32.168148 PROGRESS: =========================================================================
0:40:32.168643 INFO: Target number of precursors reached.
0:40:32.172709 INFO: fragments_df: keeping 3997 of 21891 [sum(precursor_idx_mask)=8608 sum(mass_error_mask)=21891 stop_rank=3997
0:40:32.178958 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:32.304788 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:32.834285 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:32.834772 INFO: Using score_cutoff 12.498570075702666 (fac=0.99, q=1)
0:40:32.835072 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:32.835153 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:32.835208 INFO: Updating optimization_manager: score_cutoff        : 12.389557496738433 -> 12.498570075702666
0:40:32.835262 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:32.836875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:32.839079 INFO: === checking if optimization conditions were reached ===
0:40:32.840561 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.171496
0:40:32.840669 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:40:32.840734 PROGRESS: ❌ ms2_error      : 7.1715 > 7.1715 or insufficient steps taken.
0:40:32.840794 INFO: ==============================================
0:40:32.840858 INFO: Starting optimization step 7.
0:40:32.840934 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:32.840997 INFO: Using ng extraction backend
0:40:32.841053 PROGRESS: Extracting batch of 1196 precursors
0:40:32.844734 INFO: === Search parameters used ===
0:40:32.844825 INFO: rt_error       : 805.5982666015625
0:40:32.844895 INFO: mobility_error : 0.1
0:40:32.844939 INFO: num_candidates : 3
0:40:32.844980 INFO: ms1_error      : 30
0:40:32.845018 INFO: ms2_error      : 7.171496
0:40:32.845060 INFO: fwhm_rt        : 3.0
0:40:32.845098 INFO: quant_window   : 3
0:40:32.845136 INFO: ==============================================
0:40:32.883351 INFO: performing precursor FDR with 40 features
0:40:32.883446 INFO: Decoy channel: -1
0:40:32.883471 INFO: Competetive: True
0:40:32.886368 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:32.888342 INFO: Using random state 99714 for train-test-split
0:40:32.901968 INFO: Test AUC: 0.674
0:40:32.902035 INFO: Train AUC: 0.675
0:40:32.902064 INFO: AUC difference: 0.18%
0:40:33.120139 INFO: Resetting torch num_threads to 80
0:40:33.121815 PROGRESS: === Extracted 3588 precursors and 25699 fragments ===
0:40:33.122159 INFO: === FDR correction performed with classifier version 6 ===
0:40:33.122660 PROGRESS: ============================= Precursor FDR =============================
0:40:33.122750 PROGRESS: Total precursors accumulated: 411
0:40:33.122811 PROGRESS: Target precursors: 407 (99.03%)
0:40:33.122861 PROGRESS: Decoy precursors: 4 (0.97%)
0:40:33.122907 PROGRESS: 
0:40:33.122952 PROGRESS: Precursor Summary:
0:40:33.123907 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   407; 0.001 FDR:   390
0:40:33.123996 PROGRESS: 
0:40:33.124050 PROGRESS: Protein Summary:
0:40:33.125209 PROGRESS: Channel   0:	 0.050 FDR:   387; 0.010 FDR:   387; 0.001 FDR:   372
0:40:33.125302 PROGRESS: =========================================================================
0:40:33.125526 INFO: Target number of precursors reached.
0:40:33.129998 INFO: fragments_df: keeping 4347 of 25699 [sum(precursor_idx_mask)=10005 sum(mass_error_mask)=25699 stop_rank=4347
0:40:33.135071 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:33.276370 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:33.789332 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:33.789798 INFO: Using score_cutoff 12.230355631256103 (fac=0.99, q=1)
0:40:33.790099 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:33.790182 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:33.790237 INFO: Updating optimization_manager: score_cutoff        : 12.498570075702666 -> 12.230355631256103
0:40:33.790295 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:33.791912 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:33.794203 INFO: === checking if optimization conditions were reached ===
0:40:33.795747 INFO: Updating optimization_manager: ms2_error           : 7.171496 -> 7.171496
0:40:33.795853 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:40:33.795917 PROGRESS: ✅ ms2_error      : 7.1715 <= 7.1715
0:40:33.795974 INFO: ==============================================
0:40:33.796036 PROGRESS: Optimization finished for ms2_error.
0:40:33.800843 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:33.802163 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:33.804416 INFO: Starting optimization step 0.
0:40:33.804514 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:33.804596 INFO: Using ng extraction backend
0:40:33.804660 PROGRESS: Extracting batch of 1196 precursors
0:40:33.808297 INFO: === Search parameters used ===
0:40:33.808393 INFO: rt_error       : 805.5982666015625
0:40:33.808443 INFO: mobility_error : 0.1
0:40:33.808486 INFO: num_candidates : 3
0:40:33.808529 INFO: ms1_error      : 30
0:40:33.808568 INFO: ms2_error      : 7.171496
0:40:33.808609 INFO: fwhm_rt        : 3.0
0:40:33.808648 INFO: quant_window   : 3
0:40:33.808686 INFO: ==============================================
0:40:33.845269 INFO: performing precursor FDR with 40 features
0:40:33.845359 INFO: Decoy channel: -1
0:40:33.845385 INFO: Competetive: True
0:40:33.850000 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:33.851954 INFO: Using random state 962090 for train-test-split
0:40:33.864038 INFO: Test AUC: 0.677
0:40:33.864101 INFO: Train AUC: 0.675
0:40:33.864133 INFO: AUC difference: 0.26%
0:40:34.082576 INFO: Resetting torch num_threads to 80
0:40:34.084241 PROGRESS: === Extracted 3588 precursors and 25654 fragments ===
0:40:34.084583 INFO: === FDR correction performed with classifier version 7 ===
0:40:34.085082 PROGRESS: ============================= Precursor FDR =============================
0:40:34.085172 PROGRESS: Total precursors accumulated: 409
0:40:34.085229 PROGRESS: Target precursors: 405 (99.02%)
0:40:34.085280 PROGRESS: Decoy precursors: 4 (0.98%)
0:40:34.085324 PROGRESS: 
0:40:34.085370 PROGRESS: Precursor Summary:
0:40:34.086425 PROGRESS: Channel   0:	 0.050 FDR:   405; 0.010 FDR:   405; 0.001 FDR:   391
0:40:34.086524 PROGRESS: 
0:40:34.086610 PROGRESS: Protein Summary:
0:40:34.088073 PROGRESS: Channel   0:	 0.050 FDR:   385; 0.010 FDR:   385; 0.001 FDR:   372
0:40:34.088176 PROGRESS: =========================================================================
0:40:34.088504 INFO: Target number of precursors reached.
0:40:34.092967 INFO: fragments_df: keeping 4349 of 25654 [sum(precursor_idx_mask)=9958 sum(mass_error_mask)=25654 stop_rank=4349
0:40:34.097966 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:34.210273 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:34.722935 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:34.723403 INFO: Using score_cutoff 12.225815991210936 (fac=0.99, q=1)
0:40:34.723706 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:34.723787 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:34.723841 INFO: Updating optimization_manager: score_cutoff        : 12.230355631256103 -> 12.225815991210936
0:40:34.723894 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:34.725531 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:34.727808 INFO: === checking if optimization conditions were reached ===
0:40:34.727911 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:40:34.729409 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 59.30164721748417
0:40:34.729511 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 59.3016.
0:40:34.729573 INFO: ==============================================
0:40:34.729649 INFO: Starting optimization step 1.
0:40:34.729710 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:34.729774 INFO: Using ng extraction backend
0:40:34.729830 PROGRESS: Extracting batch of 1196 precursors
0:40:34.733558 INFO: === Search parameters used ===
0:40:34.733651 INFO: rt_error       : 59.30164721748417
0:40:34.733701 INFO: mobility_error : 0.1
0:40:34.733745 INFO: num_candidates : 3
0:40:34.733787 INFO: ms1_error      : 30
0:40:34.733826 INFO: ms2_error      : 7.171496
0:40:34.733869 INFO: fwhm_rt        : 3.0
0:40:34.733910 INFO: quant_window   : 3
0:40:34.733948 INFO: ==============================================
0:40:34.768521 INFO: performing precursor FDR with 40 features
0:40:34.768602 INFO: Decoy channel: -1
0:40:34.768627 INFO: Competetive: True
0:40:34.771476 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:34.773291 INFO: Using random state 962090 for train-test-split
0:40:34.785510 INFO: Test AUC: 0.724
0:40:34.785575 INFO: Train AUC: 0.689
0:40:34.785606 INFO: AUC difference: 5.02%
0:40:34.785630 WARNING: AUC difference > 5%. This may indicate overfitting.
0:40:35.007004 INFO: Resetting torch num_threads to 80
0:40:35.008674 PROGRESS: === Extracted 3534 precursors and 21867 fragments ===
0:40:35.009041 INFO: === FDR correction performed with classifier version 7 ===
0:40:35.009530 PROGRESS: ============================= Precursor FDR =============================
0:40:35.009618 PROGRESS: Total precursors accumulated: 431
0:40:35.009677 PROGRESS: Target precursors: 427 (99.07%)
0:40:35.009737 PROGRESS: Decoy precursors: 4 (0.93%)
0:40:35.009783 PROGRESS: 
0:40:35.009826 PROGRESS: Precursor Summary:
0:40:35.010790 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   427; 0.001 FDR:   399
0:40:35.010891 PROGRESS: 
0:40:35.010947 PROGRESS: Protein Summary:
0:40:35.012107 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   407; 0.001 FDR:   379
0:40:35.012199 PROGRESS: =========================================================================
0:40:35.012427 INFO: Target number of precursors reached.
0:40:35.016508 INFO: fragments_df: keeping 4211 of 21867 [sum(precursor_idx_mask)=9416 sum(mass_error_mask)=21867 stop_rank=4211
0:40:35.021486 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:35.131031 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:35.642231 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:35.642706 INFO: Using score_cutoff 12.275781318855286 (fac=0.99, q=1)
0:40:35.643002 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:35.643086 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:35.643141 INFO: Updating optimization_manager: score_cutoff        : 12.225815991210936 -> 12.275781318855286
0:40:35.643196 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:35.644796 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:35.647098 INFO: === checking if optimization conditions were reached ===
0:40:35.647202 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:40:35.648798 INFO: Updating optimization_manager: rt_error            : 59.30164721748417 -> 18.941278907363387
0:40:35.648909 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 18.9413.
0:40:35.648975 INFO: ==============================================
0:40:35.649041 INFO: Starting optimization step 2.
0:40:35.649101 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:35.649161 INFO: Using ng extraction backend
0:40:35.649217 PROGRESS: Extracting batch of 1196 precursors
0:40:35.652805 INFO: === Search parameters used ===
0:40:35.652897 INFO: rt_error       : 18.941278907363387
0:40:35.652948 INFO: mobility_error : 0.1
0:40:35.652994 INFO: num_candidates : 3
0:40:35.653037 INFO: ms1_error      : 30
0:40:35.653077 INFO: ms2_error      : 7.171496
0:40:35.653118 INFO: fwhm_rt        : 3.0
0:40:35.653158 INFO: quant_window   : 3
0:40:35.653197 INFO: ==============================================
0:40:35.687324 INFO: performing precursor FDR with 40 features
0:40:35.687407 INFO: Decoy channel: -1
0:40:35.687433 INFO: Competetive: True
0:40:35.690043 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:35.691834 INFO: Using random state 962090 for train-test-split
0:40:35.703372 INFO: Test AUC: 0.698
0:40:35.703435 INFO: Train AUC: 0.704
0:40:35.703466 INFO: AUC difference: 0.83%
0:40:35.924382 INFO: Resetting torch num_threads to 80
0:40:35.926035 PROGRESS: === Extracted 3314 precursors and 20028 fragments ===
0:40:35.926377 INFO: === FDR correction performed with classifier version 7 ===
0:40:35.926867 PROGRESS: ============================= Precursor FDR =============================
0:40:35.926957 PROGRESS: Total precursors accumulated: 432
0:40:35.927015 PROGRESS: Target precursors: 428 (99.07%)
0:40:35.927064 PROGRESS: Decoy precursors: 4 (0.93%)
0:40:35.927109 PROGRESS: 
0:40:35.927160 PROGRESS: Precursor Summary:
0:40:35.928113 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   428; 0.001 FDR:   400
0:40:35.928203 PROGRESS: 
0:40:35.928257 PROGRESS: Protein Summary:
0:40:35.929409 PROGRESS: Channel   0:	 0.050 FDR:   408; 0.010 FDR:   408; 0.001 FDR:   380
0:40:35.929500 PROGRESS: =========================================================================
0:40:35.929734 INFO: Target number of precursors reached.
0:40:35.933577 INFO: fragments_df: keeping 3966 of 20028 [sum(precursor_idx_mask)=8576 sum(mass_error_mask)=20028 stop_rank=3966
0:40:35.938597 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:36.068252 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:36.590251 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:36.590723 INFO: Using score_cutoff 12.278052470111847 (fac=0.99, q=1)
0:40:36.591024 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:36.591105 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:36.591160 INFO: Updating optimization_manager: score_cutoff        : 12.275781318855286 -> 12.278052470111847
0:40:36.591215 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:36.592847 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:36.595083 INFO: === checking if optimization conditions were reached ===
0:40:36.595183 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:40:36.597119 INFO: Updating optimization_manager: rt_error            : 18.941278907363387 -> 18.892165646740864
0:40:36.597221 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 18.8922.
0:40:36.597286 INFO: ==============================================
0:40:36.597353 INFO: Starting optimization step 3.
0:40:36.597412 PROGRESS: === Extracting elution groups 0 to 600 ===
0:40:36.597476 INFO: Using ng extraction backend
0:40:36.597533 PROGRESS: Extracting batch of 1196 precursors
0:40:36.601180 INFO: === Search parameters used ===
0:40:36.601270 INFO: rt_error       : 18.892165646740864
0:40:36.601319 INFO: mobility_error : 0.1
0:40:36.601363 INFO: num_candidates : 3
0:40:36.601405 INFO: ms1_error      : 30
0:40:36.601445 INFO: ms2_error      : 7.171496
0:40:36.601485 INFO: fwhm_rt        : 3.0
0:40:36.601523 INFO: quant_window   : 3
0:40:36.601562 INFO: ==============================================
0:40:36.633784 INFO: performing precursor FDR with 40 features
0:40:36.633868 INFO: Decoy channel: -1
0:40:36.633893 INFO: Competetive: True
0:40:36.636460 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:36.638269 INFO: Using random state 962090 for train-test-split
0:40:36.650317 INFO: Test AUC: 0.679
0:40:36.650384 INFO: Train AUC: 0.710
0:40:36.650415 INFO: AUC difference: 4.36%
0:40:36.870538 INFO: Resetting torch num_threads to 80
0:40:36.872196 PROGRESS: === Extracted 3311 precursors and 20014 fragments ===
0:40:36.872534 INFO: === FDR correction performed with classifier version 7 ===
0:40:36.872999 PROGRESS: ============================= Precursor FDR =============================
0:40:36.873086 PROGRESS: Total precursors accumulated: 432
0:40:36.873144 PROGRESS: Target precursors: 428 (99.07%)
0:40:36.873201 PROGRESS: Decoy precursors: 4 (0.93%)
0:40:36.873247 PROGRESS: 
0:40:36.873292 PROGRESS: Precursor Summary:
0:40:36.874237 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   428; 0.001 FDR:   400
0:40:36.874325 PROGRESS: 
0:40:36.874379 PROGRESS: Protein Summary:
0:40:36.875519 PROGRESS: Channel   0:	 0.050 FDR:   408; 0.010 FDR:   408; 0.001 FDR:   380
0:40:36.875613 PROGRESS: =========================================================================
0:40:36.875818 INFO: Target number of precursors reached.
0:40:36.879449 INFO: fragments_df: keeping 3965 of 20014 [sum(precursor_idx_mask)=8567 sum(mass_error_mask)=20014 stop_rank=3965
0:40:36.884377 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:37.014794 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:37.537258 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:37.537727 INFO: Using score_cutoff 12.278052470111847 (fac=0.99, q=1)
0:40:37.538027 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:37.538108 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:37.538164 INFO: Updating optimization_manager: score_cutoff        : 12.278052470111847 -> 12.278052470111847
0:40:37.538219 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:37.539875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:37.542144 INFO: === checking if optimization conditions were reached ===
0:40:37.542261 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:40:37.543203 INFO: Updating optimization_manager: rt_error            : 18.892165646740864 -> 18.892165646740864
0:40:37.543326 INFO: Updating optimization_manager: classifier_version  : 7 -> 11
0:40:37.543420 INFO: Updating optimization_manager: score_cutoff        : 12.278052470111847 -> 12.278052470111847
0:40:37.543502 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:37.543581 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:37.543664 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 18.8922 found after 4 searches.
0:40:37.543725 INFO: ==============================================
0:40:37.543793 PROGRESS: Optimization finished for rt_error.
0:40:37.548566 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:37.549887 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:37.577247 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:40:37.577396 PROGRESS: ==============================================
0:40:37.577462 PROGRESS: ms2_error      : 7.1715
0:40:37.577519 PROGRESS: rt_error       : 18.8922
0:40:37.577566 PROGRESS: ==============================================
0:40:37.577983 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:37.701813 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:38.048734 INFO: Using ng extraction backend
0:40:38.049030 PROGRESS: Extracting batch of 240048 precursors
0:40:38.432340 INFO: === Search parameters used ===
0:40:38.432613 INFO: rt_error       : 18.892165646740864
0:40:38.432671 INFO: mobility_error : 0.1
0:40:38.432720 INFO: num_candidates : 3
0:40:38.432764 INFO: ms1_error      : 30
0:40:38.432806 INFO: ms2_error      : 7.171496
0:40:38.432850 INFO: fwhm_rt        : 3.0
0:40:38.432891 INFO: quant_window   : 3
0:40:38.432932 INFO: ==============================================
0:40:38.691086 INFO: Removed 381559 precursors with score below cutoff 12.278052470111847
0:40:38.948590 INFO: performing precursor FDR with 40 features
0:40:38.948723 INFO: Decoy channel: -1
0:40:38.948749 INFO: Competetive: True
0:40:38.975759 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:38.991857 WARNING: FDR calculation for 186591 target and 89348 decoy PSMs
0:40:38.991998 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:40:39.048944 INFO: Using random state 406006 for train-test-split
0:40:42.940307 INFO: Test AUC: 0.873
0:40:42.940445 INFO: Train AUC: 0.877
0:40:42.940479 INFO: AUC difference: 0.48%
0:40:43.235331 INFO: Resetting torch num_threads to 80
0:40:43.548554 PROGRESS: ============================= Precursor FDR =============================
0:40:43.548821 PROGRESS: Total precursors accumulated: 109,970
0:40:43.548895 PROGRESS: Target precursors: 108,882 (99.01%)
0:40:43.548948 PROGRESS: Decoy precursors: 1,088 (0.99%)
0:40:43.548996 PROGRESS: 
0:40:43.549041 PROGRESS: Precursor Summary:
0:40:43.579098 PROGRESS: Channel   0:	 0.050 FDR: 108,882; 0.010 FDR: 108,882; 0.001 FDR: 105,054
0:40:43.579365 PROGRESS: 
0:40:43.579429 PROGRESS: Protein Summary:
0:40:43.621086 PROGRESS: Channel   0:	 0.050 FDR: 10,109; 0.010 FDR: 10,109; 0.001 FDR: 10,088
0:40:43.621367 PROGRESS: =========================================================================
0:40:43.623011 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
0:40:43.805511 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
0:40:44.102381 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:40:44.198260 PROGRESS: 
0:40:44.198421 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
0:40:44.198492 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
0:40:44.198652 INFO: Initializing TimingManager
0:40:44.199161 INFO: Initializing RawFileManager
0:40:55.538456 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:40:55.542690 INFO: Determining DIA cycle
0:40:55.559107 INFO: Found cycle with start 0.00 min and length 300.
0:40:55.747239 INFO: RT (min)            : 0.0 - 26.9
0:40:55.747354 INFO: RT duration (sec)   : 1611.2
0:40:55.747389 INFO: RT duration (min)   : 26.9
0:40:55.747417 INFO: Cycle len (scans)   : 300
0:40:55.747440 INFO: Cycle len (sec)     : 1.65
0:40:55.747462 INFO: Number of cycles    : 977
0:40:55.747483 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:40:55.747536 INFO: Creating DIA data object took: 11.548264980316162
0:40:56.439360 INFO: Creating DIA data NG object took: 0.6916718482971191
0:40:56.484334 INFO: Initializing CalibrationManager
0:40:56.484652 INFO: Setting up calibration estimators ..
0:40:56.484712 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:40:56.484808 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'}' ..
0:40:56.484905 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:40:56.484958 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:40:56.485012 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}}' ..
0:40:56.485065 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:40:56.485108 INFO: Done setting up calibration estimators.
0:40:56.485294 INFO: Initializing OptimizationManager
0:40:56.485422 INFO: initial parameter: ms1_error = 30
0:40:56.485476 INFO: initial parameter: ms2_error = 30
0:40:56.485523 INFO: initial parameter: rt_error = 805.6002197265625
0:40:56.485564 INFO: initial parameter: mobility_error = 0.1
0:40:56.485602 INFO: initial parameter: num_candidates = 1
0:40:56.485639 INFO: initial parameter: fwhm_rt = 5
0:40:56.485678 INFO: initial parameter: fwhm_mobility = 0.01
0:40:56.485715 INFO: initial parameter: score_cutoff = 0
0:40:56.485752 INFO: initial parameter: classifier_version = -1
0:40:56.485825 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:40:56.486244 INFO: FDRManager: loading saved state not requested, will be initialized.
0:40:56.486282 INFO: Initializing FDRManager
0:40:56.486323 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:40:56.516377 PROGRESS: Initializing spectral library: 120,580 target precursors potentially observable (0 removed)
0:40:56.536633 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:40:56.537014 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
0:40:56.537124 PROGRESS: Starting initial search for precursors.
0:40:56.537209 INFO: Starting optimization step 0.
0:40:56.537269 PROGRESS: === Extracting elution groups 0 to 200 ===
0:40:56.537331 INFO: Using ng extraction backend
0:40:56.537401 PROGRESS: Extracting batch of 398 precursors
0:40:56.539812 INFO: === Search parameters used ===
0:40:56.539922 INFO: rt_error       : 805.6002197265625
0:40:56.539973 INFO: mobility_error : 0.1
0:40:56.540018 INFO: num_candidates : 1
0:40:56.540068 INFO: ms1_error      : 30
0:40:56.540111 INFO: ms2_error      : 30
0:40:56.540153 INFO: fwhm_rt        : 5
0:40:56.540191 INFO: quant_window   : 3
0:40:56.540228 INFO: ==============================================
0:40:56.557486 INFO: performing precursor FDR with 40 features
0:40:56.557555 INFO: Decoy channel: -1
0:40:56.557580 INFO: Competetive: True
0:40:56.558559 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:56.561149 INFO: Using random state 394692 for train-test-split
0:40:56.569142 INFO: Test AUC: 0.441
0:40:56.569199 INFO: Train AUC: 0.514
0:40:56.569229 INFO: AUC difference: 14.17%
0:40:56.569251 WARNING: AUC difference > 5%. This may indicate overfitting.
0:40:56.783926 INFO: Resetting torch num_threads to 80
0:40:56.785358 PROGRESS: === Extracted 398 precursors and 2817 fragments ===
0:40:56.785712 INFO: === FDR correction performed with classifier version -1 ===
0:40:56.786151 PROGRESS: ============================= Precursor FDR =============================
0:40:56.786246 PROGRESS: Total precursors accumulated: 0
0:40:56.786307 PROGRESS: Target precursors: 0 (0.00%)
0:40:56.786359 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:56.786403 PROGRESS: 
0:40:56.786449 PROGRESS: Precursor Summary:
0:40:56.786570 PROGRESS: 
0:40:56.786633 PROGRESS: Protein Summary:
0:40:56.786705 PROGRESS: =========================================================================
0:40:56.786891 INFO: Target number of precursors not reached yet.
0:40:56.791493 INFO: Starting optimization step 1.
0:40:56.791610 PROGRESS: === Extracting elution groups 200 to 600 ===
0:40:56.791684 INFO: Using ng extraction backend
0:40:56.791744 PROGRESS: Extracting batch of 798 precursors
0:40:56.794529 INFO: === Search parameters used ===
0:40:56.794630 INFO: rt_error       : 805.6002197265625
0:40:56.794679 INFO: mobility_error : 0.1
0:40:56.794724 INFO: num_candidates : 1
0:40:56.794764 INFO: ms1_error      : 30
0:40:56.794803 INFO: ms2_error      : 30
0:40:56.794842 INFO: fwhm_rt        : 5
0:40:56.794885 INFO: quant_window   : 3
0:40:56.794924 INFO: ==============================================
0:40:56.818722 INFO: performing precursor FDR with 40 features
0:40:56.818795 INFO: Decoy channel: -1
0:40:56.818820 INFO: Competetive: True
0:40:56.822628 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:56.824503 INFO: Using random state 713912 for train-test-split
0:40:56.834155 INFO: Test AUC: 0.491
0:40:56.834215 INFO: Train AUC: 0.512
0:40:56.834243 INFO: AUC difference: 4.19%
0:40:57.052593 INFO: Resetting torch num_threads to 80
0:40:57.055147 PROGRESS: === Extracted 1195 precursors and 8371 fragments ===
0:40:57.055546 INFO: === FDR correction performed with classifier version -1 ===
0:40:57.056018 PROGRESS: ============================= Precursor FDR =============================
0:40:57.056108 PROGRESS: Total precursors accumulated: 1
0:40:57.056165 PROGRESS: Target precursors: 1 (100.00%)
0:40:57.056216 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:57.056259 PROGRESS: 
0:40:57.056303 PROGRESS: Precursor Summary:
0:40:57.057231 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:57.057319 PROGRESS: 
0:40:57.057384 PROGRESS: Protein Summary:
0:40:57.058409 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:57.058499 PROGRESS: =========================================================================
0:40:57.058732 INFO: Target number of precursors not reached yet.
0:40:57.063580 INFO: Starting optimization step 2.
0:40:57.063686 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:40:57.063769 INFO: Using ng extraction backend
0:40:57.063832 PROGRESS: Extracting batch of 1598 precursors
0:40:57.068446 INFO: === Search parameters used ===
0:40:57.068546 INFO: rt_error       : 805.6002197265625
0:40:57.068597 INFO: mobility_error : 0.1
0:40:57.068640 INFO: num_candidates : 1
0:40:57.068682 INFO: ms1_error      : 30
0:40:57.068721 INFO: ms2_error      : 30
0:40:57.068760 INFO: fwhm_rt        : 5
0:40:57.068802 INFO: quant_window   : 3
0:40:57.068851 INFO: ==============================================
0:40:57.102309 INFO: performing precursor FDR with 40 features
0:40:57.102390 INFO: Decoy channel: -1
0:40:57.102415 INFO: Competetive: True
0:40:57.106305 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:57.108709 INFO: Using random state 482230 for train-test-split
0:40:57.122212 INFO: Test AUC: 0.515
0:40:57.122280 INFO: Train AUC: 0.495
0:40:57.122310 INFO: AUC difference: 3.93%
0:40:57.335749 INFO: Resetting torch num_threads to 80
0:40:57.338346 PROGRESS: === Extracted 2791 precursors and 19453 fragments ===
0:40:57.338719 INFO: === FDR correction performed with classifier version -1 ===
0:40:57.339184 PROGRESS: ============================= Precursor FDR =============================
0:40:57.339273 PROGRESS: Total precursors accumulated: 1
0:40:57.339340 PROGRESS: Target precursors: 1 (100.00%)
0:40:57.339394 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:57.339441 PROGRESS: 
0:40:57.339485 PROGRESS: Precursor Summary:
0:40:57.340411 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:57.340497 PROGRESS: 
0:40:57.340556 PROGRESS: Protein Summary:
0:40:57.341575 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:57.341664 PROGRESS: =========================================================================
0:40:57.341898 INFO: Target number of precursors not reached yet.
0:40:57.348433 INFO: Starting optimization step 3.
0:40:57.348551 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:40:57.348627 INFO: Using ng extraction backend
0:40:57.348686 PROGRESS: Extracting batch of 3190 precursors
0:40:57.356041 INFO: === Search parameters used ===
0:40:57.356164 INFO: rt_error       : 805.6002197265625
0:40:57.356215 INFO: mobility_error : 0.1
0:40:57.356262 INFO: num_candidates : 1
0:40:57.356308 INFO: ms1_error      : 30
0:40:57.356349 INFO: ms2_error      : 30
0:40:57.356389 INFO: fwhm_rt        : 5
0:40:57.356430 INFO: quant_window   : 3
0:40:57.356476 INFO: ==============================================
0:40:57.406178 INFO: performing precursor FDR with 40 features
0:40:57.406287 INFO: Decoy channel: -1
0:40:57.406312 INFO: Competetive: True
0:40:57.411520 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:57.414012 INFO: Using random state 500633 for train-test-split
0:40:57.435174 INFO: Test AUC: 0.490
0:40:57.435255 INFO: Train AUC: 0.494
0:40:57.435285 INFO: AUC difference: 0.87%
0:40:57.651005 INFO: Resetting torch num_threads to 80
0:40:57.655547 PROGRESS: === Extracted 5980 precursors and 41624 fragments ===
0:40:57.655913 INFO: === FDR correction performed with classifier version -1 ===
0:40:57.656378 PROGRESS: ============================= Precursor FDR =============================
0:40:57.656470 PROGRESS: Total precursors accumulated: 1
0:40:57.656529 PROGRESS: Target precursors: 1 (100.00%)
0:40:57.656592 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:57.656646 PROGRESS: 
0:40:57.656693 PROGRESS: Precursor Summary:
0:40:57.657617 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:57.657708 PROGRESS: 
0:40:57.657763 PROGRESS: Protein Summary:
0:40:57.658792 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:57.658884 PROGRESS: =========================================================================
0:40:57.659154 INFO: Target number of precursors not reached yet.
0:40:57.669478 INFO: Starting optimization step 4.
0:40:57.669609 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:40:57.669688 INFO: Using ng extraction backend
0:40:57.669750 PROGRESS: Extracting batch of 6370 precursors
0:40:57.682223 INFO: === Search parameters used ===
0:40:57.682353 INFO: rt_error       : 805.6002197265625
0:40:57.682413 INFO: mobility_error : 0.1
0:40:57.682461 INFO: num_candidates : 1
0:40:57.682505 INFO: ms1_error      : 30
0:40:57.682546 INFO: ms2_error      : 30
0:40:57.682598 INFO: fwhm_rt        : 5
0:40:57.682640 INFO: quant_window   : 3
0:40:57.682679 INFO: ==============================================
0:40:57.760061 INFO: performing precursor FDR with 40 features
0:40:57.760173 INFO: Decoy channel: -1
0:40:57.760200 INFO: Competetive: True
0:40:57.766624 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:57.770596 INFO: Using random state 527045 for train-test-split
0:40:57.810343 INFO: Test AUC: 0.495
0:40:57.810452 INFO: Train AUC: 0.505
0:40:57.810482 INFO: AUC difference: 1.87%
0:40:58.031394 INFO: Resetting torch num_threads to 80
0:40:58.035565 PROGRESS: === Extracted 12347 precursors and 86121 fragments ===
0:40:58.035938 INFO: === FDR correction performed with classifier version -1 ===
0:40:58.036403 PROGRESS: ============================= Precursor FDR =============================
0:40:58.036491 PROGRESS: Total precursors accumulated: 0
0:40:58.036551 PROGRESS: Target precursors: 0 (0.00%)
0:40:58.036602 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:58.036647 PROGRESS: 
0:40:58.036691 PROGRESS: Precursor Summary:
0:40:58.036798 PROGRESS: 
0:40:58.036860 PROGRESS: Protein Summary:
0:40:58.036932 PROGRESS: =========================================================================
0:40:58.037226 INFO: Target number of precursors not reached yet.
0:40:58.053394 INFO: Starting optimization step 5.
0:40:58.053605 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:40:58.053691 INFO: Using ng extraction backend
0:40:58.053771 PROGRESS: Extracting batch of 12737 precursors
0:40:58.076838 INFO: === Search parameters used ===
0:40:58.077013 INFO: rt_error       : 805.6002197265625
0:40:58.077068 INFO: mobility_error : 0.1
0:40:58.077118 INFO: num_candidates : 1
0:40:58.077162 INFO: ms1_error      : 30
0:40:58.077206 INFO: ms2_error      : 30
0:40:58.077250 INFO: fwhm_rt        : 5
0:40:58.077291 INFO: quant_window   : 3
0:40:58.077335 INFO: ==============================================
0:40:58.210018 INFO: performing precursor FDR with 40 features
0:40:58.210143 INFO: Decoy channel: -1
0:40:58.210169 INFO: Competetive: True
0:40:58.222535 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:58.228314 INFO: Using random state 30569 for train-test-split
0:40:58.553342 INFO: Test AUC: 0.802
0:40:58.553471 INFO: Train AUC: 0.814
0:40:58.553502 INFO: AUC difference: 1.42%
0:40:58.788994 INFO: Resetting torch num_threads to 80
0:40:58.795414 PROGRESS: === Extracted 25068 precursors and 175430 fragments ===
0:40:58.795852 INFO: === FDR correction performed with classifier version -1 ===
0:40:58.796785 PROGRESS: ============================= Precursor FDR =============================
0:40:58.796882 PROGRESS: Total precursors accumulated: 4,380
0:40:58.796943 PROGRESS: Target precursors: 4,337 (99.02%)
0:40:58.796994 PROGRESS: Decoy precursors: 43 (0.98%)
0:40:58.797040 PROGRESS: 
0:40:58.797085 PROGRESS: Precursor Summary:
0:40:58.798994 PROGRESS: Channel   0:	 0.050 FDR: 4,337; 0.010 FDR: 4,337; 0.001 FDR: 2,010
0:40:58.799103 PROGRESS: 
0:40:58.799161 PROGRESS: Protein Summary:
0:40:58.801831 PROGRESS: Channel   0:	 0.050 FDR: 2,666; 0.010 FDR: 2,666; 0.001 FDR: 1,438
0:40:58.801943 PROGRESS: =========================================================================
0:40:58.802368 INFO: Target number of precursors reached.
0:40:58.829336 INFO: fragments_df: keeping 5000 of 175430 [sum(precursor_idx_mask)=47415 sum(mass_error_mask)=175430 stop_rank=5000
0:40:58.835808 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:59.422363 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:00.101034 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:41:00.101559 INFO: Using score_cutoff 14.063864529418947 (fac=0.99, q=1)
0:41:00.101926 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:41:00.102010 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:41:00.102066 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.063864529418947
0:41:00.102127 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:00.103764 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:00.105945 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:41:00.106040 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:41:00.106119 INFO: Starting optimization step 6.
0:41:00.106180 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:00.106244 INFO: Using ng extraction backend
0:41:00.106302 PROGRESS: Extracting batch of 1196 precursors
0:41:00.109925 INFO: === Search parameters used ===
0:41:00.110021 INFO: rt_error       : 805.6002197265625
0:41:00.110074 INFO: mobility_error : 0.1
0:41:00.110118 INFO: num_candidates : 3
0:41:00.110159 INFO: ms1_error      : 30
0:41:00.110200 INFO: ms2_error      : 30
0:41:00.110241 INFO: fwhm_rt        : 3.0
0:41:00.110283 INFO: quant_window   : 3
0:41:00.110323 INFO: ==============================================
0:41:00.149822 INFO: performing precursor FDR with 40 features
0:41:00.149912 INFO: Decoy channel: -1
0:41:00.149938 INFO: Competetive: True
0:41:00.152607 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:00.154660 INFO: Using random state 378346 for train-test-split
0:41:00.166833 INFO: Test AUC: 0.692
0:41:00.166899 INFO: Train AUC: 0.632
0:41:00.166929 INFO: AUC difference: 9.55%
0:41:00.166952 WARNING: AUC difference > 5%. This may indicate overfitting.
0:41:00.386796 INFO: Resetting torch num_threads to 80
0:41:00.388455 PROGRESS: === Extracted 3583 precursors and 21961 fragments ===
0:41:00.388818 INFO: === FDR correction performed with classifier version 5 ===
0:41:00.389268 PROGRESS: ============================= Precursor FDR =============================
0:41:00.389358 PROGRESS: Total precursors accumulated: 241
0:41:00.389417 PROGRESS: Target precursors: 239 (99.17%)
0:41:00.389467 PROGRESS: Decoy precursors: 2 (0.83%)
0:41:00.389513 PROGRESS: 
0:41:00.389558 PROGRESS: Precursor Summary:
0:41:00.390460 PROGRESS: Channel   0:	 0.050 FDR:   239; 0.010 FDR:   239; 0.001 FDR:   216
0:41:00.390551 PROGRESS: 
0:41:00.390619 PROGRESS: Protein Summary:
0:41:00.391666 PROGRESS: Channel   0:	 0.050 FDR:   230; 0.010 FDR:   230; 0.001 FDR:   208
0:41:00.391760 PROGRESS: =========================================================================
0:41:00.392175 INFO: Target number of precursors reached.
0:41:00.395602 INFO: fragments_df: keeping 2778 of 21961 [sum(precursor_idx_mask)=5486 sum(mass_error_mask)=21961 stop_rank=2778
0:41:00.400623 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:00.515036 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:00.888151 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:00.888614 INFO: Using score_cutoff 14.736687346458435 (fac=0.99, q=1)
0:41:00.888908 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:00.888990 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:00.889043 INFO: Updating optimization_manager: score_cutoff        : 14.063864529418947 -> 14.736687346458435
0:41:00.889100 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:00.890777 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:00.892933 INFO: === checking if optimization conditions were reached ===
0:41:00.894263 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.171496
0:41:00.894376 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:41:00.894445 PROGRESS: ❌ ms2_error      : 7.1715 > 7.1715 or insufficient steps taken.
0:41:00.894505 INFO: ==============================================
0:41:00.894579 INFO: Starting optimization step 7.
0:41:00.894643 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:00.894705 INFO: Using ng extraction backend
0:41:00.894763 PROGRESS: Extracting batch of 1196 precursors
0:41:00.898338 INFO: === Search parameters used ===
0:41:00.898436 INFO: rt_error       : 805.6002197265625
0:41:00.898486 INFO: mobility_error : 0.1
0:41:00.898529 INFO: num_candidates : 3
0:41:00.898578 INFO: ms1_error      : 30
0:41:00.898631 INFO: ms2_error      : 7.171496
0:41:00.898672 INFO: fwhm_rt        : 3.0
0:41:00.898710 INFO: quant_window   : 3
0:41:00.898749 INFO: ==============================================
0:41:00.935262 INFO: performing precursor FDR with 40 features
0:41:00.935376 INFO: Decoy channel: -1
0:41:00.935402 INFO: Competetive: True
0:41:00.938054 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:00.939947 INFO: Using random state 157008 for train-test-split
0:41:00.951876 INFO: Test AUC: 0.682
0:41:00.951942 INFO: Train AUC: 0.661
0:41:00.951972 INFO: AUC difference: 3.25%
0:41:01.167852 INFO: Resetting torch num_threads to 80
0:41:01.169523 PROGRESS: === Extracted 3588 precursors and 25578 fragments ===
0:41:01.169870 INFO: === FDR correction performed with classifier version 6 ===
0:41:01.170343 PROGRESS: ============================= Precursor FDR =============================
0:41:01.170431 PROGRESS: Total precursors accumulated: 369
0:41:01.170491 PROGRESS: Target precursors: 366 (99.19%)
0:41:01.170545 PROGRESS: Decoy precursors: 3 (0.81%)
0:41:01.170600 PROGRESS: 
0:41:01.170646 PROGRESS: Precursor Summary:
0:41:01.171581 PROGRESS: Channel   0:	 0.050 FDR:   366; 0.010 FDR:   366; 0.001 FDR:   345
0:41:01.171669 PROGRESS: 
0:41:01.171722 PROGRESS: Protein Summary:
0:41:01.172843 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   330
0:41:01.172939 PROGRESS: =========================================================================
0:41:01.173148 INFO: Target number of precursors reached.
0:41:01.177265 INFO: fragments_df: keeping 4140 of 25578 [sum(precursor_idx_mask)=9115 sum(mass_error_mask)=25578 stop_rank=4140
0:41:01.182216 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:01.285234 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:01.765529 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:01.765996 INFO: Using score_cutoff 12.614345955848695 (fac=0.99, q=1)
0:41:01.766292 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:01.766373 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:01.766431 INFO: Updating optimization_manager: score_cutoff        : 14.736687346458435 -> 12.614345955848695
0:41:01.766487 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:01.768136 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:01.770332 INFO: === checking if optimization conditions were reached ===
0:41:01.771821 INFO: Updating optimization_manager: ms2_error           : 7.171496 -> 7.171496
0:41:01.771924 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:41:01.771987 PROGRESS: ✅ ms2_error      : 7.1715 <= 7.1715
0:41:01.772046 INFO: ==============================================
0:41:01.772113 PROGRESS: Optimization finished for ms2_error.
0:41:01.776966 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:01.778299 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:01.780433 INFO: Starting optimization step 0.
0:41:01.780533 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:01.780606 INFO: Using ng extraction backend
0:41:01.780668 PROGRESS: Extracting batch of 1196 precursors
0:41:01.784303 INFO: === Search parameters used ===
0:41:01.784400 INFO: rt_error       : 805.6002197265625
0:41:01.784451 INFO: mobility_error : 0.1
0:41:01.784495 INFO: num_candidates : 3
0:41:01.784538 INFO: ms1_error      : 30
0:41:01.784577 INFO: ms2_error      : 7.171496
0:41:01.784616 INFO: fwhm_rt        : 3.0
0:41:01.784657 INFO: quant_window   : 3
0:41:01.784694 INFO: ==============================================
0:41:01.822969 INFO: performing precursor FDR with 40 features
0:41:01.823090 INFO: Decoy channel: -1
0:41:01.823117 INFO: Competetive: True
0:41:01.825686 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:01.827565 INFO: Using random state 369771 for train-test-split
0:41:01.839606 INFO: Test AUC: 0.659
0:41:01.839675 INFO: Train AUC: 0.666
0:41:01.839705 INFO: AUC difference: 1.05%
0:41:02.054242 INFO: Resetting torch num_threads to 80
0:41:02.055888 PROGRESS: === Extracted 3588 precursors and 25555 fragments ===
0:41:02.056232 INFO: === FDR correction performed with classifier version 7 ===
0:41:02.056692 PROGRESS: ============================= Precursor FDR =============================
0:41:02.056778 PROGRESS: Total precursors accumulated: 369
0:41:02.056835 PROGRESS: Target precursors: 366 (99.19%)
0:41:02.056885 PROGRESS: Decoy precursors: 3 (0.81%)
0:41:02.056929 PROGRESS: 
0:41:02.056973 PROGRESS: Precursor Summary:
0:41:02.057918 PROGRESS: Channel   0:	 0.050 FDR:   366; 0.010 FDR:   366; 0.001 FDR:   346
0:41:02.058007 PROGRESS: 
0:41:02.058064 PROGRESS: Protein Summary:
0:41:02.059216 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   331
0:41:02.059310 PROGRESS: =========================================================================
0:41:02.059529 INFO: Target number of precursors reached.
0:41:02.063732 INFO: fragments_df: keeping 4114 of 25555 [sum(precursor_idx_mask)=9117 sum(mass_error_mask)=25555 stop_rank=4114
0:41:02.068665 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:02.192752 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:02.714592 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:02.715050 INFO: Using score_cutoff 12.614345955848695 (fac=0.99, q=1)
0:41:02.715350 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:02.715433 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:02.715488 INFO: Updating optimization_manager: score_cutoff        : 12.614345955848695 -> 12.614345955848695
0:41:02.715543 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:02.717154 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:02.719368 INFO: === checking if optimization conditions were reached ===
0:41:02.719474 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:41:02.720978 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 68.68498400414504
0:41:02.721086 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 68.6850.
0:41:02.721152 INFO: ==============================================
0:41:02.721221 INFO: Starting optimization step 1.
0:41:02.721279 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:02.721340 INFO: Using ng extraction backend
0:41:02.721396 PROGRESS: Extracting batch of 1196 precursors
0:41:02.724994 INFO: === Search parameters used ===
0:41:02.725085 INFO: rt_error       : 68.68498400414504
0:41:02.725137 INFO: mobility_error : 0.1
0:41:02.725182 INFO: num_candidates : 3
0:41:02.725223 INFO: ms1_error      : 30
0:41:02.725263 INFO: ms2_error      : 7.171496
0:41:02.725302 INFO: fwhm_rt        : 3.0
0:41:02.725344 INFO: quant_window   : 3
0:41:02.725381 INFO: ==============================================
0:41:02.761049 INFO: performing precursor FDR with 40 features
0:41:02.761139 INFO: Decoy channel: -1
0:41:02.761165 INFO: Competetive: True
0:41:02.763812 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:02.765654 INFO: Using random state 369771 for train-test-split
0:41:02.777743 INFO: Test AUC: 0.672
0:41:02.777808 INFO: Train AUC: 0.689
0:41:02.777838 INFO: AUC difference: 2.48%
0:41:02.995408 INFO: Resetting torch num_threads to 80
0:41:02.997036 PROGRESS: === Extracted 3580 precursors and 22472 fragments ===
0:41:02.997384 INFO: === FDR correction performed with classifier version 7 ===
0:41:02.997848 PROGRESS: ============================= Precursor FDR =============================
0:41:02.997936 PROGRESS: Total precursors accumulated: 464
0:41:02.997995 PROGRESS: Target precursors: 460 (99.14%)
0:41:02.998044 PROGRESS: Decoy precursors: 4 (0.86%)
0:41:02.998096 PROGRESS: 
0:41:02.998146 PROGRESS: Precursor Summary:
0:41:02.999154 PROGRESS: Channel   0:	 0.050 FDR:   460; 0.010 FDR:   460; 0.001 FDR:   351
0:41:02.999931 PROGRESS: 
0:41:02.999988 PROGRESS: Protein Summary:
0:41:03.001179 PROGRESS: Channel   0:	 0.050 FDR:   437; 0.010 FDR:   437; 0.001 FDR:   334
0:41:03.001271 PROGRESS: =========================================================================
0:41:03.001474 INFO: Target number of precursors reached.
0:41:03.005548 INFO: fragments_df: keeping 4491 of 22472 [sum(precursor_idx_mask)=10421 sum(mass_error_mask)=22472 stop_rank=4491
0:41:03.010470 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:03.127627 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:03.665087 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:03.665550 INFO: Using score_cutoff 12.052817556667327 (fac=0.99, q=1)
0:41:03.665848 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:03.665932 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:03.665985 INFO: Updating optimization_manager: score_cutoff        : 12.614345955848695 -> 12.052817556667327
0:41:03.666042 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:03.667660 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:03.669906 INFO: === checking if optimization conditions were reached ===
0:41:03.670007 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:41:03.671647 INFO: Updating optimization_manager: rt_error            : 68.68498400414504 -> 22.47602437055141
0:41:03.671747 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 22.4760.
0:41:03.671813 INFO: ==============================================
0:41:03.671881 INFO: Starting optimization step 2.
0:41:03.671940 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:03.672000 INFO: Using ng extraction backend
0:41:03.672055 PROGRESS: Extracting batch of 1196 precursors
0:41:03.675664 INFO: === Search parameters used ===
0:41:03.675754 INFO: rt_error       : 22.47602437055141
0:41:03.675803 INFO: mobility_error : 0.1
0:41:03.675846 INFO: num_candidates : 3
0:41:03.675890 INFO: ms1_error      : 30
0:41:03.675931 INFO: ms2_error      : 7.171496
0:41:03.675970 INFO: fwhm_rt        : 3.0
0:41:03.676012 INFO: quant_window   : 3
0:41:03.676050 INFO: ==============================================
0:41:03.709236 INFO: performing precursor FDR with 40 features
0:41:03.710052 INFO: Decoy channel: -1
0:41:03.710082 INFO: Competetive: True
0:41:03.712684 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:03.714463 INFO: Using random state 369771 for train-test-split
0:41:03.726416 INFO: Test AUC: 0.729
0:41:03.726480 INFO: Train AUC: 0.699
0:41:03.726508 INFO: AUC difference: 4.34%
0:41:03.945269 INFO: Resetting torch num_threads to 80
0:41:03.946927 PROGRESS: === Extracted 3304 precursors and 20093 fragments ===
0:41:03.947272 INFO: === FDR correction performed with classifier version 7 ===
0:41:03.947746 PROGRESS: ============================= Precursor FDR =============================
0:41:03.947836 PROGRESS: Total precursors accumulated: 463
0:41:03.947901 PROGRESS: Target precursors: 459 (99.14%)
0:41:03.947952 PROGRESS: Decoy precursors: 4 (0.86%)
0:41:03.947996 PROGRESS: 
0:41:03.948042 PROGRESS: Precursor Summary:
0:41:03.948991 PROGRESS: Channel   0:	 0.050 FDR:   459; 0.010 FDR:   459; 0.001 FDR:   352
0:41:03.949083 PROGRESS: 
0:41:03.949138 PROGRESS: Protein Summary:
0:41:03.950312 PROGRESS: Channel   0:	 0.050 FDR:   436; 0.010 FDR:   436; 0.001 FDR:   335
0:41:03.950403 PROGRESS: =========================================================================
0:41:03.950634 INFO: Target number of precursors reached.
0:41:03.954391 INFO: fragments_df: keeping 4188 of 20093 [sum(precursor_idx_mask)=9216 sum(mass_error_mask)=20093 stop_rank=4188
0:41:03.959372 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:04.094421 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:04.650002 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:04.650472 INFO: Using score_cutoff 12.0522812582016 (fac=0.99, q=1)
0:41:04.650777 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:04.650861 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:04.650914 INFO: Updating optimization_manager: score_cutoff        : 12.052817556667327 -> 12.0522812582016
0:41:04.650970 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:04.652577 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:04.654872 INFO: === checking if optimization conditions were reached ===
0:41:04.654974 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:41:04.656693 INFO: Updating optimization_manager: rt_error            : 22.47602437055141 -> 19.166985447014884
0:41:04.656794 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 19.1670.
0:41:04.656858 INFO: ==============================================
0:41:04.656925 INFO: Starting optimization step 3.
0:41:04.656984 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:04.657045 INFO: Using ng extraction backend
0:41:04.657101 PROGRESS: Extracting batch of 1196 precursors
0:41:04.660644 INFO: === Search parameters used ===
0:41:04.660883 INFO: rt_error       : 19.166985447014884
0:41:04.660935 INFO: mobility_error : 0.1
0:41:04.660979 INFO: num_candidates : 3
0:41:04.661022 INFO: ms1_error      : 30
0:41:04.661061 INFO: ms2_error      : 7.171496
0:41:04.661100 INFO: fwhm_rt        : 3.0
0:41:04.661139 INFO: quant_window   : 3
0:41:04.661180 INFO: ==============================================
0:41:04.692345 INFO: performing precursor FDR with 40 features
0:41:04.692429 INFO: Decoy channel: -1
0:41:04.692455 INFO: Competetive: True
0:41:04.694913 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:04.696650 INFO: Using random state 369771 for train-test-split
0:41:04.708197 INFO: Test AUC: 0.689
0:41:04.708262 INFO: Train AUC: 0.707
0:41:04.708290 INFO: AUC difference: 2.49%
0:41:04.926548 INFO: Resetting torch num_threads to 80
0:41:04.928164 PROGRESS: === Extracted 3306 precursors and 20092 fragments ===
0:41:04.928514 INFO: === FDR correction performed with classifier version 7 ===
0:41:04.928976 PROGRESS: ============================= Precursor FDR =============================
0:41:04.929075 PROGRESS: Total precursors accumulated: 464
0:41:04.929137 PROGRESS: Target precursors: 460 (99.14%)
0:41:04.929187 PROGRESS: Decoy precursors: 4 (0.86%)
0:41:04.929230 PROGRESS: 
0:41:04.929273 PROGRESS: Precursor Summary:
0:41:04.930230 PROGRESS: Channel   0:	 0.050 FDR:   460; 0.010 FDR:   460; 0.001 FDR:   350
0:41:04.930319 PROGRESS: 
0:41:04.930374 PROGRESS: Protein Summary:
0:41:04.931552 PROGRESS: Channel   0:	 0.050 FDR:   437; 0.010 FDR:   437; 0.001 FDR:   333
0:41:04.931644 PROGRESS: =========================================================================
0:41:04.931849 INFO: Target number of precursors reached.
0:41:04.935555 INFO: fragments_df: keeping 4184 of 20092 [sum(precursor_idx_mask)=9242 sum(mass_error_mask)=20092 stop_rank=4184
0:41:04.940493 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:05.075762 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:05.631944 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:05.632402 INFO: Using score_cutoff 12.069602878189087 (fac=0.99, q=1)
0:41:05.632703 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:05.632786 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:05.632841 INFO: Updating optimization_manager: score_cutoff        : 12.0522812582016 -> 12.069602878189087
0:41:05.632896 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:05.634501 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:05.636739 INFO: === checking if optimization conditions were reached ===
0:41:05.636838 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:41:05.638540 INFO: Updating optimization_manager: rt_error            : 19.166985447014884 -> 19.164602503576482
0:41:05.638652 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 19.1646.
0:41:05.638715 INFO: ==============================================
0:41:05.638784 INFO: Starting optimization step 4.
0:41:05.638841 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:05.638903 INFO: Using ng extraction backend
0:41:05.638958 PROGRESS: Extracting batch of 1196 precursors
0:41:05.642586 INFO: === Search parameters used ===
0:41:05.642677 INFO: rt_error       : 19.164602503576482
0:41:05.642727 INFO: mobility_error : 0.1
0:41:05.642772 INFO: num_candidates : 3
0:41:05.642817 INFO: ms1_error      : 30
0:41:05.642857 INFO: ms2_error      : 7.171496
0:41:05.642897 INFO: fwhm_rt        : 3.0
0:41:05.642937 INFO: quant_window   : 3
0:41:05.642976 INFO: ==============================================
0:41:05.676327 INFO: performing precursor FDR with 40 features
0:41:05.676417 INFO: Decoy channel: -1
0:41:05.676442 INFO: Competetive: True
0:41:05.679010 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:05.680839 INFO: Using random state 369771 for train-test-split
0:41:05.693167 INFO: Test AUC: 0.707
0:41:05.693236 INFO: Train AUC: 0.703
0:41:05.693265 INFO: AUC difference: 0.67%
0:41:05.912452 INFO: Resetting torch num_threads to 80
0:41:05.914063 PROGRESS: === Extracted 3306 precursors and 20086 fragments ===
0:41:05.914412 INFO: === FDR correction performed with classifier version 7 ===
0:41:05.914890 PROGRESS: ============================= Precursor FDR =============================
0:41:05.914979 PROGRESS: Total precursors accumulated: 464
0:41:05.915038 PROGRESS: Target precursors: 460 (99.14%)
0:41:05.915088 PROGRESS: Decoy precursors: 4 (0.86%)
0:41:05.915132 PROGRESS: 
0:41:05.915176 PROGRESS: Precursor Summary:
0:41:05.916119 PROGRESS: Channel   0:	 0.050 FDR:   460; 0.010 FDR:   460; 0.001 FDR:   350
0:41:05.916208 PROGRESS: 
0:41:05.916262 PROGRESS: Protein Summary:
0:41:05.917411 PROGRESS: Channel   0:	 0.050 FDR:   437; 0.010 FDR:   437; 0.001 FDR:   333
0:41:05.917500 PROGRESS: =========================================================================
0:41:05.917705 INFO: Target number of precursors reached.
0:41:05.921389 INFO: fragments_df: keeping 4189 of 20086 [sum(precursor_idx_mask)=9240 sum(mass_error_mask)=20086 stop_rank=4189
0:41:05.926338 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:06.060969 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:06.619107 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:06.619576 INFO: Using score_cutoff 12.069602878189087 (fac=0.99, q=1)
0:41:06.619872 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:06.619954 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:06.620020 INFO: Updating optimization_manager: score_cutoff        : 12.069602878189087 -> 12.069602878189087
0:41:06.620078 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:06.621685 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:06.623874 INFO: === checking if optimization conditions were reached ===
0:41:06.623975 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:41:06.624928 INFO: Updating optimization_manager: rt_error            : 19.164602503576482 -> 19.164602503576482
0:41:06.625054 INFO: Updating optimization_manager: classifier_version  : 7 -> 12
0:41:06.625146 INFO: Updating optimization_manager: score_cutoff        : 12.069602878189087 -> 12.069602878189087
0:41:06.625230 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:06.625310 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:06.625390 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 19.1646 found after 5 searches.
0:41:06.625449 INFO: ==============================================
0:41:06.625527 PROGRESS: Optimization finished for rt_error.
0:41:06.630242 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:06.631567 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:06.662044 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:41:06.662195 PROGRESS: ==============================================
0:41:06.662263 PROGRESS: ms2_error      : 7.1715
0:41:06.662319 PROGRESS: rt_error       : 19.1646
0:41:06.662377 PROGRESS: ==============================================
0:41:06.662890 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:06.784685 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:07.138762 INFO: Using ng extraction backend
0:41:07.139057 PROGRESS: Extracting batch of 240048 precursors
0:41:07.521896 INFO: === Search parameters used ===
0:41:07.522170 INFO: rt_error       : 19.164602503576482
0:41:07.522232 INFO: mobility_error : 0.1
0:41:07.522279 INFO: num_candidates : 3
0:41:07.522324 INFO: ms1_error      : 30
0:41:07.522366 INFO: ms2_error      : 7.171496
0:41:07.522406 INFO: fwhm_rt        : 3.0
0:41:07.522447 INFO: quant_window   : 3
0:41:07.522486 INFO: ==============================================
0:41:07.786366 INFO: Removed 376488 precursors with score below cutoff 12.069602878189087
0:41:08.068876 INFO: performing precursor FDR with 40 features
0:41:08.068999 INFO: Decoy channel: -1
0:41:08.069026 INFO: Competetive: True
0:41:08.094375 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:08.110379 WARNING: FDR calculation for 189084 target and 92196 decoy PSMs
0:41:08.110509 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:41:08.170094 INFO: Using random state 633178 for train-test-split
0:41:12.245483 INFO: Test AUC: 0.886
0:41:12.245625 INFO: Train AUC: 0.887
0:41:12.245656 INFO: AUC difference: 0.13%
0:41:12.539246 INFO: Resetting torch num_threads to 80
0:41:12.855516 PROGRESS: ============================= Precursor FDR =============================
0:41:12.855783 PROGRESS: Total precursors accumulated: 109,647
0:41:12.855856 PROGRESS: Target precursors: 108,562 (99.01%)
0:41:12.855912 PROGRESS: Decoy precursors: 1,085 (0.99%)
0:41:12.855959 PROGRESS: 
0:41:12.856004 PROGRESS: Precursor Summary:
0:41:12.886284 PROGRESS: Channel   0:	 0.050 FDR: 108,562; 0.010 FDR: 108,562; 0.001 FDR: 99,208
0:41:12.886550 PROGRESS: 
0:41:12.886631 PROGRESS: Protein Summary:
0:41:12.927248 PROGRESS: Channel   0:	 0.050 FDR: 10,124; 0.010 FDR: 10,124; 0.001 FDR: 10,018
0:41:12.927507 PROGRESS: =========================================================================
0:41:12.929462 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
0:41:13.124541 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
0:41:13.412620 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:41:13.494032 PROGRESS: 
0:41:13.494190 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant
0:41:13.494265 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
0:41:13.494424 INFO: Initializing TimingManager
0:41:13.494924 INFO: Initializing RawFileManager
0:41:22.801107 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:41:22.805106 INFO: Determining DIA cycle
0:41:22.821371 INFO: Found cycle with start 0.00 min and length 300.
0:41:22.986131 INFO: RT (min)            : 0.0 - 26.9
0:41:22.986240 INFO: RT duration (sec)   : 1611.2
0:41:22.986273 INFO: RT duration (min)   : 26.9
0:41:22.986306 INFO: Cycle len (scans)   : 300
0:41:22.986326 INFO: Cycle len (sec)     : 1.65
0:41:22.986347 INFO: Number of cycles    : 978
0:41:22.986366 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:41:22.986391 INFO: Creating DIA data object took: 9.491363525390625
0:41:23.643891 INFO: Creating DIA data NG object took: 0.6573808193206787
0:41:23.668238 INFO: Initializing CalibrationManager
0:41:23.668542 INFO: Setting up calibration estimators ..
0:41:23.668602 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:41:23.668676 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'}' ..
0:41:23.668739 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:41:23.668789 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:41:23.668838 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}}' ..
0:41:23.668887 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:41:23.668931 INFO: Done setting up calibration estimators.
0:41:23.669118 INFO: Initializing OptimizationManager
0:41:23.669243 INFO: initial parameter: ms1_error = 30
0:41:23.669295 INFO: initial parameter: ms2_error = 30
0:41:23.669344 INFO: initial parameter: rt_error = 805.611083984375
0:41:23.669388 INFO: initial parameter: mobility_error = 0.1
0:41:23.669430 INFO: initial parameter: num_candidates = 1
0:41:23.669468 INFO: initial parameter: fwhm_rt = 5
0:41:23.669510 INFO: initial parameter: fwhm_mobility = 0.01
0:41:23.669549 INFO: initial parameter: score_cutoff = 0
0:41:23.669588 INFO: initial parameter: classifier_version = -1
0:41:23.669653 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:41:23.669874 INFO: FDRManager: loading saved state not requested, will be initialized.
0:41:23.669924 INFO: Initializing FDRManager
0:41:23.669955 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:41:23.698223 PROGRESS: Initializing spectral library: 120,580 target precursors potentially observable (0 removed)
0:41:23.717182 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:41:23.717557 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
0:41:23.717653 PROGRESS: Starting initial search for precursors.
0:41:23.717734 INFO: Starting optimization step 0.
0:41:23.717796 PROGRESS: === Extracting elution groups 0 to 200 ===
0:41:23.717850 INFO: Using ng extraction backend
0:41:23.717909 PROGRESS: Extracting batch of 398 precursors
0:41:23.720261 INFO: === Search parameters used ===
0:41:23.720362 INFO: rt_error       : 805.611083984375
0:41:23.720413 INFO: mobility_error : 0.1
0:41:23.720456 INFO: num_candidates : 1
0:41:23.720499 INFO: ms1_error      : 30
0:41:23.720540 INFO: ms2_error      : 30
0:41:23.720579 INFO: fwhm_rt        : 5
0:41:23.720621 INFO: quant_window   : 3
0:41:23.720658 INFO: ==============================================
0:41:23.737422 INFO: performing precursor FDR with 40 features
0:41:23.737491 INFO: Decoy channel: -1
0:41:23.737517 INFO: Competetive: True
0:41:23.738414 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:23.741270 INFO: Using random state 291557 for train-test-split
0:41:23.747864 INFO: Test AUC: 0.624
0:41:23.747922 INFO: Train AUC: 0.577
0:41:23.747952 INFO: AUC difference: 8.11%
0:41:23.747974 WARNING: AUC difference > 5%. This may indicate overfitting.
0:41:23.966166 INFO: Resetting torch num_threads to 80
0:41:23.967598 PROGRESS: === Extracted 398 precursors and 2841 fragments ===
0:41:23.967944 INFO: === FDR correction performed with classifier version -1 ===
0:41:23.968408 PROGRESS: ============================= Precursor FDR =============================
0:41:23.968496 PROGRESS: Total precursors accumulated: 5
0:41:23.968556 PROGRESS: Target precursors: 5 (100.00%)
0:41:23.968608 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:23.968652 PROGRESS: 
0:41:23.968696 PROGRESS: Precursor Summary:
0:41:23.969615 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
0:41:23.969704 PROGRESS: 
0:41:23.969761 PROGRESS: Protein Summary:
0:41:23.970783 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
0:41:23.970878 PROGRESS: =========================================================================
0:41:23.971069 INFO: Target number of precursors not reached yet.
0:41:23.974827 INFO: Starting optimization step 1.
0:41:23.974932 PROGRESS: === Extracting elution groups 200 to 600 ===
0:41:23.975005 INFO: Using ng extraction backend
0:41:23.975067 PROGRESS: Extracting batch of 798 precursors
0:41:23.977849 INFO: === Search parameters used ===
0:41:23.977935 INFO: rt_error       : 805.611083984375
0:41:23.977985 INFO: mobility_error : 0.1
0:41:23.978029 INFO: num_candidates : 1
0:41:23.978074 INFO: ms1_error      : 30
0:41:23.978116 INFO: ms2_error      : 30
0:41:23.978155 INFO: fwhm_rt        : 5
0:41:23.978196 INFO: quant_window   : 3
0:41:23.978236 INFO: ==============================================
0:41:24.010223 INFO: performing precursor FDR with 40 features
0:41:24.010335 INFO: Decoy channel: -1
0:41:24.010361 INFO: Competetive: True
0:41:24.013356 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:24.014915 INFO: Using random state 158125 for train-test-split
0:41:24.023700 INFO: Test AUC: 0.574
0:41:24.023759 INFO: Train AUC: 0.579
0:41:24.023791 INFO: AUC difference: 0.80%
0:41:24.236004 INFO: Resetting torch num_threads to 80
0:41:24.238152 PROGRESS: === Extracted 1196 precursors and 8412 fragments ===
0:41:24.238502 INFO: === FDR correction performed with classifier version -1 ===
0:41:24.239022 PROGRESS: ============================= Precursor FDR =============================
0:41:24.239113 PROGRESS: Total precursors accumulated: 1
0:41:24.239173 PROGRESS: Target precursors: 1 (100.00%)
0:41:24.239225 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:24.239269 PROGRESS: 
0:41:24.239314 PROGRESS: Precursor Summary:
0:41:24.240264 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:24.240355 PROGRESS: 
0:41:24.240413 PROGRESS: Protein Summary:
0:41:24.241430 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:24.241519 PROGRESS: =========================================================================
0:41:24.241734 INFO: Target number of precursors not reached yet.
0:41:24.246376 INFO: Starting optimization step 2.
0:41:24.246483 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:41:24.246559 INFO: Using ng extraction backend
0:41:24.246647 PROGRESS: Extracting batch of 1598 precursors
0:41:24.251065 INFO: === Search parameters used ===
0:41:24.251169 INFO: rt_error       : 805.611083984375
0:41:24.251220 INFO: mobility_error : 0.1
0:41:24.251265 INFO: num_candidates : 1
0:41:24.251309 INFO: ms1_error      : 30
0:41:24.251351 INFO: ms2_error      : 30
0:41:24.251393 INFO: fwhm_rt        : 5
0:41:24.251435 INFO: quant_window   : 3
0:41:24.251476 INFO: ==============================================
0:41:24.281997 INFO: performing precursor FDR with 40 features
0:41:24.282079 INFO: Decoy channel: -1
0:41:24.282104 INFO: Competetive: True
0:41:24.285277 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:24.287200 INFO: Using random state 449399 for train-test-split
0:41:24.299042 INFO: Test AUC: 0.609
0:41:24.299104 INFO: Train AUC: 0.578
0:41:24.299135 INFO: AUC difference: 5.31%
0:41:24.299156 WARNING: AUC difference > 5%. This may indicate overfitting.
0:41:24.514961 INFO: Resetting torch num_threads to 80
0:41:24.517468 PROGRESS: === Extracted 2791 precursors and 19432 fragments ===
0:41:24.517820 INFO: === FDR correction performed with classifier version -1 ===
0:41:24.518293 PROGRESS: ============================= Precursor FDR =============================
0:41:24.518381 PROGRESS: Total precursors accumulated: 1
0:41:24.518441 PROGRESS: Target precursors: 1 (100.00%)
0:41:24.518494 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:24.518541 PROGRESS: 
0:41:24.518608 PROGRESS: Precursor Summary:
0:41:24.519544 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:24.519635 PROGRESS: 
0:41:24.519691 PROGRESS: Protein Summary:
0:41:24.520700 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:24.520788 PROGRESS: =========================================================================
0:41:24.521026 INFO: Target number of precursors not reached yet.
0:41:24.527419 INFO: Starting optimization step 3.
0:41:24.527530 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:41:24.527607 INFO: Using ng extraction backend
0:41:24.527668 PROGRESS: Extracting batch of 3190 precursors
0:41:24.534694 INFO: === Search parameters used ===
0:41:24.534796 INFO: rt_error       : 805.611083984375
0:41:24.534848 INFO: mobility_error : 0.1
0:41:24.534894 INFO: num_candidates : 1
0:41:24.534940 INFO: ms1_error      : 30
0:41:24.534983 INFO: ms2_error      : 30
0:41:24.535032 INFO: fwhm_rt        : 5
0:41:24.535074 INFO: quant_window   : 3
0:41:24.535114 INFO: ==============================================
0:41:24.583359 INFO: performing precursor FDR with 40 features
0:41:24.583456 INFO: Decoy channel: -1
0:41:24.583483 INFO: Competetive: True
0:41:24.587373 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:24.589618 INFO: Using random state 782985 for train-test-split
0:41:24.610676 INFO: Test AUC: 0.574
0:41:24.610760 INFO: Train AUC: 0.586
0:41:24.610791 INFO: AUC difference: 2.10%
0:41:24.831048 INFO: Resetting torch num_threads to 80
0:41:24.834384 PROGRESS: === Extracted 5975 precursors and 41691 fragments ===
0:41:24.834748 INFO: === FDR correction performed with classifier version -1 ===
0:41:24.835254 PROGRESS: ============================= Precursor FDR =============================
0:41:24.835351 PROGRESS: Total precursors accumulated: 1
0:41:24.835413 PROGRESS: Target precursors: 1 (100.00%)
0:41:24.835466 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:24.835513 PROGRESS: 
0:41:24.835556 PROGRESS: Precursor Summary:
0:41:24.836494 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:24.836584 PROGRESS: 
0:41:24.836642 PROGRESS: Protein Summary:
0:41:24.837718 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:24.837808 PROGRESS: =========================================================================
0:41:24.838058 INFO: Target number of precursors not reached yet.
0:41:24.850614 INFO: Starting optimization step 4.
0:41:24.850868 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:41:24.850956 INFO: Using ng extraction backend
0:41:24.851019 PROGRESS: Extracting batch of 6370 precursors
0:41:24.863206 INFO: === Search parameters used ===
0:41:24.863335 INFO: rt_error       : 805.611083984375
0:41:24.863390 INFO: mobility_error : 0.1
0:41:24.863438 INFO: num_candidates : 1
0:41:24.863481 INFO: ms1_error      : 30
0:41:24.863523 INFO: ms2_error      : 30
0:41:24.863564 INFO: fwhm_rt        : 5
0:41:24.863604 INFO: quant_window   : 3
0:41:24.863646 INFO: ==============================================
0:41:24.937500 INFO: performing precursor FDR with 40 features
0:41:24.937614 INFO: Decoy channel: -1
0:41:24.937700 INFO: Competetive: True
0:41:24.944259 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:24.947432 INFO: Using random state 959808 for train-test-split
0:41:24.985450 INFO: Test AUC: 0.604
0:41:24.985569 INFO: Train AUC: 0.579
0:41:24.985601 INFO: AUC difference: 4.39%
0:41:25.202913 INFO: Resetting torch num_threads to 80
0:41:25.206846 PROGRESS: === Extracted 12336 precursors and 86263 fragments ===
0:41:25.207206 INFO: === FDR correction performed with classifier version -1 ===
0:41:25.207669 PROGRESS: ============================= Precursor FDR =============================
0:41:25.207769 PROGRESS: Total precursors accumulated: 1
0:41:25.207829 PROGRESS: Target precursors: 1 (100.00%)
0:41:25.207881 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:25.207925 PROGRESS: 
0:41:25.207970 PROGRESS: Precursor Summary:
0:41:25.208889 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:25.208978 PROGRESS: 
0:41:25.209034 PROGRESS: Protein Summary:
0:41:25.210049 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:25.210137 PROGRESS: =========================================================================
0:41:25.210618 INFO: Target number of precursors not reached yet.
0:41:25.225698 INFO: Starting optimization step 5.
0:41:25.225925 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:41:25.226011 INFO: Using ng extraction backend
0:41:25.226079 PROGRESS: Extracting batch of 12737 precursors
0:41:25.249179 INFO: === Search parameters used ===
0:41:25.249349 INFO: rt_error       : 805.611083984375
0:41:25.249402 INFO: mobility_error : 0.1
0:41:25.249447 INFO: num_candidates : 1
0:41:25.249490 INFO: ms1_error      : 30
0:41:25.249532 INFO: ms2_error      : 30
0:41:25.249573 INFO: fwhm_rt        : 5
0:41:25.249614 INFO: quant_window   : 3
0:41:25.249652 INFO: ==============================================
0:41:28.274805 INFO: performing precursor FDR with 40 features
0:41:28.274929 INFO: Decoy channel: -1
0:41:28.274957 INFO: Competetive: True
0:41:28.285798 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:28.291458 INFO: Using random state 880544 for train-test-split
0:41:28.611505 INFO: Test AUC: 0.766
0:41:28.611619 INFO: Train AUC: 0.775
0:41:28.611649 INFO: AUC difference: 1.18%
0:41:28.842262 INFO: Resetting torch num_threads to 80
0:41:28.850249 PROGRESS: === Extracted 25053 precursors and 175597 fragments ===
0:41:28.850777 INFO: === FDR correction performed with classifier version -1 ===
0:41:28.852164 PROGRESS: ============================= Precursor FDR =============================
0:41:28.852265 PROGRESS: Total precursors accumulated: 8,279
0:41:28.852325 PROGRESS: Target precursors: 8,198 (99.02%)
0:41:28.852377 PROGRESS: Decoy precursors: 81 (0.98%)
0:41:28.852427 PROGRESS: 
0:41:28.852481 PROGRESS: Precursor Summary:
0:41:28.855592 PROGRESS: Channel   0:	 0.050 FDR: 8,198; 0.010 FDR: 8,198; 0.001 FDR: 8,198
0:41:28.855700 PROGRESS: 
0:41:28.855758 PROGRESS: Protein Summary:
0:41:28.860446 PROGRESS: Channel   0:	 0.050 FDR: 4,413; 0.010 FDR: 4,413; 0.001 FDR: 4,413
0:41:28.860554 PROGRESS: =========================================================================
0:41:28.861014 INFO: Target number of precursors reached.
0:41:28.897444 INFO: fragments_df: keeping 5000 of 175597 [sum(precursor_idx_mask)=80628 sum(mass_error_mask)=175597 stop_rank=5000
0:41:28.904306 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:30.197212 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:30.820714 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:41:30.821336 INFO: Using score_cutoff 12.078876093578339 (fac=0.99, q=1)
0:41:30.821718 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:41:30.821801 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:41:30.821856 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.078876093578339
0:41:30.821913 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:30.823589 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:30.825816 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:41:30.825915 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:41:30.826000 INFO: Starting optimization step 6.
0:41:30.826064 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:30.826129 INFO: Using ng extraction backend
0:41:30.826187 PROGRESS: Extracting batch of 1196 precursors
0:41:30.829911 INFO: === Search parameters used ===
0:41:30.830020 INFO: rt_error       : 805.611083984375
0:41:30.830070 INFO: mobility_error : 0.1
0:41:30.830115 INFO: num_candidates : 3
0:41:30.830158 INFO: ms1_error      : 30
0:41:30.830200 INFO: ms2_error      : 30
0:41:30.830245 INFO: fwhm_rt        : 3.0
0:41:30.830286 INFO: quant_window   : 3
0:41:30.830324 INFO: ==============================================
0:41:30.871066 INFO: performing precursor FDR with 40 features
0:41:30.871188 INFO: Decoy channel: -1
0:41:30.871215 INFO: Competetive: True
0:41:30.874227 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:30.876406 INFO: Using random state 427567 for train-test-split
0:41:30.889101 INFO: Test AUC: 0.640
0:41:30.889168 INFO: Train AUC: 0.626
0:41:30.889198 INFO: AUC difference: 2.32%
0:41:31.110622 INFO: Resetting torch num_threads to 80
0:41:31.112386 PROGRESS: === Extracted 3584 precursors and 21889 fragments ===
0:41:31.112735 INFO: === FDR correction performed with classifier version 5 ===
0:41:31.113222 PROGRESS: ============================= Precursor FDR =============================
0:41:31.113316 PROGRESS: Total precursors accumulated: 469
0:41:31.113376 PROGRESS: Target precursors: 465 (99.15%)
0:41:31.113426 PROGRESS: Decoy precursors: 4 (0.85%)
0:41:31.113471 PROGRESS: 
0:41:31.113517 PROGRESS: Precursor Summary:
0:41:31.114505 PROGRESS: Channel   0:	 0.050 FDR:   465; 0.010 FDR:   465; 0.001 FDR:   465
0:41:31.114617 PROGRESS: 
0:41:31.114680 PROGRESS: Protein Summary:
0:41:31.115879 PROGRESS: Channel   0:	 0.050 FDR:   444; 0.010 FDR:   444; 0.001 FDR:   444
0:41:31.115974 PROGRESS: =========================================================================
0:41:31.116853 INFO: Target number of precursors reached.
0:41:31.120986 INFO: fragments_df: keeping 4416 of 21889 [sum(precursor_idx_mask)=9860 sum(mass_error_mask)=21889 stop_rank=4416
0:41:31.127608 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:31.242080 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:31.770548 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:31.771023 INFO: Using score_cutoff 12.613509922027587 (fac=0.99, q=1)
0:41:31.771318 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:31.771399 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:31.771452 INFO: Updating optimization_manager: score_cutoff        : 12.078876093578339 -> 12.613509922027587
0:41:31.771508 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:31.773152 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:31.775431 INFO: === checking if optimization conditions were reached ===
0:41:31.776981 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.171496
0:41:31.777081 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:41:31.777144 PROGRESS: ❌ ms2_error      : 7.1715 > 7.1715 or insufficient steps taken.
0:41:31.777210 INFO: ==============================================
0:41:31.777273 INFO: Starting optimization step 7.
0:41:31.777332 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:31.777392 INFO: Using ng extraction backend
0:41:31.777448 PROGRESS: Extracting batch of 1196 precursors
0:41:31.781321 INFO: === Search parameters used ===
0:41:31.781422 INFO: rt_error       : 805.611083984375
0:41:31.781476 INFO: mobility_error : 0.1
0:41:31.781521 INFO: num_candidates : 3
0:41:31.781565 INFO: ms1_error      : 30
0:41:31.781607 INFO: ms2_error      : 7.171496
0:41:31.781647 INFO: fwhm_rt        : 3.0
0:41:31.781685 INFO: quant_window   : 3
0:41:31.781723 INFO: ==============================================
0:41:31.820164 INFO: performing precursor FDR with 40 features
0:41:31.820257 INFO: Decoy channel: -1
0:41:31.820283 INFO: Competetive: True
0:41:31.823132 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:31.825050 INFO: Using random state 702831 for train-test-split
0:41:31.838031 INFO: Test AUC: 0.723
0:41:31.838095 INFO: Train AUC: 0.656
0:41:31.838130 INFO: AUC difference: 10.21%
0:41:31.838163 WARNING: AUC difference > 5%. This may indicate overfitting.
0:41:32.065174 INFO: Resetting torch num_threads to 80
0:41:32.067125 PROGRESS: === Extracted 3588 precursors and 25604 fragments ===
0:41:32.067474 INFO: === FDR correction performed with classifier version 6 ===
0:41:32.067950 PROGRESS: ============================= Precursor FDR =============================
0:41:32.068043 PROGRESS: Total precursors accumulated: 385
0:41:32.068104 PROGRESS: Target precursors: 382 (99.22%)
0:41:32.068155 PROGRESS: Decoy precursors: 3 (0.78%)
0:41:32.068200 PROGRESS: 
0:41:32.068245 PROGRESS: Precursor Summary:
0:41:32.069222 PROGRESS: Channel   0:	 0.050 FDR:   382; 0.010 FDR:   382; 0.001 FDR:   382
0:41:32.069315 PROGRESS: 
0:41:32.069372 PROGRESS: Protein Summary:
0:41:32.070557 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   365; 0.001 FDR:   365
0:41:32.070661 PROGRESS: =========================================================================
0:41:32.070926 INFO: Target number of precursors reached.
0:41:32.075244 INFO: fragments_df: keeping 4089 of 25604 [sum(precursor_idx_mask)=9361 sum(mass_error_mask)=25604 stop_rank=4089
0:41:32.080309 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:32.187835 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:32.671848 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:32.672321 INFO: Using score_cutoff 12.201678670406341 (fac=0.99, q=1)
0:41:32.672628 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:32.672712 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:32.672768 INFO: Updating optimization_manager: score_cutoff        : 12.613509922027587 -> 12.201678670406341
0:41:32.672822 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:32.674472 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:32.676756 INFO: === checking if optimization conditions were reached ===
0:41:32.678284 INFO: Updating optimization_manager: ms2_error           : 7.171496 -> 7.171496
0:41:32.678385 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:41:32.678455 PROGRESS: ✅ ms2_error      : 7.1715 <= 7.1715
0:41:32.678514 INFO: ==============================================
0:41:32.678586 PROGRESS: Optimization finished for ms2_error.
0:41:32.685749 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:32.687095 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:32.689336 INFO: Starting optimization step 0.
0:41:32.689442 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:32.689524 INFO: Using ng extraction backend
0:41:32.689590 PROGRESS: Extracting batch of 1196 precursors
0:41:32.693280 INFO: === Search parameters used ===
0:41:32.693382 INFO: rt_error       : 805.611083984375
0:41:32.693434 INFO: mobility_error : 0.1
0:41:32.693483 INFO: num_candidates : 3
0:41:32.693525 INFO: ms1_error      : 30
0:41:32.693565 INFO: ms2_error      : 7.171496
0:41:32.693608 INFO: fwhm_rt        : 3.0
0:41:32.693649 INFO: quant_window   : 3
0:41:32.693687 INFO: ==============================================
0:41:32.741965 INFO: performing precursor FDR with 40 features
0:41:32.742066 INFO: Decoy channel: -1
0:41:32.742092 INFO: Competetive: True
0:41:32.745333 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:32.747244 INFO: Using random state 872578 for train-test-split
0:41:32.761639 INFO: Test AUC: 0.661
0:41:32.761708 INFO: Train AUC: 0.673
0:41:32.761737 INFO: AUC difference: 1.80%
0:41:32.989218 INFO: Resetting torch num_threads to 80
0:41:32.990903 PROGRESS: === Extracted 3588 precursors and 25615 fragments ===
0:41:32.991264 INFO: === FDR correction performed with classifier version 7 ===
0:41:32.991740 PROGRESS: ============================= Precursor FDR =============================
0:41:32.991839 PROGRESS: Total precursors accumulated: 386
0:41:32.991899 PROGRESS: Target precursors: 383 (99.22%)
0:41:32.991951 PROGRESS: Decoy precursors: 3 (0.78%)
0:41:32.992002 PROGRESS: 
0:41:32.992046 PROGRESS: Precursor Summary:
0:41:32.992998 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   383; 0.001 FDR:   383
0:41:32.993087 PROGRESS: 
0:41:32.993142 PROGRESS: Protein Summary:
0:41:32.994307 PROGRESS: Channel   0:	 0.050 FDR:   366; 0.010 FDR:   366; 0.001 FDR:   366
0:41:32.994398 PROGRESS: =========================================================================
0:41:32.994687 INFO: Target number of precursors reached.
0:41:32.999095 INFO: fragments_df: keeping 4101 of 25615 [sum(precursor_idx_mask)=9373 sum(mass_error_mask)=25615 stop_rank=4101
0:41:33.006261 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:33.115177 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:33.597800 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:33.598268 INFO: Using score_cutoff 12.202875506401062 (fac=0.99, q=1)
0:41:33.598587 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:33.598673 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:33.598731 INFO: Updating optimization_manager: score_cutoff        : 12.201678670406341 -> 12.202875506401062
0:41:33.598785 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:33.600431 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:33.602679 INFO: === checking if optimization conditions were reached ===
0:41:33.602784 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:41:33.604347 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 110.44252912068438
0:41:33.604448 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 110.4425.
0:41:33.604514 INFO: ==============================================
0:41:33.604586 INFO: Starting optimization step 1.
0:41:33.604651 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:33.604715 INFO: Using ng extraction backend
0:41:33.604771 PROGRESS: Extracting batch of 1196 precursors
0:41:33.608443 INFO: === Search parameters used ===
0:41:33.608537 INFO: rt_error       : 110.44252912068438
0:41:33.608590 INFO: mobility_error : 0.1
0:41:33.608637 INFO: num_candidates : 3
0:41:33.608679 INFO: ms1_error      : 30
0:41:33.608721 INFO: ms2_error      : 7.171496
0:41:33.608761 INFO: fwhm_rt        : 3.0
0:41:33.608800 INFO: quant_window   : 3
0:41:33.608839 INFO: ==============================================
0:41:33.641830 INFO: performing precursor FDR with 40 features
0:41:33.641917 INFO: Decoy channel: -1
0:41:33.641942 INFO: Competetive: True
0:41:33.646703 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:33.648556 INFO: Using random state 872578 for train-test-split
0:41:33.660922 INFO: Test AUC: 0.699
0:41:33.660989 INFO: Train AUC: 0.685
0:41:33.661018 INFO: AUC difference: 2.01%
0:41:33.886724 INFO: Resetting torch num_threads to 80
0:41:33.888391 PROGRESS: === Extracted 3588 precursors and 23728 fragments ===
0:41:33.888735 INFO: === FDR correction performed with classifier version 7 ===
0:41:33.889221 PROGRESS: ============================= Precursor FDR =============================
0:41:33.889310 PROGRESS: Total precursors accumulated: 407
0:41:33.889370 PROGRESS: Target precursors: 403 (99.02%)
0:41:33.889421 PROGRESS: Decoy precursors: 4 (0.98%)
0:41:33.889465 PROGRESS: 
0:41:33.889509 PROGRESS: Precursor Summary:
0:41:33.890479 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   403; 0.001 FDR:   384
0:41:33.890574 PROGRESS: 
0:41:33.890635 PROGRESS: Protein Summary:
0:41:33.891826 PROGRESS: Channel   0:	 0.050 FDR:   385; 0.010 FDR:   385; 0.001 FDR:   367
0:41:33.891922 PROGRESS: =========================================================================
0:41:33.892144 INFO: Target number of precursors reached.
0:41:33.896279 INFO: fragments_df: keeping 4148 of 23728 [sum(precursor_idx_mask)=9485 sum(mass_error_mask)=23728 stop_rank=4148
0:41:33.901181 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:34.018882 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:34.507334 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:34.507792 INFO: Using score_cutoff 12.202607522392274 (fac=0.99, q=1)
0:41:34.508103 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:34.508184 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:34.508240 INFO: Updating optimization_manager: score_cutoff        : 12.202875506401062 -> 12.202607522392274
0:41:34.508303 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:34.509947 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:34.512205 INFO: === checking if optimization conditions were reached ===
0:41:34.512305 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:41:34.513914 INFO: Updating optimization_manager: rt_error            : 110.44252912068438 -> 27.065694696399543
0:41:34.514013 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 27.0657.
0:41:34.514080 INFO: ==============================================
0:41:34.514149 INFO: Starting optimization step 2.
0:41:34.514210 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:34.514273 INFO: Using ng extraction backend
0:41:34.514333 PROGRESS: Extracting batch of 1196 precursors
0:41:34.518026 INFO: === Search parameters used ===
0:41:34.518128 INFO: rt_error       : 27.065694696399543
0:41:34.518183 INFO: mobility_error : 0.1
0:41:34.518234 INFO: num_candidates : 3
0:41:34.518280 INFO: ms1_error      : 30
0:41:34.518323 INFO: ms2_error      : 7.171496
0:41:34.518365 INFO: fwhm_rt        : 3.0
0:41:34.518406 INFO: quant_window   : 3
0:41:34.518448 INFO: ==============================================
0:41:34.553110 INFO: performing precursor FDR with 40 features
0:41:34.553207 INFO: Decoy channel: -1
0:41:34.553233 INFO: Competetive: True
0:41:34.556152 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:34.557923 INFO: Using random state 872578 for train-test-split
0:41:34.570471 INFO: Test AUC: 0.683
0:41:34.570541 INFO: Train AUC: 0.714
0:41:34.570578 INFO: AUC difference: 4.31%
0:41:34.798027 INFO: Resetting torch num_threads to 80
0:41:34.799691 PROGRESS: === Extracted 3270 precursors and 19812 fragments ===
0:41:34.800040 INFO: === FDR correction performed with classifier version 7 ===
0:41:34.800518 PROGRESS: ============================= Precursor FDR =============================
0:41:34.800609 PROGRESS: Total precursors accumulated: 411
0:41:34.800668 PROGRESS: Target precursors: 407 (99.03%)
0:41:34.800719 PROGRESS: Decoy precursors: 4 (0.97%)
0:41:34.800763 PROGRESS: 
0:41:34.800807 PROGRESS: Precursor Summary:
0:41:34.801778 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   407; 0.001 FDR:   382
0:41:34.801874 PROGRESS: 
0:41:34.801930 PROGRESS: Protein Summary:
0:41:34.803118 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   389; 0.001 FDR:   365
0:41:34.803215 PROGRESS: =========================================================================
0:41:34.803473 INFO: Target number of precursors reached.
0:41:34.807238 INFO: fragments_df: keeping 3750 of 19812 [sum(precursor_idx_mask)=8053 sum(mass_error_mask)=19812 stop_rank=3750
0:41:34.812162 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:34.943144 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:35.438692 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:35.439154 INFO: Using score_cutoff 12.203497768592834 (fac=0.99, q=1)
0:41:35.439448 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:35.439537 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:35.439596 INFO: Updating optimization_manager: score_cutoff        : 12.202607522392274 -> 12.203497768592834
0:41:35.439652 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:35.441280 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:35.443563 INFO: === checking if optimization conditions were reached ===
0:41:35.443664 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:41:35.445353 INFO: Updating optimization_manager: rt_error            : 27.065694696399543 -> 19.66263169886111
0:41:35.445453 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 19.6626.
0:41:35.445519 INFO: ==============================================
0:41:35.445586 INFO: Starting optimization step 3.
0:41:35.445648 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:35.445711 INFO: Using ng extraction backend
0:41:35.445767 PROGRESS: Extracting batch of 1196 precursors
0:41:35.449351 INFO: === Search parameters used ===
0:41:35.449464 INFO: rt_error       : 19.66263169886111
0:41:35.449531 INFO: mobility_error : 0.1
0:41:35.449587 INFO: num_candidates : 3
0:41:35.449633 INFO: ms1_error      : 30
0:41:35.449674 INFO: ms2_error      : 7.171496
0:41:35.449715 INFO: fwhm_rt        : 3.0
0:41:35.449761 INFO: quant_window   : 3
0:41:35.449801 INFO: ==============================================
0:41:35.488685 INFO: performing precursor FDR with 40 features
0:41:35.488794 INFO: Decoy channel: -1
0:41:35.488819 INFO: Competetive: True
0:41:35.491849 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:35.493748 INFO: Using random state 872578 for train-test-split
0:41:35.505629 INFO: Test AUC: 0.707
0:41:35.505697 INFO: Train AUC: 0.706
0:41:35.505726 INFO: AUC difference: 0.19%
0:41:35.736146 INFO: Resetting torch num_threads to 80
0:41:35.737817 PROGRESS: === Extracted 3273 precursors and 19823 fragments ===
0:41:35.738161 INFO: === FDR correction performed with classifier version 7 ===
0:41:35.738645 PROGRESS: ============================= Precursor FDR =============================
0:41:35.738738 PROGRESS: Total precursors accumulated: 411
0:41:35.738798 PROGRESS: Target precursors: 407 (99.03%)
0:41:35.738848 PROGRESS: Decoy precursors: 4 (0.97%)
0:41:35.738893 PROGRESS: 
0:41:35.738937 PROGRESS: Precursor Summary:
0:41:35.739918 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   407; 0.001 FDR:   383
0:41:35.740011 PROGRESS: 
0:41:35.740068 PROGRESS: Protein Summary:
0:41:35.741241 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   389; 0.001 FDR:   366
0:41:35.741334 PROGRESS: =========================================================================
0:41:35.741591 INFO: Target number of precursors reached.
0:41:35.745414 INFO: fragments_df: keeping 3754 of 19823 [sum(precursor_idx_mask)=8062 sum(mass_error_mask)=19823 stop_rank=3754
0:41:35.750552 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:35.862487 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:36.293165 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:36.293616 INFO: Using score_cutoff 12.203497768592834 (fac=0.99, q=1)
0:41:36.293921 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:36.294008 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:36.294065 INFO: Updating optimization_manager: score_cutoff        : 12.203497768592834 -> 12.203497768592834
0:41:36.294120 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:36.295765 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:36.298049 INFO: === checking if optimization conditions were reached ===
0:41:36.298152 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:41:36.299922 INFO: Updating optimization_manager: rt_error            : 19.66263169886111 -> 19.662631698886763
0:41:36.300024 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 19.6626.
0:41:36.300090 INFO: ==============================================
0:41:36.300159 INFO: Starting optimization step 4.
0:41:36.300220 PROGRESS: === Extracting elution groups 0 to 600 ===
0:41:36.300285 INFO: Using ng extraction backend
0:41:36.300352 PROGRESS: Extracting batch of 1196 precursors
0:41:36.304123 INFO: === Search parameters used ===
0:41:36.304225 INFO: rt_error       : 19.662631698886763
0:41:36.304281 INFO: mobility_error : 0.1
0:41:36.304329 INFO: num_candidates : 3
0:41:36.304372 INFO: ms1_error      : 30
0:41:36.304420 INFO: ms2_error      : 7.171496
0:41:36.304462 INFO: fwhm_rt        : 3.0
0:41:36.304503 INFO: quant_window   : 3
0:41:36.304543 INFO: ==============================================
0:41:36.339070 INFO: performing precursor FDR with 40 features
0:41:36.339165 INFO: Decoy channel: -1
0:41:36.339191 INFO: Competetive: True
0:41:36.341956 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:36.343779 INFO: Using random state 872578 for train-test-split
0:41:36.357073 INFO: Test AUC: 0.717
0:41:36.357146 INFO: Train AUC: 0.704
0:41:36.357177 INFO: AUC difference: 1.87%
0:41:36.584413 INFO: Resetting torch num_threads to 80
0:41:36.586094 PROGRESS: === Extracted 3275 precursors and 19829 fragments ===
0:41:36.586439 INFO: === FDR correction performed with classifier version 7 ===
0:41:36.586920 PROGRESS: ============================= Precursor FDR =============================
0:41:36.587009 PROGRESS: Total precursors accumulated: 411
0:41:36.587068 PROGRESS: Target precursors: 407 (99.03%)
0:41:36.587117 PROGRESS: Decoy precursors: 4 (0.97%)
0:41:36.587161 PROGRESS: 
0:41:36.587204 PROGRESS: Precursor Summary:
0:41:36.588179 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   407; 0.001 FDR:   383
0:41:36.588270 PROGRESS: 
0:41:36.588327 PROGRESS: Protein Summary:
0:41:36.589492 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   389; 0.001 FDR:   366
0:41:36.589584 PROGRESS: =========================================================================
0:41:36.589822 INFO: Target number of precursors reached.
0:41:36.593515 INFO: fragments_df: keeping 3758 of 19829 [sum(precursor_idx_mask)=8068 sum(mass_error_mask)=19829 stop_rank=3758
0:41:36.598511 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:36.708727 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:37.141687 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:37.142159 INFO: Using score_cutoff 12.203497768592834 (fac=0.99, q=1)
0:41:37.142458 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:37.142540 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:37.142606 INFO: Updating optimization_manager: score_cutoff        : 12.203497768592834 -> 12.203497768592834
0:41:37.142659 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:37.144292 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:37.146530 INFO: === checking if optimization conditions were reached ===
0:41:37.146639 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:41:37.147576 INFO: Updating optimization_manager: rt_error            : 19.662631698886763 -> 19.66263169886111
0:41:37.147697 INFO: Updating optimization_manager: classifier_version  : 7 -> 11
0:41:37.147803 INFO: Updating optimization_manager: score_cutoff        : 12.203497768592834 -> 12.203497768592834
0:41:37.147890 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:37.147984 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:37.148093 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 19.6626 found after 5 searches.
0:41:37.148160 INFO: ==============================================
0:41:37.148230 PROGRESS: Optimization finished for rt_error.
0:41:37.152983 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:37.154366 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:37.184402 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:41:37.184554 PROGRESS: ==============================================
0:41:37.184623 PROGRESS: ms2_error      : 7.1715
0:41:37.184679 PROGRESS: rt_error       : 19.6626
0:41:37.184742 PROGRESS: ==============================================
0:41:37.185226 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:37.314453 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:37.671099 INFO: Using ng extraction backend
0:41:37.671427 PROGRESS: Extracting batch of 240048 precursors
0:41:38.055001 INFO: === Search parameters used ===
0:41:38.055262 INFO: rt_error       : 19.66263169886111
0:41:38.055324 INFO: mobility_error : 0.1
0:41:38.055377 INFO: num_candidates : 3
0:41:38.055425 INFO: ms1_error      : 30
0:41:38.055470 INFO: ms2_error      : 7.171496
0:41:38.055511 INFO: fwhm_rt        : 3.0
0:41:38.055558 INFO: quant_window   : 3
0:41:38.055600 INFO: ==============================================
0:41:38.315935 INFO: Removed 381623 precursors with score below cutoff 12.203497768592834
0:41:38.587467 INFO: performing precursor FDR with 40 features
0:41:38.587598 INFO: Decoy channel: -1
0:41:38.587627 INFO: Competetive: True
0:41:38.613779 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:38.627845 WARNING: FDR calculation for 186574 target and 89200 decoy PSMs
0:41:38.627980 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:41:38.687486 INFO: Using random state 454814 for train-test-split
0:41:42.426989 INFO: Test AUC: 0.887
0:41:42.427128 INFO: Train AUC: 0.885
0:41:42.427159 INFO: AUC difference: 0.13%
0:41:42.731115 INFO: Resetting torch num_threads to 80
0:41:43.050281 PROGRESS: ============================= Precursor FDR =============================
0:41:43.050552 PROGRESS: Total precursors accumulated: 108,653
0:41:43.050644 PROGRESS: Target precursors: 107,578 (99.01%)
0:41:43.050700 PROGRESS: Decoy precursors: 1,075 (0.99%)
0:41:43.050750 PROGRESS: 
0:41:43.050795 PROGRESS: Precursor Summary:
0:41:43.078741 PROGRESS: Channel   0:	 0.050 FDR: 107,578; 0.010 FDR: 107,578; 0.001 FDR: 92,372
0:41:43.079007 PROGRESS: 
0:41:43.079076 PROGRESS: Protein Summary:
0:41:43.117358 PROGRESS: Channel   0:	 0.050 FDR: 10,116; 0.010 FDR: 10,116; 0.001 FDR: 9,880
0:41:43.117613 PROGRESS: =========================================================================
0:41:43.119287 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
0:41:43.298486 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
0:41:43.585998 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:41:44.191357 PROGRESS: Processing search outputs
0:41:44.191475 PROGRESS: Performing protein grouping and FDR
0:41:44.191516 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:41:44.251013 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:41:44.311830 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:41:44.372808 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:41:44.433465 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:41:44.495960 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:41:44.555845 INFO: Building combined output
0:41:44.587067 INFO: Performing protein inference
0:41:45.289758 INFO: Inference strategy: library. Using library grouping for protein inference
0:41:45.292966 INFO: Performing protein FDR
0:41:48.781332 INFO: Normalizing q-values using 10,145 targets and 3,391 decoys
0:41:48.784957 INFO: Test AUC: 1.000
0:41:48.785023 INFO: Train AUC: 1.000
0:41:48.785065 INFO: AUC difference: 0.01%
0:41:49.565894 PROGRESS: ================ Protein FDR =================
0:41:49.566099 PROGRESS: Unique protein groups in output
0:41:49.566129 PROGRESS:   1% protein FDR: 10,140
0:41:49.566150 PROGRESS: 
0:41:49.566169 PROGRESS: Unique precursor in output
0:41:49.566187 PROGRESS:   1% protein FDR: 119,450
0:41:49.566204 PROGRESS: ================================================
0:41:49.642375 PROGRESS: Building search statistics
0:41:49.798182 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
0:41:49.798389 INFO: Initializing OptimizationManager
0:41:49.798691 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
0:41:49.798778 INFO: Initializing CalibrationManager
0:41:49.799029 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
0:41:49.799111 INFO: Initializing RawFileManager
0:41:49.839343 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
0:41:49.839551 INFO: Initializing OptimizationManager
0:41:49.839772 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
0:41:49.839849 INFO: Initializing CalibrationManager
0:41:49.840074 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
0:41:49.840153 INFO: Initializing RawFileManager
0:41:49.879653 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
0:41:49.879861 INFO: Initializing OptimizationManager
0:41:49.880073 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
0:41:49.880150 INFO: Initializing CalibrationManager
0:41:49.880372 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
0:41:49.880446 INFO: Initializing RawFileManager
0:41:49.920512 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
0:41:49.920720 INFO: Initializing OptimizationManager
0:41:49.920932 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
0:41:49.921008 INFO: Initializing CalibrationManager
0:41:49.921227 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
0:41:49.921304 INFO: Initializing RawFileManager
0:41:49.961330 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
0:41:49.961531 INFO: Initializing OptimizationManager
0:41:49.961737 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
0:41:49.961812 INFO: Initializing CalibrationManager
0:41:49.962027 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
0:41:49.962101 INFO: Initializing RawFileManager
0:41:50.001950 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
0:41:50.002155 INFO: Initializing OptimizationManager
0:41:50.002364 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
0:41:50.002454 INFO: Initializing CalibrationManager
0:41:50.002685 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
0:41:50.002768 INFO: Initializing RawFileManager
0:41:50.006300 INFO: Writing stat output to disk
0:41:50.006426 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/stat.tsv to disk
0:41:50.019421 PROGRESS: Building internal statistics
0:41:50.019629 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
0:41:50.019672 INFO: Initializing TimingManager
0:41:50.019984 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
0:41:50.020025 INFO: Initializing TimingManager
0:41:50.020221 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
0:41:50.020258 INFO: Initializing TimingManager
0:41:50.020440 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
0:41:50.020477 INFO: Initializing TimingManager
0:41:50.020652 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
0:41:50.020688 INFO: Initializing TimingManager
0:41:50.020860 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
0:41:50.020896 INFO: Initializing TimingManager
0:41:50.021295 INFO: Writing internal output to disk
0:41:50.021341 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/internal.tsv to disk
0:41:50.021818 PROGRESS: Performing label free quantification
0:41:50.141613 INFO: Accumulating fragment data
0:41:50.141794 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:41:50.206910 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:41:51.734737 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:41:53.293781 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:41:54.902284 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:41:56.433464 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:41:58.455793 PROGRESS: Performing label free quantification on the precursor level
0:41:58.455961 INFO: Filtering fragments by quality
0:41:58.860779 INFO: Performing label-free quantification using directLFQ
0:42:00.123716 INFO: 119450 lfq-groups total
0:42:40.761559 INFO: using 80 processes
0:42:41.080750 INFO: lfq-object 0
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0:44:06.511109 INFO: Writing precursor output to disk
0:44:06.511552 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/precursor.matrix.tsv to disk
0:44:07.165938 PROGRESS: Performing label free quantification on the pg level
0:44:07.166049 INFO: Filtering fragments by quality
0:44:07.581896 INFO: Performing label-free quantification using directLFQ
0:44:07.969218 INFO: 10140 lfq-groups total
0:44:26.063344 INFO: using 80 processes
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0:44:32.498156 INFO: Writing pg output to disk
0:44:32.498332 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/pg.matrix.tsv to disk
0:44:32.769971 INFO: Writing psm output to disk
0:44:32.770117 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR_calibrateTol/precursors.tsv to disk
0:44:44.489640 PROGRESS: Building MBR spectral library
0:44:44.608735 INFO: Running MbrLibraryBuilder
0:44:44.853484 INFO: MBR spectral library contains 119,450 precursors, 10,140 proteins
0:44:44.853613 INFO: Writing MBR spectral library to disk
0:44:45.698452 PROGRESS: =================== Search Finished ===================
0:44:45.730462 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_a65qspd8. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 1,065,687,027,712
